From 84f782e8d23cb95569ac24098515949809d4d855 Mon Sep 17 00:00:00 2001
From: Taylor Hanayik <hanayik@gmail.com>
Date: Fri, 16 Jun 2023 11:11:33 +0100
Subject: [PATCH 1/6] add --json option and associated logic
---
.gitignore | 1 +
fslstats.cc | 1263 +++++++++++++++++++++++++++++++++++----------------
2 files changed, 867 insertions(+), 397 deletions(-)
create mode 100644 .gitignore
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..600d2d3
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.vscode
\ No newline at end of file
diff --git a/fslstats.cc b/fslstats.cc
index 03514a9..83a9873 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -15,16 +15,18 @@
#include "newimage/newimageall.h"
#include "newimage/costfns.h"
-
using namespace std;
using namespace NEWMAT;
using namespace NEWIMAGE;
-int print_usage(const string& progname) {
- cout << "Usage: fslstats [preoptions] <input> [options]" << endl << endl;
+int print_usage(const string &progname)
+{
+ cout << "Usage: fslstats [preoptions] <input> [options]" << endl
+ << endl;
cout << "preoption -t will give a separate output line for each 3D volume of a 4D timeseries" << endl;
cout << "preoption -K < indexMask > will generate seperate n submasks from indexMask, for indexvalues 1..n where n is the maximum index value in indexMask, and generate statistics for each submask" << endl;
- cout << "Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean" << endl << endl;
+ cout << "Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean" << endl
+ << endl;
cout << "-l <lthresh> : set lower threshold" << endl;
cout << "-u <uthresh> : set upper threshold" << endl;
cout << "-r : output <robust min intensity> <robust max intensity>" << endl;
@@ -44,12 +46,16 @@ int print_usage(const string& progname) {
cout << "-C : output centre-of-gravity (cog) in voxel coordinates" << endl;
cout << "-p <n> : output nth percentile (n between 0 and 100)" << endl;
cout << "-P <n> : output nth percentile (for nonzero voxels)" << endl;
- cout << "-a : use absolute values of all image intensities"<< endl;
+ cout << "-a : use absolute values of all image intensities" << endl;
cout << "-n : treat NaN or Inf as zero for subsequent stats" << endl;
cout << "-k <mask> : use the specified image (filename) for masking - overrides lower and upper thresholds" << endl;
cout << "-d <image> : take the difference between the base image and the image specified here" << endl;
cout << "-h <nbins> : output a histogram (for the thresholded/masked voxels only) with nbins" << endl;
- cout << "-H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max" << endl << endl;
+ cout << "-H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max" << endl;
+ // add --json output format option
+ // keys will correspond to the options above
+ cout << "--json : output in JSON format" << endl
+ << endl;
cout << "Note - thresholds are not inclusive ie lthresh<allowed<uthresh" << endl;
return 1;
}
@@ -57,461 +63,924 @@ int print_usage(const string& progname) {
// Some specialised nonzero functions just for speedup
// (it avoids generating masks when not absolutely necessary)
-long nonzerocount(const volume4D<float>& vol)
+long nonzerocount(const volume4D<float> &vol)
{
- long totn=0;
- for(volume4D<float>::fast_const_iterator it=vol.fbegin(), end=vol.fend(); it<end; it++ )
- if ( (*it) != 0 )
+ long totn = 0;
+ for (volume4D<float>::fast_const_iterator it = vol.fbegin(), end = vol.fend(); it < end; it++)
+ if ((*it) != 0)
totn++;
return totn;
}
-double nonzeromean(const volume4D<float>& vol)
+double nonzeromean(const volume4D<float> &vol)
{
- double total=0.0;
- long int totn=0;
- for(volume4D<float>::fast_const_iterator it=vol.fbegin(), end=vol.fend(); it<end; it++ )
- if ( (*it) != 0 ) {
- total+=(double)(*it);
+ double total = 0.0;
+ long int totn = 0;
+ for (volume4D<float>::fast_const_iterator it = vol.fbegin(), end = vol.fend(); it < end; it++)
+ if ((*it) != 0)
+ {
+ total += (double)(*it);
totn++;
}
- if (totn>0)
- total/=totn;
+ if (totn > 0)
+ total /= totn;
return total;
}
-double nonzerostddev(const volume4D<float>& vol)
+double nonzerostddev(const volume4D<float> &vol)
{
- double totv=0.0, totvv=0.0;
- long int totn=0;
- for(volume4D<float>::fast_const_iterator it=vol.fbegin(), end=vol.fend(); it<end; it++ )
- if ( (*it) != 0 ) {
- totvv+=(double)((*it)*(*it));
- totv+=(double)(*it);
+ double totv = 0.0, totvv = 0.0;
+ long int totn = 0;
+ for (volume4D<float>::fast_const_iterator it = vol.fbegin(), end = vol.fend(); it < end; it++)
+ if ((*it) != 0)
+ {
+ totvv += (double)((*it) * (*it));
+ totv += (double)(*it);
totn++;
}
- double var=0.0;
- if (totn>1) {
- double meanval = totv/totn;
- var = (totvv - totn*meanval*meanval)/(totn-1);
+ double var = 0.0;
+ if (totn > 1)
+ {
+ double meanval = totv / totn;
+ var = (totvv - totn * meanval * meanval) / (totn - 1);
}
return std::sqrt(var);
}
-template<class M>
+template <class M>
int generateNonZeroMask(const M &mask, volume4D<float> &masknz, const volume4D<float> &input)
{
- masknz = binarise(input,0.0f,0.0f,inclusive,true)*mask;
+ masknz = binarise(input, 0.0f, 0.0f, inclusive, true) * mask;
return 0;
}
-int generate_masks(volume4D<float>& mask, volume4D<float>& masknz, const volume4D<float>& input, const float& lthr, const float& uthr)
+int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4D<float> &input, const float <hr, const float &uthr)
+{
+ mask = binarise(input, lthr, uthr, exclusive);
+ return generateNonZeroMask(mask, masknz, input);
+}
+
+// print function that can handle outputting in JSON format or not
+void print_value(const string &key, const string &value, string &json, const bool jsonOutput)
{
- mask = binarise(input,lthr,uthr,exclusive);
- return generateNonZeroMask(mask,masknz,input);
+ // append the key and value to the json string
+ if (jsonOutput)
+ {
+ json.append("\"" + key + "\": \"" + value + "\", ");
+ }
+ else
+ {
+ cout << value << " ";
+ }
}
-int fmrib_main_float(int argc, char* argv[],const bool timeseriesMode, const string& indexMaskName)
+
+int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const string &indexMaskName)
{
+ // determine if the user wants to output in JSON format
+ bool jsonOutput = false;
+ for (int i = 1; i < argc; i++)
+ {
+ if (strcmp(argv[i], "--json") == 0)
+ {
+ jsonOutput = true;
+ break;
+ }
+ }
+ // if JSON output is requested, then we need to store the output as a string
+ // and then output it at the end via cout
+ // don't forget to close the json at the end with a "}"
+ string json = "";
+
cout.setf(ios::dec);
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::left, ios::adjustfield);
cout.precision(6);
volume<float> vol, inputMaster;
volume<int> indexMask;
- if ( timeseriesMode || indexMaskName != "" )
- read_volume4D(inputMaster,argv[1]);
+ if (timeseriesMode || indexMaskName != "")
+ read_volume4D(inputMaster, argv[1]);
else
- read_volume4D(vol,argv[1]);
- volume<float> & indexMaster = (timeseriesMode ) ? vol : inputMaster;
- if ( indexMaskName != "" )
- read_volume4D(indexMask,indexMaskName);
+ read_volume4D(vol, argv[1]);
+ volume<float> &indexMaster = (timeseriesMode) ? vol : inputMaster;
+ if (indexMaskName != "")
+ read_volume4D(indexMask, indexMaskName);
int nTimepoints((timeseriesMode) ? inputMaster.tsize() : 1), nIndices((indexMaskName != "") ? indexMask.max() : 1);
- for ( int timepoint=0; timepoint < nTimepoints ; timepoint++ ) {
- for ( int index=1; index <= nIndices; index++ ) {
- if ( timeseriesMode )
- vol=inputMaster[timepoint];
- volume<float> mask, masknz;
- float lthr(-numeric_limits<float>::max());
- float uthr(numeric_limits<float>::max());
- if ( indexMask.nvoxels() ) {
- if ( indexMask.dimensionality() > 3 ) {
- cerr << "Index mask must be 3D" << endl;
- return 3;
- }
- copyconvert(indexMask,mask);
- mask.binarise(index-1,index+1,exclusive);
- vol=indexMaster*mask;
- if (mask.max() < 1) {
- cout << "missing label: " << index << " in mask" << endl;
- continue;
- }
- generateNonZeroMask(mask,masknz,vol);
- }
- int narg(2);
-
- while (narg<argc) {
- string sarg(argv[narg]);
- if (sarg=="-n") {
- for (int t=0; t<vol.tsize(); t++)
- for (int z=0; z<vol.zsize(); z++)
- for (int y=0; y<vol.ysize(); y++)
- for (int x=0; x<vol.xsize(); x++)
- if (!isfinite((double)vol(x,y,z,t)))
- vol(x,y,z,t)=0;
- } else if (sarg=="-m") {
- if (mask.nvoxels()>0) cout << vol.mean(mask) << " ";
- else cout << vol.mean() << " ";
- } else if (sarg=="-M") {
- if (masknz.nvoxels()>0) cout << vol.mean(masknz) << " ";
- else {
- double nzmean=0;
- nzmean = nonzeromean(vol);
- cout << nzmean << " ";
- }
- } else if (sarg=="-X") {
- ColumnVector coord(4);
- vector<int64_t> iCoords;
- vol.min(mask,iCoords);
- coord << (Real)iCoords[7] << (Real)iCoords[8] << (Real)iCoords[9] << 1.0;
- coord = vol.niftivox2newimagevox_mat().i() * coord;
- cout << MISCMATHS::round(coord(1)) << " " <<
- MISCMATHS::round(coord(2)) << " " << MISCMATHS::round(coord(3)) << " ";
- } else if (sarg=="-x") {
- ColumnVector coord(4);
- vector<int64_t> iCoords;
- vol.min(mask,iCoords);
- coord << (Real)iCoords[0] << (Real)iCoords[1] << (Real)iCoords[2] << 1.0;
- coord = vol.niftivox2newimagevox_mat().i() * coord;
- cout << MISCMATHS::round(coord(1)) << " " <<
- MISCMATHS::round(coord(2)) << " " << MISCMATHS::round(coord(3)) << " ";
- } else if (sarg=="-w") {
- if (masknz.nvoxels()<1) { //Need to generate non-zeromask
- generate_masks(mask,masknz,vol,lthr,uthr);
- vol*=mask;
- }
- int xmin=masknz.xsize()-1,xmax(0),ymin=masknz.ysize()-1,ymax(0),zmin=masknz.zsize()-1,zmax(0),tmin=masknz.tsize()-1,tmax(0);
- for(int t=0;t<masknz.tsize();t++)
- for(int z=0;z<masknz.zsize();z++)
- for(int y=0;y<masknz.ysize();y++)
- for(int x=0;x<masknz.xsize();x++)
- if (masknz(x,y,z,t)>0.5) {
- if (x<xmin) xmin=x;
- if (x>xmax) xmax=x;
- if (y<ymin) ymin=y;
- if (y>ymax) ymax=y;
- if (z<zmin) zmin=z;
- if (z>zmax) zmax=z;
- if (t<tmin) tmin=t;
- if (t>tmax) tmax=t;
- }
- // change voxel coords from newimage to nifti convention for output
- ColumnVector v(4);
- v << xmin << ymin << zmin << 1.0;
- v = masknz.niftivox2newimagevox_mat().i() * v;
- xmin = MISCMATHS::round(v(1));
- ymin = MISCMATHS::round(v(2));
- zmin = MISCMATHS::round(v(3));
- v << xmax << ymax << zmax << 1.0;
- v = masknz.niftivox2newimagevox_mat().i() * v;
- xmax = MISCMATHS::round(v(1));
- ymax = MISCMATHS::round(v(2));
- zmax = MISCMATHS::round(v(3));
- if (xmin>xmax) { int tmp=xmax; xmax=xmin; xmin=tmp; }
- if (ymin>ymax) { int tmp=ymax; ymax=ymin; ymin=tmp; }
- if (zmin>zmax) { int tmp=zmax; zmax=zmin; zmin=tmp; }
- // now output nifti coords
- cout << xmin << " " << 1+xmax-xmin << " " << ymin << " " << 1+ymax-ymin << " " << zmin << " " << 1+zmax-zmin << " " << tmin << " " << 1+tmax-tmin << " ";
- } else if (sarg=="-e") {
- if (mask.nvoxels()<1) {
- generate_masks(mask,masknz,vol,lthr,uthr);
- vol*=mask;
- }
- ColumnVector hist;
- int nbins=1000;
- double entropy=0;
- hist = vol.histogram(nbins,mask);
- double ntot = hist.Sum();
- for (int j=1; j<=nbins; j++) {
- if (hist(j)>0) {
- entropy -= (hist(j)/ntot) * log(hist(j)/ntot);
- }
- }
- entropy /= log((double) nbins);
- cout << entropy << " ";
- } else if (sarg=="-E") {
- ColumnVector hist;
- int nbins=1000;
- double entropy=0;
- if (mask.nvoxels()<1) {
- generate_masks(mask,masknz,vol,lthr,uthr);
- vol*=mask;
- }
- hist = vol.histogram(nbins,masknz);
- double ntot = hist.Sum();
- for (int j=1; j<=nbins; j++) {
- if (hist(j)>0) {
- entropy -= (hist(j)/ntot) * log(hist(j)/ntot);
- }
- }
- entropy /= log((double) nbins);
- cout << entropy << " ";
- } else if (sarg=="-k") {
- narg++;
- volume<float> mask2;
- if (narg>=argc) {
- cerr << "Must specify an argument to -k" << endl;
- exit(2);
- }
- read_volume4D(mask,argv[narg]);
- if ( !samesize(mask,vol,3) || mask.tsize() > vol.tsize() ) {
- cerr << "Mask and image must be the same size" << endl;
- exit(3);
- }
- if (timeseriesMode && mask.tsize() != 1 ) { mask2=mask[timepoint]; }
- if ( mask.tsize() != vol.tsize() && mask.tsize() != 1)
- while (mask.tsize() < vol.tsize() ) { // copy the last max volume until the correct size is reached
- mask.addvolume(mask[mask.tsize()-1]);
- }
- mask.binarise(0.5);
- if (mask.tsize()!=1) {
- generateNonZeroMask(mask,masknz,vol);
- vol*=mask;
- }
- else {
- generateNonZeroMask(mask[0],masknz,vol);
- vol*=mask[0];
- }
- } else if (sarg=="-d") {
- narg++;
- if (narg>=argc) {
- cerr << "Must specify an argument to -d" << endl;
- exit(2);
- }
- volume4D<float> image2,image3;
- read_volume4D(image2,argv[narg]);
- if (!samesize(image2[0],vol[0])) {
- cerr << "Image used with -d must be the same size as the base image" << endl;
- exit(3);
- }
- if (timeseriesMode) { image3=image2[timepoint]; }
- if ( image2.tsize() > vol.tsize() ) {
- cerr << "Image must be the same size as the base image" << endl;
- exit(3);
- }
- if ( image2.tsize() != vol.tsize() && image2.tsize() != 1) {
- // copy the last max volume until the correct size is reached
- while (image2.tsize() < vol.tsize() ) {
- image2.addvolume(image2[image2.maxt()]);
- }
- }
- // now substract the new image from the base image
- vol -= image2;
- } else if (sarg=="-l") {
- narg++;
- if (narg<argc) {
- lthr = atof(argv[narg]);
- } else {
- cerr << "Must specify an argument to -l" << endl;
- exit(2);
- }
- generate_masks(mask,masknz,vol,lthr,uthr);
- vol*=mask;
- } else if (sarg=="-u") {
- narg++;
- if (narg<argc) {
- uthr = atof(argv[narg]);
- } else {
- cerr << "Must specify an argument to -u" << endl;
- exit(2);
- }
- generate_masks(mask,masknz,vol,lthr,uthr);
- vol*=mask;
- } else if (sarg=="-a") {
- vol = abs(vol);
- } else if (sarg=="-v") {
- if (mask.nvoxels()>0) {
- long int nvox = mask.sum();
- if (mask.tsize() == 1) nvox = nvox * vol.tsize();
- cout << (long int) nvox << " "
- << nvox * vol.xdim() * vol.ydim() * vol.zdim() << " ";
- } else {
- cout << (long int) vol.nvoxels() * vol.tsize() << " "
- << vol.nvoxels() * vol.tsize() * vol.xdim() * vol.ydim() * vol.zdim() << " ";
- }
- } else if (sarg=="-V") {
- if (masknz.nvoxels()>0) {
- cout << (long int) masknz.sum() << " "
- << masknz.sum() * vol.xdim() * vol.ydim() * vol.zdim() << " ";
- } else {
- long int nzvox;
- nzvox = nonzerocount(vol);
- cout << nzvox << " "
- << nzvox * vol.xdim() * vol.ydim() * vol.zdim() << " ";
- }
- } else if (sarg=="-D") {
- // hidden debug option!
