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From: <ts...@us...> - 2008-07-23 13:55:56
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Revision: 3877
http://teem.svn.sourceforge.net/teem/?rev=3877&view=rev
Author: tststs
Date: 2008-07-23 13:56:05 +0000 (Wed, 23 Jul 2008)
Log Message:
-----------
Integrated code from "Using Eigenvalue Derivatives for Edge Detection in
DT-MRI Data" (Schultz/Seidel, DAGM 2008). This introduces the following
tengage items:
tenGageCl1GradVec,
tenGageCl1GradMag,
tenGageCp1GradVec,
tenGageCp1GradMag,
tenGageCa1GradVec,
tenGageCa1GradMag,
tenGageTensorGradRotE
for gradients of cl1, cp1, and ca1, respectively, as well as the full
(third-order) tensor field gradient rotated to the tensor field's eigenframe
E. Moreover, the existing item tenGageEvalGrads now avoids visual artifacts
in edge maps previously caused by ill-conditioned eigenvectors.
Modified Paths:
--------------
teem/trunk/src/ten/enumsTen.c
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenGage.c
Modified: teem/trunk/src/ten/enumsTen.c
===================================================================
--- teem/trunk/src/ten/enumsTen.c 2008-07-23 13:49:00 UTC (rev 3876)
+++ teem/trunk/src/ten/enumsTen.c 2008-07-23 13:56:05 UTC (rev 3877)
@@ -620,7 +620,14 @@
tenGageTensorLogEuclidean,
tenGageTensorQuatGeoLoxK,
tenGageTensorQuatGeoLoxR,
- tenGageAniso
+ tenGageAniso,
+ tenGageCl1GradVec,
+ tenGageCl1GradMag,
+ tenGageCp1GradVec,
+ tenGageCp1GradMag,
+ tenGageCa1GradVec,
+ tenGageCa1GradMag,
+ tenGageTensorGradRotE
};
char
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2008-07-23 13:49:00 UTC (rev 3876)
+++ teem/trunk/src/ten/ten.h 2008-07-23 13:56:05 UTC (rev 3877)
@@ -435,9 +435,19 @@
tenGageTensorQuatGeoLoxR, /* 149: QGL-R interpolation */
tenGageAniso, /* 150: "an", all anisos: [TEN_ANISO_MAX+1] */
+ tenGageCl1GradVec, /* 151: gradient vector of cl1: [3] */
+ tenGageCl1GradMag, /* 152: gradient magnitude of cl1: [1] */
+ tenGageCp1GradVec, /* 153: gradient vector of cp1: [3] */
+ tenGageCp1GradMag, /* 154: gradient magnitude of cp1: [1] */
+ tenGageCa1GradVec, /* 155: gradient vector of ca1: [3] */
+ tenGageCa1GradMag, /* 156: gradient magnitude of ca1: [1] */
+ tenGageTensorGradRotE, /* 157: all tensor component gradients,
+ starting with confidence gradient.
+ Rotated such that eigenvalue
+ derivatives are on the diagonal: [21] */
tenGageLast
};
-#define TEN_GAGE_ITEM_MAX 150
+#define TEN_GAGE_ITEM_MAX 157
/*
******** tenDwiGage* enum
Modified: teem/trunk/src/ten/tenGage.c
===================================================================
--- teem/trunk/src/ten/tenGage.c 2008-07-23 13:49:00 UTC (rev 3876)
+++ teem/trunk/src/ten/tenGage.c 2008-07-23 13:56:05 UTC (rev 3877)
@@ -227,7 +227,15 @@
{tenGageTensorQuatGeoLoxK, 7, 0, {0}, 0, 0, AIR_FALSE},
{tenGageTensorQuatGeoLoxR, 7, 0, {0}, 0, 0, AIR_FALSE},
- {tenGageAniso, TEN_ANISO_MAX+1, 0, {tenGageEval0, tenGageEval1, tenGageEval2}, 0, 0, AIR_FALSE}
+ {tenGageAniso, TEN_ANISO_MAX+1, 0, {tenGageEval0, tenGageEval1, tenGageEval2}, 0, 0, AIR_FALSE},
+
+ {tenGageCl1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
+ {tenGageCl1GradMag, 1, 1, {tenGageCl1GradVec}, 0, 0, AIR_FALSE},
+ {tenGageCp1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
+ {tenGageCp1GradMag, 1, 1, {tenGageCp1GradVec}, 0, 0, AIR_FALSE},
+ {tenGageCa1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
+ {tenGageCa1GradMag, 1, 1, {tenGageCa1GradVec}, 0, 0, AIR_FALSE},
+ {tenGageTensorGradRotE, 21, 1, {tenGageTensorGrad, tenGageEval, tenGageEvec}, 0, 0, AIR_FALSE}
};
void
@@ -750,15 +758,65 @@
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvalGrads)) {
double matOut[9], tenOut[9];
+ double tmpRes[9];
int evi;
for (evi=0; evi<=2; evi++) {
ELL_3MV_OUTER(matOut, evecAns + evi*3, evecAns + evi*3);
TEN_M2T(tenOut, matOut);
- ELL_3V_SET(pvl->directAnswer[tenGageEvalGrads] + evi*3,
+ ELL_3V_SET(tmpRes + evi*3,
TEN_T_DOT(tenOut, gradDdXYZ + 0*7),
TEN_T_DOT(tenOut, gradDdXYZ + 1*7),
TEN_T_DOT(tenOut, gradDdXYZ + 2*7));
}
+
+ /* Added 2008-06-27: In case there are duplicate eigenvalues,
+ * average their derivatives to avoid visible artifacs in edge
+ * maps. Provide a smooth transition to the ill-defined case */
+ float eps=0.05; /* threshold at which we start the transition */
+
+ /* interpolation weights from relative eigenvalue distance */
+ float rel1=(evalAns[0]-evalAns[1])/(evalAns[0]+evalAns[1]);
+ float rel2=(evalAns[1]-evalAns[2])/(evalAns[1]+evalAns[2]);
+ float w1=rel1/eps-1;
+ w1*=w1;
+ float w2=rel2/eps-1;
+ w2*=w2;
+
+ if (rel1>eps) {
+ ELL_3V_COPY(pvl->directAnswer[tenGageEvalGrads], tmpRes);
+ } else {
+ if (rel2>eps) {
+ ELL_3V_SCALE_ADD2(pvl->directAnswer[tenGageEvalGrads],
+ 1-0.5*w1, tmpRes, 0.5*w1, tmpRes+3);
+ } else {
+ ELL_3V_SCALE_ADD3(pvl->directAnswer[tenGageEvalGrads],
+ 1-0.5*w1-w1*w2/6.0, tmpRes,
+ 0.5*w1-w1*w2/6.0, tmpRes+3,
+ w1*w2/3.0, tmpRes+6);
+ }
+ }
+
+ if (rel2>eps) {
+ ELL_3V_COPY(pvl->directAnswer[tenGageEvalGrads]+6, tmpRes+6);
+ } else {
+ if (rel1>eps) {
+ ELL_3V_SCALE_ADD2(pvl->directAnswer[tenGageEvalGrads]+6,
+ 1-0.5*w2, tmpRes+6, 0.5*w2, tmpRes+3);
+ } else {
+ ELL_3V_SCALE_ADD3(pvl->directAnswer[tenGageEvalGrads]+6,
+ 1-0.5*w2-w1*w2/6.0, tmpRes+6,
+ 0.5*w2-w1*w2/6.0, tmpRes+3,
+ w1*w2/3.0, tmpRes);
+ }
+ }
+
+ ELL_3V_ADD3(pvl->directAnswer[tenGageEvalGrads]+3,
+ tmpRes, tmpRes+3, tmpRes+6);
+ ELL_3V_ADD2(tmpRes, pvl->directAnswer[tenGageEvalGrads],
+ pvl->directAnswer[tenGageEvalGrads]+6);
+ ELL_3V_SUB(pvl->directAnswer[tenGageEvalGrads]+3,
+ pvl->directAnswer[tenGageEvalGrads]+3,
+ tmpRes); /* l2 = trace - l1 - l3 */
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageRotTans)) {
double phi1[7], phi2[7], phi3[7];
@@ -1367,6 +1425,218 @@
pvl->directAnswer[tenGageAniso][ci] = tenAnisoEval_d(evalAns, ci);
}
}
+
+ /* --- cl/cp/ca gradients --- */
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1GradVec)) {
+ vecTmp = pvl->directAnswer[tenGageCl1GradVec];
+
+ ELL_3V_SET(vecTmp,
+ (evalAns[0]*(-2*pvl->directAnswer[tenGageEvalGrads][3]-pvl->directAnswer[tenGageEvalGrads][6])
+ +evalAns[1]*(2*pvl->directAnswer[tenGageEvalGrads][0]+pvl->directAnswer[tenGageEvalGrads][6])
+ +evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][0]-pvl->directAnswer[tenGageEvalGrads][3]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]),
+ (evalAns[0]*(-2*pvl->directAnswer[tenGageEvalGrads][4]-pvl->directAnswer[tenGageEvalGrads][7])
+ +evalAns[1]*(2*pvl->directAnswer[tenGageEvalGrads][1]+pvl->directAnswer[tenGageEvalGrads][7])
+ +evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][1]-pvl->directAnswer[tenGageEvalGrads][4]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]),
+ (evalAns[0]*(-2*pvl->directAnswer[tenGageEvalGrads][5]-pvl->directAnswer[tenGageEvalGrads][8])
+ +evalAns[1]*(2*pvl->directAnswer[tenGageEvalGrads][2]+pvl->directAnswer[tenGageEvalGrads][8])
+ +evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][2]-pvl->directAnswer[tenGageEvalGrads][5]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]));
+ }
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1GradMag)) {
+ pvl->directAnswer[tenGageCl1GradMag][0] = ELL_3V_LEN(vecTmp);
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1GradVec)) {
+ vecTmp = pvl->directAnswer[tenGageCp1GradVec];
+
+ ELL_3V_SET(vecTmp,
+ 2*(evalAns[0]*(pvl->directAnswer[tenGageEvalGrads][3]-pvl->directAnswer[tenGageEvalGrads][6])
+ +evalAns[1]*(-pvl->directAnswer[tenGageEvalGrads][0]-2*pvl->directAnswer[tenGageEvalGrads][6])
+ +evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][0]+2*pvl->directAnswer[tenGageEvalGrads][3]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]),
+ 2*(evalAns[0]*(pvl->directAnswer[tenGageEvalGrads][4]-pvl->directAnswer[tenGageEvalGrads][7])
+ +evalAns[1]*(-pvl->directAnswer[tenGageEvalGrads][1]-2*pvl->directAnswer[tenGageEvalGrads][7])
+ +evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][1]+2*pvl->directAnswer[tenGageEvalGrads][4]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]),
+ 2*(evalAns[0]*(pvl->directAnswer[tenGageEvalGrads][5]-pvl->directAnswer[tenGageEvalGrads][8])
+ +evalAns[1]*(-pvl->directAnswer[tenGageEvalGrads][2]-2*pvl->directAnswer[tenGageEvalGrads][8])
+ +evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][2]+2*pvl->directAnswer[tenGageEvalGrads][5]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]));
+ }
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1GradMag)) {
+ pvl->directAnswer[tenGageCp1GradMag][0] = ELL_3V_LEN(vecTmp);
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1GradVec)) {
+ vecTmp = pvl->directAnswer[tenGageCa1GradVec];
+
+ ELL_3V_SET(vecTmp,
+ -3*((evalAns[0]+evalAns[1])*pvl->directAnswer[tenGageEvalGrads][6]
+ -evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][0]+pvl->directAnswer[tenGageEvalGrads][3]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]),
+ -3*((evalAns[0]+evalAns[1])*pvl->directAnswer[tenGageEvalGrads][7]
+ -evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][1]+pvl->directAnswer[tenGageEvalGrads][4]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]),
+ -3*((evalAns[0]+evalAns[1])*pvl->directAnswer[tenGageEvalGrads][8]
+ -evalAns[2]*(pvl->directAnswer[tenGageEvalGrads][2]+pvl->directAnswer[tenGageEvalGrads][5]))
+ /(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]));
+ }
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1GradMag)) {
+ pvl->directAnswer[tenGageCa1GradMag][0] = ELL_3V_LEN(vecTmp);
+ }
+
+ /* --- tensor gradient, rotated into eigenframe of the tensor itself --- */
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensorGradRotE)) {
+ /* confidence not affected by rotation */
+ ELL_3V_COPY(pvl->directAnswer[tenGageTensorGradRotE], pvl->directAnswer[tenGageTensorGrad]);
+
+ float evecsT[9], evecs[9], tmp[9], tmp2[9];
+
+ /* pre-compute relative eigenvalue differences to detect ill-conditioned case */
+ float diff0=(evalAns[0]-evalAns[1])/(evalAns[0]+evalAns[1]);
+ float diff1=(evalAns[1]-evalAns[2])/(evalAns[1]+evalAns[2]);
+ float diff2=(evalAns[0]-evalAns[2])/(evalAns[0]+evalAns[2]);
+ float diffthresh=0.05;
+
+ float rdiff0, rdiff1, rdiff2;
+ if (diff2>diffthresh) rdiff2=1.0; else rdiff2=diff2/diffthresh;
+ if (diff1>diffthresh) rdiff1=1.0; else rdiff1=diff1/diffthresh;
+ if (diff0>diffthresh) rdiff0=1.0; else rdiff0=diff0/diffthresh;
+
+ ELL_3M_COPY(evecs,evecAns);
+ ELL_3M_TRANSPOSE(evecsT,evecs);
+ int i, k;
+ for (i=0; i<3; ++i) {
+ /* first, simply rotate derivatives into eigenframe of value */
+ TEN_T2M(tmp,gradDdXYZ + i*7);
+ ell_3m_mul_f(tmp2,tmp,evecsT);
+ ell_3m_mul_f(tmp,evecs,tmp2);
+
+ /* If necessary, perform a number of additional rotations to
+ * distribute eigenvalue derivatives equally in ill-defined
+ * cases. Explanation in Schultz and Seidel, "Using Eigenvalue
+ * Derivatives for Edge Detection in DT-MRI Data", DAGM 2008*/
+ if (rdiff0<1.0) {
+ /* rotate around z axis */
+ float phi=0.5*atan((tmp[0]-tmp[4])/(2*tmp[1]));
+ float R[9],RT[9];
+ ELL_3M_ROTATE_Z_SET(R, (1.0-rdiff0)*phi);
+ ELL_3M_TRANSPOSE(RT,R);
+ ell_3m_mul_f(tmp2,tmp,RT);
+ ell_3m_mul_f(tmp,R,tmp2);
+ }
+ if (rdiff1<1.0) {
+ /* rotate around x axis */
+ float phi=0.5*atan((tmp[4]-tmp[8])/(2*tmp[5]));
+ float R[9],RT[9];
+ ELL_3M_ROTATE_X_SET(R, (1.0-rdiff1)*phi);
+ ELL_3M_TRANSPOSE(RT,R);
+ ell_3m_mul_f(tmp2,tmp,RT);
+ ell_3m_mul_f(tmp,R,tmp2);
+ }
+ if (rdiff2<1.0) {
+ float mean=(tmp[0]+tmp[4]+tmp[8])/3.0;
+ /* what's the median? */
+ int midaxis=0;
+ if ((tmp[0]>tmp[4] && tmp[4]>tmp[8])||
+ (tmp[0]<tmp[4] && tmp[4]<tmp[8]))
+ midaxis=1;
+ else if ((tmp[4]>tmp[8] && tmp[8]>tmp[0])||
+ (tmp[4]<tmp[8] && tmp[8]<tmp[0]))
+ midaxis=2;
+ int axis;
+ float submatrix[3];
+ int smallest=0;
+ /* do we first rotate around smallest or largest? */
+ if (mean>tmp[4*midaxis])
+ smallest=1;
+
+ char sign=1;
+ if ((smallest && (tmp[0]<tmp[4] && tmp[0]<tmp[8])) ||
+ (!smallest && (tmp[0]>tmp[4] && tmp[0]>tmp[8]))) {
+ axis=0;
+ submatrix[0]=tmp[4];
+ submatrix[1]=tmp[5];
+ submatrix[2]=tmp[8];
+ if (midaxis!=1) sign=-1;
+ } else if ((smallest && (tmp[4]<tmp[0] && tmp[4]<tmp[8])) ||
+ (!smallest && (tmp[4]>tmp[0] && tmp[4]>tmp[8]))) {
+ axis=1;
+ submatrix[0]=tmp[8];
+ submatrix[1]=tmp[2];
+ submatrix[2]=tmp[0];
+ if (midaxis!=2) sign=-1;
+ } else {
+ axis=2;
+ submatrix[0]=tmp[0];
+ submatrix[1]=tmp[1];
+ submatrix[2]=tmp[4];
+ if (midaxis!=0) sign=-1;
+ }
+ float isoPhi=0.0f;
+ float gamma=sign*(submatrix[0]-submatrix[2]);
+ float beta=-sign*2*submatrix[1];
+ float A=sqrt(gamma*gamma+beta*beta);
+ float C=atan2(gamma,beta);
+ isoPhi=0.5*(asin(2.0/A*(mean-0.5*(submatrix[0]+submatrix[2])))-C);
+ /* make sure we use the minimal rotation */
+ isoPhi=asin(2.0/A*(mean-0.5*(submatrix[0]+submatrix[2])));
+ if (isoPhi>0) {
+ if (fabs(M_PI-isoPhi-C)<fabs(isoPhi-C))
+ isoPhi=0.5*(M_PI-isoPhi-C);
+ else
+ isoPhi=0.5*(isoPhi-C);
+ } else if (isoPhi<0) {
+ if (fabs(-M_PI-isoPhi-C)<fabs(isoPhi-C))
+ isoPhi=0.5*(-M_PI-isoPhi-C);
+ else
+ isoPhi=0.5*(isoPhi-C);
+ }
+
+ /* perform the rotation */
+ float R[9],RT[9];
+ switch (axis) {
+ case 0:
+ ELL_3M_ROTATE_X_SET(R, (1.0-rdiff2)*isoPhi);
+ break;
+ case 1:
+ ELL_3M_ROTATE_Y_SET(R, (1.0-rdiff2)*isoPhi);
+ break;
+ default:
+ ELL_3M_ROTATE_Z_SET(R, (1.0-rdiff2)*isoPhi);
+ break;
+ }
+ ELL_3M_TRANSPOSE(RT,R);
+ ell_3m_mul_f(tmp2,tmp,RT);
+ ell_3m_mul_f(tmp,R,tmp2);
+
+ /* rotate around the now corrected evec */
+ axis=midaxis;
+ switch (midaxis) {
+ case 0:
+ ELL_3M_ROTATE_X_SET(R, (1.0-rdiff2)*0.5*atan((tmp[0]-tmp[4])/(2*tmp[1])));
+ break;
+ case 1:
+ ELL_3M_ROTATE_Y_SET(R, (1.0-rdiff2)*0.5*atan((tmp[8]-tmp[0])/(2*tmp[2])));
+ break;
+ case 2:
+ ELL_3M_ROTATE_Z_SET(R, (1.0-rdiff2)*0.5*atan((tmp[4]-tmp[8])/(2*tmp[5])));
+ break;
+ }
+ ELL_3M_TRANSPOSE(RT,R);
+ ell_3m_mul_f(tmp2,tmp,RT);
+ ell_3m_mul_f(tmp,R,tmp2);
+ }
+ /* Now, we can set the answer */
+ TEN_M2T(tmp2,tmp);
+ for (k=1; k<7; ++k) {
+ pvl->directAnswer[tenGageTensorGradRotE][3*k+i] = tmp2[k];
+ }
+ }
+ }
+
return;
}
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|
|
From: <ts...@us...> - 2008-08-01 08:33:48
|
Revision: 3882
http://teem.svn.sourceforge.net/teem/?rev=3882&view=rev
Author: tststs
Date: 2008-08-01 08:33:57 +0000 (Fri, 01 Aug 2008)
Log Message:
-----------
Declared the last two parameters of tenMakeSingle* "const" to avoid compiler
warnings.
--This line, and those below, will be ignored--
M ten/tensor.c
M ten/ten.h
Modified Paths:
--------------
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tensor.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2008-07-25 14:14:10 UTC (rev 3881)
+++ teem/trunk/src/ten/ten.h 2008-08-01 08:33:57 UTC (rev 3882)
@@ -1178,9 +1178,9 @@
TEN_EXPORT int tenEigensolve_d(double eval[3], double evec[9],
const double ten[7]);
TEN_EXPORT void tenMakeSingle_f(float ten[7],
- float conf, float eval[3], float evec[9]);
+ float conf, const float eval[3], const float evec[9]);
TEN_EXPORT void tenMakeSingle_d(double ten[7],
- double conf, double eval[3], double evec[9]);
+ double conf, const double eval[3], const double evec[9]);
TEN_EXPORT int tenMake(Nrrd *nout, const Nrrd *nconf,
const Nrrd *neval, const Nrrd *nevec);
TEN_EXPORT int tenSlice(Nrrd *nout, const Nrrd *nten,
Modified: teem/trunk/src/ten/tensor.c
===================================================================
--- teem/trunk/src/ten/tensor.c 2008-07-25 14:14:10 UTC (rev 3881)
+++ teem/trunk/src/ten/tensor.c 2008-08-01 08:33:57 UTC (rev 3882)
@@ -404,7 +404,7 @@
*/
void
-tenMakeSingle_f(float ten[7], float conf, float eval[3], float evec[9]) {
+tenMakeSingle_f(float ten[7], float conf, const float eval[3], const float evec[9]) {
double tmpMat1[9], tmpMat2[9], diag[9], evecT[9];
ELL_3M_ZERO_SET(diag);
@@ -419,7 +419,7 @@
/* HEY: copy and paste! */
void
-tenMakeSingle_d(double ten[7], double conf, double eval[3], double evec[9]) {
+tenMakeSingle_d(double ten[7], double conf, const double eval[3], const double evec[9]) {
double tmpMat1[9], tmpMat2[9], diag[9], evecT[9];
ELL_3M_ZERO_SET(diag);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2008-10-28 22:11:02
|
Revision: 3912
http://teem.svn.sourceforge.net/teem/?rev=3912&view=rev
Author: kindlmann
Date: 2008-10-28 22:10:57 +0000 (Tue, 28 Oct 2008)
Log Message:
-----------
added tenFiberStopAnisoSet, tenFiberStopDoubleSet, tenFiberStopUIntSet so that stop criteria can be set without using var-args
Modified Paths:
--------------
teem/trunk/src/ten/fiberMethods.c
teem/trunk/src/ten/ten.h
Modified: teem/trunk/src/ten/fiberMethods.c
===================================================================
--- teem/trunk/src/ten/fiberMethods.c 2008-10-16 00:31:05 UTC (rev 3911)
+++ teem/trunk/src/ten/fiberMethods.c 2008-10-28 22:10:57 UTC (rev 3912)
@@ -527,6 +527,63 @@
return ret;
}
+/* to avoid var-args */
+int
+tenFiberStopAnisoSet(tenFiberContext *tfx, int anisoType, double anisoThresh) {
+ char me[]="tenFiberStopAnisoSet", err[BIFF_STRLEN];
+
+ if (tenFiberStopSet(tfx, tenFiberStopAniso, anisoType, anisoThresh)) {
+ sprintf(err, "%s: trouble", me);
+ biffAdd(TEN, err); return 1;
+ }
+ return 0;
+}
+
+/* to avoid var-args */
+int
+tenFiberStopDoubleSet(tenFiberContext *tfx, int stop, double val) {
+ char me[]="tenFiberStopDoubleSet", err[BIFF_STRLEN];
+
+ switch (stop) {
+ case tenFiberStopLength:
+ case tenFiberStopMinLength:
+ case tenFiberStopConfidence:
+ case tenFiberStopRadius:
+ case tenFiberStopFraction:
+ if (tenFiberStopSet(tfx, stop, val)) {
+ sprintf(err, "%s: trouble", me);
+ biffAdd(TEN, err); return 1;
+ }
+ break;
+ default:
+ sprintf(err, "%s: given stop criterion %d (%s) isn't a double", me,
+ stop, airEnumStr(tenFiberStop, stop));
+ biffAdd(TEN, err); return 1;
+ }
+ return 0;
+}
+
+/* to avoid var-args */
+int
+tenFiberStopUIntSet(tenFiberContext *tfx, int stop, unsigned int val) {
+ char me[]="tenFiberStopUIntSet", err[BIFF_STRLEN];
+
+ switch (stop) {
+ case tenFiberStopNumSteps:
+ case tenFiberStopMinNumSteps:
+ if (tenFiberStopSet(tfx, stop, val)) {
+ sprintf(err, "%s: trouble", me);
+ biffAdd(TEN, err); return 1;
+ }
+ break;
+ default:
+ sprintf(err, "%s: given stop criterion %d (%s) isn't an unsigned int", me,
+ stop, airEnumStr(tenFiberStop, stop));
+ biffAdd(TEN, err); return 1;
+ }
+ return 0;
+}
+
void
tenFiberStopOn(tenFiberContext *tfx, int stop) {
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2008-10-16 00:31:05 UTC (rev 3911)
+++ teem/trunk/src/ten/ten.h 2008-10-28 22:10:57 UTC (rev 3912)
@@ -1365,6 +1365,12 @@
const double parm[NRRD_KERNEL_PARMS_NUM]);
TEN_EXPORT int tenFiberIntgSet(tenFiberContext *tfx, int intg);
TEN_EXPORT int tenFiberStopSet(tenFiberContext *tfx, int stop, ...);
+TEN_EXPORT int tenFiberStopAnisoSet(tenFiberContext *tfx,
+ int anisoType, double anisoThresh);
+TEN_EXPORT int tenFiberStopDoubleSet(tenFiberContext *tfx,
+ int stop, double val);
+TEN_EXPORT int tenFiberStopUIntSet(tenFiberContext *tfx,
+ int stop, unsigned int val);
TEN_EXPORT void tenFiberStopOn(tenFiberContext *tfx, int stop);
TEN_EXPORT void tenFiberStopOff(tenFiberContext *tfx, int stop);
TEN_EXPORT void tenFiberStopReset(tenFiberContext *tfx);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2008-11-03 23:22:03
|
Revision: 3917
http://teem.svn.sourceforge.net/teem/?rev=3917&view=rev
Author: kindlmann
Date: 2008-11-03 23:22:00 +0000 (Mon, 03 Nov 2008)
Log Message:
-----------
API NEW: added tenFiberMulti struct, tenFiberMultiNew(), tenFiberMultiNix(), and API CHANGE the use of tenFiberMultiTrace() and tenFiberMultiPolyData()
Modified Paths:
--------------
teem/trunk/src/ten/fiber.c
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tendFiber.c
Modified: teem/trunk/src/ten/fiber.c
===================================================================
--- teem/trunk/src/ten/fiber.c 2008-11-02 04:23:34 UTC (rev 3916)
+++ teem/trunk/src/ten/fiber.c 2008-11-03 23:22:00 UTC (rev 3917)
@@ -863,6 +863,34 @@
return 0;
}
+/* uses biff */
+tenFiberMulti *
+tenFiberMultiNew() {
+ char me[]="tenFiberMultiNew", err[BIFF_STRLEN];
+ tenFiberMulti *ret;
+
+ ret = AIR_CAST(tenFiberMulti *, calloc(1, sizeof(tenFiberMulti)));
+ if (ret) {
+ ret->fiber = NULL;
+ ret->fiberNum = 0;
+ ret->fiberArr = airArrayNew(AIR_CAST(void **, &(ret->fiber)),
+ &(ret->fiberNum),
+ sizeof(tenFiberSingle), 512 /* incr */);
+ if (ret->fiberArr) {
+ airArrayStructCB(ret->fiberArr,
+ AIR_CAST(void (*)(void *), tenFiberSingleInit),
+ AIR_CAST(void (*)(void *), tenFiberSingleDone));
+ } else {
+ sprintf(err, "%s: couldn't create airArray", me);
+ biffAdd(TEN, err); return NULL;
+ }
+ } else {
+ sprintf(err, "%s: couldn't create tenFiberMulti", me);
+ biffAdd(TEN, err); return NULL;
+ }
+ return ret;
+}
+
int
tenFiberMultiCheck(airArray *arr) {
char me[]="tenFiberMultiCheck", err[BIFF_STRLEN];
@@ -883,36 +911,42 @@
return 0;
}
+tenFiberMulti *
+tenFiberMultiNix(tenFiberMulti *tfm) {
+
+ if (tfm) {
+ airArrayNuke(tfm->fiberArr);
+ airFree(tfm);
+ }
+ return NULL;
+}
+
/*
******** tenFiberMultiTrace
**
** does tractography for a list of seedpoints
**
-** "tfbsArr" is an airArray that the caller has already set up to be
-** an array of tenFiberSingle pointers, with length set to represent
-** the number of tenFiberSingle's that have already been allocated
-** (and pointed to).
+** tfml has been returned from tenFiberMultiNew()
**
** This is probably the first time that an airArray is being forced on
** Teem API users in this way, since other container structs/classes
** could probably be better here. Alas.
*/
int
-tenFiberMultiTrace(tenFiberContext *tfx, airArray *tfbsArr,
+tenFiberMultiTrace(tenFiberContext *tfx, tenFiberMulti *tfml,
const Nrrd *_nseed) {
char me[]="tenFiberMultiTrace", err[BIFF_STRLEN];
airArray *mop;
const double *seedData;
double seed[3];
unsigned int seedNum, seedIdx, fibrNum, dirNum, dirIdx;
- tenFiberSingle *tfbs;
Nrrd *nseed;
- if (!(tfx && tfbsArr && _nseed)) {
+ if (!(tfx && tfml && _nseed)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(TEN, err); return 1;
}
- if (tenFiberMultiCheck(tfbsArr)) {
+ if (tenFiberMultiCheck(tfml->fiberArr)) {
sprintf(err, "%s: problem with fiber array", me);
biffAdd(TEN, err); return 1;
}
@@ -940,7 +974,6 @@
/* HEY: the correctness of the use of the airArray here is quite subtle */
fibrNum = 0;
- tfbs = AIR_CAST(tenFiberSingle *, tfbsArr->data);
for (seedIdx=0; seedIdx<seedNum; seedIdx++) {
dirNum = tenFiberDirectionNumber(tfx, seed);
if (!dirNum) {
@@ -951,35 +984,37 @@
for (dirIdx=0; dirIdx<dirNum; dirIdx++) {
if (tfx->verbose > 1) {
fprintf(stderr, "%s: dir %u/%u on seed %u/%u; len %u; # %u\n",
- me, dirIdx, dirNum, seedIdx, seedNum, tfbsArr->len, fibrNum);
+ me, dirIdx, dirNum, seedIdx, seedNum,
+ tfml->fiberArr->len, fibrNum);
}
- /* tfbsArr->len can never be < fibrNum */
- if (tfbsArr->len == fibrNum) {
- airArrayLenIncr(tfbsArr, 1);
- tfbs = AIR_CAST(tenFiberSingle *, tfbsArr->data);
+ /* tfml->fiberArr->len can never be < fibrNum */
+ if (tfml->fiberArr->len == fibrNum) {
+ airArrayLenIncr(tfml->fiberArr, 1);
}
- ELL_3V_COPY(tfbs[fibrNum].seedPos, seedData + 3*seedIdx);
- tfbs[fibrNum].dirIdx = dirIdx;
- tfbs[fibrNum].dirNum = dirNum;
+ ELL_3V_COPY(tfml->fiber[fibrNum].seedPos, seedData + 3*seedIdx);
+ tfml->fiber[fibrNum].dirIdx = dirIdx;
+ tfml->fiber[fibrNum].dirNum = dirNum;
ELL_3V_COPY(seed, seedData + 3*seedIdx);
- if (tenFiberSingleTrace(tfx, &(tfbs[fibrNum]), seed, dirIdx)) {
+ if (tenFiberSingleTrace(tfx, &(tfml->fiber[fibrNum]), seed, dirIdx)) {
sprintf(err, "%s: trouble on seed (%g,%g,%g) %u/%u, dir %u/%u", me,
seed[0], seed[1], seed[2], seedIdx, seedNum, dirIdx, dirNum);
biffAdd(TEN, err); return 1;
}
if (tfx->verbose) {
- if (tenFiberStopUnknown == tfbs[fibrNum].whyNowhere) {
+ if (tenFiberStopUnknown == tfml->fiber[fibrNum].whyNowhere) {
fprintf(stderr, "%s: (%g,%g,%g) ->\n"
" steps = %u,%u; len = %g,%g; whyStop = %s,%s\n",
me, seed[0], seed[1], seed[2],
- tfbs[fibrNum].stepNum[0], tfbs[fibrNum].stepNum[1],
- tfbs[fibrNum].halfLen[0], tfbs[fibrNum].halfLen[1],
- airEnumStr(tenFiberStop, tfbs[fibrNum].whyStop[0]),
- airEnumStr(tenFiberStop, tfbs[fibrNum].whyStop[1]));
+ tfml->fiber[fibrNum].stepNum[0],
+ tfml->fiber[fibrNum].stepNum[1],
+ tfml->fiber[fibrNum].halfLen[0],
+ tfml->fiber[fibrNum].halfLen[1],
+ airEnumStr(tenFiberStop, tfml->fiber[fibrNum].whyStop[0]),
+ airEnumStr(tenFiberStop, tfml->fiber[fibrNum].whyStop[1]));
} else {
fprintf(stderr, "%s: (%g,%g,%g) -> whyNowhere: %s\n",
me, seed[0], seed[1], seed[2],
- airEnumStr(tenFiberStop, tfbs[fibrNum].whyNowhere));
+ airEnumStr(tenFiberStop, tfml->fiber[fibrNum].whyNowhere));
}
}
fibrNum++;
@@ -988,36 +1023,45 @@
/* if the airArray got to be its length only because of the work above,
then the following will be a no-op. Otherwise, via the callbacks,
it will clear out the tenFiberSingle's that we didn't create here */
- airArrayLenSet(tfbsArr, fibrNum);
+ airArrayLenSet(tfml->fiberArr, fibrNum);
airMopOkay(mop);
return 0;
}
+/*
+******** tenFiberMultiPolyData
+**
+** converts tenFiberMulti to polydata.
+**
+** currently the tenFiberContext *tfx arg is not used, but it will
+** probably be needed in the future as the way that parameters to the
+** polydata creation process are passed.
+*/
int
tenFiberMultiPolyData(tenFiberContext *tfx,
- limnPolyData *lpld, airArray *fiberArr) {
+ limnPolyData *lpld, tenFiberMulti *tfml) {
char me[]="tenFiberMultiPolyData", err[BIFF_STRLEN];
- tenFiberSingle *fiber;
unsigned int seedIdx, vertTotalNum, fiberNum, fiberIdx, vertTotalIdx;
- if (!(tfx && lpld && fiberArr)) {
+ if (!(tfx && lpld && tfml)) {
sprintf(err, "%s: got NULL pointer", me);
biffAdd(TEN, err); return 1;
}
- if (tenFiberMultiCheck(fiberArr)) {
+ if (tenFiberMultiCheck(tfml->fiberArr)) {
sprintf(err, "%s: problem with fiber array", me);
biffAdd(TEN, err); return 1;
}
- fiber = AIR_CAST(tenFiberSingle *, fiberArr->data);
+ /* we have to count the real fibers that went somewhere, excluding
+ fibers that went nowhere (counted in tfml->fiberNum) */
vertTotalNum = 0;
fiberNum = 0;
- for (seedIdx=0; seedIdx<fiberArr->len; seedIdx++) {
- if (!(tenFiberStopUnknown == fiber[seedIdx].whyNowhere)) {
+ for (seedIdx=0; seedIdx<tfml->fiberArr->len; seedIdx++) {
+ if (!(tenFiberStopUnknown == tfml->fiber[seedIdx].whyNowhere)) {
continue;
}
- vertTotalNum += fiber[seedIdx].nvert->axis[1].size;
+ vertTotalNum += tfml->fiber[seedIdx].nvert->axis[1].size;
fiberNum++;
}
@@ -1029,14 +1073,14 @@
fiberIdx = 0;
vertTotalIdx = 0;
- for (seedIdx=0; seedIdx<fiberArr->len; seedIdx++) {
+ for (seedIdx=0; seedIdx<tfml->fiberArr->len; seedIdx++) {
double *vert;
unsigned int vertIdx, vertNum;
- if (!(tenFiberStopUnknown == fiber[seedIdx].whyNowhere)) {
+ if (!(tenFiberStopUnknown == tfml->fiber[seedIdx].whyNowhere)) {
continue;
}
- vertNum = fiber[seedIdx].nvert->axis[1].size;
- vert = AIR_CAST(double*, fiber[seedIdx].nvert->data);
+ vertNum = tfml->fiber[seedIdx].nvert->axis[1].size;
+ vert = AIR_CAST(double*, tfml->fiber[seedIdx].nvert->data);
for (vertIdx=0; vertIdx<vertNum; vertIdx++) {
ELL_3V_COPY_TT(lpld->xyzw + 4*vertTotalIdx, float, vert + 3*vertIdx);
(lpld->xyzw + 4*vertTotalIdx)[3] = 1.0;
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2008-11-02 04:23:34 UTC (rev 3916)
+++ teem/trunk/src/ten/ten.h 2008-11-03 23:22:00 UTC (rev 3917)
@@ -816,7 +816,7 @@
/* ------- available for recording for reference, not used by ten */
double seedPos[3]; /* where was the seed point */
unsigned int dirIdx; /* which direction at seedpoint to follow */
- unsigned int dirNum; /* how many directions at seedpoint could be followed */
+ unsigned int dirNum; /* how many directions at seedpnt could be followed */
/* ------- output ------- */
Nrrd *nvert; /* locations of tract vertices */
double halfLen[2]; /* (same as in tenFiberContext) */
@@ -829,6 +829,17 @@
} tenFiberSingle;
/*
+******** tenFiberMulti
+**
+** container for multiple fibers
+*/
+typedef struct {
+ tenFiberSingle *fiber;
+ unsigned int fiberNum;
+ airArray *fiberArr;
+} tenFiberMulti;
+
+/*
******** struct tenEmBimodalParm
**
** input and output parameters for tenEMBimodal (for fitting two
@@ -1393,10 +1404,12 @@
double seed[3]);
TEN_EXPORT int tenFiberSingleTrace(tenFiberContext *tfx, tenFiberSingle *tfbs,
double seed[3], unsigned int which);
-TEN_EXPORT int tenFiberMultiTrace(tenFiberContext *tfx, airArray *tfbsArr,
+TEN_EXPORT tenFiberMulti *tenFiberMultiNew(void);
+TEN_EXPORT tenFiberMulti *tenFiberMultiNix(tenFiberMulti *tfm);
+TEN_EXPORT int tenFiberMultiTrace(tenFiberContext *tfx, tenFiberMulti *tfml,
const Nrrd *nseed);
TEN_EXPORT int tenFiberMultiPolyData(tenFiberContext *tfx,
- limnPolyData *lpld, airArray *tfbsArr);
+ limnPolyData *lpld, tenFiberMulti *tfml);
/* epireg.c */
TEN_EXPORT int _tenEpiRegThresholdFind(double *DWthrP, Nrrd **nin,
Modified: teem/trunk/src/ten/tendFiber.c
===================================================================
--- teem/trunk/src/ten/tendFiber.c 2008-11-02 04:23:34 UTC (rev 3916)
+++ teem/trunk/src/ten/tendFiber.c 2008-11-03 23:22:00 UTC (rev 3917)
@@ -37,7 +37,7 @@
char *outS;
tenFiberContext *tfx;
- tenFiberSingle *tfbs, *fiber;
+ tenFiberSingle *tfbs;
NrrdKernelSpec *ksp;
double start[3], step, *_stop, *stop;
airEnum *ftypeEnum;
@@ -47,7 +47,7 @@
Nrrd *nin, *nseed, *nmat, *_nmat;
unsigned int si, stopLen, whichPath;
double matx[16]={1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1};
- airArray *fiberArr;
+ tenFiberMulti *tfml;
limnPolyData *fiberPld;
hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
@@ -259,16 +259,20 @@
fprintf(stderr, "%s: didn't get seed nrrd via \"-ns\"\n", me);
airMopError(mop); return 1;
}
+ tfml = tenFiberMultiNew();
+ airMopAdd(mop, tfml, (airMopper)tenFiberMultiNix, airMopAlways);
+ /*
fiberArr = airArrayNew(AIR_CAST(void **, &fiber), NULL,
- sizeof(tenFiberSingle), 1024 /* incr */);
+ sizeof(tenFiberSingle), 1024);
airArrayStructCB(fiberArr,
AIR_CAST(void (*)(void *), tenFiberSingleInit),
AIR_CAST(void (*)(void *), tenFiberSingleDone));
airMopAdd(mop, fiberArr, (airMopper)airArrayNuke, airMopAlways);
+ */
fiberPld = limnPolyDataNew();
airMopAdd(mop, fiberPld, (airMopper)limnPolyDataNix, airMopAlways);
- if (tenFiberMultiTrace(tfx, fiberArr, nseed)
- || tenFiberMultiPolyData(tfx, fiberPld, fiberArr)) {
+ if (tenFiberMultiTrace(tfx, tfml, nseed)
+ || tenFiberMultiPolyData(tfx, fiberPld, tfml)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble:\n%s\n", me, err);
airMopError(mop); return 1;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2008-11-17 19:02:18
|
Revision: 3979
http://teem.svn.sourceforge.net/teem/?rev=3979&view=rev
Author: kindlmann
Date: 2008-11-17 19:02:12 +0000 (Mon, 17 Nov 2008)
Log Message:
-----------
The tend commands that take a 7-component tensor can now take a 6-component tensor and it will be silently padded out to 7 components, by a significantly hacked up PARSE() macro
Modified Paths:
--------------
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/tendAnplot.c
teem/trunk/src/ten/tendAvg.c
teem/trunk/src/ten/tendBmat.c
teem/trunk/src/ten/tendEllipse.c
teem/trunk/src/ten/tendEpireg.c
teem/trunk/src/ten/tendEstim.c
teem/trunk/src/ten/tendGlyph.c
teem/trunk/src/ten/tendHelix.c
teem/trunk/src/ten/tendMake.c
teem/trunk/src/ten/tendSatin.c
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/privateTen.h 2008-11-17 19:02:12 UTC (rev 3979)
@@ -30,8 +30,9 @@
#define TEND_CMD(name, info) \
unrrduCmd tend_##name##Cmd = { #name, info, tend_##name##Main }
-/* USAGE, PARSE: both copied verbatim from unrrdu/privateUnrrdu.h */
-
+/* USAGE, PARSE: both copied verbatim from unrrdu/privateUnrrdu.h, but
+** then some hacking was added ...
+*/
#define USAGE(info) \
if (!argc) { \
hestInfo(stderr, me, (info), hparm); \
@@ -41,20 +42,53 @@
return 2; \
}
-#define PARSE() \
- if ((pret=hestParse(hopt, argc, argv, &perr, hparm))) { \
- if (1 == pret) { \
- fprintf(stderr, "%s: %s\n", me, perr); free(perr); \
- hestUsage(stderr, hopt, me, hparm); \
- airMopError(mop); \
- return 2; \
- } else { \
- /* ... like tears ... in rain. Time ... to die. */ \
- exit(1); \
- } \
+/* JUSTPARSE is called by the tend functions that do *not* take an
+** input 7-component tensor volume
+*/
+#define JUSTPARSE() \
+ if ((pret=hestParse(hopt, argc, argv, &perr, hparm))) { \
+ if (1 == pret) { \
+ fprintf(stderr, "%s: %s\n", me, perr); free(perr); \
+ hestUsage(stderr, hopt, me, hparm); \
+ airMopError(mop); \
+ return 2; \
+ } else { \
+ /* ... like tears ... in rain. Time ... to die. */ \
+ exit(1); \
+ } \
}
-
-
+
+/*
+** PARSE is called by tend functions that do take a 7-component tensor
+** volume, so that as a hack, we can process 6-component volumes as well,
+** by padding on the confidence channel (fixed at 1.0)
+*/
+#define PARSE() \
+ JUSTPARSE(); \
+ if (4 == nin->dim \
+ && 6 == nin->axis[0].size \
+ && nrrdTypeBlock != nin->type) { \
+ ptrdiff_t min[4], max[4]; \
+ Nrrd *ntmp; \
+ /* create a confidence channel by padding on 1s */ \
+ min[0] = -1; min[1] = min[2] = min[3] = 0; \
+ max[0] = nin->axis[0].size-1; \
+ max[1] = nin->axis[1].size-1; \
+ max[2] = nin->axis[2].size-1; \
+ max[3] = nin->axis[3].size-1; \
+ ntmp = nrrdNew(); \
+ if (nrrdPad_nva(ntmp, nin, min, max, nrrdBoundaryPad, 1.0) \
+ || nrrdCopy(nin, ntmp)) { \
+ char *err; \
+ airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways); \
+ fprintf(stderr, "%s: can't pad 6-comp tensor:\n%s", me, err); \
+ airMopError(mop); \
+ nrrdNuke(ntmp); \
+ return 2; \
+ } \
+ nrrdNuke(ntmp); \
+ }
+
/* qseg.c: 2-tensor estimation */
extern void _tenQball(const double b, const int gradcount,
const double svals[], const double grads[],
Modified: teem/trunk/src/ten/tendAnplot.c
===================================================================
--- teem/trunk/src/ten/tendAnplot.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendAnplot.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -68,7 +68,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_anplotInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendAvg.c
===================================================================
--- teem/trunk/src/ten/tendAvg.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendAvg.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -52,7 +52,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_avgInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendBmat.c
===================================================================
--- teem/trunk/src/ten/tendBmat.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendBmat.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -55,7 +55,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_bmatInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
Modified: teem/trunk/src/ten/tendEllipse.c
===================================================================
--- teem/trunk/src/ten/tendEllipse.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendEllipse.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -248,7 +248,7 @@
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_ellipseInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (npos) {
Modified: teem/trunk/src/ten/tendEpireg.c
===================================================================
--- teem/trunk/src/ten/tendEpireg.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendEpireg.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -116,7 +116,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_epiregInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (strcmp("kvp", gradS)) {
Modified: teem/trunk/src/ten/tendEstim.c
===================================================================
--- teem/trunk/src/ten/tendEstim.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendEstim.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -212,7 +212,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_estimInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendGlyph.c
===================================================================
--- teem/trunk/src/ten/tendGlyph.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendGlyph.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -102,7 +102,7 @@
char *perr, *err;
airArray *mop;
- Nrrd *nten, *emap, *nraw, *npos, *nslc;
+ Nrrd *nin, *emap, *nraw, *npos, *nslc;
char *outS;
limnCamera *cam, *hackcams;
limnObject *glyph;
@@ -318,7 +318,7 @@
"don't mind me");
/* input/output */
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nten, "-",
+ hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
"input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
"output file");
@@ -348,7 +348,7 @@
if (tenGlyphGen(doRT ? NULL : glyph,
doRT ? scene : NULL,
gparm,
- nten, npos, nslc)) {
+ nin, npos, nslc)) {
airMopAdd(mop, err = biffGetDone(TEN), airFree, airMopAlways);
fprintf(stderr, "%s: trouble generating glyphs:\n%s\n", me, err);
airMopError(mop); return 1;
Modified: teem/trunk/src/ten/tendHelix.c
===================================================================
--- teem/trunk/src/ten/tendHelix.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendHelix.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -190,7 +190,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_helixInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendMake.c
===================================================================
--- teem/trunk/src/ten/tendMake.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendMake.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -48,7 +48,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_makeInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendSatin.c
===================================================================
--- teem/trunk/src/ten/tendSatin.c 2008-11-17 19:00:54 UTC (rev 3978)
+++ teem/trunk/src/ten/tendSatin.c 2008-11-17 19:02:12 UTC (rev 3979)
@@ -223,7 +223,7 @@
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
USAGE(_tend_satinInfoL);
- PARSE();
+ JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
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|
|
From: <kin...@us...> - 2008-11-19 04:49:51
|
Revision: 3992
http://teem.svn.sourceforge.net/teem/?rev=3992&view=rev
Author: kindlmann
Date: 2008-11-19 04:49:46 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
adding tend about, like unu about
Modified Paths:
--------------
teem/trunk/src/ten/GNUmakefile
teem/trunk/src/ten/sources.cmake
teem/trunk/src/ten/ten.h
Added Paths:
-----------
teem/trunk/src/ten/tendAbout.c
Modified: teem/trunk/src/ten/GNUmakefile
===================================================================
--- teem/trunk/src/ten/GNUmakefile 2008-11-18 17:25:00 UTC (rev 3991)
+++ teem/trunk/src/ten/GNUmakefile 2008-11-19 04:49:46 UTC (rev 3992)
@@ -51,7 +51,7 @@
$(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o grads.o miscTen.o \
mod.o estimate.o tenGage.o tenDwiGage.o qseg.o path.o qglox.o \
fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o bvec.o \
- triple.o \
+ triple.o tendAbout.o \
tendFlotsam.o tendGrads.o tendAnplot.o tendAnvol.o tendEval.o \
tendEvec.o tendSten.o tendExpand.o tendEvq.o tendPoint.o \
tendTriple.o tendTconv.o tendAvg.o \
Modified: teem/trunk/src/ten/sources.cmake
===================================================================
--- teem/trunk/src/ten/sources.cmake 2008-11-18 17:25:00 UTC (rev 3991)
+++ teem/trunk/src/ten/sources.cmake 2008-11-19 04:49:46 UTC (rev 3992)
@@ -22,6 +22,7 @@
qseg.c
path.c
qglox.c
+ tendAbout.c
tendAnhist.c
tendAnplot.c
tendAnscale.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2008-11-18 17:25:00 UTC (rev 3991)
+++ teem/trunk/src/ten/ten.h 2008-11-19 04:49:46 UTC (rev 3992)
@@ -1481,6 +1481,7 @@
#define TEND_LIST(C) &tend_##C##Cmd,
/* removed from below (superseded by estim): F(calc) \ */
#define TEND_MAP(F) \
+F(about) \
F(grads) \
F(epireg) \
F(bmat) \
Added: teem/trunk/src/ten/tendAbout.c
===================================================================
--- teem/trunk/src/ten/tendAbout.c (rev 0)
+++ teem/trunk/src/ten/tendAbout.c 2008-11-19 04:49:46 UTC (rev 3992)
@@ -0,0 +1,86 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define INFO "Information about this program and its use"
+char *_tend_aboutInfoL =
+ (INFO
+ ". ");
+
+int
+tend_aboutMain(int argc, char **argv, char *me, hestParm *hparm) {
+ char buff[AIR_STRLEN_MED], fmt[AIR_STRLEN_MED];
+ char par1[] = "\t\t\t\t"
+ "\"tend\" is a command-line interface to much of the functionality "
+ "in \"ten\", a C library for diffusion image processing. Ten is one "
+ "library in the \"Teem\" collection of libraries. More information "
+ "about Teem is at <http://teem.sourceforge.net>.\n";
+ char par2[] = "\t\t\t\t"
+ "Users are strongly encouraged to join the teem-users mailing list: "
+ "<http://lists.sourceforge.net/lists/listinfo/teem-users>. This is "
+ "the primary forum for feedback, questions, and feature requests.\n";
+ char par3[] = "\t\t\t\t"
+ "Like \"unu\", another Teem command-line binary, it is often useful "
+ "to chain together invocations of tend with pipes, as in the "
+ "following, which estimates tensors from DWIs, takes a slice of the "
+ "tensor volume, computes the standard RGB colormap of the principal "
+ "eigenvector, and then quantizes it to an 8-bit PNG:\n";
+ char par4[] = "\ttend estim -i dwi.nhdr -B kvp -knownB0 true \\\n "
+ " | tend slice -a 2 -p 30 \\\n "
+ " | tend evecrgb -c 0 -a cl2 -gam 1.2 \\\n "
+ " | unu quantize -b 8 -min 0 -max 1 -o z30-rgb.png\n";
+ char par5[] = "\t\t\t\t"
+ "If tend repeatedly proves itself useful for your research, an "
+ "acknowledgment to that effect in your publication would be greatly "
+ "appreciated, such as (for LaTeX): "
+ "\"Dataset processing performed with the {\\tt tend} tool "
+ "part of the {\\tt Teem} toolkit available at "
+ "{\\tt\t$<$http://teem.sf.net$>$}\"\n ";
+
+ AIR_UNUSED(argc);
+ AIR_UNUSED(argv);
+ AIR_UNUSED(me);
+
+ fprintf(stdout, "\n");
+ sprintf(buff, "--- tend: Diffusion Image Processing and Analysis ---");
+ sprintf(fmt, "%%%ds\n",
+ (int)((hparm->columns-strlen(buff))/2 + strlen(buff) - 1));
+ fprintf(stdout, fmt, buff);
+ sprintf(buff, "(Teem version %s, %s)",
+ airTeemVersion, airTeemReleaseDate);
+ sprintf(fmt, "%%%ds\n",
+ (int)((hparm->columns-strlen(buff))/2 + strlen(buff) - 1));
+ fprintf(stdout, fmt, buff);
+ fprintf(stdout, "\n");
+
+ _hestPrintStr(stdout, 1, 0, 78, par1, AIR_FALSE);
+ _hestPrintStr(stdout, 1, 0, 78, par2, AIR_FALSE);
+ _hestPrintStr(stdout, 1, 0, 78, par3, AIR_FALSE);
+ _hestPrintStr(stdout, 2, 0, 78, par4, AIR_FALSE);
+ _hestPrintStr(stdout, 1, 0, 78, par5, AIR_FALSE);
+
+ return 0;
+}
+
+TEND_CMD(about, INFO);
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|
|
From: <kin...@us...> - 2008-11-19 05:00:16
|
Revision: 3993
http://teem.svn.sourceforge.net/teem/?rev=3993&view=rev
Author: kindlmann
Date: 2008-11-19 05:00:12 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
usage information not generated by an error should go to stdout, not stderr
Modified Paths:
--------------
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/tendFlotsam.c
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2008-11-19 04:49:46 UTC (rev 3992)
+++ teem/trunk/src/ten/privateTen.h 2008-11-19 05:00:12 UTC (rev 3993)
@@ -35,9 +35,9 @@
*/
#define USAGE(info) \
if (!argc) { \
- hestInfo(stderr, me, (info), hparm); \
- hestUsage(stderr, hopt, me, hparm); \
- hestGlossary(stderr, hopt, hparm); \
+ hestInfo(stdout, me, (info), hparm); \
+ hestUsage(stdout, hopt, me, hparm); \
+ hestGlossary(stdout, hopt, hparm); \
airMopError(mop); \
return 2; \
}
Modified: teem/trunk/src/ten/tendFlotsam.c
===================================================================
--- teem/trunk/src/ten/tendFlotsam.c 2008-11-19 04:49:46 UTC (rev 3992)
+++ teem/trunk/src/ten/tendFlotsam.c 2008-11-19 05:00:12 UTC (rev 3993)
@@ -51,10 +51,10 @@
maxlen = AIR_MAX(maxlen, (int)strlen(tendCmdList[i]->name));
}
- sprintf(buff, "--- Diffusion Tensor Processing and Analysis ---");
+ sprintf(buff, "--- Diffusion Image Processing and Analysis ---");
sprintf(fmt, "%%%ds\n",
(int)((hparm->columns-strlen(buff))/2 + strlen(buff) - 1));
- fprintf(stderr, fmt, buff);
+ fprintf(stdout, fmt, buff);
for (i=0; tendCmdList[i]; i++) {
len = strlen(tendCmdList[i]->name);
@@ -66,8 +66,8 @@
strcat(buff, tendCmdList[i]->name);
strcat(buff, " ... ");
len = strlen(buff);
- fprintf(stderr, "%s", buff);
- _hestPrintStr(stderr, len, len, hparm->columns,
+ fprintf(stdout, "%s", buff);
+ _hestPrintStr(stdout, len, len, hparm->columns,
tendCmdList[i]->info, AIR_FALSE);
}
}
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|
|
From: <kin...@us...> - 2008-12-09 11:02:03
|
Revision: 4035
http://teem.svn.sourceforge.net/teem/?rev=4035&view=rev
Author: kindlmann
Date: 2008-12-09 11:02:01 +0000 (Tue, 09 Dec 2008)
Log Message:
-----------
Integrating last fixes and changes from Arish Qazi based on his
two-tensor tractography work:
* If the single tensor is too planar (based on pvlData->levmarMinCp),
then the two-tensor fit will not be computed
* removed "ELL_3V_NORM(tfx->lastDir, tfx->lastDir, len);" from
_tenFiberProbe in the case of two-tensor work; the reason why this
works is not yet clear....
