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From: <kin...@us...> - 2023-07-15 14:27:22
|
Revision: 7111
http://sourceforge.net/p/teem/code/7111
Author: kindlmann
Date: 2023-07-15 14:27:19 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
fixing one oversight in hest usage update
Modified Paths:
--------------
teem/trunk/src/ten/tendGlyph.c
Modified: teem/trunk/src/ten/tendGlyph.c
===================================================================
--- teem/trunk/src/ten/tendGlyph.c 2023-07-15 14:24:54 UTC (rev 7110)
+++ teem/trunk/src/ten/tendGlyph.c 2023-07-15 14:27:19 UTC (rev 7111)
@@ -189,8 +189,8 @@
"for superquadric glyphs, how much to sharp edges form as a "
"function of differences between eigenvalues. Higher values "
"mean that edges form more easily");
- hestOptAdd(&hopt, "gsc", "scale", airTypeFloat, 1, 1, &(gparm->glyphScale), "0.01",
- "over-all glyph size in world-space");
+ hestOptAdd_1_Float(&hopt, "gsc", "scale", &(gparm->glyphScale), "0.01",
+ "over-all glyph size in world-space");
/* how glyphs will be colored */
hestOptAdd_1_Int(&hopt, "c", "evector #", &(gparm->colEvec), "0",
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-15 14:24:57
|
Revision: 7110
http://sourceforge.net/p/teem/code/7110
Author: kindlmann
Date: 2023-07-15 14:24:54 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
restoring block and unblock commands, but they are hidden
Modified Paths:
--------------
teem/trunk/src/unrrdu/CMakeLists.txt
teem/trunk/src/unrrdu/GNUmakefile
teem/trunk/src/unrrdu/block.c
teem/trunk/src/unrrdu/privateUnrrdu.h
teem/trunk/src/unrrdu/unblock.c
Modified: teem/trunk/src/unrrdu/CMakeLists.txt
===================================================================
--- teem/trunk/src/unrrdu/CMakeLists.txt 2023-07-15 14:15:33 UTC (rev 7109)
+++ teem/trunk/src/unrrdu/CMakeLists.txt 2023-07-15 14:24:54 UTC (rev 7110)
@@ -15,6 +15,7 @@
axinsert.c
axmerge.c
axsplit.c
+ block.c
ccadj.c
ccfind.c
ccmerge.c
@@ -77,10 +78,8 @@
unquantize.c
unrrdu.h
untile.c
- )
-# no longer used:
-# block.c
-# unblock.c
+ unblock.c
+)
target_sources(teem PRIVATE ${UNRRDU_SOURCES})
# This will group all the source files in the VS project by directory
Modified: teem/trunk/src/unrrdu/GNUmakefile
===================================================================
--- teem/trunk/src/unrrdu/GNUmakefile 2023-07-15 14:15:33 UTC (rev 7109)
+++ teem/trunk/src/unrrdu/GNUmakefile 2023-07-15 14:24:54 UTC (rev 7110)
@@ -61,8 +61,7 @@
ccsettle.o about.o axsplit.o axmerge.o mlut.o mrmap.o tile.o untile.o \
unorient.o env.o dist.o affine.o i2w.o w2i.o fft.o acrop.o dering.o \
diff.o cksum.o dnorm.o vidicon.o undos.o uncmt.o basinfo.o grid.o ilk.o \
- ninspect.o hack.o aabplot.o
-# no longer used: block.o unblock.o
+ ninspect.o hack.o aabplot.o block.o unblock.o
####
####
####
Modified: teem/trunk/src/unrrdu/block.c
===================================================================
--- teem/trunk/src/unrrdu/block.c 2023-07-15 14:15:33 UTC (rev 7109)
+++ teem/trunk/src/unrrdu/block.c 2023-07-15 14:24:54 UTC (rev 7110)
@@ -69,4 +69,4 @@
return 0;
}
-UNRRDU_CMD(block, INFO);
+UNRRDU_CMD_HIDE(block, INFO);
Modified: teem/trunk/src/unrrdu/privateUnrrdu.h
===================================================================
--- teem/trunk/src/unrrdu/privateUnrrdu.h 2023-07-15 14:15:33 UTC (rev 7109)
+++ teem/trunk/src/unrrdu/privateUnrrdu.h 2023-07-15 14:24:54 UTC (rev 7110)
@@ -107,6 +107,8 @@
F(flip) \
F(unorient) \
F(basinfo) \
+ F(block) \
+ F(unblock) \
F(axinfo) \
F(axinsert) \
F(axsplit) \
@@ -145,10 +147,6 @@
F(undos) \
F(uncmt) \
F(save)
-/* these two have been removed since no one uses them
-F(block) \
-F(unblock) \
-*/
/* xxx.c */
/* Declare the extern unrrduCmds unrrdu_xxxCmd, for all xxx. These are
Modified: teem/trunk/src/unrrdu/unblock.c
===================================================================
--- teem/trunk/src/unrrdu/unblock.c 2023-07-15 14:15:33 UTC (rev 7109)
+++ teem/trunk/src/unrrdu/unblock.c 2023-07-15 14:24:54 UTC (rev 7110)
@@ -68,4 +68,4 @@
return 0;
}
-UNRRDU_CMD(unblock, INFO);
+UNRRDU_CMD_HIDE(unblock, INFO);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-15 14:15:35
|
Revision: 7109
http://sourceforge.net/p/teem/code/7109
Author: kindlmann
Date: 2023-07-15 14:15:33 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
updating hest usage
Modified Paths:
--------------
teem/trunk/src/bane/gkmsHvol.c
teem/trunk/src/bane/gkmsInfo.c
teem/trunk/src/bane/gkmsMite.c
teem/trunk/src/bane/gkmsOpac.c
teem/trunk/src/bane/gkmsPvg.c
teem/trunk/src/bane/gkmsScat.c
teem/trunk/src/bane/gkmsTxf.c
teem/trunk/src/bane/privateBane.h
Modified: teem/trunk/src/bane/gkmsHvol.c
===================================================================
--- teem/trunk/src/bane/gkmsHvol.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsHvol.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -41,51 +41,49 @@
NrrdIoState *nio;
NrrdKernelSpec *ksp00, *ksp11, *ksp22;
- hestOptAdd(&opt, "s", "incV incG incH", airTypeOther, 3, 3, inc,
- "f:1.0 p:0.005 p:0.015",
- "Strategies for determining how much of the range "
- "of a quantity should be included and quantized in its axis "
- "of the histogram volume. Possibilities include:\n "
- "\b\bo \"f:<F>\": included range is some fraction of the "
- "total range, as scaled by F\n "
- "\b\bo \"p:<P>\": exclude the extremal P percent of "
- "the values\n "
- "\b\bo \"s:<S>\": included range is S times the standard "
- "deviation of the values\n "
- "\b\bo \"a:<min>,<max>\": range is from <min> to <max>",
- NULL, NULL, baneGkmsHestIncStrategy);
- hestOptAdd(&opt, "d", "dimV dimG dimH", airTypeInt, 3, 3, dim, "256 256 256",
- "Dimensions of histogram volume; number of samples along "
- "each axis");
- hestOptAdd(&opt, "k00", "kernel", airTypeOther, 1, 1, &ksp00, "tent",
- "value reconstruction kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&opt, "k11", "kernel", airTypeOther, 1, 1, &ksp11, "cubicd:1,0",
- "first derivative kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&opt, "k22", "kernel", airTypeOther, 1, 1, &ksp22, "cubicdd:1,0",
- "second derivative kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&opt, "l", NULL, airTypeInt, 0, 0, &lapl, NULL,
- "Use Laplacian instead of Hessian to approximate second "
- "directional derivative. No faster, less accurate.");
- hestOptAdd(&opt, "slow", NULL, airTypeInt, 0, 0, &slow, NULL,
- "Instead of allocating a floating point VGH volume and measuring "
- "V,G,H once, measure V,G,H multiple times on separate passes "
- "(slower, but needs less memory)");
+ hestOptAdd_3_Other(&opt, "s", "incV incG incH", inc, "f:1.0 p:0.005 p:0.015",
+ "Strategies for determining how much of the range "
+ "of a quantity should be included and quantized in its axis "
+ "of the histogram volume. Possibilities include:\n "
+ "\b\bo \"f:<F>\": included range is some fraction of the "
+ "total range, as scaled by F\n "
+ "\b\bo \"p:<P>\": exclude the extremal P percent of "
+ "the values\n "
+ "\b\bo \"s:<S>\": included range is S times the standard "
+ "deviation of the values\n "
+ "\b\bo \"a:<min>,<max>\": range is from <min> to <max>",
+ baneGkmsHestIncStrategy);
+ hestOptAdd_3_Int(&opt, "d", "dimV dimG dimH", dim, "256 256 256",
+ "Dimensions of histogram volume; number of samples along "
+ "each axis");
+ hestOptAdd_1_Other(&opt, "k00", "kernel", &ksp00, "tent",
+ "value reconstruction kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&opt, "k11", "kernel", &ksp11, "cubicd:1,0",
+ "first derivative kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&opt, "k22", "kernel", &ksp22, "cubicdd:1,0",
+ "second derivative kernel", nrrdHestKernelSpec);
+ hestOptAdd_Flag(&opt, "l", &lapl,
+ "Use Laplacian instead of Hessian to approximate second "
+ "directional derivative. No faster, less accurate.");
+ hestOptAdd_Flag(&opt, "slow", &slow,
+ "Instead of allocating a floating point VGH volume and measuring "
+ "V,G,H once, measure V,G,H multiple times on separate passes "
+ "(slower, but needs less memory)");
if (nrrdEncodingGzip->available()) {
- hestOptAdd(&opt, "gz", NULL, airTypeInt, 0, 0, &gz, NULL,
- "Use gzip compression for output histo-volume; "
- "much less disk space, slightly slower to read/write");
+ hestOptAdd_Flag(&opt, "gz", &gz,
+ "Use gzip compression for output histo-volume; "
+ "much less disk space, slightly slower to read/write");
}
- hestOptAdd(&opt, "i", "volumeIn", airTypeOther, 1, 1, &nin, NULL,
- "input scalar volume for which a transfer function is needed", NULL, NULL,
- nrrdHestNrrd);
- hestOptAdd(&opt, "o", "hvolOut", airTypeString, 1, 1, &out, NULL,
- "output histogram volume, used by \"gkms scat\" and "
- "\"gkms info\"");
+ hestOptAdd_1_Other(&opt, "i", "volumeIn", &nin, NULL,
+ "input scalar volume for which a transfer function is needed",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&opt, "o", "hvolOut", &out, NULL,
+ "output histogram volume, used by \"gkms scat\" and "
+ "\"gkms info\"");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_hvolInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_hvolInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
Modified: teem/trunk/src/bane/gkmsInfo.c
===================================================================
--- teem/trunk/src/bane/gkmsInfo.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsInfo.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -35,25 +35,24 @@
airArray *mop;
int pret, one, measr;
- hestOptAdd(&opt, "m", "measr", airTypeEnum, 1, 1, &measr, "mean",
- "How to project along the 2nd derivative axis. Possibilities "
- "include:\n "
- "\b\bo \"mean\": average value\n "
- "\b\bo \"median\": value at 50th percentile\n "
- "\b\bo \"mode\": most common value\n "
- "\b\bo \"min\", \"max\": probably not useful",
- NULL, baneGkmsMeasr);
- hestOptAdd(&opt, "one", NULL, airTypeInt, 0, 0, &one, NULL,
- "Create 1-dimensional info file; default is 2-dimensional");
- hestOptAdd(&opt, "i", "hvolIn", airTypeOther, 1, 1, &hvol, NULL,
- "input histogram volume (from \"gkms hvol\")", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "o", "infoOut", airTypeString, 1, 1, &outS, NULL,
- "output info file, used by \"gkms pvg\" and \"gkms opac\"");
+ hestOptAdd_1_Enum(&opt, "m", "measr", &measr, "mean",
+ "How to project along the 2nd derivative axis. Possibilities "
+ "include:\n "
+ "\b\bo \"mean\": average value\n "
+ "\b\bo \"median\": value at 50th percentile\n "
+ "\b\bo \"mode\": most common value\n "
+ "\b\bo \"min\", \"max\": probably not useful",
+ baneGkmsMeasr);
+ hestOptAdd_Flag(&opt, "one", &one,
+ "Create 1-dimensional info file; default is 2-dimensional");
+ hestOptAdd_1_Other(&opt, "i", "hvolIn", &hvol, NULL,
+ "input histogram volume (from \"gkms hvol\")", nrrdHestNrrd);
+ hestOptAdd_1_String(&opt, "o", "infoOut", &outS, NULL,
+ "output info file, used by \"gkms pvg\" and \"gkms opac\"");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_infoInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_infoInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
Modified: teem/trunk/src/bane/gkmsMite.c
===================================================================
--- teem/trunk/src/bane/gkmsMite.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsMite.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -36,17 +36,16 @@
airArray *mop;
int pret, E;
- hestOptAdd(&opt, "i", "opacIn", airTypeOther, 1, 1, &nin, NULL,
- "input opacity function (1 or 2 dimensional), from "
- "\"gkms opac\"",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "o", "opacOut", airTypeString, 1, 1, &out, NULL,
- "output opacity function filename");
+ hestOptAdd_1_Other(&opt, "i", "opacIn", &nin, NULL,
+ "input opacity function (1 or 2 dimensional), from "
+ "\"gkms opac\"",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&opt, "o", "opacOut", &out, NULL,
+ "output opacity function filename");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_miteInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_miteInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
if (1 == nin->axis[0].size && nin->axis[0].label && !strcmp("A", nin->axis[0].label)) {
Modified: teem/trunk/src/bane/gkmsOpac.c
===================================================================
--- teem/trunk/src/bane/gkmsOpac.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsOpac.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -36,48 +36,47 @@
int pret, radius, idim;
float sigma, gthrInfo[2], gthresh;
- hestOptAdd(&opt, "b", "bef", airTypeOther, 1, 1, &nbef, "1,1,0,1",
- "boundary emphasis function mapping from \"position\" to "
- "opacity. Can be either:\n "
- "\b\bo filename of nrrd suitable for \"unu imap\", or:\n "
- "\b\bo comma-separated list of four floats, with no spaces: "
- "\"s,w,c,a\", where\n "
- "s = shape of function, between 0.0 for box and "
- "1.0 for tent\n "
- "w = full-width half-max of function support\n "
- "c = where to center function support\n "
- "a = maximum opacity\n "
- "If all goes well, the units for \"w\" and \"c\" are voxels.",
- NULL, NULL, baneGkmsHestBEF);
- hestOptAdd(&opt, "s", "sigma", airTypeFloat, 1, 1, &sigma, "nan",
- "scaling in position calculation, accounts for thickness "
- "of transition region between materials. Lower sigmas lead to "
- "wider peaks in opacity function. "
- "Calculated automatically by default.");
- hestOptAdd(&opt, "g", "gthresh", airTypeOther, 1, 1, gthrInfo, "x0.04",
- "minimum significant gradient magnitude. Can be given "
- "in two different ways:\n "
- "\b\bo \"<float>\": specify gthresh as <float> exactly.\n "
- "\b\bo \"x<float>\": gthresh is a scaling, by <float>, of "
- "the maximum gradient magnitude in the info file.",
- NULL, NULL, baneGkmsHestGthresh);
- hestOptAdd(&opt, "r", "radius", airTypeInt, 1, 1, &radius, "0",
- "radius of median filtering to apply to opacity function, "
- "use \"0\" to signify no median filtering");
- hestOptAdd(&opt, "m", "befOut", airTypeString, 1, 1, &befS, "",
- "if boundary emphasis function given via \"-b\" "
- "is in the \"s,w,c,a\" form, then save out the "
- "corresponding nrrd to <befOut>, suitable for use in this "
- "command or \"unu imap\"");
- hestOptAdd(&opt, "i", "infoIn", airTypeOther, 1, 1, &ninfo, NULL,
- "input info file (from \"gkms info\")", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "o", "opacOut", airTypeString, 1, 1, &outS, NULL,
- "output 1D or 2D opacity function");
+ hestOptAdd_1_Other(&opt, "b", "bef", &nbef, "1,1,0,1",
+ "boundary emphasis function mapping from \"position\" to "
+ "opacity. Can be either:\n "
+ "\b\bo filename of nrrd suitable for \"unu imap\", or:\n "
+ "\b\bo comma-separated list of four floats, with no spaces: "
+ "\"s,w,c,a\", where\n "
+ "s = shape of function, between 0.0 for box and "
+ "1.0 for tent\n "
+ "w = full-width half-max of function support\n "
+ "c = where to center function support\n "
+ "a = maximum opacity\n "
+ "If all goes well, the units for \"w\" and \"c\" are voxels.",
+ baneGkmsHestBEF);
+ hestOptAdd_1_Float(&opt, "s", "sigma", &sigma, "nan",
+ "scaling in position calculation, accounts for thickness "
+ "of transition region between materials. Lower sigmas lead to "
+ "wider peaks in opacity function. "
+ "Calculated automatically by default.");
+ hestOptAdd_1_Other(&opt, "g", "gthresh", gthrInfo, "x0.04",
+ "minimum significant gradient magnitude. Can be given "
+ "in two different ways:\n "
+ "\b\bo \"<float>\": specify gthresh as <float> exactly.\n "
+ "\b\bo \"x<float>\": gthresh is a scaling, by <float>, of "
+ "the maximum gradient magnitude in the info file.",
+ baneGkmsHestGthresh);
+ hestOptAdd_1_Int(&opt, "r", "radius", &radius, "0",
+ "radius of median filtering to apply to opacity function, "
+ "use \"0\" to signify no median filtering");
+ hestOptAdd_1_String(&opt, "m", "befOut", &befS, "",
+ "if boundary emphasis function given via \"-b\" "
+ "is in the \"s,w,c,a\" form, then save out the "
+ "corresponding nrrd to <befOut>, suitable for use in this "
+ "command or \"unu imap\"");
+ hestOptAdd_1_Other(&opt, "i", "infoIn", &ninfo, NULL,
+ "input info file (from \"gkms info\")", nrrdHestNrrd);
+ hestOptAdd_1_String(&opt, "o", "opacOut", &outS, NULL,
+ "output 1D or 2D opacity function");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_opacInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_opacInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
airMopAdd(mop, nmax = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, npos = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
Modified: teem/trunk/src/bane/gkmsPvg.c
===================================================================
--- teem/trunk/src/bane/gkmsPvg.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsPvg.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -99,20 +99,17 @@
float *pos, p, min, max, sml, newsml, newmin, newmax;
NrrdRange *range;
- hestOptAdd(&opt, "inv", NULL, airTypeInt, 0, 0, &invert, NULL,
- "Draw on white background, instead of black");
- hestOptAdd(&opt, "m", "mapOut", airTypeString, 1, 1, &mapS, "",
- "save out the colormap used here, so that it can be applied "
- "to other nrrds with \"unu imap -r\"");
- hestOptAdd(&opt, "i", "infoIn", airTypeOther, 1, 1, &ninfo, NULL,
- "input info file (from \"gkms info\")", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "o", "imageOut", airTypeString, 1, 1, &outS, NULL,
- "output image, in PPM format");
+ hestOptAdd_Flag(&opt, "inv", &invert, "Draw on white background, instead of black");
+ hestOptAdd_1_String(&opt, "m", "mapOut", &mapS, "",
+ "save out the colormap used here, so that it can be applied "
+ "to other nrrds with \"unu imap -r\"");
+ hestOptAdd_1_Other(&opt, "i", "infoIn", &ninfo, NULL,
+ "input info file (from \"gkms info\")", nrrdHestNrrd);
+ hestOptAdd_1_String(&opt, "o", "imageOut", &outS, NULL, "output image, in PPM format");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_pvgInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_pvgInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
airMopAdd(mop, ndon = _baneGkmsDonNew(invert), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nposA = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
Modified: teem/trunk/src/bane/gkmsScat.c
===================================================================
--- teem/trunk/src/bane/gkmsScat.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsScat.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -38,21 +38,20 @@
int pret, E;
double _gamma;
- hestOptAdd(&opt, "g", "gamma", airTypeDouble, 1, 1, &_gamma, "1.0",
- "gamma used to brighten/darken scatterplots. "
- "gamma > 1.0 brightens; gamma < 1.0 darkens. "
- "Negative gammas invert values (like in xv). ");
- hestOptAdd(&opt, "i", "hvolIn", airTypeOther, 1, 1, &hvol, NULL,
- "input histogram volume (from \"gkms hvol\")", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "o", "vgOut vhOut", airTypeString, 2, 2, out, NULL,
- "Filenames to use for two output scatterplots, (gradient "
- "magnitude versus value, and 2nd derivative versus value); "
- "can use PGM or PNG format");
+ hestOptAdd_1_Double(&opt, "g", "gamma", &_gamma, "1.0",
+ "gamma used to brighten/darken scatterplots. "
+ "gamma > 1.0 brightens; gamma < 1.0 darkens. "
+ "Negative gammas invert values (like in xv). ");
+ hestOptAdd_1_Other(&opt, "i", "hvolIn", &hvol, NULL,
+ "input histogram volume (from \"gkms hvol\")", nrrdHestNrrd);
+ hestOptAdd_2_String(&opt, "o", "vgOut vhOut", out, NULL,
+ "Filenames to use for two output scatterplots, (gradient "
+ "magnitude versus value, and 2nd derivative versus value); "
+ "can use PGM or PNG format");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_scatInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_scatInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nvgRaw = nrrdNew();
Modified: teem/trunk/src/bane/gkmsTxf.c
===================================================================
--- teem/trunk/src/bane/gkmsTxf.c 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/gkmsTxf.c 2023-07-15 14:15:33 UTC (rev 7109)
@@ -38,39 +38,39 @@
float min[2], max[2], top[2], v0, g0, *data, v, g, gwidth, width, mwidth, tvl, tvr, vl,
vr, tmp, maxa;
- hestOptAdd(&opt, "r", "Vres Gres", airTypeInt, 2, 2, res, "256 256",
- "resolution of the transfer function in value and gradient "
- "magnitude");
- hestOptAdd(&opt, "min", "Vmin Gmin", airTypeFloat, 2, 2, min, "0.0 0.0",
- "minimum value and grad mag in txf");
- hestOptAdd(&opt, "max", "Vmax Gmax", airTypeFloat, 2, 2, max, NULL,
- "maximum value and grad mag in txf");
- hestOptAdd(&opt, "v", "base value", airTypeFloat, 1, 1, &v0, NULL,
- "data value at which to position bottom of triangle");
- hestOptAdd(&opt, "g", "gthresh", airTypeFloat, 1, 1, &g0, "0.0",
- "lowest grad mag to receive opacity");
- hestOptAdd(&opt, "gw", "gwidth", airTypeFloat, 1, 1, &gwidth, "0.0",
- "range of grad mag values over which to apply threshold "
- "at low gradient magnitudes");
- hestOptAdd(&opt, "top", "Vtop Gtop", airTypeFloat, 2, 2, top, NULL,
- "data value and grad mag at center of top of triangle");
- hestOptAdd(&opt, "w", "value width", airTypeFloat, 1, 1, &width, NULL,
- "range of values to be spanned at top of triangle");
- hestOptAdd(&opt, "mw", "value width", airTypeFloat, 1, 1, &mwidth, "0",
- "range of values to be spanned at BOTTOM of triangle");
- hestOptAdd(&opt, "step", NULL, airTypeInt, 0, 0, &step, NULL,
- "instead of assigning opacity inside a triangular region, "
- "make it more like a step function, in which opacity never "
- "decreases in increasing data value");
- hestOptAdd(&opt, "a", "max opac", airTypeFloat, 1, 1, &maxa, "1.0",
- "highest opacity to assign");
- hestOptAdd(&opt, "o", "opacOut", airTypeString, 1, 1, &out, NULL,
- "output opacity function filename");
+ /* HEY many of these ints should be unsigned, but bane never got the signed->unsigned
+ * treatment */
+ hestOptAdd_2_Int(&opt, "r", "Vres Gres", res, "256 256",
+ "resolution of the transfer function in value and gradient "
+ "magnitude");
+ hestOptAdd_2_Float(&opt, "min", "Vmin Gmin", min, "0.0 0.0",
+ "minimum value and grad mag in txf");
+ hestOptAdd_2_Float(&opt, "max", "Vmax Gmax", max, NULL,
+ "maximum value and grad mag in txf");
+ hestOptAdd_1_Float(&opt, "v", "base value", &v0, NULL,
+ "data value at which to position bottom of triangle");
+ hestOptAdd_1_Float(&opt, "g", "gthresh", &g0, "0.0",
+ "lowest grad mag to receive opacity");
+ hestOptAdd_1_Float(&opt, "gw", "gwidth", &gwidth, "0.0",
+ "range of grad mag values over which to apply threshold "
+ "at low gradient magnitudes");
+ hestOptAdd_2_Float(&opt, "top", "Vtop Gtop", top, NULL,
+ "data value and grad mag at center of top of triangle");
+ hestOptAdd_1_Float(&opt, "w", "value width", &width, NULL,
+ "range of values to be spanned at top of triangle");
+ hestOptAdd_1_Float(&opt, "mw", "value width", &mwidth, "0",
+ "range of values to be spanned at BOTTOM of triangle");
+ hestOptAdd_Flag(&opt, "step", &step,
+ "instead of assigning opacity inside a triangular region, "
+ "make it more like a step function, in which opacity never "
+ "decreases in increasing data value");
+ hestOptAdd_1_Float(&opt, "a", "max opac", &maxa, "1.0", "highest opacity to assign");
+ hestOptAdd_1_String(&opt, "o", "opacOut", &out, NULL,
+ "output opacity function filename");
mop = airMopNew();
airMopAdd(mop, opt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_baneGkms_txfInfoL);
- PARSE();
+ USAGE_PARSE(_baneGkms_txfInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/bane/privateBane.h
===================================================================
--- teem/trunk/src/bane/privateBane.h 2023-07-15 12:28:05 UTC (rev 7108)
+++ teem/trunk/src/bane/privateBane.h 2023-07-15 14:15:33 UTC (rev 7109)
@@ -31,9 +31,9 @@
/* USAGE, PARSE
all copied from unrrdu/privateUnrrdu.h */
-#define USAGE(info) \
- if (!argc) { \
- hestInfo(stderr, me, (info), hparm); \
+#define USAGE(INFO) \
+ if (!argc && !hparm->noArgsIsNoProblem) { \
+ hestInfo(stderr, me, (INFO), hparm); \
hestUsage(stderr, opt, me, hparm); \
hestGlossary(stderr, opt, hparm); \
airMopError(mop); \
@@ -40,19 +40,31 @@
return 2; \
}
-#define PARSE() \
+#define PARSE(INFO) \
if ((pret = hestParse(opt, argc, argv, &perr, hparm))) { \
if (1 == pret) { \
fprintf(stderr, "%s: %s\n", me, perr); \
free(perr); \
hestUsage(stderr, opt, me, hparm); \
+ if (hparm && hparm->noArgsIsNoProblem) { \
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me); \
+ } else { \
+ fprintf(stderr, "\nFor more info: \"%s\" or \"%s --help\"\n", me, me); \
+ } \
airMopError(mop); \
return 2; \
} else { \
exit(1); \
} \
+ } else if (opt->helpWanted) { \
+ hestInfo(stdout, me, (INFO), hparm); \
+ hestUsage(stdout, opt, me, hparm); \
+ hestGlossary(stdout, opt, hparm); \
+ return 0; \
}
+#define USAGE_PARSE(INFO) USAGE(INFO) PARSE(INFO)
+
#ifdef __cplusplus
}
#endif
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-15 12:28:07
|
Revision: 7108
http://sourceforge.net/p/teem/code/7108
Author: kindlmann
Date: 2023-07-15 12:28:05 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
really do have to use hestOptAdd here, better explaining why
Modified Paths:
--------------
teem/trunk/src/bin/miter.c
Modified: teem/trunk/src/bin/miter.c
===================================================================
--- teem/trunk/src/bin/miter.c 2023-07-15 12:27:42 UTC (rev 7107)
+++ teem/trunk/src/bin/miter.c 2023-07-15 12:28:05 UTC (rev 7108)
@@ -84,7 +84,7 @@
hestOptAdd_1_Float(&hopt, "iss", "scale", &isScale, "1.0",
"scaling of image size (from \"is\")");
hestOptAdd_3_Float(&hopt, "ads", "ka kd ks", ads, "0.1 0.6 0.3", "phong components");
- /* mite_at could be float or double */
+ /* mite_at could be float or double, so have to use older hest interface */
hestOptAdd(&hopt, "sp", "spec pow", mite_at, 1, 1, &(muu->rangeInit[miteRangeSP]),
"30", "phong specular power");
hestOptAdd_1_Other(&hopt, "k00", "kernel", &(muu->ksp[gageKernel00]), "tent",
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-15 12:27:43
|
Revision: 7107
http://sourceforge.net/p/teem/code/7107
Author: kindlmann
Date: 2023-07-15 12:27:42 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
missed one call to hestOptAdd in previous update
Modified Paths:
--------------
teem/trunk/src/bin/gprobe.c
Modified: teem/trunk/src/bin/gprobe.c
===================================================================
--- teem/trunk/src/bin/gprobe.c 2023-07-15 12:25:19 UTC (rev 7106)
+++ teem/trunk/src/bin/gprobe.c 2023-07-15 12:27:42 UTC (rev 7107)
@@ -335,10 +335,10 @@
fprintf(stderr, "%s: PANIC nsi %u != %u", me, nsi, NON_SBP_OPT_NUM);
exit(1);
}
- hestOptAdd(&hopt, "sbp", "blur spec", airTypeOther, 1, 1, &sbpCL, "",
- "complete specification of stack blur parms; "
- "over-rides all previous \"ss\" options",
- NULL, NULL, gageHestStackBlurParm);
+ hestOptAdd_1_Other(&hopt, "sbp", "blur spec", &sbpCL, "",
+ "complete specification of stack blur parms; "
+ "over-rides all previous \"ss\" options",
+ gageHestStackBlurParm);
/* These two options are needed even if sbp is used, because they are *not*
part of the gageStackBlurParm. In meet, this info is handled by the
extraFlag/extraParm construct, which is not available here */
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-15 12:25:22
|
Revision: 7106
http://sourceforge.net/p/teem/code/7106
Author: kindlmann
Date: 2023-07-15 12:25:19 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
updating hest usage
Modified Paths:
--------------
teem/trunk/src/limn/lpu_cbfit.c
teem/trunk/src/limn/lpu_ccfind.c
teem/trunk/src/limn/lpu_meas.c
teem/trunk/src/limn/lpu_psel.c
teem/trunk/src/limn/lpu_rast.c
teem/trunk/src/limn/lpu_sort.c
teem/trunk/src/limn/lpu_verts.c
Modified: teem/trunk/src/limn/lpu_cbfit.c
===================================================================
--- teem/trunk/src/limn/lpu_cbfit.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_cbfit.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -42,44 +42,39 @@
limnCBFContext fctx;
limnCBFPath *path;
- hestOptAdd(&hopt, "i", "input", airTypeOther, 1, 1, &_nin, NULL, "input xy points",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "v", "verbose", airTypeInt, 1, 1, &verbose, "1", "verbosity level");
- hestOptAdd(&hopt, "s", "synth", airTypeInt, 0, 0, &synth, NULL,
- "synthesize xy points from control points");
- hestOptAdd(&hopt, "so", "synth out", airTypeString, 1, 1, &synthOut, "",
- "if non-empty, filename in which to save synthesized xy pts");
- hestOptAdd(&hopt, "snf", NULL, airTypeInt, 0, 0, &nofit, NULL,
- "actually do not fit, just save -so synthetic "
- "output and quit");
- hestOptAdd(&hopt, "t1", "tan", airTypeDouble, 2, 2, utt1, "nan nan",
- "if non-nan, the outgoing tangent from the first point");
- hestOptAdd(&hopt, "t2", "tan", airTypeDouble, 2, 2, utt2, "nan nan",
- "if non-nan, the incoming tangent to the last point");
- hestOptAdd(&hopt, "im", "max", airTypeUInt, 1, 1, &iterMax, "0",
- "(if non-zero) max # nrp iterations to run");
- hestOptAdd(&hopt, "deltam", "delta", airTypeDouble, 1, 1, &deltaMin, "0.0005",
- "(if non-zero) stop nrp when change in spline "
- "domain sampling goes below this");
- hestOptAdd(&hopt, "distm", "dist", airTypeDouble, 1, 1, &distMin, "0.01",
- "(if non-zero) stop nrp when distance between spline "
- "and points goes below this");
- hestOptAdd(&hopt, "dists", "scl", airTypeDouble, 1, 1, &distScl, "0.25",
- "scaling on nrp distMin check");
- hestOptAdd(&hopt, "psi", "psi", airTypeDouble, 1, 1, &psi, "10", "psi, of course");
- hestOptAdd(&hopt, "ca", "angle", airTypeDouble, 1, 1, &cangle, "100",
- "angle indicating a corner");
- hestOptAdd(&hopt, "scl", "scale", airTypeDouble, 1, 1, &scale, "0",
- "scale for geometry estimation");
- hestOptAdd(&hopt, "loop", NULL, airTypeInt, 0, 0, &loop, NULL,
- "given xy points are actually a loop; BUT "
- "the first and last points need to be the same!");
- hestOptAdd(&hopt, "petc", NULL, airTypeInt, 0, 0, &petc, NULL,
- "(Press Enter To Continue) ");
+ hestOptAdd_1_Other(&hopt, "i", "input", &_nin, NULL, "input xy points", nrrdHestNrrd);
+ hestOptAdd_1_Int(&hopt, "v", "verbose", &verbose, "1", "verbosity level");
+ hestOptAdd_Flag(&hopt, "s", &synth, "synthesize xy points from control points");
+ hestOptAdd_1_String(&hopt, "so", "synth out", &synthOut, "",
+ "if non-empty, filename in which to save synthesized xy pts");
+ hestOptAdd_Flag(&hopt, "snf", &nofit,
+ "actually do not fit, just save -so synthetic "
+ "output and quit");
+ hestOptAdd_2_Double(&hopt, "t1", "tan", utt1, "nan nan",
+ "if non-nan, the outgoing tangent from the first point");
+ hestOptAdd_2_Double(&hopt, "t2", "tan", utt2, "nan nan",
+ "if non-nan, the incoming tangent to the last point");
+ hestOptAdd_1_UInt(&hopt, "im", "max", &iterMax, "0",
+ "(if non-zero) max # nrp iterations to run");
+ hestOptAdd_1_Double(&hopt, "deltam", "delta", &deltaMin, "0.0005",
+ "(if non-zero) stop nrp when change in spline "
+ "domain sampling goes below this");
+ hestOptAdd_1_Double(&hopt, "distm", "dist", &distMin, "0.01",
+ "(if non-zero) stop nrp when distance between spline "
+ "and points goes below this");
+ hestOptAdd_1_Double(&hopt, "dists", "scl", &distScl, "0.25",
+ "scaling on nrp distMin check");
+ hestOptAdd_1_Double(&hopt, "psi", "psi", &psi, "10", "psi, of course");