- cout << vol.sum() << " ";
- } else if (sarg=="-s") {
- if (mask.nvoxels()>0) cout << vol.stddev(mask) << " ";
- else cout << vol.stddev() << " ";
- } else if (sarg=="-S") {
- if (masknz.nvoxels()>0) {
- cout << vol.stddev(masknz) << " ";
- } else {
- cout << nonzerostddev(vol) << " ";
- }
- } else if (sarg=="-r") {
- vector<float> limits(vol.robustlimits(mask));
- cout << limits[0] << " " << limits[1] << " ";
- } else if (sarg=="-R") {
- cout << vol.min(mask) << " " << vol.max(mask) << " ";
- } else if (sarg=="-c") {
- ColumnVector cog(4);
- // convert from fsl mm to voxel to nifti sform coord
- cog.SubMatrix(1,3,1,1) = vol.cog();
- cog(4) = 1.0;
- cog = vol.newimagevox2mm_mat() * cog;
- cout << cog(1) << " " << cog(2) << " " << cog(3) << " " ;
- } else if (sarg=="-C") {
- ColumnVector cog(4);
- // convert from fsl mm to fsl voxel coord to nifti voxel coord
- cog.SubMatrix(1,3,1,1) = vol.cog();
- cog(4) = 1.0;
- cog = vol.niftivox2newimagevox_mat().i() * cog;
- cout << cog(1) << " " << cog(2) << " " << cog(3) << " " ;
- } else if (sarg=="-p") {
- float n;
- narg++;
- if (narg<argc) {
- n = atof(argv[narg]);
- } else {
- cerr << "Must specify an argument to -p" << endl;
- exit(2);
- }
- if ( (n<0) || (n>100) ) {
- cerr << "Percentile must be between 0 and 100" << endl;
- exit(1);
- }
- if (mask.nvoxels()>0) cout << vol.percentile((float) n/100.0, mask) << " ";
- else cout << vol.percentile((float) n/100.0) << " ";
- } else if (sarg=="-P") {
- float n;
- narg++;
- if (narg<argc) {
- n = atof(argv[narg]);
- } else {
- cerr << "Must specify an argument to -P" << endl;
- exit(2);
- }
- if ( (n<0) || (n>100) ) {
- cerr << "Percentile must be between 0 and 100" << endl;
- exit(1);
- }
- if (mask.nvoxels()<1) {
- generate_masks(mask,masknz,vol,lthr,uthr);
- vol*=mask;
- }
- cout << vol.percentile((float) n/100.0,masknz) << " ";
- } else if (sarg=="-h") {
- float n;
- narg++;
- if (narg<argc) {
- n = atof(argv[narg]);
- } else {
- cerr << "Must specify the number of bins" << endl;
- exit(2);
- }
- int nbins = (int) n;
- if (nbins<1) {
- cerr << "Must specify at least 1 bin" << endl;
- exit(1);
- }
- if (mask.nvoxels()>0) {
- cout << vol.histogram(nbins,vol.min(),vol.max(),mask) << " ";
+ for (int timepoint = 0; timepoint < nTimepoints; timepoint++)
+ {
+ if (jsonOutput)
+ {
+ if (timepoint == 0){
+ json.append("{\"volumes\": [");
} else {
- cout << vol.histogram(nbins,vol.min(),vol.max()) << " ";
+ json.append(", ");
}
- } else if (sarg=="-H") {
- float n;
- narg++;
- if (narg<argc) {
- n = atof(argv[narg]);
- } else {
- cerr << "Must specify the number of bins" << endl;
- exit(2);
+ }
+ for (int index = 1; index <= nIndices; index++)
+ {
+ // if json mode is enabled
+ if (jsonOutput)
+ {
+ if (index == 1){
+ json.append("{\"indices\": [{");
+ } else {
+ json.append(", {");
+ }
}
- int nbins = (int) n;
- if (nbins<1) {
- cerr << "Must specify at least 1 bin" << endl;
- exit(1);
+ if (timeseriesMode)
+ vol = inputMaster[timepoint];
+ volume<float> mask, masknz;
+ float lthr(-numeric_limits<float>::max());
+ float uthr(numeric_limits<float>::max());
+ if (indexMask.nvoxels())
+ {
+ if (indexMask.dimensionality() > 3)
+ {
+ cerr << "Index mask must be 3D" << endl;
+ return 3;
+ }
+ copyconvert(indexMask, mask);
+ mask.binarise(index - 1, index + 1, exclusive);
+ vol = indexMaster * mask;
+ if (mask.max() < 1)
+ {
+ cout << "missing label: " << index << " in mask" << endl;
+ continue;
+ }
+ generateNonZeroMask(mask, masknz, vol);
}
- float min=0;
- narg++;
- if (narg<argc) {
- min = atof(argv[narg]);
- } else {
- cerr << "Must specify the histogram minimum intensity" << endl;
- exit(2);
+ int narg(2);
+ bool last = false;
+ while (narg < argc)
+ {
+
+ last = !(narg < argc - 1);
+ string sarg(argv[narg]);
+ if (sarg == "-n")
+ {
+ for (int t = 0; t < vol.tsize(); t++)
+ for (int z = 0; z < vol.zsize(); z++)
+ for (int y = 0; y < vol.ysize(); y++)
+ for (int x = 0; x < vol.xsize(); x++)
+ if (!isfinite((double)vol(x, y, z, t)))
+ vol(x, y, z, t) = 0;
+ }
+ else if (sarg == "-m")
+ {
+ if (mask.nvoxels() > 0){
+ string val = to_string(vol.mean(mask));
+ print_value(sarg, val, json, jsonOutput);
+ } else {
+ string val = to_string(vol.mean());
+ print_value(sarg, val, json, jsonOutput);
+ }
+ }
+ else if (sarg == "-M")
+ {
+ if (masknz.nvoxels() > 0)
+ print_value(sarg, to_string(vol.mean(masknz)), json, jsonOutput);
+ else
+ {
+ double nzmean = 0;
+ nzmean = nonzeromean(vol);
+ string val = to_string(nzmean);
+ print_value(sarg, val, json, jsonOutput);
+ }
+ }
+ else if (sarg == "-X")
+ {
+ ColumnVector coord(4);
+ vector<int64_t> iCoords;
+ vol.min(mask, iCoords);
+ coord << (Real)iCoords[7] << (Real)iCoords[8] << (Real)iCoords[9] << 1.0;
+ coord = vol.niftivox2newimagevox_mat().i() * coord;
+ //cout << MISCMATHS::round(coord(1)) << " " << MISCMATHS::round(coord(2)) << " " << MISCMATHS::round(coord(3)) << " ";
+ auto coord1 = MISCMATHS::round(coord(1));
+ auto coord2 = MISCMATHS::round(coord(2));
+ auto coord3 = MISCMATHS::round(coord(3));
+ string coordString = "";
+ coordString.append(to_string(coord1));
+ coordString.append(" ");
+ coordString.append(to_string(coord2));
+ coordString.append(" ");
+ coordString.append(to_string(coord3));
+ print_value(
+ sarg,
+ coordString,
+ json,
+ jsonOutput);
+
+ }
+ else if (sarg == "-x")
+ {
+ ColumnVector coord(4);
+ vector<int64_t> iCoords;
+ vol.min(mask, iCoords);
+ coord << (Real)iCoords[0] << (Real)iCoords[1] << (Real)iCoords[2] << 1.0;
+ coord = vol.niftivox2newimagevox_mat().i() * coord;
+ //cout << MISCMATHS::round(coord(1)) << " " << MISCMATHS::round(coord(2)) << " " << MISCMATHS::round(coord(3)) << " ";
+ auto coord1 = MISCMATHS::round(coord(1));
+ auto coord2 = MISCMATHS::round(coord(2));
+ auto coord3 = MISCMATHS::round(coord(3));
+ string coordString = "";
+ coordString.append(to_string(coord1));
+ coordString.append(" ");
+ coordString.append(to_string(coord2));
+ coordString.append(" ");
+ coordString.append(to_string(coord3));
+ print_value(
+ sarg,
+ coordString,
+ json,
+ jsonOutput);
+ }
+ else if (sarg == "-w")
+ {
+ if (masknz.nvoxels() < 1)
+ { // Need to generate non-zeromask
+ generate_masks(mask, masknz, vol, lthr, uthr);
+ vol *= mask;
+ }
+ int xmin = masknz.xsize() - 1, xmax(0), ymin = masknz.ysize() - 1, ymax(0), zmin = masknz.zsize() - 1, zmax(0), tmin = masknz.tsize() - 1, tmax(0);
+
+ for (int t = 0; t < masknz.tsize(); t++)
+ for (int z = 0; z < masknz.zsize(); z++)
+ for (int y = 0; y < masknz.ysize(); y++)
+ for (int x = 0; x < masknz.xsize(); x++)
+ if (masknz(x, y, z, t) > 0.5)
+ {
+ if (x < xmin)
+ xmin = x;
+ if (x > xmax)
+ xmax = x;
+ if (y < ymin)
+ ymin = y;
+ if (y > ymax)
+ ymax = y;
+ if (z < zmin)
+ zmin = z;
+ if (z > zmax)
+ zmax = z;
+ if (t < tmin)
+ tmin = t;
+ if (t > tmax)
+ tmax = t;
+ }
+ // change voxel coords from newimage to nifti convention for output
+ ColumnVector v(4);
+ v << xmin << ymin << zmin << 1.0;
+ v = masknz.niftivox2newimagevox_mat().i() * v;
+ xmin = MISCMATHS::round(v(1));
+ ymin = MISCMATHS::round(v(2));
+ zmin = MISCMATHS::round(v(3));
+ v << xmax << ymax << zmax << 1.0;
+ v = masknz.niftivox2newimagevox_mat().i() * v;
+ xmax = MISCMATHS::round(v(1));
+ ymax = MISCMATHS::round(v(2));
+ zmax = MISCMATHS::round(v(3));
+ if (xmin > xmax)
+ {
+ int tmp = xmax;
+ xmax = xmin;
+ xmin = tmp;
+ }
+ if (ymin > ymax)
+ {
+ int tmp = ymax;
+ ymax = ymin;
+ ymin = tmp;
+ }
+ if (zmin > zmax)
+ {
+ int tmp = zmax;
+ zmax = zmin;
+ zmin = tmp;
+ }
+ // now output nifti coords
+ string coords = "";
+ coords.append(to_string(xmin));
+ coords.append(" ");
+ coords.append(to_string(1 + xmax - xmin));
+ coords.append(" ");
+ coords.append(to_string(ymin));
+ coords.append(" ");
+ coords.append(to_string(1 + ymax - ymin));
+ coords.append(" ");
+ coords.append(to_string(zmin));
+ coords.append(" ");
+ coords.append(to_string(1 + zmax - zmin));
+ coords.append(" ");
+ coords.append(to_string(tmin));
+ coords.append(" ");
+ coords.append(to_string(1 + tmax - tmin));
+ print_value(
+ sarg,
+ coords,
+ json,
+ jsonOutput);
+ }
+ else if (sarg == "-e")
+ {
+ if (mask.nvoxels() < 1)
+ {
+ generate_masks(mask, masknz, vol, lthr, uthr);
+ vol *= mask;
+ }
+ ColumnVector hist;
+ int nbins = 1000;
+ double entropy = 0;
+ hist = vol.histogram(nbins, mask);
+ double ntot = hist.Sum();
+ for (int j = 1; j <= nbins; j++)
+ {
+ if (hist(j) > 0)
+ {
+ entropy -= (hist(j) / ntot) * log(hist(j) / ntot);
+ }
+ }
+ entropy /= log((double)nbins);
+ print_value(
+ sarg,
+ to_string(entropy),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-E")
+ {
+ ColumnVector hist;
+ int nbins = 1000;
+ double entropy = 0;
+ if (mask.nvoxels() < 1)
+ {
+ generate_masks(mask, masknz, vol, lthr, uthr);
+ vol *= mask;
+ }
+ hist = vol.histogram(nbins, masknz);
+ double ntot = hist.Sum();
+ for (int j = 1; j <= nbins; j++)
+ {
+ if (hist(j) > 0)
+ {
+ entropy -= (hist(j) / ntot) * log(hist(j) / ntot);
+ }
+ }
+ entropy /= log((double)nbins);
+ print_value(
+ sarg,
+ to_string(entropy),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-k")
+ {
+ narg++;
+ volume<float> mask2;
+ if (narg >= argc)
+ {
+ cerr << "Must specify an argument to -k" << endl;
+ exit(2);
+ }
+ read_volume4D(mask, argv[narg]);
+ if (!samesize(mask, vol, 3) || mask.tsize() > vol.tsize())
+ {
+ cerr << "Mask and image must be the same size" << endl;
+ exit(3);
+ }
+ if (timeseriesMode && mask.tsize() != 1)
+ {
+ mask2 = mask[timepoint];
+ }
+ if (mask.tsize() != vol.tsize() && mask.tsize() != 1)
+ while (mask.tsize() < vol.tsize())
+ { // copy the last max volume until the correct size is reached
+ mask.addvolume(mask[mask.tsize() - 1]);
+ }
+ mask.binarise(0.5);
+ if (mask.tsize() != 1)
+ {
+ generateNonZeroMask(mask, masknz, vol);