* the measurement frame is applied to the whole tensor, instead of
just its eigenvectors
Modified Paths:
--------------
teem/trunk/src/ten/fiber.c
teem/trunk/src/ten/tenDwiGage.c
Modified: teem/trunk/src/ten/fiber.c
===================================================================
--- teem/trunk/src/ten/fiber.c 2008-12-08 17:38:33 UTC (rev 4034)
+++ teem/trunk/src/ten/fiber.c 2008-12-09 11:02:01 UTC (rev 4035)
@@ -55,6 +55,7 @@
char me[]="_tenFiberProbe", err[BIFF_STRLEN];
double iPos[3];
int ret = 0;
+ double tens2[2][7];
gageShapeWtoI(tfx->gtx->shape, iPos, wPos);
*gageRet = gageProbe(tfx->gtx, iPos[0], iPos[1], iPos[2]);
@@ -82,7 +83,7 @@
airEnumStr(tenDwiFiberType, tfx->fiberType));
}
switch (tfx->fiberType) {
- double evec[2][9], eval[2][3], len;
+ double evec[2][9], eval[2][3];
case tenDwiFiberType1Evec0:
if (tfx->mframeUse) {
double matTmpA[9], matTmpB[9];
@@ -106,18 +107,27 @@
break;
case tenDwiFiberType2Evec0:
/* Estimate principal diffusion direction of each tensor */
- tenEigensolve_d(eval[0], evec[0], tfx->gageTen2 + 0);
- tenEigensolve_d(eval[1], evec[1], tfx->gageTen2 + 7);
+ if (tfx->mframeUse) {
+ /* Transform both the tensors */
+ double matTmpA[9], matTmpB[9];
- if (tfx->mframeUse) {
- double vectmp[3];
- /* NOTE: only fixing first (of three) eigenvector, for both tensors */
- ELL_3MV_MUL(vectmp, tfx->mframe, evec[0]);
- ELL_3V_COPY(evec[0], vectmp);
- ELL_3MV_MUL(vectmp, tfx->mframe, evec[1]);
- ELL_3V_COPY(evec[1], vectmp);
+ TEN_T2M(matTmpA, tfx->gageTen2 + 0);
+ ELL_3M_MUL(matTmpB, tfx->mframe, matTmpA);
+ ELL_3M_MUL(matTmpA, matTmpB, tfx->mframeT);
+ TEN_M2T(tens2[0], matTmpA);
+ /* new eigen values and vectors */
+ tenEigensolve_d(eval[0], evec[0], tens2[0]);
+
+ TEN_T2M(matTmpA, tfx->gageTen2 + 7);
+ ELL_3M_MUL(matTmpB, tfx->mframe, matTmpA);
+ ELL_3M_MUL(matTmpA, matTmpB, tfx->mframeT);
+ TEN_M2T(tens2[1], matTmpA);
+ tenEigensolve_d(eval[1], evec[1], tens2[1]);
+ } else {
+ tenEigensolve_d(eval[0], evec[0], tfx->gageTen2 + 0);
+ tenEigensolve_d(eval[1], evec[1], tfx->gageTen2 + 7);
}
-
+
/* set ten2Use */
if (seedProbe) { /* we're on the *very* 1st probe per tract,
at the seed pt */
@@ -135,7 +145,11 @@
lastVec = tfx->seedEvec;
} else {
/* we're past the first step */
- ELL_3V_NORM(tfx->lastDir, tfx->lastDir, len);
+ /* Arish says: "Bug len has not been initialized and don't think
+ its needed". The first part is not a problem; "len" is in the
+ *output* argument of ELL_3V_NORM. The second part seems to be
+ true, even though Gordon can't currently see why! */
+ /* ELL_3V_NORM(tfx->lastDir, tfx->lastDir, len); */
lastVec = tfx->lastDir;
}
dot[0] = ELL_3V_DOT(lastVec, evec[0]);
@@ -158,11 +172,7 @@
/* based on ten2Use, set the rest of the needed fields */
if (tfx->mframeUse) {
- double matTmpA[9], matTmpB[9];
- TEN_T2M(matTmpA, tfx->gageTen2 + 7*(tfx->ten2Use));
- ELL_3M_MUL(matTmpB, tfx->mframe, matTmpA);
- ELL_3M_MUL(matTmpA, matTmpB, tfx->mframeT);
- TEN_M2T(tfx->fiberTen, matTmpA);
+ TEN_T_COPY(tfx->fiberTen, tens2[tfx->ten2Use]);
} else {
TEN_T_COPY(tfx->fiberTen, tfx->gageTen2 + 7*(tfx->ten2Use));
}
Modified: teem/trunk/src/ten/tenDwiGage.c
===================================================================
--- teem/trunk/src/ten/tenDwiGage.c 2008-12-08 17:38:33 UTC (rev 4034)
+++ teem/trunk/src/ten/tenDwiGage.c 2008-12-09 11:02:01 UTC (rev 4035)
@@ -306,8 +306,8 @@
egrad += 3;
for (ii=0; ii<nn; ii++) {
double argA, argB, sigA, sigB;
- argA = -pvlData->tec2->bValue*TEN_T3V_CONTR(tenA, egrad + 3*ii);
- argB = -pvlData->tec2->bValue*TEN_T3V_CONTR(tenB, egrad + 3*ii);
+ argA = -pvlData->tec1->bValue*TEN_T3V_CONTR(tenA, egrad + 3*ii);
+ argB = -pvlData->tec1->bValue*TEN_T3V_CONTR(tenB, egrad + 3*ii);
if (pvlData->levmarUseFastExp) {
sigA = airFastExp(argA);
sigB = airFastExp(argB);
@@ -315,7 +315,7 @@
sigA = exp(argA);
sigB = exp(argB);
}
- xx[ii] = pvlData->tec2->knownB0*(pp[1]*sigA + (1-pp[1])*sigB);
+ xx[ii] = pvlData->tec1->knownB0*(pp[1]*sigA + (1-pp[1])*sigB);
}
return;
}
@@ -580,106 +580,114 @@
/* Pointer to the location where the two tensor will be written */
twoTen = pvl->directAnswer[tenDwiGage2TensorPeled];
/* Estimate the DWI error, error is given as standard deviation */
- pvlData->tec2->recordErrorDwi = AIR_FALSE;
+ pvlData->tec1->recordErrorDwi = AIR_FALSE;
/* Estimate the single tensor */
- tenEstimate1TensorSingle_d(pvlData->tec2, pvlData->ten1, dwiAll);
+ tenEstimate1TensorSingle_d(pvlData->tec1, pvlData->ten1, dwiAll);
/* Get the eigenValues and eigen vectors for this tensor */
tenEigensolve_d(pvlData->ten1Eval, pvlData->ten1Evec, pvlData->ten1);
/* Get westins Cp */
Cp = tenAnisoEval_d(pvlData->ten1Eval, tenAniso_Cp1);
- /* Calculate the residual, need the variance to sqr it */
- /* residual = pvlData->tec2->errorDwi*pvlData->tec2->errorDwi; */
- /* Calculate the AIC for single tensor fit */
- /* AICSingFit = _tenComputeAIC(residual, pvlData->tec2->dwiNum, 6); */
+ /* Only do two-tensor fitting if CP is greater or equal to than a
+ user-defined threshold */
+ if (Cp >= pvlData->levmarMinCp) {
+ /* Calculate the residual, need the variance to sqr it */
+ /* residual = pvlData->tec1->errorDwi*pvlData->tec1->errorDwi; */
+ /* Calculate the AIC for single tensor fit */
+ /* AICSingFit = _tenComputeAIC(residual, pvlData->tec1->dwiNum, 6); */
- /* the CP-based test is gone; caller's responsibility */
+ /* the CP-based test is gone; caller's responsibility */
- /* rotate DW gradients by inverse of eigenvector column matrix
- and place into pvlData->nten1EigenGrads (which has been
- allocated by _tenDwiGagePvlDataNew()) */
- grad = AIR_CAST(double *, kindData->ngrad->data);
- egrad = AIR_CAST(double *, pvlData->nten1EigenGrads->data);
- for (gi=0; gi<kindData->ngrad->axis[1].size; gi++) {
- /* yes, this is also transforming some zero-length (B0) gradients;
- that's harmless */
- ELL_3MV_MUL(egrad, pvlData->ten1Evec, grad);
- grad += 3;
- egrad += 3;
- }
+ /* rotate DW gradients by inverse of eigenvector column matrix
+ and place into pvlData->nten1EigenGrads (which has been
+ allocated by _tenDwiGagePvlDataNew()) */
+ grad = AIR_CAST(double *, kindData->ngrad->data);
+ egrad = AIR_CAST(double *, pvlData->nten1EigenGrads->data);
+ for (gi=0; gi<kindData->ngrad->axis[1].size; gi++) {
+ /* yes, this is also transforming some zero-length (B0) gradients;
+ that's harmless */
+ ELL_3MV_MUL(egrad, pvlData->ten1Evec, grad);
+ grad += 3;
+ egrad += 3;
+ }
- /* Lower and upper bounds for the NLLS routine */
- loBnd[0] = 0.0;
- loBnd[1] = 0.0;
- loBnd[2] = -AIR_PI/2;
- loBnd[3] = -AIR_PI/2;
- upBnd[0] = pvlData->ten1Eval[0]*5;
- upBnd[1] = 1.0;
- upBnd[2] = AIR_PI/2;
- upBnd[3] = AIR_PI/2;
- /* Starting point for the NLLS */
- guess[0] = pvlData->ten1Eval[0];
- guess[1] = 0.5;
+ /* Lower and upper bounds for the NLLS routine */
+ loBnd[0] = 0.0;
+ loBnd[1] = 0.0;
+ loBnd[2] = -AIR_PI/2;
+ loBnd[3] = -AIR_PI/2;
+ upBnd[0] = pvlData->ten1Eval[0]*5;
+ upBnd[1] = 1.0;
+ upBnd[2] = AIR_PI/2;
+ upBnd[3] = AIR_PI/2;
+ /* Starting point for the NLLS */
+ guess[0] = pvlData->ten1Eval[0];
+ guess[1] = 0.5;
- guess[2] = AIR_PI/4;
- guess[3] = -AIR_PI/4;
- /*
- guess[2] = AIR_AFFINE(0, airDrandMT_r(pvlData->randState), 1,
- AIR_PI/6, AIR_PI/3);
- guess[3] = AIR_AFFINE(0, airDrandMT_r(pvlData->randState), 1,
- -AIR_PI/6, -AIR_PI/3);
- */
- /* Fill in the constraints for the LM optimization,
- the threshold of error difference */
- opts[0] = pvlData->levmarTau;
- opts[1] = pvlData->levmarEps1;
- opts[2] = pvlData->levmarEps2;
- opts[3] = pvlData->levmarEps3;
- /* Very imp to set this opt, note that only forward
- differences are used to approx Jacobian */
- opts[4] = pvlData->levmarDelta;
-
- /* run NLLS, results are stored back into guess[] */
- pvlData->levmarUseFastExp = AIR_FALSE;
- lmret = dlevmar_bc_dif(_tenLevmarPeledCB, guess, pvlData->tec2->dwi,
- PARAMS, pvlData->tec2->dwiNum, loBnd, upBnd,
- pvlData->levmarMaxIter, opts,
- pvlData->levmarInfo,
- NULL, NULL, pvlData);
- if (-1 == lmret) {
- ctx->errNum = 1;
- sprintf(ctx->errStr, "%s: dlevmar_bc_dif() failed!", me);
- } else {
- /* Get the AIC for the two tensor fit, use the levmarinfo
- to get the residual */
+ guess[2] = AIR_PI/4;
+ guess[3] = -AIR_PI/4;
/*
- residual = pvlData->levmarInfo[1]/pvlData->tec2->dwiNum;
- AICTwoFit = _tenComputeAIC(residual, pvlData->tec2->dwiNum, 12);
+ guess[2] = AIR_AFFINE(0, airDrandMT_r(pvlData->randState), 1,
+ AIR_PI/6, AIR_PI/3);
+ guess[3] = AIR_AFFINE(0, airDrandMT_r(pvlData->randState), 1,
+ -AIR_PI/6, -AIR_PI/3);
*/
- /* Form the tensors using the estimated pp, returned in guess */
- _tenPeledRotate2D(tenA, guess[0], pvlData->ten1Eval[2], guess[2]);
- _tenPeledRotate2D(tenB, guess[0], pvlData->ten1Eval[2], guess[3]);
- TEN_T2M(matA, tenA);
- TEN_T2M(matB, tenB);
+ /* Fill in the constraints for the LM optimization,
+ the threshold of error difference */
+ opts[0] = pvlData->levmarTau;
+ opts[1] = pvlData->levmarEps1;
+ opts[2] = pvlData->levmarEps2;
+ opts[3] = pvlData->levmarEps3;
+ /* Very imp to set this opt, note that only forward
+ differences are used to approx Jacobian */
+ opts[4] = pvlData->levmarDelta;
+
+ /* run NLLS, results are stored back into guess[] */
+ pvlData->levmarUseFastExp = AIR_FALSE;
+ lmret = dlevmar_bc_dif(_tenLevmarPeledCB, guess, pvlData->tec1->dwi,
+ PARAMS, pvlData->tec1->dwiNum, loBnd, upBnd,
+ pvlData->levmarMaxIter, opts,
+ pvlData->levmarInfo,
+ NULL, NULL, pvlData);
+ if (-1 == lmret) {
+ ctx->errNum = 1;
+ sprintf(ctx->errStr, "%s: dlevmar_bc_dif() failed!", me);
+ } else {
+ /* Get the AIC for the two tensor fit, use the levmarinfo
+ to get the residual */
+ /*
+ residual = pvlData->levmarInfo[1]/pvlData->tec1->dwiNum;
+ AICTwoFit = _tenComputeAIC(residual, pvlData->tec1->dwiNum, 12);
+ */
+ /* Form the tensors using the estimated pp, returned in guess */
+ _tenPeledRotate2D(tenA, guess[0], pvlData->ten1Eval[2], guess[2]);
+ _tenPeledRotate2D(tenB, guess[0], pvlData->ten1Eval[2], guess[3]);
+ TEN_T2M(matA, tenA);
+ TEN_T2M(matB, tenB);
- ELL_3M_TRANSPOSE(rott, pvlData->ten1Evec);
- ELL_3M_MUL(matTmp, matA, pvlData->ten1Evec);
- ELL_3M_MUL(matA, rott, matTmp);
- ELL_3M_MUL(matTmp, matB, pvlData->ten1Evec);
- ELL_3M_MUL(matB, rott, matTmp);
-
- /* Copy two two tensors */
- /* guess[1] is population fraction of first tensor */
- if (guess[1] > 0.5) {
- twoTen[7] = guess[1];
- TEN_M2T(twoTen + 0, matA);
- TEN_M2T(twoTen + 7, matB);
- } else {
- twoTen[7] = 1 - guess[1];
- TEN_M2T(twoTen + 0, matB);
- TEN_M2T(twoTen + 7, matA);
+ ELL_3M_TRANSPOSE(rott, pvlData->ten1Evec);
+ ELL_3M_MUL(matTmp, matA, pvlData->ten1Evec);
+ ELL_3M_MUL(matA, rott, matTmp);
+ ELL_3M_MUL(matTmp, matB, pvlData->ten1Evec);
+ ELL_3M_MUL(matB, rott, matTmp);
+
+ /* Copy two two tensors */
+ /* guess[1] is population fraction of first tensor */
+ if (guess[1] > 0.5) {
+ twoTen[7] = guess[1];
+ TEN_M2T(twoTen + 0, matA);
+ TEN_M2T(twoTen + 7, matB);
+ } else {
+ twoTen[7] = 1 - guess[1];
+ TEN_M2T(twoTen + 0, matB);
+ TEN_M2T(twoTen + 7, matA);
+ }
+ twoTen[0] = 1;
}
- twoTen[0] = 1;
+ } else {
+ /* its too planar- just do single tensor fit */
+ TEN_T_COPY(twoTen, pvlData->ten1);
+ TEN_T_SET(twoTen + 7, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0);
}
#undef PARAMS
#else
@@ -700,7 +708,7 @@
if (info[1] > 0) {
/* Returning the standard deviation */
pvl->directAnswer[tenDwiGage2TensorPeledError][0] =
- sqrt(info[1]/pvlData->tec2->dwiNum);
+ sqrt(info[1]/pvlData->tec1->dwiNum);
}
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenDwiGage2TensorPeledAndError)) {
@@ -833,7 +841,7 @@
pvlData->levmarEps2 = 1E-8;
pvlData->levmarEps3 = 1E-8;
pvlData->levmarDelta = 1E-8;
- pvlData->levmarMinCp = 0.08;
+ pvlData->levmarMinCp = 0.1;
/* pvlData->levmarInfo[] is output; not initialized */
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-03-23 06:05:52
|
Revision: 4208
http://teem.svn.sourceforge.net/teem/?rev=4208&view=rev
Author: kindlmann
Date: 2009-03-23 06:05:50 +0000 (Mon, 23 Mar 2009)
Log Message:
-----------
API NEW: added two more items to tenGage:
tenGageFARidgeLineAlignment and tenGageFARidgeSurfaceAlignment
for looking at the alignment between eigenvectors of the Hessian of FA,
and of the tensor itself
Modified Paths:
--------------
teem/trunk/src/ten/enumsTen.c
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenGage.c
Modified: teem/trunk/src/ten/enumsTen.c
===================================================================
--- teem/trunk/src/ten/enumsTen.c 2009-03-23 06:04:04 UTC (rev 4207)
+++ teem/trunk/src/ten/enumsTen.c 2009-03-23 06:05:50 UTC (rev 4208)
@@ -250,10 +250,12 @@
"FA hessian evec 0",
"FA hessian evec 1",
"FA hessian evec 2",
- "FA ridge surface",
- "FA valley surface",
+ "FA ridge surface strength",
+ "FA valley surface strength",
"FA laplacian",
"FA hessian eval mode",
+ "FA ridge line alignment",
+ "FA ridge surface alignment",
"FA 2nd DD",
"FA geometry tensor",
@@ -415,6 +417,8 @@
"FA valley surface strength",
"FA laplacian",
"FA hessian eval mode",
+ "FA ridge line alignment",
+ "FA ridge surface alignment",
"FA 2nd DD",
"FA geometry tensor",
"FA kappa1",
@@ -570,6 +574,8 @@
tenGageFAValleySurfaceStrength,
tenGageFALaplacian,
tenGageFAHessianEvalMode,
+ tenGageFARidgeLineAlignment,
+ tenGageFARidgeSurfaceAlignment,
tenGageFA2ndDD,
tenGageFAGeomTens,
tenGageFAKappa1,
@@ -731,10 +737,12 @@
"fahessevec0",
"fahessevec1",
"fahessevec2",
- "farsurf",
- "favsurf",
+ "farsurfstrn",
+ "favsurfstrn",
"falapl",
"fahessevalmode",
+ "farlinealn",
+ "farsurfaln",
"fa2d", "fa2dd",
"fagten", "FA geometry tensor",
"fak1", "FA kappa1",
@@ -890,6 +898,8 @@
tenGageFAValleySurfaceStrength,
tenGageFALaplacian,
tenGageFAHessianEvalMode,
+ tenGageFARidgeLineAlignment,
+ tenGageFARidgeSurfaceAlignment,
tenGageFA2ndDD, tenGageFA2ndDD,
tenGageFAGeomTens, tenGageFAGeomTens,
tenGageFAKappa1, tenGageFAKappa1,
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-03-23 06:04:04 UTC (rev 4207)
+++ teem/trunk/src/ten/ten.h 2009-03-23 06:05:50 UTC (rev 4208)
@@ -363,62 +363,64 @@
tenGageFAHessianEvec0, /* 93: "fahessevec0": [3] */
tenGageFAHessianEvec1, /* 94: "fahessevec1": [3] */
tenGageFAHessianEvec2, /* 95: "fahessevec2": [3] */
- tenGageFARidgeSurfaceStrength, /* 96: "farsurf": [1] */
- tenGageFAValleySurfaceStrength, /* 97: "favsurf": [1] */
+ tenGageFARidgeSurfaceStrength, /* 96: "farsurfstrn": [1] */
+ tenGageFAValleySurfaceStrength, /* 97: "favsurfstrn": [1] */
tenGageFALaplacian, /* 98: "falapl": [1] */
tenGageFAHessianEvalMode,/* 99: "fahessevalmode": [1] */
- tenGageFA2ndDD, /* 100: "fa2d": [1] */
+ tenGageFARidgeLineAlignment, /* 100: "farlinealn": [1] */
+ tenGageFARidgeSurfaceAlignment, /* 101: "farsurfaln": [1] */
+ tenGageFA2ndDD, /* 102: "fa2d": [1] */
- tenGageFAGeomTens, /* 101: "fagten", sym. matx w/ evals {0, K1, K2}
+ tenGageFAGeomTens, /* 103: "fagten", sym. matx w/ evals {0, K1, K2}
and evecs {grad, cdir0, cdir1}: [9] */
- tenGageFAKappa1, /* 102: "fak1", 1st princ curv: [1] */
- tenGageFAKappa2, /* 103: "fak2", 2nd princ curv (k2 <= k1): [1] */
- tenGageFATotalCurv, /* 104: "fatc", L2 norm(K1,K2): [1] */
- tenGageFAShapeIndex, /* 105: "fasi", Koen.'s shape index, ("S"): [1] */
- tenGageFAMeanCurv, /* 106: "famc", mean curvature (K1 + K2)/2: [1] */
- tenGageFAGaussCurv, /* 107: "fagc", gaussian curvature K1*K2: [1] */
- tenGageFACurvDir1, /* 108: "facdir1", 1st princ curv direction: [3] */
- tenGageFACurvDir2, /* 109: "facdir2", 2nd princ curv direction: [3] */
- tenGageFAFlowlineCurv, /* 110: "fafc", curv of normal streamline: [1] */
+ tenGageFAKappa1, /* 104: "fak1", 1st princ curv: [1] */
+ tenGageFAKappa2, /* 105: "fak2", 2nd princ curv (k2 <= k1): [1] */
+ tenGageFATotalCurv, /* 106: "fatc", L2 norm(K1,K2): [1] */
+ tenGageFAShapeIndex, /* 107: "fasi", Koen.'s shape index, ("S"): [1] */
+ tenGageFAMeanCurv, /* 108: "famc", mean curvature (K1 + K2)/2: [1] */
+ tenGageFAGaussCurv, /* 109: "fagc", gaussian curvature K1*K2: [1] */
+ tenGageFACurvDir1, /* 110: "facdir1", 1st princ curv direction: [3] */
+ tenGageFACurvDir2, /* 111: "facdir2", 2nd princ curv direction: [3] */
+ tenGageFAFlowlineCurv, /* 112: "fafc", curv of normal streamline: [1] */
- tenGageRHessian, /* 111: "rhess": [9] */
+ tenGageRHessian, /* 113: "rhess": [9] */
- tenGageModeHessian, /* 112: "mhess": [9] */
- tenGageModeHessianEval, /* 113: "mhesseval": [3] */
- tenGageModeHessianEval0, /* 114: "mhesseval0": [1] */
- tenGageModeHessianEval1, /* 115: "mhesseval1": [1] */
- tenGageModeHessianEval2, /* 116: "mhesseval2": [1] */
- tenGageModeHessianEvec, /* 117: "mhessevec": [9] */
- tenGageModeHessianEvec0, /* 118: "mhessevec0": [3] */
- tenGageModeHessianEvec1, /* 119: "mhessevec1": [3] */
- tenGageModeHessianEvec2, /* 120: "mhessevec2": [3] */
+ tenGageModeHessian, /* 114: "mhess": [9] */
+ tenGageModeHessianEval, /* 115: "mhesseval": [3] */
+ tenGageModeHessianEval0, /* 116: "mhesseval0": [1] */
+ tenGageModeHessianEval1, /* 117: "mhesseval1": [1] */
+ tenGageModeHessianEval2, /* 118: "mhesseval2": [1] */
+ tenGageModeHessianEvec, /* 119: "mhessevec": [9] */
+ tenGageModeHessianEvec0, /* 120: "mhessevec0": [3] */
+ tenGageModeHessianEvec1, /* 121: "mhessevec1": [3] */
+ tenGageModeHessianEvec2, /* 122: "mhessevec2": [3] */
- tenGageOmegaHessian, /* 121: "omhess": [9] */
- tenGageOmegaHessianEval, /* 122: "omhesseval": [3] */
- tenGageOmegaHessianEval0,/* 123: "omhesseval0": [1] */
- tenGageOmegaHessianEval1,/* 124: "omhesseval1": [1] */
- tenGageOmegaHessianEval2,/* 125: "omhesseval2": [1] */
- tenGageOmegaHessianEvec, /* 126: "omhessevec": [9] */
- tenGageOmegaHessianEvec0,/* 127: "omhessevec0": [3] */
- tenGageOmegaHessianEvec1,/* 128: "omhessevec1": [3] */
- tenGageOmegaHessianEvec2,/* 129: "omhessevec2": [3] */
- tenGageOmegaLaplacian, /* 130: "omlapl": [1] */
- tenGageOmega2ndDD, /* 131: "om2d": [1] */
+ tenGageOmegaHessian, /* 123: "omhess": [9] */
+ tenGageOmegaHessianEval, /* 124: "omhesseval": [3] */
+ tenGageOmegaHessianEval0,/* 125: "omhesseval0": [1] */
+ tenGageOmegaHessianEval1,/* 126: "omhesseval1": [1] */
+ tenGageOmegaHessianEval2,/* 127: "omhesseval2": [1] */
+ tenGageOmegaHessianEvec, /* 128: "omhessevec": [9] */
+ tenGageOmegaHessianEvec0,/* 129: "omhessevec0": [3] */
+ tenGageOmegaHessianEvec1,/* 130: "omhessevec1": [3] */
+ tenGageOmegaHessianEvec2,/* 131: "omhessevec2": [3] */
+ tenGageOmegaLaplacian, /* 132: "omlapl": [1] */
+ tenGageOmega2ndDD, /* 133: "om2d": [1] */
- tenGageTraceGradVecDotEvec0, /* 132: "trgvdotevec0": [1] */
- tenGageTraceDiffusionAlign, /* 133: "datr": [1] */
- tenGageTraceDiffusionFraction, /* 134: "dftr": [1] */
- tenGageFAGradVecDotEvec0, /* 135: "fagvdotevec0": [1] */
- tenGageFADiffusionAlign, /* 136: "dafa": [1] */
- tenGageFADiffusionFraction, /* 137: "dffa": [1] */
- tenGageOmegaGradVecDotEvec0, /* 138: "omgvdotevec0": [1] */
- tenGageOmegaDiffusionAlign, /* 139: "daom": [1] */
- tenGageOmegaDiffusionFraction, /* 140: "daom": [1] */
- tenGageConfGradVecDotEvec0, /* 141: "cnfgvdotevec0": [1] */
- tenGageConfDiffusionAlign, /* 142: "dacnf": [1] */
- tenGageConfDiffusionFraction, /* 143: "dfcnf": [1] */
+ tenGageTraceGradVecDotEvec0, /* 134: "trgvdotevec0": [1] */
+ tenGageTraceDiffusionAlign, /* 135: "datr": [1] */
+ tenGageTraceDiffusionFraction, /* 136: "dftr": [1] */
+ tenGageFAGradVecDotEvec0, /* 137: "fagvdotevec0": [1] */
+ tenGageFADiffusionAlign, /* 138: "dafa": [1] */
+ tenGageFADiffusionFraction, /* 139: "dffa": [1] */
+ tenGageOmegaGradVecDotEvec0, /* 140: "omgvdotevec0": [1] */
+ tenGageOmegaDiffusionAlign, /* 141: "daom": [1] */
+ tenGageOmegaDiffusionFraction, /* 142: "daom": [1] */
+ tenGageConfGradVecDotEvec0, /* 143: "cnfgvdotevec0": [1] */
+ tenGageConfDiffusionAlign, /* 144: "dacnf": [1] */
+ tenGageConfDiffusionFraction, /* 145: "dfcnf": [1] */
- tenGageCovariance, /* 144: "cov" 4rth order covariance tensor: [21]
+ tenGageCovariance, /* 146: "cov" 4rth order covariance tensor: [21]
in order of appearance:
0:xxxx 1:xxxy 2:xxxz 3:xxyy 4:xxyz 5:xxzz
6:xyxy 7:xyxz 8:xyyy 9:xyyz 10:xyzz
@@ -426,28 +428,28 @@
15:yyyy 16:yyyz 17:yyzz
18:yzyz 19:yzzz
20:zzzz */
- tenGageCovarianceRGRT, /* 145: "covr" covariance tensor expressed in frame
+ tenGageCovarianceRGRT, /* 147: "covr" covariance tensor expressed in frame
of R invariant gradients and rotation tangents */
- tenGageCovarianceKGRT, /* 146: "covk" covariance tensor expressed in frame
+ tenGageCovarianceKGRT, /* 148: "covk" covariance tensor expressed in frame
of K invariant gradients and rotation tangents */
- tenGageTensorLogEuclidean, /* 147: log-euclidean interpolation */
- tenGageTensorQuatGeoLoxK, /* 148: QGL-K interpolation */
- tenGageTensorQuatGeoLoxR, /* 149: QGL-R interpolation */
+ tenGageTensorLogEuclidean, /* 149: log-euclidean interpolation */
+ tenGageTensorQuatGeoLoxK, /* 150: QGL-K interpolation */
+ tenGageTensorQuatGeoLoxR, /* 152: QGL-R interpolation */
- tenGageAniso, /* 150: "an", all anisos: [TEN_ANISO_MAX+1] */
- tenGageCl1GradVec, /* 151: gradient vector of cl1: [3] */
- tenGageCl1GradMag, /* 152: gradient magnitude of cl1: [1] */
- tenGageCp1GradVec, /* 153: gradient vector of cp1: [3] */
- tenGageCp1GradMag, /* 154: gradient magnitude of cp1: [1] */
- tenGageCa1GradVec, /* 155: gradient vector of ca1: [3] */
- tenGageCa1GradMag, /* 156: gradient magnitude of ca1: [1] */
- tenGageTensorGradRotE, /* 157: all tensor component gradients,
+ tenGageAniso, /* 152: "an", all anisos: [TEN_ANISO_MAX+1] */
+ tenGageCl1GradVec, /* 153: gradient vector of cl1: [3] */
+ tenGageCl1GradMag, /* 154: gradient magnitude of cl1: [1] */
+ tenGageCp1GradVec, /* 155: gradient vector of cp1: [3] */
+ tenGageCp1GradMag, /* 156: gradient magnitude of cp1: [1] */
+ tenGageCa1GradVec, /* 157: gradient vector of ca1: [3] */
+ tenGageCa1GradMag, /* 158: gradient magnitude of ca1: [1] */
+ tenGageTensorGradRotE, /* 159: all tensor component gradients,
starting with confidence gradient.
Rotated such that eigenvalue
derivatives are on the diagonal: [21] */
tenGageLast
};
-#define TEN_GAGE_ITEM_MAX 157
+#define TEN_GAGE_ITEM_MAX 159
/*
******** tenDwiGage* enum
Modified: teem/trunk/src/ten/tenGage.c
===================================================================
--- teem/trunk/src/ten/tenGage.c 2009-03-23 06:04:04 UTC (rev 4207)
+++ teem/trunk/src/ten/tenGage.c 2009-03-23 06:05:50 UTC (rev 4208)
@@ -158,6 +158,8 @@
{tenGageFAValleySurfaceStrength, 1, 2, {tenGageConfidence, tenGageFAHessianEval}, 0, 0, AIR_FALSE},
{tenGageFALaplacian, 1, 2, {tenGageFAHessian}, 0, 0, AIR_FALSE},
{tenGageFAHessianEvalMode, 1, 2, {tenGageFAHessianEval}, 0, 0, AIR_FALSE},
+ {tenGageFARidgeLineAlignment, 1, 2, {tenGageEvec0, tenGageFAHessianEvec0, tenGageFAHessianEvalMode}, 0, 0, AIR_FALSE},
+ {tenGageFARidgeSurfaceAlignment, 1, 2, {tenGageEvec0, tenGageFAHessianEvec2, tenGageFAHessianEvalMode}, 0, 0, AIR_FALSE},
{tenGageFA2ndDD, 1, 2, {tenGageFAHessian, tenGageFANormal}, 0, 0, AIR_FALSE},
{tenGageFAGeomTens, 9, 2, {tenGageFAHessian, tenGageFAGradMag, tenGageFANormal}, 0, 0, AIR_FALSE},
@@ -1030,6 +1032,24 @@
heval = pvl->directAnswer[tenGageFAHessianEval];
pvl->directAnswer[tenGageFAHessianEvalMode][0] = airMode3_d(heval);
}
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFARidgeLineAlignment)) {
+ double *hev0, *dev0, dot, mde;
+ hev0 = pvl->directAnswer[tenGageFAHessianEvec0];
+ dev0 = pvl->directAnswer[tenGageEvec0];
+ dot = ELL_3V_DOT(hev0, dev0);
+ mde = pvl->directAnswer[tenGageFAHessianEvalMode][0];
+ mde = AIR_AFFINE(-1, mde, 1, 0, 1);
+ pvl->directAnswer[tenGageFARidgeLineAlignment][0] = mde*AIR_ABS(dot);
+ }
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFARidgeSurfaceAlignment)) {
+ double *hev2, *dev0, dot, mde;
+ hev2 = pvl->directAnswer[tenGageFAHessianEvec2];
+ dev0 = pvl->directAnswer[tenGageEvec0];
+ dot = ELL_3V_DOT(hev2, dev0);
+ mde = pvl->directAnswer[tenGageFAHessianEvalMode][0];
+ mde = AIR_AFFINE(-1, mde, 1, 1, 0);
+ pvl->directAnswer[tenGageFARidgeSurfaceAlignment][0]= mde*(1-AIR_ABS(dot));
+ }
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFA2ndDD)) {
double *hess, *norm, tmpv[3];
hess = pvl->directAnswer[tenGageFAHessian];
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-06-29 01:22:17
|
Revision: 4234
http://teem.svn.sourceforge.net/teem/?rev=4234&view=rev
Author: kindlmann
Date: 2009-06-29 01:08:18 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
bringing ten up to date with increased strictness in gage
Modified Paths:
--------------
teem/trunk/src/ten/tendSatin.c
teem/trunk/src/ten/tensor.c
Modified: teem/trunk/src/ten/tendSatin.c
===================================================================
--- teem/trunk/src/ten/tendSatin.c 2009-05-20 23:00:52 UTC (rev 4233)
+++ teem/trunk/src/ten/tendSatin.c 2009-06-29 01:08:18 UTC (rev 4234)
@@ -247,6 +247,17 @@
nrrdCenterCell, nrrdCenterCell);
shape = gageShapeNew();
airMopAdd(mop, shape, (airMopper)gageShapeNix, airMopAlways);
+ /* this is a weird mix of new and legacy code. At some point
+ prior to Wed May 27 19:23:55 CDT 2009, it was okay to pass
+ in a volume to gageShapeSet that had absolutely no notion
+ of spacing or orientation. Then gageShapeSet was used to
+ get a plausible set of space directions and space origin.
+ Now, we're setting some spacings, so that gageShapeSet can
+ do its thing, then (below) nan-ing out those spacings so
+ that the nrrd is self-consistent */
+ nout->axis[1].spacing = 1.0;
+ nout->axis[2].spacing = 1.0;
+ nout->axis[3].spacing = 1.0;
if (gageShapeSet(shape, nout, tenGageKind->baseDim)) {
airMopAdd(mop, err=biffGetDone(GAGE), airFree, airMopAlways);
fprintf(stderr, "%s: trouble doing shape:\n%s\n", me, err);
@@ -263,6 +274,9 @@
nrrdSpaceOriginSet(nout, orig);
nrrdAxisInfoSet_va(nout, nrrdAxisInfoSpaceDirection,
spd[0], spd[1], spd[2], spd[3]);
+ nout->axis[1].spacing = AIR_NAN;
+ nout->axis[2].spacing = AIR_NAN;
+ nout->axis[3].spacing = AIR_NAN;
nrrdAxisInfoSet_va(nout, nrrdAxisInfoKind,
nrrdKind3DMaskedSymMatrix, nrrdKindSpace,
nrrdKindSpace, nrrdKindSpace);
Modified: teem/trunk/src/ten/tensor.c
===================================================================
--- teem/trunk/src/ten/tensor.c 2009-05-20 23:00:52 UTC (rev 4233)
+++ teem/trunk/src/ten/tensor.c 2009-06-29 01:08:18 UTC (rev 4234)
@@ -547,6 +547,7 @@
}
nout->axis[0].label = (char *)airFree(nout->axis[0].label);
nout->axis[0].label = airStrdup("tensor");
+ nout->axis[0].kind = nrrdKind3DMaskedSymMatrix;
if (nrrdBasicInfoCopy(nout, nconf,
NRRD_BASIC_INFO_DATA_BIT
| NRRD_BASIC_INFO_TYPE_BIT
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|
|
From: <kin...@us...> - 2009-10-11 19:37:12
|
Revision: 4277
http://teem.svn.sourceforge.net/teem/?rev=4277&view=rev
Author: kindlmann
Date: 2009-10-11 19:37:05 +0000 (Sun, 11 Oct 2009)
Log Message:
-----------
fixing longstanding bugs in the definition of tenGageKind (got out of sync with tenGage enum), and one field in tenDwiGage
Modified Paths:
--------------
teem/trunk/src/ten/enumsTen.c
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenDwiGage.c
teem/trunk/src/ten/tenGage.c
Modified: teem/trunk/src/ten/enumsTen.c
===================================================================
--- teem/trunk/src/ten/enumsTen.c 2009-10-11 19:31:36 UTC (rev 4276)
+++ teem/trunk/src/ten/enumsTen.c 2009-10-11 19:37:05 UTC (rev 4277)
@@ -314,6 +314,14 @@
"qglk",
"qglr",
+ "cl1gv",
+ "cl1gm",
+ "cp1gv",
+ "cp1gm",
+ "ca1gv",
+ "ca1gm",
+ "tgrote",
+
"anisotropies"
};
@@ -395,9 +403,11 @@
"linear anisotropy (1)",
"planar anisotropy (1)",
"linear+planar anisotropy (1)",
+ "min(linear,planar) anisotropy (1)",
"linear anisotropy (2)",
"planar anisotropy (2)",
"linear+planar anisotropy (2)",
+ "min(linear,planar) anisotropy (2)",
"hessian",
"trace hessian",
"B hessian",
@@ -469,6 +479,15 @@
"log-euclidean",
"QuatGeoLoxK",
"QuatGeoLoxR",
+ "gradient vector of cl1",
+ "gradient magnitude of cl1",
+ "gradient vector of cp1",
+ "gradient magnitude of cp1",
+ "gradient vector of ca1",
+ "gradient magnitude of ca1",
+ "all tensor component gradients, starting with confidence gradient, "
+ /* !! CONCAT !! */
+ "rotated such that eigenvalue derivatives are on the diagonal",
"anisotropies"
};
@@ -596,7 +615,7 @@
tenGageModeHessianEvec,
tenGageModeHessianEvec0,
tenGageModeHessianEvec1,
- tenGageOmegaHessianEvec2,
+ tenGageModeHessianEvec2,
tenGageOmegaHessian,
tenGageOmegaHessianEval,
tenGageOmegaHessianEval0,
@@ -626,14 +645,14 @@
tenGageTensorLogEuclidean,
tenGageTensorQuatGeoLoxK,
tenGageTensorQuatGeoLoxR,
- tenGageAniso,
tenGageCl1GradVec,
tenGageCl1GradMag,
tenGageCp1GradVec,
tenGageCp1GradMag,
tenGageCa1GradVec,
tenGageCa1GradMag,
- tenGageTensorGradRotE
+ tenGageTensorGradRotE,
+ tenGageAniso,
};
const char *
@@ -784,12 +803,24 @@
"omgvdotevec0",
"daom",
"dfom",
+ "confgvdotevec0",
+ "daconf",
+ "dfconf",
"cov",
"covr",
"covk",
"logeuclidean", "logeuc",
"quatgeoloxk", "qglk",
"quatgeoloxr", "qglr",
+
+ "cl1gv",
+ "cl1gm",
+ "cp1gv",
+ "cp1gm",
+ "ca1gv",
+ "ca1gm",
+ "tgrote",
+
"an", "aniso", "anisotropies",
""
};
@@ -957,13 +988,21 @@
tenGageTensorQuatGeoLoxK, tenGageTensorQuatGeoLoxK,
tenGageTensorQuatGeoLoxR, tenGageTensorQuatGeoLoxR,
+ tenGageCl1GradVec,
+ tenGageCl1GradMag,
+ tenGageCp1GradVec,
+ tenGageCp1GradMag,
+ tenGageCa1GradVec,
+ tenGageCa1GradMag,
+ tenGageTensorGradRotE,
+
tenGageAniso, tenGageAniso, tenGageAniso
};
airEnum
_tenGage = {
"tenGage",
- TEN_GAGE_ITEM_MAX+1,
+ TEN_GAGE_ITEM_MAX,
_tenGageStr, _tenGageVal,
_tenGageDesc,
_tenGageStrEqv, _tenGageValEqv,
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-11 19:31:36 UTC (rev 4276)
+++ teem/trunk/src/ten/ten.h 2009-10-11 19:37:05 UTC (rev 4277)
@@ -415,10 +415,10 @@
tenGageFADiffusionFraction, /* 139: "dffa": [1] */
tenGageOmegaGradVecDotEvec0, /* 140: "omgvdotevec0": [1] */
tenGageOmegaDiffusionAlign, /* 141: "daom": [1] */
- tenGageOmegaDiffusionFraction, /* 142: "daom": [1] */
- tenGageConfGradVecDotEvec0, /* 143: "cnfgvdotevec0": [1] */
- tenGageConfDiffusionAlign, /* 144: "dacnf": [1] */
- tenGageConfDiffusionFraction, /* 145: "dfcnf": [1] */
+ tenGageOmegaDiffusionFraction, /* 142: "dfom": [1] */
+ tenGageConfGradVecDotEvec0, /* 143: "confgvdotevec0": [1] */
+ tenGageConfDiffusionAlign, /* 144: "daconf": [1] */
+ tenGageConfDiffusionFraction, /* 145: "dfconf": [1] */
tenGageCovariance, /* 146: "cov" 4rth order covariance tensor: [21]
in order of appearance:
@@ -432,21 +432,22 @@
of R invariant gradients and rotation tangents */
tenGageCovarianceKGRT, /* 148: "covk" covariance tensor expressed in frame
of K invariant gradients and rotation tangents */
- tenGageTensorLogEuclidean, /* 149: log-euclidean interpolation */
- tenGageTensorQuatGeoLoxK, /* 150: QGL-K interpolation */
- tenGageTensorQuatGeoLoxR, /* 152: QGL-R interpolation */
+ tenGageTensorLogEuclidean, /* 149: "logeuc" log-euclidean interp */
+ tenGageTensorQuatGeoLoxK, /* 150: "qglk" QGL-K interpolation */
+ tenGageTensorQuatGeoLoxR, /* 151: "qglr" QGL-R interpolation */
- tenGageAniso, /* 152: "an", all anisos: [TEN_ANISO_MAX+1] */
- tenGageCl1GradVec, /* 153: gradient vector of cl1: [3] */
- tenGageCl1GradMag, /* 154: gradient magnitude of cl1: [1] */
- tenGageCp1GradVec, /* 155: gradient vector of cp1: [3] */
- tenGageCp1GradMag, /* 156: gradient magnitude of cp1: [1] */
- tenGageCa1GradVec, /* 157: gradient vector of ca1: [3] */
- tenGageCa1GradMag, /* 158: gradient magnitude of ca1: [1] */
- tenGageTensorGradRotE, /* 159: all tensor component gradients,
+ tenGageCl1GradVec, /* 152: "cl1gv" gradient vector of cl1: [3] */
+ tenGageCl1GradMag, /* 153: "cl1gm" gradient magnitude of cl1: [1] */
+ tenGageCp1GradVec, /* 154: "cp1gv" gradient vector of cp1: [3] */
+ tenGageCp1GradMag, /* 155: "cp1gm" gradient magnitude of cp1: [1] */
+ tenGageCa1GradVec, /* 156: "ca1gv" gradient vector of ca1: [3] */
+ tenGageCa1GradMag, /* 157: "ca1gm" gradient magnitude of ca1: [1] */
+ tenGageTensorGradRotE, /* 158: "tgrote" all tensor component gradients,
starting with confidence gradient.