+ hestOptAdd_1_Double(&hopt, "ca", "angle", &cangle, "100", "angle indicating a corner");
+ hestOptAdd_1_Double(&hopt, "scl", "scale", &scale, "0",
+ "scale for geometry estimation");
+ hestOptAdd_Flag(&hopt, "loop", &loop,
+ "given xy points are actually a loop; BUT "
+ "the first and last points need to be the same!");
+ hestOptAdd_Flag(&hopt, "petc", &petc, "(Press Enter To Continue) ");
/*
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output nrrd filename");
- */
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output nrrd filename");
+ */
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/limn/lpu_ccfind.c
===================================================================
--- teem/trunk/src/limn/lpu_ccfind.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_ccfind.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -36,10 +36,9 @@
Nrrd *nmeas;
char *out;
- hestOptAdd(&hopt, NULL, "input", airTypeOther, 1, 1, &pld, NULL,
- "input polydata filename", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output polydata filename");
+ hestOptAdd_1_Other(&hopt, NULL, "input", &pld, NULL, "input polydata filename",
+ limnHestPolyDataLMPD);
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output polydata filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/limn/lpu_meas.c
===================================================================
--- teem/trunk/src/limn/lpu_meas.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_meas.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -37,10 +37,9 @@
Nrrd *nout;
char *out;
- hestOptAdd(&hopt, NULL, "input", airTypeOther, 1, 1, &pld, NULL,
- "input polydata filename", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output nrrd filename");
+ hestOptAdd_1_Other(&hopt, NULL, "input", &pld, NULL, "input polydata filename",
+ limnHestPolyDataLMPD);
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output nrrd filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/limn/lpu_psel.c
===================================================================
--- teem/trunk/src/limn/lpu_psel.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_psel.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -40,12 +40,11 @@
char *out;
size_t size[NRRD_DIM_MAX];
- hestOptAdd(&hopt, "r", "range", airTypeUInt, 2, 2, prange, NULL,
- "range of indices of primitives to select");
- hestOptAdd(&hopt, NULL, "input", airTypeOther, 1, 1, &pldIn, NULL,
- "input polydata filename", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output polydata filename");
+ hestOptAdd_2_UInt(&hopt, "r", "range", prange, NULL,
+ "range of indices of primitives to select");
+ hestOptAdd_1_Other(&hopt, NULL, "input", &pldIn, NULL, "input polydata filename",
+ limnHestPolyDataLMPD);
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output polydata filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/limn/lpu_rast.c
===================================================================
--- teem/trunk/src/limn/lpu_rast.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_rast.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -39,16 +39,14 @@
int type;
size_t size[NRRD_DIM_MAX];
- hestOptAdd(&hopt, "min", "min", airTypeDouble, 3, 3, min, NULL, "bottom corner");
- hestOptAdd(&hopt, "max", "max", airTypeDouble, 3, 3, max, NULL, "top corner");
- hestOptAdd(&hopt, "s", "size", airTypeSize_t, 3, 3, size, NULL,
- "number of samples along each axis");
- hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &type, "uchar",
- "type of output nrrd", NULL, nrrdType);
- hestOptAdd(&hopt, NULL, "input", airTypeOther, 1, 1, &pld, NULL,
- "input polydata filename", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output nrrd filename");
+ hestOptAdd_3_Double(&hopt, "min", "min", min, NULL, "bottom corner");
+ hestOptAdd_3_Double(&hopt, "max", "max", max, NULL, "top corner");
+ hestOptAdd_3_Size_t(&hopt, "s", "size", size, NULL,
+ "number of samples along each axis");
+ hestOptAdd_1_Enum(&hopt, "t", "type", &type, "uchar", "type of output nrrd", nrrdType);
+ hestOptAdd_1_Other(&hopt, NULL, "input", &pld, NULL, "input polydata filename",
+ limnHestPolyDataLMPD);
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output nrrd filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/limn/lpu_sort.c
===================================================================
--- teem/trunk/src/limn/lpu_sort.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_sort.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -36,12 +36,11 @@
Nrrd *nin;
char *out;
- hestOptAdd(&hopt, NULL, "input lpld", airTypeOther, 1, 1, &pld, NULL,
- "input polydata filename", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, NULL, "input nrrd", airTypeOther, 1, 1, &nin, NULL,
- "input nrrd filename", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output lpld filename");
+ hestOptAdd_1_Other(&hopt, NULL, "input lpld", &pld, NULL, "input polydata filename",
+ limnHestPolyDataLMPD);
+ hestOptAdd_1_Other(&hopt, NULL, "input nrrd", &nin, NULL, "input nrrd filename",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output lpld filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/limn/lpu_verts.c
===================================================================
--- teem/trunk/src/limn/lpu_verts.c 2023-07-15 12:13:27 UTC (rev 7105)
+++ teem/trunk/src/limn/lpu_verts.c 2023-07-15 12:25:19 UTC (rev 7106)
@@ -36,10 +36,9 @@
Nrrd *nout;
char *out;
- hestOptAdd(&hopt, NULL, "input", airTypeOther, 1, 1, &pld, NULL,
- "input polydata filename", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, NULL, "output", airTypeString, 1, 1, &out, NULL,
- "output nrrd filename");
+ hestOptAdd_1_Other(&hopt, NULL, "input", &pld, NULL, "input polydata filename",
+ limnHestPolyDataLMPD);
+ hestOptAdd_1_String(&hopt, NULL, "output", &out, NULL, "output nrrd filename");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-15 12:13:36
|
Revision: 7105
http://sourceforge.net/p/teem/code/7105
Author: kindlmann
Date: 2023-07-15 12:13:27 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
upating hest usage
Modified Paths:
--------------
teem/trunk/src/ten/tendAnhist.c
teem/trunk/src/ten/tendAnplot.c
teem/trunk/src/ten/tendAnscale.c
teem/trunk/src/ten/tendAnvol.c
teem/trunk/src/ten/tendAvg.c
teem/trunk/src/ten/tendBfit.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/tendEval.c
teem/trunk/src/ten/tendEvaladd.c
teem/trunk/src/ten/tendEvalclamp.c
teem/trunk/src/ten/tendEvalmult.c
teem/trunk/src/ten/tendEvalpow.c
teem/trunk/src/ten/tendEvec.c
teem/trunk/src/ten/tendEvecrgb.c
teem/trunk/src/ten/tendEvq.c
teem/trunk/src/ten/tendExp.c
teem/trunk/src/ten/tendExpand.c
teem/trunk/src/ten/tendFiber.c
teem/trunk/src/ten/tendGlyph.c
teem/trunk/src/ten/tendGrads.c
teem/trunk/src/ten/tendHelix.c
teem/trunk/src/ten/tendLog.c
teem/trunk/src/ten/tendMake.c
teem/trunk/src/ten/tendMconv.c
teem/trunk/src/ten/tendMfit.c
teem/trunk/src/ten/tendMsim.c
teem/trunk/src/ten/tendNorm.c
teem/trunk/src/ten/tendPoint.c
teem/trunk/src/ten/tendSatin.c
teem/trunk/src/ten/tendShrink.c
teem/trunk/src/ten/tendSim.c
teem/trunk/src/ten/tendSlice.c
teem/trunk/src/ten/tendSten.c
teem/trunk/src/ten/tendTconv.c
teem/trunk/src/ten/tendTriple.c
teem/trunk/src/ten/tendUnmf.c
Modified: teem/trunk/src/ten/tendAnhist.c
===================================================================
--- teem/trunk/src/ten/tendAnhist.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendAnhist.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -39,29 +39,26 @@
Nrrd *nin, *nout, *nwght;
char *outS;
- hestOptAdd(&hopt, "v", "westin version", airTypeInt, 1, 1, &version, "1",
- "Which version of Westin's anisotropy metric triple "
- "to use, either \"1\" or \"2\"");
- hestOptAdd(&hopt, "w", "nweight", airTypeOther, 1, 1, &nwght, "",
- "how to weigh contributions to histogram. By default "
- "(not using this option), the increment is one bin count per "
- "sample, but by giving a nrrd, the value in the nrrd at the "
- "corresponding location will be the bin count increment ",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "r", "res", airTypeInt, 1, 1, &res, NULL,
- "resolution of anisotropy plot");
- hestOptAdd(&hopt, "right", NULL, airTypeInt, 0, 0, &right, NULL,
- "sample a right-triangle-shaped region, instead of "
- "a roughly equilateral triangle. ");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_Int(&hopt, "v", "westin version", &version, "1",
+ "Which version of Westin's anisotropy metric triple "
+ "to use, either \"1\" or \"2\"");
+ hestOptAdd_1_Other(&hopt, "w", "nweight", &nwght, "",
+ "how to weigh contributions to histogram. By default "
+ "(not using this option), the increment is one bin count per "
+ "sample, but by giving a nrrd, the value in the nrrd at the "
+ "corresponding location will be the bin count increment ",
+ nrrdHestNrrd);
+ hestOptAdd_1_Int(&hopt, "r", "res", &res, NULL, "resolution of anisotropy plot");
+ hestOptAdd_Flag(&hopt, "right", &right,
+ "sample a right-triangle-shaped region, instead of "
+ "a roughly equilateral triangle. ");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_anhistInfoL);
- PARSE();
+ USAGE_PARSE(_tend_anhistInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendAnplot.c
===================================================================
--- teem/trunk/src/ten/tendAnplot.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendAnplot.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -40,32 +40,30 @@
char *perr, *err;
airArray *mop;
- int res, aniso, whole, nanout, hflip;
+ int aniso, whole, nanout, hflip;
+ unsigned int res;
Nrrd *nout;
char *outS;
- hestOptAdd(&hopt, "r", "res", airTypeInt, 1, 1, &res, "256",
- "resolution of anisotropy plot");
- hestOptAdd(&hopt, "w", NULL, airTypeInt, 0, 0, &whole, NULL,
- "sample the whole triangle of constant trace, "
- "instead of just the "
- "sixth of it in which the eigenvalues have the "
- "traditional sorted order. ");
- hestOptAdd(&hopt, "hflip", NULL, airTypeInt, 0, 0, &hflip, NULL,
- "flip the two bottom corners (swapping the place of "
- "linear and planar)");
- hestOptAdd(&hopt, "nan", NULL, airTypeInt, 0, 0, &nanout, NULL,
- "set the pixel values outside the triangle to be NaN, "
- "instead of 0");
- hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &aniso, NULL,
- "Which anisotropy metric to plot. " TEN_ANISO_DESC, NULL, tenAniso);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_UInt(&hopt, "r", "res", &res, "256", "resolution of anisotropy plot");
+ hestOptAdd_Flag(&hopt, "w", &whole,
+ "sample the whole triangle of constant trace, "
+ "instead of just the "
+ "sixth of it in which the eigenvalues have the "
+ "traditional sorted order. ");
+ hestOptAdd_Flag(&hopt, "hflip", &hflip,
+ "flip the two bottom corners (swapping the place of "
+ "linear and planar)");
+ hestOptAdd_Flag(&hopt, "nan", &nanout,
+ "set the pixel values outside the triangle to be NaN, "
+ "instead of 0");
+ hestOptAdd_1_Enum(&hopt, "a", "aniso", &aniso, NULL,
+ "Which anisotropy metric to plot. " TEN_ANISO_DESC, tenAniso);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_anplotInfoL);
- JUSTPARSE();
+ USAGE_JUSTPARSE(_tend_anplotInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendAnscale.c
===================================================================
--- teem/trunk/src/ten/tendAnscale.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendAnscale.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -42,23 +42,21 @@
float scale;
int fixDet, makePositive;
- hestOptAdd(&hopt, "s", "scale", airTypeFloat, 1, 1, &scale, NULL,
- "Amount by which to scale deviatoric component of tensor.");
- hestOptAdd(&hopt, "fd", NULL, airTypeInt, 0, 0, &fixDet, NULL,
- "instead of fixing the per-sample trace (the default), fix the "
- "determinant (ellipsoid volume)");
- hestOptAdd(&hopt, "mp", NULL, airTypeInt, 0, 0, &makePositive, NULL,
- "after changing the eigenvalues of the tensor, enforce their "
- "non-negative-ness. By default, no such constraint is imposed.");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_Float(&hopt, "s", "scale", &scale, NULL,
+ "Amount by which to scale deviatoric component of tensor.");
+ hestOptAdd_Flag(&hopt, "fd", &fixDet,
+ "instead of fixing the per-sample trace (the default), fix the "
+ "determinant (ellipsoid volume)");
+ hestOptAdd_Flag(&hopt, "mp", &makePositive,
+ "after changing the eigenvalues of the tensor, enforce their "
+ "non-negative-ness. By default, no such constraint is imposed.");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_anscaleInfoL);
- PARSE();
+ USAGE_PARSE(_tend_anscaleInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendAnvol.c
===================================================================
--- teem/trunk/src/ten/tendAnvol.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendAnvol.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -39,19 +39,16 @@
char *outS;
float thresh;
- hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &aniso, NULL,
- "Which anisotropy metric to plot. " TEN_ANISO_DESC, NULL, tenAniso);
- hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5",
- "confidence threshold");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_Enum(&hopt, "a", "aniso", &aniso, NULL,
+ "Which anisotropy metric to plot. " TEN_ANISO_DESC, tenAniso);
+ hestOptAdd_1_Float(&hopt, "t", "thresh", &thresh, "0.5", "confidence threshold");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_anvolInfoL);
- PARSE();
+ USAGE_PARSE(_tend_anvolInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendAvg.c
===================================================================
--- teem/trunk/src/ten/tendAvg.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendAvg.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -34,21 +34,20 @@
char *perr, *err;
airArray *mop;
- int ninLen, itype;
+ int itype;
+ unsigned int ninLen;
Nrrd **nin, *nout;
char *outS;
- hestOptAdd(&hopt, "i", "nin1 nin2", airTypeOther, 2, -1, &nin, NULL,
- "list of input diffusion tensor volumes", &ninLen, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &itype, "linear", "averaging method",
- NULL, tenInterpType);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_Nv_Other(&hopt, "i", "nin1 nin2", 2, -1, &nin, NULL,
+ "list of input diffusion tensor volumes", &ninLen, nrrdHestNrrd);
+ hestOptAdd_1_Enum(&hopt, "t", "type", &itype, "linear", "averaging method",
+ tenInterpType);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_avgInfoL);
- JUSTPARSE();
+ USAGE_JUSTPARSE(_tend_avgInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendBfit.c
===================================================================
--- teem/trunk/src/ten/tendBfit.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendBfit.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -43,26 +43,24 @@
hparm->respFileEnable = AIR_TRUE;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "Input nrrd. List of DWIs from different b-values must "
- "be along axis 0",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "b", "b1 b2", airTypeDouble, 2, -1, &bb, NULL,
- "b values across axis 0 of input nrrd", &bbLen);
- hestOptAdd(&hopt, "w", "w1 w2", airTypeDouble, 2, -1, &_ww, "nan nan",
- "weights for samples in non-linear fitting", &_wwLen);
- hestOptAdd(&hopt, "imax", "# iter", airTypeInt, 1, 1, &iterMax, "10",
- "max number of iterations to use in non-linear fitting, or, "
- "use 0 to do only initial linear fit");
- hestOptAdd(&hopt, "eps", "epsilon", airTypeDouble, 1, 1, &eps, "1",
- "epsilon convergence threshold for non-linear fitting");
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output tensor volume");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-",
+ "Input nrrd. List of DWIs from different b-values must "
+ "be along axis 0",
+ nrrdHestNrrd);
+ hestOptAdd_Nv_Double(&hopt, "b", "b1 b2", 2, -1, &bb, NULL,
+ "b values across axis 0 of input nrrd", &bbLen);
+ hestOptAdd_Nv_Double(&hopt, "w", "w1 w2", 2, -1, &_ww, "nan nan",
+ "weights for samples in non-linear fitting", &_wwLen);
+ hestOptAdd_1_Int(&hopt, "imax", "# iter", &iterMax, "10",
+ "max number of iterations to use in non-linear fitting, or, "
+ "use 0 to do only initial linear fit");
+ hestOptAdd_1_Double(&hopt, "eps", "epsilon", &eps, "1",
+ "epsilon convergence threshold for non-linear fitting");
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output tensor volume");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_bfitInfoL);
- PARSE();
+ USAGE_PARSE(_tend_bfitInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (!(bbLen == nin->axis[0].size)) {
Modified: teem/trunk/src/ten/tendBmat.c
===================================================================
--- teem/trunk/src/ten/tendBmat.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendBmat.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -45,14 +45,13 @@
Nrrd *ngrad, *nout;
char *outS;
- hestOptAdd(&hopt, "i", "grads", airTypeOther, 1, 1, &ngrad, NULL,
- "array of gradient directions", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-", "output B matrix");
+ hestOptAdd_1_Other(&hopt, "i", "grads", &ngrad, NULL, "array of gradient directions",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output B matrix");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_bmatInfoL);
- JUSTPARSE();
+ USAGE_JUSTPARSE(_tend_bmatInfoL);
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 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEllipse.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -216,39 +216,34 @@
mop = airMopNew();
- hestOptAdd(&hopt, "ctr", "conf thresh", airTypeFloat, 1, 1, &cthresh, "0.5",
- "Glyphs will be drawn only for tensors with confidence "
- "values greater than this threshold");
- hestOptAdd(&hopt, "gsc", "scale", airTypeFloat, 1, 1, &gscale, "1",
- "over-all glyph size");
- hestOptAdd(&hopt, "dot", "radius", airTypeFloat, 1, 1, &dotRad, "0.0",
- "radius of little dot to put in middle of ellipse, or \"0\" "
- "for no such dot");
- hestOptAdd(&hopt, "wid", "width", airTypeFloat, 1, 1, &lineWidth, "0.0",
- "with of lines for tractlets");
- hestOptAdd(&hopt, "inv", NULL, airTypeInt, 0, 0, &invert, NULL,
- "use white ellipses on black background, instead of reverse");
- hestOptAdd(&hopt, "min", "minX minY", airTypeFloat, 2, 2, min, "-1 -1",
- "when using \"-p\", minimum corner");
- hestOptAdd(&hopt, "max", "maxX maxY", airTypeFloat, 2, 2, max, "1 1",
- "when using \"-p\", maximum corner");
+ hestOptAdd_1_Float(&hopt, "ctr", "conf thresh", &cthresh, "0.5",
+ "Glyphs will be drawn only for tensors with confidence "
+ "values greater than this threshold");
+ hestOptAdd_1_Float(&hopt, "gsc", "scale", &gscale, "1", "over-all glyph size");
+ hestOptAdd_1_Float(&hopt, "dot", "radius", &dotRad, "0.0",
+ "radius of little dot to put in middle of ellipse, or \"0\" "
+ "for no such dot");
+ hestOptAdd_1_Float(&hopt, "wid", "width", &lineWidth, "0.0",
+ "with of lines for tractlets");
+ hestOptAdd_Flag(&hopt, "inv", &invert,
+ "use white ellipses on black background, instead of reverse");
+ hestOptAdd_2_Float(&hopt, "min", "minX minY", min, "-1 -1",
+ "when using \"-p\", minimum corner");
+ hestOptAdd_2_Float(&hopt, "max", "maxX maxY", max, "1 1",
+ "when using \"-p\", maximum corner");
/* input/output */
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nten, "-", "image of 2D tensors",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "p", "pos array", airTypeOther, 1, 1, &npos, "",
- "Instead of being on a grid, tensors are at arbitrary locations, "
- "as defined by this 2-by-N array of floats",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "s", "stn array", airTypeOther, 1, 1, &nstn, "",
- "Locations given by \"-p\" have this connectivity", NULL, NULL,
- nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output PostScript file");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nten, "-", "image of 2D tensors", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "p", "pos array", &npos, "",
+ "Instead of being on a grid, tensors are at arbitrary locations, "
+ "as defined by this 2-by-N array of floats",
+ nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "s", "stn array", &nstn, "",
+ "Locations given by \"-p\" have this connectivity", nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output PostScript file");
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_ellipseInfoL);
- JUSTPARSE();
+ USAGE_JUSTPARSE(_tend_ellipseInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (npos) {
Modified: teem/trunk/src/ten/tendEpireg.c
===================================================================
--- teem/trunk/src/ten/tendEpireg.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEpireg.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -45,76 +45,73 @@
char *gradS;
NrrdKernelSpec *ksp;
Nrrd **nin, **nout3D, *nout4D, *ngrad, *ngradKVP, *nbmatKVP;
- unsigned int ni, ninLen, *skip, skipNum;
- int ref, noverbose, progress, nocc, baseNum;
+ unsigned int ni, ninLen, *skip, skipNum, baseNum;
+ int ref, noverbose, progress, nocc;
float bw[2], thr, fitFrac;
double bvalue;
- hestOptAdd(&hopt, "i", "dwi0 dwi1", airTypeOther, 1, -1, &nin, NULL,
- "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, "g", "grads", airTypeString, 1, 1, &gradS, NULL,
- "array of gradient directions, in the same order as the "
- "associated DWIs were given to \"-i\", "
- "**OR** \"-g kvp\" signifies that gradient directions should "
- "be read from the key/value pairs of the DWI",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "r", "reference", airTypeInt, 1, 1, &ref, "-1",
- "which of the DW volumes (zero-based numbering) should be used "
- "as the standard, to which all other images are transformed. "
- "Using -1 (the default) means that 9 intrinsic parameters "
- "governing the relationship between the gradient direction "
- "and the resulting distortion are estimated and fitted, "
- "ensuring good registration with the non-diffusion-weighted "
- "T2 image (which is never explicitly used in registration). "
- "Otherwise, by picking a specific DWI, no distortion parameter "
- "estimation is done. ");
- hestOptAdd(&hopt, "nv", NULL, airTypeInt, 0, 0, &noverbose, NULL,
- "turn OFF verbose mode, and "
- "have no idea what stage processing is at.");
- hestOptAdd(&hopt, "p", NULL, airTypeInt, 0, 0, &progress, NULL,
- "save out intermediate steps of processing");
- hestOptAdd(&hopt, "bw", "x,y blur", airTypeFloat, 2, 2, bw, "1.0 2.0",
- "standard devs in X and Y directions of gaussian filter used "
- "to blur the DWIs prior to doing segmentation. This blurring "
- "does not effect the final resampling of registered DWIs. "
- "Use \"0.0 0.0\" to say \"no blurring\"");
- hestOptAdd(&hopt, "t", "DWI thresh", airTypeFloat, 1, 1, &thr, "nan",
- "Threshold value to use on DWIs, "
- "to do initial separation of brain and non-brain. By default, "
- "the threshold is determined automatically by histogram "
- "analysis. ");
- hestOptAdd(&hopt, "ncc", NULL, airTypeInt, 0, 0, &nocc, NULL,
- "do *NOT* do connected component (CC) analysis, after "
- "thresholding and before moment calculation. Doing CC analysis "
- "usually gives better results because it converts the "
- "thresholding output into something much closer to a "
- "real segmentation");
- hestOptAdd(&hopt, "f", "fit frac", airTypeFloat, 1, 1, &fitFrac, "0.70",
- "(only meaningful with \"-r -1\") When doing linear fitting "
- "of the intrinsic distortion parameters, it is good "
- "to ignore the slices for which the segmentation was poor. A "
- "heuristic is used to rank the slices according to segmentation "
- "quality. This option controls how many of the (best) slices "
- "contribute to the fitting. Use \"0\" to disable distortion "
- "parameter fitting. ");
- hestOptAdd(&hopt, "k", "kernel", airTypeOther, 1, 1, &ksp, "cubic:0,0.5",
- "kernel for resampling DWIs along the phase-encoding "
- "direction during final registration stage",
- NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "s", "start #", airTypeInt, 1, 1, &baseNum, "1",
- "first number to use in numbered sequence of output files.");
- hestOptAdd(&hopt, "o", "output/prefix", airTypeString, 1, 1, &outS, "-",
- "For separate 3D DWI volume inputs: prefix for output filenames; "
- "will save out one (registered) "
- "DWI for each input DWI, using the same type as the input. "
- "**OR**: For single 4D DWI input: output file name. ");
+ hestOptAdd_Nv_Other(&hopt, "i", "dwi0 dwi1", 1, -1, &nin, NULL,
+ "all the diffusion-weighted images (DWIs), as separate 3D nrrds, "
+ "**OR**: one 4D nrrd of all DWIs stacked along axis 0",
+ &ninLen, nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "g", "grads", &gradS, NULL,
+ "array of gradient directions, in the same order as the "
+ "associated DWIs were given to \"-i\", "
+ "**OR** \"-g kvp\" signifies that gradient directions should "
+ "be read from the key/value pairs of the DWI");
+ hestOptAdd_1_Int(&hopt, "r", "reference", &ref, "-1",
+ "which of the DW volumes (zero-based numbering) should be used "
+ "as the standard, to which all other images are transformed. "
+ "Using -1 (the default) means that 9 intrinsic parameters "
+ "governing the relationship between the gradient direction "
+ "and the resulting distortion are estimated and fitted, "
+ "ensuring good registration with the non-diffusion-weighted "
+ "T2 image (which is never explicitly used in registration). "
+ "Otherwise, by picking a specific DWI, no distortion parameter "
+ "estimation is done. ");
+ hestOptAdd_Flag(&hopt, "nv", &noverbose,
+ "turn OFF verbose mode, and "
+ "have no idea what stage processing is at.");
+ hestOptAdd_Flag(&hopt, "p", &progress, "save out intermediate steps of processing");
+ hestOptAdd_2_Float(&hopt, "bw", "x,y blur", bw, "1.0 2.0",
+ "standard devs in X and Y directions of gaussian filter used "
+ "to blur the DWIs prior to doing segmentation. This blurring "
+ "does not effect the final resampling of registered DWIs. "
+ "Use \"0.0 0.0\" to say \"no blurring\"");
+ hestOptAdd_1_Float(&hopt, "t", "DWI thresh", &thr, "nan",
+ "Threshold value to use on DWIs, "
+ "to do initial separation of brain and non-brain. By default, "
+ "the threshold is determined automatically by histogram "
+ "analysis.");
+ hestOptAdd_Flag(&hopt, "ncc", &nocc,
+ "do *NOT* do connected component (CC) analysis, after "
+ "thresholding and before moment calculation. Doing CC analysis "
+ "usually gives better results because it converts the "
+ "thresholding output into something much closer to a "
+ "real segmentation");
+ hestOptAdd_1_Float(&hopt, "f", "fit frac", &fitFrac, "0.70",
+ "(only meaningful with \"-r -1\") When doing linear fitting "
+ "of the intrinsic distortion parameters, it is good "
+ "to ignore the slices for which the segmentation was poor. A "
+ "heuristic is used to rank the slices according to segmentation "
+ "quality. This option controls how many of the (best) slices "
+ "contribute to the fitting. Use \"0\" to disable distortion "
+ "parameter fitting. ");
+ hestOptAdd_1_Other(&hopt, "k", "kernel", &ksp, "cubic:0,0.5",
+ "kernel for resampling DWIs along the phase-encoding "
+ "direction during final registration stage",
+ nrrdHestKernelSpec);
+ hestOptAdd_1_UInt(&hopt, "s", "start #", &baseNum, "1",
+ "first number to use in numbered sequence of output files.");
+ hestOptAdd_1_String(&hopt, "o", "output/prefix", &outS, "-",
+ "For separate 3D DWI volume inputs: prefix for output filenames; "
+ "will save out one (registered) "
+ "DWI for each input DWI, using the same type as the input. "
+ "**OR**: For single 4D DWI input: output file name. ");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_epiregInfoL);
- JUSTPARSE();
+ USAGE_JUSTPARSE(_tend_epiregInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
if (strcmp("kvp", gradS)) {
@@ -186,11 +183,11 @@
} else {
for (ni = 0; ni < ninLen; ni++) {
if (ninLen + baseNum > 99) {
- sprintf(buff, "%s%05d.nrrd", outS, ni + baseNum);
+ sprintf(buff, "%s%05u.nrrd", outS, ni + baseNum);
} else if (ninLen + baseNum > 9) {
- sprintf(buff, "%s%02d.nrrd", outS, ni + baseNum);
+ sprintf(buff, "%s%02u.nrrd", outS, ni + baseNum);
} else {
- sprintf(buff, "%s%d.nrrd", outS, ni + baseNum);
+ sprintf(buff, "%s%u.nrrd", outS, ni + baseNum);
}
if (nrrdSave(buff, nout3D[ni], NULL)) {
airMopAdd(mop, err = biffGetDone(NRRD), airFree, airMopAlways);
Modified: teem/trunk/src/ten/tendEstim.c
===================================================================
--- teem/trunk/src/ten/tendEstim.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEstim.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -50,84 +50,81 @@
tenEstimateContext *tec;
- hestOptAdd(&hopt, "old", NULL, airTypeInt, 0, 0, &oldstuff, NULL,
- "instead of the new tenEstimateContext code, use "
- "the old tenEstimateLinear code");
- hestOptAdd(&hopt, "sigma", "sigma", airTypeFloat, 1, 1, &sigma, "nan",
- "Rician noise parameter");
- hestOptAdd(&hopt, "v", "verbose", airTypeInt, 1, 1, &verbose, "0", "verbosity level");
- hestOptAdd(&hopt, "est", "estimate method", airTypeEnum, 1, 1, &estmeth, "lls",
- "estimation method to use. \"lls\": linear-least squares", NULL,
- tenEstimate1Method);
- hestOptAdd(&hopt, "wlsi", "WLS iters", airTypeUInt, 1, 1, &wlsi, "1",
- "when using weighted-least-squares (\"-est wls\"), how "
- "many iterations to do after the initial weighted fit.");
- hestOptAdd(&hopt, "fixneg", NULL, airTypeInt, 0, 0, &fixneg, NULL,
- "after estimating the tensor, ensure that there are no negative "
- "eigenvalues by adding (to all eigenvalues) the amount by which "
- "the smallest is negative (corresponding to increasing the "
- "non-DWI image value).");
- hestOptAdd(&hopt, "ee", "filename", airTypeString, 1, 1, &terrS, "",
- "Giving a filename here allows you to save out the tensor "
- "estimation error: a value which measures how much error there "
- "is between the tensor model and the given diffusion weighted "
- "measurements for each sample. By default, no such error "
- "calculation is saved.");
- hestOptAdd(&hopt, "eb", "filename", airTypeString, 1, 1, &eb0S, "",
- "In those cases where there is no B=0 reference image given "
- "(\"-knownB0 false\"), "
- "giving a filename here allows you to save out the B=0 image "
- "which is estimated from the data. By default, this image value "
- "is estimated but not saved.");
- hestOptAdd(&hopt, "t", "thresh", airTypeDouble, 1, 1, &thresh, "nan",
- "value at which to threshold the mean DWI value per pixel "
- "in order to generate the \"confidence\" mask. By default, "
- "the threshold value is calculated automatically, based on "
- "histogram analysis.");
- hestOptAdd(&hopt, "soft", "soft", airTypeFloat, 1, 1, &soft, "0",
- "how fuzzy the confidence boundary should be. By default, "
- "confidence boundary is perfectly sharp");
- hestOptAdd(&hopt, "scale", "scale", airTypeFloat, 1, 1, &scale, "1",
- "After estimating the tensor, scale all of its elements "
- "(but not the confidence value) by this amount. Can help with "
- "downstream numerical precision if values are very large "
- "or small.");
- hestOptAdd(&hopt, "mv", "min val", airTypeDouble, 1, 1, &valueMin, "1.0",
- "minimum plausible value (especially important for linear "
- "least squares estimation)");