+ vol *= mask;
+ }
+ else
+ {
+ generateNonZeroMask(mask[0], masknz, vol);
+ vol *= mask[0];
+ }
+ }
+ else if (sarg == "-d")
+ {
+ narg++;
+ if (narg >= argc)
+ {
+ cerr << "Must specify an argument to -d" << endl;
+ exit(2);
+ }
+ volume4D<float> image2, image3;
+ read_volume4D(image2, argv[narg]);
+ if (!samesize(image2[0], vol[0]))
+ {
+ cerr << "Image used with -d must be the same size as the base image" << endl;
+ exit(3);
+ }
+ if (timeseriesMode)
+ {
+ image3 = image2[timepoint];
+ }
+ if (image2.tsize() > vol.tsize())
+ {
+ cerr << "Image must be the same size as the base image" << endl;
+ exit(3);
+ }
+ if (image2.tsize() != vol.tsize() && image2.tsize() != 1)
+ {
+ // copy the last max volume until the correct size is reached
+ while (image2.tsize() < vol.tsize())
+ {
+ image2.addvolume(image2[image2.maxt()]);
+ }
+ }
+ // now substract the new image from the base image
+ vol -= image2;
+ }
+ else if (sarg == "-l")
+ {
+ narg++;
+ if (narg < argc)
+ {
+ lthr = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify an argument to -l" << endl;
+ exit(2);
+ }
+ generate_masks(mask, masknz, vol, lthr, uthr);
+ vol *= mask;
+ }
+ else if (sarg == "-u")
+ {
+ narg++;
+ if (narg < argc)
+ {
+ uthr = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify an argument to -u" << endl;
+ exit(2);
+ }
+ generate_masks(mask, masknz, vol, lthr, uthr);
+ vol *= mask;
+ }
+ else if (sarg == "-a")
+ {
+ vol = abs(vol);
+ }
+ else if (sarg == "-v")
+ {
+ if (mask.nvoxels() > 0)
+ {
+ long int nvox = mask.sum();
+ if (mask.tsize() == 1)
+ nvox = nvox * vol.tsize();
+
+ string nvox_str = "";
+ nvox_str.append(to_string(nvox));
+ nvox_str.append(" ");
+ nvox_str.append(to_string(nvox * vol.xdim() * vol.ydim() * vol.zdim()));
+ print_value(
+ sarg,
+ nvox_str,
+ json,
+ jsonOutput
+ );
+ }
+ else
+ {
+ string nvox_str = "";
+ nvox_str.append(to_string((long int)vol.nvoxels() * vol.tsize()));
+ nvox_str.append(" ");
+ nvox_str.append(to_string(vol.nvoxels() * vol.tsize() * vol.xdim() * vol.ydim() * vol.zdim()));
+ print_value(
+ sarg,
+ nvox_str,
+ json,
+ jsonOutput);
+ }
+ }
+ else if (sarg == "-V")
+ {
+ if (masknz.nvoxels() > 0)
+ {
+ string nvox_str = "";
+ nvox_str.append(to_string((long int)masknz.sum()));
+ nvox_str.append(" ");
+ nvox_str.append(to_string(masknz.sum() * vol.xdim() * vol.ydim() * vol.zdim()));
+ print_value(
+ sarg,
+ nvox_str,
+ json,
+ jsonOutput);
+ }
+ else
+ {
+ long int nzvox;
+ nzvox = nonzerocount(vol);
+ string nzvox_str = "";
+ nzvox_str.append(to_string(nzvox));
+ nzvox_str.append(" ");
+ nzvox_str.append(to_string(nzvox * vol.xdim() * vol.ydim() * vol.zdim()));
+ print_value(
+ sarg,
+ nzvox_str,
+ json,
+ jsonOutput);
+ }
+ }
+ else if (sarg == "-D")
+ {
+ // hidden debug option!
+ print_value(
+ sarg,
+ to_string(vol.sum()),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-s")
+ {
+ if (mask.nvoxels() > 0)
+ print_value(
+ sarg,
+ to_string(vol.stddev(mask)),
+ json,
+ jsonOutput
+ );
+ else
+ print_value(
+ sarg,
+ to_string(vol.stddev()),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-S")
+ {
+ if (masknz.nvoxels() > 0)
+ {
+ print_value(
+ sarg,
+ to_string(vol.stddev(masknz)),
+ json,
+ jsonOutput
+ );
+ }
+ else
+ {
+ print_value(
+ sarg,
+ to_string(nonzerostddev(vol)),
+ json,
+ jsonOutput
+ );
+ }
+ }
+ else if (sarg == "-r")
+ {
+ vector<float> limits(vol.robustlimits(mask));
+ print_value(
+ sarg,
+ to_string(limits[0]).append(" ").append(to_string(limits[1])),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-R")
+ {
+ print_value(
+ sarg,
+ to_string(vol.min(mask)).append(" ").append(to_string(vol.max(mask))),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-c")
+ {
+ ColumnVector cog(4);
+ cog.SubMatrix(1, 3, 1, 1) = vol.cog();
+ cog(4) = 1.0;
+ cog = vol.newimagevox2mm_mat() * cog;
+ print_value(
+ sarg,
+ to_string(cog(1)).append(" ").append(to_string(cog(2))).append(" ").append(to_string(cog(3))),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-C")
+ {
+ ColumnVector cog(4);
+ // convert from fsl mm to fsl voxel coord to nifti voxel coord
+ cog.SubMatrix(1, 3, 1, 1) = vol.cog();
+ cog(4) = 1.0;
+ cog = vol.niftivox2newimagevox_mat().i() * cog;
+ print_value(
+ sarg,
+ to_string(cog(1)).append(" ").append(to_string(cog(2))).append(" ").append(to_string(cog(3))),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-p")
+ {
+ float n;
+ narg++;
+ if (narg < argc)
+ {
+ n = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify an argument to -p" << endl;
+ exit(2);
+ }
+ if ((n < 0) || (n > 100))
+ {
+ cerr << "Percentile must be between 0 and 100" << endl;
+ exit(1);
+ }
+ if (mask.nvoxels() > 0)
+ print_value(
+ sarg,
+ to_string(vol.percentile((float)n / 100.0, mask)),
+ json,
+ jsonOutput
+ );
+ else
+ print_value(
+ sarg,
+ to_string(vol.percentile((float)n / 100.0)),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-P")
+ {
+ float n;
+ narg++;
+ if (narg < argc)
+ {
+ n = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify an argument to -P" << endl;
+ exit(2);
+ }
+ if ((n < 0) || (n > 100))
+ {
+ cerr << "Percentile must be between 0 and 100" << endl;
+ exit(1);
+ }
+ if (mask.nvoxels() < 1)
+ {
+ generate_masks(mask, masknz, vol, lthr, uthr);
+ vol *= mask;
+ }
+ print_value(
+ sarg,
+ to_string(vol.percentile((float)n / 100.0, masknz)),
+ json,
+ jsonOutput
+ );
+ }
+ else if (sarg == "-h")
+ {
+ float n;
+ narg++;
+ if (narg < argc)
+ {
+ n = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify the number of bins" << endl;
+ exit(2);
+ }
+ int nbins = (int)n;
+ if (nbins < 1)
+ {
+ cerr << "Must specify at least 1 bin" << endl;
+ exit(1);
+ }
+ if (mask.nvoxels() > 0)
+ {
+ auto hist = vol.histogram(nbins, vol.min(), vol.max(), mask);
+ // loop over histogram values and and build a string to print
+ string hist_str = "";
+ for (int i = 0; i < hist.Nrows(); i++)
+ {
+ hist_str += to_string(hist(i+1));
+ if (i < hist.Nrows() - 1)
+ {
+ hist_str += " ";
+ }
+ }
+ print_value(
+ sarg,
+ hist_str,
+ json,
+ jsonOutput
+ );
+ }
+ else
+ {
+ auto hist = vol.histogram(nbins, vol.min(), vol.max());
+ string hist_str = "";
+ for (int i = 0; i < hist.Nrows(); i++)
+ {
+ hist_str += to_string(hist(i+1));
+ if (i < hist.Nrows() - 1)
+ {
+ hist_str += " ";
+ }
+ }
+ print_value(
+ sarg,
+ hist_str,
+ json,
+ jsonOutput
+ );
+ }
+ }
+ else if (sarg == "-H")
+ {
+ float n;
+ narg++;
+ if (narg < argc)
+ {
+ n = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify the number of bins" << endl;
+ exit(2);
+ }
+ int nbins = (int)n;
+ if (nbins < 1)
+ {
+ cerr << "Must specify at least 1 bin" << endl;
+ exit(1);
+ }
+ float min = 0;
+ narg++;
+ if (narg < argc)
+ {
+ min = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify the histogram minimum intensity" << endl;
+ exit(2);
+ }
+ float max = 0;
+ narg++;
+ if (narg < argc)
+ {
+ max = atof(argv[narg]);
+ }
+ else
+ {
+ cerr << "Must specify the histogram maximum intensity" << endl;
+ exit(2);
+ }
+ if (mask.nvoxels() > 0)
+ {
+ auto hist = vol.histogram(nbins, min, max, mask);
+ string hist_str = "";
+ for (int i = 0; i < hist.Nrows(); i++)
+ {
+ hist_str += to_string(hist(i+1));
+ if (i < hist.Nrows() - 1)
+ {
+ hist_str += " ";
+ }
+ }
+ print_value(
+ sarg,
+ hist_str,
+ json,
+ jsonOutput
+ );
+ }
+ else
+ {
+ auto hist = vol.histogram(nbins, min, max);
+ string hist_str = "";
+ for (int i = 0; i < hist.Nrows(); i++)
+ {
+ hist_str += to_string(hist(i+1));
+ if (i < hist.Nrows() - 1)
+ {
+ hist_str += " ";
+ }
+ }
+ print_value(
+ sarg,
+ hist_str,
+ json,
+ jsonOutput
+ );
+ }
+ }
+ else
+ {
+ // only print cerr if not the --json option
+ if (sarg != "--json")
+ {
+ cerr << "Unrecognised option: " << sarg << endl;
+ exit(3);
+ } else if (sarg == "--json" && last) {
+ // remove the trailing comma and space
+ json.pop_back();
+ json.pop_back();
+ }
+ }
+
+ narg++;
}
- float max=0;
- narg++;
- if (narg<argc) {
- max = atof(argv[narg]);
- } else {
- cerr << "Must specify the histogram maximum intensity" << endl;
- exit(2);
+ // if json mode is enabled
+ if (jsonOutput)
+ {
+ // close the json object
+ json.append("}");
}
- if (mask.nvoxels()>0) {
- cout << vol.histogram(nbins,min,max,mask) << " ";
- } else {
- cout << vol.histogram(nbins,min,max) << " ";
+ if (index < nIndices && !jsonOutput)
+ {
+ cout << endl;
}
- } else {
- cerr << "Unrecognised option: " << sarg << endl;
- exit(3);
+ // cout << endl;
+ } // end nIndices
+ // if json mode is enabled
+ if (jsonOutput)
+ {
+ // close the json object
+ json.append("]}");
}
-
- narg++;
- }
- cout << endl;
- }
-
+ if (timepoint < nTimepoints - 1 && !jsonOutput)
+ {
+ cout << endl;
+ }
+ // cout << endl;
+ } // end timepoints
+ if (jsonOutput)
+ {
+ // close the json object
+ json.append("]}");
+ cout << json;
+ } else {
+ cout << endl;
}
return 0;
}
-
-
-int main(int argc,char *argv[])
+int main(int argc, char *argv[])
{
Tracer tr("main");
string progname(argv[0]);
bool timeseriesMode(false);
string indexMask("");
- while ( argc > 2 && ( string(argv[1])=="-t" || string(argv[1]) =="-K" ) ) {
- if ( string(argv[1])=="-t" )
- timeseriesMode=true;
- if ( string(argv[1])=="-K" ) {
- indexMask=string(argv[2]);
+ while (argc > 2 && (string(argv[1]) == "-t" || string(argv[1]) == "-K"))
+ {
+ if (string(argv[1]) == "-t")
+ timeseriesMode = true;
+ if (string(argv[1]) == "-K")
+ {
+ indexMask = string(argv[2]);
argv++;
argc--;
}
argv++;
argc--;
}
- if (argc < 3 )
+ if (argc < 3)
return print_usage(progname);
- try {
- return fmrib_main_float(argc,argv,timeseriesMode,indexMask);
- } catch(std::exception &e) {
+ try
+ {
+ return fmrib_main_float(argc, argv, timeseriesMode, indexMask);
+ }
+ catch (std::exception &e)
+ {
cerr << e.what() << endl;
- } catch (...) {
+ }
+ catch (...)