Rotated such that eigenvalue
derivatives are on the diagonal: [21] */
+
+ tenGageAniso, /* 159: "an", all anisos: [TEN_ANISO_MAX+1] */
tenGageLast
};
#define TEN_GAGE_ITEM_MAX 159
Modified: teem/trunk/src/ten/tenDwiGage.c
===================================================================
--- teem/trunk/src/ten/tenDwiGage.c 2009-10-11 19:31:36 UTC (rev 4276)
+++ teem/trunk/src/ten/tenDwiGage.c 2009-10-11 19:37:05 UTC (rev 4277)
@@ -112,7 +112,7 @@
airEnum
_tenDwiGage = {
"tenDwiGage",
- TEN_DWI_GAGE_ITEM_MAX+1,
+ TEN_DWI_GAGE_ITEM_MAX,
_tenDwiGageStr, _tenDwiGageVal,
NULL,
NULL, NULL,
Modified: teem/trunk/src/ten/tenGage.c
===================================================================
--- teem/trunk/src/ten/tenGage.c 2009-10-11 19:31:36 UTC (rev 4276)
+++ teem/trunk/src/ten/tenGage.c 2009-10-11 19:37:05 UTC (rev 4277)
@@ -229,7 +229,6 @@
{tenGageTensorQuatGeoLoxK, 7, 0, {0}, 0, 0, AIR_FALSE},
{tenGageTensorQuatGeoLoxR, 7, 0, {0}, 0, 0, AIR_FALSE},
- {tenGageAniso, TEN_ANISO_MAX+1, 0, {tenGageEval0, tenGageEval1, tenGageEval2}, 0, 0, AIR_FALSE},
{tenGageCl1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
{tenGageCl1GradMag, 1, 1, {tenGageCl1GradVec}, 0, 0, AIR_FALSE},
@@ -237,7 +236,8 @@
{tenGageCp1GradMag, 1, 1, {tenGageCp1GradVec}, 0, 0, AIR_FALSE},
{tenGageCa1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
{tenGageCa1GradMag, 1, 1, {tenGageCa1GradVec}, 0, 0, AIR_FALSE},
- {tenGageTensorGradRotE, 21, 1, {tenGageTensorGrad, tenGageEval, tenGageEvec}, 0, 0, AIR_FALSE}
+ {tenGageTensorGradRotE, 21, 1, {tenGageTensorGrad, tenGageEval, tenGageEvec}, 0, 0, AIR_FALSE},
+ {tenGageAniso, TEN_ANISO_MAX+1, 0, {tenGageEval0, tenGageEval1, tenGageEval2}, 0, 0, AIR_FALSE},
};
void
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-22 18:09:27
|
Revision: 4297
http://teem.svn.sourceforge.net/teem/?rev=4297&view=rev
Author: kindlmann
Date: 2009-10-22 18:09:18 +0000 (Thu, 22 Oct 2009)
Log Message:
-----------
adding more flexible modeling of DWI signals
Added Paths:
-----------
teem/trunk/src/ten/experSpec.c
teem/trunk/src/ten/modelBall.c
teem/trunk/src/ten/modelBall1Stick.c
teem/trunk/src/ten/modelCylinder.c
teem/trunk/src/ten/modelTen.c
teem/trunk/src/ten/modelTensor2.c
Added: teem/trunk/src/ten/experSpec.c
===================================================================
--- teem/trunk/src/ten/experSpec.c (rev 0)
+++ teem/trunk/src/ten/experSpec.c 2009-10-22 18:09:18 UTC (rev 4297)
@@ -0,0 +1,307 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+static int
+_experAlloc(tenExperSpec* espec, unsigned int num) {
+ static char me[]="_experAlloc";
+
+ espec->bval = airFree(espec->bval);
+ espec->grad = airFree(espec->grad);
+ espec->wght = airFree(espec->wght);
+ if (!num) {
+ biffAddf(TEN, "%s: need a non-zero number of images", me);
+ return 1;
+ }
+ espec->bval = AIR_CAST(double *, calloc(num, sizeof(double)));
+ espec->grad = AIR_CAST(double *, calloc(3*num, sizeof(double)));
+ espec->wght = AIR_CAST(double *, calloc(num, sizeof(double)));
+ if (!( espec->bval && espec->grad && espec->wght )) {
+ biffAddf(TEN, "%s: couldn't allocate for %u images", me, num);
+ return 1;
+ }
+ return 0;
+}
+
+tenExperSpec*
+tenExperSpecNew(void) {
+ tenExperSpec* espec;
+
+ espec = AIR_CAST(tenExperSpec*, calloc(1, sizeof(tenExperSpec)));
+ espec->set = AIR_FALSE;
+ espec->imgNum = 0;
+ espec->bval = NULL;
+ espec->grad = NULL;
+ espec->wght = NULL;
+ return espec;
+}
+
+int
+tenExperSpecGradSingleBValSet(tenExperSpec *espec,
+ unsigned int imgNum,
+ double bval,
+ const double *grad) {
+ static const char me[]="tenExperSpecGradSingleBValSet";
+ unsigned int ii;
+
+ if (!espec) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ if (_experAlloc(espec, imgNum)) {
+ biffAddf(TEN, "%s: couldn't allocate", me);
+ return 1;
+ }
+ for (ii=0; ii<imgNum; ii++) {
+ espec->bval[ii] = bval;
+ ELL_3V_COPY(espec->grad + 3*ii, grad + 3*ii);
+ espec->wght[ii] = 1.0;
+ }
+
+ return 0;
+}
+
+int
+tenExperSpecGradBValSet(tenExperSpec *espec,
+ unsigned int imgNum,
+ const double *bval,
+ const double *grad) {
+ static const char me[]="tenExperSpecGradBValSet";
+ unsigned int ii;
+
+ if (!espec) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ if (_experAlloc(espec, imgNum)) {
+ biffAddf(TEN, "%s: couldn't allocate", me);
+ return 1;
+ }
+ for (ii=0; ii<imgNum; ii++) {
+ espec->bval[ii] = bval[ii];
+ ELL_3V_COPY(espec->grad + 3*ii, grad + 3*ii);
+ espec->wght[ii] = 1.0;
+ }
+
+ return 0;
+}
+
+int
+tenExperSpecGradBValWghtSet(tenExperSpec *espec,
+ unsigned int imgNum,
+ const double *bval,
+ const double *grad,
+ const double *wght) {
+ static const char me[]="tenExperSpecGradBValWghtSet";
+ unsigned int ii;
+
+ if (!espec) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ if (_experAlloc(espec, imgNum)) {
+ biffAddf(TEN, "%s: couldn't allocate", me);
+ return 1;
+ }
+ for (ii=0; ii<imgNum; ii++) {
+ espec->bval[ii] = bval[ii];
+ ELL_3V_COPY(espec->grad + 3*ii, grad + 3*ii);
+ espec->wght[ii] = wght[ii];
+ }
+
+ return 0;
+}
+
+int
+tenExperSpecFromKeyValueSet(tenExperSpec *espec, const Nrrd *ndwi) {
+ static const char me[]="tenExperSpecFromKeyValueSet";
+ unsigned int *skip, skipNum, ii, imgNum;
+ Nrrd *ngrad, *nbmat;
+ airArray *mop;
+ double len, singleBval, *bval, *grad;
+
+ if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &singleBval,
+ &skip, &skipNum, ndwi)) {
+ biffAddf(TEN, "%s: trouble parsing DWI info from key/value pairs", me);
+ return 1;
+ }
+ mop = airMopNew();
+ if (ngrad) {
+ airMopAdd(mop, ngrad, (airMopper)nrrdNuke, airMopAlways);
+ }
+ if (nbmat) {
+ airMopAdd(mop, nbmat, (airMopper)nrrdNuke, airMopAlways);
+ }
+ if (skip) {
+ airMopAdd(mop, skip, airFree, airMopAlways);
+ }
+
+ if (nbmat) {
+ biffAddf(TEN, "%s: sorry, currently can't handle B-matrices here", me);
+ airMopError(mop); return 1;
+ }
+ if (skipNum) {
+ biffAddf(TEN, "%s: sorry, currently can't handle skipping (%u) here", me,
+ skipNum);
+ airMopError(mop); return 1;
+ }
+
+ imgNum = ngrad->axis[1].size;
+ bval = AIR_CAST(double *, calloc(imgNum, sizeof(double)));
+ airMopAdd(mop, bval, airFree, airMopAlways);
+ grad = AIR_CAST(double *, ngrad->data);
+ for (ii=0; ii<imgNum; ii++) {
+ len = ELL_3V_LEN(grad + 3*ii);
+ bval[ii] = singleBval*len*len;
+ if (len) {
+ ELL_3V_SCALE(grad + 3*ii, 1/len, grad + 3*ii);
+ } else {
+ ELL_3V_SET(grad + 3*ii, 0, 0, -1);
+ }
+ }
+ if (tenExperSpecGradBValSet(espec, imgNum, bval, grad)) {
+ biffAddf(TEN, "%s: trouble", me);
+ airMopError(mop); return 1;
+ }
+ airMopOkay(mop);
+ return 0;
+}
+
+tenExperSpec*
+tenExperSpecNix(tenExperSpec *espec) {
+
+ if (espec) {
+ espec->bval = airFree(espec->bval);
+ espec->grad = airFree(espec->grad);
+ espec->wght = airFree(espec->wght);
+ airFree(espec);
+ }
+ return NULL;
+}
+
+double
+_tenModel_sqe(const double *dwiMeas, const double *dwiSim,
+ const tenExperSpec *espec) {
+ unsigned int ii;
+ double sqe;
+
+ sqe = 0;
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double dd;
+ dd = dwiMeas[ii] - dwiSim[ii];
+ sqe += dd*dd;
+ }
+ return sqe;
+}
+
+double
+_tenModel_nll(const double *dwiMeas, const double *dwiSim,
+ const tenExperSpec *espec,
+ int rician, double sigma) {
+ double nll;
+ unsigned int ii;
+
+ nll = 0;
+ if (rician) {
+ for (ii=0; ii<espec->imgNum; ii++) {
+ nll += -airLogRician(dwiMeas[ii], dwiSim[ii], sigma);
+ }
+ } else {
+ double dd, ladd, denom;
+ ladd = log(sigma*sqrt(2*AIR_PI));
+ denom = 1.0/(2*sigma*sigma);
+ for (ii=0; ii<espec->imgNum; ii++) {
+ dd = dwiMeas[ii] - dwiSim[ii];
+ nll += dd*dd*denom + ladd;
+ }
+ }
+ return nll;
+}
+
+int
+tenDWMRIKeyValueFromExperSpecSet(Nrrd *ndwi, const tenExperSpec *espec) {
+ static char me[]="tenDWMRIKeyValueFromExperSpecSet";
+ char keystr[AIR_STRLEN_MED], valstr[AIR_STRLEN_MED];
+
+ if (!(ndwi && espec)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+
+ AIR_UNUSED(keystr);
+ AIR_UNUSED(valstr);
+
+ /*
+ nrrdKeyValueAdd(ndwi, tenDWMRIModalityKey, tenDWMRIModalityVal);
+ sprintf(valstr, "%g", espec->);
+ nrrdKeyValueAdd(ndwi, tenDWMRIBValueKey, valstr);
+ if (tec->_ngrad) {
+ lup = nrrdDLookup[tec->_ngrad->type];
+ for (allIdx=0; allIdx<tec->allNum; allIdx++) {
+ sprintf(keystr, tenDWMRIGradKeyFmt, allIdx);
+ sprintf(valstr, "%g %g %g",
+ lup(tec->_ngrad->data, 0 + 3*allIdx),
+ lup(tec->_ngrad->data, 1 + 3*allIdx),
+ lup(tec->_ngrad->data, 2 + 3*allIdx));
+ nrrdKeyValueAdd(ndwi, keystr, valstr);
+ }
+ } else {
+ lup = nrrdDLookup[tec->_nbmat->type];
+ for (allIdx=0; allIdx<tec->allNum; allIdx++) {
+ sprintf(keystr, tenDWMRIBmatKeyFmt, allIdx);
+ sprintf(valstr, "%g %g %g %g %g %g",
+ lup(tec->_nbmat->data, 0 + 6*allIdx),
+ lup(tec->_nbmat->data, 1 + 6*allIdx),
+ lup(tec->_nbmat->data, 2 + 6*allIdx),
+ lup(tec->_nbmat->data, 3 + 6*allIdx),
+ lup(tec->_nbmat->data, 4 + 6*allIdx),
+ lup(tec->_nbmat->data, 5 + 6*allIdx));
+ nrrdKeyValueAdd(ndwi, keystr, valstr);
+ }
+ }
+ */
+
+ return 0;
+}
+
+double
+tenExperSpecKnownB0Get(const tenExperSpec *espec, const double *dwi) {
+ unsigned int ii, nb;
+ double b0;
+
+ if (!( dwi && espec )) {
+ return AIR_NAN;
+ }
+
+ nb = 0;
+ b0 = 0.0;
+ for (ii=0; ii<espec->imgNum; ii++) {
+ if (0 == espec->bval[ii]) {
+ b0 += dwi[ii];
+ ++nb;
+ }
+ }
+ return b0/nb;
+}
+
Added: teem/trunk/src/ten/modelBall.c
===================================================================
--- teem/trunk/src/ten/modelBall.c (rev 0)
+++ teem/trunk/src/ten/modelBall.c 2009-10-22 18:09:18 UTC (rev 4297)
@@ -0,0 +1,104 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define PARM_NUM 2
+
+static void
+simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
+ unsigned int ii;
+ double b0, diff;
+
+ b0 = parm[0];
+ diff = parm[1];
+ for (ii=0; ii<espec->imgNum; ii++) {
+ dwiSim[ii] = b0*exp(-espec->bval[ii]*diff);
+ }
+ return;
+}
+
+static double
+sqe(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+}
+
+static int
+sqeFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+static double
+nll(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+}
+
+static int
+nllFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+tenModel
+_tenModelBall = {
+ "ball",
+ PARM_NUM,
+ {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
+ },
+ simulate,
+ sqe,
+ sqeFit,
+ nll,
+ nllFit
+};
+const tenModel *const tenModelBall = &_tenModelBall;
Added: teem/trunk/src/ten/modelBall1Stick.c
===================================================================
--- teem/trunk/src/ten/modelBall1Stick.c (rev 0)
+++ teem/trunk/src/ten/modelBall1Stick.c 2009-10-22 18:09:18 UTC (rev 4297)
@@ -0,0 +1,116 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define PARM_NUM 6
+
+static void
+simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
+ unsigned int ii;
+ double b0, diff, frac, vec[3];
+
+ b0 = parm[0];
+ diff = parm[1];
+ frac = parm[2];
+ vec[0] = parm[3];
+ vec[1] = parm[4];
+ vec[2] = parm[5];
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double dwiBall, dwiStck, dot;
+ dwiBall = exp(-espec->bval[ii]*diff);
+ dot = ELL_3V_DOT(vec, espec->grad + 3*ii);
+ dwiStck = exp(-espec->bval[ii]*diff*dot*dot);
+ dwiSim[ii] = b0*((1-frac)*dwiBall + frac*dwiStck);
+ }
+ return;
+}
+
+static double
+sqe(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+}
+
+static int
+sqeFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+static double
+nll(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+}
+
+static int
+nllFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+tenModel
+_tenModelBall1Stick = {
+ "ball1stick",
+ PARM_NUM,
+ {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"fraction", 0.0, 1.0, AIR_FALSE, 0},
+ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ {"z", -1.0, 1.0, AIR_TRUE, 2},
+ },
+ simulate,
+ sqe,
+ sqeFit,
+ nll,
+ nllFit
+};
+const tenModel *const tenModelBall1Stick = &_tenModelBall1Stick;
Added: teem/trunk/src/ten/modelCylinder.c
===================================================================
--- teem/trunk/src/ten/modelCylinder.c (rev 0)
+++ teem/trunk/src/ten/modelCylinder.c 2009-10-22 18:09:18 UTC (rev 4297)
@@ -0,0 +1,118 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define PARM_NUM 6
+
+static void
+simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
+ unsigned int ii;
+ double b0, length, radius, vec[3], ten[7],
+ ident[7] = {1, 1, 0, 0, 1, 0, 1};
+
+ b0 = parm[0];
+ length = parm[1];
+ radius = parm[2];
+ vec[0] = parm[3];
+ vec[1] = parm[4];
+ vec[2] = parm[5];
+ TEN_T3V_OUTER(ten, vec);
+ TEN_T_SCALE_ADD2(ten, length - radius, ten, radius, ident);
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double adc, bb;
+ bb = espec->bval[ii];
+ adc = TEN_T3V_CONTR(ten, espec->grad + 3*ii);
+ dwiSim[ii] = b0*exp(-bb*adc);
+ }
+ return;
+}
+
+static double
+sqe(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+}
+
+static int
+sqeFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+static double
+nll(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+}
+
+static int
+nllFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+tenModel
+_tenModelCylinder = {
+ "cylinder",
+ PARM_NUM,
+ {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ {"z", -1.0, 1.0, AIR_TRUE, 2},
+ },
+ simulate,
+ sqe,
+ sqeFit,
+ nll,
+ nllFit
+};
+const tenModel *const tenModelCylinder = &_tenModelCylinder;
Added: teem/trunk/src/ten/modelTen.c
===================================================================
--- teem/trunk/src/ten/modelTen.c (rev 0)
+++ teem/trunk/src/ten/modelTen.c 2009-10-22 18:09:18 UTC (rev 4297)
@@ -0,0 +1,268 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+static const tenModel *
+str2model(const char *str) {
+ const tenModel *ret = NULL;
+
+ if (!strcmp(str, "ball")) ret = tenModelBall;
+
+ if (!strcmp(str, "ball1stick")) ret = tenModelBall1Stick;
+
+ if (!strcmp(str, "cyl")) ret = tenModelCylinder;
+ if (!strcmp(str, "cylinder")) ret = tenModelCylinder;
+
+ if (!strcmp(str, "tensor2")) ret = tenModelTensor2;
+ return ret;
+}
+
+int
+tenModelParse(const tenModel **model, int *plusB0, const char *_str) {
+ static const char me[]="tenModelParse";
+ char *str, *modstr;
+ airArray *mop;
+
+ if (!( model && plusB0 && _str)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ str = airToLower(airStrdup(_str));
+ if (!str) {
+ biffAddf(TEN, "%s: couldn't strdup", me);
+ return 1;
+ }
+
+ mop = airMopNew();
+ airMopAdd(mop, str, airFree, airMopAlways);
+ if ((modstr = strchr(str, '+'))) {
+ *modstr = '\0';
+ ++modstr;
+ if (!strcmp(str, "b0")) {
+ *plusB0 = AIR_TRUE;
+ } else {
+ biffAddf(TEN, "%s: string (\"%s\") prior to \"+\" not \"b0\"", me, str);
+ airMopError(mop);
+ return 1;
+ }
+ } else {
+ *plusB0 = AIR_FALSE;
+ modstr = str;
+ }
+ if (!(*model = str2model(modstr))) {
+ biffAddf(TEN, "%s: didn't recognize \"%s\" as model", me, str);
+ airMopError(mop);
+ return 1;
+ }
+ airMopOkay(mop);
+ return 0;
+}
+
+/*
+** if nB0 is given, and if parm vector is short by one (seems to be
+** missing B0), then use that instead. Otherwise parm vector has to
+** be length that includes B0
+*/
+int
+tenModelSimulate(Nrrd *ndwi, int typeOut,
+ tenExperSpec *espec,
+ const tenModel *model,
+ const Nrrd *_nB0,
+ const Nrrd *_nparm,
+ int keyValueSet) {
+ static const char me[]="tenModelSimulate";
+ double *ddwi, *parm, (*ins)(void *v, size_t I, double d);
+ char *dwi;
+ size_t szOut[NRRD_DIM_MAX], II, numSamp;
+ const Nrrd *nB0, /* B0 as doubles */
+ *ndparm, /* parm as doubles */
+ *ndpparm, /* parm as doubles, padded */
+ *nparm; /* final parm as doubles, padded, w/ correct B0 values */
+ Nrrd *ntmp; /* non-const pointer for working */
+ airArray *mop;
+ unsigned int gpsze, /* given parm size */
+ ii;
+ int useB0, needPad;
+
+ if (!(ndwi && espec && model /* _nB0 can be NULL */ && _nparm)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+
+ gpsze = _nparm->axis[0].size;
+ if (model->parmNum - 1 == gpsze) {
+ /* got one less than needed parm #, see if we got B0 */
+ if (!_nB0) {
+ biffAddf(TEN, "%s: got %u parms, need %u, but didn't get B0 vol",
+ me, gpsze, model->parmNum);
+ return 1;
+ }
+ useB0 = AIR_TRUE;
+ needPad = AIR_TRUE;
+ } else if (model->parmNum != gpsze) {
+ biffAddf(TEN, "%s: mismatch between getting %u parms, needing %u\n",
+ me, gpsze, model->parmNum);
+ return 1;
+ } else {
+ /* model->parmNum == gpsze */
+ needPad = AIR_FALSE;
+ useB0 = !!_nB0;
+ }
+
+ mop = airMopNew();
+ /* get parms as doubles */
+ if (nrrdTypeDouble == _nparm->type) {
+ ndparm = _nparm;
+ } else {
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ if (nrrdConvert(ntmp, _nparm, nrrdTypeDouble)) {
+ biffMovef(TEN, NRRD, "%s: couldn't convert parm to %s", me,
+ airEnumStr(nrrdType, nrrdTypeDouble));
+ airMopError(mop); return 1;
+ }
+ ndparm = ntmp;
+ }
+ /* get parms the right length */
+ if (!needPad) {
+ ndpparm = ndparm;
+ } else {
+ ptrdiff_t min[NRRD_DIM_MAX], max[NRRD_DIM_MAX];
+ unsigned int ax;
+
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ for (ax=0; ax<ndparm->dim; ax++) {
+ min[ax] = (!ax ? -1 : 0);
+ max[ax] = ndparm->axis[ax].size-1;
+ }
+ if (nrrdPad_nva(ntmp, ndparm, min, max, nrrdBoundaryBleed, 0.0)) {
+ biffMovef(TEN, NRRD, "%s: couldn't pad", me);
+ airMopError(mop); return 1;
+ }
+ ndpparm = ntmp;
+ }
+ /* put in B0 values if needed */
+ if (!useB0) {
+ nparm = ndpparm;
+ } else {
+ if (nrrdTypeDouble == _nB0->type) {
+ nB0 = _nB0;
+ } else {
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ if (nrrdConvert(ntmp, _nB0, nrrdTypeDouble)) {
+ biffMovef(TEN, NRRD, "%s: couldn't convert B0 to %s", me,
+ airEnumStr(nrrdType, nrrdTypeDouble));
+ airMopError(mop); return 1;
+ }
+ nB0 = ntmp;
+ }
+ /* HEY: this is mostly likely a waste of memory,
+ but its all complicated by const-correctness */
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ if (nrrdSplice(ntmp, ndpparm, nB0, 0, 0)) {
+ biffMovef(TEN, NRRD, "%s: couldn't splice in B0", me);
+ airMopError(mop); return 1;
+ }
+ nparm = ntmp;
+ }
+
+ /* allocate output */
+ for (ii=0; ii<nparm->dim; ii++) {
+ szOut[ii] = (!ii
+ ? espec->imgNum
+ : nparm->axis[ii].size);
+ }
+ if (nrrdMaybeAlloc_nva(ndwi, typeOut, nparm->dim, szOut)) {
+ biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ airMopError(mop); return 1;
+ }
+ if (!(ddwi = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double))))) {
+ biffAddf(TEN, "%s: couldn't allocate dwi buffer", me);
+ airMopError(mop); return 1;
+ }
+ airMopAdd(mop, ddwi, airFree, airMopAlways);
+ numSamp = nrrdElementNumber(nparm)/nparm->axis[0].size;
+
+ /* set output */
+ ins = nrrdDInsert[typeOut];
+ parm = AIR_CAST(double *, nparm->data);
+ dwi = AIR_CAST(char *, ndwi->data);
+ for (II=0; II<numSamp; II++) {
+ model->simulate(ddwi, parm, espec);
+ for (ii=0; ii<espec->imgNum; ii++) {
+ ins(dwi, ii, ddwi[ii]);
+ }
+ parm += model->parmNum;
+ dwi += espec->imgNum*nrrdTypeSize[typeOut];
+ }
+
+ if (keyValueSet) {
+ if (tenDWMRIKeyValueFromExperSpecSet(ndwi, espec)) {
+ biffAddf(TEN, "%s: trouble", me);
+ airMopError(mop); return 1;
+ }
+ }
+
+ /* set basic info */
+
+ airMopOkay(mop);
+ return 0;
+}
+
+int
+tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int knownB0) {
+
+ AIR_UNUSED(nparm);
+ AIR_UNUSED(nsqeP);
+ AIR_UNUSED(model);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(ndwi);
+ AIR_UNUSED(knownB0);
+
+ return 0;
+}
+
+int
+tenModelNllFit(Nrrd *nparm, Nrrd **nnllP,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int rician, double sigma, int knownB0) {
+
+ AIR_UNUSED(nparm);
+ AIR_UNUSED(nnllP);
+ AIR_UNUSED(model);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(ndwi);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+
+ return 0;
+}
Added: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c (rev 0)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-22 18:09:18 UTC (rev 4297)
@@ -0,0 +1,121 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define PARM_NUM 6
+
+static void
+simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
+ unsigned int ii;
+ double b0, ten[7];
+
+ b0 = parm[0];
+ ten[0] = 1;
+ ten[1] = parm[1];
+ ten[2] = parm[2];
+ ten[3] = parm[3];
+ ten[4] = parm[4];
+ ten[5] = parm[5];
+ ten[6] = parm[6];
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double adc, bb;
+ bb = espec->bval[ii];
+ adc = TEN_T3V_CONTR(ten, espec->grad + 3*ii);
+ dwiSim[ii] = b0*exp(-bb*adc);
+ }
+ return;
+}
+
+static double
+sqe(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+}
+
+static int
+sqeFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+static double
+nll(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ simulate(dwiBuff, parm, espec);
+ return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+}
+
+static int
+nllFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+/* 1/sqrt(2) */
+#define OST 0.70710678118654752440
+
+tenModel
+_tenModelTensor2 = {
+ "tensor2",
+ PARM_NUM,
+ {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"Dxx", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"Dxy", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
+ {"Dxz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
+ {"Dyy", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"Dyz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
+ {"Dzz", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ },
+ simulate,
+ sqe,
+ sqeFit,
+ nll,
+ nllFit
+};
+const tenModel *const tenModelTensor2 = &_tenModelTensor2;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-22 18:10:39
|
Revision: 4298
http://teem.svn.sourceforge.net/teem/?rev=4298&view=rev
Author: kindlmann
Date: 2009-10-22 18:10:31 +0000 (Thu, 22 Oct 2009)
Log Message:
-----------
adding const to airEnums, and adding more flexible modeling of DWI signals
Modified Paths:
--------------
teem/trunk/src/ten/GNUmakefile
teem/trunk/src/ten/chan.c
teem/trunk/src/ten/enumsTen.c
teem/trunk/src/ten/estimate.c
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/sources.cmake
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tendFiber.c
Modified: teem/trunk/src/ten/GNUmakefile
===================================================================
--- teem/trunk/src/ten/GNUmakefile 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/GNUmakefile 2009-10-22 18:10:31 UTC (rev 4298)
@@ -51,7 +51,9 @@
$(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o grads.o miscTen.o \
mod.o estimate.o tenGage.o tenDwiGage.o qseg.o path.o qglox.o \
fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o bvec.o \
- triple.o tendAbout.o \
+ triple.o experSpec.o modelTen.o modelBall.o modelBall1Stick.o \
+ modelCylinder.o modelTensor2.o \
+ tendAbout.o \
tendFlotsam.o tendGrads.o tendAnplot.o tendAnvol.o tendEval.o \
tendEvec.o tendSten.o tendExpand.o tendEvq.o tendPoint.o \
tendTriple.o tendTconv.o tendAvg.o \
@@ -61,8 +63,8 @@
tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o tendBfit.o \
tendUnmf.o tendLog.o tendExp.o
$(L).TESTS = test/roistat test/tg test/tt test/tem test/rotedge \
- test/tsoid test/odf-hist test/to test/tensorDotDat \
- test/igrt test/cntr test/geode test/taniso test/csim \
+ test/tsoid test/odf-hist test/to test/tensorDotDat \
+ test/igrt test/cntr test/geode test/taniso test/csim \
test/ttriple test/tqgl
####
####
Modified: teem/trunk/src/ten/chan.c
===================================================================
--- teem/trunk/src/ten/chan.c 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/chan.c 2009-10-22 18:10:31 UTC (rev 4298)
@@ -53,8 +53,9 @@
** Parses through key-value pairs in the NRRD header to determine the
** list of diffusion-sensitizing gradient directions, or B-matrices
** (depending to what was found), according the NAMIC conventions.
-** This requires, among other things, that ndwi be have exactly one axis
-** with kind nrrdKindList, which is taken to be the DWI axis.
+** This requires, among other things, that ndwi be have exactly one
+** axis with kind nrrdKindList (or nrrdKindVector), which is taken to
+** be the DWI axis.
**
** Either *ngradP or *nbmatP is set to a newly- allocated nrrd
** containing this information, and the other one is set to NULL
Modified: teem/trunk/src/ten/enumsTen.c
===================================================================
--- teem/trunk/src/ten/enumsTen.c 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/enumsTen.c 2009-10-22 18:10:31 UTC (rev 4298)
@@ -59,7 +59,7 @@
"eval2"
};
-airEnum
+const airEnum
_tenAniso = {
"anisotropy metric",
TEN_ANISO_MAX,
@@ -68,7 +68,7 @@
NULL, NULL,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenAniso = &_tenAniso;
/* --------------------------------------------------------------------- */
@@ -117,7 +117,7 @@
tenInterpTypeQuatGeoLoxR, tenInterpTypeQuatGeoLoxR,
};
-airEnum
+const airEnum
_tenInterpType = {
"interp type",
TEN_INTERP_TYPE_MAX,
@@ -126,7 +126,7 @@
_tenInterpTypeStrEqv, _tenInterpTypeValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenInterpType = &_tenInterpType;
/* --------------------------------------------------------------------- */
@@ -999,7 +999,7 @@
tenGageAniso, tenGageAniso, tenGageAniso
};
-airEnum
+const airEnum
_tenGage = {
"tenGage",
TEN_GAGE_ITEM_MAX,
@@ -1008,7 +1008,7 @@
_tenGageStrEqv, _tenGageValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenGage = &_tenGage;
/* --------------------------------------------------------------------- */
@@ -1056,7 +1056,7 @@
tenFiberTypeZhukov, tenFiberTypeZhukov
};
-airEnum
+const airEnum
_tenFiberType = {
"tenFiberType",
TEN_FIBER_TYPE_MAX,
@@ -1065,7 +1065,7 @@
_tenFiberTypeStrEqv, _tenFiberTypeValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenFiberType = &_tenFiberType;
/* --------------------------------------------------------------------- */
@@ -1101,7 +1101,7 @@
tenDwiFiberType12BlendEvec0, tenDwiFiberType12BlendEvec0
};
-airEnum
+const airEnum
_tenDwiFiberType = {
"tenDwiFiberType",
TEN_DWI_FIBER_TYPE_MAX,
@@ -1110,7 +1110,7 @@
_tenDwiFiberTypeStrEqv, _tenDwiFiberTypeValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenDwiFiberType = &_tenDwiFiberType;
/* ----------------------------------------------------------------------- */
@@ -1174,7 +1174,7 @@
"whole fiber has too few numbers of steps"
};
-airEnum
+const airEnum
_tenFiberStop = {
"fiber stopping criteria",
TEN_FIBER_STOP_MAX,
@@ -1183,7 +1183,7 @@
_tenFiberStopStrEqv, _tenFiberStopValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenFiberStop = &_tenFiberStop;
/* ----------------------------------------------------------------------- */
@@ -1219,7 +1219,7 @@
"4rth order Runge-Kutta"
};
-airEnum
+const airEnum
_tenFiberIntg = {
"fiber integration method",
TEN_FIBER_INTG_MAX,
@@ -1228,7 +1228,7 @@
_tenFiberIntgStrEqv, _tenFiberIntgValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenFiberIntg = &_tenFiberIntg;
/* ----------------------------------------------------------------------- */
@@ -1273,7 +1273,7 @@
"superquadric (superellipsoids)"
};
-airEnum
+const airEnum
_tenGlyphType = {
"tenGlyphType",
TEN_GLYPH_TYPE_MAX,
@@ -1282,7 +1282,7 @@
_tenGlyphTypeStrEqv, _tenGlyphTypeValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenGlyphType = &_tenGlyphType;
/* ---------------------------------------------- */
@@ -1305,7 +1305,7 @@
"maximum likelihood estimate from DWI"
};
-airEnum
+const airEnum
_tenEstimate1Method = {
"single-tensor-estimation",
TEN_ESTIMATE_1_METHOD_MAX,
@@ -1314,7 +1314,7 @@
NULL, NULL,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenEstimate1Method= &_tenEstimate1Method;
/* ---------------------------------------------- */
@@ -1333,7 +1333,7 @@
"Peled"
};
-airEnum
+const airEnum
_tenEstimate2Method = {
"two-tensor-estimation",
TEN_ESTIMATE_2_METHOD_MAX,
@@ -1342,7 +1342,7 @@
NULL, NULL,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenEstimate2Method= &_tenEstimate2Method;
/* ---------------------------------------------- */
@@ -1402,7 +1402,7 @@
tenTripleTypeWheelParm, tenTripleTypeWheelParm
};
-airEnum
+const airEnum
_tenTripleType = {
"tenTripleType",
TEN_TRIPLE_TYPE_MAX,
@@ -1411,5 +1411,5 @@
_tenTripleTypeStrEqv, _tenTripleTypeValEqv,
AIR_FALSE
};
-airEnum *
+const airEnum *const
tenTripleType = &_tenTripleType;
Modified: teem/trunk/src/ten/estimate.c
===================================================================
--- teem/trunk/src/ten/estimate.c 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/estimate.c 2009-10-22 18:10:31 UTC (rev 4298)
@@ -1001,7 +1001,6 @@
const Nrrd *nB0, const Nrrd *nten,
int outType, int keyValueSet) {
static const char me[]="tenEstimate1TensorSimulateVolume";
- char keystr[AIR_STRLEN_MED], valstr[AIR_STRLEN_MED];
size_t sizeTen, sizeX, sizeY, sizeZ, NN, II;
double (*tlup)(const void *, size_t), (*blup)(const void *, size_t),
(*lup)(const void *, size_t), ten_d[7], *dwi_d, B0;
@@ -1098,6 +1097,8 @@
airMopError(mop); return 1;
}
if (keyValueSet) {
+ char keystr[AIR_STRLEN_MED], valstr[AIR_STRLEN_MED];
+
nrrdKeyValueAdd(ndwi, tenDWMRIModalityKey, tenDWMRIModalityVal);
sprintf(valstr, "%g", bValue);
nrrdKeyValueAdd(ndwi, tenDWMRIBValueKey, valstr);
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/privateTen.h 2009-10-22 18:10:31 UTC (rev 4298)
@@ -147,6 +147,15 @@
const double *wght,
unsigned int NN, int ptype, tenInterpParm *tip);
+/* modelUtil.c */
+TEN_EXPORT double _tenModel_sqe(const double *dwiMeas,
+ const double *dwiSim,
+ const tenExperSpec *espec);
+TEN_EXPORT double _tenModel_nll(const double *dwiMeas,
+ const double *dwiSim,
+ const tenExperSpec *espec,
+ int rician, double sigma);
+
#ifdef __cplusplus
}
#endif
Modified: teem/trunk/src/ten/sources.cmake
===================================================================
--- teem/trunk/src/ten/sources.cmake 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/sources.cmake 2009-10-22 18:10:31 UTC (rev 4298)
@@ -62,6 +62,12 @@
tendUnmf.c
tensor.c
triple.c
+ experSpec.c
+ modelTen.c
+ modelBall.c
+ modelBall1Stick.c
+ modelCylinder.c
+ modelTensor2.c
)
ADD_TEEM_LIBRARY(ten ${TEN_SOURCES})
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/ten.h 2009-10-22 18:10:31 UTC (rev 4298)
@@ -1075,6 +1075,68 @@
double lengthShape, lengthOrient;
} tenInterpParm;
+/* the idea is that there should be a uniform way of describing
+ DWI experiments, and as a result of calling one of the Set()
+ functions below, the information is set in tenExperSpec so that
+ combined with a diffusion model spec, DWIs can be simulated */
+typedef struct {
+ int set; /* has been set */
+ unsigned imgNum; /* total number of images, dwi or not */
+ double *bval, /* all b values: imgNum doubles */
+ *wght, /* all weights: imgNum doubles */
+ *grad; /* all gradients: 3 x imgNum doubles */
+} tenExperSpec;
+
+typedef struct {
+ char name[AIR_STRLEN_SMALL]; /* name */
+ double min, max; /* bounds */
+ int vec3; /* non-zero if this is one coeff of 3-vector */
+ unsigned int idx; /* if 3-vector, index into it */
+} tenModelParmDesc;
+
+#define TEN_MODEL_PARM_MAXNUM 15 /* adjust as needed */
+#define TEN_MODEL_B0_MAX 65536 /* pretty arbitrary */
+#define TEN_MODEL_DIFF_MAX 0.004 /* in units of mm^2/sec */
+
+/*
+******** struct tenModel
+**
+** container for information about how DWI values arise,
+** with functions that help in fitting and evaluating models
+**
+** NOTE: the current convention is to *always* have the non-DW
+** T2 image value ("B0") be the first parameter in the model.
+** The B0 value will probably be found by trivial means (i.e copied
+** from the image data), or by a different method than the rest
+** of the model parameters, but (1) its very handy to have in one
+** place all the information that, when combined with the
+** tenExperSpec, gives you a DWI value, and (2) sometimes B0 does
+** have to be estimated at the same time as the rest of the model,
+** and it would be dumb to double the number of models to be able
+** to capture this.
+*/
+typedef struct {
+ char name[AIR_STRLEN_SMALL];
+ unsigned int parmNum;
+ tenModelParmDesc parmDesc[TEN_MODEL_PARM_MAXNUM];
+ /* noise free simulation */
+ void (*simulate)(double *dwiSim, const double *parm,
+ const tenExperSpec *espec);
+ /* "sqe" == squared error in DWI values */
+ double (*sqe)(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas);
+ int (*sqeFit)(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int knownB0);
+ /* "nll" == negative log likelihood */
+ double (*nll)(double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma);
+ int (*nllFit)(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0);
+} tenModel;
+
/* defaultsTen.c */
TEN_EXPORT const char *tenBiffKey;
TEN_EXPORT const char tenDefFiberKernel[];
@@ -1125,18 +1187,18 @@
tenGradientParm *tgparm);
/* enumsTen.c */
-TEN_EXPORT airEnum *tenAniso;
-TEN_EXPORT airEnum *tenInterpType;
-TEN_EXPORT airEnum _tenGage;
-TEN_EXPORT airEnum *tenGage;
-TEN_EXPORT airEnum *tenFiberType;
-TEN_EXPORT airEnum *tenDwiFiberType;
-TEN_EXPORT airEnum *tenFiberStop;
-TEN_EXPORT airEnum *tenFiberIntg;
-TEN_EXPORT airEnum *tenGlyphType;
-TEN_EXPORT airEnum *tenEstimate1Method;
-TEN_EXPORT airEnum *tenEstimate2Method;
-TEN_EXPORT airEnum *tenTripleType;
+TEN_EXPORT const airEnum *const tenAniso;
+TEN_EXPORT const airEnum *const tenInterpType;
+TEN_EXPORT const airEnum _tenGage;
+TEN_EXPORT const airEnum *const tenGage;
+TEN_EXPORT const airEnum *const tenFiberType;
+TEN_EXPORT const airEnum *const tenDwiFiberType;
+TEN_EXPORT const airEnum *const tenFiberStop;
+TEN_EXPORT const airEnum *const tenFiberIntg;
+TEN_EXPORT const airEnum *const tenGlyphType;
+TEN_EXPORT const airEnum *const tenEstimate1Method;
+TEN_EXPORT const airEnum *const tenEstimate2Method;
+TEN_EXPORT const airEnum *const tenTripleType;
/* path.c */
TEN_EXPORT tenInterpParm *tenInterpParmNew();
@@ -1435,6 +1497,58 @@
const NrrdKernel *kern, double *kparm,
int progress, int verbose);
+/* experspec.c */
+TEN_EXPORT tenExperSpec* tenExperSpecNew(void);
+TEN_EXPORT int tenExperSpecGradSingleBValSet(tenExperSpec *espec,
+ unsigned int imgNum,
+ double bval,
+ const double *grad);
+TEN_EXPORT int tenExperSpecGradBValSet(tenExperSpec *espec,
+ unsigned int imgNum,
+ const double *bval,
+ const double *grad);
+TEN_EXPORT int tenExperSpecGradBValWghtSet(tenExperSpec *espec,
+ unsigned int imgNum,
+ const double *bval,
+ const double *grad,
+ const double *wght);
+TEN_EXPORT int tenExperSpecFromKeyValueSet(tenExperSpec *espec,
+ const Nrrd *ndwi);
+TEN_EXPORT tenExperSpec* tenExperSpecNix(tenExperSpec *espec);
+TEN_EXPORT int tenDWMRIKeyValueFromExperSpecSet(Nrrd *ndwi,
+ const tenExperSpec *espec);
+TEN_EXPORT double tenExperSpecKnownB0Get(const tenExperSpec *espec,
+ const double *dwi);
+
+/* modelTen.c */
+TEN_EXPORT int tenModelParse(const tenModel **model, int *plusB0,
+ const char *_str);
+TEN_EXPORT int tenModelSimulate(Nrrd *ndwi, int typeOut,
+ tenExperSpec *espec,
+ const tenModel *model,
+ const Nrrd *nB0, /* maybe NULL */
+ const Nrrd *nparm,
+ int keyValueSet);
+TEN_EXPORT int tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int knownB0);
+TEN_EXPORT int tenModelNllFit(Nrrd *nparm, Nrrd **nnllP,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int rician, double sigma, int knownB0);
+
+
+/* have to keep in sync with modelUtil.c/tenModelParse() */
+/* modelBall.c */
+TEN_EXPORT const tenModel *const tenModelBall;
+/* modelBall1Stick.c */
+TEN_EXPORT const tenModel *const tenModelBall1Stick;
+/* modelCylinder.c */
+TEN_EXPORT const tenModel *const tenModelCylinder;
+/* modelTensor2.c */
+TEN_EXPORT const tenModel *const tenModelTensor2;
+
/* mod.c */
TEN_EXPORT int tenSizeNormalize(Nrrd *nout, const Nrrd *nin, double weight[3],
double amount, double target);
Modified: teem/trunk/src/ten/tendFiber.c
===================================================================
--- teem/trunk/src/ten/tendFiber.c 2009-10-22 18:09:18 UTC (rev 4297)
+++ teem/trunk/src/ten/tendFiber.c 2009-10-22 18:10:31 UTC (rev 4298)
@@ -40,7 +40,7 @@
tenFiberSingle *tfbs;
NrrdKernelSpec *ksp;
double start[3], step, *_stop, *stop;
- airEnum *ftypeEnum;
+ const airEnum *ftypeEnum;
char *ftypeS;
int E, intg, useDwi, allPaths, verbose, worldSpace, worldSpaceOut,
ftype, ftypeDef;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-22 22:27:19
|
Revision: 4310
http://teem.svn.sourceforge.net/teem/?rev=4310&view=rev
Author: kindlmann
Date: 2009-10-22 22:27:12 +0000 (Thu, 22 Oct 2009)
Log Message:
-----------
improving tenModel code, added tend msim
Modified Paths:
--------------
teem/trunk/src/ten/GNUmakefile
teem/trunk/src/ten/experSpec.c
teem/trunk/src/ten/modelTen.c
teem/trunk/src/ten/modelTensor2.c
teem/trunk/src/ten/sources.cmake
teem/trunk/src/ten/ten.h
Modified: teem/trunk/src/ten/GNUmakefile
===================================================================
--- teem/trunk/src/ten/GNUmakefile 2009-10-22 19:43:13 UTC (rev 4309)
+++ teem/trunk/src/ten/GNUmakefile 2009-10-22 22:27:12 UTC (rev 4310)
@@ -58,7 +58,7 @@
tendEvec.o tendSten.o tendExpand.o tendEvq.o tendPoint.o \
tendTriple.o tendTconv.o tendAvg.o \
tendAnhist.o tendMake.o tendSatin.o tendShrink.o tendGlyph.o \
- tendFiber.o tendEpireg.o tendBmat.o tendEstim.o tendSim.o \
+ tendFiber.o tendEpireg.o tendBmat.o tendEstim.o tendSim.o tendMsim.o \
tendSlice.o tendEllipse.o tendEvecrgb.o tendNorm.o tendAnscale.o \
tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o tendBfit.o \
tendUnmf.o tendLog.o tendExp.o
Modified: teem/trunk/src/ten/experSpec.c
===================================================================
--- teem/trunk/src/ten/experSpec.c 2009-10-22 19:43:13 UTC (rev 4309)
+++ teem/trunk/src/ten/experSpec.c 2009-10-22 22:27:12 UTC (rev 4310)
@@ -34,6 +34,7 @@
biffAddf(TEN, "%s: need a non-zero number of images", me);
return 1;
}
+ espec->imgNum = num;
espec->bval = AIR_CAST(double *, calloc(num, sizeof(double)));
espec->grad = AIR_CAST(double *, calloc(3*num, sizeof(double)));
espec->wght = AIR_CAST(double *, calloc(num, sizeof(double)));
@@ -243,44 +244,27 @@
tenDWMRIKeyValueFromExperSpecSet(Nrrd *ndwi, const tenExperSpec *espec) {
static char me[]="tenDWMRIKeyValueFromExperSpecSet";
char keystr[AIR_STRLEN_MED], valstr[AIR_STRLEN_MED];
+ double maxb, bb;
+ unsigned int ii;
if (!(ndwi && espec)) {
biffAddf(TEN, "%s: got NULL pointer", me);
return 1;
}
- AIR_UNUSED(keystr);
- AIR_UNUSED(valstr);
-
- /*
nrrdKeyValueAdd(ndwi, tenDWMRIModalityKey, tenDWMRIModalityVal);
- sprintf(valstr, "%g", espec->);
- nrrdKeyValueAdd(ndwi, tenDWMRIBValueKey, valstr);
- if (tec->_ngrad) {
- lup = nrrdDLookup[tec->_ngrad->type];
- for (allIdx=0; allIdx<tec->allNum; allIdx++) {
- sprintf(keystr, tenDWMRIGradKeyFmt, allIdx);
- sprintf(valstr, "%g %g %g",
- lup(tec->_ngrad->data, 0 + 3*allIdx),
- lup(tec->_ngrad->data, 1 + 3*allIdx),
- lup(tec->_ngrad->data, 2 + 3*allIdx));
- nrrdKeyValueAdd(ndwi, keystr, valstr);
- }
- } else {
- lup = nrrdDLookup[tec->_nbmat->type];
- for (allIdx=0; allIdx<tec->allNum; allIdx++) {
- sprintf(keystr, tenDWMRIBmatKeyFmt, allIdx);
- sprintf(valstr, "%g %g %g %g %g %g",
- lup(tec->_nbmat->data, 0 + 6*allIdx),
- lup(tec->_nbmat->data, 1 + 6*allIdx),
- lup(tec->_nbmat->data, 2 + 6*allIdx),
- lup(tec->_nbmat->data, 3 + 6*allIdx),
- lup(tec->_nbmat->data, 4 + 6*allIdx),
- lup(tec->_nbmat->data, 5 + 6*allIdx));
- nrrdKeyValueAdd(ndwi, keystr, valstr);
- }
- }
- */
+ maxb = tenExperSpecMaxBGet(espec);
+ sprintf(valstr, "%g", maxb);
+ nrrdKeyValueAdd(ndwi, tenDWMRIBValueKey, valstr);
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double vec[3];
+ sprintf(keystr, tenDWMRIGradKeyFmt, ii);
+ ELL_3V_COPY(vec, espec->grad + 3*ii);
+ bb = espec->bval[ii];
+ ELL_3V_SCALE(vec, sqrt(bb/maxb), vec);
+ sprintf(valstr, "%g %g %g", vec[0], vec[1], vec[2]);
+ nrrdKeyValueAdd(ndwi, keystr, valstr);
+ }
return 0;
}
@@ -305,3 +289,18 @@
return b0/nb;
}
+double
+tenExperSpecMaxBGet(const tenExperSpec *espec) {
+ unsigned int ii;
+ double bval;
+
+ if (!( espec )) {
+ return AIR_NAN;
+ }
+
+ bval = -1;
+ for (ii=0; ii<espec->imgNum; ii++) {
+ bval = AIR_MAX(bval, espec->bval[ii]);
+ }
+ return bval;
+}
Modified: teem/trunk/src/ten/modelTen.c
===================================================================
--- teem/trunk/src/ten/modelTen.c 2009-10-22 19:43:13 UTC (rev 4309)
+++ teem/trunk/src/ten/modelTen.c 2009-10-22 22:27:12 UTC (rev 4310)
@@ -79,10 +79,37 @@
return 0;
}
+int
+tenModelFromAxisLearn(const tenModel **modelP,
+ const NrrdAxisInfo *axinfo) {
+ static const char me[]="tenModelFromAxisLearn";
+
+ if (!(modelP && axinfo)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ /* first try to learn model from "kind" */
+ if (nrrdKind3DSymMatrix == axinfo->kind
+ || nrrdKind3DMaskedSymMatrix == axinfo->kind) {
+ *modelP = tenModelTensor2;
+ } else if (airStrlen(axinfo->label)) {
+ /* try to parse from label */
+
+ } else {
+ biffAddf(TEN, "%s: don't have kind or label info to learn model", me);
+ *modelP = NULL;
+ return 1;
+ }
+
+ return 0;
+}
+
/*
** if nB0 is given, and if parm vector is short by one (seems to be
** missing B0), then use that instead. Otherwise parm vector has to
** be length that includes B0
+**
+** basic and axis info is derived from _nparm
*/
int
tenModelSimulate(Nrrd *ndwi, int typeOut,
@@ -103,26 +130,32 @@
airArray *mop;
unsigned int gpsze, /* given parm size */
ii;
- int useB0, needPad;
+ int useB0, needPad, axmap[NRRD_DIM_MAX];
if (!(ndwi && espec && model /* _nB0 can be NULL */ && _nparm)) {
biffAddf(TEN, "%s: got NULL pointer", me);
return 1;
}
+ if (!espec->imgNum) {
+ biffAddf(TEN, "%s: given espec wants 0 images, unset?", me);
+ return 1;
+ }
gpsze = _nparm->axis[0].size;
if (model->parmNum - 1 == gpsze) {
/* got one less than needed parm #, see if we got B0 */
if (!_nB0) {
- biffAddf(TEN, "%s: got %u parms, need %u, but didn't get B0 vol",
- me, gpsze, model->parmNum);
+ biffAddf(TEN, "%s: got %u parms, need %u (for %s), "
+ "but didn't get B0 vol",
+ me, gpsze, model->parmNum, model->name);
return 1;
}
useB0 = AIR_TRUE;
needPad = AIR_TRUE;
} else if (model->parmNum != gpsze) {
- biffAddf(TEN, "%s: mismatch between getting %u parms, needing %u\n",
- me, gpsze, model->parmNum);
+ biffAddf(TEN, "%s: mismatch between getting %u parms, "
+ "needing %u (for %s)\n",
+ me, gpsze, model->parmNum, model->name);
return 1;
} else {
/* model->parmNum == gpsze */
@@ -190,11 +223,14 @@
nparm = ntmp;
}
- /* allocate output */
+ /* allocate output (and set axmap) */
for (ii=0; ii<nparm->dim; ii++) {
szOut[ii] = (!ii
? espec->imgNum
: nparm->axis[ii].size);
+ axmap[ii] = (!ii
+ ? -1
+ : AIR_CAST(int, ii));
}
if (nrrdMaybeAlloc_nva(ndwi, typeOut, nparm->dim, szOut)) {
biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
@@ -227,7 +263,20 @@
}
}
- /* set basic info */
+ if (nrrdAxisInfoCopy(ndwi, _nparm, axmap, NRRD_AXIS_INFO_SIZE_BIT)
+ || nrrdBasicInfoCopy(ndwi, _nparm,
+ NRRD_BASIC_INFO_DATA_BIT
+ | NRRD_BASIC_INFO_TYPE_BIT
+ | NRRD_BASIC_INFO_BLOCKSIZE_BIT
+ | NRRD_BASIC_INFO_DIMENSION_BIT
+ | NRRD_BASIC_INFO_CONTENT_BIT
+ | NRRD_BASIC_INFO_COMMENTS_BIT
+ | (nrrdStateKeyValuePairsPropagate
+ ? 0
+ : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
+ biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ airMopError(mop); return 1;
+ }
airMopOkay(mop);
return 0;
Modified: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c 2009-10-22 19:43:13 UTC (rev 4309)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-22 22:27:12 UTC (rev 4310)
@@ -23,7 +23,7 @@
#include "ten.h"
#include "privateTen.h"
-#define PARM_NUM 6
+#define PARM_NUM 7
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
Modified: teem/trunk/src/ten/sources.cmake
===================================================================
--- teem/trunk/src/ten/sources.cmake 2009-10-22 19:43:13 UTC (rev 4309)
+++ teem/trunk/src/ten/sources.cmake 2009-10-22 22:27:12 UTC (rev 4310)
@@ -55,6 +55,7 @@
tendSatin.c
tendShrink.c
tendSim.c
+ tendMsim.c
tendSlice.c
tendSten.c
tendTconv.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-22 19:43:13 UTC (rev 4309)
+++ teem/trunk/src/ten/ten.h 2009-10-22 22:27:12 UTC (rev 4310)
@@ -1515,14 +1515,17 @@
TEN_EXPORT int tenExperSpecFromKeyValueSet(tenExperSpec *espec,
const Nrrd *ndwi);
TEN_EXPORT tenExperSpec* tenExperSpecNix(tenExperSpec *espec);
+TEN_EXPORT double tenExperSpecKnownB0Get(const tenExperSpec *espec,
+ const double *dwi);
+TEN_EXPORT double tenExperSpecMaxBGet(const tenExperSpec *espec);
TEN_EXPORT int tenDWMRIKeyValueFromExperSpecSet(Nrrd *ndwi,
const tenExperSpec *espec);
-TEN_EXPORT double tenExperSpecKnownB0Get(const tenExperSpec *espec,
- const double *dwi);
/* modelTen.c */
TEN_EXPORT int tenModelParse(const tenModel **model, int *plusB0,
const char *_str);
+TEN_EXPORT int tenModelFromAxisLearn(const tenModel **model,
+ const NrrdAxisInfo *axinfo);
TEN_EXPORT int tenModelSimulate(Nrrd *ndwi, int typeOut,
tenExperSpec *espec,
const tenModel *model,
@@ -1538,7 +1541,6 @@
const tenExperSpec *espec, const Nrrd *ndwi,
int rician, double sigma, int knownB0);
-
/* have to keep in sync with modelUtil.c/tenModelParse() */
/* modelBall.c */
TEN_EXPORT const tenModel *const tenModelBall;
@@ -1605,6 +1607,7 @@
F(epireg) \
F(bmat) \
F(estim) \
+F(msim) \
F(sim) \
F(make) \
F(avg) \
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-23 04:36:55
|
Revision: 4314
http://teem.svn.sourceforge.net/teem/?rev=4314&view=rev
Author: kindlmann
Date: 2009-10-23 04:36:46 +0000 (Fri, 23 Oct 2009)
Log Message:
-----------
mv modelTen.c tenModel.c
Added Paths:
-----------
teem/trunk/src/ten/tenModel.c
Removed Paths:
-------------
teem/trunk/src/ten/modelTen.c
Deleted: teem/trunk/src/ten/modelTen.c
===================================================================
--- teem/trunk/src/ten/modelTen.c 2009-10-23 04:36:21 UTC (rev 4313)
+++ teem/trunk/src/ten/modelTen.c 2009-10-23 04:36:46 UTC (rev 4314)
@@ -1,335 +0,0 @@
-/*
- Teem: Tools to process and visualize scientific data and images
- Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
- Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
-
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public License
- (LGPL) as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
- The terms of redistributing and/or modifying this software also
- include exceptions to the LGPL that facilitate static linking.