- hestOptAdd(&hopt, "B", "B-list", airTypeString, 1, 1, &bmatS, NULL,
- "6-by-N list of B-matrices characterizing "
- "the diffusion weighting for each "
- "image. \"tend bmat\" is one source for such a matrix; see "
- "its usage info for specifics on how the coefficients of "
- "the B-matrix are ordered. "
- "An unadorned plain text file is a great way to "
- "specify the B-matrix.\n **OR**\n "
- "Can say just \"-B kvp\" to try to learn B matrices from "
- "key/value pair information in input images.");
- 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,
- "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 "
- "B-matrices, there are one or more with zero norm, which are "
- "simply averaged to find the B=0 reference image value\n "
- "\b\bo if \"false\": there may or may not be diffusion-weighted "
- "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 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, "-",
- "output tensor volume");
+ hestOptAdd_Flag(&hopt, "old", &oldstuff,
+ "instead of the new tenEstimateContext code, use "
+ "the old tenEstimateLinear code");
+ hestOptAdd_1_Float(&hopt, "sigma", "sigma", &sigma, "nan", "Rician noise parameter");
+ hestOptAdd_1_Int(&hopt, "v", "verbose", &verbose, "0", "verbosity level");
+ hestOptAdd_1_Enum(&hopt, "est", "estimate method", &estmeth, "lls",
+ "estimation method to use. \"lls\": linear-least squares",
+ tenEstimate1Method);
+ hestOptAdd_1_UInt(&hopt, "wlsi", "WLS iters", &wlsi, "1",
+ "when using weighted-least-squares (\"-est wls\"), how "
+ "many iterations to do after the initial weighted fit.");
+ hestOptAdd_Flag(&hopt, "fixneg", &fixneg,
+ "after estimating the tensor, ensure that there are no negative "
+ "eigenvalues by adding (to all eigenvalues) the amount by which "
+ "the smallest is negative (corresponding to increasing the "
+ "non-DWI image value).");
+ hestOptAdd_1_String(&hopt, "ee", "filename", &terrS, "",
+ "Giving a filename here allows you to save out the tensor "
+ "estimation error: a value which measures how much error there "
+ "is between the tensor model and the given diffusion weighted "
+ "measurements for each sample. By default, no such error "
+ "calculation is saved.");
+ hestOptAdd_1_String(&hopt, "eb", "filename", &eb0S, "",
+ "In those cases where there is no B=0 reference image given "
+ "(\"-knownB0 false\"), "
+ "giving a filename here allows you to save out the B=0 image "
+ "which is estimated from the data. By default, this image value "
+ "is estimated but not saved.");
+ hestOptAdd_1_Double(&hopt, "t", "thresh", &thresh, "nan",
+ "value at which to threshold the mean DWI value per pixel "
+ "in order to generate the \"confidence\" mask. By default, "
+ "the threshold value is calculated automatically, based on "
+ "histogram analysis.");
+ hestOptAdd_1_Float(&hopt, "soft", "soft", &soft, "0",
+ "how fuzzy the confidence boundary should be. By default, "
+ "confidence boundary is perfectly sharp");
+ hestOptAdd_1_Float(&hopt, "scale", "scale", &scale, "1",
+ "After estimating the tensor, scale all of its elements "
+ "(but not the confidence value) by this amount. Can help with "
+ "downstream numerical precision if values are very large "
+ "or small.");
+ hestOptAdd_1_Double(&hopt, "mv", "min val", &valueMin, "1.0",
+ "minimum plausible value (especially important for linear "
+ "least squares estimation)");
+ hestOptAdd_1_String(&hopt, "B", "B-list", &bmatS, NULL,
+ "6-by-N list of B-matrices characterizing "
+ "the diffusion weighting for each "
+ "image. \"tend bmat\" is one source for such a matrix; see "
+ "its usage info for specifics on how the coefficients of "
+ "the B-matrix are ordered. "
+ "An unadorned plain text file is a great way to "
+ "specify the B-matrix.\n **OR**\n "
+ "Can say just \"-B kvp\" to try to learn B matrices from "
+ "key/value pair information in input images.");
+ hestOptAdd_1_Double(&hopt, "b", "b", &bval, "nan",
+ "\"b\" diffusion-weighting factor (units of sec/mm^2)");
+ hestOptAdd_1_Bool(&hopt, "knownB0", "bool", &knownB0, NULL,
+ "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 "
+ "B-matrices, there are one or more with zero norm, which are "
+ "simply averaged to find the B=0 reference image value\n "
+ "\b\bo if \"false\": there may or may not be diffusion-weighted "
+ "images among the input; the B=0 image value is going to be "
+ "estimated along with the diffusion model");
+ hestOptAdd_Nv_Other(&hopt, "i", "dwi0 dwi1", 1, -1, &nin, "-",
+ "all the diffusion-weighted images (DWIs), as separate 3D nrrds, "
+ "**OR**: One 4D nrrd of all DWIs stacked along axis 0",
+ &ninLen, nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output tensor volume");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_estimInfoL);
- JUSTPARSE();
+ USAGE_JUSTPARSE(_tend_estimInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendEval.c
===================================================================
--- teem/trunk/src/ten/tendEval.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEval.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -32,34 +32,32 @@
char *perr, *err;
airArray *mop;
- int ret, *comp, compLen, cc;
+ int ret;
+ unsigned int *comp, compLen, cc;
Nrrd *nin, *nout;
char *outS;
float thresh, *edata, *tdata, eval[3], evec[9];
size_t N, I, sx, sy, sz;
- hestOptAdd(&hopt, "c", "c0 ", airTypeInt, 1, 3, &comp, NULL,
- "which eigenvalues should be saved out. \"0\" for the "
- "largest, \"1\" for the middle, \"2\" for the smallest, "
- "\"0 1\", \"1 2\", \"0 1 2\" or similar for more than one",
- &compLen);
- hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5",
- "confidence threshold");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_Nv_UInt(&hopt, "c", "c0 ", 1, 3, &comp, NULL,
+ "which eigenvalues should be saved out. \"0\" for the "
+ "largest, \"1\" for the middle, \"2\" for the smallest, "
+ "\"0 1\", \"1 2\", \"0 1 2\" or similar for more than one",
+ &compLen);
+ hestOptAdd_1_Float(&hopt, "t", "thresh", &thresh, "0.5", "confidence threshold");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evalInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evalInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
for (cc = 0; cc < compLen; cc++) {
- if (!AIR_IN_CL(0, comp[cc], 2)) {
- fprintf(stderr, "%s: requested component %d (%d of 3) not in [0..2]\n", me,
- comp[cc], cc + 1);
+ if (!(comp[cc] <= 2)) {
+ fprintf(stderr, "%s: requested component %u (%u of %u) not in [0..2]\n", me,
+ comp[cc], cc + 1, compLen);
airMopError(mop);
return 1;
}
Modified: teem/trunk/src/ten/tendEvaladd.c
===================================================================
--- teem/trunk/src/ten/tendEvaladd.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvaladd.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -39,17 +39,14 @@
char *outS;
float val;
- hestOptAdd(&hopt, "v", "value", airTypeFloat, 1, 1, &val, NULL,
- "Value to add to all eigenvalues");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_Float(&hopt, "v", "value", &val, NULL, "Value to add to all eigenvalues");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evaladdInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evaladdInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendEvalclamp.c
===================================================================
--- teem/trunk/src/ten/tendEvalclamp.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvalclamp.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -39,23 +39,21 @@
char *outS;
float min, max;
- hestOptAdd(&hopt, "min", "min", airTypeFloat, 1, 1, &min, NULL,
- "Eigenvalues are clamped from below by this (the minimum "
- "output eigenvalue). Use \"nan\" to signify that no "
- "minimum clamping should be done.");
- hestOptAdd(&hopt, "max", "max", airTypeFloat, 1, 1, &max, "nan",
- "Eigenvalues are clamped from above by this (the maximum "
- "output eigenvalue). Use \"nan\" to signify that no "
- "maximum clamping should be done.");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_Float(&hopt, "min", "min", &min, NULL,
+ "Eigenvalues are clamped from below by this (the minimum "
+ "output eigenvalue). Use \"nan\" to signify that no "
+ "minimum clamping should be done.");
+ hestOptAdd_1_Float(&hopt, "max", "max", &max, "nan",
+ "Eigenvalues are clamped from above by this (the maximum "
+ "output eigenvalue). Use \"nan\" to signify that no "
+ "maximum clamping should be done.");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evalclampInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evalclampInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendEvalmult.c
===================================================================
--- teem/trunk/src/ten/tendEvalmult.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvalmult.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -37,17 +37,15 @@
char *outS;
float val;
- hestOptAdd(&hopt, "v", "value", airTypeFloat, 1, 1, &val, NULL,
- "Value to multiply eigenvalues by");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_Float(&hopt, "v", "value", &val, NULL,
+ "Value to multiply eigenvalues by");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evalmultInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evalmultInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendEvalpow.c
===================================================================
--- teem/trunk/src/ten/tendEvalpow.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvalpow.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -37,17 +37,15 @@
char *outS;
float expo;
- hestOptAdd(&hopt, "p", "power", airTypeFloat, 1, 1, &expo, NULL,
- "Power to which to raise all the eigenvalues.");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output tensor volume");
+ hestOptAdd_1_Float(&hopt, "p", "power", &expo, NULL,
+ "Power to which to raise all the eigenvalues.");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output tensor volume");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evalpowInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evalpowInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendEvec.c
===================================================================
--- teem/trunk/src/ten/tendEvec.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvec.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -32,28 +32,26 @@
char *perr, *err;
airArray *mop;
- int ret, *comp, compLen, cc;
+ int ret, *comp;
+ unsigned int cc, compLen;
Nrrd *nin, *nout;
char *outS;
float thresh, *edata, *tdata, eval[3], evec[9], scl;
size_t N, I, sx, sy, sz;
- hestOptAdd(&hopt, "c", "c0 ", airTypeInt, 1, 3, &comp, NULL,
- "which eigenvalues should be saved out. \"0\" for the "
- "largest, \"1\" for the middle, \"2\" for the smallest, "
- "\"0 1\", \"1 2\", \"0 1 2\" or similar for more than one",
- &compLen);
- hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5",
- "confidence threshold");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_Nv_Int(&hopt, "c", "c0 ", 1, 3, &comp, NULL,
+ "which eigenvalues should be saved out. \"0\" for the "
+ "largest, \"1\" for the middle, \"2\" for the smallest, "
+ "\"0 1\", \"1 2\", \"0 1 2\" or similar for more than one",
+ &compLen);
+ hestOptAdd_1_Float(&hopt, "t", "thresh", &thresh, "0.5", "confidence threshold");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evecInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evecInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
for (cc = 0; cc < compLen; cc++) {
Modified: teem/trunk/src/ten/tendEvecrgb.c
===================================================================
--- teem/trunk/src/ten/tendEvecrgb.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvecrgb.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -42,30 +42,28 @@
rgbp = tenEvecRGBParmNew();
airMopAdd(mop, rgbp, AIR_CAST(airMopper, tenEvecRGBParmNix), airMopAlways);
- hestOptAdd(&hopt, "c", "evec index", airTypeUInt, 1, 1, &(rgbp->which), NULL,
- "which eigenvector will be colored. \"0\" for the "
- "principal, \"1\" for the middle, \"2\" for the minor");
- hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &(rgbp->aniso), NULL,
- "Which anisotropy to use for modulating the saturation "
- "of the colors. " TEN_ANISO_DESC,
- NULL, tenAniso);
- hestOptAdd(&hopt, "t", "thresh", airTypeDouble, 1, 1, &(rgbp->confThresh), "0.5",
- "confidence threshold");
- hestOptAdd(&hopt, "bg", "background", airTypeDouble, 1, 1, &(rgbp->bgGray), "0",
- "gray level to use for voxels who's confidence is zero ");
- hestOptAdd(&hopt, "gr", "gray", airTypeDouble, 1, 1, &(rgbp->isoGray), "0",
- "the gray level to desaturate towards as anisotropy "
- "decreases (while confidence remains 1.0)");
- hestOptAdd(&hopt, "gam", "gamma", airTypeDouble, 1, 1, &(rgbp->gamma), "1",
- "gamma to use on color components");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_UInt(&hopt, "c", "evec index", &(rgbp->which), NULL,
+ "which eigenvector will be colored. \"0\" for the "
+ "principal, \"1\" for the middle, \"2\" for the minor");
+ hestOptAdd_1_Enum(&hopt, "a", "aniso", &(rgbp->aniso), NULL,
+ "Which anisotropy to use for modulating the saturation "
+ "of the colors. " TEN_ANISO_DESC,
+ tenAniso);
+ hestOptAdd_1_Double(&hopt, "t", "thresh", &(rgbp->confThresh), "0.5",
+ "confidence threshold");
+ hestOptAdd_1_Double(&hopt, "bg", "background", &(rgbp->bgGray), "0",
+ "gray level to use for voxels who's confidence is zero ");
+ hestOptAdd_1_Double(&hopt, "gr", "gray", &(rgbp->isoGray), "0",
+ "the gray level to desaturate towards as anisotropy "
+ "decreases (while confidence remains 1.0)");
+ hestOptAdd_1_Double(&hopt, "gam", "gamma", &(rgbp->gamma), "1",
+ "gamma to use on color components");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evecrgbInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evecrgbInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendEvq.c
===================================================================
--- teem/trunk/src/ten/tendEvq.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendEvq.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -24,12 +24,13 @@
#define INFO "Quantize directions of diffusion"
static const char *_tend_evqInfoL
- = (INFO ". Because VTK doesn't do multi-dimensional colormaps, we have to "
- "quantize directions of diffusion (usually just the principal eigenvector) "
- "in order to create the usual XYZ<->RGB coloring. Because "
- "eigenvector directions are poorly defined in regions of low "
- "anisotropy, the length of the vector (pre-quantization) is modulated "
- "by anisotropy, requiring the selection of some anisotropy metric.");
+ = (INFO
+ ". Because VTK doesn't do multi-dimensional colormaps (circa year 2000), we "
+ "have to quantize directions of diffusion (usually just the principal eigenvector) "
+ "in order to create the usual XYZ<->RGB coloring. Because eigenvector directions "
+ "are poorly defined in regions of low anisotropy, the length of the vector "
+ "(pre-quantization) is modulated by anisotropy, requiring the selection of some "
+ "anisotropy metric.");
static int
tend_evqMain(int argc, const char **argv, const char *me, hestParm *hparm) {
@@ -38,32 +39,30 @@
char *perr, *err;
airArray *mop;
- int which, aniso, dontScaleByAniso;
+ int aniso, dontScaleByAniso;
+ unsigned int which;
Nrrd *nin, *nout;
char *outS;
- hestOptAdd(&hopt, "c", "evec index", airTypeInt, 1, 1, &which, "0",
- "Which eigenvector should be quantized: \"0\" for the "
- "direction of fastest diffusion (eigenvector associated "
- "with largest eigenvalue), \"1\" or \"2\" for other two "
- "eigenvectors (associated with middle and smallest eigenvalue)");
- hestOptAdd(&hopt, "a", "aniso", airTypeEnum, 1, 1, &aniso, NULL,
- "Which anisotropy metric to scale the eigenvector "
- "with. " TEN_ANISO_DESC,
- NULL, tenAniso);
- hestOptAdd(&hopt, "ns", NULL, airTypeInt, 0, 0, &dontScaleByAniso, NULL,
- "Don't attenuate the color by anisotropy. By default (not "
- "using this option), regions with low or no anisotropy are "
- "very dark colors or black");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output image (floating point)");
+ hestOptAdd_1_UInt(&hopt, "c", "evec index", &which, "0",
+ "Which eigenvector should be quantized: \"0\" for the "
+ "direction of fastest diffusion (eigenvector associated "
+ "with largest eigenvalue), \"1\" or \"2\" for other two "
+ "eigenvectors (associated with middle and smallest eigenvalue)");
+ hestOptAdd_1_Enum(&hopt, "a", "aniso", &aniso, NULL,
+ "Scale the eigenvector with this anisotropy metric. " TEN_ANISO_DESC,
+ tenAniso);
+ hestOptAdd_Flag(&hopt, "ns", &dontScaleByAniso,
+ "Don't attenuate the color by anisotropy. By default (not "
+ "using this option), regions with low or no anisotropy are "
+ "very dark colors or black");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output image (floating point)");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_evqInfoL);
- PARSE();
+ USAGE_PARSE(_tend_evqInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendExp.c
===================================================================
--- teem/trunk/src/ten/tendExp.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendExp.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -36,14 +36,13 @@
Nrrd *nin, *nout;
char *outS;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL, "output image");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, NULL, "output image");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
- USAGE(_tend_expInfoL);
- PARSE();
+ USAGE_PARSE(_tend_expInfoL);
airMopAdd(mop, hopt, (airMopper)hestParseFree, airMopAlways);
nout = nrrdNew();
Modified: teem/trunk/src/ten/tendExpand.c
===================================================================
--- teem/trunk/src/ten/tendExpand.c 2023-07-15 12:12:55 UTC (rev 7104)
+++ teem/trunk/src/ten/tendExpand.c 2023-07-15 12:13:27 UTC (rev 7105)
@@ -45,31 +45,30 @@
int orientRed, orientRedWithOrigin, mfRed;
float scale, thresh;
- hestOptAdd(&hopt, "t", "thresh", airTypeFloat, 1, 1, &thresh, "0.5",
- "confidence level to threshold output tensors at. Should "
- "be between 0.0 and 1.0.");
- hestOptAdd(&hopt, "s", "scale", airTypeFloat, 1, 1, &scale, "1.0",
- "how to scale values before saving as 9-value tensor. Useful "
- "for visualization tools which assume certain characteristic "
- "ranges of eigenvalues");
- hestOptAdd(&hopt, "unmf", NULL, airTypeInt, 0, 0, &mfRed, NULL,
- "apply and remove the measurement frame, if it exists");
- hestOptAdd(&hopt, "ro", NULL, airTypeInt, 0, 0, &orientRed, NULL,
- "reduce general image orientation to axis-aligned spacings");
- hestOptAdd(&hopt, "roo", NULL, airTypeInt, 0, 0, &orientRedWithOrigin, NULL,
- "reduce general image orientation to axis-aligned spacings, "
- "while also making some effort to set axis mins from "
- "space origin");
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, "-",
- "input diffusion tensor volume, with 7 values per sample", NULL, NULL,
- nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, NULL,
- "output tensor volume, with the 9 matrix components per sample");
+ hestOptAdd_1_Float(&hopt, "t", "thresh", &thresh, "0.5",
+ "confidence level to threshold output tensors at. Should "
+ "be between 0.0 and 1.0.");
+ hestOptAdd_1_Float(&hopt, "s", "scale", &scale, "1.0",
+ "how to scale values before saving as 9-value tensor. Useful "
+ "for visualization tools which assume certain characteristic "
+ "ranges of eigenvalues");
+ hestOptAdd_Flag(&hopt, "unmf", &mfRed,
+ "apply and remove the measurement frame, if it exists");
+ hestOptAdd_Flag(&hopt, "ro", &orientRed,
+ "reduce general image orientation to axis-aligned spacings");
+ hestOptAdd_Flag(&hopt, "roo", &orientRedWithOrigin,
+ "reduce general image orientation to axis-aligned spacings, "
+ "while also making some effort to set axis mins from "
+ "space origin");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-",
+ "input diffusion tensor volume, with 7 values per sample",
+ nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, NULL,
+ ...
[truncated message content] |
|
From: <kin...@us...> - 2023-07-15 12:12:57
|
Revision: 7104
http://sourceforge.net/p/teem/code/7104
Author: kindlmann
Date: 2023-07-15 12:12:55 +0000 (Sat, 15 Jul 2023)
Log Message:
-----------
like in unu: the PARSE (and the tend-specific JUSTPARSE) macros now take the INFO string, because it is part of how they respond to --help
Modified Paths:
--------------
teem/trunk/src/ten/privateTen.h
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2023-07-14 16:58:11 UTC (rev 7103)
+++ teem/trunk/src/ten/privateTen.h 2023-07-15 12:12:55 UTC (rev 7104)
@@ -29,9 +29,9 @@
/* USAGE, PARSE: both copied verbatim from unrrdu/privateUnrrdu.h, but
** then some hacking was added . . .
*/
-#define USAGE(info) \
+#define USAGE(INFO) \
if (!argc && !hparm->noArgsIsNoProblem) { \
- hestInfo(stdout, me, (info), hparm); \
+ hestInfo(stdout, me, (INFO), hparm); \
hestUsage(stdout, hopt, me, hparm); \
hestGlossary(stdout, hopt, hparm); \
airMopError(mop); \
@@ -38,10 +38,10 @@
return 0; \
}
-/* JUSTPARSE is called by the tend functions that do *not* take an
+/* JUSTPARSE is used by the tend functions that do *not* take an
** input 7-component tensor volume
*/
-#define JUSTPARSE() \
+#define JUSTPARSE(INFO) \
if ((pret = hestParse(hopt, argc, argv, &perr, hparm))) { \
if (1 == pret) { \
fprintf(stderr, "%s: %s\n", me, perr); \
@@ -65,12 +65,12 @@
}
/*
-** PARSE is called by tend functions that do take a 7-component tensor
+** PARSE is used 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(); \
+#define PARSE(INFO) \
+ JUSTPARSE(INFO); \
if (4 == nin->dim && 6 == nin->axis[0].size && nrrdTypeBlock != nin->type) { \
ptrdiff_t padmin[4], padmax[4]; \
Nrrd *npadtmp; \
@@ -94,6 +94,10 @@
nrrdNuke(npadtmp); \
}
+/* convenience macros now that using INFO is part of how PARSE responds to --help */
+#define USAGE_PARSE(INFO) USAGE(INFO) PARSE(INFO)
+#define USAGE_JUSTPARSE(INFO) USAGE(INFO) JUSTPARSE(INFO)
+
/* enumsTen.c */
extern const airEnum _tenGage;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-14 16:58:13
|
Revision: 7103
http://sourceforge.net/p/teem/code/7103
Author: kindlmann
Date: 2023-07-14 16:58:11 +0000 (Fri, 14 Jul 2023)
Log Message:
-----------
clarifying comment
Modified Paths:
--------------
teem/trunk/src/unrrdu/privateUnrrdu.h
Modified: teem/trunk/src/unrrdu/privateUnrrdu.h
===================================================================
--- teem/trunk/src/unrrdu/privateUnrrdu.h 2023-07-14 16:32:21 UTC (rev 7102)
+++ teem/trunk/src/unrrdu/privateUnrrdu.h 2023-07-14 16:58:11 UTC (rev 7103)
@@ -286,7 +286,8 @@
return 0; \
}
-/* For the (many) times that USAGE and PARSE are used together */
+/* For the (many) times that USAGE and PARSE are used together, useful
+ now that using INFO is part of how PARSE responds to --help */
#define USAGE_OR_PARSE(INFO) \
USAGE(INFO) \
PARSE(INFO)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-14 16:32:23
|
Revision: 7102
http://sourceforge.net/p/teem/code/7102
Author: kindlmann
Date: 2023-07-14 16:32:21 +0000 (Fri, 14 Jul 2023)
Log Message:
-----------
more comments about the new functions
Modified Paths:
--------------
teem/trunk/src/hest/adders.c
Modified: teem/trunk/src/hest/adders.c
===================================================================
--- teem/trunk/src/hest/adders.c 2023-07-14 12:29:56 UTC (rev 7101)
+++ teem/trunk/src/hest/adders.c 2023-07-14 16:32:21 UTC (rev 7102)
@@ -54,8 +54,39 @@
type (like void* is the generic pointer type), and, we're not doing compile-time checks
on the non-NULL-ity of hestCB->destroy. So it all devolves back to plain void*. Still,
the hestOptAdd_*_Other function are generated here to slightly simplify the hestOptAdd
-call, since there is no more NULL and NULL for sawP and enum. Actually, there is a way
-around a type-checking black hole: extreme attentiveness!
+call, since there is no more NULL and NULL for sawP and enum. The only way around this
+particular type-checking black hole is still extreme attentiveness.
+
+Two other design points of note:
+
+(1) If we're moving to more type checking, why not make the default values be something
+other than a mere string? Why isn't the default typed in a way analogous to the newly
+typed valueP? This is a great idea, and it was actually briefly tried, but then
+abandoned. One of the original good ideas that made hest work (when it was created) was
+the recognition that if the point is to get values out of argv strings collected from the
+command-line, then you are absolutely unavoidably in the business of parsing values from
+strings, at which point you are losing zero expressivity to have the default also
+expressed as a string, and, as a happy side-effect, the type of the string was the same
+for all cases. So nothing in hest ever learned to *copy* values from a given default
+value array, it *only* *parses* values from strings. So couldn't all the functions
+generated below take typed default values and generate the default string? Yes, but the
+code is annoying, and it seems fishy to have a string-->value route for user-supplied
+options, but a value-->string-->value route for options using their default, and it risks
+confusion to have the hestGlossary-generated usage info show a default string (and it in
+that context it really does need to be a string) that doesn't seem to match the
+compiled-time value array. Also, the cases where the default is not known at compile
+(and is instead learned only at run-time) are so rare that the cost of converting that
+default value to a string is acceptable. If hest (in Teem v3) learns to copy values from
+a given default value array, this may be revisited.
+
+(2) Why the underscores in the names? Teem is pretty consistent about usingCamelCase for
+everything, no? Yes, except when it gets in the way of legibility, like the airInsane_*
+enum values, the airFP_* enum values, and nrrdWrap_nva, nrrdAlloc_nva ... (and the
+snake_case ell and tijk libraries). The "hestOptAdd" prefix needs to stay the same (we're
+not going to have both hestOptAdd() and hest_opt_add_*() in one library, when other
+necessary functions like hestOptFree() are not going to change. So then the question is:
+which is more reader-friendly: hestOptAddNvUInt or hestOpt_Nv_UInt? Obviously the
+second, and that matters more that superficial consistency.
*/
/* --------------------------------------------------------------- 1 == kind */
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|
|
From: <kin...@us...> - 2023-07-14 12:29:57
|
Revision: 7101
http://sourceforge.net/p/teem/code/7101
Author: kindlmann
Date: 2023-07-14 12:29:56 +0000 (Fri, 14 Jul 2023)
Log Message:
-----------
updating how multi-line piping works to move away from csh towards bash and friends, making output respect hparm->columns
Modified Paths:
--------------
teem/trunk/src/ten/tendAbout.c
Modified: teem/trunk/src/ten/tendAbout.c
===================================================================
--- teem/trunk/src/ten/tendAbout.c 2023-07-14 12:28:18 UTC (rev 7100)
+++ teem/trunk/src/ten/tendAbout.c 2023-07-14 12:29:56 UTC (rev 7101)
@@ -58,10 +58,10 @@
"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 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";
AIR_UNUSED(argc);
AIR_UNUSED(argv);
@@ -76,10 +76,10 @@
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, hparm->columns, par1, AIR_FALSE);
+ _hestPrintStr(stdout, 1, 0, hparm->columns, par2, AIR_FALSE);
+ _hestPrintStr(stdout, 1, 0, hparm->columns, par3, AIR_FALSE);
+ _hestPrintStr(stdout, 2, 0, hparm->columns, par4, AIR_FALSE);
return 0;
}
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|
|
From: <kin...@us...> - 2023-07-14 12:28:21
|
Revision: 7100
http://sourceforge.net/p/teem/code/7100
Author: kindlmann
Date: 2023-07-14 12:28:18 +0000 (Fri, 14 Jul 2023)
Log Message:
-----------
using new hparm->noArgsIsNoProblem and nrrdHestNrrdNoTTY
Modified Paths:
--------------
teem/trunk/src/ten/tendUnmf.c
Modified: teem/trunk/src/ten/tendUnmf.c
===================================================================
--- teem/trunk/src/ten/tendUnmf.c 2023-07-14 12:27:09 UTC (rev 7099)
+++ teem/trunk/src/ten/tendUnmf.c 2023-07-14 12:28:18 UTC (rev 7100)
@@ -39,13 +39,10 @@
Nrrd *nin, *nout;
char *outS;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
- "input diffusion tensor volume "
- "(sorry, can't use usual default of \"-\" for stdin "
- "because of hest quirk)",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
- "output tensor volume");
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, "-", "input diffusion tensor volume ",
+ nrrdHestNrrdNoTTY);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output tensor volume");
mop = airMopNew();
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
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|
|
From: <kin...@us...> - 2023-07-14 12:27:11
|
Revision: 7099
http://sourceforge.net/p/teem/code/7099
Author: kindlmann
Date: 2023-07-14 12:27:09 +0000 (Fri, 14 Jul 2023)
Log Message:
-----------
copying from unu new handling of hparm->noArgsIsNoProblem so that commands can have defaults for all options
Modified Paths:
--------------
teem/trunk/src/ten/privateTen.h
Modified: teem/trunk/src/ten/privateTen.h
===================================================================
--- teem/trunk/src/ten/privateTen.h 2023-07-13 23:23:48 UTC (rev 7098)
+++ teem/trunk/src/ten/privateTen.h 2023-07-14 12:27:09 UTC (rev 7099)
@@ -30,7 +30,7 @@
** then some hacking was added . . .
*/
#define USAGE(info) \
- if (!argc) { \
+ if (!argc && !hparm->noArgsIsNoProblem) { \
hestInfo(stdout, me, (info), hparm); \
hestUsage(stdout, hopt, me, hparm); \
hestGlossary(stdout, hopt, hparm); \
@@ -47,7 +47,11 @@
fprintf(stderr, "%s: %s\n", me, perr); \
free(perr); \
hestUsage(stderr, hopt, me, hparm); \
- fprintf(stderr, "\nFor more info: \"%s\" or \"%s ... --help\"\n", me, me); \
+ if (hparm && hparm->noArgsIsNoProblem) { \
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me); \
+ } else { \
+ fprintf(stderr, "\nFor more info: \"%s\" or \"%s --help\"\n", me, me); \
+ } \
airMopError(mop); \
return 2; \
} else { \
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|
|
From: <kin...@us...> - 2023-07-13 23:23:50
|
Revision: 7098
http://sourceforge.net/p/teem/code/7098
Author: kindlmann
Date: 2023-07-13 23:23:48 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
turning OFF hparm->elideSingleOtherDefault (or, no longer turning it on), since it needlessly obscured what the -i input option to most unu commands was
Modified Paths:
--------------
teem/trunk/src/bin/unu.c
Modified: teem/trunk/src/bin/unu.c
===================================================================
--- teem/trunk/src/bin/unu.c 2023-07-13 23:05:20 UTC (rev 7097)
+++ teem/trunk/src/bin/unu.c 2023-07-13 23:23:48 UTC (rev 7098)
@@ -64,12 +64,17 @@
airMopAdd(mop, hparm, hestParmFree_vp, airMopAlways);
hparm->elideSingleEnumType = AIR_TRUE;
hparm->elideSingleOtherType = AIR_TRUE;
- hparm->elideSingleOtherDefault = AIR_TRUE;
+ /*
+ * This prevents clarifying that the default input is "-" i.e. stdin, and it was
+ * explicitly turned off in multiple commands (such as resample). In the interests of
+ * clarity, no longer want to elide this info.