+ {
// do nothing - just exit without garbage message
}
return -1;
-
}
--
GitLab
From 08e56c4632edf175221ec9c263dc1b77efb99e92 Mon Sep 17 00:00:00 2001
From: Taylor Hanayik <hanayik@gmail.com>
Date: Fri, 16 Jun 2023 14:08:31 +0100
Subject: [PATCH 2/6] add previous avwutils tests and new fslstats test
---
.gitignore | 3 +-
tests/avscale/feedsRun | 116 +++++++++++++++
tests/fix_orient/feedsRun | 166 ++++++++++++++++++++++
tests/fslchpixdim/feedsRun | 58 ++++++++
tests/fslcomplex/feedsRun | 132 +++++++++++++++++
tests/fslcreatehd/feedsRun | 265 +++++++++++++++++++++++++++++++++++
tests/fslcreatehd/mni2mm.xml | 44 ++++++
tests/fslstats/feedsRun | 180 ++++++++++++++++++++++++
8 files changed, 963 insertions(+), 1 deletion(-)
create mode 100755 tests/avscale/feedsRun
create mode 100755 tests/fix_orient/feedsRun
create mode 100755 tests/fslchpixdim/feedsRun
create mode 100755 tests/fslcomplex/feedsRun
create mode 100755 tests/fslcreatehd/feedsRun
create mode 100644 tests/fslcreatehd/mni2mm.xml
create mode 100755 tests/fslstats/feedsRun
diff --git a/.gitignore b/.gitignore
index 600d2d3..49b91c2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
-.vscode
\ No newline at end of file
+.vscode
+pyfeeds-out
\ No newline at end of file
diff --git a/tests/avscale/feedsRun b/tests/avscale/feedsRun
new file mode 100755
index 0000000..32062a0
--- /dev/null
+++ b/tests/avscale/feedsRun
@@ -0,0 +1,116 @@
+#!/usr/bin/env fslpython
+
+# test avscale with different input affines
+
+
+import sys
+import os
+
+import fsl.utils.run as run
+
+import numpy as np
+
+
+PI = np.pi
+PION2 = np.pi / 2
+
+
+# Each test has the form (input-affine, expected-output)
+# where expected-output comprises:
+# - scales
+# - translations
+# - rotations
+# - skews
+# - L/R orientation (preserved or swapped)
+tests = [
+
+ ([[1, 0, 0, 0],
+ [0, 1, 0, 0],
+ [0, 0, 1, 0],
+ [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, 0, 0), (0, 0, 0), 'preserved']),
+ ([[2, 0, 0, 0],
+ [0, 2, 0, 0],
+ [0, 0, 2, 0],
+ [0, 0, 0, 1]], [(2, 2, 2), (0, 0, 0), (0, 0, 0), (0, 0, 0), 'preserved']),
+ ([[-2, 0, 0, 0],
+ [ 0, 2, 0, 0],
+ [ 0, 0, 2, 0],
+ [ 0, 0, 0, 1]], [(2, 2, 2), (0, 0, 0), (0, 0, PI), (0, 0, 0), 'swapped']),
+ ([[0, 0, 1, 0],
+ [0, 1, 0, 0],
+ [1, 0, 0, 0],
+ [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, -PION2, 0), (0, 0, 0), 'swapped']),
+ ([[ 0, 0, -1, 0],
+ [ 0, -1, 0, 0],
+ [-1, 0, 0, 0],
+ [ 0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (-PI, PION2, 0), (0, 0, 0), 'preserved']),
+ ([[0, 1, 0, 0],
+ [1, 0, 0, 0],
+ [0, 0, 1, 0],
+ [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, 0, PION2), (0, 0, 0), 'swapped']),
+ ([[1, 0, 0, 0],
+ [0, 0, 1, 0],
+ [0, 1, 0, 0],
+ [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (PION2, 0, 0), (0, 0, 0), 'swapped']),
+ ([[-2, 0, 0, 90],
+ [ 0, 2, 0, -126],
+ [ 0, 0, 2, -72],
+ [ 0, 0, 0, 1]], [(2, 2, 2), (90, -126, -72), (0, 0, PI), (0, 0, 0), 'swapped']),
+
+]
+
+def read_avscale_output(output):
+ lines = output.split('\n')
+ # scales
+ # translations
+ # rotations
+ # skews
+ # l/r orientation (preserved or swapped)
+ scales = [l for l in lines if l.startswith('Scales ')] [0]
+ translations = [l for l in lines if l.startswith('Translations ')] [0]
+ rotations = [l for l in lines if l.startswith('Rotation Angles')][0]
+ skews = [l for l in lines if l.startswith('Skews ')] [0]
+ orient = [l for l in lines if l.startswith('Left-Right ')] [0]
+
+ scales = [float(s) for s in scales .split()[-3:]]
+ translations = [float(s) for s in translations.split()[-3:]]
+ rotations = [float(s) for s in rotations .split()[-3:]]
+ skews = [float(s) for s in skews .split()[-3:]]
+ orient = orient.split()[-1]
+
+ return {
+ 'scales' : np.array(scales),
+ 'translations' : np.array(translations),
+ 'rotations' : np.array(rotations),
+ 'skews' : np.array(skews),
+ 'orient' : orient.lower(),
+ }
+
+
+def test_avscale():
+
+ for affine, expected in tests:
+ affine = np.array(affine)
+ np.savetxt('affine.mat', affine, '%0.6f')
+ print(affine)
+ output = run.runfsl('avscale --allparams affine.mat')
+ output = read_avscale_output(output)
+
+ scales, translations, rotations, skews, orient = expected
+
+ try:
+ assert np.all(np.isclose(scales, output['scales']))
+ assert np.all(np.isclose(translations, output['translations']))
+ assert np.all(np.isclose(rotations, output['rotations']))
+ assert np.all(np.isclose(skews, output['skews']))
+ assert orient == output['orient']
+ except AssertionError:
+ print(affine)
+ print(output)
+ raise
+
+
+if __name__ == '__main__':
+ if len(sys.argv) > 1:
+ os.chdir(sys.argv[1])
+ test_avscale()
diff --git a/tests/fix_orient/feedsRun b/tests/fix_orient/feedsRun
new file mode 100755
index 0000000..0e0e575
--- /dev/null
+++ b/tests/fix_orient/feedsRun
@@ -0,0 +1,166 @@
+#!/usr/bin/env fslpython
+"""Test the standard recipe for fixing a broken orientation, from "The labels
+in FSLView are wrong or missing and no conversion to NIfTI can fix this", on
+this page:
+
+https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
+
+ If this really cannot be fixed at the conversion stage, then it is
+ possible to fix by the follow (only to be attempted after reading the
+ following section on background information on NIfTI orientation):
+ fslorient -deleteorient imagename ; fslswapdim imagename a b c imagename ;
+ fslorient -setqformcode 1 imagename ; where a b c need to be chosen,
+ usually by trial and error, so that the image after this is in the same
+ orientation (as viewed in FSLView) as the MNI152 images. However, unless
+ you have some way of telling left from right in the image (e.g. by a
+ vitamin capsule or clearly known structural asymmetry) this method can
+ easily result in an incorrect left-right labelling and so should not be
+ attempted.
+
+The recipe involves:
+
+ 1. resetting the image affines
+
+ 2. transposing the data array until it is in a
+ RAS orientation
+
+ 3. Enabling the qform affine which, after step
+ 1, should be a diagonal matrix with pixdims
+ as scaling parameters.
+
+Specifically, the recipe is as follows:
+
+ # 1. clear the sform/qform affines
+ fslorient -deleteorient image
+
+ # 2. rotate the data into RAS orientation (exact
+ # command depends on original data orientation)
+ fslswapdim image x z y image
+
+ # 3. reset the qform code. The qform should be
+ # a diagonal matrix, and the image data array
+ # should be in RAS orientation, so after this
+ # step the image should be labelled correctly.
+ fslorient -setqformcode 1 image
+
+
+This recipe makes some key assumptions:
+
+ - fslorient -deleteorient (step 1) deleting/
+ clearing the affines - the qform must be
+ reset to be a scaling matrix.
+
+ - fslswapdim (step 2) not touching the affines
+ when the s/qform codes are 0
+
+These are required so that, in step 3, the qform is a diagonal matrix with
+correct scaling paramaters.
+
+Some bugs were introduced in FSL 6.0.0 (fixed in FSL 6.0.6) which broke the
+above assumptions:
+
+ - fslorient -deleteorient was not clearing the original
+ affines
+ - fslswapdim was applying the rotations/flips to both the
+ data, and to the s/qforms, even if the s/qform codes were
+ set to 0.
+"""
+
+import numpy as np
+import nibabel as nib
+import os
+import subprocess as sp
+import shlex
+import sys
+import traceback
+
+def sprun(cmd):
+ sp.run(shlex.split(cmd), check=True)
+
+
+# Test the original recipe for fixing the
+# orientation of an image, as described above
+def test_fix_orient():
+
+ data = np.random.random((10, 10, 10))
+ orig_qform = np.array([[2, 0, 0, 10],
+ [0, 2, 0, -20],
+ [0, 0, 2, 50],
+ [0, 0, 0, 1]])
+ image = nib.Nifti1Image(data, np.eye(4))
+ image.set_sform(np.eye(4), 0)
+ image.set_qform(orig_qform, 1)
+
+ image.to_filename('orig.nii.gz')
+ sprun('imcp orig cleared')
+ sprun('fslorient -deleteorient cleared')
+ sprun('fslswapdim cleared x z y swapped')
+ sprun('imcp swapped fixed')
+ sprun('fslorient -setqformcode 1 fixed')
+
+ fixed = nib.load('fixed.nii.gz')
+
+ new_data = fixed.get_fdata()
+ new_qform, qcode = fixed.get_qform(coded=True)
+ _, scode = fixed.get_sform(coded=True)
+
+ # new qform should be a scaling matrix (not
+ # necessarily equivalent to the original
+ assert qcode == 1
+ assert scode == 0
+ assert np.all(np.isclose(new_qform, np.diag([2, 2, 2, 1])))
+ assert np.all(np.isclose(new_data, data.transpose((0, 2, 1))))
+
+
+# An alternate strategy which involves
+# explicitly clobbering the qform
+def test_fix_orient_alternate():
+ # original qform
+ data = np.random.random((10, 10, 10))
+ orig_qform = np.array([[2, 0, 0, 10],
+ [0, 2, 0, -20],
+ [0, 0, 2, 50],
+ [0, 0, 0, 1]])
+ image = nib.Nifti1Image(data, np.eye(4))
+ image.set_sform(np.eye(4), 0)
+ image.set_qform(orig_qform, 1)
+
+ image.to_filename('orig.nii.gz')
+ sprun('imcp orig cleared')
+ sprun('fslorient -deleteorient cleared')
+ sprun('fslswapdim cleared x z y swapped')
+ sprun('imcp swapped fixed1')
+ sprun('fslorient -setqform 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 fixed1')
+ sprun('imcp fixed1 fixed')
+ sprun('fslorient -setqformcode 1 fixed')
+
+ fixed = nib.load('fixed.nii.gz')
+
+ new_data = fixed.get_fdata()
+ new_qform, qcode = fixed.get_qform(coded=True)
+ _, scode = fixed.get_sform(coded=True)
+
+ # new qform should be a scaling matrix (not
+ # necessarily equivalent to the original
+ assert qcode == 1
+ assert scode == 0
+ assert np.all(np.isclose(new_qform, np.diag([2, 2, 2, 1])))
+ assert np.all(np.isclose(new_data, data.transpose((0, 2, 1))))
+
+
+if __name__ == '__main__':
+ tests = [test_fix_orient,
+ test_fix_orient_alternate]
+
+ result = 0
+ for test in tests:
+ try:
+ os.chdir(sys.argv[1])
+ test()
+ print(f'\nTest {test.__name__} PASSED')
+ except Exception as e:
+ print(f'\nTest {test.__name__} FAILED')
+ traceback.print_exc()
+ result = 1
+
+ sys.exit(result)
diff --git a/tests/fslchpixdim/feedsRun b/tests/fslchpixdim/feedsRun
new file mode 100755
index 0000000..56bcee4
--- /dev/null
+++ b/tests/fslchpixdim/feedsRun
@@ -0,0 +1,58 @@
+#!/usr/bin/env fslpython
+
+import os
+import sys
+import subprocess as sp
+
+import numpy as np
+import nibabel as nib
+
+
+def create_image(shape, pixdim):
+ pixdim = list(pixdim)
+ data = np.random.random(shape).astype(np.float32)
+ hdr = nib.Nifti1Header()
+
+ hdr.set_data_dtype(np.float32)
+ hdr.set_data_shape(shape)
+ hdr.set_zooms(pixdim[:len(shape)])
+
+ return nib.Nifti1Image(data, np.eye(4), hdr)
+
+
+def check_image(origimg, changedimg, exppixdim):
+
+ gotshape = changedimg.shape
+ gotpixdim = list(changedimg.header.get_zooms())
+ gotdata = changedimg.get_fdata()
+
+ assert origimg.shape == gotshape
+ assert gotpixdim == exppixdim
+ assert np.all(origimg.get_fdata() == gotdata)
+
+
+def run_tests():
+ # (image shape, command, exppixdims)
+ tests = [
+ ((5, 5, 5), '2 2 2', (2, 2, 2)),
+ ((5, 5, 5), '2 2 2 2', (2, 2, 2)),
+ ((5, 5, 5, 5), '2 2 2', (2, 2, 2, 1)),
+ ((5, 5, 5, 5), '2 2 2 2', (2, 2, 2, 2)),
+ ]
+
+ for shape, cmd, exppixdim in tests:
+
+ imgfile = 'image.nii.gz'
+ img = create_image(shape, [1] * len(shape))
+ img.to_filename(imgfile)
+
+ try:
+ sp.run(['fslchpixdim', imgfile] + list(cmd.split()))
+ check_image(img, nib.load(imgfile), list(exppixdim))
+
+ finally:
+ os.remove(imgfile)
+
+
+if __name__ == '__main__':
+ sys.exit(run_tests())
diff --git a/tests/fslcomplex/feedsRun b/tests/fslcomplex/feedsRun
new file mode 100755
index 0000000..a84cc1d
--- /dev/null
+++ b/tests/fslcomplex/feedsRun
@@ -0,0 +1,132 @@
+#!/usr/bin/env fslpython
+"""Test that fslcomplex produces correct outputs. Specifically tests that the
+output files have orientation info that matches that of the input files.
