Menu
▾
▴
[Teem-commit] SF.net SVN: teem:[5912] teem/trunk/src
|
From: <kin...@us...> - 2013-06-20 04:01:08
|
Revision: 5912
http://sourceforge.net/p/teem/code/5912
Author: kindlmann
Date: 2013-06-20 04:01:05 +0000 (Thu, 20 Jun 2013)
Log Message:
-----------
adding pullFlagZeroZ, pullFlag.zeroZ, and puller -zz
Modified Paths:
--------------
teem/trunk/src/bin/puller.c
teem/trunk/src/pull/actionPull.c
teem/trunk/src/pull/parmPull.c
teem/trunk/src/pull/pointPull.c
teem/trunk/src/pull/popcntl.c
teem/trunk/src/pull/pull.h
Modified: teem/trunk/src/bin/puller.c
===================================================================
--- teem/trunk/src/bin/puller.c 2013-06-20 03:56:30 UTC (rev 5911)
+++ teem/trunk/src/bin/puller.c 2013-06-20 04:01:05 UTC (rev 5912)
@@ -712,7 +712,7 @@
int energyFromStrength, nixAtVolumeEdgeSpace, constraintBeforeSeedThresh,
binSingle, liveThresholdOnInit, permuteOnRebin, noPopCntlWithZeroAlpha,
useBetaForGammaLearn, restrictiveAddToBins, noAdd, unequalShapesAllow,
- popCntlEnoughTest;
+ popCntlEnoughTest, zeroZ;
int verbose;
int interType, allowCodimension3Constraints, scaleIsTau, useHalton,
pointPerVoxel;
@@ -830,6 +830,8 @@
"butter:16,0.8", "windowing to create locality with additive "
"scale-space interaction (\"-int add\")",
NULL, NULL, pullHestEnergySpec);
+ hestOptAdd(&hopt, "zz", "bool", airTypeBool, 1, 1, &zeroZ, "false",
+ "always constrain Z=0, to process 2D images");
hestOptAdd(&hopt, "efs", "bool", airTypeBool, 1, 1,
&energyFromStrength, "false",
"whether or not strength contributes to particle-image energy");
@@ -1076,6 +1078,7 @@
pctx = pullContextNew();
airMopAdd(mop, pctx, (airMopper)pullContextNix, airMopAlways);
if (pullVerboseSet(pctx, verbose)
+ || pullFlagSet(pctx, pullFlagZeroZ, zeroZ)
|| pullFlagSet(pctx, pullFlagEnergyFromStrength, energyFromStrength)
|| pullFlagSet(pctx, pullFlagNixAtVolumeEdgeSpace, nixAtVolumeEdgeSpace)
|| pullFlagSet(pctx, pullFlagConstraintBeforeSeedThresh,
Modified: teem/trunk/src/pull/actionPull.c
===================================================================
--- teem/trunk/src/pull/actionPull.c 2013-06-20 03:56:30 UTC (rev 5911)
+++ teem/trunk/src/pull/actionPull.c 2013-06-20 04:01:05 UTC (rev 5912)
@@ -1102,6 +1102,9 @@
biffAddf(PULL, "%s: trouble", me);
return 1;
}
+ if (task->pctx->flag.zeroZ) {
+ point->pos[2] = 0;
+ }
return 0;
}
@@ -1121,7 +1124,8 @@
if (task->pctx->pointNum > _PULL_PROGRESS_POINT_NUM_MIN
&& !task->pctx->flag.binSingle
&& task->pctx->progressBinMod
- && 0 == myBinIdx % task->pctx->progressBinMod) {
+ && 0 == myBinIdx % task->pctx->progressBinMod
+ && task->pctx->verbose) {
printf("."); fflush(stdout);
}
point = myBin->point[myPointIdx];
Modified: teem/trunk/src/pull/parmPull.c
===================================================================
--- teem/trunk/src/pull/parmPull.c 2013-06-20 03:56:30 UTC (rev 5911)
+++ teem/trunk/src/pull/parmPull.c 2013-06-20 04:01:05 UTC (rev 5912)
@@ -83,6 +83,7 @@
flag->allowCodimension3Constraints = AIR_FALSE;
flag->scaleIsTau = AIR_FALSE;