+ * hparm->elideSingleOtherDefault = AIR_TRUE;
+ */
hparm->elideSingleNonExistFloatDefault = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
hparm->elideSingleEmptyStringDefault = AIR_TRUE;
hparm->elideMultipleEmptyStringDefault = AIR_TRUE;
- /* so that we look for, and know how to handle, seeing "--help" */
+ /* say that we look for, and know how to handle, seeing "--help" */
hparm->respectDashDashHelp = AIR_TRUE;
/* Try to dynamically learn number of columns. Learning the terminal size will probably
work if stdout is the terminal, but not if we're piping elsewhere (as is common with
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|
|
From: <kin...@us...> - 2023-07-13 23:05:23
|
Revision: 7097
http://sourceforge.net/p/teem/code/7097
Author: kindlmann
Date: 2023-07-13 23:05:20 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
make some more things unsigned that should always have been so
Modified Paths:
--------------
teem/trunk/src/alan/alan.h
teem/trunk/src/alan/coreAlan.c
teem/trunk/src/alan/methodsAlan.c
Modified: teem/trunk/src/alan/alan.h
===================================================================
--- teem/trunk/src/alan/alan.h 2023-07-13 23:04:28 UTC (rev 7096)
+++ teem/trunk/src/alan/alan.h 2023-07-13 23:05:20 UTC (rev 7097)
@@ -108,15 +108,15 @@
typedef struct alanContext_t {
/* INPUT ----------------------------- */
unsigned int dim, /* either 2 or 3 */
- size[3]; /* number of texels in X, Y, (Z) */
+ size[3], /* number of texels in X, Y, (Z) */
+ numThreads, /* # of threads, if airThreadCapable */
+ frameInterval, /* # of iterations between which to an image */
+ saveInterval, /* # of iterations between which to save all state */
+ maxIteration; /* cap on # of iterations, or 0 if there is no limit */
int verbose, wrap, /* do toroidal boundary wrapping */
textureType, /* what kind are we (from alanTextureType* enum) */
oversample, /* oversampling of tensors to texels */
homogAniso, /* homogenous anisotropy approximation */
- numThreads, /* # of threads, if airThreadCapable */
- frameInterval, /* # of iterations between which to an image */
- saveInterval, /* # of iterations between which to save all state */
- maxIteration, /* cap on # of iterations, or 0 if there is no limit */
constFilename; /* always use the same filename when saving frames */
alan_t K, F, /* simulation variables */
deltaX, /* size of spatial grid discretization */
@@ -137,13 +137,13 @@
int (*perIteration)(struct alanContext_t *, int iter);
/* INTERNAL -------------------------- */
- int iter; /* current iteration */
- Nrrd *_nlev[2], /* levels of morphogens, alternating buffers */
- *nlev; /* pointer to last iterations output */
- Nrrd *nparm; /* alpha, beta values for all texels */
- alan_t averageChange; /* average amount of "change" in last iteration */
- int changeCount; /* # of contributions to averageChange */
- /* to control update of averageChange and changeCount */
+ int iter; /* current iteration */
+ Nrrd *_nlev[2], /* levels of morphogens, alternating buffers */
+ *nlev; /* pointer to last iterations output */
+ Nrrd *nparm; /* alpha, beta values for all texels */
+ alan_t averageChange; /* average amount of "change" in last iteration */
+ unsigned int changeCount; /* # of contributions to averageChange
+ to control update of averageChange and changeCount */
airThreadMutex *changeMutex;
/* to synchronize separate iterations of simulation */
airThreadBarrier *iterBarrier;
Modified: teem/trunk/src/alan/coreAlan.c
===================================================================
--- teem/trunk/src/alan/coreAlan.c 2023-07-13 23:04:28 UTC (rev 7096)
+++ teem/trunk/src/alan/coreAlan.c 2023-07-13 23:05:20 UTC (rev 7097)
@@ -223,8 +223,9 @@
*tpx, *tmx, *tpy, *tmy, /* *tpz, *tmz, */
*lev0, *lev1, *parm, deltaT, alpha, beta, A, B, *v[27], lapA, lapB, corrA, corrB,
deltaA, deltaB, diffA, diffB, change;
- int dim, iter, stop, startW, endW, idx, px, mx, py, my, pz, mz, startY, endY, startZ,
- endZ, sx, sy, sz, x, y, z;
+ int dim, stop, startW, endW, idx, px, mx, py, my, pz, mz, startY, endY, startZ, endZ,
+ sx, sy, sz, x, y, z;
+ unsigned int iter;
alanTask *task;
task = (alanTask *)_task;
@@ -455,7 +456,8 @@
int /* Biff: 1 */
alanRun(alanContext *actx) {
static const char me[] = "alanRun";
- int tid, hack = AIR_FALSE;
+ int hack = AIR_FALSE;
+ unsigned int tid;
alanTask task[ALAN_THREAD_MAX];
if (_alanCheck(actx)) {
Modified: teem/trunk/src/alan/methodsAlan.c
===================================================================
--- teem/trunk/src/alan/methodsAlan.c 2023-07-13 23:04:28 UTC (rev 7096)
+++ teem/trunk/src/alan/methodsAlan.c 2023-07-13 23:05:20 UTC (rev 7097)
@@ -208,6 +208,7 @@
alanParmSet(alanContext *actx, int whichParm, double parm) {
static const char me[] = "alanParmSet";
int parmI;
+ unsigned int parmUI;
GOT_NULL;
DIM_SET;
@@ -239,15 +240,15 @@
actx->textureType = parmI;
break;
case alanParmNumThreads:
- parmI = !!parm;
+ parmUI = AIR_UINT(parm);
if (!airThreadCapable) {
fprintf(stderr,
"%s: WARNING: no multi-threading available, so 1 thread "
- "will be used, not %d\n",
- me, parmI);
- parmI = 1;
+ "will be used, not %u\n",
+ me, parmUI);
+ parmUI = 1;
}
- actx->numThreads = parmI;
+ actx->numThreads = parmUI;
break;
case alanParmHomogAniso:
parmI = !!parm;
@@ -254,16 +255,16 @@
actx->homogAniso = parmI;
break;
case alanParmSaveInterval:
- parmI = !!parm;
- actx->saveInterval = parmI;
+ parmUI = AIR_UINT(parm);
+ actx->saveInterval = parmUI;
break;
case alanParmFrameInterval:
- parmI = !!parm;
- actx->frameInterval = parmI;
+ parmUI = AIR_UINT(parm);
+ actx->frameInterval = parmUI;
break;
case alanParmMaxIteration:
- parmI = !!parm;
- actx->maxIteration = parmI;
+ parmUI = AIR_UINT(parm);
+ actx->maxIteration = parmUI;
break;
case alanParmConstantFilename:
parmI = !!parm;
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|
|
From: <kin...@us...> - 2023-07-13 23:04:30
|
Revision: 7096
http://sourceforge.net/p/teem/code/7096
Author: kindlmann
Date: 2023-07-13 23:04:28 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
make some more things unsigned that should always have been so
Modified Paths:
--------------
teem/trunk/src/hoover/hoover.h
teem/trunk/src/hoover/rays.c
Modified: teem/trunk/src/hoover/hoover.h
===================================================================
--- teem/trunk/src/hoover/hoover.h 2023-07-13 23:01:51 UTC (rev 7095)
+++ teem/trunk/src/hoover/hoover.h 2023-07-13 23:04:28 UTC (rev 7096)
@@ -116,8 +116,8 @@
void *user; /* passed to all callbacks */
/******** 5) stuff about multi-threading */
- unsigned int numThreads; /* number of threads to spawn per rendering */
- int workIdx; /* next work assignment (such as a scanline) */
+ unsigned int numThreads, /* number of threads to spawn per rendering */
+ workIdx; /* next work assignment (such as a scanline) */
airThreadMutex *workMutex; /* mutex around work assignment */
/*
Modified: teem/trunk/src/hoover/rays.c
===================================================================
--- teem/trunk/src/hoover/rays.c 2023-07-13 23:01:51 UTC (rev 7095)
+++ teem/trunk/src/hoover/rays.c 2023-07-13 23:04:28 UTC (rev 7096)
@@ -139,31 +139,31 @@
_hooverThreadBody(void *_arg) {
_hooverThreadArg *arg;
void *thread;
- int ret, /* to catch return values from callbacks */
- sampleI, /* which sample we're on */
- inside, /* we're inside the volume */
- vI, uI; /* integral coords in image */
- double tmp, mm, /* lowest position in index space, for all axes */
- Mx, My, Mz, /* highest position in index space on each axis */
- u, v, /* floating-point coords in image */
- uvScale, /* how to scale (u,v) to go from image to
- near plane, according to ortho or perspective */
- lx, ly, lz, /* half edge-lengths of volume */
- rayLen = 0, /* length of segment formed by ray line intersecting
- the near and far clipping planes */
- rayT, /* current position along ray (world-space) */
- rayDirW[3], /* unit-length ray direction (world-space) */
- rayDirI[3], /* rayDirW transformed into index space;
- not unit length, but a unit change in
- world space along rayDirW translates to
- this change in index space along rayDirI */
- rayPosW[3], /* current ray location (world-space) */
- rayPosI[3], /* current ray location (index-space) */
- rayStartW[3], /* ray start on near plane (world-space) */
- rayStartI[3], /* ray start on near plane (index-space) */
- rayStep, /* distance between samples (world-space) */
- vOff[3], uOff[3]; /* offsets in arg->ec->wU and arg->ec->wV
- directions towards start of ray */
+ int ret, /* to catch return values from callbacks */
+ inside; /* we're inside the volume */
+ unsigned int sampleI, /* which sample we're on */
+ vI, uI; /* integral coords in image */
+ double tmp, mm, /* lowest position in index space, for all axes */
+ Mx, My, Mz, /* highest position in index space on each axis */
+ u, v, /* floating-point coords in image */
+ uvScale, /* how to scale (u,v) to go from image to
+ near plane, according to ortho or perspective */
+ lx, ly, lz, /* half edge-lengths of volume */
+ rayLen = 0, /* length of segment formed by ray line intersecting
+ the near and far clipping planes */
+ rayT, /* current position along ray (world-space) */
+ rayDirW[3], /* unit-length ray direction (world-space) */
+ rayDirI[3], /* rayDirW transformed into index space;
+ not unit length, but a unit change in
+ world space along rayDirW translates to
+ this change in index space along rayDirI */
+ rayPosW[3], /* current ray location (world-space) */
+ rayPosI[3], /* current ray location (index-space) */
+ rayStartW[3], /* ray start on near plane (world-space) */
+ rayStartI[3], /* ray start on near plane (index-space) */
+ rayStep, /* distance between samples (world-space) */
+ vOff[3], uOff[3]; /* offsets in arg->ec->wU and arg->ec->wV
+ directions towards start of ray */
arg = (_hooverThreadArg *)_arg;
if ((ret = (arg->ctx->threadBegin)(&thread,
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|
|
From: <kin...@us...> - 2023-07-13 23:01:55
|
Revision: 7095
http://sourceforge.net/p/teem/code/7095
Author: kindlmann
Date: 2023-07-13 23:01:51 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
updating hest usage
Modified Paths:
--------------
teem/trunk/src/unrrdu/aabplot.c
teem/trunk/src/unrrdu/acrop.c
teem/trunk/src/unrrdu/affine.c
teem/trunk/src/unrrdu/axdelete.c
teem/trunk/src/unrrdu/axinfo.c
teem/trunk/src/unrrdu/axinsert.c
teem/trunk/src/unrrdu/axmerge.c
teem/trunk/src/unrrdu/axsplit.c
teem/trunk/src/unrrdu/basinfo.c
teem/trunk/src/unrrdu/ccadj.c
teem/trunk/src/unrrdu/ccfind.c
teem/trunk/src/unrrdu/ccmerge.c
teem/trunk/src/unrrdu/cmedian.c
teem/trunk/src/unrrdu/convert.c
teem/trunk/src/unrrdu/crop.c
teem/trunk/src/unrrdu/dering.c
teem/trunk/src/unrrdu/dhisto.c
teem/trunk/src/unrrdu/dice.c
teem/trunk/src/unrrdu/diff.c
teem/trunk/src/unrrdu/dist.c
teem/trunk/src/unrrdu/fft.c
teem/trunk/src/unrrdu/gamma.c
teem/trunk/src/unrrdu/hack.c
teem/trunk/src/unrrdu/heq.c
teem/trunk/src/unrrdu/histax.c
teem/trunk/src/unrrdu/histo.c
teem/trunk/src/unrrdu/i2w.c
teem/trunk/src/unrrdu/ilk.c
teem/trunk/src/unrrdu/imap.c
teem/trunk/src/unrrdu/inset.c
teem/trunk/src/unrrdu/jhisto.c
teem/trunk/src/unrrdu/join.c
teem/trunk/src/unrrdu/lut.c
teem/trunk/src/unrrdu/lut2.c
teem/trunk/src/unrrdu/ninspect.c
Modified: teem/trunk/src/unrrdu/aabplot.c
===================================================================
--- teem/trunk/src/unrrdu/aabplot.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/aabplot.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -40,21 +40,18 @@
unsigned int plen;
double vrange[2], *single;
- hestOptAdd(&opt, "l", "len", airTypeUInt, 1, 1, &plen, "78",
- "number of characters in box plot");
- hestOptAdd(&opt, "r", "min max", airTypeDouble, 2, 2, vrange, "0 100",
- "values to use as absolute min and max (unfortunately "
- "has to be same for all scanlines (rows).");
- hestOptAdd(&opt, "rs", "show", airTypeBool, 1, 1, &rshow, "false",
- "show range above plots");
- hestOptAdd(&opt, "ms", "show", airTypeBool, 1, 1, &medshow, "false",
- "print the median value");
+ hestOptAdd_1_UInt(&opt, "l", "len", &plen, "78", "number of characters in box plot");
+ hestOptAdd_2_Double(&opt, "r", "min max", vrange, "0 100",
+ "values to use as absolute min and max (unfortunately "
+ "has to be same for all scanlines (rows).");
+ hestOptAdd_1_Bool(&opt, "rs", "show", &rshow, "false", "show range above plots");
+ hestOptAdd_1_Bool(&opt, "ms", "show", &medshow, "false", "print the median value");
OPT_ADD_NIN(_nin, "input nrrd");
- hestOptAdd(&opt, "s", "single", airTypeOther, 1, 1, &_nsingle, "",
- "if given a 1D nrrd here that matches the number of "
- "rows in the \"-i\" input, interpret it as a list of values "
- "that should be indicated with \"X\"s in the plots.",
- NULL, NULL, nrrdHestNrrd);
+ hestOptAdd_1_Other(&opt, "s", "single", &_nsingle, "",
+ "if given a 1D nrrd here that matches the number of "
+ "rows in the \"-i\" input, interpret it as a list of values "
+ "that should be indicated with \"X\"s in the plots.",
+ nrrdHestNrrd);
mop = airMopNew();
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
Modified: teem/trunk/src/unrrdu/acrop.c
===================================================================
--- teem/trunk/src/unrrdu/acrop.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/acrop.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -47,34 +47,34 @@
Nrrd *nbounds;
char *boundsSave;
- hestOptAdd(&opt, "a,axes", "ax0", airTypeUInt, 0, -1, &axes, "",
- "the axes (if any) that should NOT be cropped", &axesLen);
- hestOptAdd(&opt, "m,measure", "measr", airTypeEnum, 1, 1, &measr, NULL,
- "How to measure slices (along axes to crop) as scalars, "
- "to form 1-D array analyzed to determine cropping extent. "
- "All the measures from \"unu project\" can be used, but "
- "those that make more sense here include:\n "
- "\b\bo \"max\", \"mean\", \"median\", "
- "\"variance\": (self-explanatory)\n "
- "\b\bo \"stdv\": standard deviation\n "
- "\b\bo \"cov\": coefficient of variation\n "
- "\b\bo \"product\", \"sum\": product or sum of all values\n "
- "\b\bo \"L1\", \"L2\", \"NL2\", \"RMS\", \"Linf\": "
- "different norms.",
- NULL, nrrdMeasure);
- hestOptAdd(&opt, "f,frac", "frac", airTypeDouble, 1, 1, &frac, "0.1",
- "threshold of cumulative sum of 1-D array at which to crop. "
- "Needs to be in interval [0.0,0.5).");
- hestOptAdd(&opt, "off,offset", "offset", airTypeInt, 1, 1, &offset, "1",
- "how much to offset the numerically determined cropping; "
- "positive offsets means expanding the interval of kept "
- "indices (less cropping)");
- hestOptAdd(&opt, "b,bounds", "filename", airTypeString, 1, 1, &boundsSave, "",
- "if a filename is given here, the automatically determined "
- "min and max bounds for cropping are saved to this file "
- "as a 2-D array; first scanline is for -min, second is for -max. "
- "Unfortunately nothing using the \"m\" and \"M\" semantics "
- "(above) can currently be saved in the bounds file.");
+ hestOptAdd_Nv_UInt(&opt, "a,axes", "ax0", 0, -1, &axes, "",
+ "the axes (if any) that should NOT be cropped", &axesLen);
+ hestOptAdd_1_Enum(&opt, "m,measure", "measr", &measr, NULL,
+ "How to measure slices (along axes to crop) as scalars, "
+ "to form 1-D array analyzed to determine cropping extent. "
+ "All the measures from \"unu project\" can be used, but "
+ "those that make more sense here include:\n "
+ "\b\bo \"max\", \"mean\", \"median\", "
+ "\"variance\": (self-explanatory)\n "
+ "\b\bo \"stdv\": standard deviation\n "
+ "\b\bo \"cov\": coefficient of variation\n "
+ "\b\bo \"product\", \"sum\": product or sum of all values\n "
+ "\b\bo \"L1\", \"L2\", \"NL2\", \"RMS\", \"Linf\": "
+ "different norms.",
+ nrrdMeasure);
+ hestOptAdd_1_Double(&opt, "f,frac", "frac", &frac, "0.1",
+ "threshold of cumulative sum of 1-D array at which to crop. "
+ "Needs to be in interval [0.0,0.5).");
+ hestOptAdd_1_Int(&opt, "off,offset", "offset", &offset, "1",
+ "how much to offset the numerically determined cropping; "
+ "positive offsets means expanding the interval of kept "
+ "indices (less cropping)");
+ hestOptAdd_1_String(&opt, "b,bounds", "filename", &boundsSave, "",
+ "if a filename is given here, the automatically determined "
+ "min and max bounds for cropping are saved to this file "
+ "as a 2-D array; first scanline is for -min, second is for -max. "
+ "Unfortunately nothing using the \"m\" and \"M\" semantics "
+ "(above) can currently be saved in the bounds file.");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/affine.c
===================================================================
--- teem/trunk/src/unrrdu/affine.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/affine.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -43,24 +43,23 @@
airArray *mop;
unsigned int ai, nn;
- hestOptAdd(&opt, NULL, "minIn", airTypeOther, 1, 1, &minIn, NULL,
- "Lower end of input value range.", NULL, NULL, nrrdHestIter);
- hestOptAdd(&opt, NULL, "in", airTypeOther, 1, 1, &in, NULL, "Input value.", NULL, NULL,
- nrrdHestIter);
- hestOptAdd(&opt, NULL, "maxIn", airTypeOther, 1, 1, &maxIn, NULL,
- "Upper end of input value range.", NULL, NULL, nrrdHestIter);
- hestOptAdd(&opt, NULL, "minOut", airTypeOther, 1, 1, &minOut, NULL,
- "Lower end of output value range.", NULL, NULL, nrrdHestIter);
- hestOptAdd(&opt, NULL, "maxOut", airTypeOther, 1, 1, &maxOut, NULL,
- "Upper end of output value range.", NULL, NULL, nrrdHestIter);
- hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &type, "default",
- "type to convert all nrrd inputs to, prior to "
- "doing operation. This also determines output type. "
- "By default (not using this option), the types of the input "
- "nrrds are left unchanged.",
- NULL, NULL, &unrrduHestMaybeTypeCB);
- hestOptAdd(&opt, "clamp", "bool", airTypeBool, 1, 1, &clamp, "false",
- "clamp output values to specified output range");
+ hestOptAdd_1_Other(&opt, NULL, "minIn", &minIn, NULL,
+ "Lower end of input value range.", nrrdHestIter);
+ hestOptAdd_1_Other(&opt, NULL, "in", &in, NULL, "Input value.", nrrdHestIter);
+ hestOptAdd_1_Other(&opt, NULL, "maxIn", &maxIn, NULL,
+ "Upper end of input value range.", nrrdHestIter);
+ hestOptAdd_1_Other(&opt, NULL, "minOut", &minOut, NULL,
+ "Lower end of output value range.", nrrdHestIter);
+ hestOptAdd_1_Other(&opt, NULL, "maxOut", &maxOut, NULL,
+ "Upper end of output value range.", nrrdHestIter);
+ hestOptAdd_1_Other(&opt, "t,type", "type", &type, "default",
+ "type to convert all nrrd inputs to, prior to "
+ "doing operation. This also determines output type. "
+ "By default (not using this option), the types of the input "
+ "nrrds are left unchanged.",
+ &unrrduHestMaybeTypeCB);
+ hestOptAdd_1_Bool(&opt, "clamp", "bool", &clamp, "false",
+ "clamp output values to specified output range");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
Modified: teem/trunk/src/unrrdu/axdelete.c
===================================================================
--- teem/trunk/src/unrrdu/axdelete.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/axdelete.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -27,9 +27,7 @@
= (INFO ". Singleton axes have only a single sample along them. "
"The underlying linear ordering of the samples is "
"unchanged, and the information about the other axes is "
- "shifted downwards as needed. As a total hack, if you give "
- "-1 as the axis, this will do a matlab-style \"squeeze\", in which "
- "any and all singleton axes are removed.\n "
+ "shifted downwards as needed.\n "
"* Uses nrrdAxesDelete");
static int
@@ -41,8 +39,12 @@
unsigned axis;
airArray *mop;
- hestOptAdd(&opt, "a,axis", "axis", airTypeInt, 1, 1, &_axis, NULL,
- "dimension (axis index) of the axis to remove");
+ /* really needs to be signed int, because of hack */
+ hestOptAdd_1_Int(&opt, "a,axis", "axis", &_axis, NULL,
+ "dimension (axis index) of the axis to remove. "
+ "As a total hack, if you give -1 as the axis, "
+ "this will do a matlab-style \"squeeze\", in which "
+ "any and all singleton axes are removed.");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/axinfo.c
===================================================================
--- teem/trunk/src/unrrdu/axinfo.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/axinfo.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -38,16 +38,15 @@
double mm[2], spc, sdir[NRRD_SPACE_DIM_MAX];
airArray *mop;
- hestOptAdd(&opt, "a,axes", "ax0", airTypeUInt, 1, -1, &axes, NULL,
- "the one or more axes that should be modified", &axesLen);
- hestOptAdd(&opt, "l,label", "label", airTypeString, 1, 1, &label, "",
- "label to associate with axis");
- hestOptAdd(&opt, "u,units", "units", airTypeString, 1, 1, &units, "",
- "units of measurement");
- mmIdx = hestOptAdd(&opt, "mm,minmax", "min max", airTypeString, 2, 2, mmStr, "nan nan",
- "min and max values along axis");
- spIdx = hestOptAdd(&opt, "sp,spacing", "spacing", airTypeDouble, 1, 1, &spc, "nan",
- "spacing between samples along axis");
+ hestOptAdd_Nv_UInt(&opt, "a,axes", "ax0", 1, -1, &axes, NULL,
+ "the one or more axes that should be modified", &axesLen);
+ hestOptAdd_1_String(&opt, "l,label", "label", &label, "",
+ "label to associate with axis");
+ hestOptAdd_1_String(&opt, "u,units", "units", &units, "", "units of measurement");
+ mmIdx = hestOptAdd_2_String(&opt, "mm,minmax", "min max", mmStr, "nan nan",
+ "min and max values along axis");
+ spIdx = hestOptAdd_1_Double(&opt, "sp,spacing", "spacing", &spc, "nan",
+ "spacing between samples along axis");
/* There used to be a complaint here about how hest doesn't allow
you to learn whether the option was parsed from the supplied
default versus from the command-line itself. That issue has been
@@ -56,19 +55,19 @@
parsing from a string here is still needed here, because here we
need to allow the string that represents "no centering"; this
is a current weakness of airEnumStr.
- hestOptAdd(&opt, "c,center", "center", airTypeEnum, 1, 1, ¢, "unknown",
- "centering of axis: \"cell\" or \"node\"",
- NULL, nrrdCenter);
+ hestOptAdd_1_Enum(&opt, "c,center", "center", ¢, "unknown",
+ "centering of axis: \"cell\" or \"node\"",
+ nrrdCenter);
*/
- hestOptAdd(&opt, "c,center", "center", airTypeString, 1, 1, ¢erStr, "",
- "axis centering: \"cell\" or \"node\". Not using this option "
- "leaves the centering as it is on input");
- hestOptAdd(&opt, "dir,direction", "svec", airTypeString, 1, 1, &_dirStr, "",
- "(NOTE: must quote vector) The \"space direction\": the vector "
- "in space spanned by incrementing (by one) the axis index.");
- hestOptAdd(&opt, "k,kind", "kind", airTypeString, 1, 1, &kindStr, "",
- "axis kind. Not using this option "
- "leaves the kind as it is on input");
+ hestOptAdd_1_String(&opt, "c,center", "center", ¢erStr, "",
+ "axis centering: \"cell\" or \"node\". Not using this option "
+ "leaves the centering as it is on input");
+ hestOptAdd_1_String(&opt, "dir,direction", "svec", &_dirStr, "",
+ "(NOTE: must quote vector) The \"space direction\": the vector "
+ "in space spanned by incrementing (by one) the axis index.");
+ hestOptAdd_1_String(&opt, "k,kind", "kind", &kindStr, "",
+ "axis kind. Not using this option "
+ "leaves the kind as it is on input");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/axinsert.c
===================================================================
--- teem/trunk/src/unrrdu/axinsert.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/axinsert.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -42,25 +42,25 @@
hparm->elideSingleOtherDefault = AIR_FALSE;
OPT_ADD_AXIS(axis, "dimension (axis index) at which to insert the new axis");
- hestOptAdd(&opt, "l,label", "label", airTypeString, 1, 1, &label, "",
- "label to associate with new axis");
- opi = hestOptAdd(&opt, "k,kind", "kind", airTypeEnum, 1, 1, &kind, "stub",
- "axis kind to associate with new axis", NULL, nrrdKind);
- hestOptAdd(&opt, "mm,minmax", "min max", airTypeDouble, 2, 2, mm, "nan nan",
- "min and max values along new axis");
- centOptIdx = hestOptAdd(&opt, "c,center", "center", airTypeEnum, 1, 1, ¢er, "cell",
- "centering of inserted axis: \"cell\" or \"node\"", NULL,
- nrrdCenter);
- hestOptAdd(&opt, "s,size", "size", airTypeUInt, 1, 1, &size, "1",
- "after inserting stub axis, also pad out to some length, "
- "according to the \"-b\" option");
- hestOptAdd(&opt, "b,boundary", "behavior", airTypeOther, 1, 1, &bspec, "bleed",
- "How to handle samples beyond the input bounds:\n "
- "\b\bo \"pad:<val>\": use specified value\n "
- "\b\bo \"bleed\": extend border values outward\n "
- "\b\bo \"mirror\": repeated reflections\n "
- "\b\bo \"wrap\": wrap-around to other side",
- NULL, NULL, nrrdHestBoundarySpec);
+ hestOptAdd_1_String(&opt, "l,label", "label", &label, "",
+ "label to associate with new axis");
+ opi = hestOptAdd_1_Enum(&opt, "k,kind", "kind", &kind, "stub",
+ "axis kind to associate with new axis", nrrdKind);
+ hestOptAdd_2_Double(&opt, "mm,minmax", "min max", mm, "nan nan",
+ "min and max values along new axis");
+ centOptIdx = hestOptAdd_1_Enum(&opt, "c,center", "center", ¢er, "cell",
+ "centering of inserted axis: \"cell\" or \"node\"",
+ nrrdCenter);
+ hestOptAdd_1_UInt(&opt, "s,size", "size", &size, "1",
+ "after inserting stub axis, also pad out to some length, "
+ "according to the \"-b\" option");
+ hestOptAdd_1_Other(&opt, "b,boundary", "behavior", &bspec, "bleed",
+ "How to handle samples beyond the input bounds:\n "
+ "\b\bo \"pad:<val>\": use specified value\n "
+ "\b\bo \"bleed\": extend border values outward\n "
+ "\b\bo \"mirror\": repeated reflections\n "
+ "\b\bo \"wrap\": wrap-around to other side",
+ nrrdHestBoundarySpec);
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/axmerge.c
===================================================================
--- teem/trunk/src/unrrdu/axmerge.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/axmerge.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -35,17 +35,17 @@
hestOpt *opt = NULL;
char *out, *err;
Nrrd *nin, *nout[2];
- int *axes, pret, ni;
- unsigned int ii, jj, axesLen;
+ int pret;
+ unsigned int ni, ii, jj, *axes, axesLen;
airArray *mop;
- hestOptAdd(&opt, "a,axis", "ax0", airTypeInt, 1, -1, &axes, NULL,
- "axis (or axes) to merge. Each axis index identified is the "
- "lower of the pair of axes that will be merged. Saying \"-a 2\" "
- "means to merge axis 2 and axis 3 into axis 2. If multiple "
- "merges are to be done, the indices listed here are for "
- "the axes prior to any merging.",
- &axesLen);
+ hestOptAdd_Nv_UInt(&opt, "a,axis", "ax0", 1, -1, &axes, NULL,
+ "axis (or axes) to merge. Each axis index identified is the "
+ "lower of the pair of axes that will be merged. Saying \"-a 2\" "
+ "means to merge axis 2 and axis 3 into axis 2. If multiple "
+ "merges are to be done, the indices listed here are for "
+ "the axes prior to any merging.",
+ &axesLen);
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
@@ -55,6 +55,7 @@
USAGE_OR_PARSE(_unrrdu_axmergeInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
+ /* make two nout buffers, will alternate between them */
airMopAdd(mop, nout[0] = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
airMopAdd(mop, nout[1] = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
Modified: teem/trunk/src/unrrdu/axsplit.c
===================================================================
--- teem/trunk/src/unrrdu/axsplit.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/axsplit.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -40,9 +40,9 @@
airArray *mop;
OPT_ADD_AXIS(axis, "dimension (axis index) to split at");
- hestOptAdd(&opt, "s,size", "fast, slow sizes", airTypeSize_t, 2, 2, size, NULL,
- "fast and slow axis sizes to produce as result of splitting "
- "given axis.");
+ hestOptAdd_2_Size_t(&opt, "s,size", "fast, slow sizes", size, NULL,
+ "fast and slow axis sizes to produce as result of splitting "
+ "given axis.");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/basinfo.c
===================================================================
--- teem/trunk/src/unrrdu/basinfo.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/basinfo.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -45,34 +45,36 @@
int space, nixkvp;
unsigned int spaceDim, kvpLen, dkeyLen, cIdx, ii;
- hestOptAdd(&opt, "spc,space", "space", airTypeString, 1, 1, &spcStr, "",
- "identify the space (e.g. \"RAS\", \"LPS\") in which the array "
- "conceptually lives, from the nrrdSpace airEnum, which in turn "
- "determines the dimension of the space. Or, use an integer>0 to "
- "give the dimension of a space that nrrdSpace doesn't know about. "
- "By default (not using this option), the enclosing space is "
- "set as unknown.");
- hestOptAdd(&opt, "orig,origin", "origin", airTypeString, 1, 1, &_origStr, "",
- "(NOTE: must quote vector) the origin in space of the array: "
- "the location of the center "
- "of the first sample, of the form \"(x,y,z)\" (or however "
- "many coefficients are needed for the chosen space). Quoting the "
- "vector is needed to stop interpretation from the shell");
+ /* no point in invoking this if no options are used, so even though every option has a
+ default, we refrain from setting hparm->noArgsIsNoProblem */
+ hestOptAdd_1_String(&opt, "spc,space", "space", &spcStr, "",
+ "identify the space (e.g. \"RAS\", \"LPS\") in which the array "
+ "conceptually lives, from the nrrdSpace airEnum, which in turn "
+ "determines the dimension of the space. Or, use an integer>0 to "
+ "give the dimension of a space that nrrdSpace doesn't know about. "
+ "By default (not using this option), the enclosing space is "
+ "set as unknown.");
+ hestOptAdd_1_String(&opt, "orig,origin", "origin", &_origStr, "",
+ "(NOTE: must quote vector) the origin in space of the array: "
+ "the location of the center "
+ "of the first sample, of the form \"(x,y,z)\" (or however "
+ "many coefficients are needed for the chosen space). Quoting the "
+ "vector is needed to stop interpretation from the shell");
/* HEY: copy and paste from unrrdu/make.c */
- hestOptAdd(&opt, "kv,keyvalue", "key/val", airTypeString, 1, -1, &kvp, "",
- "key/value string pairs to be stored in nrrd. Each key/value "
- "pair must be a single string (put it in \"\"s "
- "if the key or the value contain spaces). The format of each "
- "pair is \"<key>:=<value>\", with no spaces before or after "
- "\":=\".",
- &kvpLen);
- hestOptAdd(&opt, "dk,delkey", "key", airTypeString, 1, -1, &dkey, "",
- "keys to be deleted (erased) from key/value pairs", &dkeyLen);