-
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-#include "ten.h"
-#include "privateTen.h"
-
-const char *
-tenModelPrefixStr = "DWMRI_model";
-
-static const tenModel *
-str2model(const char *str) {
- const tenModel *ret = NULL;
-
- if (!strcmp(str, TEN_MODEL_STR_BALL)) ret = tenModelBall;
- if (!strcmp(str, TEN_MODEL_STR_1STICK)) ret = tenModel1Stick;
- if (!strcmp(str, TEN_MODEL_STR_BALL1STICK)) ret = tenModelBall1Stick;
- if (!strcmp(str, TEN_MODEL_STR_CYLINDER)) ret = tenModelCylinder;
- if (!strcmp(str, TEN_MODEL_STR_TENSOR2)) ret = tenModelTensor2;
- return ret;
-}
-
-int
-tenModelParse(const tenModel **model, int *plusB0,
- int requirePrefix, const char *_str) {
- static const char me[]="tenModelParse";
- char *str, *modstr, prefix[AIR_STRLEN_MED], *pre;
- airArray *mop;
-
- if (!( model && plusB0 && _str)) {
- biffAddf(TEN, "%s: got NULL pointer", me);
- return 1;
- }
- str = airToLower(airStrdup(_str));
- if (!str) {
- biffAddf(TEN, "%s: couldn't strdup", me);
- return 1;
- }
- mop = airMopNew();
- airMopAdd(mop, str, airFree, airMopAlways);
- sprintf(prefix, "%s:", tenModelPrefixStr);
- pre = strstr(str, prefix);
- if (pre) {
- str += strlen(prefix);
- } else {
- if (requirePrefix) {
- biffAddf(TEN, "%s: didn't see prefix \"%s\" in \"%s\"", me,
- prefix, _str);
- airMopError(mop); return 1;
- }
- }
-
- if ((modstr = strchr(str, '+'))) {
- *modstr = '\0';
- ++modstr;
- if (!strcmp(str, "b0")) {
- *plusB0 = AIR_TRUE;
- } else {
- biffAddf(TEN, "%s: string (\"%s\") prior to \"+\" not \"b0\"", me, str);
- airMopError(mop);
- return 1;
- }
- } else {
- *plusB0 = AIR_FALSE;
- modstr = str;
- }
- if (!(*model = str2model(modstr))) {
- biffAddf(TEN, "%s: didn't recognize \"%s\" as model", me, str);
- airMopError(mop);
- return 1;
- }
- airMopOkay(mop);
- return 0;
-}
-
-int
-tenModelFromAxisLearn(const tenModel **modelP,
- int *plusB0,
- const NrrdAxisInfo *axinfo) {
- static const char me[]="tenModelFromAxisLearn";
-
- if (!(modelP && plusB0 && axinfo)) {
- biffAddf(TEN, "%s: got NULL pointer", me);
- return 1;
- }
- *plusB0 = AIR_FALSE;
- /* first try to learn model from "kind" */
- if (nrrdKind3DSymMatrix == axinfo->kind
- || nrrdKind3DMaskedSymMatrix == axinfo->kind) {
- *modelP = tenModelTensor2;
- } else if (airStrlen(axinfo->label)) {
- /* try to parse from label */
- if (tenModelParse(modelP, plusB0, AIR_TRUE, axinfo->label)) {
- biffAddf(TEN, "%s: couldn't parse label \"%s\"", me, axinfo->label);
- *modelP = NULL;
- return 1;
- }
- } else {
- biffAddf(TEN, "%s: don't have kind or label info to learn model", me);
- *modelP = NULL;
- return 1;
- }
-
- return 0;
-}
-
-/*
-** if nB0 is given, and if parm vector is short by one (seems to be
-** missing B0), then use that instead. Otherwise parm vector has to
-** be length that includes B0
-**
-** basic and axis info is derived from _nparm
-*/
-int
-tenModelSimulate(Nrrd *ndwi, int typeOut,
- tenExperSpec *espec,
- const tenModel *model,
- const Nrrd *_nB0,
- const Nrrd *_nparm,
- int keyValueSet) {
- static const char me[]="tenModelSimulate";
- double *ddwi, *parm, (*ins)(void *v, size_t I, double d);
- char *dwi;
- size_t szOut[NRRD_DIM_MAX], II, numSamp;
- const Nrrd *nB0, /* B0 as doubles */
- *ndparm, /* parm as doubles */
- *ndpparm, /* parm as doubles, padded */
- *nparm; /* final parm as doubles, padded, w/ correct B0 values */
- Nrrd *ntmp; /* non-const pointer for working */
- airArray *mop;
- unsigned int gpsze, /* given parm size */
- ii;
- int useB0, needPad, axmap[NRRD_DIM_MAX];
-
- if (!(ndwi && espec && model /* _nB0 can be NULL */ && _nparm)) {
- biffAddf(TEN, "%s: got NULL pointer", me);
- return 1;
- }
- if (!espec->imgNum) {
- biffAddf(TEN, "%s: given espec wants 0 images, unset?", me);
- return 1;
- }
-
- gpsze = _nparm->axis[0].size;
- if (model->parmNum - 1 == gpsze) {
- /* got one less than needed parm #, see if we got B0 */
- if (!_nB0) {
- biffAddf(TEN, "%s: got %u parms, need %u (for %s), "
- "but didn't get B0 vol",
- me, gpsze, model->parmNum, model->name);
- return 1;
- }
- useB0 = AIR_TRUE;
- needPad = AIR_TRUE;
- } else if (model->parmNum != gpsze) {
- biffAddf(TEN, "%s: mismatch between getting %u parms, "
- "needing %u (for %s)\n",
- me, gpsze, model->parmNum, model->name);
- return 1;
- } else {
- /* model->parmNum == gpsze */
- needPad = AIR_FALSE;
- useB0 = !!_nB0;
- }
-
- mop = airMopNew();
- /* get parms as doubles */
- if (nrrdTypeDouble == _nparm->type) {
- ndparm = _nparm;
- } else {
- ntmp = nrrdNew();
- airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
- if (nrrdConvert(ntmp, _nparm, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert parm to %s", me,
- airEnumStr(nrrdType, nrrdTypeDouble));
- airMopError(mop); return 1;
- }
- ndparm = ntmp;
- }
- /* get parms the right length */
- if (!needPad) {
- ndpparm = ndparm;
- } else {
- ptrdiff_t min[NRRD_DIM_MAX], max[NRRD_DIM_MAX];
- unsigned int ax;
-
- ntmp = nrrdNew();
- airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
- for (ax=0; ax<ndparm->dim; ax++) {
- min[ax] = (!ax ? -1 : 0);
- max[ax] = ndparm->axis[ax].size-1;
- }
- if (nrrdPad_nva(ntmp, ndparm, min, max, nrrdBoundaryBleed, 0.0)) {
- biffMovef(TEN, NRRD, "%s: couldn't pad", me);
- airMopError(mop); return 1;
- }
- ndpparm = ntmp;
- }
- /* put in B0 values if needed */
- if (!useB0) {
- nparm = ndpparm;
- } else {
- if (nrrdTypeDouble == _nB0->type) {
- nB0 = _nB0;
- } else {
- ntmp = nrrdNew();
- airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
- if (nrrdConvert(ntmp, _nB0, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert B0 to %s", me,
- airEnumStr(nrrdType, nrrdTypeDouble));
- airMopError(mop); return 1;
- }
- nB0 = ntmp;
- }
- /* HEY: this is mostly likely a waste of memory,
- but its all complicated by const-correctness */
- ntmp = nrrdNew();
- airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
- if (nrrdSplice(ntmp, ndpparm, nB0, 0, 0)) {
- biffMovef(TEN, NRRD, "%s: couldn't splice in B0", me);
- airMopError(mop); return 1;
- }
- nparm = ntmp;
- }
-
- /* allocate output (and set axmap) */
- for (ii=0; ii<nparm->dim; ii++) {
- szOut[ii] = (!ii
- ? espec->imgNum
- : nparm->axis[ii].size);
- axmap[ii] = (!ii
- ? -1
- : AIR_CAST(int, ii));
- }
- if (nrrdMaybeAlloc_nva(ndwi, typeOut, nparm->dim, szOut)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
- airMopError(mop); return 1;
- }
- if (!(ddwi = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double))))) {
- biffAddf(TEN, "%s: couldn't allocate dwi buffer", me);
- airMopError(mop); return 1;
- }
- airMopAdd(mop, ddwi, airFree, airMopAlways);
- numSamp = nrrdElementNumber(nparm)/nparm->axis[0].size;
-
- /* set output */
- ins = nrrdDInsert[typeOut];
- parm = AIR_CAST(double *, nparm->data);
- dwi = AIR_CAST(char *, ndwi->data);
- for (II=0; II<numSamp; II++) {
- model->simulate(ddwi, parm, espec);
- for (ii=0; ii<espec->imgNum; ii++) {
- ins(dwi, ii, ddwi[ii]);
- }
- parm += model->parmNum;
- dwi += espec->imgNum*nrrdTypeSize[typeOut];
- }
-
- if (keyValueSet) {
- if (tenDWMRIKeyValueFromExperSpecSet(ndwi, espec)) {
- biffAddf(TEN, "%s: trouble", me);
- airMopError(mop); return 1;
- }
- }
-
- if (nrrdAxisInfoCopy(ndwi, _nparm, axmap, NRRD_AXIS_INFO_SIZE_BIT)
- || nrrdBasicInfoCopy(ndwi, _nparm,
- NRRD_BASIC_INFO_DATA_BIT
- | NRRD_BASIC_INFO_TYPE_BIT
- | NRRD_BASIC_INFO_BLOCKSIZE_BIT
- | NRRD_BASIC_INFO_DIMENSION_BIT
- | NRRD_BASIC_INFO_CONTENT_BIT
- | NRRD_BASIC_INFO_COMMENTS_BIT
- | (nrrdStateKeyValuePairsPropagate
- ? 0
- : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
- airMopError(mop); return 1;
- }
-
- airMopOkay(mop);
- return 0;
-}
-
-int
-tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
- const tenModel *model,
- const tenExperSpec *espec, const Nrrd *ndwi,
- int knownB0) {
-
- AIR_UNUSED(nparm);
- AIR_UNUSED(nsqeP);
- AIR_UNUSED(model);
- AIR_UNUSED(espec);
- AIR_UNUSED(ndwi);
- AIR_UNUSED(knownB0);
-
- return 0;
-}
-
-int
-tenModelNllFit(Nrrd *nparm, Nrrd **nnllP,
- const tenModel *model,
- const tenExperSpec *espec, const Nrrd *ndwi,
- int rician, double sigma, int knownB0) {
-
- AIR_UNUSED(nparm);
- AIR_UNUSED(nnllP);
- AIR_UNUSED(model);
- AIR_UNUSED(espec);
- AIR_UNUSED(ndwi);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- AIR_UNUSED(knownB0);
-
- return 0;
-}
Copied: teem/trunk/src/ten/tenModel.c (from rev 4313, teem/trunk/src/ten/modelTen.c)
===================================================================
--- teem/trunk/src/ten/tenModel.c (rev 0)
+++ teem/trunk/src/ten/tenModel.c 2009-10-23 04:36:46 UTC (rev 4314)
@@ -0,0 +1,335 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+const char *
+tenModelPrefixStr = "DWMRI_model";
+
+static const tenModel *
+str2model(const char *str) {
+ const tenModel *ret = NULL;
+
+ if (!strcmp(str, TEN_MODEL_STR_BALL)) ret = tenModelBall;
+ if (!strcmp(str, TEN_MODEL_STR_1STICK)) ret = tenModel1Stick;
+ if (!strcmp(str, TEN_MODEL_STR_BALL1STICK)) ret = tenModelBall1Stick;
+ if (!strcmp(str, TEN_MODEL_STR_CYLINDER)) ret = tenModelCylinder;
+ if (!strcmp(str, TEN_MODEL_STR_TENSOR2)) ret = tenModelTensor2;
+ return ret;
+}
+
+int
+tenModelParse(const tenModel **model, int *plusB0,
+ int requirePrefix, const char *_str) {
+ static const char me[]="tenModelParse";
+ char *str, *modstr, prefix[AIR_STRLEN_MED], *pre;
+ airArray *mop;
+
+ if (!( model && plusB0 && _str)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ str = airToLower(airStrdup(_str));
+ if (!str) {
+ biffAddf(TEN, "%s: couldn't strdup", me);
+ return 1;
+ }
+ mop = airMopNew();
+ airMopAdd(mop, str, airFree, airMopAlways);
+ sprintf(prefix, "%s:", tenModelPrefixStr);
+ pre = strstr(str, prefix);
+ if (pre) {
+ str += strlen(prefix);
+ } else {
+ if (requirePrefix) {
+ biffAddf(TEN, "%s: didn't see prefix \"%s\" in \"%s\"", me,
+ prefix, _str);
+ airMopError(mop); return 1;
+ }
+ }
+
+ if ((modstr = strchr(str, '+'))) {
+ *modstr = '\0';
+ ++modstr;
+ if (!strcmp(str, "b0")) {
+ *plusB0 = AIR_TRUE;
+ } else {
+ biffAddf(TEN, "%s: string (\"%s\") prior to \"+\" not \"b0\"", me, str);
+ airMopError(mop);
+ return 1;
+ }
+ } else {
+ *plusB0 = AIR_FALSE;
+ modstr = str;
+ }
+ if (!(*model = str2model(modstr))) {
+ biffAddf(TEN, "%s: didn't recognize \"%s\" as model", me, str);
+ airMopError(mop);
+ return 1;
+ }
+ airMopOkay(mop);
+ return 0;
+}
+
+int
+tenModelFromAxisLearn(const tenModel **modelP,
+ int *plusB0,
+ const NrrdAxisInfo *axinfo) {
+ static const char me[]="tenModelFromAxisLearn";
+
+ if (!(modelP && plusB0 && axinfo)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ *plusB0 = AIR_FALSE;
+ /* first try to learn model from "kind" */
+ if (nrrdKind3DSymMatrix == axinfo->kind
+ || nrrdKind3DMaskedSymMatrix == axinfo->kind) {
+ *modelP = tenModelTensor2;
+ } else if (airStrlen(axinfo->label)) {
+ /* try to parse from label */
+ if (tenModelParse(modelP, plusB0, AIR_TRUE, axinfo->label)) {
+ biffAddf(TEN, "%s: couldn't parse label \"%s\"", me, axinfo->label);
+ *modelP = NULL;
+ return 1;
+ }
+ } else {
+ biffAddf(TEN, "%s: don't have kind or label info to learn model", me);
+ *modelP = NULL;
+ return 1;
+ }
+
+ return 0;
+}
+
+/*
+** if nB0 is given, and if parm vector is short by one (seems to be
+** missing B0), then use that instead. Otherwise parm vector has to
+** be length that includes B0
+**
+** basic and axis info is derived from _nparm
+*/
+int
+tenModelSimulate(Nrrd *ndwi, int typeOut,
+ tenExperSpec *espec,
+ const tenModel *model,
+ const Nrrd *_nB0,
+ const Nrrd *_nparm,
+ int keyValueSet) {
+ static const char me[]="tenModelSimulate";
+ double *ddwi, *parm, (*ins)(void *v, size_t I, double d);
+ char *dwi;
+ size_t szOut[NRRD_DIM_MAX], II, numSamp;
+ const Nrrd *nB0, /* B0 as doubles */
+ *ndparm, /* parm as doubles */
+ *ndpparm, /* parm as doubles, padded */
+ *nparm; /* final parm as doubles, padded, w/ correct B0 values */
+ Nrrd *ntmp; /* non-const pointer for working */
+ airArray *mop;
+ unsigned int gpsze, /* given parm size */
+ ii;
+ int useB0, needPad, axmap[NRRD_DIM_MAX];
+
+ if (!(ndwi && espec && model /* _nB0 can be NULL */ && _nparm)) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ if (!espec->imgNum) {
+ biffAddf(TEN, "%s: given espec wants 0 images, unset?", me);
+ return 1;
+ }
+
+ gpsze = _nparm->axis[0].size;
+ if (model->parmNum - 1 == gpsze) {
+ /* got one less than needed parm #, see if we got B0 */
+ if (!_nB0) {
+ biffAddf(TEN, "%s: got %u parms, need %u (for %s), "
+ "but didn't get B0 vol",
+ me, gpsze, model->parmNum, model->name);
+ return 1;
+ }
+ useB0 = AIR_TRUE;
+ needPad = AIR_TRUE;
+ } else if (model->parmNum != gpsze) {
+ biffAddf(TEN, "%s: mismatch between getting %u parms, "
+ "needing %u (for %s)\n",
+ me, gpsze, model->parmNum, model->name);
+ return 1;
+ } else {
+ /* model->parmNum == gpsze */
+ needPad = AIR_FALSE;
+ useB0 = !!_nB0;
+ }
+
+ mop = airMopNew();
+ /* get parms as doubles */
+ if (nrrdTypeDouble == _nparm->type) {
+ ndparm = _nparm;
+ } else {
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ if (nrrdConvert(ntmp, _nparm, nrrdTypeDouble)) {
+ biffMovef(TEN, NRRD, "%s: couldn't convert parm to %s", me,
+ airEnumStr(nrrdType, nrrdTypeDouble));
+ airMopError(mop); return 1;
+ }
+ ndparm = ntmp;
+ }
+ /* get parms the right length */
+ if (!needPad) {
+ ndpparm = ndparm;
+ } else {
+ ptrdiff_t min[NRRD_DIM_MAX], max[NRRD_DIM_MAX];
+ unsigned int ax;
+
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ for (ax=0; ax<ndparm->dim; ax++) {
+ min[ax] = (!ax ? -1 : 0);
+ max[ax] = ndparm->axis[ax].size-1;
+ }
+ if (nrrdPad_nva(ntmp, ndparm, min, max, nrrdBoundaryBleed, 0.0)) {
+ biffMovef(TEN, NRRD, "%s: couldn't pad", me);
+ airMopError(mop); return 1;
+ }
+ ndpparm = ntmp;
+ }
+ /* put in B0 values if needed */
+ if (!useB0) {
+ nparm = ndpparm;
+ } else {
+ if (nrrdTypeDouble == _nB0->type) {
+ nB0 = _nB0;
+ } else {
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ if (nrrdConvert(ntmp, _nB0, nrrdTypeDouble)) {
+ biffMovef(TEN, NRRD, "%s: couldn't convert B0 to %s", me,
+ airEnumStr(nrrdType, nrrdTypeDouble));
+ airMopError(mop); return 1;
+ }
+ nB0 = ntmp;
+ }
+ /* HEY: this is mostly likely a waste of memory,
+ but its all complicated by const-correctness */
+ ntmp = nrrdNew();
+ airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
+ if (nrrdSplice(ntmp, ndpparm, nB0, 0, 0)) {
+ biffMovef(TEN, NRRD, "%s: couldn't splice in B0", me);
+ airMopError(mop); return 1;
+ }
+ nparm = ntmp;
+ }
+
+ /* allocate output (and set axmap) */
+ for (ii=0; ii<nparm->dim; ii++) {
+ szOut[ii] = (!ii
+ ? espec->imgNum
+ : nparm->axis[ii].size);
+ axmap[ii] = (!ii
+ ? -1
+ : AIR_CAST(int, ii));
+ }
+ if (nrrdMaybeAlloc_nva(ndwi, typeOut, nparm->dim, szOut)) {
+ biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ airMopError(mop); return 1;
+ }
+ if (!(ddwi = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double))))) {
+ biffAddf(TEN, "%s: couldn't allocate dwi buffer", me);
+ airMopError(mop); return 1;
+ }
+ airMopAdd(mop, ddwi, airFree, airMopAlways);
+ numSamp = nrrdElementNumber(nparm)/nparm->axis[0].size;
+
+ /* set output */
+ ins = nrrdDInsert[typeOut];
+ parm = AIR_CAST(double *, nparm->data);
+ dwi = AIR_CAST(char *, ndwi->data);
+ for (II=0; II<numSamp; II++) {
+ model->simulate(ddwi, parm, espec);
+ for (ii=0; ii<espec->imgNum; ii++) {
+ ins(dwi, ii, ddwi[ii]);
+ }
+ parm += model->parmNum;
+ dwi += espec->imgNum*nrrdTypeSize[typeOut];
+ }
+
+ if (keyValueSet) {
+ if (tenDWMRIKeyValueFromExperSpecSet(ndwi, espec)) {
+ biffAddf(TEN, "%s: trouble", me);
+ airMopError(mop); return 1;
+ }
+ }
+
+ if (nrrdAxisInfoCopy(ndwi, _nparm, axmap, NRRD_AXIS_INFO_SIZE_BIT)
+ || nrrdBasicInfoCopy(ndwi, _nparm,
+ NRRD_BASIC_INFO_DATA_BIT
+ | NRRD_BASIC_INFO_TYPE_BIT
+ | NRRD_BASIC_INFO_BLOCKSIZE_BIT
+ | NRRD_BASIC_INFO_DIMENSION_BIT
+ | NRRD_BASIC_INFO_CONTENT_BIT
+ | NRRD_BASIC_INFO_COMMENTS_BIT
+ | (nrrdStateKeyValuePairsPropagate
+ ? 0
+ : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
+ biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ airMopError(mop); return 1;
+ }
+
+ airMopOkay(mop);
+ return 0;
+}
+
+int
+tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int knownB0) {
+
+ AIR_UNUSED(nparm);
+ AIR_UNUSED(nsqeP);
+ AIR_UNUSED(model);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(ndwi);
+ AIR_UNUSED(knownB0);
+
+ return 0;
+}
+
+int
+tenModelNllFit(Nrrd *nparm, Nrrd **nnllP,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int rician, double sigma, int knownB0) {
+
+ AIR_UNUSED(nparm);
+ AIR_UNUSED(nnllP);
+ AIR_UNUSED(model);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(ndwi);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+
+ return 0;
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-26 22:40:16
|
Revision: 4321
http://teem.svn.sourceforge.net/teem/?rev=4321&view=rev
Author: kindlmann
Date: 2009-10-26 22:40:09 +0000 (Mon, 26 Oct 2009)
Log Message:
-----------
under construction
Modified Paths:
--------------
teem/trunk/src/ten/GNUmakefile
teem/trunk/src/ten/experSpec.c
teem/trunk/src/ten/modelBall.c
teem/trunk/src/ten/modelBall1Stick.c
teem/trunk/src/ten/modelCylinder.c
teem/trunk/src/ten/modelTensor2.c
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/sources.cmake
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenModel.c
teem/trunk/src/ten/tendEstim.c
Added Paths:
-----------
teem/trunk/src/ten/model1Stick.c
teem/trunk/src/ten/tendMfit.c
Modified: teem/trunk/src/ten/GNUmakefile
===================================================================
--- teem/trunk/src/ten/GNUmakefile 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/GNUmakefile 2009-10-26 22:40:09 UTC (rev 4321)
@@ -51,14 +51,15 @@
$(L).OBJS = tensor.o chan.o aniso.o glyph.o enumsTen.o grads.o miscTen.o \
mod.o estimate.o tenGage.o tenDwiGage.o qseg.o path.o qglox.o \
fiberMethods.o fiber.o epireg.o defaultsTen.o bimod.o bvec.o \
- triple.o experSpec.o modelTen.o modelBall.o modelBall1Stick.o \
- modelCylinder.o modelTensor2.o \
+ triple.o experSpec.o tenModel.o modelBall.o model1Stick.o \
+ modelBall1Stick.o modelCylinder.o modelTensor2.o \
tendAbout.o \
tendFlotsam.o tendGrads.o tendAnplot.o tendAnvol.o tendEval.o \
tendEvec.o tendSten.o tendExpand.o tendEvq.o tendPoint.o \
tendTriple.o tendTconv.o tendAvg.o \
tendAnhist.o tendMake.o tendSatin.o tendShrink.o tendGlyph.o \
- tendFiber.o tendEpireg.o tendBmat.o tendEstim.o tendSim.o tendMsim.o \
+ tendFiber.o tendEpireg.o tendBmat.o tendEstim.o tendSim.o \
+ tendMsim.o tendMfit.o \
tendSlice.o tendEllipse.o tendEvecrgb.o tendNorm.o tendAnscale.o \
tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o tendBfit.o \
tendUnmf.o tendLog.o tendExp.o
Modified: teem/trunk/src/ten/experSpec.c
===================================================================
--- teem/trunk/src/ten/experSpec.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/experSpec.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -137,11 +137,35 @@
int
tenExperSpecFromKeyValueSet(tenExperSpec *espec, const Nrrd *ndwi) {
static const char me[]="tenExperSpecFromKeyValueSet";
- unsigned int *skip, skipNum, ii, imgNum;
+ unsigned int *skip, skipNum, ii, imgNum, dwiax;
Nrrd *ngrad, *nbmat;
airArray *mop;
double len, singleBval, *bval, *grad;
+ for (dwiax=0; dwiax<ndwi->dim; dwiax++) {
+ if (nrrdKindList == ndwi->axis[dwiax].kind
+ || nrrdKindVector == ndwi->axis[dwiax].kind) {
+ break;
+ }
+ }
+ if (0 != dwiax) {
+ biffAddf(TEN, "%s: need dwis (kind %s or %s) along axis 0, not %u", me,
+ airEnumStr(nrrdKind, nrrdKindList),
+ airEnumStr(nrrdKind, nrrdKindVector), dwiax);
+ return 1;
+ }
+ for (ii=dwiax+1; ii<ndwi->dim; ii++) {
+ if (nrrdKindList == ndwi->axis[ii].kind
+ || nrrdKindVector == ndwi->axis[ii].kind) {
+ break;
+ }
+ }
+ if (ii < ndwi->dim) {
+ biffAddf(TEN, "%s: saw on %u another %s or %s kind axis, after 0", me,
+ ii, airEnumStr(nrrdKind, nrrdKindList),
+ airEnumStr(nrrdKind, nrrdKindVector));
+ return 1;
+ }
if (tenDWMRIKeyValueParse(&ngrad, &nbmat, &singleBval,
&skip, &skipNum, ndwi)) {
biffAddf(TEN, "%s: trouble parsing DWI info from key/value pairs", me);
Added: teem/trunk/src/ten/model1Stick.c
===================================================================
--- teem/trunk/src/ten/model1Stick.c (rev 0)
+++ teem/trunk/src/ten/model1Stick.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -0,0 +1,158 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define PARM_NUM 5
+#define PARM_DESC \
+ { \
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ {"x", -1.0, 1.0, AIR_TRUE, 0}, \
+ {"y", -1.0, 1.0, AIR_TRUE, 1}, \
+ {"z", -1.0, 1.0, AIR_TRUE, 2}, \
+ }
+static const tenModelParmDesc
+const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
+
+static void
+simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
+ unsigned int ii;
+ double b0, diff, vec[3];
+
+ b0 = parm[0];
+ diff = parm[1];
+ vec[0] = parm[2];
+ vec[1] = parm[3];
+ vec[2] = parm[4];
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double dot;
+ dot = ELL_3V_DOT(vec, espec->grad + 3*ii);
+ dwiSim[ii] = b0*exp(-espec->bval[ii]*diff*dot*dot);
+ }
+ return;
+}
+
+static void
+prand(double *parm, airRandMTState *rng) {
+ unsigned int ii;
+
+ for (ii=0; ii<PARM_NUM; ii++) {
+ if (pdesc[ii].vec3) {
+ /* its unit vector */
+ double xx, yy, zz, theta, rr;
+
+ zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
+ theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
+ rr = sqrt(1 - zz*zz);
+ xx = rr*cos(theta);
+ yy = rr*sin(theta);
+ parm[ii + 0] = xx;
+ parm[ii + 1] = yy;
+ parm[ii + 2] = zz;
+ /* bump ii by 2; next for loop will increment past */
+ ii += 2;
+ } else {
+ parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
+ pdesc[ii].min, pdesc[ii].max);
+ }
+ }
+ return;
+}
+
+SQE;
+
+static void
+sqeGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ return;
+}
+
+static int
+sqeFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+NLL;
+
+static void
+nllGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ return;
+}
+
+static int
+nllFit(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0) {
+ unsigned int pp;
+
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ AIR_UNUSED(knownB0);
+ for (pp=0; pp<PARM_NUM; pp++) {
+ parm[pp] = parmInit[pp];
+ }
+ return 0;
+}
+
+tenModel
+_tenModel1Stick = {
+ TEN_MODEL_STR_1STICK,
+ PARM_NUM,
+ PARM_DESC,
+ simulate,
+ prand,
+ sqe, sqeGrad, sqeFit,
+ nll, nllGrad, nllFit
+};
+const tenModel *const tenModel1Stick = &_tenModel1Stick;
Modified: teem/trunk/src/ten/modelBall.c
===================================================================
--- teem/trunk/src/ten/modelBall.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/modelBall.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -24,6 +24,13 @@
#include "privateTen.h"
#define PARM_NUM 2
+#define PARM_DESC \
+ { \
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0} \
+ }
+static const tenModelParmDesc
+const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
@@ -38,14 +45,29 @@
return;
}
-static double
-sqe(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
+static void
+prand(double *parm, airRandMTState *rng) {
- simulate(dwiBuff, parm, espec);
- return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+ parm[0] = AIR_AFFINE(0, airDrandMT_r(rng), 1, pdesc[0].min, pdesc[0].max);
+ parm[1] = AIR_AFFINE(0, airDrandMT_r(rng), 1, pdesc[1].min, pdesc[1].max);
+ return;
}
+SQE;
+
+static void
+sqeGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ return;
+}
+
static int
sqeFit(double *parm, const tenExperSpec *espec,
const double *dwiMeas, const double *parmInit,
@@ -61,13 +83,22 @@
return 0;
}
-static double
-nll(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
+NLL;
- simulate(dwiBuff, parm, espec);
- return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+static void
+nllGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ return;
}
static int
@@ -89,16 +120,12 @@
tenModel
_tenModelBall = {
- "ball",
+ TEN_MODEL_STR_BALL,
PARM_NUM,
- {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
- },
+ PARM_DESC,
simulate,
- sqe,
- sqeFit,
- nll,
- nllFit
+ prand,
+ sqe, sqeGrad, sqeFit,
+ nll, nllGrad, nllFit
};
const tenModel *const tenModelBall = &_tenModelBall;
Modified: teem/trunk/src/ten/modelBall1Stick.c
===================================================================
--- teem/trunk/src/ten/modelBall1Stick.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/modelBall1Stick.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -24,6 +24,17 @@
#include "privateTen.h"
#define PARM_NUM 6
+#define PARM_DESC \
+ { \
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ {"fraction", 0.0, 1.0, AIR_FALSE, 0}, \
+ {"x", -1.0, 1.0, AIR_TRUE, 0}, \
+ {"y", -1.0, 1.0, AIR_TRUE, 1}, \
+ {"z", -1.0, 1.0, AIR_TRUE, 2} \
+ }
+static const tenModelParmDesc
+const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
@@ -46,14 +57,48 @@
return;
}
-static double
-sqe(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
+static void
+prand(double *parm, airRandMTState *rng) {
+ unsigned int ii;
- simulate(dwiBuff, parm, espec);
- return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+ for (ii=0; ii<PARM_NUM; ii++) {
+ if (pdesc[ii].vec3) {
+ /* its unit vector */
+ double xx, yy, zz, theta, rr;
+
+ zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
+ theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
+ rr = sqrt(1 - zz*zz);
+ xx = rr*cos(theta);
+ yy = rr*sin(theta);
+ parm[ii + 0] = xx;
+ parm[ii + 1] = yy;
+ parm[ii + 2] = zz;
+ /* bump ii by 2, anticipating completion of this for-loop iter */
+ ii += 2;
+ } else {
+ parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
+ pdesc[ii].min, pdesc[ii].max);
+ }
+ }
+ return;
}
+SQE;
+
+static void
+sqeGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ return;
+}
+
static int
sqeFit(double *parm, const tenExperSpec *espec,
const double *dwiMeas, const double *parmInit,
@@ -69,13 +114,22 @@
return 0;
}
-static double
-nll(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
+NLL;
- simulate(dwiBuff, parm, espec);
- return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+static void
+nllGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ return;
}
static int
@@ -97,20 +151,12 @@
tenModel
_tenModelBall1Stick = {
- "ball1stick",
+ TEN_MODEL_STR_BALL1STICK,
PARM_NUM,
- {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"fraction", 0.0, 1.0, AIR_FALSE, 0},
- {"x", -1.0, 1.0, AIR_TRUE, 0},
- {"y", -1.0, 1.0, AIR_TRUE, 1},
- {"z", -1.0, 1.0, AIR_TRUE, 2},
- },
+ PARM_DESC,
simulate,
- sqe,
- sqeFit,
- nll,
- nllFit
+ prand,
+ sqe, sqeGrad, sqeFit,
+ nll, nllGrad, nllFit
};
const tenModel *const tenModelBall1Stick = &_tenModelBall1Stick;
Modified: teem/trunk/src/ten/modelCylinder.c
===================================================================
--- teem/trunk/src/ten/modelCylinder.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/modelCylinder.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -24,6 +24,17 @@
#include "privateTen.h"
#define PARM_NUM 6
+#define PARM_DESC \
+ { \
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
+ {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ {"x", -1.0, 1.0, AIR_TRUE, 0}, \
+ {"y", -1.0, 1.0, AIR_TRUE, 1}, \
+ {"z", -1.0, 1.0, AIR_TRUE, 2}, \
+ }
+static const tenModelParmDesc
+const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
@@ -48,14 +59,48 @@
return;
}
-static double
-sqe(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
+static void
+prand(double *parm, airRandMTState *rng) {
+ unsigned int ii;
- simulate(dwiBuff, parm, espec);
- return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+ for (ii=0; ii<PARM_NUM; ii++) {
+ if (pdesc[ii].vec3) {
+ /* its unit vector */
+ double xx, yy, zz, theta, rr;
+
+ zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
+ theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
+ rr = sqrt(1 - zz*zz);
+ xx = rr*cos(theta);
+ yy = rr*sin(theta);
+ parm[ii + 0] = xx;
+ parm[ii + 1] = yy;
+ parm[ii + 2] = zz;
+ /* bump ii by 2, anticipating completion of this for-loop iter */
+ ii += 2;
+ } else {
+ parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
+ pdesc[ii].min, pdesc[ii].max);
+ }
+ }
+ return;
}
+SQE;
+
+static void
+sqeGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ return;
+}
+
static int
sqeFit(double *parm, const tenExperSpec *espec,
const double *dwiMeas, const double *parmInit,
@@ -71,13 +116,22 @@
return 0;
}
-static double
-nll(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
+NLL;
- simulate(dwiBuff, parm, espec);
- return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+static void
+nllGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ return;
}
static int
@@ -99,20 +153,12 @@
tenModel
_tenModelCylinder = {
- "cylinder",
+ TEN_MODEL_STR_CYLINDER,
PARM_NUM,
- {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"x", -1.0, 1.0, AIR_TRUE, 0},
- {"y", -1.0, 1.0, AIR_TRUE, 1},
- {"z", -1.0, 1.0, AIR_TRUE, 2},
- },
+ PARM_DESC,
simulate,
- sqe,
- sqeFit,
- nll,
- nllFit
+ prand,
+ sqe, sqeGrad, sqeFit,
+ nll, nllGrad, nllFit
};
const tenModel *const tenModelCylinder = &_tenModelCylinder;
Modified: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -24,6 +24,20 @@
#include "privateTen.h"
#define PARM_NUM 7
+/* 1/sqrt(2) */
+#define OST 0.70710678118654752440
+#define PARM_DESC \
+ { \
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
+ {"Dxx", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ {"Dxy", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0}, \
+ {"Dxz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0}, \
+ {"Dyy", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ {"Dyz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0}, \
+ {"Dzz", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
+ }
+static const tenModelParmDesc
+const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
@@ -47,38 +61,166 @@
return;
}
-static double
-sqe(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
+static void
+prand(double *parm, airRandMTState *rng) {
+ unsigned int ii;
- simulate(dwiBuff, parm, espec);
- return _tenModel_sqe(dwiMeas, dwiBuff, espec);
+ for (ii=0; ii<PARM_NUM; ii++) {
+ if (pdesc[ii].vec3) {
+ /* its unit vector */
+ double xx, yy, zz, theta, rr;
+
+ zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
+ theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
+ rr = sqrt(1 - zz*zz);
+ xx = rr*cos(theta);
+ yy = rr*sin(theta);
+ parm[ii + 0] = xx;
+ parm[ii + 1] = yy;
+ parm[ii + 2] = zz;
+ /* bump ii by 2, anticipating completion of this for-loop iter */
+ ii += 2;
+ } else {
+ parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
+ pdesc[ii].min, pdesc[ii].max);
+ }
+ }
+ return;
}
-static int
-sqeFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int knownB0) {
- unsigned int pp;
+SQE;
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
+static void
+sqeGrad(double *grad, const double *parm0,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int knownB0) {
+ double parm1[PARM_NUM], sqe0, sqe1, dp;
+ unsigned int ii, i0;
+
+ i0 = knownB0 ? 1 : 0;
+ for (ii=i0; ii<PARM_NUM; ii++) {
+ parm1[ii] = parm0[ii];
}
- return 0;
+ sqe0 = sqe(parm0, espec, dwiBuff, dwiMeas);
+ for (ii=i0; ii<PARM_NUM; ii++) {
+ dp = (pdesc[ii].max - pdesc[ii].min)/3000;
+ parm1[ii] += dp;
+ sqe1 = sqe(parm1, espec, dwiBuff, dwiMeas);
+ grad[ii] = (sqe1 - sqe0)/dp;
+ parm1[ii] = parm0[ii];
+ }
+ if (knownB0) {
+ grad[ii] = 0;
+ }
+ return;
}
+static void
+parmAdd(double *parm1, const double scl,
+ const double *grad, const double *parm0) {
+ unsigned int ii;
+
+ for (ii=0; ii<PARM_NUM; ii++) {
+ parm1[ii] = scl*grad[ii] + parm0[ii];
+ parm1[ii] = AIR_CLAMP(pdesc[ii].min, parm1[ii], pdesc[ii].max);
+ }
+}
+
static double
-nll(double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
+parmDist(const double *parmA, const double *parmB) {
+ unsigned int ii;
+ double dist, dd;
- simulate(dwiBuff, parm, espec);
- return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma);
+ dist = 0;
+ for (ii=0; ii<PARM_NUM; ii++) {
+ dd = (parmA[ii] - parmB[ii])/(pdesc[ii].max - pdesc[ii].min);
+ dist += dd*dd;
+ }
+ return sqrt(dist);
}
+static char *
+parmSprint(char str[AIR_STRLEN_MED], double *parm) {
+ sprintf(str, "(%g) [%g %g %g; %g %g; %g]", parm[0],
+ parm[1], parm[2], parm[3],
+ parm[4], parm[5],
+ parm[6]);
+ return str;
+}
+
+#define PARM_COPY(A, B) \
+ { \
+ unsigned int pidx; \
+ for (pidx=0; pidx<PARM_NUM; pidx++) { \
+ A[pidx] = B[pidx]; \
+ } \
+ }
+
+static double
+sqeFit(double *parm, double *convFrac, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ const double *parmInit, int knownB0,
+ unsigned int maxIter, double convEps) {
+ static const char me[]= TEN_MODEL_STR_TENSOR2 ":sqeFit";
+ unsigned int ii, i0, iter;
+ double step, bak, opp, val, tval,
+ dist, tparm[PARM_NUM], grad[PARM_NUM];
+ char str[AIR_STRLEN_MED];
+
+ i0 = knownB0 ? 1 : 0;
+ PARM_COPY(parm, parmInit);
+ val = sqe(parm, espec, dwiBuff, dwiMeas);
+ sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
+ step = 0;
+ for (ii=i0; ii<PARM_NUM; ii++) {
+ step += (pdesc[ii].max - pdesc[ii].min)/(10*grad[ii]);
+ }
+ step /= (PARM_NUM - i0);
+ fprintf(stderr, "!%s: at %s\n", me, parmSprint(str, parm));
+ fprintf(stderr, "!%s: initial step = %g\n", me, step);
+
+ opp = 1.5;
+ bak = 0.1;
+ iter = 0;
+ do {
+ do {
+ parmAdd(tparm, -step, grad, parm);
+ tval = sqe(tparm, espec, dwiBuff, dwiMeas);
+ if (tval > val) {
+ step *= bak;
+ }
+ } while (tval > val);
+ fprintf(stderr, "!%s: step %g got to tval %g at %s\n", me,
+ step, tval, parmSprint(str, tparm));
+ dist = parmDist(tparm, parm);
+ val = tval;
+ PARM_COPY(parm, tparm);
+ step *= opp;
+ iter++;
+ } while ((iter < maxIter) && (dist > convEps));
+ *convFrac = dist/convEps;
+ return val;
+}
+
+NLL;
+
+static void
+nllGrad(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma) {
+
+ AIR_UNUSED(grad);
+ AIR_UNUSED(parm);
+ AIR_UNUSED(espec);
+ AIR_UNUSED(dwiBuff);
+ AIR_UNUSED(dwiMeas);
+ AIR_UNUSED(rician);
+ AIR_UNUSED(sigma);
+ return;
+}
+
static int
nllFit(double *parm, const tenExperSpec *espec,
const double *dwiMeas, const double *parmInit,
@@ -96,26 +238,14 @@
return 0;
}
-/* 1/sqrt(2) */
-#define OST 0.70710678118654752440
-
tenModel
_tenModelTensor2 = {
- "tensor2",
+ TEN_MODEL_STR_TENSOR2,
PARM_NUM,
- {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"Dxx", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"Dxy", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
- {"Dxz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
- {"Dyy", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"Dyz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
- {"Dzz", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- },
+ PARM_DESC,
simulate,
- sqe,
- sqeFit,
- nll,
- nllFit
+ prand,
+ sqe, sqeGrad, sqeFit,
+ nll, nllGrad, nllFit
};
const tenModel *const tenModelTensor2 = &_tenModelTensor2;
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/privateTen.h 2009-10-26 22:40:09 UTC (rev 4321)
@@ -156,6 +156,35 @@
const tenExperSpec *espec,
int rician, double sigma);
+/* model*.c */
+/*
+** NOTE: these functions rely on the "simulate" function defined
+** per-model (which is why these functions can't all use the same
+** underlying function definition, unless the simulate function
+** was passed as a callback, which would incur some more function
+** call overhead)
+*/
+#define SQE \
+static double \
+sqe(const double *parm, const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas) { \
+ \
+ simulate(dwiBuff, parm, espec); \
+ return _tenModel_sqe(dwiMeas, dwiBuff, espec); \
+}
+
+#define NLL \
+static double \
+nll(const double *parm, const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ int rician, double sigma) { \
+ \
+ simulate(dwiBuff, parm, espec); \
+ return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma); \
+}
+
+
+
#ifdef __cplusplus
}
#endif
Modified: teem/trunk/src/ten/sources.cmake
===================================================================
--- teem/trunk/src/ten/sources.cmake 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/sources.cmake 2009-10-26 22:40:09 UTC (rev 4321)
@@ -56,6 +56,7 @@
tendShrink.c
tendSim.c
tendMsim.c
+ tendMfit.c
tendSlice.c
tendSten.c
tendTconv.c
@@ -64,8 +65,9 @@
tensor.c
triple.c
experSpec.c
- modelTen.c
+ tenModel.c
modelBall.c
+ model1Stick.c
modelBall1Stick.c
modelCylinder.c
modelTensor2.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/ten.h 2009-10-26 22:40:09 UTC (rev 4321)
@@ -1122,16 +1122,26 @@
/* noise free simulation */
void (*simulate)(double *dwiSim, const double *parm,
const tenExperSpec *espec);
+ /* random parameter vector */
+ void (*random)(double *parm, airRandMTState *rng);
/* "sqe" == squared error in DWI values */
- double (*sqe)(double *parm, const tenExperSpec *espec,
+ double (*sqe)(const double *parm, const tenExperSpec *espec,
double *dwiBuff, const double *dwiMeas);
- int (*sqeFit)(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int knownB0);
+ void (*sqeGrad)(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas);
+ int (*sqeFit)(double *parm, double *convFrac, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ const double *parmInit, int knownB0,
+ unsigned int maxIter, double convEps);
/* "nll" == negative log likelihood */
- double (*nll)(double *parm, const tenExperSpec *espec,
+ double (*nll)(const double *parm, const tenExperSpec *espec,
double *dwiBuff, const double *dwiMeas,
int rician, double sigma);
+ void (*nllGrad)(double *grad, const double *parm,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ int rician, double sigma);
int (*nllFit)(double *parm, const tenExperSpec *espec,
const double *dwiMeas, const double *parmInit,
int rician, double sigma, int knownB0);
@@ -1521,10 +1531,11 @@
TEN_EXPORT int tenDWMRIKeyValueFromExperSpecSet(Nrrd *ndwi,
const tenExperSpec *espec);
-/* modelTen.c */
+/* tenModel.c */
+TEN_EXPORT const char *tenModelPrefixStr;
TEN_EXPORT int tenModelParse(const tenModel **model, int *plusB0,
- const char *_str);
-TEN_EXPORT int tenModelFromAxisLearn(const tenModel **model,
+ int requirePrefix, const char *_str);
+TEN_EXPORT int tenModelFromAxisLearn(const tenModel **model, int *plusB0,
const NrrdAxisInfo *axinfo);
TEN_EXPORT int tenModelSimulate(Nrrd *ndwi, int typeOut,
tenExperSpec *espec,
@@ -1535,20 +1546,28 @@
TEN_EXPORT int tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
- int knownB0);
+ int knownB0, int saveB0, int typeOut,
+ unsigned int maxIter, double convEps);
TEN_EXPORT int tenModelNllFit(Nrrd *nparm, Nrrd **nnllP,
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
int rician, double sigma, int knownB0);
-/* have to keep in sync with modelUtil.c/tenModelParse() */
+/* have to keep in sync with modelTen.c/tenModelParse() */
/* modelBall.c */
+#define TEN_MODEL_STR_BALL "ball"
TEN_EXPORT const tenModel *const tenModelBall;
+/* model1Stick.c */
+#define TEN_MODEL_STR_1STICK "1stick"
+TEN_EXPORT const tenModel *const tenModel1Stick;
/* modelBall1Stick.c */
+#define TEN_MODEL_STR_BALL1STICK "ball1stick"
TEN_EXPORT const tenModel *const tenModelBall1Stick;
/* modelCylinder.c */
+#define TEN_MODEL_STR_CYLINDER "cylinder"
TEN_EXPORT const tenModel *const tenModelCylinder;
/* modelTensor2.c */
+#define TEN_MODEL_STR_TENSOR2 "tensor2"
TEN_EXPORT const tenModel *const tenModelTensor2;
/* mod.c */
@@ -1607,8 +1626,9 @@
F(epireg) \
F(bmat) \
F(estim) \
+F(sim) \
+F(mfit) \
F(msim) \
-F(sim) \
F(make) \
F(avg) \
F(helix) \
Modified: teem/trunk/src/ten/tenModel.c
===================================================================
--- teem/trunk/src/ten/tenModel.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/tenModel.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -75,8 +75,7 @@
*plusB0 = AIR_TRUE;
} else {
biffAddf(TEN, "%s: string (\"%s\") prior to \"+\" not \"b0\"", me, str);
- airMopError(mop);
- return 1;
+ airMopError(mop); return 1;
}
} else {
*plusB0 = AIR_FALSE;
@@ -84,8 +83,7 @@
}
if (!(*model = str2model(modstr))) {
biffAddf(TEN, "%s: didn't recognize \"%s\" as model", me, str);
- airMopError(mop);
- return 1;
+ airMopError(mop); return 1;
}
airMopOkay(mop);
return 0;
@@ -304,15 +302,94 @@
tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
- int knownB0) {
+ int knownB0, int saveB0, int typeOut,
+ unsigned int maxIter, double convEps) {
+ static const char me[]="tenModelSqeFit";
+ double *ddwi, *dwibuff, dparm[TEN_MODEL_PARM_MAXNUM],
+ (*ins)(void *v, size_t I, double d),
+ (*lup)(const void *v, size_t I);
+ airArray *mop;
+ unsigned int saveParmNum, dwiNum, ii;
+ size_t szOut[NRRD_DIM_MAX], II, numSamp;
+ int axmap[NRRD_DIM_MAX];
+ const char *dwi;
+ char *parm;
- AIR_UNUSED(nparm);
- AIR_UNUSED(nsqeP);
- AIR_UNUSED(model);
- AIR_UNUSED(espec);
- AIR_UNUSED(ndwi);
- AIR_UNUSED(knownB0);
+ if (!( nparm && model && espec && ndwi )) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ if (!( nrrdTypeFloat == typeOut || nrrdTypeDouble == typeOut )) {
+ biffAddf(TEN, "%s: typeOut must be %s or %s, not %s", me,
+ airEnumStr(nrrdType, nrrdTypeFloat),
+ airEnumStr(nrrdType, nrrdTypeDouble),
+ airEnumStr(nrrdType, typeOut));
+ return 1;
+ }
+ dwiNum = ndwi->axis[0].size;
+ if (!( espec->imgNum != dwiNum )) {
+ biffAddf(TEN, "%s: espec expects %u images but dwi has %u on axis 0",
+ me, espec->imgNum, AIR_CAST(unsigned int, dwiNum));
+ return 1;
+ }
+
+ /* allocate output (and set axmap) */
+ saveParmNum = saveB0 ? model->parmNum : model->parmNum-1;
+ for (ii=0; ii<nparm->dim; ii++) {
+ szOut[ii] = (!ii
+ ? saveParmNum
+ : ndwi->axis[ii].size);
+ axmap[ii] = (!ii
+ ? -1
+ : AIR_CAST(int, ii));
+ }
+ if (nrrdMaybeAlloc_nva(nparm, typeOut, ndwi->dim, szOut)) {
+ biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ airMopError(mop); return 1;
+ }
+ ddwi = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double)));
+ dwibuff = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double)));
+ if (!(ddwi && dwibuff)) {
+ biffAddf(TEN, "%s: couldn't allocate dwi buffers", me);
+ airMopError(mop); return 1;
+ }
+ airMopAdd(mop, ddwi, airFree, airMopAlways);
+ airMopAdd(mop, dwibuff, airFree, airMopAlways);
+ /* set output */
+ numSamp = nrrdElementNumber(ndwi)/ndwi->axis[0].size;
+ ins = nrrdDInsert[typeOut];
+ lup = nrrdDLookup[ndwi->type];
+ parm = AIR_CAST(char *, nparm->data);
+ dwi = AIR_CAST(char *, ndwi->data);
+ for (II=0; II<numSamp; II++) {
+ for (ii=0; ii<dwiNum; ii++) {
+ ddwi[ii] = lup(dwi, ii);
+ }
+ /* fit to dparm */
+ for (ii=0; ii<saveParmNum; ii++) {
+ ins(parm, ii, dparm[ii]);
+ }
+ parm += saveParmNum*nrrdTypeSize[typeOut];
+ dwi += espec->imgNum*nrrdTypeSize[ndwi->type];
+ }
+
+ if (nrrdAxisInfoCopy(nparm, ndwi, axmap, NRRD_AXIS_INFO_SIZE_BIT)
+ || nrrdBasicInfoCopy(nparm, ndwi,
+ NRRD_BASIC_INFO_DATA_BIT
+ | NRRD_BASIC_INFO_TYPE_BIT
+ | NRRD_BASIC_INFO_BLOCKSIZE_BIT
+ | NRRD_BASIC_INFO_DIMENSION_BIT
+ | NRRD_BASIC_INFO_CONTENT_BIT
+ | NRRD_BASIC_INFO_COMMENTS_BIT
+ | (nrrdStateKeyValuePairsPropagate
+ ? 0
+ : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
+ biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ airMopError(mop); return 1;
+ }
+
+ airMopOkay(mop);
return 0;