+"""
+
+import numpy as np
+import nibabel as nib
+import subprocess as sp
+import os.path as op
+import shlex
+import sys
+import traceback
+
+from fsl.utils.tempdir import tempdir
+from fsl.data.image import addExt
+
+
+def sprun(cmd):
+ print(f'RUN {cmd}')
+ sp.run(shlex.split(cmd), check=True)
+
+
+def imtest(path):
+ try:
+ addExt(path)
+ return True
+ except Exception:
+ return False
+
+
+# radio=[True|False] -> whether or not
+# to add a flip on the affine X axis
+def create_test_input_data(radio, seed=1):
+
+ np.random.seed(seed)
+
+ real = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
+ imag = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
+ affine = np.diag([3, 3, 3, 1])
+
+ if radio:
+ affine[0, 0] *= -1
+ affine[:3, 3] = [37, 20, 30]
+ real = np.flip(real, 0)
+ imag = np.flip(imag, 0)
+ else:
+ affine[:3, 3] = [10, 20, 30]
+
+ comp = real + imag * 1j
+ abso = np.abs(comp)
+ phase = np.arctan2(comp.imag, comp.real)
+ comp4d = np.concatenate((comp.reshape(10, 10, 10, 1),
+ comp.reshape(10, 10, 10, 1)), 3)
+
+ real = nib.Nifti1Image(real, affine)
+ imag = nib.Nifti1Image(imag, affine)
+ comp = nib.Nifti1Image(comp, affine)
+ comp4d = nib.Nifti1Image(comp4d, affine)
+ abso = nib.Nifti1Image(abso, affine)
+ phase = nib.Nifti1Image(phase, affine)
+
+ real .set_qform(*real .get_sform(coded=True))
+ imag .set_qform(*comp .get_sform(coded=True))
+ comp .set_qform(*comp .get_sform(coded=True))
+ comp4d.set_qform(*comp4d.get_sform(coded=True))
+ abso .set_qform(*abso .get_sform(coded=True))
+ phase .set_qform(*phase .get_sform(coded=True))
+
+ real .to_filename('real_in.nii.gz')
+ imag .to_filename('imag_in.nii.gz')
+ comp .to_filename('complex_in.nii.gz')
+ comp4d.to_filename('complex4d_in.nii.gz')
+ abso .to_filename('abs_in.nii.gz')
+ phase .to_filename('phase_in.nii.gz')
+
+
+def compare_images(file1, file2):
+ img1 = nib.load(addExt(file1))
+ img2 = nib.load(addExt(file2))
+ data1 = np.asanyarray(img1.dataobj)
+ data2 = np.asanyarray(img2.dataobj)
+ assert img1.header['sform_code'] == img2.header['sform_code']
+ assert img1.header['qform_code'] == img2.header['qform_code']
+ assert np.all(np.isclose(img1.get_sform(), img2.get_sform()))
+ assert np.all(np.isclose(img1.get_qform(), img2.get_qform()))
+ assert np.all(np.isclose(img1.header['pixdim'], img2.header['pixdim']))
+ assert np.all(np.isclose(data1, data2))
+
+
+def test_fslcomplex_call(args, infiles, outfiles, radio):
+ with tempdir():
+ create_test_input_data(radio)
+ sprun(f'fslcomplex {args} {infiles} {outfiles}')
+ for outfile in outfiles.split(' '):
+
+ if not imtest(outfile):
+ continue
+
+ prefix = outfile.split('_')[0]
+ infile = f'{prefix}_in'
+
+ print(f'Comparing {outfile} against {infile}')
+
+ compare_images(infile, outfile)
+
+
+if __name__ == '__main__':
+ tests = [
+ ('-realabs', 'complex_in', 'abs_out'),
+ ('-realphase', 'complex_in', 'phase_out'),
+ ('-realpolar', 'complex_in', 'abs_out phase_out'),
+ ('-realcartesian', 'complex_in', 'real_out imag_out'),
+ ('-complex', 'real_in imag_in', 'complex_out'),
+ ('-complexpolar', 'abs_in phase_in', 'complex_out'),
+ ('-copyonly', 'complex_in', 'complex_out'),
+ ('-complexsplit', 'complex4d_in', 'complex_out 0 0'),
+ ('-complexsplit', 'complex4d_in', 'complex_out 1 1'),
+ ('-complexmerge', 'complex_in complex_in', 'complex4d_out'),
+ ]
+
+ result = 0
+ for radio in [True, False]:
+ for args, infiles, outfiles in tests:
+ try:
+ test_fslcomplex_call(args, infiles, outfiles, radio)
+ print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] PASSED')
+ except Exception as e:
+ print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] FAILED')
+ traceback.print_exc()
+ result = 1
+
+ sys.exit(result)
diff --git a/tests/fslcreatehd/feedsRun b/tests/fslcreatehd/feedsRun
new file mode 100755
index 0000000..339553d
--- /dev/null
+++ b/tests/fslcreatehd/feedsRun
@@ -0,0 +1,265 @@
+#!/usr/bin/env fslpython
+
+import os
+import os.path as op
+import sys
+import subprocess as sp
+
+import numpy as np
+import nibabel as nib
+
+
+THISDIR = op.dirname(op.abspath(__file__))
+
+
+# 2=char, 4=short, 8=int, 16=float, 64=double
+DTYPE_MAPPING = {
+ 2 : np.uint8,
+ 4 : np.int16,
+ 8 : np.int32,
+ 16 : np.float32,
+ 64 : np.float64
+}
+
+MNI152_2MM_AFFINE = np.array([[-2, 0, 0, 90],
+ [ 0, 2, 0, -126],
+ [ 0, 0, 2, -72],
+ [ 0, 0, 0, 1]])
+
+
+def validate_result(imgfile, expshape, exppixdim, exporigin, expdtype):
+
+ img = nib.load(imgfile)
+ hdr = img.header
+ expshape = list(expshape)
+ exppixdim = list(exppixdim)
+ exporigin = list(exporigin)
+
+ if (len(expshape) == 3) or \
+ expshape[3] in (0, 1):
+ expndims = 3
+ else:
+ expndims = 4
+
+ expaffine = np.diag(exppixdim[:3] + [1])
+ expaffine[0, 0] *= -1
+ expaffine[:3, 3] = exporigin
+ expaffine[0, 3] *= exppixdim[0]
+ expaffine[1, 3] *= -exppixdim[1]
+ expaffine[2, 3] *= -exppixdim[2]
+
+ assert len(img.shape) == expndims
+ assert list(img.shape) == expshape[ :expndims]
+ assert list(hdr.get_zooms()) == exppixdim[:expndims]
+ assert img.get_data_dtype() == expdtype
+ assert np.all(np.isclose(img.affine, expaffine))
+
+
+def create_image(shape, pixdim, origin, dtype):
+ pixdim = list(pixdim)
+ affine = np.diag(pixdim[:3] + [1])
+ affine[:3, 3] = origin
+ data = np.random.randint(1, 100, shape).astype(dtype)
+ hdr = nib.Nifti1Header()
+
+ hdr.set_data_dtype(dtype)
+ hdr.set_data_shape(shape)
+ hdr.set_zooms(pixdim[:len(shape)])
+
+ return nib.Nifti1Image(data, affine, hdr)
+
+
+def test_new_file():
+ tests = [
+
+ # 4th dim of size 0 or 1 should
+ # result in a 3D image (this
+ # is coded in validate_result)
+ ' 5 5 5 0 2 2 2 0 0 0 0 2',
+ ' 5 5 5 0 2 2 2 1 0 0 0 2',
+ ' 5 5 5 1 2 2 2 1 0 0 0 2',
+ ' 5 5 5 1 2 2 2 1 0 0 0 4',
+ ' 5 5 5 1 2 2 2 1 0 0 0 8',
+ ' 5 5 5 1 2 2 2 1 0 0 0 16',
+ ' 5 5 5 1 2 2 2 1 1 2 3 64',
+ ' 5 5 5 1 0.5 1.5 1.25 1 0 0 0 2',
+ ' 5 5 5 1 0.5 1.5 1.25 1.5 0 0 0 2',
+ ' 5 5 5 1 0.5 1.5 1.25 0.5 0 0 0 2',
+ '30 30 30 5 5 10 3 5 10 20 10 2',
+ ]
+
+ for test in tests:
+ args = list(test.split())
+ imgfile = 'image.nii.gz'
+
+ try:
+ os.remove(imgfile)
+ except:
+ pass
+
+ print(['fslcreatehd'] + args + [imgfile])
+
+ sp.run(['fslcreatehd'] + args + [imgfile])
+
+ args = [float(a) for a in args]
+ expshape = args[:4]
+ exppixdim = args[4:8]
+ exporigin = args[8:11]
+ expdtype = DTYPE_MAPPING[args[11]]
+
+ try:
+ validate_result(
+ imgfile, expshape, exppixdim, exporigin, expdtype)
+ finally:
+ os.remove(imgfile)
+
+
+def test_existing_file():
+
+ # each test is a tuple containing:
+ # - dtype_of_existing_image
+ # - shape_of_existing_image
+ # - exp_shape (set to None if image should not be overwritten)
+ # - fslcreatehd_args
+ tests = [
+ # 4th dim of 0 or 1 should result in a 3D image
+ (2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 2'),
+ (2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 1 2 3 2'),
+ (2, (5, 5, 5), None, '5 5 5 1 2 2 2 2 0 0 0 2'),
+
+ # dtype arg should be ignored for existing images
+ (2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 4'),
+ (4, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 2'),
+
+ # data should be overwritten if any
+ # of the first 3 dims are different,
+ # or if a 4th dim is specified
+ (2, (5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 4'),
+ (2, (5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 1 2 3 2'),
+ (2, (5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 1 2 3 2'),
+
+ # 4D - same rules apply
+ (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 4'),
+ (4, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 1 2 3 2'),
+
+ # data overwritten if nelements
+ # change
+ (2, (5, 5, 5, 5), (5, 5, 5), '5 5 5 0 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), (5, 5, 5), '5 5 5 1 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 1 2 3 2'),
+ (2, (5, 5, 5, 5), (5, 5, 5, 2), '5 5 5 2 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 0 0 0 2'),
+ (2, (5, 5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 1 2 3 2'),
+ ]
+
+ for (dtype, shape, expshape, args) in tests:
+ imgfile = 'image.nii.gz'
+ dtype = DTYPE_MAPPING[dtype]
+ args = list(args.split())
+ img = create_image(shape, (1, 1, 1, 1), (0, 0, 0), dtype)
+
+ img.to_filename(imgfile)
+
+ sp.run(['fslcreatehd'] + args + [imgfile])
+
+ checkdata = expshape is None
+
+ if expshape is None:
+ expshape = shape
+
+ args = [float(a) for a in args]
+ exppixdim = args[4:8]
+ exporigin = args[8:11]
+
+ try:
+ validate_result(imgfile, expshape, exppixdim, exporigin, dtype)
+
+ if checkdata:
+ data = np.asanyarray(img.dataobj)
+ datacopy = np.asanyarray(nib.load(imgfile).dataobj)
+ assert np.all(data == datacopy)
+
+ finally:
+ os.remove(imgfile)
+
+
+def test_new_file_xml():
+ xmlfile = op.join(THISDIR, 'mni2mm.xml')
+ sp.run(['fslcreatehd', xmlfile, 'mni.nii.gz'])
+ img = nib.load('mni.nii.gz')
+
+ assert img.shape == (91, 109, 91)
+ assert img.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+ assert img.header['intent_code'] == 10
+ assert img.header['intent_p1'] == 20
+ assert img.header['intent_p2'] == 30
+ assert img.header['intent_p3'] == 40
+
+
+def test_existing_file_xml_same_shape():
+ xmlfile = op.join(THISDIR, 'mni2mm.xml')
+ img = create_image((91, 109, 91), (3, 3, 3), (5, 5, 5), np.float32)
+ img.to_filename('image.nii.gz')
+
+ sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
+
+ result = nib.load('image.nii.gz')
+
+ assert result.shape == (91, 109, 91)
+ assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+
+ # bug in FSL<=6.0.4 caused intent codes to not be set
+ assert result.header['intent_code'] == 10
+ assert result.header['intent_p1'] == 20
+ assert result.header['intent_p2'] == 30
+ assert result.header['intent_p3'] == 40
+ assert np.all(result.affine == MNI152_2MM_AFFINE)
+
+ # data should be preserved
+ assert np.all(result.get_fdata() == img.get_fdata())
+
+
+def test_existing_file_xml_different_shape():
+
+ xmlfile = op.join(THISDIR, 'mni2mm.xml')
+ img = create_image((20, 20, 20), (3, 3, 3), (5, 5, 5), np.float32)