- hestOptAdd(&opt, "xkv,nixkeyvalue", NULL, airTypeBool, 0, 0, &nixkvp, NULL,
- "nix (clear) all key/value pairs");
- cIdx = hestOptAdd(&opt, "c,content", "content", airTypeString, 1, 1, &content, "",
- "Specifies the content string of the nrrd, which is built upon "
- "by many nrrd function to record a history of operations");
+ hestOptAdd_Nv_String(&opt, "kv,keyvalue", "key/val", 1, -1, &kvp, "",
+ "key/value string pairs to be stored in nrrd. Each key/value "
+ "pair must be a single string (put it in \"\"s "
+ "if the key or the value contain spaces). The format of each "
+ "pair is \"<key>:=<value>\", with no spaces before or after "
+ "\":=\".",
+ &kvpLen);
+ hestOptAdd_Nv_String(&opt, "dk,delkey", "key", 1, -1, &dkey, "",
+ "keys to be deleted (erased) from key/value pairs", &dkeyLen);
+ hestOptAdd_Flag(&opt, "xkv,nixkeyvalue", &nixkvp, "nix (clear) all key/value pairs");
+ cIdx = hestOptAdd_1_String(
+ &opt, "c,content", "content", &content, "",
+ "Specifies the content string of the nrrd, which is built upon "
+ "by many nrrd function to record a history of operations");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/ccadj.c
===================================================================
--- teem/trunk/src/unrrdu/ccadj.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/ccadj.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -38,10 +38,10 @@
int pret;
unsigned int conny;
- hestOptAdd(&opt, "c,connect", "connectivity", airTypeUInt, 1, 1, &conny, NULL,
- "what kind of connectivity to use: the number of coordinates "
- "that vary in order to traverse the neighborhood of a given "
- "sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
+ hestOptAdd_1_UInt(&opt, "c,connect", "connectivity", &conny, NULL,
+ "what kind of connectivity to use: the number of coordinates "
+ "that vary in order to traverse the neighborhood of a given "
+ "sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/ccfind.c
===================================================================
--- teem/trunk/src/unrrdu/ccfind.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/ccfind.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -37,22 +37,22 @@
int type, pret;
unsigned int conny;
- hestOptAdd(&opt, "v,values", "filename", airTypeString, 1, 1, &valS, "",
- "Giving a filename here allows you to save out the values "
- "associated with each connect component. This can be used "
- "later with \"ccmerge -d\". By default, no record of the "
- "original CC values is kept.");
- hestOptAdd(&opt, "t,type", "type", airTypeOther, 1, 1, &type, "default",
- "type to use for output, to store the CC ID values. By default "
- "(not using this option), the type used will be the smallest of "
- "uchar, ushort, or int, that can represent all the CC ID values. "
- "Using this option allows one to specify the integral type to "
- "be used.",
- NULL, NULL, &unrrduHestMaybeTypeCB);
- hestOptAdd(&opt, "c,connect", "connectivity", airTypeUInt, 1, 1, &conny, NULL,
- "what kind of connectivity to use: the number of coordinates "
- "that vary in order to traverse the neighborhood of a given "
- "sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
+ hestOptAdd_1_String(&opt, "v,values", "filename", &valS, "",
+ "Giving a filename here allows you to save out the values "
+ "associated with each connect component. This can be used "
+ "later with \"ccmerge -d\". By default, no record of the "
+ "original CC values is kept.");
+ hestOptAdd_1_Other(&opt, "t,type", "type", &type, "default",
+ "type to use for output, to store the CC ID values. By default "
+ "(not using this option), the type used will be the smallest of "
+ "uchar, ushort, or int, that can represent all the CC ID values. "
+ "Using this option allows one to specify the integral type to "
+ "be used.",
+ &unrrduHestMaybeTypeCB);
+ hestOptAdd_1_UInt(&opt, "c,connect", "connectivity", &conny, NULL,
+ "what kind of connectivity to use: the number of coordinates "
+ "that vary in order to traverse the neighborhood of a given "
+ "sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/ccmerge.c
===================================================================
--- teem/trunk/src/unrrdu/ccmerge.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/ccmerge.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -40,36 +40,36 @@
int pret, maxSize, dir, maxNeigh, revalue;
unsigned int conny;
- hestOptAdd(&opt, "d,directed", "dir", airTypeInt, 1, 1, &dir, "0",
- "do value-driven merging. Using (positive) \"1\" says that "
- "dark islands get merged with bright surrounds, while \"-1\" "
- "says the opposite. By default, merging can go either way. ");
- hestOptAdd(&opt, "s,size", "max size", airTypeInt, 1, 1, &maxSize, "0",
- "a cap on the CC size that will be absorbed into its "
- "surround. CCs larger than this are deemed too significant "
- "to mess with. Or, use \"0\" to remove any such restriction "
- "on merging.");
- hestOptAdd(&opt, "n,neighbor", "max # neigh", airTypeInt, 1, 1, &maxNeigh, "1",
- "a cap on the number of neighbors that a CC may have if it is "
- "to be be merged. \"1\" allows only islands to be merged, "
- "\"2\" does merging with bigger of two neighbors, etc, while "
- "\"0\" says that number of neighbors is no constraint");
- hestOptAdd(&opt, "c,connect", "connectivity", airTypeUInt, 1, 1, &conny, NULL,
- "what kind of connectivity to use: the number of coordinates "
- "that vary in order to traverse the neighborhood of a given "
- "sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
- hestOptAdd(&opt, "revalue", NULL, airTypeInt, 0, 0, &revalue, NULL,
- "If this option is given, then after the merging, the CCs "
- "are re-assigned their original datavalues, as given by "
- "the \"-v\" option");
+ hestOptAdd_1_Int(&opt, "d,directed", "dir", &dir, "0",
+ "do value-driven merging. Using (positive) \"1\" says that "
+ "dark islands get merged with bright surrounds, while \"-1\" "
+ "says the opposite. By default, merging can go either way. ");
+ hestOptAdd_1_Int(&opt, "s,size", "max size", &maxSize, "0",
+ "a cap on the CC size that will be absorbed into its "
+ "surround. CCs larger than this are deemed too significant "
+ "to mess with. Or, use \"0\" to remove any such restriction "
+ "on merging.");
+ hestOptAdd_1_Int(&opt, "n,neighbor", "max # neigh", &maxNeigh, "1",
+ "a cap on the number of neighbors that a CC may have if it is "
+ "to be be merged. \"1\" allows only islands to be merged, "
+ "\"2\" does merging with bigger of two neighbors, etc, while "
+ "\"0\" says that number of neighbors is no constraint");
+ hestOptAdd_1_UInt(&opt, "c,connect", "connectivity", &conny, NULL,
+ "what kind of connectivity to use: the number of coordinates "
+ "that vary in order to traverse the neighborhood of a given "
+ "sample. In 2D: \"1\": 4-connected, \"2\": 8-connected");
+ hestOptAdd_Flag(&opt, "revalue", &revalue,
+ "If this option is given, then after the merging, the CCs "
+ "are re-assigned their original datavalues, as given by "
+ "the \"-v\" option");
OPT_ADD_NIN(nin, "input nrrd");
- hestOptAdd(&opt, "v,values", "values", airTypeOther, 1, 1, &nval, "",
- "result of using \"ccfind -v\", the record of which values "
- "were originally associated with each CC. This is required "
- "for value-directed merging (with non-zero \"-d\" option), "
- "or if the \"-revalue\" option is given, "
- "but is not needed otherwise",
- NULL, NULL, nrrdHestNrrd);
+ hestOptAdd_1_Other(&opt, "v,values", "values", &nval, "",
+ "result of using \"ccfind -v\", the record of which values "
+ "were originally associated with each CC. This is required "
+ "for value-directed merging (with non-zero \"-d\" option), "
+ "or if the \"-revalue\" option is given, "
+ "but is not needed otherwise",
+ nrrdHestNrrd);
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
Modified: teem/trunk/src/unrrdu/cmedian.c
===================================================================
--- teem/trunk/src/unrrdu/cmedian.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/cmedian.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -46,36 +46,36 @@
airArray *mop;
float wght;
- hestOptAdd(&opt, "r,radius", "radius", airTypeUInt, 1, 1, &radius, NULL,
- "how big a window to filter over. \"-r 1\" leads to a "
- "3x3 window in an image, and a 3x3x3 window in a volume");
- hestOptAdd(&opt, "mode", NULL, airTypeInt, 0, 0, &mode, NULL,
- "By default, median filtering is done. Using this option "
- "enables mode filtering, in which the most common value is "
- "used as output");
- hestOptAdd(&opt, "b,bins", "num", airTypeUInt, 1, 1, &bins, "256",
- "# of bins in histogram. It is in your interest to minimize "
- "this number, since big histograms mean slower execution "
- "times. 8-bit data needs at most 256 bins.");
- hestOptAdd(&opt, "w,weight", "weight", airTypeFloat, 1, 1, &wght, "1.0",
- "How much higher to preferentially weight samples that are "
- "closer to the center of the window. \"1.0\" weight means that "
- "all samples are uniformly weighted over the window, which "
- "facilitates a simple speed-up. ");
+ hestOptAdd_1_UInt(&opt, "r,radius", "radius", &radius, NULL,
+ "how big a window to filter over. \"-r 1\" leads to a "
+ "3x3 window in an image, and a 3x3x3 window in a volume");
+ hestOptAdd_Flag(&opt, "mode", &mode,
+ "By default, median filtering is done. Using this option "
+ "enables mode filtering, in which the most common value is "
+ "used as output");
+ hestOptAdd_1_UInt(&opt, "b,bins", "num", &bins, "256",
+ "# of bins in histogram. It is in your interest to minimize "
+ "this number, since big histograms mean slower execution "
+ "times. 8-bit data needs at most 256 bins.");
+ hestOptAdd_1_Float(&opt, "w,weight", "weight", &wght, "1.0",
+ "How much higher to preferentially weight samples that are "
+ "closer to the center of the window. \"1.0\" weight means that "
+ "all samples are uniformly weighted over the window, which "
+ "facilitates a simple speed-up. ");
/* FYI: these are weights which are just high enough to preserve
an island of N contiguous high pixels in a row:
1: 7.695
2: 6.160
3: 4.829 (actually only the middle pixel remains */
- hestOptAdd(&opt, "p,pad", NULL, airTypeInt, 0, 0, &pad, NULL,
- "Pad the input (with boundary method \"bleed\"), "
- "and crop the output, so as to "
- "overcome our cheapness and correctly "
- "handle the border. Obviously, this takes more memory.");
- hestOptAdd(&opt, "c,channel", NULL, airTypeInt, 0, 0, &chan, NULL,
- "Slice the input along axis 0, run filtering on all slices, "
- "and join the results back together. This is the way you'd "
- "want to process color (multi-channel) images or volumes.");
+ hestOptAdd_Flag(&opt, "p,pad", &pad,
+ "Pad the input (with boundary method \"bleed\"), "
+ "and crop the output, so as to "
+ "overcome our cheapness and correctly "
+ "handle the border. Obviously, this takes more memory.");
+ hestOptAdd_Flag(&opt, "c,channel", &chan,
+ "Slice the input along axis 0, run filtering on all slices, "
+ "and join the results back together. This is the way you'd "
+ "want to process color (multi-channel) images or volumes.");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/convert.c
===================================================================
--- teem/trunk/src/unrrdu/convert.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/convert.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -44,9 +44,9 @@
OPT_ADD_TYPE(type, "type to convert to", NULL);
OPT_ADD_NIN(nin, "input nrrd");
- hestOptAdd(&opt, "clamp", NULL, airTypeInt, 0, 0, &doClamp, NULL,
- "clamp input values to representable range of values of "
- "output type, to avoid wrap-around problems");
+ hestOptAdd_Flag(&opt, "clamp", &doClamp,
+ "clamp input values to representable range of values of "
+ "output type, to avoid wrap-around problems");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
Modified: teem/trunk/src/unrrdu/crop.c
===================================================================
--- teem/trunk/src/unrrdu/crop.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/crop.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -38,6 +38,10 @@
airArray *mop;
Nrrd *_nbounds;
+ /* one might think this is a candidate for hparm->noArgsIsNoProblem, but really
+ the "-b" option is an alternative to -min,-max: it is not the case that neither
+ one can be used. It is a weakness of hest that we can't say: "either -b, or,
+ both -min and -max, must be set" */
OPT_ADD_BOUND("min,minimum", 0, minOff, "0",
"low corner of bounding box.\n "
"\b\bo <int> gives 0-based index\n "
Modified: teem/trunk/src/unrrdu/dering.c
===================================================================
--- teem/trunk/src/unrrdu/dering.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/dering.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -44,39 +44,38 @@
/* HEY is this needed? (to display -rk and -tk kernels) */
hparm->elideSingleOtherDefault = AIR_FALSE;
- hestOptAdd(&opt, "c,center", "x y", airTypeDouble, 2, 2, center, NULL,
- "center of rings, in index space of fastest two axes");
- hestOptAdd(&opt, "v,verbose", "v", airTypeInt, 1, 1, &verbose, "0", "verbosity level");
- hestOptAdd(&opt, "li,linterp", "bool", airTypeBool, 1, 1, &linterp, "false",
- "whether to use linear interpolation during polar transform");
- hestOptAdd(&opt, "vs,vertseam", "bool", airTypeBool, 1, 1, &vertSeam, "false",
- "whether to dering left and right sides separately "
- "(requires an even value for -tn thetanum)");
- hestOptAdd(&opt, "tn,thetanum", "# smpls", airTypeUInt, 1, 1, &thetaNum, "20",
- "# of theta samples");
- hestOptAdd(&opt, "rs,radscale", "scale", airTypeDouble, 1, 1, &radScale, "1.0",
- "scaling on radius in polar transform");
- hestOptAdd(&opt, "rk,radiuskernel", "kern", airTypeOther, 1, 1, &rkspec, "gauss:3,4",
- "kernel for high-pass filtering along radial direction", NULL, NULL,
- nrrdHestKernelSpec);
- hestOptAdd(&opt, "tk,thetakernel", "kern", airTypeOther, 1, 1, &tkspec, "box",
- "kernel for blurring along theta direction.", NULL, NULL,
- nrrdHestKernelSpec);
- hestOptAdd(&opt, "cp,clampperc", "lo hi", airTypeDouble, 2, 2, clampPerc, "0.0 0.0",
- "when clamping values as part of ring estimation, the "
- "clamping range is set to exclude this percent of values "
- "from the low and high end of the data range");
- hestOptAdd(&opt, "m,mask", "mask", airTypeOther, 1, 1, &nmask, "",
- "optional: after deringing, output undergoes a lerp, "
- "parameterized by this array, from the background value "
- "(via \"-b\") where mask=0 to the original deringing "
- "output where mask=1. This lerp is effectively the same "
- "as a \"unu 3op lerp\", so this should either be match the "
- "input in size, or match its slices along the slowest axis.",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "b,back", "val", airTypeDouble, 1, 1, &backval, "0.0",
- "when using a mask (\"-m\"), the background value to "
- "lerp with.");
+ hestOptAdd_2_Double(&opt, "c,center", "x y", center, NULL,
+ "center of rings, in index space of fastest two axes");
+ hestOptAdd_1_Int(&opt, "v,verbose", "v", &verbose, "0", "verbosity level");
+ hestOptAdd_1_Bool(&opt, "li,linterp", "bool", &linterp, "false",
+ "whether to use linear interpolation during polar transform");
+ hestOptAdd_1_Bool(&opt, "vs,vertseam", "bool", &vertSeam, "false",
+ "whether to dering left and right sides separately "
+ "(requires an even value for -tn thetanum)");
+ hestOptAdd_1_UInt(&opt, "tn,thetanum", "# smpls", &thetaNum, "20",
+ "# of theta samples");
+ hestOptAdd_1_Double(&opt, "rs,radscale", "scale", &radScale, "1.0",
+ "scaling on radius in polar transform");
+ hestOptAdd_1_Other(&opt, "rk,radiuskernel", "kern", &rkspec, "gauss:3,4",
+ "kernel for high-pass filtering along radial direction",
+ nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&opt, "tk,thetakernel", "kern", &tkspec, "box",
+ "kernel for blurring along theta direction.", nrrdHestKernelSpec);
+ hestOptAdd_2_Double(&opt, "cp,clampperc", "lo hi", clampPerc, "0.0 0.0",
+ "when clamping values as part of ring estimation, the "
+ "clamping range is set to exclude this percent of values "
+ "from the low and high end of the data range");
+ hestOptAdd_1_Other(&opt, "m,mask", "mask", &nmask, "",
+ "optional: after deringing, output undergoes a lerp, "
+ "parameterized by this array, from the background value "
+ "(via \"-b\") where mask=0 to the original deringing "
+ "output where mask=1. This lerp is effectively the same "
+ "as a \"unu 3op lerp\", so this should either be match the "
+ "input in size, or match its slices along the slowest axis.",
+ nrrdHestNrrd);
+ hestOptAdd_1_Double(&opt, "b,back", "val", &backval, "0.0",
+ "when using a mask (\"-m\"), the background value to "
+ "lerp with.");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/dhisto.c
===================================================================
--- teem/trunk/src/unrrdu/dhisto.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/dhisto.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -38,20 +38,19 @@
airArray *mop;
double max;
- hestOptAdd(&opt, "h,height", "height", airTypeUInt, 1, 1, &size, NULL,
- "height of output image (horizontal size is determined by "
- "number of bins in input histogram).");
- hestOptAdd(&opt, "nolog", NULL, airTypeInt, 0, 0, &nolog, NULL,
- "do not show the log-scaled histogram with decade tick-marks");
- hestOptAdd(&opt, "notick", NULL, airTypeInt, 0, 0, ¬ick, NULL,
- "do not draw the log decade tick marks");
- hestOptAdd(&opt, "max,maximum", "max # hits", airTypeDouble, 1, 1, &max, "nan",
- "constrain the top of the drawn histogram to be at this "
- "number of hits. This will either scale the drawn histogram "
- "downward or clip its top, depending on whether the given max "
- "is higher or lower than the actual maximum bin count. By "
- "not using this option (the default), the actual maximum bin "
- "count is used");
+ hestOptAdd_1_UInt(&opt, "h,height", "height", &size, NULL,
+ "height of output image (horizontal size is determined by "
+ "number of bins in input histogram).");
+ hestOptAdd_Flag(&opt, "nolog", &nolog,
+ "do not show the log-scaled histogram with decade tick-marks");
+ hestOptAdd_Flag(&opt, "notick", ¬ick, "do not draw the log decade tick marks");
+ hestOptAdd_1_Double(&opt, "max,maximum", "max # hits", &max, "nan",
+ "constrain the top of the drawn histogram to be at this "
+ "number of hits. This will either scale the drawn histogram "
+ "downward or clip its top, depending on whether the given max "
+ "is higher or lower than the actual maximum bin count. By "
+ "not using this option (the default), the actual maximum bin "
+ "count is used");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/dice.c
===================================================================
--- teem/trunk/src/unrrdu/dice.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/dice.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -42,26 +42,26 @@
OPT_ADD_AXIS(axis, "axis to slice along");
OPT_ADD_NIN(nin, "input nrrd");
- hestOptAdd(&opt, "s,start", "start", airTypeUInt, 1, 1, &start, "0",
- "integer value to start numbering with");
- hestOptAdd(&opt, "ff,format", "form", airTypeString, 1, 1, &ftmpl, "",
- "a printf-style format to use for generating all "
- "filenames. Use this to override the number of characters "
- "used to represent the slice position, or the file format "
- "of the output, e.g. \"-ff %03d.ppm\" for 000.ppm, "
- "001.ppm, etc. By default (not using this option), slices "
- "are saved in NRRD format (or PNM or PNG where possible) "
- "with shortest possible filenames.");
+ hestOptAdd_1_UInt(&opt, "s,start", "start", &start, "0",
+ "integer value to start numbering with");
+ hestOptAdd_1_String(&opt, "ff,format", "form", &ftmpl, "",
+ "a printf-style format to use for generating all "
+ "filenames. Use this to override the number of characters "
+ "used to represent the slice position, or the file format "
+ "of the output, e.g. \"-ff %03d.ppm\" for 000.ppm, "
+ "001.ppm, etc. By default (not using this option), slices "
+ "are saved in NRRD format (or PNM or PNG where possible) "
+ "with shortest possible filenames.");
/* the fact that we're using unsigned int instead of size_t is
its own kind of sanity check */
- hestOptAdd(&opt, "l,limit", "max#", airTypeUInt, 1, 1, &sanity, "9999",
- "a sanity check on how many slice files should be saved "
- "out, to prevent accidentally dicing the wrong axis "
- "or the wrong array. Can raise this value if needed.");
- hestOptAdd(&opt, "o,output", "prefix", airTypeString, 1, 1, &base, NULL,
- "output filename prefix (excluding info set via \"-ff\"), "
- "basically to set path of output files (so be sure to end "
- "with \"/\".");
+ hestOptAdd_1_UInt(&opt, "l,limit", "max#", &sanity, "9999",
+ "a sanity check on how many slice files should be saved "
+ "out, to prevent accidentally dicing the wrong axis "
+ "or the wrong array. Can raise this value if needed.");
+ hestOptAdd_1_String(&opt, "o,output", "prefix", &base, NULL,
+ "output filename prefix (excluding info set via \"-ff\"), "
+ "basically to set path of output files (so be sure to end "
+ "with \"/\".");
mop = airMopNew();
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
Modified: teem/trunk/src/unrrdu/diff.c
===================================================================
--- teem/trunk/src/unrrdu/diff.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/diff.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -42,21 +42,20 @@
char explain[AIR_STRLEN_LARGE + 1];
mop = airMopNew();
- hestOptAdd(&opt, NULL, "ninA", airTypeOther, 1, 1, &ninA, NULL, "First input nrrd.",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, NULL, "ninB", airTypeOther, 1, 1, &ninB, NULL, "Second input nrrd.",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "eps,epsilon", "eps", airTypeDouble, 1, 1, &epsilon, "0.0",
- "threshold for allowable difference in values in "
- "data values");
- hestOptAdd(&opt, "q,quiet", NULL, airTypeInt, 0, 0, &quiet, NULL,
- "be quiet (like regular diff), so that nothing is printed "
- "if the nrrds are the same");
- hestOptAdd(&opt, "x,exit", NULL, airTypeInt, 0, 0, &exitstat, NULL,
- "use the exit status (like regular diff) to indicate if "
- "there was a significant difference (as if it's an error)");
- hestOptAdd(&opt, "od,onlydata", NULL, airTypeInt, 0, 0, &onlyData, NULL,
- "Compare data values only, excluding array meta-data");
+ hestOptAdd_1_Other(&opt, NULL, "ninA", &ninA, NULL, "First input nrrd.", nrrdHestNrrd);
+ hestOptAdd_1_Other(&opt, NULL, "ninB", &ninB, NULL, "Second input nrrd.",
+ nrrdHestNrrd);
+ hestOptAdd_1_Double(&opt, "eps,epsilon", "eps", &epsilon, "0.0",
+ "threshold for allowable difference in values in "
+ "data values");
+ hestOptAdd_Flag(&opt, "q,quiet", &quiet,
+ "be quiet (like regular diff), so that nothing is printed "
+ "if the nrrds are the same");
+ hestOptAdd_Flag(&opt, "x,exit", &exitstat,
+ "use the exit status (like regular diff) to indicate if "
+ "there was a significant difference (as if it's an error)");
+ hestOptAdd_Flag(&opt, "od,onlydata", &onlyData,
+ "Compare data values only, excluding array meta-data");
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
USAGE_OR_PARSE(_unrrdu_diffInfoL);
Modified: teem/trunk/src/unrrdu/dist.c
===================================================================
--- teem/trunk/src/unrrdu/dist.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/dist.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -44,20 +44,20 @@
double thresh, bias;
airArray *mop;
- hestOptAdd(&opt, "th,thresh", "val", airTypeDouble, 1, 1, &thresh, NULL,
- "threshold value to separate inside from outside");
- hestOptAdd(&opt, "b,bias", "val", airTypeDouble, 1, 1, &bias, "0.0",
- "if non-zero, bias the distance transform by this amount "
- "times the difference in value from the threshold");
- hestOptAdd(&opt, "t,type", "type", airTypeEnum, 1, 1, &typeOut, "float",
- "type to save output in", NULL, nrrdType);
- hestOptAdd(&opt, "sgn", NULL, airTypeInt, 0, 0, &sign, NULL,
- "also compute signed (negative) distances inside objects, "
- "instead of leaving them as zero");
- hestOptAdd(&opt, "inv", NULL, airTypeInt, 0, 0, &invert, NULL,
- "values *below* threshold are considered interior to object. "
- "By default (not using this option), values above threshold "
- "are considered interior. ");
+ hestOptAdd_1_Double(&opt, "th,thresh", "val", &thresh, NULL,
+ "threshold value to separate inside from outside");
+ hestOptAdd_1_Double(&opt, "b,bias", "val", &bias, "0.0",
+ "if non-zero, bias the distance transform by this amount "
+ "times the difference in value from the threshold");
+ hestOptAdd_1_Enum(&opt, "t,type", "type", &typeOut, "float", "type to save output in",
+ nrrdType);
+ hestOptAdd_Flag(&opt, "sgn", &sign,
+ "also compute signed (negative) distances inside objects, "
+ "instead of leaving them as zero");
+ hestOptAdd_Flag(&opt, "inv", &invert,
+ "values *below* threshold are considered interior to object. "
+ "By default (not using this option), values above threshold "
+ "are considered interior. ");
OPT_ADD_NIN(nin, "input nrrd");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/fft.c
===================================================================
--- teem/trunk/src/unrrdu/fft.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/fft.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -79,34 +79,34 @@
FILE *fwise;
unsigned int *axes, axesLen;
- hestOptAdd(&opt, NULL, "dir", airTypeEnum, 1, 1, &sign, NULL,
- "forward (\"forw\", \"f\") or backward/inverse "
- "(\"back\", \"b\") transform ",
- NULL, direction_enm);
- hestOptAdd(&opt, "a,axes", "ax0", airTypeUInt, 1, -1, &axes, NULL,
- "the one or more axes that should be transformed", &axesLen);
- hestOptAdd(&opt, "pr,planrigor", "pr", airTypeEnum, 1, 1, &rigor, "est",
- "rigor with which fftw plan is constructed. Options include:\n "
- "\b\bo \"e\", \"est\", \"estimate\": only an estimate\n "
- "\b\bo \"m\", \"meas\", \"measure\": standard amount of "
- "measurements of system properties\n "
- "\b\bo \"p\", \"pat\", \"patient\": slower, more measurements\n "
- "\b\bo \"x\", \"ex\", \"exhaustive\": slowest, most measurements",
- NULL, nrrdFFTWPlanRigor);
- hestOptAdd(&opt, "r,rescale", "bool", airTypeBool, 1, 1, &rescale, "true",
- "scale fftw output (by sqrt(1/N)) so that forward and backward "
- "transforms will get back to original values");
- hestOptAdd(&opt, "w,wisdom", "filename", airTypeString, 1, 1, &wispath, "",
- "A filename here is used to read in fftw wisdom (if the file "
- "exists already), and is used to save out updated wisdom "
- "after the transform. By default (not using this option), "
- "no wisdom is read or saved. Note: no wisdom is gained "
- "(that is, learned by FFTW) with planning rigor \"estimate\".");
+ hestOptAdd_1_Enum(&opt, NULL, "dir", &sign, NULL,
+ "forward (\"forw\", \"f\") or backward/inverse "
+ "(\"back\", \"b\") transform ",
+ direction_enm);
+ hestOptAdd_Nv_UInt(&opt, "a,axes", "ax0", 1, -1, &axes, NULL,
+ "the one or more axes that should be transformed", &axesLen);
+ hestOptAdd_1_Enum(&opt, "pr,planrigor", "pr", &rigor, "est",
+ "rigor with which fftw plan is constructed. Options include:\n "
+ "\b\bo \"e\", \"est\", \"estimate\": only an estimate\n "
+ "\b\bo \"m\", \"meas\", \"measure\": standard amount of "
+ "measurements of system properties\n "
+ "\b\bo \"p\", \"pat\", \"patient\": slower, more measurements\n "
+ "\b\bo \"x\", \"ex\", \"exhaustive\": slowest, most measurements",
+ nrrdFFTWPlanRigor);
+ hestOptAdd_1_Bool(&opt, "r,rescale", "bool", &rescale, "true",
+ "scale fftw output (by sqrt(1/N)) so that forward and backward "
+ "transforms will get back to original values");
+ hestOptAdd_1_String(&opt, "w,wisdom", "filename", &wispath, "",
+ "A filename here is used to read in fftw wisdom (if the file "
+ "exists already), and is used to save out updated wisdom "
+ "after the transform. By default (not using this option), "
+ "no wisdom is read or saved. Note: no wisdom is gained "
+ "(that is, learned by FFTW) with planning rigor \"estimate\".");
OPT_ADD_NIN(_nin, "input nrrd");
- hestOptAdd(&opt, "ri,realinput", NULL, airTypeInt, 0, 0, &realInput, NULL,
- "input is real-valued, so insert new length-2 axis 0 "
- "and set complex component to 0.0. Axes to transform "
- "(indicated by \"-a\") will be incremented accordingly.");
+ hestOptAdd_Flag(&opt, "ri,realinput", &realInput,
+ "input is real-valued, so insert new length-2 axis 0 "
+ "and set complex component to 0.0. Axes to transform "
+ "(indicated by \"-a\") will be incremented accordingly.");
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
Modified: teem/trunk/src/unrrdu/gamma.c
===================================================================
--- teem/trunk/src/unrrdu/gamma.c 2023-07-13 22:59:01 UTC (rev 7094)
+++ teem/trunk/src/unrrdu/gamma.c 2023-07-13 23:01:51 UTC (rev 7095)
@@ -41,21 +41,21 @@
int pret, blind8BitRange, srgb, forward, E;
NrrdRange *range;
- hestOptAdd(&opt, "g,gamma", "gamma", airTypeString, 1, 1, &GammaS, NULL,
- "gamma > 1.0 brightens; gamma < 1.0 darkens. "
- "Negative gammas invert values (like in xv). "
- "Or, can used \"srgb\" for ~2.2 gamma of sRGB encoding, or "
- "\"1/srgb\" for ~0.455 gamma of inverse sRGB encoding");
- hestOptAdd(&opt, "min,minimum", "value", airTypeDouble, 1, 1, &min, "nan",
- "Value to implicitly map to 0.0 prior to calling pow(). "
- "Defaults to lowest value found in input nrrd.");
- hestOptAdd(&opt, "max,maximum", "value", airTypeDouble, 1, 1, &max, "nan",
- "Value to implicitly map to 1.0 prior to calling pow(). "
- "Defaults to highest value found in input nrrd.");
- hestOptAdd(&opt, "blind8", "bool", airTypeBool, 1, 1, &blind8BitRange,
- nrrdStateBlind8BitRange ? "true" : "false",
- "Whether to know the range of 8-bit data blindly "
- "(uchar is always [0,255], signed char is [-128,127]).");
+ hestOptAdd_1_String(&opt, "g,gamma", "gamma", &GammaS, NULL,
+ "gamma > 1.0 brightens; gamma < 1.0 darkens. "
+ "Negative gammas invert values (like in xv). "
+ "Or, can used \"srgb\" for ~2.2 gamma of sRGB encoding, or "
+ "\"1/srgb\" for ~0.455 gamma of inverse sRGB encoding");
+ hestOptAdd_1_Double(&opt, "min,minimum", "value", &min, "nan",
+ "Value to implicitly map to 0.0 prior to calling pow(). "
+ "Defaults to lowest value found in input nrrd.");
+ hestOptAdd_1_Double(&opt, "max,maximum", "value", &max, "nan",
+ "Value to implicitly map to 1.0 prior to calling pow(). "
+ "Defaults to highest value found in input nrrd.");
+ hestOpt...