}
Modified: teem/trunk/src/ten/tendEstim.c
===================================================================
--- teem/trunk/src/ten/tendEstim.c 2009-10-26 22:39:34 UTC (rev 4320)
+++ teem/trunk/src/ten/tendEstim.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -27,7 +27,7 @@
char *_tend_estimInfoL =
(INFO
". The tensor coefficient weightings associated with "
- "each of the DWIs, the B-matrix, is given either as a seperate array, "
+ "each of the DWIs, the B-matrix, is given either as a separate array, "
"(see \"tend bmat\" usage info for details), or by the key-value pairs "
"in the DWI nrrd header. A \"confidence\" value is computed with the "
"tensor, based on a soft thresholding of the sum of all the DWIs, "
@@ -193,7 +193,7 @@
hestOptAdd(&hopt, "b", "b", airTypeDouble, 1, 1, &bval, "nan",
"\"b\" diffusion-weighting factor (units of sec/mm^2)");
hestOptAdd(&hopt, "knownB0", "bool", airTypeBool, 1, 1, &knownB0, NULL,
- "Determines of the B=0 non-diffusion-weighted reference image "
+ "Indicates if the B=0 non-diffusion-weighted reference image "
"is known, or if it has to be estimated along with the tensor "
"elements.\n "
"\b\bo if \"true\": in the given list of diffusion gradients or "
@@ -203,7 +203,7 @@
"images among the input; the B=0 image value is going to be "
"estimated along with the diffusion model");
hestOptAdd(&hopt, "i", "dwi0 dwi1", airTypeOther, 1, -1, &nin, "-",
- "all the diffusion-weighted images (DWIs), as seperate 3D nrrds, "
+ "all the diffusion-weighted images (DWIs), as separate 3D nrrds, "
"**OR**: One 4D nrrd of all DWIs stacked along axis 0",
&ninLen, NULL, nrrdHestNrrd);
hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
Added: teem/trunk/src/ten/tendMfit.c
===================================================================
--- teem/trunk/src/ten/tendMfit.c (rev 0)
+++ teem/trunk/src/ten/tendMfit.c 2009-10-26 22:40:09 UTC (rev 4321)
@@ -0,0 +1,101 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define INFO "Estimate models from a set of DW images"
+char *_tend_mfitInfoL =
+ (INFO
+ ". More docs here.");
+
+int
+tend_mfitMain(int argc, char **argv, char *me, hestParm *hparm) {
+ int pret;
+ hestOpt *hopt = NULL;
+ char *perr, *err;
+ airArray *mop;
+
+ Nrrd *nin, *nout;
+ char *outS;
+ int EE, knownB0, verbose, mlfit;
+ unsigned int maxIter;
+ double valueMin, thresh, sigma;
+ const tenModel *model;
+
+ hestOptAdd(&hopt, "v", "verbose", airTypeInt, 1, 1, &verbose, "0",
+ "verbosity level");
+ hestOptAdd(&hopt, "ml", NULL, airTypeInt, 0, 0, &mlfit, NULL,
+ "do ML fitting, rather than least-squares, which also "
+ "requires setting \"-sigma\"");
+ hestOptAdd(&hopt, "sigma", "sigma", airTypeDouble, 1, 1, &sigma, "nan",
+ "Rician noise parameter");
+ hestOptAdd(&hopt, "maxi", "max iters", airTypeUInt, 1, 1, &maxIter, "10",
+ "maximum allowable iterations for fitting.");
+ hestOptAdd(&hopt, "knownB0", "bool", airTypeBool, 1, 1, &knownB0, NULL,
+ "Indicates if the B=0 non-diffusion-weighted reference image "
+ "is known (\"true\"), or if it has to be estimated along with "
+ "the other model parameters (\"false\")");
+ hestOptAdd(&hopt, "i", "dwi", airTypeOther, 1, 1, &nin, "-",
+ "all the diffusion-weighted images in one 4D nrrd",
+ NULL, NULL, nrrdHestNrrd);
+ hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
+ "output tensor volume");
+
+ mop = airMopNew();
+ airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
+ USAGE(_tend_mfitInfoL);
+ JUSTPARSE();
+ airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
+
+ nout = nrrdNew();
+ airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
+
+ /*
+ if (tenModelSqeFit(nout, NULL,
+ const tenModel *model,
+ const tenExperSpec *espec, const Nrrd *ndwi,
+ int knownB0, int saveB0, int typeOut,
+ unsigned int maxIter, double convEps);
+
+ if (tenEstimate1TensorVolume4D(tec, nout, &nB0,
+ airStrlen(terrS)
+ ? &nterr
+ : NULL,
+ nin4d, nrrdTypeFloat)) {
+ airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble doing estimation:\n%s\n", me, err);
+ airMopError(mop); return 1;
+ }
+
+ */
+ if (nrrdSave(outS, nout, NULL)) {
+ airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
+ airMopError(mop); return 1;
+ }
+
+ airMopOkay(mop);
+ return 0;
+}
+/* TEND_CMD(mfit, INFO); */
+unrrduCmd tend_mfitCmd = { "mfit", INFO, tend_mfitMain };
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-27 20:23:41
|
Revision: 4323
http://teem.svn.sourceforge.net/teem/?rev=4323&view=rev
Author: kindlmann
Date: 2009-10-27 20:23:29 +0000 (Tue, 27 Oct 2009)
Log Message:
-----------
tenModel stuff still under construction
Modified Paths:
--------------
teem/trunk/src/ten/experSpec.c
teem/trunk/src/ten/model1Stick.c
teem/trunk/src/ten/modelBall.c
teem/trunk/src/ten/modelBall1Stick.c
teem/trunk/src/ten/modelCylinder.c
teem/trunk/src/ten/modelTensor2.c
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenModel.c
teem/trunk/src/ten/tendMfit.c
Modified: teem/trunk/src/ten/experSpec.c
===================================================================
--- teem/trunk/src/ten/experSpec.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/experSpec.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -29,7 +29,7 @@
espec->bval = airFree(espec->bval);
espec->grad = airFree(espec->grad);
- espec->wght = airFree(espec->wght);
+ /* espec->wght = airFree(espec->wght); */
if (!num) {
biffAddf(TEN, "%s: need a non-zero number of images", me);
return 1;
@@ -37,8 +37,8 @@
espec->imgNum = num;
espec->bval = AIR_CAST(double *, calloc(num, sizeof(double)));
espec->grad = AIR_CAST(double *, calloc(3*num, sizeof(double)));
- espec->wght = AIR_CAST(double *, calloc(num, sizeof(double)));
- if (!( espec->bval && espec->grad && espec->wght )) {
+ /* espec->wght = AIR_CAST(double *, calloc(num, sizeof(double))); */
+ if (!( espec->bval && espec->grad /* && espec->wght */ )) {
biffAddf(TEN, "%s: couldn't allocate for %u images", me, num);
return 1;
}
@@ -54,7 +54,7 @@
espec->imgNum = 0;
espec->bval = NULL;
espec->grad = NULL;
- espec->wght = NULL;
+ /* espec->wght = NULL; */
return espec;
}
@@ -77,7 +77,7 @@
for (ii=0; ii<imgNum; ii++) {
espec->bval[ii] = bval;
ELL_3V_COPY(espec->grad + 3*ii, grad + 3*ii);
- espec->wght[ii] = 1.0;
+ /* espec->wght[ii] = 1.0; */
}
return 0;
@@ -102,12 +102,13 @@
for (ii=0; ii<imgNum; ii++) {
espec->bval[ii] = bval[ii];
ELL_3V_COPY(espec->grad + 3*ii, grad + 3*ii);
- espec->wght[ii] = 1.0;
+ /* espec->wght[ii] = 1.0; */
}
return 0;
}
+/*
int
tenExperSpecGradBValWghtSet(tenExperSpec *espec,
unsigned int imgNum,
@@ -133,6 +134,7 @@
return 0;
}
+*/
int
tenExperSpecFromKeyValueSet(tenExperSpec *espec, const Nrrd *ndwi) {
@@ -219,37 +221,51 @@
if (espec) {
espec->bval = airFree(espec->bval);
espec->grad = airFree(espec->grad);
- espec->wght = airFree(espec->wght);
+ /* espec->wght = airFree(espec->wght); */
airFree(espec);
}
return NULL;
}
double
-_tenModel_sqe(const double *dwiMeas, const double *dwiSim,
- const tenExperSpec *espec) {
+_tenExperSpec_sqe(const double *dwiMeas, const double *dwiSim,
+ const tenExperSpec *espec, int knownB0) {
unsigned int ii;
double sqe;
sqe = 0;
- for (ii=0; ii<espec->imgNum; ii++) {
- double dd;
- dd = dwiMeas[ii] - dwiSim[ii];
- sqe += dd*dd;
+ if (knownB0) {
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double dd;
+ if (!espec->bval[ii]) {
+ continue;
+ }
+ dd = dwiMeas[ii] - dwiSim[ii];
+ sqe += dd*dd;
+ }
+ } else {
+ for (ii=0; ii<espec->imgNum; ii++) {
+ double dd;
+ dd = dwiMeas[ii] - dwiSim[ii];
+ sqe += dd*dd;
+ }
}
return sqe;
}
double
-_tenModel_nll(const double *dwiMeas, const double *dwiSim,
- const tenExperSpec *espec,
- int rician, double sigma) {
+_tenExperSpec_nll(const double *dwiMeas, const double *dwiSim,
+ const tenExperSpec *espec,
+ int rician, double sigma, int knownB0) {
double nll;
unsigned int ii;
nll = 0;
if (rician) {
for (ii=0; ii<espec->imgNum; ii++) {
+ if (knownB0 && !espec->bval[ii]) {
+ continue;
+ }
nll += -airLogRician(dwiMeas[ii], dwiSim[ii], sigma);
}
} else {
@@ -257,6 +273,9 @@
ladd = log(sigma*sqrt(2*AIR_PI));
denom = 1.0/(2*sigma*sigma);
for (ii=0; ii<espec->imgNum; ii++) {
+ if (knownB0 && !espec->bval[ii]) {
+ continue;
+ }
dd = dwiMeas[ii] - dwiSim[ii];
nll += dd*dd*denom + ladd;
}
Modified: teem/trunk/src/ten/model1Stick.c
===================================================================
--- teem/trunk/src/ten/model1Stick.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/model1Stick.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -53,106 +53,29 @@
return;
}
-static void
-prand(double *parm, airRandMTState *rng) {
- unsigned int ii;
-
- for (ii=0; ii<PARM_NUM; ii++) {
- if (pdesc[ii].vec3) {
- /* its unit vector */
- double xx, yy, zz, theta, rr;
-
- zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
- theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
- rr = sqrt(1 - zz*zz);
- xx = rr*cos(theta);
- yy = rr*sin(theta);
- parm[ii + 0] = xx;
- parm[ii + 1] = yy;
- parm[ii + 2] = zz;
- /* bump ii by 2; next for loop will increment past */
- ii += 2;
- } else {
- parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
- pdesc[ii].min, pdesc[ii].max);
- }
- }
- return;
+static char *
+parmSprint(char str[AIR_STRLEN_MED], const double *parm) {
+ sprintf(str, "(%g) %g (%g,%g,%g)", parm[0], parm[1],
+ parm[2], parm[3], parm[4]);
+ return str;
}
-SQE;
+_TEN_PARM_RAND
+_TEN_PARM_STEP
+_TEN_PARM_DIST
+_TEN_PARM_COPY
-static void
-sqeGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- return;
-}
+_TEN_SQE
+_TEN_SQE_GRAD_STUB
+_TEN_SQE_FIT_STUB
-static int
-sqeFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int knownB0) {
- unsigned int pp;
+_TEN_NLL
+_TEN_NLL_GRAD_STUB
+_TEN_NLL_FIT_STUB
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
-NLL;
-
-static void
-nllGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- return;
-}
-
-static int
-nllFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int rician, double sigma, int knownB0) {
- unsigned int pp;
-
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
tenModel
_tenModel1Stick = {
TEN_MODEL_STR_1STICK,
- PARM_NUM,
- PARM_DESC,
- simulate,
- prand,
- sqe, sqeGrad, sqeFit,
- nll, nllGrad, nllFit
+ _TEN_MODEL_FIELDS
};
const tenModel *const tenModel1Stick = &_tenModel1Stick;
Modified: teem/trunk/src/ten/modelBall.c
===================================================================
--- teem/trunk/src/ten/modelBall.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/modelBall.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -45,46 +45,23 @@
return;
}
-static void
-prand(double *parm, airRandMTState *rng) {
-
- parm[0] = AIR_AFFINE(0, airDrandMT_r(rng), 1, pdesc[0].min, pdesc[0].max);
- parm[1] = AIR_AFFINE(0, airDrandMT_r(rng), 1, pdesc[1].min, pdesc[1].max);
- return;
+static char *
+parmSprint(char str[AIR_STRLEN_MED], const double *parm) {
+ sprintf(str, "(%g) %g", parm[0], parm[1]);
+ return str;
}
-SQE;
+_TEN_PARM_RAND
+_TEN_PARM_STEP
+_TEN_PARM_DIST
+_TEN_PARM_COPY
-static void
-sqeGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- return;
-}
+_TEN_SQE
+_TEN_SQE_GRAD_STUB
+_TEN_SQE_FIT_STUB
-static int
-sqeFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int knownB0) {
- unsigned int pp;
+_TEN_NLL
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
-NLL;
-
static void
nllGrad(double *grad, const double *parm,
const tenExperSpec *espec,
@@ -101,7 +78,7 @@
return;
}
-static int
+static double
nllFit(double *parm, const tenExperSpec *espec,
const double *dwiMeas, const double *parmInit,
int rician, double sigma, int knownB0) {
@@ -121,11 +98,6 @@
tenModel
_tenModelBall = {
TEN_MODEL_STR_BALL,
- PARM_NUM,
- PARM_DESC,
- simulate,
- prand,
- sqe, sqeGrad, sqeFit,
- nll, nllGrad, nllFit
+ _TEN_MODEL_FIELDS
};
const tenModel *const tenModelBall = &_tenModelBall;
Modified: teem/trunk/src/ten/modelBall1Stick.c
===================================================================
--- teem/trunk/src/ten/modelBall1Stick.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/modelBall1Stick.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -57,106 +57,29 @@
return;
}
-static void
-prand(double *parm, airRandMTState *rng) {
- unsigned int ii;
-
- for (ii=0; ii<PARM_NUM; ii++) {
- if (pdesc[ii].vec3) {
- /* its unit vector */
- double xx, yy, zz, theta, rr;
-
- zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
- theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
- rr = sqrt(1 - zz*zz);
- xx = rr*cos(theta);
- yy = rr*sin(theta);
- parm[ii + 0] = xx;
- parm[ii + 1] = yy;
- parm[ii + 2] = zz;
- /* bump ii by 2, anticipating completion of this for-loop iter */
- ii += 2;
- } else {
- parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
- pdesc[ii].min, pdesc[ii].max);
- }
- }
- return;
+static char *
+parmSprint(char str[AIR_STRLEN_MED], const double *parm) {
+ sprintf(str, "(%g) %g * (%g + %g*(%g,%g,%g))", parm[0],
+ parm[1], 1-parm[2], parm[2], parm[3], parm[4], parm[5]);
+ return str;
}
-SQE;
+_TEN_PARM_RAND
+_TEN_PARM_STEP
+_TEN_PARM_DIST
+_TEN_PARM_COPY
-static void
-sqeGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- return;
-}
+_TEN_SQE
+_TEN_SQE_GRAD_STUB
+_TEN_SQE_FIT_STUB
-static int
-sqeFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int knownB0) {
- unsigned int pp;
+_TEN_NLL
+_TEN_NLL_GRAD_STUB
+_TEN_NLL_FIT_STUB
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
-NLL;
-
-static void
-nllGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- return;
-}
-
-static int
-nllFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int rician, double sigma, int knownB0) {
- unsigned int pp;
-
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
tenModel
_tenModelBall1Stick = {
TEN_MODEL_STR_BALL1STICK,
- PARM_NUM,
- PARM_DESC,
- simulate,
- prand,
- sqe, sqeGrad, sqeFit,
- nll, nllGrad, nllFit
+ _TEN_MODEL_FIELDS
};
const tenModel *const tenModelBall1Stick = &_tenModelBall1Stick;
Modified: teem/trunk/src/ten/modelCylinder.c
===================================================================
--- teem/trunk/src/ten/modelCylinder.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/modelCylinder.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -59,106 +59,29 @@
return;
}
-static void
-prand(double *parm, airRandMTState *rng) {
- unsigned int ii;
+_TEN_PARM_RAND
+_TEN_PARM_STEP
+_TEN_PARM_DIST
+_TEN_PARM_COPY
- for (ii=0; ii<PARM_NUM; ii++) {
- if (pdesc[ii].vec3) {
- /* its unit vector */
- double xx, yy, zz, theta, rr;
-
- zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
- theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
- rr = sqrt(1 - zz*zz);
- xx = rr*cos(theta);
- yy = rr*sin(theta);
- parm[ii + 0] = xx;
- parm[ii + 1] = yy;
- parm[ii + 2] = zz;
- /* bump ii by 2, anticipating completion of this for-loop iter */
- ii += 2;
- } else {
- parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
- pdesc[ii].min, pdesc[ii].max);
- }
- }
- return;
+static char *
+parmSprint(char str[AIR_STRLEN_MED], const double *parm) {
+ sprintf(str, "(%g) %g x %g (%g,%g,%g)", parm[0],
+ parm[1], parm[2], parm[3], parm[4], parm[5]);
+ return str;
}
-SQE;
+_TEN_SQE
+_TEN_SQE_GRAD_STUB
+_TEN_SQE_FIT_STUB
-static void
-sqeGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- return;
-}
+_TEN_NLL
+_TEN_NLL_GRAD_STUB
+_TEN_NLL_FIT_STUB
-static int
-sqeFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int knownB0) {
- unsigned int pp;
-
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
-NLL;
-
-static void
-nllGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
-
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- return;
-}
-
-static int
-nllFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int rician, double sigma, int knownB0) {
- unsigned int pp;
-
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
tenModel
_tenModelCylinder = {
TEN_MODEL_STR_CYLINDER,
- PARM_NUM,
- PARM_DESC,
- simulate,
- prand,
- sqe, sqeGrad, sqeFit,
- nll, nllGrad, nllFit
+ _TEN_MODEL_FIELDS
};
const tenModel *const tenModelCylinder = &_tenModelCylinder;
Modified: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -61,35 +61,22 @@
return;
}
-static void
-prand(double *parm, airRandMTState *rng) {
- unsigned int ii;
-
- for (ii=0; ii<PARM_NUM; ii++) {
- if (pdesc[ii].vec3) {
- /* its unit vector */
- double xx, yy, zz, theta, rr;
-
- zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0);
- theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI);
- rr = sqrt(1 - zz*zz);
- xx = rr*cos(theta);
- yy = rr*sin(theta);
- parm[ii + 0] = xx;
- parm[ii + 1] = yy;
- parm[ii + 2] = zz;
- /* bump ii by 2, anticipating completion of this for-loop iter */
- ii += 2;
- } else {
- parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0,
- pdesc[ii].min, pdesc[ii].max);
- }
- }
- return;
+static char *
+parmSprint(char str[AIR_STRLEN_MED], const double *parm) {
+ sprintf(str, "(%g) [%g %g %g; %g %g; %g]", parm[0],
+ parm[1], parm[2], parm[3],
+ parm[4], parm[5],
+ parm[6]);
+ return str;
}
-SQE;
+_TEN_PARM_RAND
+_TEN_PARM_STEP
+_TEN_PARM_DIST
+_TEN_PARM_COPY
+_TEN_SQE
+
static void
sqeGrad(double *grad, const double *parm0,
const tenExperSpec *espec,
@@ -102,11 +89,11 @@
for (ii=i0; ii<PARM_NUM; ii++) {
parm1[ii] = parm0[ii];
}
- sqe0 = sqe(parm0, espec, dwiBuff, dwiMeas);
+ sqe0 = sqe(parm0, espec, dwiBuff, dwiMeas, knownB0);
for (ii=i0; ii<PARM_NUM; ii++) {
- dp = (pdesc[ii].max - pdesc[ii].min)/3000;
+ dp = (pdesc[ii].max - pdesc[ii].min)*_TEN_PARM_GRAD_EPS;
parm1[ii] += dp;
- sqe1 = sqe(parm1, espec, dwiBuff, dwiMeas);
+ sqe1 = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0);
grad[ii] = (sqe1 - sqe0)/dp;
parm1[ii] = parm0[ii];
}
@@ -116,136 +103,64 @@
return;
}
-static void
-parmAdd(double *parm1, const double scl,
- const double *grad, const double *parm0) {
- unsigned int ii;
-
- for (ii=0; ii<PARM_NUM; ii++) {
- parm1[ii] = scl*grad[ii] + parm0[ii];
- parm1[ii] = AIR_CLAMP(pdesc[ii].min, parm1[ii], pdesc[ii].max);
- }
-}
-
static double
-parmDist(const double *parmA, const double *parmB) {
- unsigned int ii;
- double dist, dd;
-
- dist = 0;
- for (ii=0; ii<PARM_NUM; ii++) {
- dd = (parmA[ii] - parmB[ii])/(pdesc[ii].max - pdesc[ii].min);
- dist += dd*dd;
- }
- return sqrt(dist);
-}
-
-static char *
-parmSprint(char str[AIR_STRLEN_MED], double *parm) {
- sprintf(str, "(%g) [%g %g %g; %g %g; %g]", parm[0],
- parm[1], parm[2], parm[3],
- parm[4], parm[5],
- parm[6]);
- return str;
-}
-
-#define PARM_COPY(A, B) \
- { \
- unsigned int pidx; \
- for (pidx=0; pidx<PARM_NUM; pidx++) { \
- A[pidx] = B[pidx]; \
- } \
- }
-
-static double
sqeFit(double *parm, double *convFrac, const tenExperSpec *espec,
double *dwiBuff, const double *dwiMeas,
const double *parmInit, int knownB0,
- unsigned int maxIter, double convEps) {
+ unsigned int minIter, unsigned int maxIter, double convEps) {
static const char me[]= TEN_MODEL_STR_TENSOR2 ":sqeFit";
- unsigned int ii, i0, iter;
+ unsigned int i0, iter;
double step, bak, opp, val, tval,
dist, tparm[PARM_NUM], grad[PARM_NUM];
char str[AIR_STRLEN_MED];
+ int done;
i0 = knownB0 ? 1 : 0;
- PARM_COPY(parm, parmInit);
- val = sqe(parm, espec, dwiBuff, dwiMeas);
+ parmCopy(parm, parmInit);
+ val = sqe(parm, espec, dwiBuff, dwiMeas, knownB0);
sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
- step = 0;
- for (ii=i0; ii<PARM_NUM; ii++) {
- step += (pdesc[ii].max - pdesc[ii].min)/(10*grad[ii]);
- }
- step /= (PARM_NUM - i0);
- fprintf(stderr, "!%s: at %s\n", me, parmSprint(str, parm));
- fprintf(stderr, "!%s: initial step = %g\n", me, step);
+ step = 10;
+ fprintf(stderr, "!%s: -------- at %s\n", me, parmSprint(str, parm));
+ fprintf(stderr, "!%s: initial step = %g, convEps = %g\n",
+ me, step, convEps);
- opp = 1.5;
+ opp = 1.1;
bak = 0.1;
iter = 0;
do {
do {
- parmAdd(tparm, -step, grad, parm);
- tval = sqe(tparm, espec, dwiBuff, dwiMeas);
+ parmStep(tparm, -step, grad, parm);
+ tval = sqe(tparm, espec, dwiBuff, dwiMeas, knownB0);
if (tval > val) {
step *= bak;
+ fprintf(stderr, "!%s(%u): tval %g > val %g ==> step -> %g\n",
+ me, iter, tval, val, step);
}
} while (tval > val);
- fprintf(stderr, "!%s: step %g got to tval %g at %s\n", me,
- step, tval, parmSprint(str, tparm));
dist = parmDist(tparm, parm);
+ fprintf(stderr, "!%s(%u): step %g (dist %g) -> %g @ %s\n", me, iter,
+ step, dist, tval, parmSprint(str, tparm));
val = tval;
- PARM_COPY(parm, tparm);
+ parmCopy(parm, tparm);
+ sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
step *= opp;
iter++;
- } while ((iter < maxIter) && (dist > convEps));
+ done = (iter < minIter
+ ? AIR_FALSE
+ : (iter > maxIter) || dist < convEps);
+ } while (!done);
*convFrac = dist/convEps;
return val;
}
-NLL;
+_TEN_NLL
+_TEN_NLL_GRAD_STUB
+_TEN_NLL_FIT_STUB
-static void
-nllGrad(double *grad, const double *parm,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int rician, double sigma) {
- AIR_UNUSED(grad);
- AIR_UNUSED(parm);
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiBuff);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- return;
-}
-
-static int
-nllFit(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int rician, double sigma, int knownB0) {
- unsigned int pp;
-
- AIR_UNUSED(espec);
- AIR_UNUSED(dwiMeas);
- AIR_UNUSED(rician);
- AIR_UNUSED(sigma);
- AIR_UNUSED(knownB0);
- for (pp=0; pp<PARM_NUM; pp++) {
- parm[pp] = parmInit[pp];
- }
- return 0;
-}
-
tenModel
_tenModelTensor2 = {
TEN_MODEL_STR_TENSOR2,
- PARM_NUM,
- PARM_DESC,
- simulate,
- prand,
- sqe, sqeGrad, sqeFit,
- nll, nllGrad, nllFit
+ _TEN_MODEL_FIELDS
};
const tenModel *const tenModelTensor2 = &_tenModelTensor2;
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/privateTen.h 2009-10-27 20:23:29 UTC (rev 4323)
@@ -147,44 +147,197 @@
const double *wght,
unsigned int NN, int ptype, tenInterpParm *tip);
-/* modelUtil.c */
-TEN_EXPORT double _tenModel_sqe(const double *dwiMeas,
- const double *dwiSim,
- const tenExperSpec *espec);
-TEN_EXPORT double _tenModel_nll(const double *dwiMeas,
- const double *dwiSim,
- const tenExperSpec *espec,
- int rician, double sigma);
+/* experSpec.c */
+TEN_EXPORT double _tenExperSpec_sqe(const double *dwiMeas,
+ const double *dwiSim,
+ const tenExperSpec *espec,
+ int knownB0);
+TEN_EXPORT double _tenExperSpec_nll(const double *dwiMeas,
+ const double *dwiSim,
+ const tenExperSpec *espec,
+ int rician, double sigma,
+ int knownB0);
/* model*.c */
+
+#define _TEN_PARM_GRAD_EPS 0.0001
+
/*
-** NOTE: these functions rely on the "simulate" function defined
-** per-model (which is why these functions can't all use the same
-** underlying function definition, unless the simulate function
-** was passed as a callback, which would incur some more function
-** call overhead)
+** NOTE: these functions rely on per-model information (like PARM_NUM)
+** or functions (like "simulate"), which is why these functions can't
+** all use same common underlying function, since more information would
+** have to be passed (annoying for rapid hacking), and the function
+** call overhead might be doubled
*/
-#define SQE \
-static double \
-sqe(const double *parm, const tenExperSpec *espec, \
- double *dwiBuff, const double *dwiMeas) { \
- \
- simulate(dwiBuff, parm, espec); \
- return _tenModel_sqe(dwiMeas, dwiBuff, espec); \
+#define _TEN_PARM_RAND \
+static void \
+parmRand(double *parm, airRandMTState *rng, int knownB0) { \
+ unsigned int ii; \
+ \
+ for (ii=knownB0 ? 1 : 0; ii<PARM_NUM; ii++) { \
+ if (pdesc[ii].vec3) { \
+ /* its unit vector */ \
+ double xx, yy, zz, theta, rr; \
+ \
+ zz = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, -1.0, 1.0); \
+ theta = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, 0.0, 2*AIR_PI); \
+ rr = sqrt(1 - zz*zz); \
+ xx = rr*cos(theta); \
+ yy = rr*sin(theta); \
+ parm[ii + 0] = xx; \
+ parm[ii + 1] = yy; \
+ parm[ii + 2] = zz; \
+ /* bump ii by 2, anticipating end of this for-loop iteration */ \
+ ii += 2; \
+ } else { \
+ parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, \
+ pdesc[ii].min, pdesc[ii].max); \
+ } \
+ } \
+ return; \
}
-#define NLL \
+#define _TEN_PARM_STEP \
+static void \
+parmStep(double *parm1, const double scl, \
+ const double *grad, const double *parm0) { \
+ unsigned int ii; \
+ \
+ for (ii=0; ii<PARM_NUM; ii++) { \
+ parm1[ii] = scl*grad[ii] + parm0[ii]; \
+ parm1[ii] = AIR_CLAMP(pdesc[ii].min, parm1[ii], pdesc[ii].max); \
+ if (pdesc[ii].vec3 && 2 == pdesc[ii].vecIdx) { \
+ double len; \
+ ELL_3V_NORM(parm1 + ii - 2, parm1 + ii - 2, len); \
+ } \
+ } \
+}
+
+#define _TEN_PARM_DIST \
+static double \
+parmDist(const double *parmA, const double *parmB) { \
+ unsigned int ii; \
+ double dist, dd; \
+ \
+ dist = 0; \
+ for (ii=0; ii<PARM_NUM; ii++) { \
+ dd = (parmA[ii] - parmB[ii])/(pdesc[ii].max - pdesc[ii].min); \
+ dist += dd*dd; \
+ } \
+ return sqrt(dist); \
+}
+
+#define _TEN_PARM_COPY \
+static void \
+parmCopy(double *parmA, const double *parmB) { \
+ unsigned int ii; \
+ \
+ for (ii=0; ii<PARM_NUM; ii++) { \
+ parmA[ii] = parmB[ii]; \
+ } \
+ return; \
+}
+
+#define _TEN_SQE \
static double \
-nll(const double *parm, const tenExperSpec *espec, \
- double *dwiBuff, const double *dwiMeas, \
- int rician, double sigma) { \
+sqe(const double *parm, const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, int knownB0) { \
\
simulate(dwiBuff, parm, espec); \
- return _tenModel_nll(dwiMeas, dwiBuff, espec, rician, sigma); \
+ return _tenExperSpec_sqe(dwiMeas, dwiBuff, espec, knownB0); \
}
+#define _TEN_SQE_GRAD_STUB \
+static void \
+sqeGrad(double *grad, const double *parm, \
+ const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ int knownB0) { \
+ \
+ AIR_UNUSED(grad); \
+ AIR_UNUSED(parm); \
+ AIR_UNUSED(espec); \
+ AIR_UNUSED(dwiBuff); \
+ AIR_UNUSED(dwiMeas); \
+ AIR_UNUSED(knownB0); \
+ return; \
+}
+#define _TEN_SQE_FIT_STUB \
+static double \
+sqeFit(double *parm, double *convFrac, const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ const double *parmInit, int knownB0, \
+ unsigned int minIter, unsigned int maxIter, double convEps) { \
+ unsigned int pp; \
+ \
+ AIR_UNUSED(convFrac); \
+ AIR_UNUSED(espec); \
+ AIR_UNUSED(dwiBuff); \
+ AIR_UNUSED(dwiMeas); \
+ AIR_UNUSED(knownB0); \
+ AIR_UNUSED(minIter); \
+ AIR_UNUSED(maxIter); \
+ AIR_UNUSED(convEps); \
+ for (pp=0; pp<PARM_NUM; pp++) { \
+ parm[pp] = parmInit[pp]; \
+ } \
+ return 0; \
+}
+#define _TEN_NLL \
+ static double \
+nll(const double *parm, const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ int rician, double sigma, int knownB0) { \
+ \
+ simulate(dwiBuff, parm, espec); \
+ return _tenExperSpec_nll(dwiMeas, dwiBuff, espec, \
+ rician, sigma, knownB0); \
+}
+
+#define _TEN_NLL_GRAD_STUB \
+static void \
+nllGrad(double *grad, const double *parm, \
+ const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ int rician, double sigma) { \
+ \
+ AIR_UNUSED(grad); \
+ AIR_UNUSED(parm); \
+ AIR_UNUSED(espec); \
+ AIR_UNUSED(dwiBuff); \
+ AIR_UNUSED(dwiMeas); \
+ AIR_UNUSED(rician); \
+ AIR_UNUSED(sigma); \
+ return; \
+}
+
+#define _TEN_NLL_FIT_STUB \
+static double \
+nllFit(double *parm, const tenExperSpec *espec, \
+ const double *dwiMeas, const double *parmInit, \
+ int rician, double sigma, int knownB0) { \
+ unsigned int pp; \
+ \
+ AIR_UNUSED(espec); \
+ AIR_UNUSED(dwiMeas); \
+ AIR_UNUSED(rician); \
+ AIR_UNUSED(sigma); \
+ AIR_UNUSED(knownB0); \
+ for (pp=0; pp<PARM_NUM; pp++) { \
+ parm[pp] = parmInit[pp]; \
+ } \
+ return 0; \
+}
+
+#define _TEN_MODEL_FIELDS \
+ PARM_NUM, PARM_DESC, \
+ simulate, \
+ parmSprint, parmRand, parmStep, parmDist, parmCopy, \
+ sqe, sqeGrad, sqeFit, \
+ nll, nllGrad, nllFit
+
#ifdef __cplusplus
}
#endif
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/ten.h 2009-10-27 20:23:29 UTC (rev 4323)
@@ -1083,7 +1083,7 @@
int set; /* has been set */
unsigned imgNum; /* total number of images, dwi or not */
double *bval, /* all b values: imgNum doubles */
- *wght, /* all weights: imgNum doubles */
+ /* *wght, all weights, but not yet used */
*grad; /* all gradients: 3 x imgNum doubles */
} tenExperSpec;
@@ -1091,11 +1091,11 @@
char name[AIR_STRLEN_SMALL]; /* name */
double min, max; /* bounds */
int vec3; /* non-zero if this is one coeff of 3-vector */
- unsigned int idx; /* if 3-vector, index into it */
+ unsigned int vecIdx; /* if 3-vector, index into it */
} tenModelParmDesc;
#define TEN_MODEL_PARM_MAXNUM 15 /* adjust as needed */
-#define TEN_MODEL_B0_MAX 65536 /* pretty arbitrary */
+#define TEN_MODEL_B0_MAX 10000 /* HEY: completely arbitrary! */
#define TEN_MODEL_DIFF_MAX 0.004 /* in units of mm^2/sec */
/*
@@ -1122,29 +1122,37 @@
/* noise free simulation */
void (*simulate)(double *dwiSim, const double *parm,
const tenExperSpec *espec);
- /* random parameter vector */
- void (*random)(double *parm, airRandMTState *rng);
+ /* parameter vector operations */
+ char *(*sprint)(char str[AIR_STRLEN_MED], const double *parm);
+ void (*rand)(double *parm, airRandMTState *rng, int knownB0);
+ void (*step)(double *parm1, const double scl,
+ const double *grad, const double *parm0);
+ double (*dist)(const double *parmA, const double *parmB);
+ void (*copy)(double *parmA, const double *parmB);
+
/* "sqe" == squared error in DWI values */
double (*sqe)(const double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas);
+ double *dwiBuff, const double *dwiMeas, int knownB0);
void (*sqeGrad)(double *grad, const double *parm,
const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas);
- int (*sqeFit)(double *parm, double *convFrac, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- const double *parmInit, int knownB0,
- unsigned int maxIter, double convEps);
+ double *dwiBuff, const double *dwiMeas,
+ int knownB0);
+ double (*sqeFit)(double *parm, double *convFrac, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ const double *parmInit, int knownB0,
+ unsigned int minIter, unsigned int maxIter,
+ double convEps);
/* "nll" == negative log likelihood */
double (*nll)(const double *parm, const tenExperSpec *espec,
double *dwiBuff, const double *dwiMeas,
- int rician, double sigma);
+ int rician, double sigma, int knownB0);
void (*nllGrad)(double *grad, const double *parm,
const tenExperSpec *espec,
double *dwiBuff, const double *dwiMeas,
int rician, double sigma);
- int (*nllFit)(double *parm, const tenExperSpec *espec,
- const double *dwiMeas, const double *parmInit,
- int rician, double sigma, int knownB0);
+ double (*nllFit)(double *parm, const tenExperSpec *espec,
+ const double *dwiMeas, const double *parmInit,
+ int rician, double sigma, int knownB0);
} tenModel;
/* defaultsTen.c */
@@ -1517,11 +1525,13 @@
unsigned int imgNum,
const double *bval,
const double *grad);
+/*
TEN_EXPORT int tenExperSpecGradBValWghtSet(tenExperSpec *espec,
unsigned int imgNum,
const double *bval,
const double *grad,
const double *wght);
+*/
TEN_EXPORT int tenExperSpecFromKeyValueSet(tenExperSpec *espec,
const Nrrd *ndwi);
TEN_EXPORT tenExperSpec* tenExperSpecNix(tenExperSpec *espec);
@@ -1547,7 +1557,9 @@
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
int knownB0, int saveB0, int typeOut,
- unsigned int maxIter, double convEps);
+ unsigned int minIter, unsigned int maxIter,
+ unsigned int starts, double convEps,
+ airRandMTState *rng);
TEN_EXPORT int tenModelNllFit(Nrrd *nparm, Nrrd **nnllP,
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
Modified: teem/trunk/src/ten/tenModel.c
===================================================================
--- teem/trunk/src/ten/tenModel.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/tenModel.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -303,22 +303,30 @@
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
int knownB0, int saveB0, int typeOut,
- unsigned int maxIter, double convEps) {
+ unsigned int minIter, unsigned int maxIter,
+ unsigned int starts, double convEps, airRandMTState *_rng) {
static const char me[]="tenModelSqeFit";
- double *ddwi, *dwibuff, dparm[TEN_MODEL_PARM_MAXNUM],
+ double *ddwi, *dwibuff, sqe, sqeBest, convFrac,
+ dparm[TEN_MODEL_PARM_MAXNUM],
+ dparmBest[TEN_MODEL_PARM_MAXNUM],
(*ins)(void *v, size_t I, double d),
(*lup)(const void *v, size_t I);
airArray *mop;
- unsigned int saveParmNum, dwiNum, ii;
+ unsigned int saveParmNum, dwiNum, ii, lablen;
size_t szOut[NRRD_DIM_MAX], II, numSamp;
int axmap[NRRD_DIM_MAX];
const char *dwi;
char *parm;
+ airRandMTState *rng;
if (!( nparm && model && espec && ndwi )) {
biffAddf(TEN, "%s: got NULL pointer", me);
return 1;
}
+ if (!( starts > 0 )) {
+ biffAddf(TEN, "%s: need non-zero starts", me);
+ return 1;
+ }
if (!( nrrdTypeFloat == typeOut || nrrdTypeDouble == typeOut )) {
biffAddf(TEN, "%s: typeOut must be %s or %s, not %s", me,
airEnumStr(nrrdType, nrrdTypeFloat),
@@ -327,15 +335,16 @@
return 1;
}
dwiNum = ndwi->axis[0].size;
- if (!( espec->imgNum != dwiNum )) {
+ if (espec->imgNum != dwiNum) {
biffAddf(TEN, "%s: espec expects %u images but dwi has %u on axis 0",
me, espec->imgNum, AIR_CAST(unsigned int, dwiNum));
return 1;
}
/* allocate output (and set axmap) */
+ mop = airMopNew();
saveParmNum = saveB0 ? model->parmNum : model->parmNum-1;
- for (ii=0; ii<nparm->dim; ii++) {
+ for (ii=0; ii<ndwi->dim; ii++) {
szOut[ii] = (!ii
? saveParmNum
: ndwi->axis[ii].size);
@@ -357,19 +366,46 @@
airMopAdd(mop, dwibuff, airFree, airMopAlways);
/* set output */
+ airRandMTStateGlobalInit();
+ rng = _rng ? _rng : airRandMTStateGlobal;
numSamp = nrrdElementNumber(ndwi)/ndwi->axis[0].size;
+ lup = nrrdDLookup[ndwi->type];
ins = nrrdDInsert[typeOut];
- lup = nrrdDLookup[ndwi->type];
parm = AIR_CAST(char *, nparm->data);
dwi = AIR_CAST(char *, ndwi->data);
for (II=0; II<numSamp; II++) {
+ char pstr[AIR_STRLEN_MED];
+ unsigned int ss;
for (ii=0; ii<dwiNum; ii++) {
ddwi[ii] = lup(dwi, ii);
}
- /* fit to dparm */
+ sqeBest = DBL_MAX;
+ for (ss=0; ss<starts; ss++) {
+ fprintf(stderr, "!%s: II %u ss %u -------\n",
+ me, AIR_CAST(unsigned int, II), ss);
+ if (knownB0) {
+ dparm[0] = tenExperSpecKnownB0Get(espec, ddwi);
+ fprintf(stderr, "!%s: b0 = %g\n", me, dparm[0]);
+ }
+ model->rand(dparm, rng, knownB0);
+ fprintf(stderr, "!%s: rand -> %s\n", me,
+ model->sprint(pstr, dparm));
+ sqe = model->sqeFit(dparm, &convFrac, espec, dwibuff, ddwi,
+ dparm, knownB0, minIter, maxIter, convEps);
+ if (sqe < sqeBest) {
+ fprintf(stderr, "!%s: %g < %g --> %s\n", me,
+ sqe, sqeBest, model->sprint(pstr, dparm));
+ sqeBest = sqe;
+ model->copy(dparmBest, dparm);
+ }
+ }
for (ii=0; ii<saveParmNum; ii++) {
- ins(parm, ii, dparm[ii]);
+ ins(parm, ii, saveB0 ? dparmBest[ii] : dparmBest[ii+1]);
+ fprintf(stderr, "!%s: saving parm[%u] = %g\n", me,
+ saveB0 ? ii : ii+1,
+ saveB0 ? dparmBest[ii] : dparmBest[ii+1]);
}
+ /* possibly save sqeBest */
parm += saveParmNum*nrrdTypeSize[typeOut];
dwi += espec->imgNum*nrrdTypeSize[ndwi->type];
}
@@ -388,6 +424,16 @@
biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
airMopError(mop); return 1;
}
+ lablen = (strlen(tenModelPrefixStr)
+ + strlen(":")
+ + (saveB0 ? strlen("B0+") : 0)
+ + strlen(model->name)
+ + 1);
+ nparm->axis[0].label = AIR_CAST(char *, calloc(lablen, sizeof(char)));
+ sprintf(nparm->axis[0].label, "%s:%s%s",
+ tenModelPrefixStr,
+ saveB0 ? "B0+" : "",
+ model->name);
airMopOkay(mop);
return 0;
Modified: teem/trunk/src/ten/tendMfit.c
===================================================================
--- teem/trunk/src/ten/tendMfit.c 2009-10-27 20:22:33 UTC (rev 4322)
+++ teem/trunk/src/ten/tendMfit.c 2009-10-27 20:23:29 UTC (rev 4323)
@@ -36,25 +36,39 @@
airArray *mop;
Nrrd *nin, *nout;
- char *outS;
- int EE, knownB0, verbose, mlfit;
- unsigned int maxIter;
- double valueMin, thresh, sigma;
+ char *outS, *modS;
+ int knownB0, saveB0, verbose, mlfit, typeOut;
+ unsigned int maxIter, minIter, starts;
+ double sigma, eps;
const tenModel *model;
+ tenExperSpec *espec;
hestOptAdd(&hopt, "v", "verbose", airTypeInt, 1, 1, &verbose, "0",
"verbosity level");
+ hestOptAdd(&hopt, "m", "model", airTypeString, 1, 1, &modS, NULL,
+ "which model to fit. Use optional \"b0+\" prefix to "
+ "indicate that the B0 image should also be saved.");
+ hestOptAdd(&hopt, "ns", "# starts", airTypeUInt, 1, 1, &starts, "1",
+ "number of random starting points at which to initialize "
+ "fitting");
hestOptAdd(&hopt, "ml", NULL, airTypeInt, 0, 0, &mlfit, NULL,
"do ML fitting, rather than least-squares, which also "
"requires setting \"-sigma\"");
hestOptAdd(&hopt, "sigma", "sigma", airTypeDouble, 1, 1, &sigma, "nan",
"Rician noise parameter");
- hestOptAdd(&hopt, "maxi", "max iters", airTypeUInt, 1, 1, &maxIter, "10",
- "maximum allowable iterations for fitting.");
+ hestOptAdd(&hopt, "eps", "eps", airTypeDouble, 1, 1, &eps, "0.01",
+ "convergence epsilon");
+ hestOptAdd(&hopt, "mini", "min iters", airTypeUInt, 1, 1, &minIter, "3",
+ "minimum required # iterations for fitting.");
+ hestOptAdd(&hopt, "maxi", "max iters", airTypeUInt, 1, 1, &maxIter, "100",
+ "maximum allowable # iterations for fitting.");
hestOptAdd(&hopt, "knownB0", "bool", airTypeBool, 1, 1, &knownB0, NULL,
"Indicates if the B=0 non-diffusion-weighted reference image "
"is known (\"true\"), or if it has to be estimated along with "
"the other model parameters (\"false\")");
+ hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &typeOut, "float",
+ "output type of DWIs",
+ NULL, nrrdType);
hestOptAdd(&hopt, "i", "dwi", airTypeOther, 1, 1, &nin, "-",
"all the diffusion-weighted images in one 4D nrrd",
NULL, NULL, nrrdHestNrrd);
@@ -67,27 +81,28 @@
JUSTPARSE();
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
+ espec = tenExperSpecNew();
+ airMopAdd(mop, espec, (airMopper)tenExperSpecNix, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
-
- /*
- if (tenModelSqeFit(nout, NULL,
- const tenModel *model,
- const tenExperSpec *espec, const Nrrd *ndwi,
- int knownB0, int saveB0, int typeOut,
- unsigned int maxIter, double convEps);
-
- if (tenEstimate1TensorVolume4D(tec, nout, &nB0,
- airStrlen(terrS)
- ? &nterr
- : NULL,
- nin4d, nrrdTypeFloat)) {
+ if (tenModelParse(&model, &saveB0, AIR_FALSE, modS)) {
airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
- fprintf(stderr, "%s: trouble doing estimation:\n%s\n", me, err);
+ fprintf(stderr, "%s: trouble parsing model \"%s\":\n%s\n", me, modS, err);
airMopError(mop); return 1;
}
+ if (tenExperSpecFromKeyValueSet(espec, nin)) {
+ airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble getting exper from kvp:\n%s\n", me, err);
+ airMopError(mop); return 1;
+ }
+ if (tenModelSqeFit(nout, NULL, model, espec, nin,
+ knownB0, saveB0, typeOut,
+ minIter, maxIter, starts, eps, NULL)) {
+ airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble fitting:\n%s\n", me, err);
+ airMopError(mop); return 1;
+ }
- */
if (nrrdSave(outS, nout, NULL)) {
airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-28 02:41:11
|
Revision: 4327
http://teem.svn.sourceforge.net/teem/?rev=4327&view=rev
Author: kindlmann
Date: 2009-10-28 02:41:05 +0000 (Wed, 28 Oct 2009)
Log Message:
-----------
tenModel still under construction
Modified Paths:
--------------
teem/trunk/src/ten/experSpec.c
teem/trunk/src/ten/model1Stick.c
teem/trunk/src/ten/modelBall.c
teem/trunk/src/ten/modelBall1Stick.c
teem/trunk/src/ten/modelCylinder.c
teem/trunk/src/ten/modelTensor2.c
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenMacros.h
teem/trunk/src/ten/tenModel.c
Modified: teem/trunk/src/ten/experSpec.c
===================================================================
--- teem/trunk/src/ten/experSpec.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/experSpec.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -242,6 +242,10 @@
}
dd = dwiMeas[ii] - dwiSim[ii];
sqe += dd*dd;
+ /*
+ fprintf(stderr, "!%s: dwi[%u]: %g - %g -> %g\n", "_tenExperSpec_sqe",
+ ii, dwiMeas[ii], dwiSim[ii], sqe);
+ */
}
} else {
for (ii=0; ii<espec->imgNum; ii++) {
Modified: teem/trunk/src/ten/model1Stick.c
===================================================================
--- teem/trunk/src/ten/model1Stick.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/model1Stick.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -24,16 +24,14 @@
#include "privateTen.h"
#define PARM_NUM 5
-#define PARM_DESC \
- { \
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- {"x", -1.0, 1.0, AIR_TRUE, 0}, \
- {"y", -1.0, 1.0, AIR_TRUE, 1}, \
- {"z", -1.0, 1.0, AIR_TRUE, 2}, \
- }
static const tenModelParmDesc
-const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
+const parmDesc[] = {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ {"z", -1.0, 1.0, AIR_TRUE, 2}
+};
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
Modified: teem/trunk/src/ten/modelBall.c
===================================================================
--- teem/trunk/src/ten/modelBall.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/modelBall.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -24,13 +24,11 @@
#include "privateTen.h"
#define PARM_NUM 2
-#define PARM_DESC \
- { \
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0} \
- }
static const tenModelParmDesc
-const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
+const parmDesc[] = {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
+};
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
Modified: teem/trunk/src/ten/modelBall1Stick.c
===================================================================
--- teem/trunk/src/ten/modelBall1Stick.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/modelBall1Stick.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -24,17 +24,15 @@
#include "privateTen.h"
#define PARM_NUM 6
-#define PARM_DESC \
- { \
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- {"fraction", 0.0, 1.0, AIR_FALSE, 0}, \
- {"x", -1.0, 1.0, AIR_TRUE, 0}, \
- {"y", -1.0, 1.0, AIR_TRUE, 1}, \
- {"z", -1.0, 1.0, AIR_TRUE, 2} \
- }
static const tenModelParmDesc
-const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
+const parmDesc[] = {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"fraction", 0.0, 1.0, AIR_FALSE, 0},
+ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ {"z", -1.0, 1.0, AIR_TRUE, 2}
+};
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
Modified: teem/trunk/src/ten/modelCylinder.c
===================================================================
--- teem/trunk/src/ten/modelCylinder.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/modelCylinder.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -24,17 +24,15 @@
#include "privateTen.h"
#define PARM_NUM 6
-#define PARM_DESC \
- { \
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
- {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- {"x", -1.0, 1.0, AIR_TRUE, 0}, \
- {"y", -1.0, 1.0, AIR_TRUE, 1}, \
- {"z", -1.0, 1.0, AIR_TRUE, 2}, \
- }
static const tenModelParmDesc
-const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
+const parmDesc[] = {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ {"z", -1.0, 1.0, AIR_TRUE, 2}
+};
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
Modified: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -26,36 +26,28 @@
#define PARM_NUM 7
/* 1/sqrt(2) */
#define OST 0.70710678118654752440
-#define PARM_DESC \
- { \
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0}, \