+
+ img.to_filename('image.nii.gz')
+
+ sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
+
+ result = nib.load('image.nii.gz')
+
+ assert result.shape == (91, 109, 91)
+ assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+ assert result.header['intent_code'] == 10
+ assert result.header['intent_p1'] == 20
+ assert result.header['intent_p2'] == 30
+ assert result.header['intent_p3'] == 40
+ assert np.all(result.affine == MNI152_2MM_AFFINE)
+
+ # data should be cleared
+ assert np.all(result.get_fdata() == 0)
+
+
+def main():
+ outdir = sys.argv[1]
+ os.chdir(outdir)
+
+ test_new_file()
+ test_existing_file()
+ test_new_file_xml()
+ test_existing_file_xml_same_shape()
+ test_existing_file_xml_different_shape()
+
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/tests/fslcreatehd/mni2mm.xml b/tests/fslcreatehd/mni2mm.xml
new file mode 100644
index 0000000..06b8043
--- /dev/null
+++ b/tests/fslcreatehd/mni2mm.xml
@@ -0,0 +1,44 @@
+<nifti_image
+ image_offset = '352'
+ ndim = '3'
+ nx = '91'
+ ny = '109'
+ nz = '91'
+ nt = '1'
+ dx = '2'
+ dy = '2'
+ dz = '2'
+ dt = '1'
+ datatype = '4'
+ nvox = '902629'
+ nbyper = '2'
+ scl_slope = '1'
+ scl_inter = '0'
+ intent_code = '10'
+ intent_p1 = '20'
+ intent_p2 = '30'
+ intent_p3 = '40'
+ intent_name = ''
+ toffset = '0'
+ xyz_units = '2'
+ time_units = '8'
+ freq_dim = '0'
+ phase_dim = '0'
+ slice_dim = '0'
+ descrip = 'FSL5.0'
+ aux_file = ''
+ qform_code = '4'
+ qfac = '-1'
+ quatern_b = '0'
+ quatern_c = '1'
+ quatern_d = '0'
+ qoffset_x = '90'
+ qoffset_y = '-126'
+ qoffset_z = '-72'
+ sform_code = '4'
+ sto_xyz_matrix = '-2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1'
+ slice_code = '0'
+ slice_start = '0'
+ scl_end = '0'
+ scl_duration = '0'
+/>
diff --git a/tests/fslstats/feedsRun b/tests/fslstats/feedsRun
new file mode 100755
index 0000000..c6d1305
--- /dev/null
+++ b/tests/fslstats/feedsRun
@@ -0,0 +1,180 @@
+#!/usr/bin/env fslpython
+
+# test fslstats with a bunch of different options
+#
+# Usage: fslstats [preoptions] <input> [options]
+#
+# preoption -t will give a separate output line for each 3D volume of a 4D timeseries
+# preoption -K < indexMask > will generate seperate n submasks from indexMask, for indexvalues 1..n where n is the maximum index value in indexMask, and generate statistics for each submask
+# Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean
+
+# -l <lthresh> : set lower threshold
+# -u <uthresh> : set upper threshold
+# -r : output <robust min intensity> <robust max intensity>
+# -R : output <min intensity> <max intensity>
+# -e : output mean entropy ; mean(-i*ln(i))
+# -E : output mean entropy (of nonzero voxels)
+# -v : output <voxels> <volume>
+# -V : output <voxels> <volume> (for nonzero voxels)
+# -m : output mean
+# -M : output mean (for nonzero voxels)
+# -s : output standard deviation
+# -S : output standard deviation (for nonzero voxels)
+# -w : output smallest ROI <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> containing nonzero voxels
+# -x : output co-ordinates of maximum voxel
+# -X : output co-ordinates of minimum voxel
+# -c : output centre-of-gravity (cog) in mm coordinates
+# -C : output centre-of-gravity (cog) in voxel coordinates
+# -p <n> : output nth percentile (n between 0 and 100)
+# -P <n> : output nth percentile (for nonzero voxels)
+# -a : use absolute values of all image intensities
+# -n : treat NaN or Inf as zero for subsequent stats
+# -k <mask> : use the specified image (filename) for masking - overrides lower and upper thresholds
+# -d <image> : take the difference between the base image and the image specified here
+# -h <nbins> : output a histogram (for the thresholded/masked voxels only) with nbins
+# -H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max
+
+# Note - thresholds are not inclusive ie lthresh<allowed<uthresh
+
+import sys
+import os
+import fsl.utils.run as run
+import numpy as np
+import nibabel as nib
+
+# set the random seed so that the tests are reproducible
+np.random.seed(0)
+
+options = [
+ {"option": "-r", "expected": "0.018533 0.978824"},
+ {"option": "-R", "expected": "0.000546 0.999809"},
+ {"option": "-e", "expected": "0.906103"},
+ {"option": "-E", "expected": "0.906103"},
+ {"option": "-v", "expected": "1000 1000.000000"},
+ {"option": "-V", "expected": "1000 1000.000000"},
+ {"option": "-m", "expected": "0.495922"},
+ {"option": "-M", "expected": "0.495922"},
+ {"option": "-s", "expected": "0.290744"},
+ {"option": "-S", "expected": "0.290744"},
+ {"option": "-w", "expected": "0 10 0 10 0 10 0 1"},
+ {"option": "-x", "expected": "9 7 4"},
+ {"option": "-X", "expected": "8 2 1"},
+ {"option": "-c", "expected": "4.498706 4.545873 4.613188"},
+ {"option": "-C", "expected": "4.498706 4.545873 4.613188"},
+ {"option": "-p 50", "expected": "0.482584"},
+ {"option": "-P 50", "expected": "0.482584"},
+]
+
+# create a list of tests and expected results
+tests = []
+for option in options:
+ tests.append(
+ {
+ "preoptions": "",
+ "mask": "",
+ "options": option["option"],
+ "expected": option["expected"],
+ }
+ )
+
+tests_with_preoptions = [
+ {
+ "preoptions": "-K",
+ "mask": "mask.nii.gz",
+ "options": "-m",
+ "expected": "0.948930 \n0.947671 \n1.003258 \n1.010696",
+ },
+ {
+ "preoptions": "-t -K",
+ "mask": "mask.nii.gz",
+ "options": "-m",
+ "expected": "0.459736 \n0.476035 \n0.504080 \n0.549485 \n0.489194 \n0.471636 \n0.499178 \n0.461211",
+ },
+ {
+ "preoptions": "-t",
+ "mask": "",
+ "options": "-m",
+ "expected": "0.496675 \n0.487950",
+ },
+]
+
+# taken from fslchpixdim test
+def create_image(shape, pixdim):
+ pixdim = list(pixdim)
+ data = np.random.random(shape).astype(np.float32)
+ hdr = nib.Nifti1Header()
+ hdr.set_data_dtype(np.float32)
+ hdr.set_data_shape(shape)
+ hdr.set_zooms(pixdim[:len(shape)])
+
+ return nib.Nifti1Image(data, np.eye(4), hdr)
+
+def create_mask(input_img, n_rois=4):
+ '''
+ Create a mask image from the input image.
+ The mask image will have n_rois different values with random sizes randomly placed in the image.
+ '''
+ data = input_img.get_fdata()
+ mask = np.zeros_like(data)
+ for i in range(n_rois + 1):
+ roi_size = np.random.randint(1, data.size)
+ roi_value = i
+ roi = np.random.choice(data.size, roi_size, replace=False)
+ mask.flat[roi] = roi_value
+ return nib.Nifti1Image(mask, input_img.affine, input_img.header)
+
+
+def test_fslstats():
+ imgfile = 'test.nii.gz'
+ shape = (10,10,10)
+ img = create_image(shape, [1] * len(shape))
+ img.to_filename(imgfile)
+ mask = create_mask(img)
+ mask.to_filename('mask.nii.gz')
+
+ # run the tests witoout preoptions
+ for test in tests:
+ cmd = f"fslstats {test['preoptions']} {test['mask']} {imgfile} {test['options']}"
+ # remove any double spaces from empty test options
+ cmd = " ".join(cmd.split())
+ print(cmd)
+ output = run.runfsl(cmd)
+ # trim any trailing whitespace from the output (fslstats adds a newline at the end)
+ output = output.rstrip()
+ try:
+ assert output == test["expected"]
+ except AssertionError:
+ print(cmd)
+ print(output)
+ print(test["expected"])
+ raise
+
+ # run the tests with preoptions
+ imgfile = 'test_4d.nii.gz'
+ shape = (10,10,10, 2)
+ img = create_image(shape, [1] * len(shape))
+ img.to_filename(imgfile)
+ for test in tests_with_preoptions:
+ cmd = f"fslstats {test['preoptions']} {test['mask']} {imgfile} {test['options']}"
+ # remove any double spaces from empty test options
+ cmd = " ".join(cmd.split())
+ print(cmd, flush=True)
+ output = run.runfsl(cmd)
+ # trim any trailing whitespace from the output (fslstats adds a newline at the end)
+ output = output.rstrip()
+ try:
+ assert output == test["expected"]
+ except AssertionError:
+ print('Failed test')
+ print(cmd)
+ print('Output')
+ print(output)
+ print('Expected')
+ print(test["expected"])
+ raise
+
+
+if __name__ == "__main__":
+ if len(sys.argv) > 1:
+ os.chdir(sys.argv[1])
+ test_fslstats()
--
GitLab
From df55aff586ac0d50054bfff32f55c2a7d5090bce Mon Sep 17 00:00:00 2001
From: Taylor Hanayik <hanayik@gmail.com>
Date: Tue, 20 Jun 2023 16:00:32 +0100
Subject: [PATCH 3/6] add json lib; update unit tests; add lfs
---
.gitattributes | 1 +
fslstats.cc | 570 ++++++++++++-----------------
tests/fslstats/feedsRun | 50 +--
tests/fslstats/imageForDiff.nii.gz | 3 +
tests/fslstats/mask.nii.gz | 3 +
tests/fslstats/test.nii.gz | 3 +
tests/fslstats/test_4d.nii.gz | 3 +
7 files changed, 268 insertions(+), 365 deletions(-)
create mode 100644 .gitattributes
create mode 100644 tests/fslstats/imageForDiff.nii.gz
create mode 100644 tests/fslstats/mask.nii.gz
create mode 100644 tests/fslstats/test.nii.gz
create mode 100644 tests/fslstats/test_4d.nii.gz
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..07f0463
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+*.nii.gz filter=lfs diff=lfs merge=lfs -text
diff --git a/fslstats.cc b/fslstats.cc
index 83a9873..8e90fd2 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -8,21 +8,27 @@
#include <limits>
#include <string>
+#include <typeinfo>
#include "utils/fsl_isfinite.h"
#include "armawrap/newmat.h"
#include "miscmaths/miscmaths.h"
#include "newimage/newimageall.h"
#include "newimage/costfns.h"
+#include "nlohmann/json.hpp"
using namespace std;
using namespace NEWMAT;
using namespace NEWIMAGE;
+using json = nlohmann::json;
int print_usage(const string &progname)
{
cout << "Usage: fslstats [preoptions] <input> [options]" << endl
<< endl;
+ // add --json output format option
+ // keys will correspond to the options above
+ cout << "preoption -json: output in JSON format to standard out" << endl;
cout << "preoption -t will give a separate output line for each 3D volume of a 4D timeseries" << endl;
cout << "preoption -K < indexMask > will generate seperate n submasks from indexMask, for indexvalues 1..n where n is the maximum index value in indexMask, and generate statistics for each submask" << endl;
cout << "Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean" << endl