[truncated message content] |
|
From: <kin...@us...> - 2023-07-13 22:59:03
|
Revision: 7094
http://sourceforge.net/p/teem/code/7094
Author: kindlmann
Date: 2023-07-13 22:59:01 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
make USAGE macro play better with hestParm->noArgsIsNoProblem
Modified Paths:
--------------
teem/trunk/src/unrrdu/privateUnrrdu.h
Modified: teem/trunk/src/unrrdu/privateUnrrdu.h
===================================================================
--- teem/trunk/src/unrrdu/privateUnrrdu.h 2023-07-13 22:46:18 UTC (rev 7093)
+++ teem/trunk/src/unrrdu/privateUnrrdu.h 2023-07-13 22:59:01 UTC (rev 7094)
@@ -225,7 +225,7 @@
** don't use this macro) had already been this way.
*/
#define USAGE(INFO) \
- if (!argc) { \
+ if (!argc && !hparm->noArgsIsNoProblem) { \
hestInfo(stdout, me, (INFO), hparm); \
hestUsage(stdout, opt, me, hparm); \
hestGlossary(stdout, opt, hparm); \
@@ -267,7 +267,11 @@
/* Its gotten too annoying to always get this glossary; */ \
/* unu <cmd> --help will print it. */ \
/* hestGlossary(stderr, opt, hparm); */ \
- fprintf(stderr, "\nFor more info: \"%s\" or \"%s ... --help\"\n", me, me); \
+ if (hparm && hparm->noArgsIsNoProblem) { \
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me); \
+ } else { \
+ fprintf(stderr, "\nFor more info: \"%s\" or \"%s --help\"\n", me, me); \
+ } \
} \
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...> - 2023-07-13 22:46:28
|
Revision: 7093
http://sourceforge.net/p/teem/code/7093
Author: kindlmann
Date: 2023-07-13 22:46:18 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
updating hest usage, and exploting hparm->noArgsIsNoProblem and either isatty(STDIN_FILENO) or nrrdHestNrrdNoTTY to gracefully handle being invoked with no args, while not being piped to
Modified Paths:
--------------
teem/trunk/src/unrrdu/block.c
teem/trunk/src/unrrdu/ccsettle.c
teem/trunk/src/unrrdu/cksum.c
teem/trunk/src/unrrdu/dnorm.c
teem/trunk/src/unrrdu/grid.c
teem/trunk/src/unrrdu/head.c
teem/trunk/src/unrrdu/minmax.c
teem/trunk/src/unrrdu/unorient.c
teem/trunk/src/unrrdu/unquantize.c
Modified: teem/trunk/src/unrrdu/block.c
===================================================================
--- teem/trunk/src/unrrdu/block.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/block.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -42,11 +42,9 @@
airArray *mop;
int pret;
- /* if we gave a default for this, then there it would fine to have
- no command-line arguments whatsoever, and then the user would not
- know how to get the basic usage information */
- hestOptAdd(&opt, "i", "nin", airTypeOther, 1, 1, &nin, NULL, "input nrrd", NULL, NULL,
- nrrdHestNrrd);
+ /* nrrdHestNrrdNoTTY simplifies this, just like unquantize and unorient */
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_Other(&opt, "i", "nin", &nin, "-", "input nrrd", nrrdHestNrrdNoTTY);
OPT_ADD_NOUT(out, "output nrrd");
mop = airMopNew();
Modified: teem/trunk/src/unrrdu/ccsettle.c
===================================================================
--- teem/trunk/src/unrrdu/ccsettle.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/ccsettle.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -35,12 +35,13 @@
int pret;
mop = airMopNew();
- hestOptAdd(&opt, "i,input", "nin", airTypeOther, 1, 1, &nin, NULL, "input nrrd", NULL,
- NULL, nrrdHestNrrd);
- hestOptAdd(&opt, "v,values", "filename", airTypeString, 1, 1, &valS, "",
- "Giving a filename here allows you to save out the mapping "
- "from new (settled) values to old values, in the form of a "
- "1-D lookup table");
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_Other(&opt, "i,input", "nin", &nin, "-",
+ "input nrrd. By default try to read from stdin", nrrdHestNrrdNoTTY);
+ hestOptAdd_1_String(&opt, "v,values", "filename", &valS, "",
+ "Giving a filename here allows you to save out the mapping "
+ "from new (settled) values to old values, in the form of a "
+ "1-D lookup table");
OPT_ADD_NOUT(out, "output nrrd");
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
Modified: teem/trunk/src/unrrdu/cksum.c
===================================================================
--- teem/trunk/src/unrrdu/cksum.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/cksum.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -22,6 +22,8 @@
#include "unrrdu.h"
#include "privateUnrrdu.h"
+#include <unistd.h> /* for isatty() and STDIN_FILENO */
+
#define INFO "Compute 32-bit CRC of nrrd data (same as via \"cksum\")"
static const char *_unrrdu_cksumInfoL
= (INFO ". Unlike other commands, this doesn't produce a nrrd. It only "
@@ -37,6 +39,11 @@
char stmp[AIR_STRLEN_SMALL + 1], ends[AIR_STRLEN_SMALL + 1];
size_t nn;
+ if (!strcmp("-", inS) && isatty(STDIN_FILENO)) {
+ biffAddf(me, "declining to try reading Nrrd from stdin as tty (terminal)");
+ return 1;
+ }
+
mop = airMopNew();
airMopAdd(mop, nrrd = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nrrd, inS, NULL)) {
@@ -59,36 +66,49 @@
hestOpt *opt = NULL;
char *err, **inS;
airArray *mop;
- int pret, endian, printend;
+ int pret, endian, printend, okay;
unsigned int ni, ninLen;
mop = airMopNew();
- hestOptAdd(&opt, "en,endian", "end", airTypeEnum, 1, 1, &endian,
- airEnumStr(airEndian, airMyEndian()),
- "Endianness in which to compute CRC; \"little\" for Intel and "
- "friends; \"big\" for everyone else. "
- "Defaults to endianness of this machine",
- NULL, airEndian);
- hestOptAdd(&opt, "pen,printendian", "bool", airTypeBool, 1, 1, &printend, "false",
- "whether or not to indicate after the CRC value the endianness "
- "with which the CRC was computed; doing so clarifies "
- "that the CRC result depends on endianness and may remove "
- "confusion in comparing results on platforms of different "
- "endianness");
- hestOptAdd(&opt, NULL, "nin1", airTypeString, 1, -1, &inS, NULL, "input nrrd(s)",
- &ninLen);
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_Enum(&opt, "en,endian", "end", &endian,
+ airEnumStr(airEndian, airMyEndian()),
+ "Endianness in which to compute CRC; \"little\" for Intel and "
+ "friends; \"big\" for everyone else. "
+ "Defaults to endianness of this machine",
+ airEndian);
+ hestOptAdd_1_Bool(&opt, "pen,printendian", "bool", &printend, "false",
+ "whether or not to indicate after the CRC value the endianness "
+ "with which the CRC was computed; doing so clarifies "
+ "that the CRC result depends on endianness and may remove "
+ "confusion in comparing results on platforms of different "
+ "endianness");
+ hestOptAdd_Nv_String(&opt, NULL, "nin1", 1, -1, &inS, "-",
+ "input nrrd(s). By default tries to read from stdin", &ninLen);
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
USAGE_OR_PARSE(_unrrdu_cksumInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
+ /* HEY "okay" logic copied from head.c */
+ okay = AIR_FALSE;
for (ni = 0; ni < ninLen; ni++) {
if (unrrdu_cksumDoit(me, inS[ni], endian, printend, stdout)) {
airMopAdd(mop, err = biffGetDone(me), airFree, airMopAlways);
fprintf(stderr, "%s: trouble with \"%s\":\n%s", me, inS[ni], err);
/* continue working on the remaining files */
+ } else {
+ okay = AIR_TRUE;
}
}
+ if (!okay) {
+ /* none of the given files could be read; something is wrong */
+ if (ninLen > 1) {
+ fprintf(stderr, "\n%s: Unable to read any file\n", me);
+ }
+ hestUsage(stderr, opt, me, hparm);
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me);
+ }
airMopOkay(mop);
return 0;
Modified: teem/trunk/src/unrrdu/dnorm.c
===================================================================
--- teem/trunk/src/unrrdu/dnorm.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/dnorm.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -45,27 +45,28 @@
hestOpt *opt = NULL;
char *err;
airArray *mop;
-
- hestOptAdd(&opt, "h,header", NULL, airTypeInt, 0, 0, &headerOnly, NULL,
- "output header of nrrd file only, not the data itself");
- hestOptAdd(&opt, "v,version", "version", airTypeEnum, 1, 1, &version, "alpha",
- "what version of canonical meta-data to convert to; "
- "\"alpha\" is what has been used for Diderot until at least "
- "2016",
- NULL, nrrdMetaDataCanonicalVersion);
- hestOptAdd(&opt, "to", NULL, airTypeInt, 0, 0, &trivialOrient, NULL,
- "(*t*rivial *o*rientation) "
- "even if the input nrrd comes with full orientation or "
- "per-axis min-max info, ignore it and instead assert the "
- "identity mapping between index and world space");
- hestOptAdd(&opt, "rc,recenter", NULL, airTypeInt, 0, 0, &recenter, NULL,
- "re-locate output spaceOrigin so that field is centered "
- "around origin of space coordinates");
- hestOptAdd(&opt, "sp,spacing", "scl", airTypeDouble, 1, 1, &newSpacing, "1.0",
- "when having to contrive orientation information and there's "
- "no per-axis min/max or spacing, this is the sample spacing "
- "to assert");
- OPT_ADD_NIN(nin, "input image");
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_Flag(&opt, "h,header", &headerOnly,
+ "output header of nrrd file only, not the data itself");
+ hestOptAdd_1_Enum(&opt, "v,version", "version", &version, "alpha",
+ "what version of canonical meta-data to convert to; "
+ "\"alpha\" is what has been used for Diderot until at least "
+ "2016",
+ nrrdMetaDataCanonicalVersion);
+ hestOptAdd_Flag(&opt, "to", &trivialOrient,
+ "(*t*rivial *o*rientation) "
+ "even if the input nrrd comes with full orientation or "
+ "per-axis min-max info, ignore it and instead assert the "
+ "identity mapping between index and world space");
+ hestOptAdd_Flag(&opt, "rc,recenter", &recenter,
+ "re-locate output spaceOrigin so that field is centered "
+ "around origin of space coordinates");
+ hestOptAdd_1_Double(&opt, "sp,spacing", "scl", &newSpacing, "1.0",
+ "when having to contrive orientation information and there's "
+ "no per-axis min/max or spacing, this is the sample spacing "
+ "to assert");
+ hestOptAdd_1_Other(&opt, "i,input", "nin", &nin, "-",
+ "input image. By default reads from stdin", nrrdHestNrrdNoTTY);
OPT_ADD_NOUT(outS, "output filename");
mop = airMopNew();
Modified: teem/trunk/src/unrrdu/grid.c
===================================================================
--- teem/trunk/src/unrrdu/grid.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/grid.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -22,6 +22,8 @@
#include "unrrdu.h"
#include "privateUnrrdu.h"
+#include <unistd.h> /* for isatty() and STDIN_FILENO */
+
static int /* Biff: 1 */
gridGen(Nrrd *nout, int typeOut, const Nrrd *nin, int psz, int psg) {
static const char me[] = "gridGen";
@@ -151,20 +153,16 @@
Nrrd *nin, *nout;
int typeOut, psz, psg;
NrrdIoState *nio;
-
- hestOptAdd(&opt, "i,input", "nin", airTypeString, 1, 1, &inS, NULL,
- "input nrrd. That this argument is required instead of "
- "optional, as with most unu commands, is a quirk caused by the "
- "need to have \"unu grid\" generate usage info, combined "
- "with the fact that the other arguments have sensible "
- "defaults");
- hestOptAdd(&opt, "ps", NULL, airTypeInt, 0, 0, &psz, NULL,
- "instead of the default behavior of flattening all but the "
- "fastest axis, preserve the sizes of axes, so that the output "
- "is more like that of the input");
- hestOptAdd(&opt, "pg", NULL, airTypeInt, 0, 0, &psg, NULL,
- "(overrides -ps) generate a 2D array that represents "
- "the sampling grid in the way that \"gprobe -pg\" understands");
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_String(&opt, "i,input", "nin", &inS, "-",
+ "input nrrd. By default reads from stdin");
+ hestOptAdd_Flag(&opt, "ps", &psz,
+ "instead of the default behavior of flattening all but the "
+ "fastest axis, preserve the sizes of axes, so that the output "
+ "is more like that of the input");
+ hestOptAdd_Flag(&opt, "pg", &psg,
+ "(overrides -ps) generate a 2D array that represents "
+ "the sampling grid in the way that \"gprobe -pg\" understands");
OPT_ADD_TYPE(typeOut, "type of output", "double");
OPT_ADD_NOUT(outS, "output nrrd");
@@ -174,6 +172,15 @@
USAGE_OR_PARSE(_unrrdu_gridInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
+ if (!strcmp("-", inS) && isatty(STDIN_FILENO)) {
+ fprintf(stderr, "%s: declining to try reading Nrrd from stdin as tty (terminal)\n/",
+ me);
+ hestUsage(stderr, opt, me, hparm);
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me);
+ airMopError(mop);
+ return 1;
+ }
+
nio = nrrdIoStateNew();
airMopAdd(mop, nio, (airMopper)nrrdIoStateNix, airMopAlways);
nin = nrrdNew();
Modified: teem/trunk/src/unrrdu/head.c
===================================================================
--- teem/trunk/src/unrrdu/head.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/head.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -22,6 +22,8 @@
#include "unrrdu.h"
#include "privateUnrrdu.h"
+#include <unistd.h> /* for isatty() and STDIN_FILENO */
+
#define INFO "Print header of one or more nrrd files"
static const char *_unrrdu_headInfoL
= (INFO ". The value of this is simply to print the contents of nrrd "
@@ -32,14 +34,18 @@
"* Uses nrrdOneLine");
static int /* Biff: 1 */
-unrrdu_headDoit(const char *me, NrrdIoState *nio, char *inS, FILE *fout) {
+unrrdu_headDoit(const char *me, NrrdIoState *nio, const char *inS, FILE *fout) {
airArray *mop;
unsigned int len;
FILE *fin;
+ if (!strcmp("-", inS) && isatty(STDIN_FILENO)) {
+ biffAddf(me, "declining to try reading Nrrd from stdin as tty (terminal)");
+ return 1;
+ }
mop = airMopNew();
if (!(fin = airFopen(inS, stdin, "rb"))) {
- biffAddf(me, "%s: couldn't fopen(\"%s\",\"rb\"): %s\n", me, inS, strerror(errno));
+ biffAddf(me, "couldn't fopen(\"%s\",\"rb\"): %s\n", inS, strerror(errno));
airMopError(mop);
return 1;
}
@@ -46,17 +52,17 @@
airMopAdd(mop, fin, (airMopper)airFclose, airMopAlways);
if (nrrdOneLine(&len, nio, fin)) {
- biffAddf(me, "%s: error getting first line of file \"%s\"", me, inS);
+ biffAddf(me, "error getting first line of file \"%s\"", inS);
airMopError(mop);
return 1;
}
if (!len) {
- biffAddf(me, "%s: immediately hit EOF\n", me);
+ biffAddf(me, "immediately hit EOF\n");
airMopError(mop);
return 1;
}
if (!(nrrdFormatNRRD->contentStartsLike(nio))) {
- biffAddf(me, "%s: first line (\"%s\") isn't a nrrd magic\n", me, nio->line);
+ biffAddf(me, "first line (\"%s\") isn't a nrrd magic\n", nio->line);
airMopError(mop);
return 1;
}
@@ -85,12 +91,13 @@
char *err, **inS;
NrrdIoState *nio;
airArray *mop;
- int pret;
+ int pret, okay;
unsigned int ni, ninLen;
mop = airMopNew();
- hestOptAdd(&opt, NULL, "nin1", airTypeString, 1, -1, &inS, NULL, "input nrrd(s)",
- &ninLen);
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_Nv_String(&opt, NULL, "nin1", 1, -1, &inS, "-",
+ "input nrrd(s). By default tries to read from stdin", &ninLen);
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
USAGE_OR_PARSE(_unrrdu_headInfoL);
@@ -99,6 +106,7 @@
nio = nrrdIoStateNew();
airMopAdd(mop, nio, (airMopper)nrrdIoStateNix, airMopAlways);
+ okay = AIR_FALSE;
for (ni = 0; ni < ninLen; ni++) {
if (ninLen > 1) {
fprintf(stdout, "==> %s <==\n", inS[ni]);
@@ -107,11 +115,22 @@
airMopAdd(mop, err = biffGetDone(me), airFree, airMopAlways);
fprintf(stderr, "%s: trouble reading from \"%s\":\n%s", me, inS[ni], err);
/* continue working on the remaining files */
+ } else {
+ /* processed at least one file ok */
+ okay = AIR_TRUE;
}
if (ninLen > 1 && ni < ninLen - 1) {
fprintf(stdout, "\n");
}
}
+ if (!okay) {
+ /* none of the given files could be read; something is wrong */
+ if (ninLen > 1) {
+ fprintf(stderr, "\n%s: Unable to read from any file\n", me);
+ }
+ hestUsage(stderr, opt, me, hparm);
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me);
+ }
airMopOkay(mop);
return 0;
Modified: teem/trunk/src/unrrdu/minmax.c
===================================================================
--- teem/trunk/src/unrrdu/minmax.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/minmax.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -22,6 +22,8 @@
#include "unrrdu.h"
#include "privateUnrrdu.h"
+#include <unistd.h> /* for isatty() and STDIN_FILENO */
+
#define INFO "Print out min and max values in one or more nrrds"
static const char *_unrrdu_minmaxInfoL
= (INFO ". Unlike other commands, this doesn't produce a nrrd. It only "
@@ -36,6 +38,11 @@
NrrdRange *range;
airArray *mop;
+ if (!strcmp("-", inS) && isatty(STDIN_FILENO)) {
+ biffAddf(me, "declining to try reading Nrrd from stdin as tty (terminal)");
+ return 1;
+ }
+
mop = airMopNew();
airMopAdd(mop, nrrd = nrrdNew(), (airMopper)nrrdNuke, airMopAlways);
if (nrrdLoad(nrrd, inS, NULL)) {
@@ -80,11 +87,12 @@
hestOpt *opt = NULL;
char *err, **inS;
airArray *mop;
- int pret, blind8BitRange, singleLine;
+ int pret, blind8BitRange, singleLine, okay;
unsigned int ni, ninLen;
#define B8DEF "false"
mop = airMopNew();
+ hparm->noArgsIsNoProblem = AIR_TRUE;
hestOptAdd_1_Bool(&opt, "blind8", "bool", &blind8BitRange,
B8DEF, /* NOTE: not using nrrdStateBlind8BitRange here
for consistency with previous behavior */
@@ -103,12 +111,14 @@
"and max, possibly followed by the single word \"non-existent\" if and "
"only if there were non-existent values. If there are multiple inputs, "
"the input filename is printed first on the per-input single line.");
- hestOptAdd_Nv_String(&opt, NULL, "nin1", 1, -1, &inS, NULL, "input nrrd(s)", &ninLen);
+ hestOptAdd_Nv_String(&opt, NULL, "nin1", 1, -1, &inS, "-", "input nrrd(s)", &ninLen);
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
USAGE_OR_PARSE(_unrrdu_minmaxInfoL);
airMopAdd(mop, opt, (airMopper)hestParseFree, airMopAlways);
+ /* HEY "okay" logic copied from head.c */
+ okay = AIR_FALSE;
for (ni = 0; ni < ninLen; ni++) {
if (ninLen > 1) {
if (singleLine) {
@@ -121,11 +131,22 @@
airMopAdd(mop, err = biffGetDone(me), airFree, airMopAlways);
fprintf(stderr, "%s: trouble with \"%s\":\n%s", me, inS[ni], err);
/* continue working on the remaining files */
+ } else {
+ /* processed at least one file ok */
+ okay = AIR_TRUE;
}
if (ninLen > 1 && ni < ninLen - 1 && !singleLine) {
fprintf(stdout, "\n");
}
}
+ if (!okay) {
+ /* none of the given files could be read; something is wrong */
+ if (ninLen > 1) {
+ fprintf(stderr, "\n%s: Unable to read data from any file\n", me);
+ }
+ hestUsage(stderr, opt, me, hparm);
+ fprintf(stderr, "\nFor more info: \"%s --help\"\n", me);
+ }
airMopOkay(mop);
return 0;
Modified: teem/trunk/src/unrrdu/unorient.c
===================================================================
--- teem/trunk/src/unrrdu/unorient.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/unorient.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -35,14 +35,22 @@
int setMinsFromOrigin;
airArray *mop;
- /* if we gave a default for this, then there it would fine to have
- no command-line arguments whatsoever, and then the user would not
- know how to get the basic usage information */
- hestOptAdd(&opt, "i,input", "nin", airTypeOther, 1, 1, &nin, NULL,
- "input nrrd "
- "(sorry, can't use usual default of \"-\" for stdin "
- "because of hest quirk)",
- NULL, NULL, nrrdHestNrrd);
+ /*
+ * with new nrrdHestNrrdNoTTY, can let "-" be default input as normal; no more need
+ * for this awkwardness:
+ *
+ * / * if we gave a default for this, then there it would fine to have
+ * no command-line arguments whatsoever, and then the user would not
+ * know how to get the basic usage information * /
+ * hestOptAdd(&opt, "i,input", "nin", airTypeOther, 1, 1, &nin, NULL,
+ * "input nrrd "
+ * "(sorry, can't use usual default of \"-\" for stdin "
+ * "because of hest quirk)",
+ * NULL, NULL, nrrdHestNrrd);
+ */
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_Other(&opt, "i,input", "nin", &nin, "-",
+ "input nrrd. By default reads from stdin", nrrdHestNrrdNoTTY);
hestOptAdd_Flag(&opt, "smfo", &setMinsFromOrigin,
"set some axis mins based on space origin (hack)");
OPT_ADD_NOUT(out, "output nrrd");
Modified: teem/trunk/src/unrrdu/unquantize.c
===================================================================
--- teem/trunk/src/unrrdu/unquantize.c 2023-07-13 22:28:30 UTC (rev 7092)
+++ teem/trunk/src/unrrdu/unquantize.c 2023-07-13 22:46:18 UTC (rev 7093)
@@ -38,14 +38,19 @@
double oldMin, oldMax;
airArray *mop;
- /* mandatory arg so that "unu unquantize" produces usage info */
- hestOptAdd(&opt, "i,input", "nin", airTypeOther, 1, 1, &nin, NULL,
- "input nrrd. That this argument is required instead of "
- "optional, as with most unu commands, is a quirk caused by the "
- "need to have \"unu unquantize\" generate usage info, combined "
- "with the fact that all the other arguments have sensible "
- "defaults",
- NULL, NULL, nrrdHestNrrd);
+ /*
+ * with new nrrdHestNrrdNoTTY, can let "-" be default input as normal; no more need
+ * for this awkwardness:
+ * hestOptAdd(&opt, "i,input", "nin", airTypeOther, 1, 1, &nin, NULL,
+ * "input nrrd. That this argument is required instead of "
+ * "optional, as with most unu commands, is a quirk caused by the "
+ * "need to have \"unu unquantize\" generate usage info, combined "
+ * "with the fact that all the other arguments have sensible "
+ * "defaults",
+ * NULL, NULL, nrrdHestNrrd);
+ */
+ hparm->noArgsIsNoProblem = AIR_TRUE;
+ hestOptAdd_1_Other(&opt, "i,input", "nin", &nin, "-", "input nrrd", nrrdHestNrrdNoTTY);
hestOptAdd_1_Double(&opt, "min,minimum", "value", &oldMin, "nan",
"Lowest value prior to quantization. Defaults to "
"nin->oldMin if it exists, otherwise 0.0");
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|
|
From: <kin...@us...> - 2023-07-13 22:28:31
|
Revision: 7092
http://sourceforge.net/p/teem/code/7092
Author: kindlmann
Date: 2023-07-13 22:28:30 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
API NEW: nrrdHestNrrdNoTTY for parsing a Nrrd via hest callbacks (hestCB), but with the restriction that - does not work as a synonym for stdin if stdin is a terminal: we only want to try to read from files being piped in. This enables some LONG-wanted functionality in unu, wherein the -i input can default to -, while still allowing 'unu cmd' to trigger some usage info
Modified Paths:
--------------
teem/trunk/src/nrrd/hestNrrd.c
teem/trunk/src/nrrd/nrrd.h
Modified: teem/trunk/src/nrrd/hestNrrd.c
===================================================================
--- teem/trunk/src/nrrd/hestNrrd.c 2023-07-13 21:46:17 UTC (rev 7091)
+++ teem/trunk/src/nrrd/hestNrrd.c 2023-07-13 22:28:30 UTC (rev 7092)
@@ -22,52 +22,86 @@
#include "nrrd.h"
#include "privateNrrd.h"
+#include <unistd.h> /* for isatty() and STDIN_FILENO */
+
/* ---------------------------- Nrrd ----------------------------- */
/*
-** _nrrdHestNrrdParse()
-**
-** Converts a filename into a nrrd for the sake of hest.
-** There is no HestMaybeNrrdParse because this already does that:
-** when we get an empty string, we give back a NULL pointer, and
-** that is just fine
+_nrrdHestNrrdParseOkTTY() and _nrrdHestNrrdParseNoTTY ()
+
+Converts a filename into a nrrd for the sake of hest.
+There is no HestMaybeNrrdParse because this already does that:
+when we get an empty string, we give back a NULL pointer, and
+that is just fine
*/
+
static int
-_nrrdHestNrrdParse(void *ptr, const char *str, char err[AIR_STRLEN_HUGE + 1]) {
- static const char me[] = "_nrrdHestNrrdParse";
+parserBoth(void *ptr,
+ const char *filename,
+ char err[AIR_STRLEN_HUGE + 1],
+ const char *me,
+ int disallowTTY) {
char *nerr;
Nrrd **nrrdP;
airArray *mop;
- if (!(ptr && str)) {
+ if (!(ptr && filename)) {
sprintf(err, "%s: got NULL pointer", me);
return 1;
}
nrrdP = (Nrrd **)ptr;
- if (airStrlen(str)) {
+ *nrrdP = NULL;
+ if (airStrlen(filename)) {
+ if (disallowTTY && !strcmp("-", filename) && isatty(STDIN_FILENO)) {
+ sprintf(err, "%s: declining to try reading Nrrd from stdin as tty (terminal)", me);
+ return 1;
+ }
mop = airMopNew();
*nrrdP = nrrdNew();
airMopAdd(mop, *nrrdP, (airMopper)nrrdNuke, airMopOnError);
- if (nrrdLoad(*nrrdP, str, NULL)) {
+ /* else no concerns about filename being "-" and stdin being a terminal */
+ if (nrrdLoad(*nrrdP, filename, NULL)) {
airMopAdd(mop, nerr = biffGetDone(NRRD), airFree, airMopOnError);
airStrcpy(err, AIR_STRLEN_HUGE + 1, nerr);
airMopError(mop);
+ *nrrdP = NULL;
return (strstr(err, "EOF") ? 2 : 1);
}
airMopOkay(mop);
- } else {
- /* they gave us an empty string, we give back no nrrd,
- but its not an error condition */
- *nrrdP = NULL;
}
+ /* else they gave us an empty string filename, so we give back no nrrd,
+ and its not an error condition */
return 0;
}
-static const hestCB _nrrdHestNrrd = {sizeof(Nrrd *), "nrrd", _nrrdHestNrrdParse,
+static int
+parserOkTTY(void *ptr, const char *filename, char err[AIR_STRLEN_HUGE + 1]) {
+ return parserBoth(ptr,
+ filename,
+ err,
+ "_nrrdHestNrrdParse", /* mimic old name */
+ AIR_FALSE /* not disallowing TTY */);
+}
+
+static int
+parserNoTTY(void *ptr, const char *filename, char err[AIR_STRLEN_HUGE + 1]) {
+ return parserBoth(ptr,
+ filename,
+ err,
+ "_nrrdHestNrrdParse(NoTTY)",
+ AIR_TRUE /* yes disallow TTY */);
+}
+
+static const hestCB _nrrdHestNrrd = {sizeof(Nrrd *), "nrrd", parserOkTTY,
(airMopper)nrrdNuke};
const hestCB *const nrrdHestNrrd = &_nrrdHestNrrd;
+static const hestCB _nrrdHestNrrdNoTTY = {sizeof(Nrrd *), "nrrd", parserNoTTY,
+ (airMopper)nrrdNuke};
+
+const hestCB *const nrrdHestNrrdNoTTY = &_nrrdHestNrrdNoTTY;
+
/* ------------------------ NrrdKernelSpec -------------------------- */
static int
Modified: teem/trunk/src/nrrd/nrrd.h
===================================================================
--- teem/trunk/src/nrrd/nrrd.h 2023-07-13 21:46:17 UTC (rev 7091)
+++ teem/trunk/src/nrrd/nrrd.h 2023-07-13 22:28:30 UTC (rev 7092)
@@ -1098,6 +1098,7 @@
/******** things useful with hest */
/* hestNrrd.c */
NRRD_EXPORT const hestCB *const nrrdHestNrrd;
+NRRD_EXPORT const hestCB *const nrrdHestNrrdNoTTY;
NRRD_EXPORT const hestCB *const nrrdHestKernelSpec;
NRRD_EXPORT const hestCB *const nrrdHestBoundarySpec;
NRRD_EXPORT const hestCB *const nrrdHestIter;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-13 21:46:20
|
Revision: 7091
http://sourceforge.net/p/teem/code/7091
Author: kindlmann
Date: 2023-07-13 21:46:17 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
oops left in a debugging printf
Modified Paths:
--------------
teem/trunk/src/hest/parseHest.c
Modified: teem/trunk/src/hest/parseHest.c
===================================================================
--- teem/trunk/src/hest/parseHest.c 2023-07-13 21:27:52 UTC (rev 7090)
+++ teem/trunk/src/hest/parseHest.c 2023-07-13 21:46:17 UTC (rev 7091)
@@ -873,7 +873,9 @@
/* if not using the default, we're done with this option */
if (!udflt[op]) continue;
prms[op] = airStrdup(opt[op].dflt);
- fprintf(stderr, "!%s: prms[%d] = |%s|\n", me, op, prms[op]);
+ if (parm->verbosity) {
+ printf("%s: prms[%d] = |%s|\n", me, op, prms[op]);
+ }
if (prms[op]) {
airMopAdd(mop, prms[op], airFree, airMopAlways);
airOneLinify(prms[op]);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-13 21:27:54
|
Revision: 7090
http://sourceforge.net/p/teem/code/7090
Author: kindlmann
Date: 2023-07-13 21:27:52 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
updating hest usage, and clarifying usage info
Modified Paths:
--------------
teem/trunk/src/unrrdu/data.c
Modified: teem/trunk/src/unrrdu/data.c
===================================================================
--- teem/trunk/src/unrrdu/data.c 2023-07-13 21:20:35 UTC (rev 7089)
+++ teem/trunk/src/unrrdu/data.c 2023-07-13 21:27:52 UTC (rev 7090)
@@ -28,7 +28,7 @@
"stand-alone decoder, in case this Teem build lacks an optional "
"data encoding required for a given nrrd file. Caveats: "
"Will start copying characters from the datafile "
- "to output file until EOF is hit, so this won't work "
+ "to stdout until EOF is hit, so this won't work "
"correctly if the datafile has extraneous content at the end. Will "
"skip lines (as per \"line skip:\" header field) if needed, but can only "
"skip bytes (as per \"byte skip:\") if the encoding is NOT a compression. "
@@ -49,7 +49,7 @@
int car, pret;
mop = airMopNew();
- hestOptAdd(&opt, NULL, "nin", airTypeString, 1, 1, &inS, NULL, "input nrrd");
+ hestOptAdd_1_String(&opt, NULL, "nin", &inS, NULL, "input nrrd");
airMopAdd(mop, opt, hestOptFree_vp, airMopAlways);
USAGE_OR_PARSE(_unrrdu_dataInfoL);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-13 21:20:37
|
Revision: 7089
http://sourceforge.net/p/teem/code/7089
Author: kindlmann
Date: 2023-07-13 21:20:35 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
Some bug fixes related to updating "unu head":
* in extractUnflagged(): test for getting min # of parms for
variable parm option was in the wrong place: should be inside
test that some # of parms were given on the command-line
(so that an unflagged variable parm option can take them from default)
* in _hestDefaults(): since r1005 2002-10-03 the test for whether
enough parms were supplied by default was incorrectly contingent on
hestParm->elideMultipleEmptyStringDefault, even though that option
only controls the generation of usage info. wtf.
* lots of changes of "!%s ..." to "%s ..." since the former is
intended just for transient debugging
Modified Paths:
--------------
teem/trunk/src/hest/parseHest.c
Modified: teem/trunk/src/hest/parseHest.c
===================================================================
--- teem/trunk/src/hest/parseHest.c 2023-07-13 16:26:32 UTC (rev 7088)
+++ teem/trunk/src/hest/parseHest.c 2023-07-13 21:20:35 UTC (rev 7089)
@@ -145,7 +145,7 @@
}
/* else not a show-stopper argument */
if (parm->verbosity) {
- printf("!%s:________ newArgc = %d, oldArgc = %d -> \"%s\"\n", me, newArgc, oldArgc,
+ printf("%s:________ newArgc = %d, oldArgc = %d -> \"%s\"\n", me, newArgc, oldArgc,
oldArgv[oldArgc]);
printArgv(newArgc, newArgv, " ");
}
@@ -181,7 +181,7 @@
oldArgc++;
if (parm->verbosity) {
printArgv(newArgc, newArgv, " ");
- printf("!%s: ^^^^^^^ newArgc = %d, oldArgc = %d\n", me, newArgc, oldArgc);
+ printf("%s: ^^^^^^^ newArgc = %d, oldArgc = %d\n", me, newArgc, oldArgc);
}
}
newArgv[newArgc] = NULL;
@@ -475,9 +475,9 @@
numOpts = hestOptNum(opt);
if (parm->verbosity)
- printf("!%s: (a) looking for flag |%s| in numOpts=%d options\n", me, flag, numOpts);
+ printf("%s: (a) looking for flag |%s| in numOpts=%d options\n", me, flag, numOpts);
for (op = 0; op < numOpts; op++) {
- if (parm->verbosity) printf("!%s: op = %d\n", me, op);
+ if (parm->verbosity) printf("%s: op = %d\n", me, op);
if (!opt[op].flag) continue;
if (strchr(opt[op].flag, parm->multiFlagSep)) {
strcpy(copy, opt[op].flag);
@@ -598,21 +598,21 @@
int a, np, flag, endflag, numOpts, op;
a = 0;
- if (parm->verbosity) printf("!%s: *argcP = %d\n", me, *argcP);
+ if (parm->verbosity) printf("%s: *argcP = %d\n", me, *argcP);
while (a <= *argcP - 1) {
if (parm->verbosity) {
- printf("!%s: ----------------- a = %d -> argv[a] = %s\n", me, a, argv[a]);
+ printf("%s: ----------------- a = %d -> argv[a] = %s\n", me, a, argv[a]);
}
flag = whichFlag(opt, argv[a], parm);
- if (parm->verbosity) printf("!%s: A: a = %d -> flag = %d\n", me, a, flag);
+ if (parm->verbosity) printf("%s: A: a = %d -> flag = %d\n", me, a, flag);
if (!(0 <= flag)) {
/* not a flag, move on */
a++;
- if (parm->verbosity) printf("!%s: !(0 <= %d), so: continue\n", me, flag);
+ if (parm->verbosity) printf("%s: !(0 <= %d), so: continue\n", me, flag);
continue;
}
/* see if we can associate some parameters with the flag */
- if (parm->verbosity) printf("!%s: flag = %d; any parms?\n", me, flag);
+ if (parm->verbosity) printf("%s: flag = %d; any parms?\n", me, flag);
np = 0;
endflag = 0;
while (np < _hestMax(opt[flag].max) /* */
@@ -620,7 +620,7 @@
&& -1 == (endflag = whichFlag(opt, argv[a + np + 1], parm))) {
np++;
if (parm->verbosity)
- printf("!%s: np --> %d with flag = %d; endflag = %d\n", me, np, flag, endflag);
+ printf("%s: np --> %d with flag = %d; endflag = %d\n", me, np, flag, endflag);
}
/* we stopped because we got the max number of parameters, or
because we hit the end of the command line, or
@@ -629,7 +629,7 @@
we stopped because of whichFlag()'s return value,
endflag has been set to that return value */
if (parm->verbosity)
- printf("!%s: B: stopped with np = %d; flag = %d; endflag = %d\n", me, np, flag,
+ printf("%s: B: stopped with np = %d; flag = %d; endflag = %d\n", me, np, flag,
endflag);
if (np < (int)opt[flag].min) { /* HEY scrutinize casts */
/* didn't get minimum number of parameters */
@@ -655,7 +655,7 @@
}
nprm[flag] = np;
if (parm->verbosity) {
- printf("!%s:________ a=%d, *argcP = %d -> flag = %d\n", me, a, *argcP, flag);
+ printf("%s:________ a=%d, *argcP = %d -> flag = %d\n", me, a, *argcP, flag);
printArgv(*argcP, argv, " ");
}
/* lose the flag argument */
@@ -674,8 +674,8 @@
}
if (parm->verbosity) {
printArgv(*argcP, argv, " ");
- printf("!%s:^^^^^^^^ *argcP = %d\n", me, *argcP);
- printf("!%s: prms[%d] = %s\n", me, flag, prms[flag] ? prms[flag] : "(null)");
+ printf("%s:^^^^^^^^ *argcP = %d\n", me, *argcP);
+ printf("%s: prms[%d] = %s\n", me, flag, prms[flag] ? prms[flag] : "(null)");
}
}
@@ -715,20 +715,20 @@
return 0;
}
if (parm->verbosity) {
- printf("!%s numOpts %d != unflag1st %d: have some (of %d) unflagged options\n", me,
+ printf("%s numOpts %d != unflag1st %d: have some (of %d) unflagged options\n", me,
numOpts, unflag1st, numOpts);
}
for (unflagVar = unflag1st; unflagVar != numOpts;
unflagVar = _hestNextUnflagged(unflagVar + 1, opt, numOpts)) {
- if ((int)opt[unflagVar].min
- < _hestMax(opt[unflagVar].max)) /* HEY scrutinize casts */
+ if (AIR_INT(opt[unflagVar].min) < _hestMax(opt[unflagVar].max)) {
break;
+ }
}
/* now, if there is a variable parameter unflagged opt, unflagVar is its
index in opt[], or else unflagVar is numOpts */
if (parm->verbosity) {
- printf("!%s unflagVar %d\n", me, unflagVar);
+ printf("%s unflagVar %d\n", me, unflagVar);
}
/* grab parameters for all unflagged opts before opt[t] */
@@ -735,7 +735,7 @@
for (op = _hestNextUnflagged(0, opt, numOpts); op < unflagVar;
op = _hestNextUnflagged(op + 1, opt, numOpts)) {
if (parm->verbosity) {
- printf("!%s op = %d; unflagVar = %d\n", me, op, unflagVar);
+ printf("%s op = %d; unflagVar = %d\n", me, op, unflagVar);
}
np = opt[op].min; /* min == max */
if (!(np <= *argcP)) {
@@ -777,26 +777,30 @@
/* now we grab the parameters of the sole variable parameter unflagged opt,
if it exists (unflagVar < numOpts) */
if (parm->verbosity) {
- printf("!%s (still here) unflagVar %d vs numOpts %d\n", me, unflagVar, numOpts);
+ printf("%s (still here) unflagVar %d vs numOpts %d (nvp %d)\n", me, unflagVar,
+ numOpts, nvp);
}
if (unflagVar < numOpts) {
if (parm->verbosity) {
- printf("!%s unflagVar=%d: min, nvp, max = %d %d %d\n", me, unflagVar,
+ printf("%s unflagVar=%d: min, nvp, max = %d %d %d\n", me, unflagVar,
opt[unflagVar].min, nvp, _hestMax(opt[unflagVar].max));
}
/* we'll do error checking for unexpected args later */
nvp = AIR_MIN(nvp, _hestMax(opt[unflagVar].max));
- if (nvp < (int)opt[unflagVar].min) { /* HEY scrutinize casts */
- sprintf(err, "%sdidn't get minimum of %d arg%s for %s (got %d)", ME,
- opt[unflagVar].min, opt[unflagVar].min > 1 ? "s" : "",
- identStr(ident, opt + unflagVar, parm, AIR_TRUE), nvp);
- return 1;
- }
if (nvp) {
unsigned int gotp = 0;
+ /* pre-2023: this check used to be done regardless of nvp, but that incorrectly
+ triggered this error message when there were zero given parms, but the default
+ could have supplied them */
+ if (nvp < AIR_INT(opt[unflagVar].min)) {
+ sprintf(err, "%sdidn't get minimum of %d arg%s for %s (got %d)", ME,
+ opt[unflagVar].min, opt[unflagVar].min > 1 ? "s" : "",
+ identStr(ident, opt + unflagVar, parm, AIR_TRUE), nvp);
+ return 1;
+ }
prms[unflagVar] = extractToStr(argcP, argv, 0, nvp, &gotp, parm);
if (parm->verbosity) {
- printf("!%s extracted %u to new string |%s| (*argcP now %d)\n", me, gotp,
+ printf("%s extracted %u to new string |%s| (*argcP now %d)\n", me, gotp,
prms[unflagVar], *argcP);
}
airMopAdd(pmop, prms[unflagVar], airFree, airMopAlways);
@@ -845,23 +849,31 @@
default. In either case, nprm[op] will be zero, and in both cases,
we need to use the default information. */
udflt[op] = (0 == nprm[op]);
- /*
- fprintf(stderr, "%s nprm[%d] = %u --> udflt[%d] = %d\n", me,
- op, nprm[op], op, udflt[op]);
- */
+ /* fprintf(stderr, "%s nprm[%d] = %u --> udflt[%d] = %d\n", me,
+ * op, nprm[op], op, udflt[op]); */
break;
case 5:
/* -------- multiple optional parameters -------- */
- /* we'll use the default if the flag didn't appear (if there is a
- flag) Otherwise, if nprm[op] is zero, then the user is saying,
- I want zero parameters */
- udflt[op] = opt[op].flag && !appr[op];
+ /* we'll use the default if there is a flag and it didn't appear,
+ Otherwise (with a flagged option), if nprm[op] is zero, we'll use the default
+ if user has given zero parameters, yet the the option requires at least one.