- {"Dxx", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- {"Dxy", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0}, \
- {"Dxz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0}, \
- {"Dyy", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- {"Dyz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0}, \
- {"Dzz", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}, \
- }
static const tenModelParmDesc
-const pdesc[TEN_MODEL_PARM_MAXNUM] = PARM_DESC;
+const parmDesc[] = {
+ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ {"Dxx", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"Dxy", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
+ {"Dxz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
+ {"Dyy", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ {"Dyz", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
+ {"Dzz", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
+};
static void
simulate(double *dwiSim, const double *parm, const tenExperSpec *espec) {
unsigned int ii;
- double b0, ten[7];
+ double b0;
b0 = parm[0];
- ten[0] = 1;
- ten[1] = parm[1];
- ten[2] = parm[2];
- ten[3] = parm[3];
- ten[4] = parm[4];
- ten[5] = parm[5];
- ten[6] = parm[6];
for (ii=0; ii<espec->imgNum; ii++) {
double adc, bb;
bb = espec->bval[ii];
- adc = TEN_T3V_CONTR(ten, espec->grad + 3*ii);
+ /* safe because TEN_T3V_CONTR never looks at parm[0] */
+ adc = TEN_T3V_CONTR(parm, espec->grad + 3*ii);
dwiSim[ii] = b0*exp(-bb*adc);
}
return;
@@ -75,30 +67,40 @@
_TEN_PARM_DIST
_TEN_PARM_COPY
-_TEN_SQE
+static double
+sqe(const double *parm, const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas, int knownB0) {
+ simulate(dwiBuff, parm, espec);
+ return _tenExperSpec_sqe(dwiBuff, dwiMeas, espec, knownB0);
+}
+
static void
sqeGrad(double *grad, const double *parm0,
const tenExperSpec *espec,
double *dwiBuff, const double *dwiMeas,
int knownB0) {
- double parm1[PARM_NUM], sqe0, sqe1, dp;
+ double parm1[PARM_NUM], sqeForw, sqeBack, dp;
unsigned int ii, i0;
i0 = knownB0 ? 1 : 0;
- for (ii=i0; ii<PARM_NUM; ii++) {
+ for (ii=0; ii<PARM_NUM; ii++) {
+ /* have to copy all parms, even B0 with knownB0, and even if we
+ aren't going to diddle these values, because the
+ simulation depends on knowing the values */
parm1[ii] = parm0[ii];
}
- sqe0 = sqe(parm0, espec, dwiBuff, dwiMeas, knownB0);
for (ii=i0; ii<PARM_NUM; ii++) {
- dp = (pdesc[ii].max - pdesc[ii].min)*_TEN_PARM_GRAD_EPS;
- parm1[ii] += dp;
- sqe1 = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0);
- grad[ii] = (sqe1 - sqe0)/dp;
+ dp = (parmDesc[ii].max - parmDesc[ii].min)*TEN_MODEL_PARM_GRAD_EPS;
+ parm1[ii] = parm0[ii] + dp;
+ sqeForw = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0);
+ parm1[ii] = parm0[ii] - dp;
+ sqeBack = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0);
+ grad[ii] = (sqeForw - sqeBack)/(2*dp);
parm1[ii] = parm0[ii];
}
if (knownB0) {
- grad[ii] = 0;
+ grad[0] = 0;
}
return;
}
@@ -108,40 +110,31 @@
double *dwiBuff, const double *dwiMeas,
const double *parmInit, int knownB0,
unsigned int minIter, unsigned int maxIter, double convEps) {
- static const char me[]= TEN_MODEL_STR_TENSOR2 ":sqeFit";
- unsigned int i0, iter;
- double step, bak, opp, val, tval,
- dist, tparm[PARM_NUM], grad[PARM_NUM];
- char str[AIR_STRLEN_MED];
+ /* static const char me[]= TEN_MODEL_STR_TENSOR2 ":sqeFit"; */
+ unsigned int iter;
+ double step, bak, opp, val, testval,
+ dist, testparm[PARM_NUM], grad[PARM_NUM];
int done;
- i0 = knownB0 ? 1 : 0;
+ step = 1;
parmCopy(parm, parmInit);
val = sqe(parm, espec, dwiBuff, dwiMeas, knownB0);
sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
- step = 10;
- fprintf(stderr, "!%s: -------- at %s\n", me, parmSprint(str, parm));
- fprintf(stderr, "!%s: initial step = %g, convEps = %g\n",
- me, step, convEps);
- opp = 1.1;
+ opp = 2;
bak = 0.1;
iter = 0;
do {
do {
- parmStep(tparm, -step, grad, parm);
- tval = sqe(tparm, espec, dwiBuff, dwiMeas, knownB0);
- if (tval > val) {
+ parmStep(testparm, -step, grad, parm);
+ testval = sqe(testparm, espec, dwiBuff, dwiMeas, knownB0);
+ if (testval > val) {
step *= bak;
- fprintf(stderr, "!%s(%u): tval %g > val %g ==> step -> %g\n",
- me, iter, tval, val, step);
}
- } while (tval > val);
- dist = parmDist(tparm, parm);
- fprintf(stderr, "!%s(%u): step %g (dist %g) -> %g @ %s\n", me, iter,
- step, dist, tval, parmSprint(str, tparm));
- val = tval;
- parmCopy(parm, tparm);
+ } while (testval > val);
+ dist = parmDist(testparm, parm);
+ val = testval;
+ parmCopy(parm, testparm);
sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
step *= opp;
iter++;
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/privateTen.h 2009-10-28 02:41:05 UTC (rev 4327)
@@ -159,9 +159,6 @@
int knownB0);
/* model*.c */
-
-#define _TEN_PARM_GRAD_EPS 0.0001
-
/*
** NOTE: these functions rely on per-model information (like PARM_NUM)
** or functions (like "simulate"), which is why these functions can't
@@ -175,7 +172,7 @@
unsigned int ii; \
\
for (ii=knownB0 ? 1 : 0; ii<PARM_NUM; ii++) { \
- if (pdesc[ii].vec3) { \
+ if (parmDesc[ii].vec3) { \
/* its unit vector */ \
double xx, yy, zz, theta, rr; \
\
@@ -191,7 +188,7 @@
ii += 2; \
} else { \
parm[ii] = AIR_AFFINE(0.0, airDrandMT_r(rng), 1.0, \
- pdesc[ii].min, pdesc[ii].max); \
+ parmDesc[ii].min, parmDesc[ii].max); \
} \
} \
return; \
@@ -205,8 +202,8 @@
\
for (ii=0; ii<PARM_NUM; ii++) { \
parm1[ii] = scl*grad[ii] + parm0[ii]; \
- parm1[ii] = AIR_CLAMP(pdesc[ii].min, parm1[ii], pdesc[ii].max); \
- if (pdesc[ii].vec3 && 2 == pdesc[ii].vecIdx) { \
+ parm1[ii] = AIR_CLAMP(parmDesc[ii].min, parm1[ii], parmDesc[ii].max); \
+ if (parmDesc[ii].vec3 && 2 == parmDesc[ii].vecIdx) { \
double len; \
ELL_3V_NORM(parm1 + ii - 2, parm1 + ii - 2, len); \
} \
@@ -221,7 +218,7 @@
\
dist = 0; \
for (ii=0; ii<PARM_NUM; ii++) { \
- dd = (parmA[ii] - parmB[ii])/(pdesc[ii].max - pdesc[ii].min); \
+ dd = (parmA[ii] - parmB[ii])/(parmDesc[ii].max - parmDesc[ii].min); \
dist += dd*dd; \
} \
return sqrt(dist); \
@@ -332,7 +329,7 @@
}
#define _TEN_MODEL_FIELDS \
- PARM_NUM, PARM_DESC, \
+ PARM_NUM, parmDesc, \
simulate, \
parmSprint, parmRand, parmStep, parmDist, parmCopy, \
sqe, sqeGrad, sqeFit, \
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/ten.h 2009-10-28 02:41:05 UTC (rev 4327)
@@ -1094,9 +1094,9 @@
unsigned int vecIdx; /* if 3-vector, index into it */
} tenModelParmDesc;
-#define TEN_MODEL_PARM_MAXNUM 15 /* adjust as needed */
-#define TEN_MODEL_B0_MAX 10000 /* HEY: completely arbitrary! */
-#define TEN_MODEL_DIFF_MAX 0.004 /* in units of mm^2/sec */
+#define TEN_MODEL_B0_MAX 10000 /* HEY: completely arbitrary! */
+#define TEN_MODEL_DIFF_MAX 0.004 /* in units of mm^2/sec */
+#define TEN_MODEL_PARM_GRAD_EPS 0.00002 /* for gradient calculations */
/*
******** struct tenModel
@@ -1118,7 +1118,7 @@
typedef struct {
char name[AIR_STRLEN_SMALL];
unsigned int parmNum;
- tenModelParmDesc parmDesc[TEN_MODEL_PARM_MAXNUM];
+ const tenModelParmDesc *parmDesc;
/* noise free simulation */
void (*simulate)(double *dwiSim, const double *parm,
const tenExperSpec *espec);
Modified: teem/trunk/src/ten/tenMacros.h
===================================================================
--- teem/trunk/src/ten/tenMacros.h 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/tenMacros.h 2009-10-28 02:41:05 UTC (rev 4327)
@@ -241,6 +241,7 @@
(t)[4] = (a)[1]*(a)[1], (t)[5] = (a)[1]*(a)[2], \
(t)[6] = (a)[2]*(a)[2])
+/* NOTE: never looks at (t)[0] */
#define TEN_T3V_CONTR(t, v) ( \
(v)[0]*(t)[1]*(v)[0] + (v)[0]*(t)[2]*(v)[1] + (v)[0]*(t)[3]*(v)[2] \
+ (v)[1]*(t)[2]*(v)[0] + (v)[1]*(t)[4]*(v)[1] + (v)[1]*(t)[5]*(v)[2] \
Modified: teem/trunk/src/ten/tenModel.c
===================================================================
--- teem/trunk/src/ten/tenModel.c 2009-10-27 20:26:24 UTC (rev 4326)
+++ teem/trunk/src/ten/tenModel.c 2009-10-28 02:41:05 UTC (rev 4327)
@@ -307,8 +307,7 @@
unsigned int starts, double convEps, airRandMTState *_rng) {
static const char me[]="tenModelSqeFit";
double *ddwi, *dwibuff, sqe, sqeBest, convFrac,
- dparm[TEN_MODEL_PARM_MAXNUM],
- dparmBest[TEN_MODEL_PARM_MAXNUM],
+ *dparm, *dparmBest,
(*ins)(void *v, size_t I, double d),
(*lup)(const void *v, size_t I);
airArray *mop;
@@ -342,7 +341,15 @@
}
/* allocate output (and set axmap) */
+ dparm = AIR_CAST(double *, calloc(model->parmNum, sizeof(double)));
+ dparmBest = AIR_CAST(double *, calloc(model->parmNum, sizeof(double)));
+ if (!( dparm && dparmBest )) {
+ biffAddf(TEN, "%s: couldn't allocate parm vecs", me);
+ return 1;
+ }
mop = airMopNew();
+ airMopAdd(mop, dparm, airFree, airMopAlways);
+ airMopAdd(mop, dparmBest, airFree, airMopAlways);
saveParmNum = saveB0 ? model->parmNum : model->parmNum-1;
for (ii=0; ii<ndwi->dim; ii++) {
szOut[ii] = (!ii
@@ -381,29 +388,19 @@
}
sqeBest = DBL_MAX;
for (ss=0; ss<starts; ss++) {
- fprintf(stderr, "!%s: II %u ss %u -------\n",
- me, AIR_CAST(unsigned int, II), ss);
if (knownB0) {
dparm[0] = tenExperSpecKnownB0Get(espec, ddwi);
- fprintf(stderr, "!%s: b0 = %g\n", me, dparm[0]);
}
model->rand(dparm, rng, knownB0);
- fprintf(stderr, "!%s: rand -> %s\n", me,
- model->sprint(pstr, dparm));
sqe = model->sqeFit(dparm, &convFrac, espec, dwibuff, ddwi,
dparm, knownB0, minIter, maxIter, convEps);
if (sqe < sqeBest) {
- fprintf(stderr, "!%s: %g < %g --> %s\n", me,
- sqe, sqeBest, model->sprint(pstr, dparm));
sqeBest = sqe;
model->copy(dparmBest, dparm);
}
}
for (ii=0; ii<saveParmNum; ii++) {
ins(parm, ii, saveB0 ? dparmBest[ii] : dparmBest[ii+1]);
- fprintf(stderr, "!%s: saving parm[%u] = %g\n", me,
- saveB0 ? ii : ii+1,
- saveB0 ? dparmBest[ii] : dparmBest[ii+1]);
}
/* possibly save sqeBest */
parm += saveParmNum*nrrdTypeSize[typeOut];
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-28 13:36:08
|
Revision: 4328
http://teem.svn.sourceforge.net/teem/?rev=4328&view=rev
Author: kindlmann
Date: 2009-10-28 13:35:58 +0000 (Wed, 28 Oct 2009)
Log Message:
-----------
still hacking tenModel
Modified Paths:
--------------
teem/trunk/src/ten/GNUmakefile
teem/trunk/src/ten/model1Stick.c
teem/trunk/src/ten/modelBall.c
teem/trunk/src/ten/modelBall1Stick.c
teem/trunk/src/ten/modelCylinder.c
teem/trunk/src/ten/modelTensor2.c
teem/trunk/src/ten/privateTen.h
teem/trunk/src/ten/sources.cmake
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenModel.c
Added Paths:
-----------
teem/trunk/src/ten/tendMconv.c
Modified: teem/trunk/src/ten/GNUmakefile
===================================================================
--- teem/trunk/src/ten/GNUmakefile 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/GNUmakefile 2009-10-28 13:35:58 UTC (rev 4328)
@@ -59,7 +59,7 @@
tendTriple.o tendTconv.o tendAvg.o \
tendAnhist.o tendMake.o tendSatin.o tendShrink.o tendGlyph.o \
tendFiber.o tendEpireg.o tendBmat.o tendEstim.o tendSim.o \
- tendMsim.o tendMfit.o \
+ tendMsim.o tendMfit.o tendMconv.o \
tendSlice.o tendEllipse.o tendEvecrgb.o tendNorm.o tendAnscale.o \
tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o tendBfit.o \
tendUnmf.o tendLog.o tendExp.o
Modified: teem/trunk/src/ten/model1Stick.c
===================================================================
--- teem/trunk/src/ten/model1Stick.c 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/model1Stick.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -26,11 +26,11 @@
#define PARM_NUM 5
static const tenModelParmDesc
const parmDesc[] = {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"x", -1.0, 1.0, AIR_TRUE, 0},
- {"y", -1.0, 1.0, AIR_TRUE, 1},
- {"z", -1.0, 1.0, AIR_TRUE, 2}
+ /* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ /* 1 */ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ /* 2 */ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ /* 3 */ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ /* 4 */ {"z", -1.0, 1.0, AIR_TRUE, 2}
};
static void
@@ -58,14 +58,40 @@
return str;
}
+_TEN_PARM_ALLOC
_TEN_PARM_RAND
_TEN_PARM_STEP
_TEN_PARM_DIST
_TEN_PARM_COPY
+static int
+parmConvert(double *parmDst, const double *parmSrc,
+ const tenModel *modelSrc) {
+ int lossy;
+
+ parmDst[0] = parmSrc[0];
+ if (modelSrc == tenModelBall) {
+
+ } else if (modelSrc == tenModel1Stick) {
+
+ } else if (modelSrc == tenModelBall1Stick) {
+
+ } else if (modelSrc == tenModelCylinder) {
+
+ } else if (modelSrc == tenModelTensor2) {
+
+ } else {
+ unsigned int ii;
+ for (ii=0; ii<PARM_NUM; ii++) {
+ parmDst[ii] = AIR_NAN;
+ }
+ }
+ return lossy;
+}
+
_TEN_SQE
-_TEN_SQE_GRAD_STUB
-_TEN_SQE_FIT_STUB
+_TEN_SQE_GRAD_CENTDIFF
+_TEN_SQE_FIT(tenModel1Stick)
_TEN_NLL
_TEN_NLL_GRAD_STUB
Modified: teem/trunk/src/ten/modelBall.c
===================================================================
--- teem/trunk/src/ten/modelBall.c 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/modelBall.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -26,8 +26,8 @@
#define PARM_NUM 2
static const tenModelParmDesc
const parmDesc[] = {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
+ /* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ /* 1 */ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
};
static void
@@ -49,14 +49,41 @@
return str;
}
+_TEN_PARM_ALLOC
_TEN_PARM_RAND
_TEN_PARM_STEP
_TEN_PARM_DIST
_TEN_PARM_COPY
+static int
+parmConvert(double *parmDst, const double *parmSrc,
+ const tenModel *modelSrc) {
+ int ret;
+
+ parmDst[0] = parmSrc[0];
+ if (modelSrc == tenModelBall) {
+
+ } else if (modelSrc == tenModel1Stick) {
+
+ } else if (modelSrc == tenModelBall1Stick) {
+
+ } else if (modelSrc == tenModelCylinder) {
+
+ } else if (modelSrc == tenModelTensor2) {
+
+ } else {
+ unsigned int ii;
+ for (ii=0; ii<PARM_NUM; ii++) {
+ parmDst[ii] = AIR_NAN;
+ }
+ ret = 2;
+ }
+ return ret;
+}
+
_TEN_SQE
-_TEN_SQE_GRAD_STUB
-_TEN_SQE_FIT_STUB
+_TEN_SQE_GRAD_CENTDIFF
+_TEN_SQE_FIT(tenModelBall)
_TEN_NLL
Modified: teem/trunk/src/ten/modelBall1Stick.c
===================================================================
--- teem/trunk/src/ten/modelBall1Stick.c 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/modelBall1Stick.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -26,12 +26,12 @@
#define PARM_NUM 6
static const tenModelParmDesc
const parmDesc[] = {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"fraction", 0.0, 1.0, AIR_FALSE, 0},
- {"x", -1.0, 1.0, AIR_TRUE, 0},
- {"y", -1.0, 1.0, AIR_TRUE, 1},
- {"z", -1.0, 1.0, AIR_TRUE, 2}
+ /* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ /* 1 */ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ /* 2 */ {"fraction", 0.0, 1.0, AIR_FALSE, 0},
+ /* 3 */ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ /* 4 */ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ /* 5 */ {"z", -1.0, 1.0, AIR_TRUE, 2}
};
static void
@@ -62,14 +62,40 @@
return str;
}
+_TEN_PARM_ALLOC
_TEN_PARM_RAND
_TEN_PARM_STEP
_TEN_PARM_DIST
_TEN_PARM_COPY
+static int
+parmConvert(double *parmDst, const double *parmSrc,
+ const tenModel *modelSrc) {
+ int lossy;
+
+ parmDst[0] = parmSrc[0];
+ if (modelSrc == tenModelBall) {
+
+ } else if (modelSrc == tenModel1Stick) {
+
+ } else if (modelSrc == tenModelBall1Stick) {
+
+ } else if (modelSrc == tenModelCylinder) {
+
+ } else if (modelSrc == tenModelTensor2) {
+
+ } else {
+ unsigned int ii;
+ for (ii=0; ii<PARM_NUM; ii++) {
+ parmDst[ii] = AIR_NAN;
+ }
+ }
+ return lossy;
+}
+
_TEN_SQE
-_TEN_SQE_GRAD_STUB
-_TEN_SQE_FIT_STUB
+_TEN_SQE_GRAD_CENTDIFF
+_TEN_SQE_FIT(tenModelBall1Stick)
_TEN_NLL
_TEN_NLL_GRAD_STUB
Modified: teem/trunk/src/ten/modelCylinder.c
===================================================================
--- teem/trunk/src/ten/modelCylinder.c 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/modelCylinder.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -26,12 +26,12 @@
#define PARM_NUM 6
static const tenModelParmDesc
const parmDesc[] = {
- {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
- {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
- {"x", -1.0, 1.0, AIR_TRUE, 0},
- {"y", -1.0, 1.0, AIR_TRUE, 1},
- {"z", -1.0, 1.0, AIR_TRUE, 2}
+ /* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
+ /* 1 */ {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ /* 2 */ {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
+ /* 3 */ {"x", -1.0, 1.0, AIR_TRUE, 0},
+ /* 4 */ {"y", -1.0, 1.0, AIR_TRUE, 1},
+ /* 5 */ {"z", -1.0, 1.0, AIR_TRUE, 2}
};
static void
@@ -57,6 +57,7 @@
return;
}
+_TEN_PARM_ALLOC
_TEN_PARM_RAND
_TEN_PARM_STEP
_TEN_PARM_DIST
@@ -69,9 +70,34 @@
return str;
}
+static int
+parmConvert(double *parmDst, const double *parmSrc,
+ const tenModel *modelSrc) {
+ int lossy;
+
+ parmDst[0] = parmSrc[0];
+ if (modelSrc == tenModelBall) {
+
+ } else if (modelSrc == tenModel1Stick) {
+
+ } else if (modelSrc == tenModelBall1Stick) {
+
+ } else if (modelSrc == tenModelCylinder) {
+
+ } else if (modelSrc == tenModelTensor2) {
+
+ } else {
+ unsigned int ii;
+ for (ii=0; ii<PARM_NUM; ii++) {
+ parmDst[ii] = AIR_NAN;
+ }
+ }
+ return lossy;
+}
+
_TEN_SQE
-_TEN_SQE_GRAD_STUB
-_TEN_SQE_FIT_STUB
+_TEN_SQE_GRAD_CENTDIFF
+_TEN_SQE_FIT(tenModelCylinder)
_TEN_NLL
_TEN_NLL_GRAD_STUB
Modified: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -62,90 +62,66 @@
return str;
}
+_TEN_PARM_ALLOC
_TEN_PARM_RAND
_TEN_PARM_STEP
_TEN_PARM_DIST
_TEN_PARM_COPY
-static double
-sqe(const double *parm, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas, int knownB0) {
+static int
+parmConvert(double *parmDst, const double *parmSrc,
+ const tenModel *modelSrc) {
+ int ret;
- simulate(dwiBuff, parm, espec);
- return _tenExperSpec_sqe(dwiBuff, dwiMeas, espec, knownB0);
-}
-
-static void
-sqeGrad(double *grad, const double *parm0,
- const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- int knownB0) {
- double parm1[PARM_NUM], sqeForw, sqeBack, dp;
- unsigned int ii, i0;
-
- i0 = knownB0 ? 1 : 0;
- for (ii=0; ii<PARM_NUM; ii++) {
- /* have to copy all parms, even B0 with knownB0, and even if we
- aren't going to diddle these values, because the
- simulation depends on knowing the values */
- parm1[ii] = parm0[ii];
+ if (modelSrc == tenModelBall) {
+ TEN_T_SET(parmDst, parmSrc[0],
+ parmSrc[1], 0, 0,
+ parmSrc[1], 0,
+ parmSrc[1]);
+ ret = 0;
+ } else if (modelSrc == tenModel1Stick) {
+ double ten[7];
+ TEN_T3V_OUTER(ten, parmSrc + 2);
+ TEN_T_SCALE(parmDst, parmSrc[1], ten);
+ parmDst[0] = parmSrc[0];
+ ret = 0;
+ } else if (modelSrc == tenModelBall1Stick) {
+ double stick[7], ball[7], diff, frac;
+ diff = parmSrc[1];
+ frac = parmSrc[2];
+ TEN_T3V_OUTER(stick, parmSrc + 3);
+ TEN_T_SCALE(stick, diff, stick);
+ TEN_T_SET(ball, 1, diff, 0, 0, diff, 0, diff);
+ TEN_T_LERP(parmDst, frac, ball, stick);
+ parmDst[0] = parmSrc[0];
+ ret = 1;
+ } else if (modelSrc == tenModelCylinder) {
+ double stick[7], ball[7], len, rad;
+ len = parmSrc[1];
+ rad = parmSrc[2];
+ TEN_T3V_OUTER(stick, parmSrc + 3);
+ TEN_T_SCALE(stick, len, stick);
+ TEN_T_SET(ball, 1, rad, 0, 0, rad, 0, rad);
+ TEN_T_ADD(parmDst, ball, stick);
+ parmDst[0] = parmSrc[0];
+ ret = 0;
+ } else if (modelSrc == tenModelTensor2) {
+ parmCopy(parmDst, parmSrc);
+ ret = 0;
+ } else {
+ unsigned int ii;
+ for (ii=0; ii<PARM_NUM; ii++) {
+ parmDst[ii] = AIR_NAN;
+ }
+ ret = 2;
}
- for (ii=i0; ii<PARM_NUM; ii++) {
- dp = (parmDesc[ii].max - parmDesc[ii].min)*TEN_MODEL_PARM_GRAD_EPS;
- parm1[ii] = parm0[ii] + dp;
- sqeForw = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0);
- parm1[ii] = parm0[ii] - dp;
- sqeBack = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0);
- grad[ii] = (sqeForw - sqeBack)/(2*dp);
- parm1[ii] = parm0[ii];
- }
- if (knownB0) {
- grad[0] = 0;
- }
- return;
+ return ret;
}
-static double
-sqeFit(double *parm, double *convFrac, const tenExperSpec *espec,
- double *dwiBuff, const double *dwiMeas,
- const double *parmInit, int knownB0,
- unsigned int minIter, unsigned int maxIter, double convEps) {
- /* static const char me[]= TEN_MODEL_STR_TENSOR2 ":sqeFit"; */
- unsigned int iter;
- double step, bak, opp, val, testval,
- dist, testparm[PARM_NUM], grad[PARM_NUM];
- int done;
+_TEN_SQE
+_TEN_SQE_GRAD_CENTDIFF
+_TEN_SQE_FIT(tenModelTensor2)
- step = 1;
- parmCopy(parm, parmInit);
- val = sqe(parm, espec, dwiBuff, dwiMeas, knownB0);
- sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
-
- opp = 2;
- bak = 0.1;
- iter = 0;
- do {
- do {
- parmStep(testparm, -step, grad, parm);
- testval = sqe(testparm, espec, dwiBuff, dwiMeas, knownB0);
- if (testval > val) {
- step *= bak;
- }
- } while (testval > val);
- dist = parmDist(testparm, parm);
- val = testval;
- parmCopy(parm, testparm);
- sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
- step *= opp;
- iter++;
- done = (iter < minIter
- ? AIR_FALSE
- : (iter > maxIter) || dist < convEps);
- } while (!done);
- *convFrac = dist/convEps;
- return val;
-}
-
_TEN_NLL
_TEN_NLL_GRAD_STUB
_TEN_NLL_FIT_STUB
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/privateTen.h 2009-10-28 13:35:58 UTC (rev 4328)
@@ -158,14 +158,35 @@
int rician, double sigma,
int knownB0);
+/* tenModel.c */
+TEN_EXPORT double _tenModelSqeFitSingle(const tenModel *model,
+ double *testParm, double *grad,
+ double *parm, double *convFrac,
+ const tenExperSpec *espec,
+ double *dwiBuff,
+ const double *dwiMeas,
+ const double *parmInit,
+ int knownB0,
+ unsigned int minIter,
+ unsigned int maxIter,
+ double convEps);
+
/* model*.c */
/*
** NOTE: these functions rely on per-model information (like PARM_NUM)
-** or functions (like "simulate"), which is why these functions can't
-** all use same common underlying function, since more information would
+** or functions (like "simulate"), which is why these functions don't
+** all use some common underlying function: more information would
** have to be passed (annoying for rapid hacking), and the function
** call overhead might be doubled
*/
+
+#define _TEN_PARM_ALLOC \
+static double * \
+parmAlloc(void) { \
+ \
+ return AIR_CAST(double *, calloc(PARM_NUM, sizeof(double))); \
+}
+
#define _TEN_PARM_RAND \
static void \
parmRand(double *parm, airRandMTState *rng, int knownB0) { \
@@ -244,22 +265,61 @@
return _tenExperSpec_sqe(dwiMeas, dwiBuff, espec, knownB0); \
}
-#define _TEN_SQE_GRAD_STUB \
-static void \
-sqeGrad(double *grad, const double *parm, \
- const tenExperSpec *espec, \
- double *dwiBuff, const double *dwiMeas, \
- int knownB0) { \
- \
- AIR_UNUSED(grad); \
- AIR_UNUSED(parm); \
- AIR_UNUSED(espec); \
- AIR_UNUSED(dwiBuff); \
- AIR_UNUSED(dwiMeas); \
- AIR_UNUSED(knownB0); \
- return; \
+#define _TEN_SQE_GRAD_CENTDIFF \
+static void \
+sqeGrad(double *grad, const double *parm0, \
+ const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ int knownB0) { \
+ double parm1[PARM_NUM], sqeForw, sqeBack, dp; \
+ unsigned int ii, i0; \
+ \
+ i0 = knownB0 ? 1 : 0; \
+ for (ii=0; ii<PARM_NUM; ii++) { \
+ /* have to copy all parms, even B0 with knownB0, and even if we \
+ aren't going to diddle these values, because the \
+ simulation depends on knowing the values */ \
+ parm1[ii] = parm0[ii]; \
+ } \
+ for (ii=i0; ii<PARM_NUM; ii++) { \
+ dp = (parmDesc[ii].max - parmDesc[ii].min)*TEN_MODEL_PARM_GRAD_EPS; \
+ parm1[ii] = parm0[ii] + dp; \
+ sqeForw = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0); \
+ parm1[ii] = parm0[ii] - dp; \
+ sqeBack = sqe(parm1, espec, dwiBuff, dwiMeas, knownB0); \
+ grad[ii] = (sqeForw - sqeBack)/(2*dp); \
+ parm1[ii] = parm0[ii]; \
+ if (parmDesc[ii].vec3 && 2 == parmDesc[ii].vecIdx) { \
+ double dot, *gg; \
+ const double *vv; \
+ gg = grad + ii - 2; \
+ vv = parm0 + ii - 2; \
+ dot = ELL_3V_DOT(gg, vv); \
+ ELL_3V_SCALE_INCR(gg, -dot, vv); \
+ } \
+ } \
+ if (knownB0) { \
+ grad[0] = 0; \
+ } \
+ return; \
}
+#define _TEN_SQE_FIT(model) \
+static double \
+sqeFit(double *parm, double *convFrac, const tenExperSpec *espec, \
+ double *dwiBuff, const double *dwiMeas, \
+ const double *parmInit, int knownB0, \
+ unsigned int minIter, unsigned int maxIter, double convEps) { \
+ double testparm[PARM_NUM], grad[PARM_NUM]; \
+ \
+ return _tenModelSqeFitSingle((model), \
+ testparm, grad, \
+ parm, convFrac, \
+ espec, dwiBuff, dwiMeas, \
+ parmInit, knownB0, \
+ minIter, maxIter, convEps); \
+}
+
#define _TEN_SQE_FIT_STUB \
static double \
sqeFit(double *parm, double *convFrac, const tenExperSpec *espec, \
@@ -328,12 +388,13 @@
return 0; \
}
-#define _TEN_MODEL_FIELDS \
- PARM_NUM, parmDesc, \
- simulate, \
- parmSprint, parmRand, parmStep, parmDist, parmCopy, \
- sqe, sqeGrad, sqeFit, \
- nll, nllGrad, nllFit
+#define _TEN_MODEL_FIELDS \
+ PARM_NUM, parmDesc, \
+ simulate, \
+ parmSprint, parmAlloc, parmRand, \
+ parmStep, parmDist, parmCopy, parmConvert, \
+ sqe, sqeGrad, sqeFit, \
+ nll, nllGrad, nllFit
#ifdef __cplusplus
}
Modified: teem/trunk/src/ten/sources.cmake
===================================================================
--- teem/trunk/src/ten/sources.cmake 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/sources.cmake 2009-10-28 13:35:58 UTC (rev 4328)
@@ -57,6 +57,7 @@
tendSim.c
tendMsim.c
tendMfit.c
+ tendMconv.c
tendSlice.c
tendSten.c
tendTconv.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/ten.h 2009-10-28 13:35:58 UTC (rev 4328)
@@ -1115,7 +1115,7 @@
** and it would be dumb to double the number of models to be able
** to capture this.
*/
-typedef struct {
+typedef struct tenModel_t {
char name[AIR_STRLEN_SMALL];
unsigned int parmNum;
const tenModelParmDesc *parmDesc;
@@ -1124,11 +1124,14 @@
const tenExperSpec *espec);
/* parameter vector operations */
char *(*sprint)(char str[AIR_STRLEN_MED], const double *parm);
+ double *(*alloc)(void);
void (*rand)(double *parm, airRandMTState *rng, int knownB0);
void (*step)(double *parm1, const double scl,
const double *grad, const double *parm0);
double (*dist)(const double *parmA, const double *parmB);
void (*copy)(double *parmA, const double *parmB);
+ int (*convert)(double *parmDst, const double *parmSrc,
+ const struct tenModel_t *modelSrc);
/* "sqe" == squared error in DWI values */
double (*sqe)(const double *parm, const tenExperSpec *espec,
@@ -1564,8 +1567,16 @@
const tenModel *model,
const tenExperSpec *espec, const Nrrd *ndwi,
int rician, double sigma, int knownB0);
-
-/* have to keep in sync with modelTen.c/tenModelParse() */
+TEN_EXPORT int tenModelConvert(Nrrd *nparmDst, int *convRet,
+ const tenModel *modelDst,
+ const Nrrd *nparmSrc,
+ const tenModel *modelSrc);
+
+/*
+** Have to keep this list of model declarations in sync with:
+** * modelTen.c/tenModelParse()
+** * all model*.c/parmConvert()
+*/
/* modelBall.c */
#define TEN_MODEL_STR_BALL "ball"
TEN_EXPORT const tenModel *const tenModelBall;
@@ -1640,6 +1651,7 @@
F(estim) \
F(sim) \
F(mfit) \
+F(mconv) \
F(msim) \
F(make) \
F(avg) \
Modified: teem/trunk/src/ten/tenModel.c
===================================================================
--- teem/trunk/src/ten/tenModel.c 2009-10-28 02:41:05 UTC (rev 4327)
+++ teem/trunk/src/ten/tenModel.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -24,7 +24,7 @@
#include "privateTen.h"
const char *
-tenModelPrefixStr = "DWMRI_model";
+tenModelPrefixStr = "DWMRI_model:";
static const tenModel *
str2model(const char *str) {
@@ -42,31 +42,31 @@
tenModelParse(const tenModel **model, int *plusB0,
int requirePrefix, const char *_str) {
static const char me[]="tenModelParse";
- char *str, *modstr, prefix[AIR_STRLEN_MED], *pre;
+ char *str, *modstr, *pre;
airArray *mop;
if (!( model && plusB0 && _str)) {
biffAddf(TEN, "%s: got NULL pointer", me);
return 1;
}
- str = airToLower(airStrdup(_str));
+ str = airStrdup(_str);
if (!str) {
biffAddf(TEN, "%s: couldn't strdup", me);
return 1;
}
mop = airMopNew();
airMopAdd(mop, str, airFree, airMopAlways);
- sprintf(prefix, "%s:", tenModelPrefixStr);
- pre = strstr(str, prefix);
+ pre = strstr(str, tenModelPrefixStr);
if (pre) {
- str += strlen(prefix);
+ str += strlen(tenModelPrefixStr);
} else {
if (requirePrefix) {
biffAddf(TEN, "%s: didn't see prefix \"%s\" in \"%s\"", me,
- prefix, _str);
+ tenModelPrefixStr, _str);
airMopError(mop); return 1;
}
}
+ airToLower(str);
if ((modstr = strchr(str, '+'))) {
*modstr = '\0';
@@ -100,7 +100,8 @@
return 1;
}
*plusB0 = AIR_FALSE;
- /* first try to learn model from "kind" */
+ /* first try to learn model from axis "kind" */
+ /* HEY should probably also support 3 vector for stick? */
if (nrrdKind3DSymMatrix == axinfo->kind
|| nrrdKind3DMaskedSymMatrix == axinfo->kind) {
*modelP = tenModelTensor2;
@@ -298,6 +299,58 @@
return 0;
}
+/*
+** _tenModelSqeFitSingle
+**
+** callable function (as opposed to tenModel method) for doing
+** sqe fitting. Requires PARM_NUM length buffers testParm and grad
+*/
+double
+_tenModelSqeFitSingle(const tenModel *model,
+ double *testParm, double *grad,
+ double *parm, double *convFrac,
+ const tenExperSpec *espec,
+ double *dwiBuff, const double *dwiMeas,
+ const double *parmInit, int knownB0,
+ unsigned int minIter, unsigned int maxIter,
+ double convEps) {
+ /* static const char me[]="_tenModelSqeFitSingle"; */
+ unsigned int iter;
+ double step, bak, opp, val, testval, dist, td;
+ int done;
+
+ step = 1;
+ model->copy(parm, parmInit);
+ val = model->sqe(parm, espec, dwiBuff, dwiMeas, knownB0);
+ model->sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
+
+ opp = 2;
+ bak = 0.1;
+ iter = 0;
+ dist = convEps*8;
+ do {
+ do {
+ model->step(testParm, -step, grad, parm);
+ testval = model->sqe(testParm, espec, dwiBuff, dwiMeas, knownB0);
+ if (testval > val) {
+ step *= bak;
+ }
+ } while (testval > val);
+ td = model->dist(testParm, parm);
+ dist = (td + dist)/2;
+ val = testval;
+ model->copy(parm, testParm);
+ model->sqeGrad(grad, parm, espec, dwiBuff, dwiMeas, knownB0);
+ step *= opp;
+ iter++;
+ done = (iter < minIter
+ ? AIR_FALSE
+ : (iter > maxIter) || dist < convEps);
+ } while (!done);
+ *convFrac = dist/convEps;
+ return val;
+}
+
int
tenModelSqeFit(Nrrd *nparm, Nrrd **nsqeP,
const tenModel *model,
@@ -422,12 +475,11 @@
airMopError(mop); return 1;
}
lablen = (strlen(tenModelPrefixStr)
- + strlen(":")
+ (saveB0 ? strlen("B0+") : 0)
+ strlen(model->name)
+ 1);
nparm->axis[0].label = AIR_CAST(char *, calloc(lablen, sizeof(char)));
- sprintf(nparm->axis[0].label, "%s:%s%s",
+ sprintf(nparm->axis[0].label, "%s%s%s",
tenModelPrefixStr,
saveB0 ? "B0+" : "",
model->name);
@@ -453,3 +505,124 @@
return 0;
}
+
+/*
+** copy the B0 info if we have it
+** use the same type on the way out.
+*/
+int
+tenModelConvert(Nrrd *nparmDst, int *convRetP, const tenModel *modelDst,
+ const Nrrd *nparmSrc, const tenModel *_modelSrc) {
+ static char me[]="tenModelConvert";
+ const tenModel *modelSrc;
+ double *dpdst, *dpsrc, (*lup)(const void *v, size_t I),
+ (*ins)(void *v, size_t I, double d);
+ size_t szOut[NRRD_DIM_MAX], II, NN, tsize;
+ airArray *mop;
+ int withB0, axmap[NRRD_DIM_MAX], convRet;
+ unsigned int parmNumDst, parmNumSrc, ii, lablen;
+ const char *parmSrc;
+ char *parmDst;
+
+ if (!( nparmDst && modelDst && nparmSrc )) {
+ biffAddf(TEN, "%s: got NULL pointer", me);
+ return 1;
+ }
+ if (!_modelSrc) {
+ /* we have to try to learn the source model from the nrrd */
+ if (tenModelFromAxisLearn(&modelSrc, &withB0, nparmSrc->axis + 0)) {
+ biffAddf(TEN, "%s: couldn't learn model from src nparm", me);
+ return 1;
+ }
+ } else {
+ modelSrc = _modelSrc;
+ if (modelSrc->parmNum == nparmSrc->axis[0].size) {
+ withB0 = AIR_TRUE;
+ } if (modelSrc->parmNum-1 == nparmSrc->axis[0].size) {
+ withB0 = AIR_FALSE;
+ } else {
+ biffAddf(TEN, "%s: axis[0].size %u is not \"%s\" parmnum %u or 1 less",
+ me, AIR_CAST(unsigned int, nparmSrc->axis[0].size),
+ modelSrc->name, modelSrc->parmNum);
+ return 1;
+ }
+ }
+
+ mop = airMopNew();
+ dpdst = modelDst->alloc();
+ airMopAdd(mop, dpdst, airFree, airMopAlways);
+ dpsrc = modelSrc->alloc();
+ airMopAdd(mop, dpsrc, airFree, airMopAlways);
+ lup = nrrdDLookup[nparmSrc->type];
+ ins = nrrdDInsert[nparmSrc->type];
+ parmNumDst = withB0 ? modelDst->parmNum : modelDst->parmNum-1;
+ parmNumSrc = nparmSrc->axis[0].size;
+ for (ii=0; ii<nparmSrc->dim; ii++) {
+ szOut[ii] = (!ii
+ ? parmNumDst
+ : nparmSrc->axis[ii].size);
+ axmap[ii] = (!ii
+ ? -1
+ : AIR_CAST(int, ii));
+ }
+ if (nrrdMaybeAlloc_nva(nparmDst, nparmSrc->type, nparmSrc->dim, szOut)) {
+ biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ airMopError(mop); return 1;
+ }
+
+ NN = nrrdElementNumber(nparmSrc)/nparmSrc->axis[0].size;
+ tsize = nrrdTypeSize[nparmSrc->type];
+ parmSrc = AIR_CAST(char *, nparmSrc->data);
+ parmDst = AIR_CAST(char *, nparmDst->data);
+ if (!withB0) {
+ dpsrc[0] = 0;
+ }
+ /* do first one for error check */
+ for (II=0; II<NN; II++) {
+ for (ii=0; ii<parmNumSrc; ii++) {
+ dpsrc[withB0 ? ii : ii+1] = lup(parmSrc, ii);
+ }
+ convRet = modelDst->convert(dpdst, dpsrc, modelSrc);
+ if (2 == convRet) { /* HEY should be enum for this value */
+ biffAddf(TEN, "%s: error converting from \"%s\" to \"%s\"", me,
+ modelSrc->name, modelDst->name);
+ airMopError(mop); return 1;
+ }
+ for (ii=0; ii<parmNumDst; ii++) {
+ ins(parmDst, ii, dpdst[ii]);
+ }
+ parmSrc += parmNumSrc*tsize;
+ parmDst += parmNumDst*tsize;
+ }
+ if (convRetP) {
+ *convRetP = convRet;
+ }
+
+ if (nrrdAxisInfoCopy(nparmDst, nparmSrc, axmap, NRRD_AXIS_INFO_SIZE_BIT)
+ || nrrdBasicInfoCopy(nparmDst, nparmSrc,
+ NRRD_BASIC_INFO_DATA_BIT
+ | NRRD_BASIC_INFO_TYPE_BIT
+ | NRRD_BASIC_INFO_BLOCKSIZE_BIT
+ | NRRD_BASIC_INFO_DIMENSION_BIT
+ | NRRD_BASIC_INFO_CONTENT_BIT
+ | NRRD_BASIC_INFO_COMMENTS_BIT
+ | (nrrdStateKeyValuePairsPropagate
+ ? 0
+ : NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
+ biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ airMopError(mop); return 1;
+ }
+ /* HEY: COPY AND PASTE! from above. perhaps make helper functions? */
+ lablen = (strlen(tenModelPrefixStr)
+ + (withB0 ? strlen("B0+") : 0)
+ + strlen(modelDst->name)
+ + 1);
+ nparmDst->axis[0].label = AIR_CAST(char *, calloc(lablen, sizeof(char)));
+ sprintf(nparmDst->axis[0].label, "%s%s%s",
+ tenModelPrefixStr,
+ withB0 ? "B0+" : "",
+ modelDst->name);
+
+ airMopOkay(mop);
+ return 0;
+}
Added: teem/trunk/src/ten/tendMconv.c
===================================================================
--- teem/trunk/src/ten/tendMconv.c (rev 0)
+++ teem/trunk/src/ten/tendMconv.c 2009-10-28 13:35:58 UTC (rev 4328)
@@ -0,0 +1,97 @@
+/*
+ Teem: Tools to process and visualize scientific data and images
+ Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann
+ Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ (LGPL) as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ The terms of redistributing and/or modifying this software also
+ include exceptions to the LGPL that facilitate static linking.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+#include "ten.h"
+#include "privateTen.h"
+
+#define INFO "convert from one model to another"
+char *_tend_mconvInfoL =
+ (INFO
+ ". More docs here.");
+
+int
+tend_mconvMain(int argc, char **argv, char *me, hestParm *hparm) {
+ int pret;
+ hestOpt *hopt = NULL;
+ char *perr, *err;
+ airArray *mop;
+
+ Nrrd *nin, *nout;
+ char *outS, *modelSrcS, *modelDstS;
+ const tenModel *modelDst, *modelSrc;
+ int saveB0;
+
+ hestOptAdd(&hopt, "mo", "model", airTypeString, 1, 1, &modelDstS, NULL,
+ "which model to convert to");
+ hestOptAdd(&hopt, "mi", "model", airTypeString, 1, 1, &modelSrcS, "",
+ "model converting from; if not set, will try to determine "
+ "from input nrrd");
+ hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
+ "input nrrd of model parms",
+ NULL, NULL, nrrdHestNrrd);
+ hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
+ "output nrrd of model parms");
+
+ mop = airMopNew();
+ airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
+ USAGE(_tend_mconvInfoL);
+ JUSTPARSE();
+ airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
+
+ nout = nrrdNew();
+ airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
+ if (tenModelParse(&modelDst, &saveB0, AIR_FALSE, modelDstS)) {
+ airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble parsing model \"%s\":\n%s\n", me,
+ modelDstS, err);
+ airMopError(mop); return 1;
+ }
+ if (saveB0) {
+ printf("%s: warning: saving B0 is determined by input nrrd "
+ "having B0 info.\n", me);
+ }
+ if (airStrlen(modelSrcS)) {
+ if (tenModelParse(&modelSrc, &saveB0, AIR_FALSE, modelSrcS)) {
+ airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble parsing model \"%s\":\n%s\n", me,
+ modelSrcS, err);
+ airMopError(mop); return 1;
+ }
+ } else {
+ modelSrc = NULL;
+ }
+ if (tenModelConvert(nout, NULL, modelDst, nin, modelSrc)) {
+ airMopAdd(mop, err=biffGetDone(TEN), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble converting:\n%s\n", me, err);
+ airMopError(mop); return 1;
+ }
+ if (nrrdSave(outS, nout, NULL)) {
+ airMopAdd(mop, err=biffGetDone(NRRD), airFree, airMopAlways);
+ fprintf(stderr, "%s: trouble writing:\n%s\n", me, err);
+ airMopError(mop); return 1;
+ }
+
+ airMopOkay(mop);
+ return 0;
+}
+/* TEND_CMD(mconv, INFO); */
+unrrduCmd tend_mconvCmd = { "mconv", INFO, tend_mconvMain };
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|
|
From: <kin...@us...> - 2009-10-29 12:08:24
|
Revision: 4338
http://teem.svn.sourceforge.net/teem/?rev=4338&view=rev
Author: kindlmann
Date: 2009-10-29 12:08:18 +0000 (Thu, 29 Oct 2009)
Log Message:
-----------
comments
Modified Paths:
--------------
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenModel.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-10-29 12:08:04 UTC (rev 4337)
+++ teem/trunk/src/ten/ten.h 2009-10-29 12:08:18 UTC (rev 4338)
@@ -1090,8 +1090,9 @@
typedef struct {
char name[AIR_STRLEN_SMALL]; /* name */
double min, max; /* bounds */
- int vec3; /* non-zero if this is one coeff of 3-vector */
- unsigned int vecIdx; /* if 3-vector, index into it */
+ int vec3; /* non-zero if this is a coefficient
+ of a UNIT-LENGTH 3-vector */
+ unsigned int vecIdx; /* if part of vector, index into it */
} tenModelParmDesc;
#define TEN_MODEL_B0_MAX 10000 /* HEY: completely arbitrary! */
Modified: teem/trunk/src/ten/tenModel.c
===================================================================
--- teem/trunk/src/ten/tenModel.c 2009-10-29 12:08:04 UTC (rev 4337)
+++ teem/trunk/src/ten/tenModel.c 2009-10-29 12:08:18 UTC (rev 4338)
@@ -576,7 +576,6 @@
if (!withB0) {
dpsrc[0] = 0;
}
- /* do first one for error check */
for (II=0; II<NN; II++) {
for (ii=0; ii<parmNumSrc; ii++) {
dpsrc[withB0 ? ii : ii+1] = lup(parmSrc, ii);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-10-30 13:42:42
|
Revision: 4339
http://teem.svn.sourceforge.net/teem/?rev=4339&view=rev
Author: kindlmann
Date: 2009-10-30 13:42:36 +0000 (Fri, 30 Oct 2009)
Log Message:
-----------
fixing warning message while tenModel->convert is still largely unimplemented
Modified Paths:
--------------
teem/trunk/src/ten/model1Stick.c
teem/trunk/src/ten/modelBall.c
teem/trunk/src/ten/modelBall1Stick.c
teem/trunk/src/ten/modelCylinder.c
teem/trunk/src/ten/modelTensor2.c
Modified: teem/trunk/src/ten/model1Stick.c
===================================================================
--- teem/trunk/src/ten/model1Stick.c 2009-10-29 12:08:18 UTC (rev 4338)
+++ teem/trunk/src/ten/model1Stick.c 2009-10-30 13:42:36 UTC (rev 4339)
@@ -25,7 +25,7 @@
#define PARM_NUM 5
static const tenModelParmDesc
-const parmDesc[] = {
+parmDesc[] = {
/* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
/* 1 */ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
/* 2 */ {"x", -1.0, 1.0, AIR_TRUE, 0},
@@ -67,8 +67,9 @@
static int
parmConvert(double *parmDst, const double *parmSrc,
const tenModel *modelSrc) {
- int lossy;
+ int ret;
+ ret = 0;
parmDst[0] = parmSrc[0];
if (modelSrc == tenModelBall) {
@@ -85,8 +86,9 @@
for (ii=0; ii<PARM_NUM; ii++) {
parmDst[ii] = AIR_NAN;
}
+ ret = 2;
}
- return lossy;
+ return ret;
}
_TEN_SQE
Modified: teem/trunk/src/ten/modelBall.c
===================================================================
--- teem/trunk/src/ten/modelBall.c 2009-10-29 12:08:18 UTC (rev 4338)
+++ teem/trunk/src/ten/modelBall.c 2009-10-30 13:42:36 UTC (rev 4339)
@@ -25,7 +25,7 @@
#define PARM_NUM 2
static const tenModelParmDesc
-const parmDesc[] = {
+parmDesc[] = {
/* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
/* 1 */ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0}
};
@@ -60,6 +60,7 @@
const tenModel *modelSrc) {
int ret;
+ ret = 0;
parmDst[0] = parmSrc[0];
if (modelSrc == tenModelBall) {
Modified: teem/trunk/src/ten/modelBall1Stick.c
===================================================================
--- teem/trunk/src/ten/modelBall1Stick.c 2009-10-29 12:08:18 UTC (rev 4338)
+++ teem/trunk/src/ten/modelBall1Stick.c 2009-10-30 13:42:36 UTC (rev 4339)
@@ -25,7 +25,7 @@
#define PARM_NUM 6
static const tenModelParmDesc
-const parmDesc[] = {
+parmDesc[] = {
/* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
/* 1 */ {"diffusivity", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
/* 2 */ {"fraction", 0.0, 1.0, AIR_FALSE, 0},
@@ -71,8 +71,9 @@
static int
parmConvert(double *parmDst, const double *parmSrc,
const tenModel *modelSrc) {
- int lossy;
+ int ret;
+ ret = 0;
parmDst[0] = parmSrc[0];
if (modelSrc == tenModelBall) {
@@ -89,8 +90,9 @@
for (ii=0; ii<PARM_NUM; ii++) {
parmDst[ii] = AIR_NAN;
}
+ ret = 2;
}
- return lossy;
+ return ret;
}
_TEN_SQE
Modified: teem/trunk/src/ten/modelCylinder.c
===================================================================
--- teem/trunk/src/ten/modelCylinder.c 2009-10-29 12:08:18 UTC (rev 4338)
+++ teem/trunk/src/ten/modelCylinder.c 2009-10-30 13:42:36 UTC (rev 4339)
@@ -25,7 +25,7 @@
#define PARM_NUM 6
static const tenModelParmDesc
-const parmDesc[] = {
+parmDesc[] = {
/* 0 */ {"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
/* 1 */ {"length", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
/* 2 */ {"radius", 0.0, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
@@ -73,8 +73,9 @@
static int
parmConvert(double *parmDst, const double *parmSrc,
const tenModel *modelSrc) {
- int lossy;
+ int ret;
+ ret = 0;
parmDst[0] = parmSrc[0];
if (modelSrc == tenModelBall) {
@@ -91,8 +92,9 @@
for (ii=0; ii<PARM_NUM; ii++) {
parmDst[ii] = AIR_NAN;
}
+ ret = 2;
}
- return lossy;
+ return ret;
}
_TEN_SQE
Modified: teem/trunk/src/ten/modelTensor2.c
===================================================================
--- teem/trunk/src/ten/modelTensor2.c 2009-10-29 12:08:18 UTC (rev 4338)
+++ teem/trunk/src/ten/modelTensor2.c 2009-10-30 13:42:36 UTC (rev 4339)
@@ -27,7 +27,7 @@
/* 1/sqrt(2) */
#define OST 0.70710678118654752440
static const tenModelParmDesc
-const parmDesc[] = {
+parmDesc[] = {
{"B0", 0.0, TEN_MODEL_B0_MAX, AIR_FALSE, 0},
{"Dxx", -TEN_MODEL_DIFF_MAX, TEN_MODEL_DIFF_MAX, AIR_FALSE, 0},
{"Dxy", -TEN_MODEL_DIFF_MAX*OST, TEN_MODEL_DIFF_MAX*OST, AIR_FALSE, 0},
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|
|
From: <ts...@us...> - 2009-11-04 03:29:37
|
Revision: 4352
http://teem.svn.sourceforge.net/teem/?rev=4352&view=rev
Author: tststs
Date: 2009-11-04 03:29:26 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Integrated code that implements tenGage kinds to compute Hessian of
cl/cp/ca. Needed to implement the linearity and planarity ridges from
Schultz/Theisel/Seidel: "Crease Surfaces: From Theory to Extraction and
Application to Diffusion Tensor MRI." IEEE TVCG 2010.