@@ -51,11 +57,7 @@ int print_usage(const string &progname)
cout << "-k <mask> : use the specified image (filename) for masking - overrides lower and upper thresholds" << endl;
cout << "-d <image> : take the difference between the base image and the image specified here" << endl;
cout << "-h <nbins> : output a histogram (for the thresholded/masked voxels only) with nbins" << endl;
- cout << "-H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max" << endl;
- // add --json output format option
- // keys will correspond to the options above
- cout << "--json : output in JSON format" << endl
- << endl;
+ cout << "-H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max" << endl;
cout << "Note - thresholds are not inclusive ie lthresh<allowed<uthresh" << endl;
return 1;
}
@@ -120,38 +122,35 @@ int generate_masks(volume4D<float> &mask, volume4D<float> &masknz, const volume4
return generateNonZeroMask(mask, masknz, input);
}
-// print function that can handle outputting in JSON format or not
-void print_value(const string &key, const string &value, string &json, const bool jsonOutput)
+// print function that can handle outputting in JSON format or not. Use a template to allow for different types
+template <typename T>
+void update_json(string key, T &value, json &j)
{
- // append the key and value to the json string
- if (jsonOutput)
- {
- json.append("\"" + key + "\": \"" + value + "\", ");
- }
- else
- {
- cout << value << " ";
- }
+ j[key] = value;
}
+template <typename T>
+void update_json(string key, initializer_list<T> &value, json &j)
+{
+ j[key] = value;
+}
-int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const string &indexMaskName)
+template <typename T>
+void update_json(string key, vector<T> &value, json &j)
{
- // determine if the user wants to output in JSON format
- bool jsonOutput = false;
- for (int i = 1; i < argc; i++)
- {
- if (strcmp(argv[i], "--json") == 0)
- {
- jsonOutput = true;
- break;
- }
- }
- // if JSON output is requested, then we need to store the output as a string
- // and then output it at the end via cout
- // don't forget to close the json at the end with a "}"
- string json = "";
-
+ j[key] = value;
+}
+
+void update_json(string key, ColumnVector &value, json &j)
+{
+ j[key] = value;
+}
+
+int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const string &indexMaskName, const bool jsonMode = false)
+{
+
+ json js;
+
cout.setf(ios::dec);
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::left, ios::adjustfield);
@@ -167,27 +166,16 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
read_volume4D(indexMask, indexMaskName);
int nTimepoints((timeseriesMode) ? inputMaster.tsize() : 1), nIndices((indexMaskName != "") ? indexMask.max() : 1);
+ // initialise the volumes array in the json object. This will get appended to later
+ js["volumes"] = json::array();
+
for (int timepoint = 0; timepoint < nTimepoints; timepoint++)
{
- if (jsonOutput)
- {
- if (timepoint == 0){
- json.append("{\"volumes\": [");
- } else {
- json.append(", ");
- }
- }
+ json tp = json::object();
+ tp["indices"] = json::array();
for (int index = 1; index <= nIndices; index++)
{
- // if json mode is enabled
- if (jsonOutput)
- {
- if (index == 1){
- json.append("{\"indices\": [{");
- } else {
- json.append(", {");
- }
- }
+ json idx = json::object();
if (timeseriesMode)
vol = inputMaster[timepoint];
volume<float> mask, masknz;
@@ -229,23 +217,41 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
else if (sarg == "-m")
{
if (mask.nvoxels() > 0){
- string val = to_string(vol.mean(mask));
- print_value(sarg, val, json, jsonOutput);
+ auto val = vol.mean(mask);
+ if (jsonMode){
+ update_json(sarg, val, idx);
+ } else {
+ cout << val << " ";
+ }
} else {
- string val = to_string(vol.mean());
- print_value(sarg, val, json, jsonOutput);
+ // print_value(sarg, val, json, jsonMode);
+ auto val = vol.mean();
+ if (jsonMode){
+ update_json(sarg, val, idx);
+ } else {
+ cout << val << " ";
+ }
}
}
else if (sarg == "-M")
{
- if (masknz.nvoxels() > 0)
- print_value(sarg, to_string(vol.mean(masknz)), json, jsonOutput);
+ if (masknz.nvoxels() > 0){
+ auto val = vol.mean(masknz);
+ if (jsonMode){
+ update_json(sarg, val, idx);
+ } else {
+ cout << val << " ";
+ }
+ }
else
{
double nzmean = 0;
nzmean = nonzeromean(vol);
- string val = to_string(nzmean);
- print_value(sarg, val, json, jsonOutput);
+ if (jsonMode){
+ update_json(sarg, nzmean, idx);
+ } else {
+ cout << nzmean << " ";
+ }
}
}
else if (sarg == "-X")
@@ -259,17 +265,12 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
auto coord1 = MISCMATHS::round(coord(1));
auto coord2 = MISCMATHS::round(coord(2));
auto coord3 = MISCMATHS::round(coord(3));
- string coordString = "";
- coordString.append(to_string(coord1));
- coordString.append(" ");
- coordString.append(to_string(coord2));
- coordString.append(" ");
- coordString.append(to_string(coord3));
- print_value(
- sarg,
- coordString,
- json,
- jsonOutput);
+ auto coordList = {coord1, coord2, coord3};
+ if (jsonMode){
+ update_json(sarg, coordList, idx);
+ } else {
+ cout << coord1 << " " << coord2 << " " << coord3 << " ";
+ }
}
else if (sarg == "-x")
@@ -283,17 +284,12 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
auto coord1 = MISCMATHS::round(coord(1));
auto coord2 = MISCMATHS::round(coord(2));
auto coord3 = MISCMATHS::round(coord(3));
- string coordString = "";
- coordString.append(to_string(coord1));
- coordString.append(" ");
- coordString.append(to_string(coord2));
- coordString.append(" ");
- coordString.append(to_string(coord3));
- print_value(
- sarg,
- coordString,
- json,
- jsonOutput);
+ auto coordList = {coord1, coord2, coord3};
+ if (jsonMode){
+ update_json(sarg, coordList, idx);
+ } else {
+ cout << coord1 << " " << coord2 << " " << coord3 << " ";
+ }
}
else if (sarg == "-w")
{
@@ -357,28 +353,12 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
zmax = zmin;
zmin = tmp;
}
- // now output nifti coords
- string coords = "";
- coords.append(to_string(xmin));
- coords.append(" ");
- coords.append(to_string(1 + xmax - xmin));
- coords.append(" ");
- coords.append(to_string(ymin));
- coords.append(" ");
- coords.append(to_string(1 + ymax - ymin));
- coords.append(" ");
- coords.append(to_string(zmin));
- coords.append(" ");
- coords.append(to_string(1 + zmax - zmin));
- coords.append(" ");
- coords.append(to_string(tmin));
- coords.append(" ");
- coords.append(to_string(1 + tmax - tmin));
- print_value(
- sarg,
- coords,
- json,
- jsonOutput);
+ vector<int> coords = {xmin, 1 + xmax - xmin, ymin, 1 + ymax - ymin, zmin, 1 + zmax - zmin, tmin, 1 + tmax - tmin};
+ if (jsonMode){
+ update_json(sarg, coords, idx);
+ } else {
+ cout << coords[0] << " " << coords[1] << " " << coords[2] << " " << coords[3] << " " << coords[4] << " " << coords[5] << " " << coords[6] << " " << coords[7] << " ";
+ }
}
else if (sarg == "-e")
{
@@ -400,12 +380,11 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
}
}
entropy /= log((double)nbins);
- print_value(
- sarg,
- to_string(entropy),
- json,
- jsonOutput
- );
+ if (jsonMode){
+ update_json(sarg, entropy, idx);
+ } else {
+ cout << entropy << " ";
+ }
}
else if (sarg == "-E")
{
@@ -427,12 +406,11 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
}
}
entropy /= log((double)nbins);
- print_value(
- sarg,
- to_string(entropy),
- json,
- jsonOutput
- );
+ if (jsonMode){
+ update_json(sarg, entropy, idx);
+ } else {
+ cout << entropy << " ";
+ }
}
else if (sarg == "-k")
{
@@ -547,125 +525,125 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
if (mask.tsize() == 1)
nvox = nvox * vol.tsize();
- string nvox_str = "";
- nvox_str.append(to_string(nvox));
- nvox_str.append(" ");
- nvox_str.append(to_string(nvox * vol.xdim() * vol.ydim() * vol.zdim()));
- print_value(
- sarg,
- nvox_str,
- json,
- jsonOutput
- );
+ auto volume_v = nvox * vol.xdim() * vol.ydim() * vol.zdim();
+ // promote nvox to float to maintain types in list
+ auto nvox_volume = {static_cast<float>(nvox), volume_v};
+ if (jsonMode){
+ update_json(sarg, nvox_volume, idx);
+ } else {
+ cout << nvox << " " << volume_v << " ";
+ }
}
else
{
- string nvox_str = "";
- nvox_str.append(to_string((long int)vol.nvoxels() * vol.tsize()));
- nvox_str.append(" ");
- nvox_str.append(to_string(vol.nvoxels() * vol.tsize() * vol.xdim() * vol.ydim() * vol.zdim()));
- print_value(
- sarg,
- nvox_str,
- json,
- jsonOutput);
+ long int nvox = vol.nvoxels() * vol.tsize();
+ auto volume_v = nvox * vol.xdim() * vol.ydim() * vol.zdim();
+ // promote nvox to float to maintain types in list
+ auto nvox_volume = {static_cast<float>(nvox), volume_v};
+ if (jsonMode){
+ update_json(sarg, nvox_volume, idx);
+ } else {
+ cout << nvox << " " << volume_v << " ";
+ }
}
}
else if (sarg == "-V")
{
if (masknz.nvoxels() > 0)
{
- string nvox_str = "";
- nvox_str.append(to_string((long int)masknz.sum()));
- nvox_str.append(" ");
- nvox_str.append(to_string(masknz.sum() * vol.xdim() * vol.ydim() * vol.zdim()));
- print_value(
- sarg,
- nvox_str,
- json,
- jsonOutput);
+ long int nvox = masknz.sum();
+ auto volume_V = nvox * vol.xdim() * vol.ydim() * vol.zdim();
+ // promote nvox to float to maintain types in list
+ auto nvox_volume = {static_cast<float>(nvox), volume_V};
+ if (jsonMode){
+ update_json(sarg, nvox_volume, idx);
+ } else {
+ cout << nvox << " " << volume_V << " ";
+ }
}
else
{
long int nzvox;
nzvox = nonzerocount(vol);
- string nzvox_str = "";
- nzvox_str.append(to_string(nzvox));
- nzvox_str.append(" ");
- nzvox_str.append(to_string(nzvox * vol.xdim() * vol.ydim() * vol.zdim()));
- print_value(
- sarg,
- nzvox_str,
- json,
- jsonOutput);
+ auto volume_V = nzvox * vol.xdim() * vol.ydim() * vol.zdim();
+ // promate nzvox to float to maintain types in list
+ auto nvox_volume = {static_cast<float>(nzvox), volume_V};
+ if (jsonMode){
+ update_json(sarg, nvox_volume, idx);
+ } else {
+ cout << nzvox << " " << volume_V << " ";
+ }
}
}
else if (sarg == "-D")
{
// hidden debug option!