+ If an unflagged option can have zero parms, and user has given zero parms,
+ then we don't use the default */
+ udflt[op] = (opt[op].flag
+ ? !appr[op] /* option is flagged and flag didn't appear */
+ /* else: option is unflagged, and there were no given parms,
+ and yet the option requires at least one parm */
+ : !nprm[op] && opt[op].min >= 1);
+ /* fprintf(stderr,
+ * "!%s: opt[%d].flag = %d; appr[op] = %d; nprm[op] = %d; opt[op].min = %d "
+ * "--> udflt[op] = %d\n",
+ * me, op, !!opt[op].flag, appr[op], nprm[op], opt[op].min, udflt[op]); */
break;
}
/* if not using the default, we're done with this option */
if (!udflt[op]) continue;
prms[op] = airStrdup(opt[op].dflt);
- /* fprintf(stderr, "%s: prms[%d] = |%s|\n", me, op, prms[op]); */
+ fprintf(stderr, "!%s: prms[%d] = |%s|\n", me, op, prms[op]);
if (prms[op]) {
airMopAdd(mop, prms[op], airFree, airMopAlways);
airOneLinify(prms[op]);
@@ -868,19 +880,23 @@
tmpS = airStrdup(prms[op]);
nprm[op] = airStrntok(tmpS, " ");
airFree(tmpS);
- /* printf("!%s: nprm[%d] in default = %u\n", me, op, nprm[op]); */
- if ((int)opt[op].min < _hestMax(opt[op].max)) { /* HEY scrutinize casts */
- if (!(AIR_IN_CL((int)opt[op].min, (int)nprm[op],
- _hestMax(opt[op].max)) /* HEY scrutinize casts */
- || (airTypeString == opt[op].type
- && parm->elideMultipleEmptyStringDefault))) {
+ }
+ /* fprintf(stderr,
+ * "!%s: after default; nprm[%d] = %u; varparm = %d (min %d vs max %d)\n", me,
+ * op, nprm[op], AIR_INT(opt[op].min) < _hestMax(opt[op].max),
+ * ((int)opt[op].min), _hestMax(opt[op].max)); */
+ if (AIR_INT(opt[op].min) < _hestMax(opt[op].max)) {
+ if (!AIR_IN_CL(AIR_INT(opt[op].min), AIR_INT(nprm[op]), _hestMax(opt[op].max))) {
+ if (-1 == opt[op].max) {
+ sprintf(err, "%s# parameters (in default) for %s is %d, but need %d or more",
+ ME, identStr(ident, opt + op, parm, AIR_TRUE), nprm[op], opt[op].min);
+ } else {
sprintf(err,
- "%s# parameters (in default) for %s is %d, "
- "but need between %d and %d",
+ "%s# parameters (in default) for %s is %d, but need between %d and %d",
ME, identStr(ident, opt + op, parm, AIR_TRUE), nprm[op], opt[op].min,
_hestMax(opt[op].max));
- return 1;
}
+ return 1;
}
}
}
@@ -1263,8 +1279,8 @@
}
}
if (parm->verbosity) {
- printf("!%s: nprm[%d] = %u\n", me, op, nprm[op]);
- printf("!%s: new array (size %u*%u) is at 0x%p\n", me, nprm[op],
+ printf("%s: nprm[%d] = %u\n", me, op, nprm[op]);
+ printf("%s: new array (size %u*%u) is at 0x%p\n", me, nprm[op],
(unsigned int)size, *((void **)vP));
}
if (*((void **)vP)) {
@@ -1454,7 +1470,7 @@
argc = argr + _argc - nrf;
if (PARM->verbosity) {
- printf("!%s: nrf = %d; argr = %d; _argc = %d --> argc = %d\n", me, nrf, argr, _argc,
+ printf("%s: nrf = %d; argr = %d; _argc = %d --> argc = %d\n", me, nrf, argr, _argc,
argc);
}
argv = AIR_CALLOC(argc + 1, char *);
@@ -1548,7 +1564,7 @@
}
/* -------- now, the actual parsing of values */
- if (PARM->verbosity) printf("%s: #### calling hestSetValues\n", me);
+ if (PARM->verbosity) printf("%s: #### calling setValues\n", me);
/* this will also set hestOpt->parmStr */
ret = setValues(prms, udflt, nprm, appr, opt, err, PARM, mop);
if (ret) {
@@ -1556,7 +1572,7 @@
return ret;
}
- if (PARM->verbosity) printf("%s: #### hestSetValues done!\n", me);
+ if (PARM->verbosity) printf("%s: #### setValues done!\n", me);
#undef PARM
parseEnd:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-13 16:26:37
|
Revision: 7088
http://sourceforge.net/p/teem/code/7088
Author: kindlmann
Date: 2023-07-13 16:26:32 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
fixed use of hestOptAdd_1_Enum
Modified Paths:
--------------
teem/trunk/src/bin/overrgb.c
Modified: teem/trunk/src/bin/overrgb.c
===================================================================
--- teem/trunk/src/bin/overrgb.c 2023-07-13 12:27:54 UTC (rev 7087)
+++ teem/trunk/src/bin/overrgb.c 2023-07-13 16:26:32 UTC (rev 7088)
@@ -100,7 +100,7 @@
"intent in the sRGB chunk of the PNG file format. Can be "
"absolute, relative, perceptual, saturation, or none. This is "
"independent of using \"srgb\" as the -g gamma",
- NULL, nrrdFormatPNGsRGBIntent);
+ nrrdFormatPNGsRGBIntent);
hestOptAdd_3_Double(&hopt, "b", "background", back, "0 0 0",
"background color to composite against; white is "
"1 1 1, not 255 255 255.");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kin...@us...> - 2023-07-13 12:27:58
|
Revision: 7087
http://sourceforge.net/p/teem/code/7087
Author: kindlmann
Date: 2023-07-13 12:27:54 +0000 (Thu, 13 Jul 2023)
Log Message:
-----------
updated hest usage
Modified Paths:
--------------
teem/trunk/src/bin/deconv.c
teem/trunk/src/bin/emap.c
teem/trunk/src/bin/gprobe.c
teem/trunk/src/bin/ilk.c
teem/trunk/src/bin/miter.c
teem/trunk/src/bin/mrender.c
teem/trunk/src/bin/overrgb.c
teem/trunk/src/bin/pprobe.c
teem/trunk/src/bin/qbert.c
teem/trunk/src/bin/spots.c
teem/trunk/src/bin/talkweb.c
teem/trunk/src/bin/ungantry.c
teem/trunk/src/bin/vprobe.c
Modified: teem/trunk/src/bin/deconv.c
===================================================================
--- teem/trunk/src/bin/deconv.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/deconv.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -57,29 +57,27 @@
airMopAdd(mop, hparm, AIR_CAST(airMopper, hestParmFree), airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hparm->respectDashDashHelp = AIR_TRUE;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL, "input volume", NULL,
- NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
- "\"kind\" of volume (\"scalar\", \"vector\", "
- "\"tensor\", or \"dwi\")",
- NULL, NULL, meetHestGageKind);
- hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &ksp, NULL,
- "convolution kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "mi", "max # iters", airTypeUInt, 1, 1, &maxIter, "100",
- "maximum number of iterations with which to compute the "
- "deconvolution");
- hestOptAdd(&hopt, "e", "epsilon", airTypeDouble, 1, 1, &epsilon, "0.00000001",
- "convergence threshold");
- hestOptAdd(&hopt, "s", "step", airTypeDouble, 1, 1, &step, "1.0",
- "scaling of value update");
- hestOptAdd(&hopt, "t", "type", airTypeOther, 1, 1, &otype, "default",
- "type to save output as. By default (not using this option), "
- "the output type is the same as the input type",
- NULL, NULL, &unrrduHestMaybeTypeCB);
- hestOptAdd(&hopt, "sep", "bool", airTypeBool, 1, 1, &separ, "false",
- "use fast separable deconvolution instead of brain-dead "
- "brute-force iterative method");
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-", "output volume");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, NULL, "input volume", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "k", "kind", &kind, NULL,
+ "\"kind\" of volume (\"scalar\", \"vector\", "
+ "\"tensor\", or \"dwi\")",
+ meetHestGageKind);
+ hestOptAdd_1_Other(&hopt, "k00", "kernel", &ksp, NULL, "convolution kernel",
+ nrrdHestKernelSpec);
+ hestOptAdd_1_UInt(&hopt, "mi", "max # iters", &maxIter, "100",
+ "maximum number of iterations with which to compute the "
+ "deconvolution");
+ hestOptAdd_1_Double(&hopt, "e", "epsilon", &epsilon, "0.00000001",
+ "convergence threshold");
+ hestOptAdd_1_Double(&hopt, "s", "step", &step, "1.0", "scaling of value update");
+ hestOptAdd_1_Other(&hopt, "t", "type", &otype, "default",
+ "type to save output as. By default (not using this option), "
+ "the output type is the same as the input type",
+ &unrrduHestMaybeTypeCB);
+ hestOptAdd_1_Bool(&hopt, "sep", "bool", &separ, "false",
+ "use fast separable deconvolution instead of brain-dead "
+ "brute-force iterative method");
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output volume");
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, deconvInfo, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestOptFree), airMopAlways);
Modified: teem/trunk/src/bin/emap.c
===================================================================
--- teem/trunk/src/bin/emap.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/emap.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -45,8 +45,8 @@
char *outS, *errS, *debugS;
airArray *mop;
float amb[3], *linfo, *debug, *map, vscl;
- unsigned li, ui, vi;
- int qn, bits, method, doerr;
+ unsigned int li, ui, vi, bits;
+ int qn, method, doerr;
limnLight *light;
limnCamera *cam;
double u, v, r, w, V2W[9], diff, WW[3], VV[3];
@@ -59,35 +59,34 @@
hparm->respectDashDashHelp = AIR_TRUE;
cam = limnCameraNew();
airMopAdd(mop, cam, (airMopper)limnCameraNix, airMopAlways);
- hestOptAdd(&hopt, "i", "nlight", airTypeOther, 1, 1, &nlight, NULL,
- "input nrrd containing light information", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "b", "# bits", airTypeInt, 1, 1, &bits, "16",
- "number of bits to use for normal quantization, "
- "between 8 and 16 inclusive. ");
- hestOptAdd(&hopt, "amb", "ambient RGB", airTypeFloat, 3, 3, amb, "0 0 0",
- "ambient light color");
- hestOptAdd(&hopt, "fr", "from point", airTypeDouble, 3, 3, cam->from, "1 0 0",
- "position of camera, used to determine view vector");
- hestOptAdd(&hopt, "at", "at point", airTypeDouble, 3, 3, cam->at, "0 0 0",
- "camera look-at point, used to determine view vector");
- hestOptAdd(&hopt, "up", "up vector", airTypeDouble, 3, 3, cam->up, "0 0 1",
- "camera pseudo-up vector, used to determine view coordinates");
- hestOptAdd(&hopt, "rh", NULL, airTypeInt, 0, 0, &(cam->rightHanded), NULL,
- "use a right-handed UVN frame (V points down)");
- hestOptAdd(&hopt, "vs", "view-dir scaling", airTypeFloat, 1, 1, &vscl, "1",
- "scaling along view-direction of location of "
- "view-space lights");
- hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, NULL,
- "file to write output envmap to");
- hestOptAdd(&hopt, "d", "filename", airTypeString, 1, 1, &debugS, "",
- "Use this option to save out (to the given filename) a rendering "
- "of the front (on the left) and back (on the right) of a sphere "
- "as shaded with the new environment map. U increases "
- "right-ward, V increases downward. The back sphere half is "
- "rendered as though the front half was removed");
- hestOptAdd(&hopt, "err", NULL, airTypeInt, 0, 0, &doerr, NULL,
- "If using \"-d\", make the image represent the error between the "
- "real and quantized vector");
+ hestOptAdd_1_Other(&hopt, "i", "nlight", &nlight, NULL,
+ "input nrrd containing light information", nrrdHestNrrd);
+ hestOptAdd_1_UInt(&hopt, "b", "# bits", &bits, "16",
+ "number of bits to use for normal quantization, "
+ "between 8 and 16 inclusive. ");
+ hestOptAdd_3_Float(&hopt, "amb", "ambient RGB", amb, "0 0 0", "ambient light color");
+ hestOptAdd_3_Double(&hopt, "fr", "from point", cam->from, "1 0 0",
+ "position of camera, used to determine view vector");
+ hestOptAdd_3_Double(&hopt, "at", "at point", cam->at, "0 0 0",
+ "camera look-at point, used to determine view vector");
+ hestOptAdd_3_Double(&hopt, "up", "up vector", cam->up, "0 0 1",
+ "camera pseudo-up vector, used to determine view coordinates");
+ hestOptAdd_Flag(&hopt, "rh", &(cam->rightHanded),
+ "use a right-handed UVN frame (V points down)");
+ hestOptAdd_1_Float(&hopt, "vs", "view-dir scaling", &vscl, "1",
+ "scaling along view-direction of location of "
+ "view-space lights");
+ hestOptAdd_1_String(&hopt, "o", "filename", &outS, NULL,
+ "file to write output envmap to");
+ hestOptAdd_1_String(&hopt, "d", "filename", &debugS, "",
+ "Use this option to save out (to the given filename) a rendering "
+ "of the front (on the left) and back (on the right) of a sphere "
+ "as shaded with the new environment map. U increases "
+ "right-ward, V increases downward. The back sphere half is "
+ "rendered as though the front half was removed");
+ hestOptAdd_Flag(&hopt, "err", &doerr,
+ "If using \"-d\", make the image represent the error between the "
+ "real and quantized vector");
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, emapInfo, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
@@ -122,7 +121,7 @@
method = limnQN8octa;
break;
default:
- fprintf(stderr, "%s: requested #bits (%d) not in valid range [8,16]\n", me, bits);
+ fprintf(stderr, "%s: requested #bits (%u) not in valid range [8,16]\n", me, bits);
airMopError(mop);
return 1;
}
Modified: teem/trunk/src/bin/gprobe.c
===================================================================
--- teem/trunk/src/bin/gprobe.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/gprobe.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -272,64 +272,65 @@
airMopAdd(mop, hparm, AIR_CAST(airMopper, hestParmFree), airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hparm->respectDashDashHelp = AIR_TRUE;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL, "input volume", NULL,
- NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
- "\"kind\" of volume (\"scalar\", \"vector\", "
- "\"tensor\", or \"dwi\")",
- NULL, NULL, meetHestGageKind);
- hestOptAdd(&hopt, "v", "verbosity", airTypeInt, 1, 1, &verbose, "1",
- "verbosity level");
- hestOptAdd(&hopt, "q", "query", airTypeString, 1, 1, &whatS, NULL,
- "the quantity (scalar, vector, or matrix) to learn by probing");
- hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc, "0.0",
- "For curvature-based queries, use zero when gradient "
- "magnitude is below this");
- hestOptAdd(&hopt, "ofs", "ofs", airTypeInt, 0, 0, &orientationFromSpacing, NULL,
- "If only per-axis spacing is available, use that to "
- "contrive full orientation info");
- hestOptAdd(&hopt, "seed", "N", airTypeUInt, 1, 1, &seed, "42",
- "RNG seed; mostly for debugging");
- hestOptAdd(&hopt, "c", "bool", airTypeBool, 1, 1, &clamp, "false",
- "clamp positions as part of probing");
- hestOptAdd(&hopt, "ev", "thresh val", airTypeDouble, 2, 2, edgeFracInfo, "1 0",
- "if using position clamping (with \"-c true\"), the fraction "
- "of values invented for the kernel support, or \"edge frac\" "
- "is saved per probe (0 means kernel support was entirely within "
- "data; 1 means everything was invented). "
- "If this frac exceeds the first \"thresh\" "
- "value given here, then the saved value for the probe will be "
- "the second value \"val\" given here");
- hestOptAdd(&hopt, "zz", "bool", airTypeBool, 1, 1, &zeroZ, "false",
- "enable \"zeroZ\" behavior in gage that partially "
- "implements working with 3D images as if they are 2D");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, NULL, "input volume", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "k", "kind", &kind, NULL,
+ "\"kind\" of volume (\"scalar\", \"vector\", "
+ "\"tensor\", or \"dwi\")",
+ meetHestGageKind);
+ hestOptAdd_1_Int(&hopt, "v", "verbosity", &verbose, "1", "verbosity level");
+ hestOptAdd_1_String(&hopt, "q", "query", &whatS, NULL,
+ "the quantity (scalar, vector, or matrix) to learn by probing");
+ hestOptAdd_1_Double(&hopt, "gmc", "min gradmag", &gmc, "0.0",
+ "For curvature-based queries, use zero when gradient "
+ "magnitude is below this");
+ hestOptAdd_Flag(&hopt, "ofs", &orientationFromSpacing,
+ "If only per-axis spacing is available, use that to "
+ "contrive full orientation info");
+ hestOptAdd_1_UInt(&hopt, "seed", "N", &seed, "42", "RNG seed; mostly for debugging");
+ hestOptAdd_1_Bool(&hopt, "c", "bool", &clamp, "false",
+ "clamp positions as part of probing");
+ hestOptAdd_2_Double(&hopt, "ev", "thresh val", edgeFracInfo, "1 0",
+ "if using position clamping (with \"-c true\"), the fraction "
+ "of values invented for the kernel support, or \"edge frac\" "
+ "is saved per probe (0 means kernel support was entirely within "
+ "data; 1 means everything was invented). "
+ "If this frac exceeds the first \"thresh\" "
+ "value given here, then the saved value for the probe will be "
+ "the second value \"val\" given here");
+ hestOptAdd_1_Bool(&hopt, "zz", "bool", &zeroZ, "false",
+ "enable \"zeroZ\" behavior in gage that partially "
+ "implements working with 3D images as if they are 2D");
- hestOptAdd(&hopt, "k00", "kern00", airTypeOther, 1, 1, &k00, "tent",
- "kernel for gageKernel00", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k11", "kern11", airTypeOther, 1, 1, &k11, "cubicd:1,0",
- "kernel for gageKernel11", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k22", "kern22", airTypeOther, 1, 1, &k22, "cubicdd:1,0",
- "kernel for gageKernel22", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "rn", NULL, airTypeInt, 0, 0, &renorm, NULL,
- "renormalize kernel weights at each new sample location. "
- "\"Accurate\" kernels don't need this; doing it always "
- "makes things go slower");
+ hestOptAdd_1_Other(&hopt, "k00", "kern00", &k00, "tent", "kernel for gageKernel00",
+ nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k11", "kern11", &k11, "cubicd:1,0",
+ "kernel for gageKernel11", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k22", "kern22", &k22, "cubicdd:1,0",
+ "kernel for gageKernel22", nrrdHestKernelSpec);
+ hestOptAdd_Flag(&hopt, "rn", &renorm,
+ "renormalize kernel weights at each new sample location. "
+ "\"Accurate\" kernels don't need this; doing it always "
+ "makes things go slower");
nsi = 0;
- nonSbpOpi[nsi++] = hestOptAdd(&hopt, "ssn", "SS #", airTypeUInt, 1, 1, &numSS, "0",
- "how many scale-space samples to evaluate, or, "
- "0 to turn-off all scale-space behavior");
- nonSbpOpi[nsi++] = hestOptAdd(&hopt, "ssr", "scale range", airTypeDouble, 2, 2,
- rangeSS, "nan nan", "range of scales in scale-space");
- nonSbpOpi[nsi++] = hestOptAdd(&hopt, "ssu", NULL, airTypeInt, 0, 0, &uniformSS, NULL,
- "do uniform samples along sigma, and not (by default) "
- "samples according to the effective diffusion scale");
- nonSbpOpi[nsi++] = hestOptAdd(&hopt, "sso", NULL, airTypeInt, 0, 0, &optimSS, NULL,
- "if not using \"-ssu\", use pre-computed optimal "
- "sigmas when possible");
- nonSbpOpi[nsi++] = hestOptAdd(&hopt, "kssb", "kernel", airTypeOther, 1, 1, &kSSblur,
- "dgauss:1,5", "blurring kernel, to sample scale space",
- NULL, NULL, nrrdHestKernelSpec);
+ nonSbpOpi[nsi++] /* */
+ = hestOptAdd_1_UInt(&hopt, "ssn", "SS #", &numSS, "0",
+ "how many scale-space samples to evaluate, or, "
+ "0 to turn-off all scale-space behavior");
+ nonSbpOpi[nsi++] /* */
+ = hestOptAdd_2_Double(&hopt, "ssr", "scale range", rangeSS, "nan nan",
+ "range of scales in scale-space");
+ nonSbpOpi[nsi++] /* */
+ = hestOptAdd_Flag(&hopt, "ssu", &uniformSS,
+ "do uniform samples along sigma, and not (by default) "
+ "samples according to the effective diffusion scale");
+ nonSbpOpi[nsi++] /* */
+ = hestOptAdd_Flag(&hopt, "sso", &optimSS,
+ "if not using \"-ssu\", use pre-computed optimal "
+ "sigmas when possible");
+ nonSbpOpi[nsi++] /* */
+ = hestOptAdd_1_Other(&hopt, "kssb", "kernel", &kSSblur, "dgauss:1,5",
+ "blurring kernel, to sample scale space", nrrdHestKernelSpec);
if (nsi != NON_SBP_OPT_NUM) {
fprintf(stderr, "%s: PANIC nsi %u != %u", me, nsi, NON_SBP_OPT_NUM);
exit(1);
@@ -341,56 +342,55 @@
/* These two options are needed even if sbp is used, because they are *not*
part of the gageStackBlurParm. In meet, this info is handled by the
extraFlag/extraParm construct, which is not available here */
- hestOptAdd(&hopt, "ssnd", NULL, airTypeInt, 0, 0, &normdSS, NULL,
- "normalize derivatives by scale");
- hestOptAdd(&hopt, "ssnb", "bias", airTypeDouble, 1, 1, &biasSS, "0.0",
- "bias on scale-based derivative normalization");
+ hestOptAdd_Flag(&hopt, "ssnd", &normdSS, "normalize derivatives by scale");
+ hestOptAdd_1_Double(&hopt, "ssnb", "bias", &biasSS, "0.0",
+ "bias on scale-based derivative normalization");
- hestOptAdd(&hopt, "ssf", "SS read/save format", airTypeString, 1, 1, &stackFnameFormat,
- "",
- "printf-style format (including a \"%u\") for the "
- "filenames from which to read "
- "pre-blurred volumes computed for the stack, if they "
- "exist and match the stack parameters, and where to save "
- "them if they had to be re-computed. Leave this as empty "
- "string to disable this.");
+ hestOptAdd_1_String(&hopt, "ssf", "SS read/save format", &stackFnameFormat, "",
+ "printf-style format (including a \"%u\") for the "
+ "filenames from which to read "
+ "pre-blurred volumes computed for the stack, if they "
+ "exist and match the stack parameters, and where to save "
+ "them if they had to be re-computed. Leave this as empty "
+ "string to disable this.");
- hestOptAdd(&hopt, "kssr", "kernel", airTypeOther, 1, 1, &kSS, "hermite",
- "kernel for reconstructing from scale space samples", NULL, NULL,
- nrrdHestKernelSpec);
- hestOptAdd(&hopt, "sit", "sit", airTypeBool, 1, 1, &scaleIsTau, "false",
- "in some places, scale should be interpreted as tau, not "
- "sigma. Currently limited to grid probing (via \"-pg\")");
+ hestOptAdd_1_Other(&hopt, "kssr", "kernel", &kSS, "hermite",
+ "kernel for reconstructing from scale space samples",
+ nrrdHestKernelSpec);
+ hestOptAdd_1_Bool(&hopt, "sit", "sit", &scaleIsTau, "false",
+ "in some places, scale should be interpreted as tau, not "
+ "sigma. Currently limited to grid probing (via \"-pg\")");
- hestOptAdd(&hopt, "s", "sclX sclY sxlZ", airTypeDouble, 3, 3, scale, "1 1 1",
- "scaling factor for resampling on each axis "
- "(>1.0: supersampling); use \"-ssp\" (and \"-psi\") "
- "to specify scale position of sampling");
- hestOptAdd(&hopt, "ssp", "pos", airTypeDouble, 1, 1, &posSS, "0",
- "when using scale-space, scale-position at which to probe");
- hestOptAdd(&hopt, "pg", "nrrd", airTypeOther, 1, 1, &_ngrid, "",
- "overrides \"-s\": "
- "2-D nrrd which specifies origin and direction vectors "
- "for sampling grid",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "pi", "nrrd", airTypeOther, 1, 1, &_npos, "",
- "overrides \"-pg\": probes at this list of 3-vec or "
- "4-vec positions",
- NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "pp", "pos", airTypeDouble, 3, 4, &pntPos, "nan nan nan",
- "overrides \"-pi\": only sample at this specified point", &pntPosNum);
- hestOptAdd(&hopt, "eps", "epsilon", airTypeDouble, 1, 1, &eps, "0",
- "if non-zero, and if query is a scalar, and if using \"pp\" "
- "to query at a single point, then do epsilon offset probes "
- "to calculate discrete differences, to find the numerical "
- "gradient and hessian (for debugging)");
- hestOptAdd(&hopt, "psi", "p", airTypeBool, 1, 1, &probeSpaceIndex, "false",
- "whether the probe location specification (by any of "
- "the four previous flags) are in index space");
+ hestOptAdd_3_Double(&hopt, "s", "sclX sclY sxlZ", scale, "1 1 1",
+ "scaling factor for resampling on each axis "
+ "(>1.0: supersampling); use \"-ssp\" (and \"-psi\") "
+ "to specify scale position of sampling");
+ hestOptAdd_1_Double(&hopt, "ssp", "pos", &posSS, "0",
+ "when using scale-space, scale-position at which to probe");
+ hestOptAdd_1_Other(&hopt, "pg", "nrrd", &_ngrid, "",
+ "overrides \"-s\": "
+ "2-D nrrd which specifies origin and direction vectors "
+ "for sampling grid",
+ nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "pi", "nrrd", &_npos, "",
+ "overrides \"-pg\": probes at this list of 3-vec or "
+ "4-vec positions",
+ nrrdHestNrrd);
+ hestOptAdd_Nv_Double(&hopt, "pp", "pos", 3, 4, &pntPos, "nan nan nan",
+ "overrides \"-pi\": only sample at this specified point",
+ &pntPosNum);
+ hestOptAdd_1_Double(&hopt, "eps", "epsilon", &eps, "0",
+ "if non-zero, and if query is a scalar, and if using \"pp\" "
+ "to query at a single point, then do epsilon offset probes "
+ "to calculate discrete differences, to find the numerical "
+ "gradient and hessian (for debugging)");
+ hestOptAdd_1_Bool(&hopt, "psi", "p", &probeSpaceIndex, "false",
+ "whether the probe location specification (by any of "
+ "the four previous flags) are in index space");
- hestOptAdd(&hopt, "t", "type", airTypeEnum, 1, 1, &otype, "float",
- "type of output volume", NULL, nrrdType);
- hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-", "output volume");
+ hestOptAdd_1_Enum(&hopt, "t", "type", &otype, "float", "type of output volume",
+ nrrdType);
+ hestOptAdd_1_String(&hopt, "o", "nout", &outS, "-", "output volume");
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, probeInfo, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, AIR_CAST(airMopper, hestOptFree), airMopAlways);
Modified: teem/trunk/src/bin/ilk.c
===================================================================
--- teem/trunk/src/bin/ilk.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/ilk.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -68,62 +68,62 @@
(which may be a hest bug) */
hparm->columns = AIR_MAX(59, wsz.ws_col - 2);
- hestOptAdd(&hopt, "i", "image", airTypeOther, 1, 1, &nin, "-", "input image", NULL,
- NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "0", "origin", airTypeOther, 1, 1, &origInfo, "p:0,0",
- "where to location (0,0) prior to applying transforms.\n "
- "\b\bo \"u:<float>,<float>\" locate origin in a unit box "
- "[0,1]x[0,1] which covers the original image\n "
- "\b\bo \"p:<float>,<float>\" locate origin at a particular "
- "pixel location, in the index space of the image",
- NULL, NULL, mossHestOrigin);
- hestOptAdd(&hopt, "t", "xform0", airTypeOther, 1, -1, &matList, NULL,
- "transform(s) to apply to image. Transforms "
- "are applied in the order in which they appear.\n "
- "\b\bo \"identity\": no geometric transform, just resampling\n "
- "\b\bo \"translate:x,y\": shift image by vector (x,y), as "
- "measured in pixels\n "
- "\b\bo \"rotate:ang\": rotate CCW by ang degrees\n "
- "\b\bo \"scale:xs,ys\": scale by xs in X, and ys in Y\n "
- "\b\bo \"shear:fix,amnt\": shear by amnt, keeping fixed "
- "the pixels along a direction <fix> degrees from the X axis\n "
- "\b\bo \"flip:ang\": flip along axis an angle <ang> degrees from "
- "the X axis\n "
- "\b\bo \"a,b,tx,c,d,ty\": specify the transform explicitly "
- "in row-major order (opposite of PostScript) ",
- &matListLen, NULL, mossHestTransform);
- hestOptAdd(&hopt, "k", "kernel", airTypeOther, 1, 1, &ksp, "cubic:0,0.5",
- "reconstruction kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "min", "xMin yMin", airTypeDouble, 2, 2, min, "nan nan",
- "lower bounding corner of output image. Default (by not "
- "using this option) is the lower corner of input image. ");
- hestOptAdd(&hopt, "max", "xMax yMax", airTypeDouble, 2, 2, max, "nan nan",
- "upper bounding corner of output image. Default (by not "
- "using this option) is the upper corner of input image. ");
- hestOptAdd(&hopt, "b", "boundary", airTypeEnum, 1, 1, &bound, "bleed",
- "what to do when sampling outside original image.\n "
- "\b\bo \"bleed\": copy values at image border outward\n "
- "\b\bo \"wrap\": do wrap-around on image locations\n "
- "\b\bo \"pad\": use a given background value (via \"-bg\")",
- NULL, nrrdBoundary);
- bkgIdx = hestOptAdd(&hopt, "bg", "bg0 bg1", airTypeDouble, 1, -1, &_bkg, "nan",
- "background color to use with boundary behavior \"pad\". "
- "Defaults to all zeroes.",
- &_bkgLen);
- hestOptAdd(&hopt, "s", "xSize ySize", airTypeOther, 2, 2, scale, "x1 x1",
- "For each axis, information about how many samples in output:\n "
- "\b\bo \"x<float>\": number of output samples is some scaling of "
- " the number input of samples; multiplied by <float>\n "
- "\b\bo \"<int>\": specify exact number of samples",
- NULL, NULL, &unrrduHestScaleCB);
- hestOptAdd(&hopt, "a", "avg #", airTypeUInt, 1, 1, &avgNum, "0",
- "number of averages (if there there is only one "
- "rotation as transform)");
- hestOptAdd(&hopt, "db", "x y", airTypeInt, 2, 2, debug, "-1 -1",
- "if both non-negative, turn on verbose debugging for this output "
- "image pixel");
- hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, "-",
- "file to write output nrrd to");
+ hestOptAdd_1_Other(&hopt, "i", "image", &nin, "-", "input image", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "0", "origin", &origInfo, "p:0,0",