Modified Paths:
--------------
teem/trunk/src/ten/enumsTen.c
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tenGage.c
Modified: teem/trunk/src/ten/enumsTen.c
===================================================================
--- teem/trunk/src/ten/enumsTen.c 2009-11-03 20:26:11 UTC (rev 4351)
+++ teem/trunk/src/ten/enumsTen.c 2009-11-04 03:29:26 UTC (rev 4352)
@@ -316,12 +316,42 @@
"cl1gv",
"cl1gm",
+ "cl1gn",
"cp1gv",
"cp1gm",
+ "cp1gn",
"ca1gv",
"ca1gm",
+ "ca1gn",
"tgrote",
-
+ "eval hessian",
+ "cl1 hessian",
+ "cl1 hessian evals",
+ "cl1 hessian eval 0",
+ "cl1 hessian eval 1",
+ "cl1 hessian eval 2",
+ "cl1 hessian evecs",
+ "cl1 hessian evec 0",
+ "cl1 hessian evec 1",
+ "cl1 hessian evec 2",
+ "cp1 hessian",
+ "cp1 hessian evals",
+ "cp1 hessian eval 0",
+ "cp1 hessian eval 1",
+ "cp1 hessian eval 2",
+ "cp1 hessian evecs",
+ "cp1 hessian evec 0",
+ "cp1 hessian evec 1",
+ "cp1 hessian evec 2",
+ "ca1 hessian",
+ "ca1 hessian evals",
+ "ca1 hessian eval 0",
+ "ca1 hessian eval 1",
+ "ca1 hessian eval 2",
+ "ca1 hessian evecs",
+ "ca1 hessian evec 0",
+ "ca1 hessian evec 1",
+ "ca1 hessian evec 2",
"anisotropies"
};
@@ -481,13 +511,44 @@
"QuatGeoLoxR",
"gradient vector of cl1",
"gradient magnitude of cl1",
+ "normal of cl1",
"gradient vector of cp1",
"gradient magnitude of cp1",
+ "normal of cp1",
"gradient vector of ca1",
"gradient magnitude of ca1",
+ "normal of ca1",
"all tensor component gradients, starting with confidence gradient, "
/* !! CONCAT !! */
"rotated such that eigenvalue derivatives are on the diagonal",
+ "eigenvalue hessians",
+ "cl1 hessian",
+ "cl1 hessian evals",
+ "cl1 hessian eval 0",
+ "cl1 hessian eval 1",
+ "cl1 hessian eval 2",
+ "cl1 hessian evecs",
+ "cl1 hessian evec 0",
+ "cl1 hessian evec 1",
+ "cl1 hessian evec 2",
+ "cp1 hessian",
+ "cp1 hessian evals",
+ "cp1 hessian eval 0",
+ "cp1 hessian eval 1",
+ "cp1 hessian eval 2",
+ "cp1 hessian evecs",
+ "cp1 hessian evec 0",
+ "cp1 hessian evec 1",
+ "cp1 hessian evec 2",
+ "ca1 hessian",
+ "ca1 hessian evals",
+ "ca1 hessian eval 0",
+ "ca1 hessian eval 1",
+ "ca1 hessian eval 2",
+ "ca1 hessian evecs",
+ "ca1 hessian evec 0",
+ "ca1 hessian evec 1",
+ "ca1 hessian evec 2",
"anisotropies"
};
@@ -647,11 +708,42 @@
tenGageTensorQuatGeoLoxR,
tenGageCl1GradVec,
tenGageCl1GradMag,
+ tenGageCl1Normal,
tenGageCp1GradVec,
tenGageCp1GradMag,
+ tenGageCp1Normal,
tenGageCa1GradVec,
tenGageCa1GradMag,
+ tenGageCa1Normal,
tenGageTensorGradRotE,
+ tenGageEvalHessian, /* Hessian of the eigenvalues: [27] */
+ tenGageCl1Hessian, /* Hessian of cl1: [9] */
+ tenGageCl1HessianEval, /* Hessian eigenvalues of cl1: [3] */
+ tenGageCl1HessianEval0, /* First Hessian eigenvalue of cl1: [1] */
+ tenGageCl1HessianEval1, /* Second Hessian eigenvalue of cl1: [1] */
+ tenGageCl1HessianEval2, /* Third Hessian eigenvalue of cl1: [1] */
+ tenGageCl1HessianEvec, /* Hessian eigenvectors of cl1: [9] */
+ tenGageCl1HessianEvec0, /* First Hessian eigenvector of cl1: [3] */
+ tenGageCl1HessianEvec1, /* Second Hessian eigenvector of cl1: [3] */
+ tenGageCl1HessianEvec2, /* Third Hessian eigenvector of cl1: [3] */
+ tenGageCp1Hessian, /* Hessian of cp1: [9] */
+ tenGageCp1HessianEval, /* Hessian eigenvalues of cp1: [3] */
+ tenGageCp1HessianEval0, /* First Hessian eigenvalue of cp1: [1] */
+ tenGageCp1HessianEval1, /* Second Hessian eigenvalue of cp1: [1] */
+ tenGageCp1HessianEval2, /* Third Hessian eigenvalue of cp1: [1] */
+ tenGageCp1HessianEvec, /* Hessian eigenvectors of cp1: [9] */
+ tenGageCp1HessianEvec0, /* First Hessian eigenvector of cp1: [3] */
+ tenGageCp1HessianEvec1, /* Second Hessian eigenvector of cp1: [3] */
+ tenGageCp1HessianEvec2, /* Third Hessian eigenvector of cp1: [3] */
+ tenGageCa1Hessian, /* Hessian of cp1: [9] */
+ tenGageCa1HessianEval, /* Hessian eigenvalues of cp1: [3] */
+ tenGageCa1HessianEval0, /* First Hessian eigenvalue of cp1: [1] */
+ tenGageCa1HessianEval1, /* Second Hessian eigenvalue of cp1: [1] */
+ tenGageCa1HessianEval2, /* Third Hessian eigenvalue of cp1: [1] */
+ tenGageCa1HessianEvec, /* Hessian eigenvectors of cp1: [9] */
+ tenGageCa1HessianEvec0, /* First Hessian eigenvector of cp1: [3] */
+ tenGageCa1HessianEvec1, /* Second Hessian eigenvector of cp1: [3] */
+ tenGageCa1HessianEvec2, /* Third Hessian eigenvector of cp1: [3] */
tenGageAniso,
};
@@ -815,12 +907,42 @@
"cl1gv",
"cl1gm",
+ "cl1gn",
"cp1gv",
"cp1gm",
+ "cp1gn",
"ca1gv",
"ca1gm",
+ "ca1gn",
"tgrote",
-
+ "evalhess",
+ "cl1hess",
+ "cl1hesseval",
+ "cl1hesseval1",
+ "cl1hesseval2",
+ "cl1hesseval3",
+ "cl1hessevec",
+ "cl1hessevec1",
+ "cl1hessevec2",
+ "cl1hessevec3",
+ "cp1hess",
+ "cp1hesseval",
+ "cp1hesseval1",
+ "cp1hesseval2",
+ "cp1hesseval3",
+ "cp1hessevec",
+ "cp1hessevec1",
+ "cp1hessevec2",
+ "cp1hessevec3",
+ "ca1hess",
+ "ca1hesseval",
+ "ca1hesseval1",
+ "ca1hesseval2",
+ "ca1hesseval3",
+ "ca1hessevec",
+ "ca1hessevec1",
+ "ca1hessevec2",
+ "ca1hessevec3",
"an", "aniso", "anisotropies",
""
};
@@ -987,15 +1109,45 @@
tenGageTensorLogEuclidean, tenGageTensorLogEuclidean,
tenGageTensorQuatGeoLoxK, tenGageTensorQuatGeoLoxK,
tenGageTensorQuatGeoLoxR, tenGageTensorQuatGeoLoxR,
-
+
tenGageCl1GradVec,
tenGageCl1GradMag,
+ tenGageCl1Normal,
tenGageCp1GradVec,
tenGageCp1GradMag,
+ tenGageCp1Normal,
tenGageCa1GradVec,
tenGageCa1GradMag,
+ tenGageCa1Normal,
tenGageTensorGradRotE,
-
+ tenGageEvalHessian,
+ tenGageCl1Hessian,
+ tenGageCl1HessianEval,
+ tenGageCl1HessianEval0,
+ tenGageCl1HessianEval1,
+ tenGageCl1HessianEval2,
+ tenGageCl1HessianEvec,
+ tenGageCl1HessianEvec0,
+ tenGageCl1HessianEvec1,
+ tenGageCl1HessianEvec2,
+ tenGageCp1Hessian,
+ tenGageCp1HessianEval,
+ tenGageCp1HessianEval0,
+ tenGageCp1HessianEval1,
+ tenGageCp1HessianEval2,
+ tenGageCp1HessianEvec,
+ tenGageCp1HessianEvec0,
+ tenGageCp1HessianEvec1,
+ tenGageCp1HessianEvec2,
+ tenGageCa1Hessian,
+ tenGageCa1HessianEval,
+ tenGageCa1HessianEval0,
+ tenGageCa1HessianEval1,
+ tenGageCa1HessianEval2,
+ tenGageCa1HessianEvec,
+ tenGageCa1HessianEvec0,
+ tenGageCa1HessianEvec1,
+ tenGageCa1HessianEvec2,
tenGageAniso, tenGageAniso, tenGageAniso
};
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-11-03 20:26:11 UTC (rev 4351)
+++ teem/trunk/src/ten/ten.h 2009-11-04 03:29:26 UTC (rev 4352)
@@ -438,19 +438,50 @@
tenGageCl1GradVec, /* 152: "cl1gv" gradient vector of cl1: [3] */
tenGageCl1GradMag, /* 153: "cl1gm" gradient magnitude of cl1: [1] */
- tenGageCp1GradVec, /* 154: "cp1gv" gradient vector of cp1: [3] */
- tenGageCp1GradMag, /* 155: "cp1gm" gradient magnitude of cp1: [1] */
- tenGageCa1GradVec, /* 156: "ca1gv" gradient vector of ca1: [3] */
- tenGageCa1GradMag, /* 157: "ca1gm" gradient magnitude of ca1: [1] */
- tenGageTensorGradRotE, /* 158: "tgrote" all tensor component gradients,
+ tenGageCl1Normal, /* 154: "cl1gn" normal of cl1: [3] */
+ tenGageCp1GradVec, /* 155: "cp1gv" gradient vector of cp1: [3] */
+ tenGageCp1GradMag, /* 156: "cp1gm" gradient magnitude of cp1: [1] */
+ tenGageCp1Normal, /* 157: "cl1gn" normal of cp1: [3] */
+ tenGageCa1GradVec, /* 158: "ca1gv" gradient vector of ca1: [3] */
+ tenGageCa1GradMag, /* 159: "ca1gm" gradient magnitude of ca1: [1] */
+ tenGageCa1Normal, /* 160: "cl1gn" normal of ca1: [3] */
+ tenGageTensorGradRotE, /* 161: "tgrote" all tensor component gradients,
starting with confidence gradient.
Rotated such that eigenvalue
derivatives are on the diagonal: [21] */
+ tenGageEvalHessian, /* 162: "evalhess" Hessian of the eigenvalues: [27] */
+ tenGageCl1Hessian, /* 163: "cl1hess" Hessian of cl1: [9] */
+ tenGageCl1HessianEval, /* 164: "cl1hesseval" Hessian evals of cl1: [3] */
+ tenGageCl1HessianEval0,/* 165: "cl1hesseval1" First Hess eval of cl1: [1] */
+ tenGageCl1HessianEval1,/* 166: "cl1hesseval2" Second Hess eval of cl1: [1] */
+ tenGageCl1HessianEval2,/* 167: "cl1hesseval3" Third Hess eval of cl1: [1] */
+ tenGageCl1HessianEvec, /* 168: "cl1hessevec" Hessian evecs of cl1: [9] */
+ tenGageCl1HessianEvec0,/* 169: "cl1hessevec1" First Hess evec of cl1: [3] */
+ tenGageCl1HessianEvec1,/* 170: "cl1hessevec2" Second Hess evec of cl1: [3] */
+ tenGageCl1HessianEvec2,/* 171: "cl1hessevec3" Third Hess evec of cl1: [3] */
+ tenGageCp1Hessian, /* 172: "cp1hess" Hessian of cp1: [9] */
+ tenGageCp1HessianEval, /* 173: "cp1hesseval" Hessian evals of cp1: [3] */
+ tenGageCp1HessianEval0,/* 174: "cp1hesseval1" First Hess eval of cp1: [1] */
+ tenGageCp1HessianEval1,/* 175: "cp1hesseval2" Second Hess eval of cp1: [1] */
+ tenGageCp1HessianEval2,/* 176: "cp1hesseval3" Third Hess eval of cp1: [1] */
+ tenGageCp1HessianEvec, /* 177: "cp1hessevec" Hessian evecs of cp1: [9] */
+ tenGageCp1HessianEvec0,/* 178: "cp1hessevec1" First Hess evec of cp1: [3] */
+ tenGageCp1HessianEvec1,/* 179: "cp1hessevec2" Second Hess evec of cp1: [3] */
+ tenGageCp1HessianEvec2,/* 180: "cp1hessevec3" Third Hess evec of cp1: [3] */
+ tenGageCa1Hessian, /* 181: "ca1hess" Hessian of ca1: [9] */
+ tenGageCa1HessianEval, /* 182: "ca1hesseval" Hessian evals of ca1: [3] */
+ tenGageCa1HessianEval0,/* 183: "ca1hesseval1" First Hess eval of ca1: [1] */
+ tenGageCa1HessianEval1,/* 184: "ca1hesseval2" Second Hess eval of ca1: [1] */
+ tenGageCa1HessianEval2,/* 185: "ca1hesseval3" Third Hess eval of ca1: [1] */
+ tenGageCa1HessianEvec, /* 186: "ca1hessevec" Hessian evecs of ca1: [9] */
+ tenGageCa1HessianEvec0,/* 187: "ca1hessevec1" First Hess evec of ca1: [3] */
+ tenGageCa1HessianEvec1,/* 188: "ca1hessevec2" Second Hess evec of ca1: [3] */
+ tenGageCa1HessianEvec2,/* 189: "ca1hessevec3" Third Hess evec of ca1: [3] */
- tenGageAniso, /* 159: "an", all anisos: [TEN_ANISO_MAX+1] */
+ tenGageAniso, /* 190: "an", all anisos: [TEN_ANISO_MAX+1] */
tenGageLast
};
-#define TEN_GAGE_ITEM_MAX 159
+#define TEN_GAGE_ITEM_MAX 190
/*
******** tenDwiGage* enum
Modified: teem/trunk/src/ten/tenGage.c
===================================================================
--- teem/trunk/src/ten/tenGage.c 2009-11-03 20:26:11 UTC (rev 4351)
+++ teem/trunk/src/ten/tenGage.c 2009-11-04 03:29:26 UTC (rev 4352)
@@ -228,16 +228,45 @@
{tenGageTensorLogEuclidean, 7, 0, {0}, 0, 0, AIR_FALSE},
{tenGageTensorQuatGeoLoxK, 7, 0, {0}, 0, 0, AIR_FALSE},
{tenGageTensorQuatGeoLoxR, 7, 0, {0}, 0, 0, AIR_FALSE},
-
-
{tenGageCl1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
{tenGageCl1GradMag, 1, 1, {tenGageCl1GradVec}, 0, 0, AIR_FALSE},
+ {tenGageCl1Normal, 3, 1, {tenGageCl1GradVec, tenGageCl1GradMag}, 0, 0, AIR_FALSE},
{tenGageCp1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
{tenGageCp1GradMag, 1, 1, {tenGageCp1GradVec}, 0, 0, AIR_FALSE},
+ {tenGageCp1Normal, 3, 1, {tenGageCp1GradVec, tenGageCp1GradMag}, 0, 0, AIR_FALSE},
{tenGageCa1GradVec, 3, 1, {tenGageTrace, tenGageEval, tenGageEvalGrads}, 0, 0, AIR_FALSE},
{tenGageCa1GradMag, 1, 1, {tenGageCa1GradVec}, 0, 0, AIR_FALSE},
+ {tenGageCa1Normal, 3, 1, {tenGageCa1GradVec, tenGageCa1GradMag}, 0, 0, AIR_FALSE},
{tenGageTensorGradRotE, 21, 1, {tenGageTensorGrad, tenGageEval, tenGageEvec}, 0, 0, AIR_FALSE},
- {tenGageAniso, TEN_ANISO_MAX+1, 0, {tenGageEval0, tenGageEval1, tenGageEval2}, 0, 0, AIR_FALSE},
+ {tenGageEvalHessian, 27, 2, {tenGageTensorGradRotE, tenGageHessian, tenGageEval}, 0, 0, AIR_FALSE },
+ {tenGageCl1Hessian, 9, 2, {tenGageTensorGradRotE, tenGageEvalHessian}, 0, 0, AIR_FALSE },
+ {tenGageCl1HessianEval, 3, 2, {tenGageCl1Hessian}, 0, 0, AIR_FALSE },
+ {tenGageCl1HessianEval0, 1, 2, {tenGageCl1HessianEval}, tenGageCl1HessianEval, 0, AIR_FALSE},
+ {tenGageCl1HessianEval1, 1, 2, {tenGageCl1HessianEval}, tenGageCl1HessianEval, 1, AIR_FALSE},
+ {tenGageCl1HessianEval2, 1, 2, {tenGageCl1HessianEval}, tenGageCl1HessianEval, 2, AIR_FALSE},
+ {tenGageCl1HessianEvec, 9, 2, {tenGageCl1Hessian}, 0, 0, AIR_FALSE },
+ {tenGageCl1HessianEvec0, 3, 2, {tenGageCl1HessianEvec}, tenGageCl1HessianEvec, 0, AIR_FALSE},
+ {tenGageCl1HessianEvec1, 3, 2, {tenGageCl1HessianEvec}, tenGageCl1HessianEvec, 3, AIR_FALSE},
+ {tenGageCl1HessianEvec2, 3, 2, {tenGageCl1HessianEvec}, tenGageCl1HessianEvec, 6, AIR_FALSE},
+ {tenGageCp1Hessian, 9, 2, {tenGageTensorGradRotE, tenGageEvalHessian}, 0, 0, AIR_FALSE },
+ {tenGageCp1HessianEval, 3, 2, {tenGageCp1Hessian}, 0, 0, AIR_FALSE },
+ {tenGageCp1HessianEval0, 1, 2, {tenGageCp1HessianEval}, tenGageCp1HessianEval, 0, AIR_FALSE},
+ {tenGageCp1HessianEval1, 1, 2, {tenGageCp1HessianEval}, tenGageCp1HessianEval, 1, AIR_FALSE},
+ {tenGageCp1HessianEval2, 1, 2, {tenGageCp1HessianEval}, tenGageCp1HessianEval, 2, AIR_FALSE},
+ {tenGageCp1HessianEvec, 9, 2, {tenGageCp1Hessian}, 0, 0, AIR_FALSE },
+ {tenGageCp1HessianEvec0, 3, 2, {tenGageCp1HessianEvec}, tenGageCp1HessianEvec, 0, AIR_FALSE},
+ {tenGageCp1HessianEvec1, 3, 2, {tenGageCp1HessianEvec}, tenGageCp1HessianEvec, 3, AIR_FALSE},
+ {tenGageCp1HessianEvec2, 3, 2, {tenGageCp1HessianEvec}, tenGageCp1HessianEvec, 6, AIR_FALSE},
+ {tenGageCa1Hessian, 9, 2, {tenGageTensorGradRotE, tenGageEvalHessian}, 0, 0, AIR_FALSE },
+ {tenGageCa1HessianEval, 3, 2, {tenGageCa1Hessian}, 0, 0, AIR_FALSE },
+ {tenGageCa1HessianEval0, 1, 2, {tenGageCa1HessianEval}, tenGageCa1HessianEval, 0, AIR_FALSE},
+ {tenGageCa1HessianEval1, 1, 2, {tenGageCa1HessianEval}, tenGageCa1HessianEval, 1, AIR_FALSE},
+ {tenGageCa1HessianEval2, 1, 2, {tenGageCa1HessianEval}, tenGageCa1HessianEval, 2, AIR_FALSE},
+ {tenGageCa1HessianEvec, 9, 2, {tenGageCa1Hessian}, 0, 0, AIR_FALSE },
+ {tenGageCa1HessianEvec0, 3, 2, {tenGageCa1HessianEvec}, tenGageCa1HessianEvec, 0, AIR_FALSE},
+ {tenGageCa1HessianEvec1, 3, 2, {tenGageCa1HessianEvec}, tenGageCa1HessianEvec, 3, AIR_FALSE},
+ {tenGageCa1HessianEvec2, 3, 2, {tenGageCa1HessianEvec}, tenGageCa1HessianEvec, 6, AIR_FALSE},
+ {tenGageAniso, TEN_ANISO_MAX+1, 0, {tenGageEval0, tenGageEval1, tenGageEval2}, 0, 0, AIR_FALSE}
};
void
@@ -998,16 +1027,12 @@
ELL_3M_SCALE(matTmp, 3.0/2, matTmp);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFAHessianEvec)) {
- /* HEY: cut-and-paste from tenGageEvec, with minimal changes */
- double fakeTen[7];
- TEN_M2T(fakeTen, pvl->directAnswer[tenGageFAHessian]);
- tenEigensolve_d(pvl->directAnswer[tenGageFAHessianEval],
- pvl->directAnswer[tenGageFAHessianEvec], fakeTen);
+ ell_3m_eigensolve_d(pvl->directAnswer[tenGageFAHessianEval],
+ pvl->directAnswer[tenGageFAHessianEvec],
+ pvl->directAnswer[tenGageFAHessian], AIR_TRUE);
} else if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFAHessianEval)) {
- double fakeTen[7];
- TEN_M2T(fakeTen, pvl->directAnswer[tenGageFAHessian]);
- /* else eigenvectors are NOT needed, but eigenvalues ARE needed */
- tenEigensolve_d(pvl->directAnswer[tenGageFAHessianEval], NULL, fakeTen);
+ ell_3m_eigenvalues_d(pvl->directAnswer[tenGageFAHessianEval],
+ pvl->directAnswer[tenGageFAHessian], AIR_TRUE);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageFARidgeSurfaceStrength)) {
double ev;
@@ -1170,16 +1195,12 @@
ELL_3M_SCALE(matTmp, tmp0, matTmp);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageModeHessianEvec)) {
- /* HEY: cut-and-paste from tenGageFAHessianEvec */
- double fakeTen[7];
- TEN_M2T(fakeTen, pvl->directAnswer[tenGageModeHessian]);
- tenEigensolve_d(pvl->directAnswer[tenGageModeHessianEval],
- pvl->directAnswer[tenGageModeHessianEvec], fakeTen);
+ ell_3m_eigensolve_d(pvl->directAnswer[tenGageModeHessianEval],
+ pvl->directAnswer[tenGageModeHessianEvec],
+ pvl->directAnswer[tenGageModeHessian], AIR_TRUE);
} else if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageModeHessianEval)) {
- double fakeTen[7];
- TEN_M2T(fakeTen, pvl->directAnswer[tenGageModeHessian]);
- /* else eigenvectors are NOT needed, but eigenvalues ARE needed */
- tenEigensolve_d(pvl->directAnswer[tenGageModeHessianEval], NULL, fakeTen);
+ ell_3m_eigenvalues_d(pvl->directAnswer[tenGageModeHessianEval],
+ pvl->directAnswer[tenGageModeHessian], AIR_TRUE);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageOmegaHessian)) {
@@ -1198,16 +1219,12 @@
ELL_3MV_SCALE_OUTER_INCR(matTmp, 0.5, faGrad, modeGrad);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageOmegaHessianEvec)) {
- /* HEY: cut-and-paste from tenGageFAHessianEvec */
- double fakeTen[7];
- TEN_M2T(fakeTen, pvl->directAnswer[tenGageOmegaHessian]);
- tenEigensolve_d(pvl->directAnswer[tenGageOmegaHessianEval],
- pvl->directAnswer[tenGageOmegaHessianEvec], fakeTen);
+ ell_3m_eigensolve_d(pvl->directAnswer[tenGageOmegaHessianEval],
+ pvl->directAnswer[tenGageOmegaHessianEvec],
+ pvl->directAnswer[tenGageOmegaHessian], AIR_TRUE);
} else if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageOmegaHessianEval)) {
- double fakeTen[7];
- TEN_M2T(fakeTen, pvl->directAnswer[tenGageOmegaHessian]);
- /* else eigenvectors are NOT needed, but eigenvalues ARE needed */
- tenEigensolve_d(pvl->directAnswer[tenGageOmegaHessianEval], NULL, fakeTen);
+ ell_3m_eigenvalues_d(pvl->directAnswer[tenGageOmegaHessianEval],
+ pvl->directAnswer[tenGageOmegaHessian], AIR_TRUE);
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageOmegaLaplacian)) {
double *hess;
@@ -1465,8 +1482,12 @@
/(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1GradMag)) {
- pvl->directAnswer[tenGageCl1GradMag][0] = ELL_3V_LEN(vecTmp);
+ magTmp = pvl->directAnswer[tenGageCl1GradMag][0] = ELL_3V_LEN(vecTmp);
}
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1Normal)) {
+ ELL_3V_SCALE(pvl->directAnswer[tenGageCl1Normal],
+ magTmp ? 1/magTmp : 0, vecTmp);
+ }
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1GradVec)) {
vecTmp = pvl->directAnswer[tenGageCp1GradVec];
@@ -1486,8 +1507,12 @@
/(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1GradMag)) {
- pvl->directAnswer[tenGageCp1GradMag][0] = ELL_3V_LEN(vecTmp);
+ magTmp = pvl->directAnswer[tenGageCp1GradMag][0] = ELL_3V_LEN(vecTmp);
}
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1Normal)) {
+ ELL_3V_SCALE(pvl->directAnswer[tenGageCp1Normal],
+ magTmp ? 1/magTmp : 0, vecTmp);
+ }
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1GradVec)) {
vecTmp = pvl->directAnswer[tenGageCa1GradVec];
@@ -1504,8 +1529,12 @@
/(pvl->directAnswer[tenGageTrace][0]*pvl->directAnswer[tenGageTrace][0]));
}
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1GradMag)) {
- pvl->directAnswer[tenGageCa1GradMag][0] = ELL_3V_LEN(vecTmp);
+ magTmp = pvl->directAnswer[tenGageCa1GradMag][0] = ELL_3V_LEN(vecTmp);
}
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1Normal)) {
+ ELL_3V_SCALE(pvl->directAnswer[tenGageCa1Normal],
+ magTmp ? 1/magTmp : 0, vecTmp);
+ }
/* --- tensor gradient, rotated into eigenframe of the tensor itself --- */
if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageTensorGradRotE)) {
@@ -1680,6 +1709,240 @@
}
}
+ /* --- Eigenvalue Hessians: rotate partial second derivatives into
+ * eigenframe and take into account correction factor based on
+ * eigenvector derivatives --- */
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageEvalHessian)) {
+ /* some aliases for convenience: */
+ double *thess = pvl->directAnswer[tenGageHessian];
+ double *evhess = pvl->directAnswer[tenGageEvalHessian];
+ double *tgradE = pvl->directAnswer[tenGageTensorGradRotE];
+ int dira, dirb; /* directions of first/second partial derivative */
+ int k; /* number of the eigenvalue */
+ double evecsT[9], tmp[9];
+ /* HEY: some copy-paste from tenGageEvalGrads */
+ double eps=0.05; /* treshold for handling degeneracies */
+ double rel1, rel2, rel3, w1, w2;
+ /* interpolation weights from relative eigenvalue distance */
+ rel1=evalAns[0]*evalAns[0]+evalAns[1]*evalAns[1];
+ if (rel1>1e-10)
+ rel1=(evalAns[0]-evalAns[1])*(evalAns[0]-evalAns[1])/rel1;
+ rel2=evalAns[0]*evalAns[0]+evalAns[2]*evalAns[2];
+ if (rel2>1e-10)
+ rel2=(evalAns[0]-evalAns[2])*(evalAns[0]-evalAns[2])/rel2;
+ rel3=evalAns[1]*evalAns[1]+evalAns[2]*evalAns[2];
+ if (rel3>1e-10)
+ rel3=(evalAns[1]-evalAns[2])*(evalAns[1]-evalAns[2])/rel3;
+ w1=rel1/eps-1;
+ w1*=w1;
+ w2=rel2/eps-1;
+ w2*=w2;
+
+ ELL_3M_TRANSPOSE(evecsT,evecAns);
+ for (dira=0; dira<3; dira++) {
+ for (dirb=0; dirb<=dira; dirb++) { /* exploit symmetry of Hessian */
+ double rdiff1,rdiff2;
+ double l1res, l2res, l3res;
+ /* collect second partial derivatives in dira,dirb */
+ double H[9];
+ ELL_3V_SET(H, thess[9+3*dirb+dira], thess[18+3*dirb+dira],
+ thess[27+3*dirb+dira]);
+ ELL_3V_SET(H+3, thess[18+3*dirb+dira], thess[36+3*dirb+dira],
+ thess[45+3*dirb+dira]);
+ ELL_3V_SET(H+6, thess[27+3*dirb+dira], thess[45+3*dirb+dira],
+ thess[54+3*dirb+dira]);
+ /* rotate into eigenframe of value */
+ ell_3m_mul_d(tmp,H,evecsT);
+ ell_3m_mul_d(H,evecAns,tmp);
+
+ /* we have to divide by rdiff=lambda_1-lambda_2; the following
+ * is a heuristic to avoid numerical problems in case rdiff is
+ * near zero */
+ if (rel1>eps) rdiff1=1.0/(evalAns[0]-evalAns[1]);
+ else if (rel1>1e-10) rdiff1=(rel1/eps)/(evalAns[0]-evalAns[1]);
+ else rdiff1=0;
+
+ if (rel2>eps) rdiff2=1.0/(evalAns[0]-evalAns[2]);
+ else if (rel2>1e-10) rdiff2=(rel2/eps)/(evalAns[0]-evalAns[2]);
+ else rdiff2=0;
+
+ l1res=H[0]+2*(tgradE[6+dira]*tgradE[6+dirb]*rdiff1+
+ tgradE[9+dira]*tgradE[9+dirb]*rdiff2);
+
+ if (rel1>eps) rdiff1=1.0/(evalAns[1]-evalAns[0]);
+ else if (rel1>1e-10) rdiff1=(rel1/eps)/(evalAns[1]-evalAns[0]);
+ else rdiff1=0;
+
+ if (rel3>eps) rdiff2=1.0/(evalAns[1]-evalAns[2]);
+ else if (rel3>1e-10) rdiff2=(rel3/eps)/(evalAns[1]-evalAns[2]);
+ else rdiff2=0;
+ l2res=H[4]+2*(tgradE[6+dira]*tgradE[6+dirb]*rdiff1+
+ tgradE[15+dira]*tgradE[15+dirb]*rdiff2);
+
+ if (rel2>eps) rdiff1=1.0/(evalAns[2]-evalAns[0]);
+ else if (rel2>1e-10) rdiff1=(rel2/eps)/(evalAns[2]-evalAns[0]);
+ else rdiff1=0;
+
+ if (rel3>eps) rdiff2=1.0/(evalAns[2]-evalAns[1]);
+ else if (rel3>1e-10) rdiff2=(rel3/eps)/(evalAns[2]-evalAns[1]);
+ else rdiff2=0;
+
+ l3res=H[8]+2*(tgradE[9+dira]*tgradE[9+dirb]*rdiff1+
+ tgradE[15+dira]*tgradE[15+dirb]*rdiff2);
+
+ if (rel1>eps)
+ evhess[3*dirb+dira]=l1res;
+ else {
+ if (rel2>eps)
+ evhess[3*dirb+dira]=(1-0.5*w1)*l1res+0.5*w1*l2res;
+ else
+ evhess[3*dirb+dira]=(1-0.5*w1-w1*w2/6.0)*l1res+
+ (0.5*w1-w1*w2/6.0)*l2res+
+ w1*w2/3.0*l3res;
+ }
+
+ if (rel2>eps)
+ evhess[18+3*dirb+dira]=l3res;
+ else {
+ if (rel1>eps)
+ evhess[18+3*dirb+dira]=(1-0.5*w2)*l3res+0.5*w2*l2res;
+ else
+ evhess[18+3*dirb+dira]=(1-0.5*w2-w1*w2/6.0)*l3res+
+ (0.5*w2-w1*w2/6.0)*l2res+
+ w1*w2/3.0*l1res;
+ }
+ evhess[9+3*dirb+dira]=l1res+l2res+l3res - evhess[3*dirb+dira] -
+ evhess[18+3*dirb+dira];
+ }
+ }
+ for (dira=0; dira<2; dira++) {
+ for (dirb=dira+1; dirb<3; dirb++) { /* copy over symmetric values */
+ for (k=0; k<3; k++) {
+ evhess[9*k+3*dirb+dira]=evhess[9*k+3*dira+dirb];
+ }
+ }
+ }
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1Hessian)) {
+ int dira, dirb;
+ double *cl1hess = pvl->directAnswer[tenGageCl1Hessian];
+ double *tgradE = pvl->directAnswer[tenGageTensorGradRotE];
+ double *evhess = pvl->directAnswer[tenGageEvalHessian];
+ /* A and B come out of the quotient rule; cf. appendix of Schultz
+ * et al., TVCG 2010 for more details */
+ double B = (evalAns[0]+evalAns[1]+evalAns[2])*
+ (evalAns[0]+evalAns[1]+evalAns[2]);
+ for (dira=0; dira<3; dira++) {
+ for (dirb=0; dirb<=dira; dirb++) { /* again, exploit Hessian symmetry */
+ double A = evalAns[0]*(-2*tgradE[12+dira]-tgradE[18+dira])+
+ evalAns[1]*(2*tgradE[3+dira]+tgradE[18+dira])+
+ evalAns[2]*(tgradE[3+dira]-tgradE[12+dira]);
+ double Ad = tgradE[3+dirb]*(-2*tgradE[12+dira]-tgradE[18+dira])+
+ evalAns[0]*(-2*evhess[9+3*dirb+dira]-evhess[18+3*dirb+dira])+
+ tgradE[12+dirb]*(2*tgradE[3+dira]+tgradE[18+dira])+
+ evalAns[1]*(2*evhess[3*dirb+dira]+evhess[18+3*dirb+dira])+
+ tgradE[18+dirb]*(tgradE[3+dira]-tgradE[12+dira])+
+ evalAns[2]*(evhess[3*dirb+dira]-evhess[9+3*dirb+dira]);
+ double Bd = 2*(evalAns[0]+evalAns[1]+evalAns[2])*
+ (tgradE[3+dirb]+tgradE[12+dirb]+tgradE[18+dirb]);
+ cl1hess[3*dirb+dira]=Ad/B-A/B*Bd/B;
+ }
+ }
+ for (dira=0; dira<2; dira++) {
+ for (dirb=dira+1; dirb<3; dirb++) { /* copy over symmetric values */
+ cl1hess[3*dirb+dira]=cl1hess[3*dira+dirb];
+ }
+ }
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1HessianEvec)) {
+ ell_3m_eigensolve_d(pvl->directAnswer[tenGageCl1HessianEval],
+ pvl->directAnswer[tenGageCl1HessianEvec],
+ pvl->directAnswer[tenGageCl1Hessian], AIR_TRUE);
+ } else if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCl1HessianEval)) {
+ ell_3m_eigenvalues_d(pvl->directAnswer[tenGageCl1HessianEval],
+ pvl->directAnswer[tenGageCl1Hessian], AIR_TRUE);
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1Hessian)) {
+ int dira, dirb;
+ double *cp1hess = pvl->directAnswer[tenGageCp1Hessian];
+ double *tgradE = pvl->directAnswer[tenGageTensorGradRotE];
+ double *evhess = pvl->directAnswer[tenGageEvalHessian];
+ double B = (evalAns[0]+evalAns[1]+evalAns[2])*
+ (evalAns[0]+evalAns[1]+evalAns[2]);
+ for (dira=0; dira<3; dira++) {
+ for (dirb=0; dirb<=dira; dirb++) { /* again, exploit Hessian symmetry */
+ double A = 2*(evalAns[0]*(tgradE[12+dira]-tgradE[18+dira])+
+ evalAns[1]*(-tgradE[3+dira]-2*tgradE[18+dira])+
+ evalAns[2]*(tgradE[3+dira]+2*tgradE[12+dira]));
+ double Ad=2*(evalAns[0]*(evhess[9+3*dirb+dira]-evhess[18+3*dirb+dira])+
+ evalAns[1]*(-evhess[3*dirb+dira]-2*evhess[18+3*dirb+dira])+
+ evalAns[2]*(evhess[3*dirb+dira]+2*evhess[9+3*dirb+dira])+
+ tgradE[3+dirb]*(tgradE[12+dira]-tgradE[18+dira])+
+ tgradE[12+dirb]*(-tgradE[3+dira]-2*tgradE[18+dira])+
+ tgradE[18+dirb]*(tgradE[3+dira]+2*tgradE[12+dira]));
+ double Bd = 2*(evalAns[0]+evalAns[1]+evalAns[2])*
+ (tgradE[3+dirb]+tgradE[12+dirb]+tgradE[18+dirb]);
+ cp1hess[3*dirb+dira]=Ad/B-A/B*Bd/B;
+ }
+ }
+ for (dira=0; dira<2; dira++) {
+ for (dirb=dira+1; dirb<3; dirb++) { /* copy over symmetric values */
+ cp1hess[3*dirb+dira]=cp1hess[3*dira+dirb];
+ }
+ }
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1HessianEvec)) {
+ ell_3m_eigensolve_d(pvl->directAnswer[tenGageCp1HessianEval],
+ pvl->directAnswer[tenGageCp1HessianEvec],
+ pvl->directAnswer[tenGageCp1Hessian], AIR_TRUE);
+ } else if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCp1HessianEval)) {
+ ell_3m_eigenvalues_d(pvl->directAnswer[tenGageCp1HessianEval],
+ pvl->directAnswer[tenGageCp1Hessian], AIR_TRUE);
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1Hessian)) {
+ int dira, dirb;
+ double *ca1hess = pvl->directAnswer[tenGageCa1Hessian];
+ double *tgradE = pvl->directAnswer[tenGageTensorGradRotE];
+ double *evhess = pvl->directAnswer[tenGageEvalHessian];
+ double B = (evalAns[0]+evalAns[1]+evalAns[2])*
+ (evalAns[0]+evalAns[1]+evalAns[2]);
+ for (dira=0; dira<3; dira++) {
+ for (dirb=0; dirb<=dira; dirb++) { /* again, exploit Hessian symmetry */
+ double A = 3*(evalAns[0]*tgradE[18+dira]+evalAns[1]*tgradE[18+dira]+
+ evalAns[2]*(-tgradE[3+dira]-tgradE[12+dira]));
+ double Ad = 3*(tgradE[3+dirb]*tgradE[18+dira]+
+ tgradE[12+dirb]*tgradE[18+dira]+
+ tgradE[18+dirb]*(-tgradE[3+dira]-tgradE[12+dira])+
+ evalAns[0]*evhess[18+3*dirb+dira]+
+ evalAns[1]*evhess[18+3*dirb+dira]+
+ evalAns[2]*(-evhess[3*dirb+dira]-evhess[9+3*dirb+dira]));
+ double Bd = 2*(evalAns[0]+evalAns[1]+evalAns[2])*
+ (tgradE[3+dirb]+tgradE[12+dirb]+tgradE[18+dirb]);
+ /* above formulas are true for cs, so flip sign here */
+ ca1hess[3*dirb+dira]=-Ad/B+A/B*Bd/B;
+ }
+ }
+ for (dira=0; dira<2; dira++) {
+ for (dirb=dira+1; dirb<3; dirb++) { /* copy over symmetric values */
+ ca1hess[3*dirb+dira]=ca1hess[3*dira+dirb];
+ }
+ }
+ }
+
+ if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1HessianEvec)) {
+ ell_3m_eigensolve_d(pvl->directAnswer[tenGageCa1HessianEval],
+ pvl->directAnswer[tenGageCa1HessianEvec],
+ pvl->directAnswer[tenGageCa1Hessian], AIR_TRUE);
+ } else if (GAGE_QUERY_ITEM_TEST(pvl->query, tenGageCa1HessianEval)) {
+ ell_3m_eigenvalues_d(pvl->directAnswer[tenGageCa1HessianEval],
+ pvl->directAnswer[tenGageCa1Hessian], AIR_TRUE);
+ }
+
return;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-11-13 22:48:41
|
Revision: 4370
http://teem.svn.sourceforge.net/teem/?rev=4370&view=rev
Author: kindlmann
Date: 2009-11-13 22:48:33 +0000 (Fri, 13 Nov 2009)
Log Message:
-----------
biff rewrite: _f -> _va and new biffMove_va
Modified Paths:
--------------
teem/trunk/src/ten/aniso.c
teem/trunk/src/ten/bimod.c
teem/trunk/src/ten/bvec.c
teem/trunk/src/ten/chan.c
teem/trunk/src/ten/epireg.c
teem/trunk/src/ten/estimate.c
teem/trunk/src/ten/fiber.c
teem/trunk/src/ten/fiberMethods.c
teem/trunk/src/ten/glyph.c
teem/trunk/src/ten/grads.c
teem/trunk/src/ten/miscTen.c
teem/trunk/src/ten/mod.c
teem/trunk/src/ten/path.c
teem/trunk/src/ten/qglox.c
teem/trunk/src/ten/tenDwiGage.c
teem/trunk/src/ten/tenModel.c
teem/trunk/src/ten/tendEstim.c
teem/trunk/src/ten/tendSatin.c
teem/trunk/src/ten/tensor.c
teem/trunk/src/ten/test/csim.c
teem/trunk/src/ten/triple.c
Modified: teem/trunk/src/ten/aniso.c
===================================================================
--- teem/trunk/src/ten/aniso.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/aniso.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -995,7 +995,7 @@
}
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 2,
AIR_CAST(size_t, res), AIR_CAST(size_t, res))) {
- biffMovef(TEN, NRRD, "%s: ", me);
+ biffMove_va(TEN, NRRD, "%s: ", me);
return 1;
}
out = (float *)nout->data;
@@ -1058,7 +1058,7 @@
size[2] = sz = nin->axis[3].size;
N = sx*sy*sz;
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 3, sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
out = (float *)nout->data;
@@ -1101,7 +1101,7 @@
}
ELL_3V_SET(map, 1, 2, 3);
if (nrrdAxisInfoCopy(nout, nin, map, NRRD_AXIS_INFO_SIZE_BIT)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
if (nrrdBasicInfoCopy(nout, nin,
@@ -1129,7 +1129,7 @@
}
if (nwght) {
if (nrrdCheck(nwght)) {
- biffMovef(TEN, NRRD, "%s: trouble with weighting nrrd", me);
+ biffMove_va(TEN, NRRD, "%s: trouble with weighting nrrd", me);
return 1;
}
if (nrrdElementNumber(nwght)
@@ -1161,7 +1161,7 @@
}
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 2,
AIR_CAST(size_t, res), AIR_CAST(size_t, yres))) {
- biffMovef(TEN, NRRD, "%s: ", me);
+ biffMove_va(TEN, NRRD, "%s: ", me);
return 1;
}
out = (float *)nout->data;
Modified: teem/trunk/src/ten/bimod.c
===================================================================
--- teem/trunk/src/ten/bimod.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/bimod.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -76,7 +76,7 @@
airMopAdd(mop, nhisto, (airMopper)nrrdNuke, airMopOnError);
airMopAdd(mop, nhisto, (airMopper)nrrdNix, airMopOnOkay);
if (nrrdConvert(nhisto, _nhisto, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: trouble converting histogram to double", me);
+ biffMove_va(TEN, NRRD, "%s: trouble converting histogram to double", me);
airMopError(mop); return 1;
}
biparm->N = nhisto->axis[0].size;
@@ -100,8 +100,8 @@
biparm->histo[i] /= sum;
}
if (!AIR_EXISTS(medianD)) {
- biffMovef(TEN, NRRD,
- "%s: got empty histogram? (median calculation failed)", me);
+ biffMove_va(TEN, NRRD,
+ "%s: got empty histogram? (median calculation failed)", me);
airMopError(mop); return 1;
}
median = (int)medianD;
Modified: teem/trunk/src/ten/bvec.c
===================================================================
--- teem/trunk/src/ten/bvec.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/bvec.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -128,7 +128,7 @@
nrrdAxisInfoGet_nva(nin, nrrdAxisInfoSize, size);
size[0] = 3;
if (nrrdMaybeAlloc_nva(nout, nrrdTypeDouble, nin->dim, size)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
for (ii=1; ii<nin->dim; ii++) {
@@ -136,10 +136,10 @@
}
map[0] = -1;
if (nrrdAxisInfoCopy(nout, nin, map, NRRD_AXIS_INFO_NONE)) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis info", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't copy axis info", me);
return 1;
}
-
+
/* process all b vectors */
vecSize = nin->axis[0].size*nrrdTypeSize[nin->type];
vecNum = nrrdElementNumber(nin)/nin->axis[0].size;
Modified: teem/trunk/src/ten/chan.c
===================================================================
--- teem/trunk/src/ten/chan.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/chan.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -166,7 +166,7 @@
if (nrrdMaybeAlloc_va(ninfo, nrrdTypeDouble, 2,
AIR_CAST(size_t, valNum),
AIR_CAST(size_t, dwiNum))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
info = (double *)(ninfo->data);
@@ -352,10 +352,10 @@
if (nrrdConvert(ngrad, _ngrad, nrrdTypeDouble)
|| nrrdMaybeAlloc_va(nbmat, nrrdTypeDouble, 2,
AIR_CAST(size_t, 6), ngrad->axis[1].size)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
airMopError(mop); return 1;
}
-
+
DD = ngrad->axis[1].size;
G = (double*)(ngrad->data);
bmat = (double*)(nbmat->data);
@@ -398,19 +398,19 @@
airMopAdd(mop, nbmat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (knownB0) {
if (nrrdConvert(nbmat, _nbmat, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert given bmat to doubles", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't convert given bmat to doubles", me);
airMopError(mop); return 1;
}
} else {
airMopAdd(mop, ntmp=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ntmp, _nbmat, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert given bmat to doubles", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't convert given bmat to doubles", me);
airMopError(mop); return 1;
}
ELL_2V_SET(padmin, 0, 0);
ELL_2V_SET(padmax, 6, _nbmat->axis[1].size-1);
if (nrrdPad_nva(nbmat, ntmp, padmin, padmax, nrrdBoundaryPad, -1)) {
- biffMovef(TEN, NRRD, "%s: couldn't pad given bmat", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't pad given bmat", me);
airMopError(mop); return 1;
}
}
@@ -423,7 +423,7 @@
bmat += nbmat->axis[0].size;
}
if (ell_Nm_pseudo_inv(nemat, nbmat)) {
- biffMovef(TEN, ELL, "%s: trouble pseudo-inverting B-matrix", me);
+ biffMove_va(TEN, ELL, "%s: trouble pseudo-inverting B-matrix", me);
airMopError(mop); return 1;
}
airMopOkay(mop);
@@ -588,10 +588,10 @@
ndwi = nrrdNew();
airMopAdd(mop, ndwi, (airMopper)nrrdNuke, airMopAlways);
if (nrrdJoin(ndwi, (const Nrrd**)_ndwi, dwiLen, 0, AIR_TRUE)) {
- biffMovef(TEN, NRRD, "%s: trouble joining inputs", me);
+ biffMove_va(TEN, NRRD, "%s: trouble joining inputs", me);
airMopError(mop); return 1;
}
-
+
nrrdAxisInfoCopy(ndwi, _ndwi[0], amap, NRRD_AXIS_INFO_NONE);
if (tenEstimateLinear4D(nten, nterrP, nB0P,
ndwi, _nbmat, knownB0, thresh, soft, b)) {
@@ -668,7 +668,7 @@
mop = airMopNew();
airMopAdd(mop, nbmat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(nbmat, _nbmat, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: trouble converting to doubles", me);
+ biffMove_va(TEN, NRRD, "%s: trouble converting to doubles", me);
airMopError(mop); return 1;
}
airMopAdd(mop, nemat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
@@ -699,8 +699,8 @@
(int)AIR_MIN(1024, range->max - range->min + 1),
nrrdTypeFloat);
if (E) {
- biffMovef(TEN, NRRD,
- "%s: trouble histograming to find DW threshold", me);
+ biffMove_va(TEN, NRRD,
+ "%s: trouble histograming to find DW threshold", me);
airMopError(mop); return 1;
}
if (_tenFindValley(&thresh, nhist, 0.75, AIR_FALSE)) {
@@ -711,7 +711,7 @@
}
if (nrrdMaybeAlloc_va(nten, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7), sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
airMopError(mop); return 1;
}
if (nterrP) {
@@ -875,7 +875,7 @@
mop = airMopNew();
airMopAdd(mop, nbmat=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(nbmat, _nbmat, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert B matrix", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't convert B matrix", me);
return 1;
}
@@ -897,7 +897,7 @@
}
if (nrrdMaybeAlloc_va(ndwi, nrrdTypeFloat, 4,
AIR_CAST(size_t, DD), sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
dwi = (float*)(ndwi->data);
@@ -1049,7 +1049,7 @@
sz = nin->axis[3].size;
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7), sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: couldn't alloc output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't alloc output", me);
return 1;
}
nout->axis[0].label = airStrdup("c,Dxx,Dxy,Dxz,Dyy,Dyz,Dzz");
Modified: teem/trunk/src/ten/epireg.c
===================================================================
--- teem/trunk/src/ten/epireg.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/epireg.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -36,12 +36,12 @@
} else {
airMopAdd(mop, nout=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdJoin(nout, (const Nrrd**)nmulti, len, 0, AIR_TRUE)) {
- biffMovef(TEN, NRRD, "%s: couldn't join %s for output", me, desc);
+ biffMove_va(TEN, NRRD, "%s: couldn't join %s for output", me, desc);
airMopError(mop); return 1;
}
}
if (nrrdSave(fname, nout, NULL)) {
- biffMovef(TEN, NRRD, "%s: trouble saving %s to \"%s\"", me, desc, fname);
+ biffMove_va(TEN, NRRD, "%s: trouble saving %s to \"%s\"", me, desc, fname);
airMopError(mop); return 1;
}
fprintf(stderr, "%s: saved %s to \"%s\"\n", me, desc, fname);
@@ -79,12 +79,12 @@
return 1;
}
if (nrrdCheck(ndwi[ni])) {
- biffMovef(TEN, NRRD,
- "%s: basic nrrd validity failed on ndwi[%d]", me, ni);
+ biffMove_va(TEN, NRRD,
+ "%s: basic nrrd validity failed on ndwi[%d]", me, ni);
return 1;
}
if (!nrrdSameSize(ndwi[0], ndwi[ni], AIR_TRUE)) {
- biffMovef(TEN, NRRD, "%s: ndwi[%d] is different from ndwi[0]", me, ni);
+ biffMove_va(TEN, NRRD, "%s: ndwi[%d] is different from ndwi[0]", me, ni);
return 1;
}
}
@@ -132,8 +132,8 @@
fprintf(stderr, "%2u ", (unsigned int)ni); fflush(stderr);
}
if (nrrdCopy(nblur[ni], ndwi[ni])) {
- biffMovef(TEN, NRRD, "%s: trouble copying ndwi[%u]",
- me, (unsigned int)ni);
+ biffMove_va(TEN, NRRD, "%s: trouble copying ndwi[%u]",
+ me, (unsigned int)ni);
return 1;
}
}
@@ -183,8 +183,8 @@
ndwi[ni]->axis[0].min = 0; ndwi[ni]->axis[0].max = sx-1;
ndwi[ni]->axis[1].min = 0; ndwi[ni]->axis[1].max = sy-1;