flag->startSkipsPoints = AIR_FALSE; /* must be false by default */
+ flag->zeroZ = AIR_FALSE;
return;
}
@@ -325,6 +326,9 @@
case pullFlagStartSkipsPoints:
pctx->flag.startSkipsPoints = flag;
break;
+ case pullFlagZeroZ:
+ pctx->flag.zeroZ = flag;
+ break;
default:
biffAddf(me, "%s: sorry, flag %d valid but not handled?", me, which);
return 1;
Modified: teem/trunk/src/pull/pointPull.c
===================================================================
--- teem/trunk/src/pull/pointPull.c 2013-06-20 03:56:30 UTC (rev 5911)
+++ teem/trunk/src/pull/pointPull.c 2013-06-20 04:01:05 UTC (rev 5912)
@@ -690,6 +690,9 @@
iPos[k] = vidx[k] + pctx->initParm.jitter*(airDrandMT_r(rng)-0.5);
}
gageShapeItoW(seedShape, point->pos, iPos);
+ if (pctx->flag.zeroZ) {
+ point->pos[2] = 0.0;
+ }
if (0 && _pullVerbose) {
printf("!%s: pointIdx %u -> vidx %u %u %u (%u)\n"
@@ -873,6 +876,9 @@
}
}
_pullUnitToWorld(pctx, scaleVol, point->pos, rpos);
+ if (pctx->flag.zeroZ) {
+ point->pos[2] = 0.0;
+ }
/*
verbo = (AIR_ABS(-0.246015 - point->pos[0]) < 0.1 &&
AIR_ABS(-144.78 - point->pos[0]) < 0.1 &&
@@ -976,6 +982,9 @@
/* Copy nrrd point into pullPoint */
ELL_4V_COPY(point->pos, posData + 4*pointIdx);
+ if (pctx->flag.zeroZ) {
+ point->pos[2] = 0.0;
+ }
/*
if (AIR_ABS(247.828 - point->pos[0]) < 0.1 &&
Modified: teem/trunk/src/pull/popcntl.c
===================================================================
--- teem/trunk/src/pull/popcntl.c 2013-06-20 03:56:30 UTC (rev 5911)
+++ teem/trunk/src/pull/popcntl.c 2013-06-20 04:01:05 UTC (rev 5912)
@@ -70,12 +70,17 @@
if (point->neighPointNum && task->pctx->targetDim
&& task->pctx->flag.popCntlEnoughTest) {
- unsigned int plenty;
- plenty = (1 == task->pctx->targetDim
+ unsigned int plenty, tardim;
+ tardim = task->pctx->targetDim;
+ if (task->pctx->flag.zeroZ && tardim > 1) {
+ /* GLK unsure of tardim == 1 logic here */
+ tardim -= 1;
+ }
+ plenty = (1 == tardim
? 3
- : (2 == task->pctx->targetDim
+ : (2 == tardim
? 7
- : (3 == task->pctx->targetDim
+ : (3 == tardim
? 13 /* = 1 + 12
= 1 + coordination number of 3D sphere packing */
: 0 /* shouldn't get here */)));
@@ -126,6 +131,9 @@
/* we had no neighbors, have to pretend like we did */
airNormalRand_r(noffavg + 0, noffavg + 1, task->rng);
airNormalRand_r(noffavg + 2, noffavg + 3, task->rng);
+ if (!task->pctx->flag.zeroZ) {
+ noffavg[2] = 0;
+ }
if (!task->pctx->haveScale) {
noffavg[3] = 0;
}
Modified: teem/trunk/src/pull/pull.h
===================================================================
--- teem/trunk/src/pull/pull.h 2013-06-20 03:56:30 UTC (rev 5911)
+++ teem/trunk/src/pull/pull.h 2013-06-20 04:01:05 UTC (rev 5912)
@@ -802,6 +802,10 @@
/* pullStart should skip initializing the points */
pullFlagStartSkipsPoints,
+ /* constrain the third world-space coordinate ("z") to be zero, at all
+ times, so that pull can be used to process 2D images */
+ pullFlagZeroZ,
+
pullFlagLast
};
@@ -818,7 +822,8 @@
binSingle,
allowCodimension3Constraints,
scaleIsTau,
- startSkipsPoints;
+ startSkipsPoints,
+ zeroZ;
} pullFlag;
/*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|