+ "where to location (0,0) prior to applying transforms.\n "
+ "\b\bo \"u:<float>,<float>\" locate origin in a unit box "
+ "[0,1]x[0,1] which covers the original image\n "
+ "\b\bo \"p:<float>,<float>\" locate origin at a particular "
+ "pixel location, in the index space of the image",
+ mossHestOrigin);
+ hestOptAdd_Nv_Other(&hopt, "t", "xform0", 1, -1, &matList, NULL,
+ "transform(s) to apply to image. Transforms "
+ "are applied in the order in which they appear.\n "
+ "\b\bo \"identity\": no geometric transform, just resampling\n "
+ "\b\bo \"translate:x,y\": shift image by vector (x,y), as "
+ "measured in pixels\n "
+ "\b\bo \"rotate:ang\": rotate CCW by ang degrees\n "
+ "\b\bo \"scale:xs,ys\": scale by xs in X, and ys in Y\n "
+ "\b\bo \"shear:fix,amnt\": shear by amnt, keeping fixed "
+ "the pixels along a direction <fix> degrees from the X axis\n "
+ "\b\bo \"flip:ang\": flip along axis an angle <ang> degrees from "
+ "the X axis\n "
+ "\b\bo \"a,b,tx,c,d,ty\": specify the transform explicitly "
+ "in row-major order (opposite of PostScript) ",
+ &matListLen, mossHestTransform);
+ hestOptAdd_1_Other(&hopt, "k", "kernel", &ksp, "cubic:0,0.5", "reconstruction kernel",
+ nrrdHestKernelSpec);
+ hestOptAdd_2_Double(&hopt, "min", "xMin yMin", min, "nan nan",
+ "lower bounding corner of output image. Default (by not "
+ "using this option) is the lower corner of input image. ");
+ hestOptAdd_2_Double(&hopt, "max", "xMax yMax", max, "nan nan",
+ "upper bounding corner of output image. Default (by not "
+ "using this option) is the upper corner of input image. ");
+ hestOptAdd_1_Enum(&hopt, "b", "boundary", &bound, "bleed",
+ "what to do when sampling outside original image.\n "
+ "\b\bo \"bleed\": copy values at image border outward\n "
+ "\b\bo \"wrap\": do wrap-around on image locations\n "
+ "\b\bo \"pad\": use a given background value (via \"-bg\")",
+ nrrdBoundary);
+ bkgIdx
+ = hestOptAdd_Nv_Double(&hopt, "bg", "bg0 bg1", 1, -1, &_bkg, "nan",
+ "background color to use with boundary behavior \"pad\". "
+ "Defaults to all zeroes.",
+ &_bkgLen);
+ hestOptAdd_2_Other(&hopt, "s", "xSize ySize", scale, "x1 x1",
+ "For each axis, information about how many samples in output:\n "
+ "\b\bo \"x<float>\": number of output samples is some scaling of "
+ " the number input of samples; multiplied by <float>\n "
+ "\b\bo \"<int>\": specify exact number of samples",
+ &unrrduHestScaleCB);
+ hestOptAdd_1_UInt(&hopt, "a", "avg #", &avgNum, "0",
+ "number of averages (if there there is only one "
+ "rotation as transform)");
+ hestOptAdd_2_Int(&hopt, "db", "x y", debug, "-1 -1",
+ "if both non-negative, turn on verbose debugging for this output "
+ "image pixel");
+ hestOptAdd_1_String(&hopt, "o", "filename", &outS, "-",
+ "file to write output nrrd to");
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, ilkInfo, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/bin/miter.c
===================================================================
--- teem/trunk/src/bin/miter.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/miter.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -54,80 +54,79 @@
hparm->respectDashDashHelp = AIR_TRUE;
hparm->respFileEnable = AIR_TRUE;
hparm->elideMultipleNonExistFloatDefault = AIR_TRUE;
- hestOptAdd(&hopt, "i", "nsin", airTypeOther, 1, 1, &(muu->nsin), "",
- "input scalar volume to render", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "vi", "nvin", airTypeOther, 1, 1, &(muu->nvin), "",
- "input vector volume to render", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "ti", "ntin", airTypeOther, 1, 1, &(muu->ntin), "",
- "input tensor volume to render", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "txf", "nin", airTypeOther, 1, -1, &(muu->ntxf), NULL,
- "one or more transfer functions", &(muu->ntxfNum), NULL, nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "i", "nsin", &(muu->nsin), "",
+ "input scalar volume to render", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "vi", "nvin", &(muu->nvin), "",
+ "input vector volume to render", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "ti", "ntin", &(muu->ntin), "",
+ "input tensor volume to render", nrrdHestNrrd);
+ hestOptAdd_Nv_Other(&hopt, "txf", "nin", 1, -1, &(muu->ntxf), NULL,
+ "one or more transfer functions", &(muu->ntxfNum), nrrdHestNrrd);
limnHestCameraOptAdd(&hopt, muu->hctx->cam, NULL, "0 0 0", "0 0 1", NULL, NULL, NULL,
"nan nan", "nan nan", "20");
- hestOptAdd(&hopt, "offfr", NULL, airTypeInt, 0, 0, &offfr, NULL,
- "the given eye point (\"-fr\") is to be interpreted "
- "as an offset from the at point.");
- hestOptAdd(&hopt, "ffr", "fake from", airTypeDouble, 3, 3, &(muu->fakeFrom),
- "nan nan nan",
- "eye point to use for view-dependent transfer functions. "
- "By default (not using this option), the point used is the "
- "normally specified camera eye point.");
- hestOptAdd(&hopt, "turn", "angle", airTypeDouble, 1, 1, &turn, "0.0",
- "angle (degrees) by which to rotate the from point around "
- "true up, for making stereo pairs. Positive means move "
- "towards positive U (the right)");
- hestOptAdd(&hopt, "am", "ambient", airTypeFloat, 3, 3, muu->lit->amb, "1 1 1",
- "ambient light color");
- hestOptAdd(&hopt, "ld", "light pos", airTypeFloat, 3, 3, muu->lit->_dir[0], "0 0 -1",
- "view space light position (extended to infinity)");
- hestOptAdd(&hopt, "is", "image size", airTypeInt, 2, 2, muu->hctx->imgSize, "256 256",
- "image dimensions");
- hestOptAdd(&hopt, "iss", "scale", airTypeFloat, 1, 1, &isScale, "1.0",
- "scaling of image size (from \"is\")");
- hestOptAdd(&hopt, "ads", "ka kd ks", airTypeFloat, 3, 3, ads, "0.1 0.6 0.3",
- "phong components");
+ hestOptAdd_Flag(&hopt, "offfr", &offfr,
+ "the given eye point (\"-fr\") is to be interpreted "
+ "as an offset from the at point.");
+ hestOptAdd_3_Double(&hopt, "ffr", "fake from", muu->fakeFrom, "nan nan nan",
+ "eye point to use for view-dependent transfer functions. "
+ "By default (not using this option), the point used is the "
+ "normally specified camera eye point.");
+ hestOptAdd_1_Double(&hopt, "turn", "angle", &turn, "0.0",
+ "angle (degrees) by which to rotate the from point around "
+ "true up, for making stereo pairs. Positive means move "
+ "towards positive U (the right)");
+ hestOptAdd_3_Float(&hopt, "am", "ambient", muu->lit->amb, "1 1 1",
+ "ambient light color");
+ hestOptAdd_3_Float(&hopt, "ld", "light pos", muu->lit->_dir[0], "0 0 -1",
+ "view space light position (extended to infinity)");
+ hestOptAdd_2_UInt(&hopt, "is", "image size", muu->hctx->imgSize, "256 256",
+ "image dimensions");
+ hestOptAdd_1_Float(&hopt, "iss", "scale", &isScale, "1.0",
+ "scaling of image size (from \"is\")");
+ hestOptAdd_3_Float(&hopt, "ads", "ka kd ks", ads, "0.1 0.6 0.3", "phong components");
+ /* mite_at could be float or double */
hestOptAdd(&hopt, "sp", "spec pow", mite_at, 1, 1, &(muu->rangeInit[miteRangeSP]),
"30", "phong specular power");
- hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &(muu->ksp[gageKernel00]),
- "tent", "value reconstruction kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &(muu->ksp[gageKernel11]),
- "cubicd:1,0", "first derivative kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &(muu->ksp[gageKernel22]),
- "cubicdd:1,0", "second derivative kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "ss", "shading spec", airTypeString, 1, 1, &shadeStr,
- "phong:gage(scalar:n)", "how to do shading");
- hestOptAdd(&hopt, "ns", "normal spec", airTypeString, 1, 1, &normalStr, "",
- "\"normal\" to use for those miteVal's that need one");
- hestOptAdd(&hopt, "side", "normal side", airTypeInt, 1, 1, &(muu->normalSide), "1",
- "how to interpret gradients as normals:\n "
- "\b\bo \"1\": normal points to lower values (higher == "
- "more \"inside\")\n "
- "\b\bo \"0\": \"two-sided\": dot-products are abs()'d\n "
- "\b\bo \"-1\": normal points to higher values (lower == "
- "more \"inside\")");
- hestOptAdd(&hopt, "rn", NULL, airTypeBool, 0, 0, &renorm, NULL,
- "renormalize kernel weights at each new sample location. "
- "\"Accurate\" kernels don't need this; doing it always "
- "makes things go slower");
- hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc, "0.0",
- "For curvature-based transfer functions, set curvature to "
- "zero when gradient magnitude is below this");
- hestOptAdd(&hopt, "step", "size", airTypeDouble, 1, 1, &(muu->rayStep), "0.01",
- "step size along ray in world space");
- hestOptAdd(&hopt, "ref", "size", airTypeDouble, 1, 1, &(muu->refStep), "0.01",
- "\"reference\" step size (world space) for doing "
- "opacity correction in compositing");
- hestOptAdd(&hopt, "vp", "verbose pixel", airTypeInt, 2, 2, verbPix, "-1 -1",
- "pixel for which to turn on verbose messages");
- hestOptAdd(&hopt, "n1", "near1", airTypeDouble, 1, 1, &(muu->opacNear1), "0.99",
- "opacity close enough to 1.0 to terminate ray");
- hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1, &(muu->hctx->numThreads), "1",
- (airThreadCapable
- ? "number of threads hoover should use"
- : "if pthreads where enabled in this Teem build, this is how "
- "you would control the number of threads hoover should use"));
- hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, NULL,
- "file to write output nrrd to");
+ hestOptAdd_1_Other(&hopt, "k00", "kernel", &(muu->ksp[gageKernel00]), "tent",
+ "value reconstruction kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k11", "kernel", &(muu->ksp[gageKernel11]), "cubicd:1,0",
+ "first derivative kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k22", "kernel", &(muu->ksp[gageKernel22]), "cubicdd:1,0",
+ "second derivative kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_String(&hopt, "ss", "shading spec", &shadeStr, "phong:gage(scalar:n)",
+ "how to do shading");
+ hestOptAdd_1_String(&hopt, "ns", "normal spec", &normalStr, "",
+ "\"normal\" to use for those miteVal's that need one");
+ hestOptAdd_1_Int(&hopt, "side", "normal side", &(muu->normalSide), "1",
+ "how to interpret gradients as normals:\n "
+ "\b\bo \"1\": normal points to lower values (higher == "
+ "more \"inside\")\n "
+ "\b\bo \"0\": \"two-sided\": dot-products are abs()'d\n "
+ "\b\bo \"-1\": normal points to higher values (lower == "
+ "more \"inside\")");
+ hestOptAdd_Flag(&hopt, "rn", &renorm,
+ "renormalize kernel weights at each new sample location. "
+ "\"Accurate\" kernels don't need this; doing it always "
+ "makes things go slower");
+ hestOptAdd_1_Double(&hopt, "gmc", "min gradmag", &gmc, "0.0",
+ "For curvature-based transfer functions, set curvature to "
+ "zero when gradient magnitude is below this");
+ hestOptAdd_1_Double(&hopt, "step", "size", &(muu->rayStep), "0.01",
+ "step size along ray in world space");
+ hestOptAdd_1_Double(&hopt, "ref", "size", &(muu->refStep), "0.01",
+ "\"reference\" step size (world space) for doing "
+ "opacity correction in compositing");
+ hestOptAdd_2_Int(&hopt, "vp", "verbose pixel", verbPix, "-1 -1",
+ "pixel for which to turn on verbose messages");
+ hestOptAdd_1_Double(&hopt, "n1", "near1", &(muu->opacNear1), "0.99",
+ "opacity close enough to 1.0 to terminate ray");
+ hestOptAdd_1_UInt(&hopt, "nt", "# threads", &(muu->hctx->numThreads), "1",
+ (airThreadCapable
+ ? "number of threads hoover should use"
+ : "if pthreads where enabled in this Teem build, this is how "
+ "you would control the number of threads hoover should use"));
+ hestOptAdd_1_String(&hopt, "o", "filename", &outS, NULL,
+ "file to write output nrrd to");
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, miteInfo, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/bin/mrender.c
===================================================================
--- teem/trunk/src/bin/mrender.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/mrender.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -460,54 +460,55 @@
uu = mrendUserNew();
airMopAdd(mop, uu, (airMopper)mrendUserNix, airMopAlways);
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &(uu->nin), NULL,
- "input nrrd to render", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &(uu->kind), NULL,
- "\"kind\" of volume (\"scalar\", \"vector\", or \"tensor\")", NULL, NULL,
- meetHestGageKind);
+ hestOptAdd_1_Other(&hopt, "i", "nin", &(uu->nin), NULL, "input nrrd to render",
+ nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "k", "kind", &(uu->kind), NULL,
+ "\"kind\" of volume (\"scalar\", \"vector\", or \"tensor\")",
+ meetHestGageKind);
limnHestCameraOptAdd(&hopt, uu->hctx->cam, NULL, "0 0 0", "0 0 1", NULL, NULL, NULL,
"nan nan", "nan nan", "20");
- hestOptAdd(&hopt, "offfr", NULL, airTypeInt, 0, 0, &offfr, NULL,
- "the given eye point (\"-fr\") is to be interpreted "
- "as an offset from the at point.");
- hestOptAdd(&hopt, "turn", "angle", airTypeDouble, 1, 1, &turn, "0.0",
- "angle (degrees) by which to rotate the from point around "
- "true up, for making stereo pairs. Positive means move "
- "towards positive U (the right)");
- hestOptAdd(&hopt, "is", "image size", airTypeInt, 2, 2, uu->hctx->imgSize, "256 256",
- "image dimensions");
- hestOptAdd(&hopt, "iss", "scale", airTypeFloat, 1, 1, &isScale, "1.0",
- "scaling of image size (from \"is\")");
- hestOptAdd(&hopt, "k00", "kernel", airTypeOther, 1, 1, &(uu->ksp[gageKernel00]),
- "tent", "value reconstruction kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k11", "kernel", airTypeOther, 1, 1, &(uu->ksp[gageKernel11]),
- "cubicd:1,0", "first derivative kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k22", "kernel", airTypeOther, 1, 1, &(uu->ksp[gageKernel22]),
- "cubicdd:1,0", "second derivative kernel", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "rn", NULL, airTypeBool, 0, 0, &renorm, NULL,
- "renormalize kernel weights at each new sample location. "
- "\"Accurate\" kernels don't need this; doing it always "
- "makes things go slower");
- hestOptAdd(&hopt, "q", "query", airTypeString, 1, 1, &whatS, NULL,
- "the quantity (scalar, vector, or matrix) to learn by probing");
- hestOptAdd(&hopt, "m", "measure", airTypeEnum, 1, 1, &(uu->measr), NULL,
- "how to collapse list of ray samples into one scalar. " NRRD_MEASURE_DESC,
- NULL, nrrdMeasure);
- hestOptAdd(&hopt, "gmc", "min gradmag", airTypeDouble, 1, 1, &gmc, "0.0",
- "For curvature-related queries, set answer to zero when "
- "gradient magnitude is below this");
- hestOptAdd(&hopt, "fn", "from nan", airTypeDouble, 1, 1, &(uu->fromNaN), "nan",
- "When histo-based measures generate NaN answers, the "
- "value that should be substituted for NaN.");
- hestOptAdd(&hopt, "step", "size", airTypeDouble, 1, 1, &(uu->rayStep), "0.01",
- "step size along ray in world space");
- hestOptAdd(&hopt, "nt", "# threads", airTypeInt, 1, 1, &(uu->hctx->numThreads), "1",
- "number of threads hoover should use");
- hestOptAdd(&hopt, "vp", "img coords", airTypeInt, 2, 2, &(uu->verbPixel), "-1 -1",
- "pixel coordinates for which to turn on all verbose "
- "debugging messages, or \"-1 -1\" to disable this.");
- hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &(uu->outS), "-",
- "file to write output nrrd to. Defaults to stdout (\"-\").");
+ hestOptAdd_Flag(&hopt, "offfr", &offfr,
+ "the given eye point (\"-fr\") is to be interpreted "
+ "as an offset from the at point.");
+ hestOptAdd_1_Double(&hopt, "turn", "angle", &turn, "0.0",
+ "angle (degrees) by which to rotate the from point around "
+ "true up, for making stereo pairs. Positive means move "
+ "towards positive U (the right)");
+ hestOptAdd_2_UInt(&hopt, "is", "image size", uu->hctx->imgSize, "256 256",
+ "image dimensions");
+ hestOptAdd_1_Float(&hopt, "iss", "scale", &isScale, "1.0",
+ "scaling of image size (from \"is\")");
+ hestOptAdd_1_Other(&hopt, "k00", "kernel", &(uu->ksp[gageKernel00]), "tent",
+ "value reconstruction kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k11", "kernel", &(uu->ksp[gageKernel11]), "cubicd:1,0",
+ "first derivative kernel", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k22", "kernel", &(uu->ksp[gageKernel22]), "cubicdd:1,0",
+ "second derivative kernel", nrrdHestKernelSpec);
+ hestOptAdd_Flag(&hopt, "rn", &renorm,
+ "renormalize kernel weights at each new sample location. "
+ "\"Accurate\" kernels don't need this; doing it always "
+ "makes things go slower");
+ hestOptAdd_1_String(&hopt, "q", "query", &whatS, NULL,
+ "the quantity (scalar, vector, or matrix) to learn by probing");
+ hestOptAdd_1_Enum(&hopt, "m", "measure", &(uu->measr), NULL,
+ "how to collapse list of "
+ "ray samples into one scalar. " NRRD_MEASURE_DESC,
+ nrrdMeasure);
+ hestOptAdd_1_Double(&hopt, "gmc", "min gradmag", &gmc, "0.0",
+ "For curvature-related queries, set answer to zero when "
+ "gradient magnitude is below this");
+ hestOptAdd_1_Double(&hopt, "fn", "from nan", &(uu->fromNaN), "nan",
+ "When histo-based measures generate NaN answers, the "
+ "value that should be substituted for NaN.");
+ hestOptAdd_1_Double(&hopt, "step", "size", &(uu->rayStep), "0.01",
+ "step size along ray in world space");
+ hestOptAdd_1_UInt(&hopt, "nt", "# threads", &(uu->hctx->numThreads), "1",
+ "number of threads hoover should use");
+ hestOptAdd_2_Int(&hopt, "vp", "img coords", uu->verbPixel, "-1 -1",
+ "pixel coordinates for which to turn on all verbose "
+ "debugging messages, or \"-1 -1\" to disable this.");
+ hestOptAdd_1_String(&hopt, "o", "filename", &(uu->outS), "-",
+ "file to write output nrrd to. Defaults to stdout (\"-\").");
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, info, AIR_TRUE, AIR_TRUE,
Modified: teem/trunk/src/bin/overrgb.c
===================================================================
--- teem/trunk/src/bin/overrgb.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/overrgb.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -78,37 +78,36 @@
hparm = hestParmNew();
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->respectDashDashHelp = AIR_TRUE;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
- "input nrrd to composite", NULL, NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "c", "contrast", airTypeDouble, 1, 1, &contr, "0.0",
- "contrast to apply to RGB values, before gamma. \"0.0\" "
- "means no change, \"1.0\" means thresholding, \"-1.0\" "
- "means a complete washout.");
- hestOptAdd(&hopt, "cfp", "fixed point", airTypeDouble, 1, 1, &cfp, "0.5",
- "component level that doesn't change with contrast");
- hestOptAdd(&hopt, "g", "gamma", airTypeString, 1, 1, &gammaS, "1.0",
- "gamma to apply to image data, after contrast. Can be "
- "a number (<1 to darken >1 to brighten) or the string "
- "\"srgb\" to apply the roughly 2.2 gamma associated "
- "with sRGB (see https://en.wikipedia.org/wiki/SRGB). ");
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, NULL, "input nrrd to composite",
+ nrrdHestNrrd);
+ hestOptAdd_1_Double(&hopt, "c", "contrast", &contr, "0.0",
+ "contrast to apply to RGB values, before gamma. \"0.0\" "
+ "means no change, \"1.0\" means thresholding, \"-1.0\" "
+ "means a complete washout.");
+ hestOptAdd_1_Double(&hopt, "cfp", "fixed point", &cfp, "0.5",
+ "component level that doesn't change with contrast");
+ hestOptAdd_1_String(&hopt, "g", "gamma", &gammaS, "1.0",
+ "gamma to apply to image data, after contrast. Can be "
+ "a number (<1 to darken >1 to brighten) or the string "
+ "\"srgb\" to apply the roughly 2.2 gamma associated "
+ "with sRGB (see https://en.wikipedia.org/wiki/SRGB). ");
srgbIdx = /* HEY copied to unrrdu/quantize.c */
- hestOptAdd(&hopt, "srgb", "intent", airTypeEnum, 1, 1, &srgb, "none",
- /* the default is "none" for backwards compatibility: until now
- Teem's support of PNG hasn't handled the sRGB intent, so
- we shouldn't start using it without being asked */
- "If saving to PNG (when supported), how to set the rendering "
- "intent in the sRGB chunk of the PNG file format. Can be "
- "absolute, relative, perceptual, saturation, or none. This is "
- "independent of using \"srgb\" as the -g gamma",
- NULL, nrrdFormatPNGsRGBIntent);
- hestOptAdd(&hopt, "b", "background", airTypeDouble, 3, 3, back, "0 0 0",
- "background color to composite against; white is "
- "1 1 1, not 255 255 255.");
- hestOptAdd(&hopt, "bi", "nbg", airTypeOther, 1, 1, &_nbg, "",
- "8-bit RGB background image to composite against", NULL, NULL,
- nrrdHestNrrd);
- hestOptAdd(&hopt, "o", "filename", airTypeString, 1, 1, &outS, NULL,
- "file to write output PPM image to");
+ hestOptAdd_1_Enum(&hopt, "srgb", "intent", &srgb, "none",
+ /* the default is "none" for backwards compatibility: until now
+ Teem's support of PNG hasn't handled the sRGB intent, so
+ we shouldn't start using it without being asked */
+ "If saving to PNG (when supported), how to set the rendering "
+ "intent in the sRGB chunk of the PNG file format. Can be "
+ "absolute, relative, perceptual, saturation, or none. This is "
+ "independent of using \"srgb\" as the -g gamma",
+ NULL, nrrdFormatPNGsRGBIntent);
+ hestOptAdd_3_Double(&hopt, "b", "background", back, "0 0 0",
+ "background color to composite against; white is "
+ "1 1 1, not 255 255 255.");
+ hestOptAdd_1_Other(&hopt, "bi", "nbg", &_nbg, "",
+ "8-bit RGB background image to composite against", nrrdHestNrrd);
+ hestOptAdd_1_String(&hopt, "o", "filename", &outS, NULL,
+ "file to write output PPM image to");
hestParseOrDie(hopt, argc - 1, argv + 1, hparm, me, overInfo, AIR_TRUE, AIR_TRUE,
AIR_TRUE);
airMopAdd(mop, hopt, (airMopper)hestOptFree, airMopAlways);
Modified: teem/trunk/src/bin/pprobe.c
===================================================================
--- teem/trunk/src/bin/pprobe.c 2023-07-13 11:59:58 UTC (rev 7086)
+++ teem/trunk/src/bin/pprobe.c 2023-07-13 12:27:54 UTC (rev 7087)
@@ -82,76 +82,74 @@
airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
hparm->elideSingleOtherType = AIR_TRUE;
hparm->respectDashDashHelp = AIR_TRUE;
- hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL, "input volume", NULL,
- NULL, nrrdHestNrrd);
- hestOptAdd(&hopt, "k", "kind", airTypeOther, 1, 1, &kind, NULL,
- "\"kind\" of volume (\"scalar\", \"vector\", or \"tensor\")", NULL, NULL,
- meetHestGageKind);
- hestOptAdd(&hopt, "p", "x y z", airTypeFloat, 3, 3, pos, NULL,
- "the position in space at which to probe");
- hestOptAdd(&hopt, "wsp", NULL, airTypeInt, 0, 0, &worldSpace, NULL,
- "if using this option, position (\"-p\") will be in world "
- "space, instead of index space (the default)");
- hestOptAdd(&hopt, "pi", "lpld in", airTypeOther, 1, 1, &lpld, "",
- "input polydata (overrides \"-p\")", NULL, NULL, limnHestPolyDataLMPD);
- hestOptAdd(&hopt, "pl", "x y z s", airTypeFloat, 4, 4, lineInfo, "0 0 0 0",
- "probe along line, instead of at point. "
- "The \"-p\" three coords are the line start point. "
- "If \"s\" is zero, (x,y,z) is the line end point. "
- "If \"s\" is non-zero, (x,y,z) is the line direction, "
- "which is scaled to have length \"s\", "
- "and then used as the step between line samples. ");
- hestOptAdd(&hopt, "pln", "num", airTypeUInt, 1, 1, &lineStepNum, "0",
- "if non-zero, number of steps of probing to do along line, "
- "which overrides \"-p\" and \"-pi\"");
- hestOptAdd(&hopt, "v", "verbosity", airTypeInt, 1, 1, &verbose, "1",
- "verbosity level");
- hestOptAdd(&hopt, "q", "query", airTypeString, 1, 1, &whatS, NULL,
- "the quantity (scalar, vector, or matrix) to learn by probing");
- hestOptAdd(&hopt, "eps", "epsilon", airTypeDouble, 1, 1, &eps, "0",
- "if non-zero, and if query is a scalar, epsilon around probe "
- "location where we will do discrete differences to find the "
- "gradient and hessian (for debugging)");
- hestOptAdd(&hopt, "k00", "kern00", airTypeOther, 1, 1, &k00, "tent",
- "kernel for gageKernel00", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k11", "kern11", airTypeOther, 1, 1, &k11, "cubicd:1,0",
- "kernel for gageKernel11", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "k22", "kern22", airTypeOther, 1, 1, &k22, "cubicdd:1,0",
- "kernel for gageKernel22", NULL, NULL, nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "i", "nin", &nin, NULL, "input volume", nrrdHestNrrd);
+ hestOptAdd_1_Other(&hopt, "k", "kind", &kind, NULL,
+ "\"kind\" of volume (\"scalar\", \"vector\", or \"tensor\")",
+ meetHestGageKind);
+ hestOptAdd_3_Float(&hopt, "p", "x y z", pos, NULL,
+ "the position in space at which to probe");
+ hestOptAdd_Flag(&hopt, "wsp", &worldSpace,
+ "if using this option, position (\"-p\") will be in world "
+ "space, instead of index space (the default)");
+ hestOptAdd_1_Other(&hopt, "pi", "lpld in", &lpld, "",
+ "input polydata (overrides \"-p\")", limnHestPolyDataLMPD);
+ hestOptAdd_4_Float(&hopt, "pl", "x y z s", lineInfo, "0 0 0 0",
+ "probe along line, instead of at point. "
+ "The \"-p\" three coords are the line start point. "
+ "If \"s\" is zero, (x,y,z) is the line end point. "
+ "If \"s\" is non-zero, (x,y,z) is the line direction, "
+ "which is scaled to have length \"s\", "
+ "and then used as the step between line samples. ");
+ hestOptAdd_1_UInt(&hopt, "pln", "num", &lineStepNum, "0",
+ "if non-zero, number of steps of probing to do along line, "
+ "which overrides \"-p\" and \"-pi\"");
+ hestOptAdd_1_Int(&hopt, "v", "verbosity", &verbose, "1", "verbosity level");
+ hestOptAdd_1_String(&hopt, "q", "query", &whatS, NULL,
+ "the quantity (scalar, vector, or matrix) to learn by probing");
+ hestOptAdd_1_Double(&hopt, "eps", "epsilon", &eps, "0",
+ "if non-zero, and if query is a scalar, epsilon around probe "
+ "location where we will do discrete differences to find the "
+ "gradient and hessian (for debugging)");
+ hestOptAdd_1_Other(&hopt, "k00", "kern00", &k00, "tent", /* */
+ "kernel for gageKernel00", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k11", "kern11", &k11, "cubicd:1,0",
+ "kernel for gageKernel11", nrrdHestKernelSpec);
+ hestOptAdd_1_Other(&hopt, "k22", "kern22", &k22, "cubicdd:1,0",
+ "kernel for gageKernel22", nrrdHestKernelSpec);
- hestOptAdd(&hopt, "ssn", "SS #", airTypeUInt, 1, 1, &numSS, "0",
- "how many scale-space samples to evaluate, or, "
- "0 to turn-off all scale-space behavior");
- hestOptAdd(&hopt, "ssr", "scale range", airTypeDouble, 2, 2, rangeSS, "nan nan",
- "range of scales in scale-space");
- hestOptAdd(&hopt, "sss", "scale save path", airTypeString, 1, 1, &stackSavePath, "",
- "give a non-empty path string (like \"./\") to save out "
- "the pre-blurred volumes computed for the stack");
- hestOptAdd(&hopt, "ssp", "SS pos", airTypeDouble, 1, 1, &posSS, "0",
- "position at which to sample in scale-space");
- hestOptAdd(&hopt, "kssblur", "kernel", airTypeOther, 1, 1, &kSSblur, "dgauss:1,5",
- "blurring kernel, to sample scale space", NULL, NULL, nrrdHestKernelSpec);
- hestOptAdd(&hopt, "kss", "kernel", airTypeOther, 1, 1, &kSS, "tent",
- "kernel for reconstructing from scale space samples", NULL, NULL,
- nrrdHestKernelSpec);
- hestOptAdd(&hopt, "ssnd", "ssnd", airTypeInt, 1, 1, &SSnormd, "0",
- "enable derivative normalization based on scale space");
- hestOptAdd(&hopt, "ssu", NULL, airTypeInt, 0, 0, &SSuniform, NULL,
- "do uniform samples along sigma, and not (by default) "
- "samples according to the logarithm of diffusion time");
+ hestOptAdd_1_UInt(&hopt, "ssn", "SS #", &numSS, "0",
+ "how many scale-space samples to evaluate, or, "
+ "0 to turn-off all scale-space behavior");
+ hestOptAdd_2_Double(&hopt, "ssr", "scale range", rangeSS, "nan nan",
+ "range of scales in scale-space");
+ hestOptAdd_1_String(&hopt, "sss", "scale save path", &stackSavePath, "",
+ "give a non-empty path string (like \"./\") to save out "
+ "the pre-blurred volumes computed for the stack");
+ hestOptAdd_1_Doubl...
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