if (nrrdSpatialResample(nblur[ni], ndwi[ni], rinfo)) {
- biffMovef(TEN, NRRD, "%s: trouble blurring ndwi[%u]",
- me, (unsigned int)ni);
+ biffMove_va(TEN, NRRD, "%s: trouble blurring ndwi[%u]",
+ me, (unsigned int)ni);
airMopError(mop); return 1;
}
ndwi[ni]->axis[0].min = savemin[0]; ndwi[ni]->axis[0].max = savemax[0];
@@ -227,7 +227,8 @@
ntmp->axis[0].max = max;
for (ni=0; ni<ninLen; ni++) {
if (nrrdHisto(ntmp, nin[ni], NULL, NULL, bins, nrrdTypeFloat)) {
- biffMovef(TEN, NRRD, "%s: problem forming histogram of DWI %d", me, ni);
+ biffMove_va(TEN, NRRD,
+ "%s: problem forming histogram of DWI %d", me, ni);
airMopError(mop); return 1;
}
if (!ni) {
@@ -236,8 +237,9 @@
E = nrrdArithBinaryOp(nhist, nrrdBinaryOpAdd, nhist, ntmp);
}
if (E) {
- biffMovef(TEN, NRRD, "%s: problem updating histogram sum on DWI %d",
- me, ni);
+ biffMove_va(TEN, NRRD,
+ "%s: problem updating histogram sum on DWI %d",
+ me, ni);
airMopError(mop); return 1;
}
}
@@ -251,10 +253,10 @@
}
*/
if (nrrdHistoThresholdOtsu(DWthrP, nhist, expo)) {
- biffMovef(TEN, NRRD, "%s: problem finding DWI threshold", me);
+ biffMove_va(TEN, NRRD, "%s: problem finding DWI threshold", me);
airMopError(mop); return 1;
}
-
+
airMopOkay(mop);
return 0;
}
@@ -289,8 +291,8 @@
}
if (nrrdMaybeAlloc_va(nthresh[ni], nrrdTypeUChar, 3,
sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: trouble allocating threshold %u",
- me, (unsigned int)ni);
+ biffMove_va(TEN, NRRD, "%s: trouble allocating threshold %u",
+ me, (unsigned int)ni);
airMopError(mop); return 1;
}
thr = (unsigned char *)(nthresh[ni]->data);
@@ -358,8 +360,8 @@
|| nrrdCCMerge(ncc, ncc, nval, -1, big-1, 0, conny)
|| nrrdCCRevalue(nthr[ni], ncc, nval)) {
if (big) {
- biffMovef(TEN, NRRD,
- "%s: trouble with 3-D processing nthr[%d]", me, ni);
+ biffMove_va(TEN, NRRD,
+ "%s: trouble with 3-D processing nthr[%d]", me, ni);
return 1;
} else {
biffAddf(TEN, "%s: got size 0 for biggest bright CC of nthr[%d]",
@@ -377,8 +379,8 @@
|| nrrdCCRevalue(nslc, ncc, nval)
|| nrrdSplice(nthr[ni], nthr[ni], nslc, 2, z) ) {
if (big) {
- biffMovef(TEN, NRRD, "%s: trouble processing slice %d of nthr[%d]",
- me, z, ni);
+ biffMove_va(TEN, NRRD, "%s: trouble processing slice %d of nthr[%d]",
+ me, z, ni);
return 1;
} else {
/* biggest bright CC on this slice had size 0
@@ -431,8 +433,8 @@
}
if (nrrdMaybeAlloc_va(nmom[ni], nrrdTypeDouble, 2,
AIR_CAST(size_t, 5), sz)) {
- biffMovef(TEN, NRRD,
- "%s: couldn't allocate nmom[%u]", me, (unsigned int)ni);
+ biffMove_va(TEN, NRRD,
+ "%s: couldn't allocate nmom[%u]", me, (unsigned int)ni);
return 1;
}
nrrdAxisInfoSet_va(nmom[ni], nrrdAxisInfoLabel, "mx,my,h,s,t", "z");
@@ -523,7 +525,7 @@
AIR_CAST(size_t, sz),
AIR_CAST(size_t, ninLen),
AIR_CAST(size_t, ninLen))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate transform nrrd", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate transform nrrd", me);
return 1;
}
nrrdAxisInfoSet_va(npxfr, nrrdAxisInfoLabel,
@@ -574,7 +576,7 @@
if (nrrdMaybeAlloc_va(nmat[z], nrrdTypeDouble, 2,
AIR_CAST(size_t, (1 == order ? 3 : 9)),
AIR_CAST(size_t, npairs))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate fitting matrices", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate fitting matrices", me);
airMopError(mop); return 1;
}
airMopAdd(mop, ninv[z]=nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
@@ -587,7 +589,7 @@
|| nrrdMaybeAlloc_va(nvec, nrrdTypeDouble, 2,
AIR_CAST(size_t, 1),
AIR_CAST(size_t, npairs))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate HST nrrd", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate HST nrrd", me);
airMopError(mop); return 1;
}
nrrdAxisInfoSet_va(nhst, nrrdAxisInfoLabel,
@@ -644,7 +646,7 @@
}
} else {
if (ell_Nm_pseudo_inv(ninv[z], nmat[z])) {
- biffMovef(TEN, ELL, "%s: trouble estimating model (slice %d)", me, z);
+ biffMove_va(TEN, ELL, "%s: trouble estimating model (slice %d)", me, z);
airMopError(mop); return 1;
}
}
@@ -668,9 +670,9 @@
}
}
if (ell_Nm_mul(nans, ninv[z], nvec)) {
- biffMovef(TEN, ELL,
- "%s: trouble estimating model (slice %d): Sx, Sy, Sz",
- me, z);
+ biffMove_va(TEN, ELL,
+ "%s: trouble estimating model (slice %d): Sx, Sy, Sz",
+ me, z);
airMopError(mop); return 1;
}
ans = (double *)(nans->data);
@@ -727,9 +729,9 @@
}
}
if (ell_Nm_mul(nans, ninv[z], nvec)) {
- biffMovef(TEN, ELL,
- "%s: trouble estimating model (slice %d): Tx, Ty, Tz",
- me, z);
+ biffMove_va(TEN, ELL,
+ "%s: trouble estimating model (slice %d): Tx, Ty, Tz",
+ me, z);
airMopError(mop); return 1;
}
ans = (double *)(nans->data);
@@ -776,7 +778,7 @@
|| nrrdProject(ntB, ntA, 0, nrrdMeasureSum, nrrdTypeFloat)
|| nrrdProject(nl2, ntB, 0, nrrdMeasureSum, nrrdTypeFloat)
|| nrrdArithBinaryOp(ntA, nrrdBinaryOpDivide, nsd, nl2)) {
- biffMovef(TEN, NRRD, "%s: trouble doing CC projections", me);
+ biffMove_va(TEN, NRRD, "%s: trouble doing CC projections", me);
airMopError(mop); return 1;
}
if (verb) {
@@ -784,7 +786,7 @@
}
if (prog && _tenEpiRegSave("regtmp-messy.txt", ntA,
NULL, 0, "segmentation uncertainty")) {
- biffMovef(TEN, NRRD, "%s: EpiRegSave failed", me);
+ biffMove_va(TEN, NRRD, "%s: EpiRegSave failed", me);
airMopError(mop); return 1;
}
/* now ntA stores the per-slice messiness */
@@ -999,7 +1001,7 @@
|| nrrdMaybeAlloc_va(nidx, nrrdTypeInt, 2,
AIR_CAST(size_t, 2*supp),
AIR_CAST(size_t, sy))) {
- biffMovef(TEN, NRRD, "%s: trouble allocating buffers", me);
+ biffMove_va(TEN, NRRD, "%s: trouble allocating buffers", me);
airMopError(mop); return 1;
}
for (ni=0; ni<ninLen; ni++) {
@@ -1010,7 +1012,7 @@
|| ((!ni) && nrrdSlice(nslcB, ndone[ni], 2, 0)) /* only when 0==ni */
|| nrrdAxesSwap(ntmp, nin[ni], 0, 1)
|| nrrdConvert(nfin, ntmp, nrrdTypeFloat)) {
- biffMovef(TEN, NRRD, "%s: trouble prepping at ni=%d", me, ni);
+ biffMove_va(TEN, NRRD, "%s: trouble prepping at ni=%d", me, ni);
airMopError(mop); return 1;
}
for (zi=0; zi<sz; zi++) {
@@ -1020,7 +1022,7 @@
|| _tenEpiRegSliceWarp(nslcB, nslcA, nwght, nidx, kern, kparm,
hh, ss, tt, cx, cy)
|| nrrdSplice(ndone[ni], ndone[ni], nslcB, 2, zi)) {
- biffMovef(TEN, NRRD, "%s: trouble on slice %d if ni=%d", me, zi, ni);
+ biffMove_va(TEN, NRRD, "%s: trouble on slice %d if ni=%d", me, zi, ni);
/* because the _tenEpiReg calls above don't use biff */
airMopError(mop); return 1;
}
@@ -1077,10 +1079,10 @@
airMopAdd(mop, nhst = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, ngrad = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ngrad, _ngrad, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: trouble converting gradients to doubles", me);
+ biffMove_va(TEN, NRRD, "%s: trouble converting gradients to doubles", me);
airMopError(mop); return 1;
}
-
+
/* ------ blur */
if (_tenEpiRegBlur(nbuffA, nin, ninLen, bwX, bwY, verbose)) {
biffAddf(TEN, "%s: trouble %s", me, (bwX || bwY) ? "blurring" : "copying");
@@ -1233,10 +1235,10 @@
airMopAdd(mop, ndwigrad, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ngrad, _ngrad, nrrdTypeDouble)
|| nrrdConvert(ndwigrad, _ngrad, nrrdTypeDouble)) { /* HACK applies */
- biffMovef(TEN, NRRD, "%s: trouble converting gradients to doubles", me);
+ biffMove_va(TEN, NRRD, "%s: trouble converting gradients to doubles", me);
airMopError(mop); return 1;
}
-
+
nin = (Nrrd **)calloc(ninLen, sizeof(Nrrd*));
ndwi = (Nrrd **)calloc(ninLen, sizeof(Nrrd*));
nout = (Nrrd **)calloc(ninLen, sizeof(Nrrd*));
@@ -1265,8 +1267,8 @@
airMopAdd(mop, ndwiOut[dwiIdx], (airMopper)nrrdNuke, airMopAlways);
if (nrrdSlice(ndwi[dwiIdx], _nin, dwiAx,
AIR_CAST(unsigned int, ninIdx))) {
- biffMovef(TEN, NRRD, "%s: trouble slicing at %d on axis %u",
- me, ninIdx, dwiAx);
+ biffMove_va(TEN, NRRD, "%s: trouble slicing at %d on axis %u",
+ me, ninIdx, dwiAx);
airMopError(mop); return 1;
}
/* NOTE: this works because dwiIdx <= ninIdx */
@@ -1308,8 +1310,8 @@
nout[ninIdx] = nrrdNew();
airMopAdd(mop, nout[ninIdx], (airMopper)nrrdNuke, airMopAlways);
if (nrrdSlice(nout[ninIdx], _nin, dwiAx, ninIdx)) {
- biffMovef(TEN, NRRD, "%s: trouble slicing at %d on axis %u",
- me, dwiIdx, dwiAx);
+ biffMove_va(TEN, NRRD, "%s: trouble slicing at %d on axis %u",
+ me, dwiIdx, dwiAx);
airMopError(mop); return 1;
}
/*
@@ -1318,7 +1320,7 @@
}
}
if (nrrdJoin(_nout, (const Nrrd**)nout, ninLen, dwiAx, AIR_TRUE)) {
- biffMovef(TEN, NRRD, "%s: trouble joining output", me);
+ biffMove_va(TEN, NRRD, "%s: trouble joining output", me);
airMopError(mop); return 1;
}
nrrdAxisInfoCopy(_nout, _nin, NULL, NRRD_AXIS_INFO_NONE);
@@ -1332,7 +1334,7 @@
/* note that we're ALWAYS copying the key/value pairs- its just
too annoying to have to set nrrdStateKeyValuePairsPropagate
in order for the DWI-specific key/value pairs to be set */
- biffMovef(TEN, NRRD, "%s:", me);
+ biffMove_va(TEN, NRRD, "%s:", me);
airMopError(mop); return 1;
}
Modified: teem/trunk/src/ten/estimate.c
===================================================================
--- teem/trunk/src/ten/estimate.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/estimate.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -639,7 +639,7 @@
if (!E) size[1] = tec->dwiNum;
if (!E) E |= nrrdMaybeAlloc_nva(tec->nwght, nrrdTypeDouble, 2, size);
if (E) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate dwi nrrds", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate dwi nrrds", me);
return 1;
}
/* nrrdSave("0-nbmat.txt", tec->nbmat, NULL); */
@@ -738,9 +738,9 @@
if (!tec->simulate) {
/* HEY: ignores weights! */
if (ell_Nm_pseudo_inv(tec->nemat, tec->nbmat)) {
- biffMovef(TEN, ELL, "%s: trouble pseudo-inverting %ux%u B-matrix", me,
- AIR_CAST(unsigned int, tec->nbmat->axis[1].size),
- AIR_CAST(unsigned int, tec->nbmat->axis[0].size));
+ biffMove_va(TEN, ELL, "%s: trouble pseudo-inverting %ux%u B-matrix", me,
+ AIR_CAST(unsigned int, tec->nbmat->axis[1].size),
+ AIR_CAST(unsigned int, tec->nbmat->axis[0].size));
return 1;
}
}
@@ -1053,7 +1053,7 @@
}
if (nrrdMaybeAlloc_va(ndwi, outType, 4,
AIR_CAST(size_t, tec->allNum), sizeX, sizeY, sizeZ)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate DWI output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate DWI output", me);
airMopError(mop); return 1;
}
NN = sizeX * sizeY * sizeZ;
@@ -1093,7 +1093,7 @@
ndwi->axis[0].kind = nrrdKindList;
if (nrrdBasicInfoCopy(ndwi, nten,
NRRD_BASIC_INFO_ALL ^ NRRD_BASIC_INFO_SPACE)) {
- biffMovef(TEN, NRRD, "%s:", me);
+ biffMove_va(TEN, NRRD, "%s:", me);
airMopError(mop); return 1;
}
if (keyValueSet) {
@@ -1221,10 +1221,10 @@
wght[dwiIdx + tec->dwiNum*dwiIdx] = dwi*dwi/sum;
}
if (ell_Nm_wght_pseudo_inv(tec->nemat, tec->nbmat, tec->nwght)) {
- biffMovef(TEN, ELL, "%s(1): trouble wght-pseudo-inverting %ux%u B-matrix",
- me,
- AIR_CAST(unsigned int, tec->nbmat->axis[1].size),
- AIR_CAST(unsigned int, tec->nbmat->axis[0].size));
+ biffMove_va(TEN, ELL,
+ "%s(1): trouble wght-pseudo-inverting %ux%u B-matrix", me,
+ AIR_CAST(unsigned int, tec->nbmat->axis[1].size),
+ AIR_CAST(unsigned int, tec->nbmat->axis[0].size));
return 1;
}
/*
@@ -1266,9 +1266,9 @@
nrrdSave("nbmat.txt", tec->nbmat, NULL);
nrrdSave("nwght.txt", tec->nwght, NULL);
*/
- biffMovef(TEN, ELL, "%s(2): trouble w/ %ux%u B-matrix (iter %u)", me,
- AIR_CAST(unsigned int, tec->nbmat->axis[1].size),
- AIR_CAST(unsigned int, tec->nbmat->axis[0].size), iter);
+ biffMove_va(TEN, ELL, "%s(2): trouble w/ %ux%u B-matrix (iter %u)", me,
+ AIR_CAST(unsigned int, tec->nbmat->axis[1].size),
+ AIR_CAST(unsigned int, tec->nbmat->axis[0].size), iter);
return 1;
}
_tenEstimate1Tensor_LLS(tec);
@@ -1856,7 +1856,7 @@
return 1;
}
if (nrrdCheck(ndwi)) {
- biffMovef(TEN, NRRD, "%s: DWI volume not valid", me);
+ biffMove_va(TEN, NRRD, "%s: DWI volume not valid", me);
return 1;
}
if (!( 4 == ndwi->dim && 7 <= ndwi->axis[0].size )) {
@@ -1914,14 +1914,14 @@
if (nrrdMaybeAlloc_va(nten, outType, 4,
sizeTen, sizeX, sizeY, sizeZ)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate tensor output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate tensor output", me);
airMopError(mop); return 1;
}
if (nB0P) {
*nB0P = nrrdNew();
if (nrrdMaybeAlloc_va(*nB0P, outType, 3,
sizeX, sizeY, sizeZ)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate B0 output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate B0 output", me);
airMopError(mop); return 1;
}
airMopAdd(mop, *nB0P, (airMopper)nrrdNuke, airMopOnError);
@@ -1942,7 +1942,7 @@
| (nrrdStateKeyValuePairsPropagate
? 0
: NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't creatting fitting error output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't creatting fitting error output", me);
airMopError(mop); return 1;
}
ELL_3V_SET(axmap, 1, 2, 3);
Modified: teem/trunk/src/ten/fiber.c
===================================================================
--- teem/trunk/src/ten/fiber.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/fiber.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -739,7 +739,7 @@
AIR_CAST(size_t, 3),
AIR_CAST(size_t, (fptsArr[0]->len
+ fptsArr[1]->len - 1)))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate fiber nrrd", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate fiber nrrd", me);
airMopError(mop); return 1;
}
fiber = (double*)(nfiber->data);
@@ -976,7 +976,7 @@
nseed = nrrdNew();
airMopAdd(mop, nseed, AIR_CAST(airMopper, nrrdNuke), airMopAlways);
if (nrrdConvert(nseed, _nseed, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert seed list", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't convert seed list", me);
return 1;
}
seedData = AIR_CAST(const double *, nseed->data);
Modified: teem/trunk/src/ten/fiberMethods.c
===================================================================
--- teem/trunk/src/ten/fiberMethods.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/fiberMethods.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -127,15 +127,15 @@
if ( !(tfx->gtx = gageContextNew())
|| !(tfx->pvl = gagePerVolumeNew(tfx->gtx, vol, kind))
|| (gagePerVolumeAttach(tfx->gtx, tfx->pvl)) ) {
- biffMovef(TEN, GAGE, "%s: gage trouble", me);
+ biffMove_va(TEN, GAGE, "%s: gage trouble", me);
free(tfx); return NULL;
}
-
+
tfx->nin = vol;
tfx->ksp = nrrdKernelSpecNew();
if (nrrdKernelSpecParse(tfx->ksp, tenDefFiberKernel)) {
- biffMovef(TEN, NRRD, "%s: couldn't parse tenDefFiberKernel \"%s\"",
- me, tenDefFiberKernel);
+ biffMove_va(TEN, NRRD, "%s: couldn't parse tenDefFiberKernel \"%s\"",
+ me, tenDefFiberKernel);
return NULL;
}
if (tenFiberKernelSet(tfx, tfx->ksp->kernel, tfx->ksp->parm)) {
@@ -702,10 +702,10 @@
nrrdKernelSpecSet(tfx->ksp, kern, parm);
if (gageKernelSet(tfx->gtx, gageKernel00,
tfx->ksp->kernel, tfx->ksp->parm)) {
- biffMovef(TEN, GAGE, "%s: problem setting kernel", me);
+ biffMove_va(TEN, GAGE, "%s: problem setting kernel", me);
return 1;
}
-
+
return 0;
}
@@ -784,7 +784,7 @@
}
if (gageQuerySet(tfx->gtx, tfx->pvl, tfx->query)
|| gageUpdate(tfx->gtx)) {
- biffMovef(TEN, GAGE, "%s: trouble with gage", me);
+ biffMove_va(TEN, GAGE, "%s: trouble with gage", me);
return 1;
}
if (tfx->useDwi) {
Modified: teem/trunk/src/ten/glyph.c
===================================================================
--- teem/trunk/src/ten/glyph.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/glyph.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -235,7 +235,7 @@
}
if (!npos) {
if (gageShapeSet(shape, nten, tenGageKind->baseDim)) {
- biffMovef(TEN, GAGE, "%s: trouble", me);
+ biffMove_va(TEN, GAGE, "%s: trouble", me);
airMopError(mop); return 1;
}
}
Modified: teem/trunk/src/ten/grads.c
===================================================================
--- teem/trunk/src/ten/grads.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/grads.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -67,7 +67,7 @@
static const char me[]="tenGradientCheck";
if (nrrdCheck(ngrad)) {
- biffMovef(TEN, NRRD, "%s: basic validity check failed", me);
+ biffMove_va(TEN, NRRD, "%s: basic validity check failed", me);
return 1;
}
if (!( 3 == ngrad->axis[0].size && 2 == ngrad->dim )) {
@@ -109,7 +109,7 @@
if (nrrdMaybeAlloc_va(ngrad, nrrdTypeDouble, 2,
AIR_CAST(size_t, 3), AIR_CAST(size_t, num))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
airSrandMT(seed);
@@ -154,7 +154,7 @@
unsigned int gi, num;
if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: trouble converting input to double", me);
+ biffMove_va(TEN, NRRD, "%s: trouble converting input to double", me);
return 1;
}
if (tenGradientCheck(nout, nrrdTypeDouble, 3)) {
@@ -387,10 +387,10 @@
return 1;
}
if (nrrdConvert(nout, nin, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: can't initialize output with input", me);
+ biffMove_va(TEN, NRRD, "%s: can't initialize output with input", me);
return 1;
}
-
+
rstate = airRandMTStateNew(tgparm->seed);
lastLen = 1.0;
do {
@@ -452,10 +452,10 @@
airMopAdd(mop, npos[1], (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(npos[0], nin, nrrdTypeDouble)
|| nrrdConvert(npos[1], nin, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: trouble allocating temp buffers", me);
+ biffMove_va(TEN, NRRD, "%s: trouble allocating temp buffers", me);
airMopError(mop); return 1;
}
-
+
pos = (double*)(npos[0]->data);
for (ii=0; ii<num; ii++) {
ELL_3V_NORM(pos, pos, len);
@@ -596,7 +596,7 @@
} else {
fprintf(stderr, "%s: .......................... (no balancing)\n", me);
if (nrrdConvert(nout, npos[oldIdx], nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't set output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't set output", me);
airMopError(mop); return 1;
}
}
Modified: teem/trunk/src/ten/miscTen.c
===================================================================
--- teem/trunk/src/ten/miscTen.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/miscTen.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -55,7 +55,7 @@
if (nrrdMaybeAlloc_nva(nout, (nrrdTypeDefault == rgbp->typeOut
? nin->type
: rgbp->typeOut), nin->dim, size)) {
- biffMovef(TEN, NRRD, "%s: couldn't alloc output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't alloc output", me);
return 1;
}
odataUC = AIR_CAST(unsigned char *, nout->data);
@@ -99,7 +99,7 @@
}
}
if (nrrdAxisInfoCopy(nout, nin, NULL, (NRRD_AXIS_INFO_SIZE_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis info", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't copy axis info", me);
return 1;
}
nout->axis[0].kind = nrrdKind3Color;
@@ -181,7 +181,7 @@
sz = nin->axis[3].size;
if (nrrdMaybeAlloc_va(nout, nrrdTypeShort, 3,
sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: can't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: can't allocate output", me);
return 1;
}
N = sx*sy*sz;
@@ -200,7 +200,7 @@
ELL_3V_SET(map, 1, 2, 3);
if (nrrdAxisInfoCopy(nout, nin, map, (NRRD_AXIS_INFO_SIZE_BIT
| NRRD_AXIS_INFO_KIND_BIT) )) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
if (nrrdBasicInfoCopy(nout, nin,
@@ -217,7 +217,7 @@
static const char me[]="tenBMatrixCheck";
if (nrrdCheck(nbmat)) {
- biffMovef(TEN, NRRD, "%s: basic validity check failed", me);
+ biffMove_va(TEN, NRRD, "%s: basic validity check failed", me);
return 1;
}
if (!( 6 == nbmat->axis[0].size && 2 == nbmat->dim )) {
@@ -292,7 +292,7 @@
nrrdKernelBCCubicD, dparm, &bins, NULL)
|| nrrdSimpleResample(nhistDD, ntmpB,
nrrdKernelBCCubicDD, dparm, &bins, NULL)) {
- biffMovef(TEN, NRRD, "%s: trouble processing histogram", me);
+ biffMove_va(TEN, NRRD, "%s: trouble processing histogram", me);
airMopError(mop); return 1;
}
if (save) {
Modified: teem/trunk/src/ten/mod.c
===================================================================
--- teem/trunk/src/ten/mod.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/mod.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -68,7 +68,7 @@
}
if (nout != nin) {
if (nrrdCopy(nout, nin)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
}
Modified: teem/trunk/src/ten/path.c
===================================================================
--- teem/trunk/src/ten/path.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/path.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -673,7 +673,7 @@
AIR_CAST(size_t, 7),
AIR_CAST(size_t, 6),
AIR_CAST(size_t, 2*NN + 1))) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
airMopError(mop); return 1;
}
geod = AIR_CAST(double *, ngeod->data);
@@ -707,7 +707,7 @@
if (!E) E |= nrrdResampleRenormalizeSet(rsmc, AIR_TRUE);
if (!E) E |= nrrdResampleExecute(rsmc, ntt);
if (E) {
- biffMovef(TEN, NRRD, "%s: problem upsampling course solution", me);
+ biffMove_va(TEN, NRRD, "%s: problem upsampling course solution", me);
airMopError(mop); return 1;
}
*numIter += subIter;
@@ -806,7 +806,7 @@
if (nrrdMaybeAlloc_va(nout, nrrdTypeDouble, 2,
AIR_CAST(size_t, 7),
AIR_CAST(size_t, num))) {
- biffMovef(TEN, NRRD, "%s: trouble allocating output", me);
+ biffMove_va(TEN, NRRD, "%s: trouble allocating output", me);
airMopError(mop); return 1;
}
out = AIR_CAST(double *, nout->data);
@@ -978,7 +978,7 @@
return 1;
}
if (!nrrdSameSize(nin[0], nin[ninIdx], AIR_TRUE)) {
- biffMovef(TEN, NRRD, "%s: nin[0] doesn't match nin[%u]", me, ninIdx);
+ biffMove_va(TEN, NRRD, "%s: nin[0] doesn't match nin[%u]", me, ninIdx);
return 1;
}
if (nin[0]->type != nin[ninIdx]->type) {
@@ -991,7 +991,7 @@
mop = airMopNew();
if (nrrdCopy(nout, nin[0])) {
- biffMovef(TEN, NRRD, "%s: couldn't initialize output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't initialize output", me);
airMopError(mop); return 1;
}
if (_tip) {
Modified: teem/trunk/src/ten/qglox.c
===================================================================
--- teem/trunk/src/ten/qglox.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/qglox.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -528,7 +528,7 @@
/* compute iterated weighted mean, stored in qOut */
if (ell_q_avgN_d(qOut, &qiter, tip->qIn, tip->qBuff, wght,
NN, tip->convEps, tip->maxIter)) {
- biffMovef(TEN, ELL, "%s: problem doing quaternion mean", me);
+ biffMove_va(TEN, ELL, "%s: problem doing quaternion mean", me);
return 1;
}
/*
Modified: teem/trunk/src/ten/tenDwiGage.c
===================================================================
--- teem/trunk/src/ten/tenDwiGage.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/tenDwiGage.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -748,7 +748,7 @@
int E;
if (tenDwiGageKindCheck(kind)) {
- biffMovef(GAGE, TEN, "%s: kindData not ready for use", me);
+ biffMove_va(GAGE, TEN, "%s: kindData not ready for use", me);
return NULL;
}
kindData = AIR_CAST(tenDwiGageKindData *, kind->data);
@@ -782,7 +782,7 @@
kindData->thresh, kindData->soft);
if (!E) E |= tenEstimateUpdate(tec);
if (E) {
- biffMovef(GAGE, TEN, "%s: trouble setting %u estimation", me, num);
+ biffMove_va(GAGE, TEN, "%s: trouble setting %u estimation", me, num);
return NULL;
}
}
@@ -1092,7 +1092,7 @@
kindData = AIR_CAST(tenDwiGageKindData *, dwiKind->data);
if (nrrdConvert(kindData->ngrad, ngrad, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: trouble converting", me);
+ biffMove_va(TEN, NRRD, "%s: trouble converting", me);
return 1;
}
dwiKind->valLen = kindData->ngrad->axis[1].size;
Modified: teem/trunk/src/ten/tenModel.c
===================================================================
--- teem/trunk/src/ten/tenModel.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/tenModel.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -188,8 +188,8 @@
ntmp = nrrdNew();
airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ntmp, _nparm, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert parm to %s", me,
- airEnumStr(nrrdType, nrrdTypeDouble));
+ biffMove_va(TEN, NRRD, "%s: couldn't convert parm to %s", me,
+ airEnumStr(nrrdType, nrrdTypeDouble));
airMopError(mop); return 1;
}
ndparm = ntmp;
@@ -208,7 +208,7 @@
max[ax] = ndparm->axis[ax].size-1;
}
if (nrrdPad_nva(ntmp, ndparm, min, max, nrrdBoundaryBleed, 0.0)) {
- biffMovef(TEN, NRRD, "%s: couldn't pad", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't pad", me);
airMopError(mop); return 1;
}
ndpparm = ntmp;
@@ -223,8 +223,8 @@
ntmp = nrrdNew();
airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
if (nrrdConvert(ntmp, _nB0, nrrdTypeDouble)) {
- biffMovef(TEN, NRRD, "%s: couldn't convert B0 to %s", me,
- airEnumStr(nrrdType, nrrdTypeDouble));
+ biffMove_va(TEN, NRRD, "%s: couldn't convert B0 to %s", me,
+ airEnumStr(nrrdType, nrrdTypeDouble));
airMopError(mop); return 1;
}
nB0 = ntmp;
@@ -234,7 +234,7 @@
ntmp = nrrdNew();
airMopAdd(mop, ntmp, (airMopper)nrrdNuke, airMopAlways);
if (nrrdSplice(ntmp, ndpparm, nB0, 0, 0)) {
- biffMovef(TEN, NRRD, "%s: couldn't splice in B0", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't splice in B0", me);
airMopError(mop); return 1;
}
nparm = ntmp;
@@ -250,7 +250,7 @@
: AIR_CAST(int, ii));
}
if (nrrdMaybeAlloc_nva(ndwi, typeOut, nparm->dim, szOut)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
airMopError(mop); return 1;
}
if (!(ddwi = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double))))) {
@@ -291,10 +291,10 @@
| (nrrdStateKeyValuePairsPropagate
? 0
: NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
airMopError(mop); return 1;
}
-
+
airMopOkay(mop);
return 0;
}
@@ -413,7 +413,7 @@
: AIR_CAST(int, ii));
}
if (nrrdMaybeAlloc_nva(nparm, typeOut, ndwi->dim, szOut)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
airMopError(mop); return 1;
}
ddwi = AIR_CAST(double *, calloc(espec->imgNum, sizeof(double)));
@@ -470,7 +470,7 @@
| (nrrdStateKeyValuePairsPropagate
? 0
: NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
airMopError(mop); return 1;
}
lablen = (strlen(tenModelPrefixStr)
@@ -565,10 +565,10 @@
: AIR_CAST(int, ii));
}
if (nrrdMaybeAlloc_nva(nparmDst, nparmSrc->type, nparmSrc->dim, szOut)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
airMopError(mop); return 1;
}
-
+
NN = nrrdElementNumber(nparmSrc)/nparmSrc->axis[0].size;
tsize = nrrdTypeSize[nparmSrc->type];
parmSrc = AIR_CAST(char *, nparmSrc->data);
@@ -607,7 +607,7 @@
| (nrrdStateKeyValuePairsPropagate
? 0
: NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't copy axis or basic info", me);
airMopError(mop); return 1;
}
/* HEY: COPY AND PASTE! from above. perhaps make helper functions? */
Modified: teem/trunk/src/ten/tendEstim.c
===================================================================
--- teem/trunk/src/ten/tendEstim.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/tendEstim.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -99,7 +99,8 @@
ndwi[dwiIdx] = nrrdNew();
airMopAdd(mop, ndwi[dwiIdx], (airMopper)nrrdNuke, airMopAlways);
if (nrrdSlice(ndwi[dwiIdx], nin4d, dwiAx, slIdx)) {
- biffMovef(TEN, NRRD, "%s: trouble slicing DWI at index %u", me, slIdx);
+ biffMove_va(TEN, NRRD,
+ "%s: trouble slicing DWI at index %u", me, slIdx);
airMopError(mop); return 1;
}
}
Modified: teem/trunk/src/ten/tendSatin.c
===================================================================
--- teem/trunk/src/ten/tendSatin.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/tendSatin.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -135,10 +135,10 @@
AIR_CAST(size_t, 3), size[0], size[1], size[2]) ||
nrrdMaybeAlloc_va(nevec=nrrdNew(), nrrdTypeFloat, 4,
AIR_CAST(size_t, 9), size[0], size[1], size[2])) {
- biffMovef(TEN, NRRD, "%s: trouble allocating temp nrrds", me);
+ biffMove_va(TEN, NRRD, "%s: trouble allocating temp nrrds", me);
return 1;
}
-
+
conf = (float *)nconf->data;
eval = (float *)neval->data;
evec = (float *)nevec->data;
Modified: teem/trunk/src/ten/tensor.c
===================================================================
--- teem/trunk/src/ten/tensor.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/tensor.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -173,7 +173,7 @@
N = sx*sy*sz;
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 4,
AIR_CAST(size_t, 9), sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
for (I=0; I<=N-1; I++) {
@@ -188,7 +188,7 @@
}
if (nrrdAxisInfoCopy(nout, nin, NULL,
NRRD_AXIS_INFO_SIZE_BIT)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
/* by call above we just copied axis-0 kind, which might be wrong;
@@ -250,7 +250,7 @@
}
if (nrrdMaybeAlloc_va(tseven, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7), sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: trouble allocating output", me);
+ biffMove_va(TEN, NRRD, "%s: trouble allocating output", me);
return 1;
}
seven = (float *)tseven->data;
@@ -265,7 +265,7 @@
}
if (nrrdAxisInfoCopy(tseven, tnine, NULL,
NRRD_AXIS_INFO_SIZE_BIT)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
/* by call above we just copied axis-0 kind, which might be wrong;
@@ -471,7 +471,7 @@
return 1;
}
if (nrrdCheck(nconf) || nrrdCheck(neval) || nrrdCheck(nevec)) {
- biffMovef(TEN, NRRD, "%s: didn't get three valid nrrds", me);
+ biffMove_va(TEN, NRRD, "%s: didn't get three valid nrrds", me);
return 1;
}
if (!( 3 == nconf->dim && nrrdTypeFloat == nconf->type )) {
@@ -525,7 +525,7 @@
/* finally */
if (nrrdMaybeAlloc_va(nout, nrrdTypeFloat, 4,
AIR_CAST(size_t, 7), sx, sy, sz)) {
- biffMovef(TEN, NRRD, "%s: couldn't allocate output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't allocate output", me);
return 1;
}
N = sx*sy*sz;
@@ -542,7 +542,7 @@
}
ELL_4V_SET(map, -1, 0, 1, 2);
if (nrrdAxisInfoCopy(nout, nconf, map, NRRD_AXIS_INFO_SIZE_BIT)) {
- biffMovef(TEN, NRRD, "%s: trouble", me);
+ biffMove_va(TEN, NRRD, "%s: trouble", me);
return 1;
}
nout->axis[0].label = (char *)airFree(nout->axis[0].label);
@@ -558,10 +558,10 @@
| (nrrdStateKeyValuePairsPropagate
? 0
: NRRD_BASIC_INFO_KEYVALUEPAIRS_BIT))) {
- biffMovef(TEN, NRRD, "%s:", me);
+ biffMove_va(TEN, NRRD, "%s:", me);
return 1;
}
-
+
return 0;
}
@@ -607,7 +607,7 @@
if (3 == dim) {
if (nrrdSlice(nslice, nten, axis+1, pos)
|| nrrdAxesInsert(nout, nslice, axis+1)) {
- biffMovef(TEN, NRRD, "%s: trouble making slice", me);
+ biffMove_va(TEN, NRRD, "%s: trouble making slice", me);
airMopError(mop); return 1;
}
} else {
@@ -636,7 +636,7 @@
|| nrrdSlice(ncoeff[2], nslice, 0, ci[2])
|| nrrdSlice(ncoeff[3], nslice, 0, ci[3])
|| nrrdJoin(nout, (const Nrrd **)ncoeff, 4, 0, AIR_TRUE)) {
- biffMovef(TEN, NRRD, "%s: trouble collecting coefficients", me);
+ biffMove_va(TEN, NRRD, "%s: trouble collecting coefficients", me);
airMopError(mop); return 1;
}
}
Modified: teem/trunk/src/ten/test/csim.c
===================================================================
--- teem/trunk/src/ten/test/csim.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/test/csim.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -28,7 +28,7 @@
Nrrd *ntbuff, tenEstimateContext *tec, double *dwibuff, double sigma,
double bvalue, double B0, unsigned int NN, int randrot,
double _tenOrig[7]) {
- char me[]="csimDo", err[BIFF_STRLEN];
+ char me[]="csimDo";
double *tbuff;
unsigned int II, taa, tbb, cc;
@@ -37,9 +37,8 @@
&& 2 == ntbuff->dim
&& 7 == ntbuff->axis[0].size
&& NN == ntbuff->axis[1].size)) {
- sprintf(err, "%s: ntbuff not allocated for 2-by-%u array of %s", me,
- NN, airEnumStr(nrrdType, nrrdTypeDouble));
- biffAdd(TEN, err); return 1;
+ biffAddf(TEN, "%s: ntbuff not allocated for 2-by-%u array of %s", me,
+ NN, airEnumStr(nrrdType, nrrdTypeDouble)); return 1;
}
/* find all tensors from simulated DWIs */
@@ -77,8 +76,7 @@
if (tenEstimate1TensorSimulateSingle_d(tec, dwibuff, sigma,
bvalue, B0, tenOrig)
|| tenEstimate1TensorSingle_d(tec, tbuff, dwibuff)) {
- sprintf(err, "%s: trouble on exp %u/%u", me, II, NN);
- biffAdd(TEN, err); return 1;
+ biffAddf(TEN, "%s: trouble on exp %u/%u", me, II, NN); return 1;
}
if (randrot) {
TEN_T2M(matA, tbuff);
Modified: teem/trunk/src/ten/triple.c
===================================================================
--- teem/trunk/src/ten/triple.c 2009-11-13 22:42:10 UTC (rev 4369)
+++ teem/trunk/src/ten/triple.c 2009-11-13 22:48:33 UTC (rev 4370)
@@ -446,10 +446,10 @@
nrrdAxisInfoGet_nva(nten, nrrdAxisInfoSize, size);
size[0] = 3;
if (nrrdMaybeAlloc_nva(nout, nten->type, nten->dim, size)) {
- biffMovef(TEN, NRRD, "%s: couldn't alloc output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't alloc output", me);
return 1;
}
-
+
NN = nrrdElementNumber(nten)/7;
lup = nrrdDLookup[nten->type];
ins = nrrdDInsert[nten->type];
@@ -465,7 +465,7 @@
}
}
if (nrrdAxisInfoCopy(nout, nten, NULL, (NRRD_AXIS_INFO_SIZE_BIT))) {
- biffMovef(TEN, NRRD, "%s: couldn't copy axis info", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't copy axis info", me);
return 1;
}
nout->axis[0].kind = nrrdKindUnknown;
@@ -507,7 +507,7 @@
}
if (nrrdCopy(nout, nin)) {
- biffMovef(TEN, NRRD, "%s: couldn't initialize output", me);
+ biffMove_va(TEN, NRRD, "%s: couldn't initialize output", me);
return 1;
}
lup = nrrdDLookup[nin->type];
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-11-18 21:18:43
|
Revision: 4399
http://teem.svn.sourceforge.net/teem/?rev=4399&view=rev
Author: kindlmann
Date: 2009-11-18 21:18:36 +0000 (Wed, 18 Nov 2009)
Log Message:
-----------
added tenEigenvalueMultiply tend evalmult
Modified Paths:
--------------
teem/trunk/src/ten/GNUmakefile
teem/trunk/src/ten/mod.c
teem/trunk/src/ten/sources.cmake
teem/trunk/src/ten/ten.h
Modified: teem/trunk/src/ten/GNUmakefile
===================================================================
--- teem/trunk/src/ten/GNUmakefile 2009-11-18 18:02:00 UTC (rev 4398)
+++ teem/trunk/src/ten/GNUmakefile 2009-11-18 21:18:36 UTC (rev 4399)
@@ -61,7 +61,8 @@
tendFiber.o tendEpireg.o tendBmat.o tendEstim.o tendSim.o \
tendMsim.o tendMfit.o tendMconv.o \
tendSlice.o tendEllipse.o tendEvecrgb.o tendNorm.o tendAnscale.o \
- tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendHelix.o tendBfit.o \
+ tendEvalpow.o tendEvalclamp.o tendEvaladd.o tendEvalmult.o \
+ tendHelix.o tendBfit.o \
tendUnmf.o tendLog.o tendExp.o
$(L).TESTS = test/roistat test/tg test/tt test/tem test/rotedge \
test/tsoid test/odf-hist test/to test/tensorDotDat \
Modified: teem/trunk/src/ten/mod.c
===================================================================
--- teem/trunk/src/ten/mod.c 2009-11-18 18:02:00 UTC (rev 4398)
+++ teem/trunk/src/ten/mod.c 2009-11-18 21:18:36 UTC (rev 4399)
@@ -41,6 +41,7 @@
funcEigenvalueClamp,
funcEigenvaluePower,
funcEigenvalueAdd,
+ funcEigenvalueMultiply,
funcLog,
funcExp,
funcLast
@@ -190,6 +191,19 @@
tout += 7;
}
break;
+ case funcEigenvalueMultiply:
+ for (II=0; II<=NN-1; II++) {
+ /* HEY: this doesn't require eigensolve */
+ tenEigensolve_f(eval, evec, tin);
+ ELL_3V_SET_TT(eval, float,
+ eval[0]*parm->val,
+ eval[1]*parm->val,
+ eval[2]*parm->val);
+ tenMakeSingle_f(tout, tin[0], eval, evec);
+ tin += 7;
+ tout += 7;
+ }
+ break;
case funcLog:
for (II=0; II<=NN-1; II++) {
tenEigensolve_f(eval, evec, tin);
@@ -327,6 +341,24 @@
}
/*
+******** tenEigenvalueMultiply
+**
+** multiplies eigenvalues by something
+*/
+int
+tenEigenvalueMultiply(Nrrd *nout, const Nrrd *nin, double val) {
+ static const char me[]="tenEigenvalueMultiply";
+ funcParm parm;
+
+ parm.val = val;
+ if (theFunc(nout, nin, funcEigenvalueMultiply, &parm)) {
+ biffAddf(TEN, "%s: trouble", me);
+ return 1;
+ }
+ return 0;
+}
+
+/*
******** tenLog
**
** takes the logarithm (by taking the log of the eigenvalues)
Modified: teem/trunk/src/ten/sources.cmake
===================================================================
--- teem/trunk/src/ten/sources.cmake 2009-11-18 18:02:00 UTC (rev 4398)
+++ teem/trunk/src/ten/sources.cmake 2009-11-18 21:18:36 UTC (rev 4399)
@@ -36,6 +36,7 @@
tendEstim.c
tendEval.c
tendEvaladd.c
+ tendEvalmult.c
tendEvalclamp.c
tendEvalpow.c
tendEvec.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-11-18 18:02:00 UTC (rev 4398)
+++ teem/trunk/src/ten/ten.h 2009-11-18 21:18:36 UTC (rev 4399)
@@ -1635,6 +1635,7 @@
TEN_EXPORT int tenEigenvalueClamp(Nrrd *nout, const Nrrd *nin,
double min, double max);
TEN_EXPORT int tenEigenvalueAdd(Nrrd *nout, const Nrrd *nin, double val);
+TEN_EXPORT int tenEigenvalueMultiply(Nrrd *nout, const Nrrd *nin, double val);
TEN_EXPORT int tenLog(Nrrd *nout, const Nrrd *nin);
TEN_EXPORT int tenExp(Nrrd *nout, const Nrrd *nin);
@@ -1705,6 +1706,7 @@
F(evalpow) \
F(evalclamp) \
F(evaladd) \
+F(evalmult) \
F(log) \
F(exp) \
F(evec) \
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2009-12-12 11:23:44
|
Revision: 4453
http://teem.svn.sourceforge.net/teem/?rev=4453&view=rev
Author: kindlmann
Date: 2009-12-12 11:23:36 +0000 (Sat, 12 Dec 2009)
Log Message:
-----------
API NEW: added tenRotateSingle_f for rotating a single tensor
Modified Paths:
--------------
teem/trunk/src/ten/ten.h
teem/trunk/src/ten/tensor.c
Modified: teem/trunk/src/ten/ten.h
===================================================================
--- teem/trunk/src/ten/ten.h 2009-12-12 11:22:19 UTC (rev 4452)
+++ teem/trunk/src/ten/ten.h 2009-12-12 11:23:36 UTC (rev 4453)
@@ -1296,6 +1296,8 @@
/* tensor.c */
TEN_EXPORT int tenVerbose;
+TEN_EXPORT void tenRotateSingle_f(float tenOut[7],
+ const float rot[9], const float tenIn[7]);
TEN_EXPORT int tenTensorCheck(const Nrrd *nin,
int wantType, int want4D, int useBiff);
TEN_EXPORT int tenMeasurementFrameReduce(Nrrd *nout, const Nrrd *nin);
Modified: teem/trunk/src/ten/tensor.c
===================================================================
--- teem/trunk/src/ten/tensor.c 2009-12-12 11:22:19 UTC (rev 4452)
+++ teem/trunk/src/ten/tensor.c 2009-12-12 11:23:36 UTC (rev 4453)
@@ -26,6 +26,19 @@
int tenVerbose = 0;
+void
+tenRotateSingle_f(float tenOut[7], const float rot[9], const float tenIn[7]) {
+ float rotT[9], matIn[9], tmp[9], matOut[9];
+
+ ELL_3M_TRANSPOSE(rotT, rot);
+ TEN_T2M(matIn, tenIn);
+ ELL_3M_MUL(tmp, matIn, rotT);
+ ELL_3M_MUL(matOut, rot, tmp);
+ TEN_M2T(tenOut, matOut);
+ tenOut[0] = tenIn[0];
+ return;
+}
+
/*
******** tenTensorCheck()
**
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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