- print_value(
- sarg,
- to_string(vol.sum()),
- json,
- jsonOutput
- );
+ auto sum = vol.sum();
+ if (jsonMode){
+ update_json(sarg, sum, idx);
+ } else {
+ cout << sum << " ";
+ }
}
else if (sarg == "-s")
{
- if (mask.nvoxels() > 0)
- print_value(
- sarg,
- to_string(vol.stddev(mask)),
- json,
- jsonOutput
- );
- else
- print_value(
- sarg,
- to_string(vol.stddev()),
- json,
- jsonOutput
- );
+ if (mask.nvoxels() > 0){
+ auto stddev = vol.stddev(mask);
+ if (jsonMode){
+ update_json(sarg, stddev, idx);
+ } else {
+ cout << stddev << " ";
+ }
+ }
+ else {
+ auto stddev = vol.stddev();
+ if (jsonMode){
+ update_json(sarg, stddev, idx);
+ } else {
+ cout << stddev << " ";
+ }
+ }
}
else if (sarg == "-S")
{
if (masknz.nvoxels() > 0)
{
- print_value(
- sarg,
- to_string(vol.stddev(masknz)),
- json,
- jsonOutput
- );
+ auto stddev = vol.stddev(masknz);
+ if (jsonMode){
+ update_json(sarg, stddev, idx);
+ } else {
+ cout << stddev << " ";
+ }
}
else
{
- print_value(
- sarg,
- to_string(nonzerostddev(vol)),
- json,
- jsonOutput
- );
+ auto stddev = nonzerostddev(vol);
+ if (jsonMode){
+ update_json(sarg, stddev, idx);
+ } else {
+ cout << stddev << " ";
+ }
}
}
else if (sarg == "-r")
{
vector<float> limits(vol.robustlimits(mask));
- print_value(
- sarg,
- to_string(limits[0]).append(" ").append(to_string(limits[1])),
- json,
- jsonOutput
- );
+ if (jsonMode){
+ update_json(sarg, limits, idx);
+ } else {
+ cout << limits[0] << " " << limits[1] << " ";
+ }
}
else if (sarg == "-R")
{
- print_value(
- sarg,
- to_string(vol.min(mask)).append(" ").append(to_string(vol.max(mask))),
- json,
- jsonOutput
- );
+ auto min_R = vol.min(mask);
+ auto max_R = vol.max(mask);
+ auto minmax_R = {min_R, max_R};
+ if (jsonMode){
+ update_json(sarg, minmax_R, idx);
+ } else {
+ cout << min_R << " " << max_R << " ";
+ }
}
else if (sarg == "-c")
{
@@ -673,12 +651,15 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
cog.SubMatrix(1, 3, 1, 1) = vol.cog();
cog(4) = 1.0;
cog = vol.newimagevox2mm_mat() * cog;
- print_value(
- sarg,
- to_string(cog(1)).append(" ").append(to_string(cog(2))).append(" ").append(to_string(cog(3))),
- json,
- jsonOutput
- );
+ // remove the last element
+ cog = cog.Rows(1, 3);
+ // reshape to a row vector
+ cog = cog.t();
+ if (jsonMode){
+ update_json(sarg, cog, idx);
+ } else {
+ cout << cog(1) << " " << cog(2) << " " << cog(3) << " ";
+ }
}
else if (sarg == "-C")
{
@@ -687,12 +668,15 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
cog.SubMatrix(1, 3, 1, 1) = vol.cog();
cog(4) = 1.0;
cog = vol.niftivox2newimagevox_mat().i() * cog;
- print_value(
- sarg,
- to_string(cog(1)).append(" ").append(to_string(cog(2))).append(" ").append(to_string(cog(3))),
- json,
- jsonOutput
- );
+ // remove the last element
+ cog = cog.Rows(1, 3);
+ // reshape to a row vector
+ cog = cog.t();
+ if (jsonMode){
+ update_json(sarg, cog, idx);
+ } else {
+ cout << cog(1) << " " << cog(2) << " " << cog(3) << " ";
+ }
}
else if (sarg == "-p")
{
@@ -712,20 +696,22 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
cerr << "Percentile must be between 0 and 100" << endl;
exit(1);
}
- if (mask.nvoxels() > 0)
- print_value(
- sarg,
- to_string(vol.percentile((float)n / 100.0, mask)),
- json,
- jsonOutput
- );
- else
- print_value(
- sarg,
- to_string(vol.percentile((float)n / 100.0)),
- json,
- jsonOutput
- );
+ if (mask.nvoxels() > 0){
+ auto percentile_p = vol.percentile((float)n / 100.0, mask);
+ if (jsonMode){
+ update_json(sarg, percentile_p, idx);
+ } else {
+ cout << percentile_p << " ";
+ }
+ }
+ else {
+ auto percentile_p = vol.percentile((float)n / 100.0);
+ if (jsonMode){
+ update_json(sarg, percentile_p, idx);
+ } else {
+ cout << percentile_p << " ";
+ }
+ }
}
else if (sarg == "-P")
{
@@ -750,12 +736,12 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
generate_masks(mask, masknz, vol, lthr, uthr);
vol *= mask;
}
- print_value(
- sarg,
- to_string(vol.percentile((float)n / 100.0, masknz)),
- json,
- jsonOutput
- );
+ auto percentile_P = vol.percentile((float)n / 100.0, masknz);
+ if (jsonMode){
+ update_json(sarg, percentile_P, idx);
+ } else {
+ cout << percentile_P << " ";
+ }
}
else if (sarg == "-h")
{
@@ -779,41 +765,20 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
if (mask.nvoxels() > 0)
{
auto hist = vol.histogram(nbins, vol.min(), vol.max(), mask);
- // loop over histogram values and and build a string to print
- string hist_str = "";
- for (int i = 0; i < hist.Nrows(); i++)
- {
- hist_str += to_string(hist(i+1));
- if (i < hist.Nrows() - 1)
- {
- hist_str += " ";
- }
+ if (jsonMode){
+ update_json(sarg, hist, idx);
+ } else {
+ cout << hist << " ";
}
- print_value(
- sarg,
- hist_str,
- json,
- jsonOutput
- );
}
else
{
auto hist = vol.histogram(nbins, vol.min(), vol.max());
- string hist_str = "";
- for (int i = 0; i < hist.Nrows(); i++)
- {
- hist_str += to_string(hist(i+1));
- if (i < hist.Nrows() - 1)
- {
- hist_str += " ";
- }
+ if (jsonMode){
+ update_json(sarg, hist, idx);
+ } else {
+ cout << hist << " ";
}
- print_value(
- sarg,
- hist_str,
- json,
- jsonOutput
- );
}
}
else if (sarg == "-H")
@@ -859,91 +824,41 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
}
if (mask.nvoxels() > 0)
{
- auto hist = vol.histogram(nbins, min, max, mask);
- string hist_str = "";
- for (int i = 0; i < hist.Nrows(); i++)
- {
- hist_str += to_string(hist(i+1));
- if (i < hist.Nrows() - 1)
- {
- hist_str += " ";
- }
+ auto hist = vol.histogram(nbins,min,max,mask);
+ if (jsonMode){
+ update_json(sarg, hist, idx);
+ } else {
+ cout << hist << " ";
}
- print_value(
- sarg,
- hist_str,
- json,
- jsonOutput
- );
}
else
{
auto hist = vol.histogram(nbins, min, max);
- string hist_str = "";
- for (int i = 0; i < hist.Nrows(); i++)
- {
- hist_str += to_string(hist(i+1));
- if (i < hist.Nrows() - 1)
- {
- hist_str += " ";
- }
+ if (jsonMode){
+ update_json(sarg, hist, idx);
+ } else {
+ cout << hist << " ";
}
- print_value(
- sarg,
- hist_str,
- json,
- jsonOutput
- );
}
}
else
{
- // only print cerr if not the --json option
- if (sarg != "--json")
- {
- cerr << "Unrecognised option: " << sarg << endl;
- exit(3);
- } else if (sarg == "--json" && last) {
- // remove the trailing comma and space
- json.pop_back();
- json.pop_back();
- }
+ cerr << "Unrecognised option: " << sarg << endl;
+ exit(3);
}
-
narg++;
}
- // if json mode is enabled
- if (jsonOutput)
- {
- // close the json object
- json.append("}");
- }
- if (index < nIndices && !jsonOutput)
- {
+ tp["indices"] += idx;
+ if (!jsonMode)
cout << endl;
- }
- // cout << endl;
} // end nIndices
- // if json mode is enabled
- if (jsonOutput)
- {
- // close the json object
- json.append("]}");
- }
- if (timepoint < nTimepoints - 1 && !jsonOutput)
- {
- cout << endl;
- }
- // cout << endl;
+ // append the timepoint to the the volumes array
+ js["volumes"] += tp;
} // end timepoints
- if (jsonOutput)
- {
- // close the json object
- json.append("]}");
- cout << json;
- } else {
- cout << endl;
- }
+ if (jsonMode){
+ // print the json with 4 spaces of indentation
+ cout << js.dump(4) << endl;
+ }
return 0;
}
@@ -953,11 +868,14 @@ int main(int argc, char *argv[])
Tracer tr("main");
string progname(argv[0]);
bool timeseriesMode(false);
+ bool jsonMode(false);
string indexMask("");
- while (argc > 2 && (string(argv[1]) == "-t" || string(argv[1]) == "-K"))
+ while (argc > 2 && (string(argv[1]) == "-t" || string(argv[1]) == "-K" || string(argv[1]) == "-json"))
{
if (string(argv[1]) == "-t")
timeseriesMode = true;
+ if (string(argv[1]) == "-json")
+ jsonMode = true;
if (string(argv[1]) == "-K")
{
indexMask = string(argv[2]);
@@ -971,7 +889,7 @@ int main(int argc, char *argv[])
return print_usage(progname);
try
{
- return fmrib_main_float(argc, argv, timeseriesMode, indexMask);
+ return fmrib_main_float(argc, argv, timeseriesMode, indexMask, jsonMode);
}
catch (std::exception &e)
{
diff --git a/tests/fslstats/feedsRun b/tests/fslstats/feedsRun
index c6d1305..a007f1d 100755
--- a/tests/fslstats/feedsRun
+++ b/tests/fslstats/feedsRun
@@ -53,6 +53,8 @@ options = [
{"option": "-v", "expected": "1000 1000.000000"},
{"option": "-V", "expected": "1000 1000.000000"},
{"option": "-m", "expected": "0.495922"},
+ {"option": "-m -a", "expected": "0.495922"},
+ {"option": "-m -a -n", "expected": "0.495922"},
{"option": "-M", "expected": "0.495922"},
{"option": "-s", "expected": "0.290744"},
{"option": "-S", "expected": "0.290744"},
@@ -63,6 +65,12 @@ options = [
{"option": "-C", "expected": "4.498706 4.545873 4.613188"},
{"option": "-p 50", "expected": "0.482584"},
{"option": "-P 50", "expected": "0.482584"},
+ {"option": "-m -h 10 -c", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000 \n 4.498706 4.545873 4.613188"},
+ {"option": "-m -h 10", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+ {"option": "-h 10", "expected": "101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+ {"option": "-H 10 0 1", "expected": "98.000000 \n102.000000 \n107.000000 \n108.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+ {"option": "-l 0.25 -u 0.75 -m", "expected": "0.495150"},
+ {"option": "-d imageForDiff.nii.gz -m", "expected": "0.000000"},
]
# create a list of tests and expected results
@@ -82,55 +90,24 @@ tests_with_preoptions = [
"preoptions": "-K",
"mask": "mask.nii.gz",
"options": "-m",
- "expected": "0.948930 \n0.947671 \n1.003258 \n1.010696",
+ "expected": "1.078044 \n1.028827 \n0.986428 \n1.020869",
},
{
"preoptions": "-t -K",
"mask": "mask.nii.gz",
"options": "-m",
- "expected": "0.459736 \n0.476035 \n0.504080 \n0.549485 \n0.489194 \n0.471636 \n0.499178 \n0.461211",
+ "expected": "0.526682 \n0.515652 \n0.492337 \n0.511661 \n0.551362 \n0.513176 \n0.494091 \n0.509208",
},
{
"preoptions": "-t",
"mask": "",
"options": "-m",
- "expected": "0.496675 \n0.487950",
+ "expected": "0.503236 \n0.504035",
},
]
-# taken from fslchpixdim test
-def create_image(shape, pixdim):
- pixdim = list(pixdim)
- data = np.random.random(shape).astype(np.float32)
- hdr = nib.Nifti1Header()
- hdr.set_data_dtype(np.float32)
- hdr.set_data_shape(shape)
- hdr.set_zooms(pixdim[:len(shape)])
-
- return nib.Nifti1Image(data, np.eye(4), hdr)
-
-def create_mask(input_img, n_rois=4):
- '''
- Create a mask image from the input image.
- The mask image will have n_rois different values with random sizes randomly placed in the image.
- '''
- data = input_img.get_fdata()
- mask = np.zeros_like(data)
- for i in range(n_rois + 1):
- roi_size = np.random.randint(1, data.size)
- roi_value = i
- roi = np.random.choice(data.size, roi_size, replace=False)
- mask.flat[roi] = roi_value
- return nib.Nifti1Image(mask, input_img.affine, input_img.header)
-
-
def test_fslstats():
imgfile = 'test.nii.gz'
- shape = (10,10,10)
- img = create_image(shape, [1] * len(shape))
- img.to_filename(imgfile)
- mask = create_mask(img)
- mask.to_filename('mask.nii.gz')
# run the tests witoout preoptions
for test in tests:
@@ -151,9 +128,6 @@ def test_fslstats():
# run the tests with preoptions
imgfile = 'test_4d.nii.gz'
- shape = (10,10,10, 2)
- img = create_image(shape, [1] * len(shape))
- img.to_filename(imgfile)
for test in tests_with_preoptions:
cmd = f"fslstats {test['preoptions']} {test['mask']} {imgfile} {test['options']}"
# remove any double spaces from empty test options
@@ -175,6 +149,4 @@ def test_fslstats():
if __name__ == "__main__":
- if len(sys.argv) > 1:
- os.chdir(sys.argv[1])
test_fslstats()
diff --git a/tests/fslstats/imageForDiff.nii.gz b/tests/fslstats/imageForDiff.nii.gz
new file mode 100644
index 0000000..f4d00fe
--- /dev/null
+++ b/tests/fslstats/imageForDiff.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:14105cd775bf8e192299695a90848e285690c2dafb086bdd8830c5665fb0394b
+size 3716
diff --git a/tests/fslstats/mask.nii.gz b/tests/fslstats/mask.nii.gz
new file mode 100644
index 0000000..3a7c155
--- /dev/null
+++ b/tests/fslstats/mask.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d9a0b1719ca95cf36b44ddcde54121fa28411d060ab0d288303c80935eb429b1
+size 786
diff --git a/tests/fslstats/test.nii.gz b/tests/fslstats/test.nii.gz
new file mode 100644
index 0000000..f4d00fe
--- /dev/null
+++ b/tests/fslstats/test.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:14105cd775bf8e192299695a90848e285690c2dafb086bdd8830c5665fb0394b
+size 3716
diff --git a/tests/fslstats/test_4d.nii.gz b/tests/fslstats/test_4d.nii.gz
new file mode 100644
index 0000000..247023d
--- /dev/null
+++ b/tests/fslstats/test_4d.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a48fc73f54d9aba889968a99d58339d495950301970f166166bede44dd38e623
+size 7304
--
GitLab
From 475ab8aa0e0cf382ed6414d16e4a983ba596837b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 26 Jun 2023 11:22:31 +0100
Subject: [PATCH 4/6] TEST: avscale is part of flirt, not avwutils
---
tests/avscale/feedsRun | 116 -----------------------------------------
1 file changed, 116 deletions(-)
delete mode 100755 tests/avscale/feedsRun
diff --git a/tests/avscale/feedsRun b/tests/avscale/feedsRun
deleted file mode 100755
index 32062a0..0000000
--- a/tests/avscale/feedsRun
+++ /dev/null
@@ -1,116 +0,0 @@
-#!/usr/bin/env fslpython
-
-# test avscale with different input affines
-
-
-import sys
-import os
-
-import fsl.utils.run as run
-
-import numpy as np
-
-
-PI = np.pi
-PION2 = np.pi / 2
-
-
-# Each test has the form (input-affine, expected-output)
-# where expected-output comprises:
-# - scales
-# - translations
-# - rotations
-# - skews
-# - L/R orientation (preserved or swapped)
-tests = [
-
- ([[1, 0, 0, 0],
- [0, 1, 0, 0],
- [0, 0, 1, 0],
- [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, 0, 0), (0, 0, 0), 'preserved']),
- ([[2, 0, 0, 0],
- [0, 2, 0, 0],
- [0, 0, 2, 0],
- [0, 0, 0, 1]], [(2, 2, 2), (0, 0, 0), (0, 0, 0), (0, 0, 0), 'preserved']),
- ([[-2, 0, 0, 0],
- [ 0, 2, 0, 0],
- [ 0, 0, 2, 0],
- [ 0, 0, 0, 1]], [(2, 2, 2), (0, 0, 0), (0, 0, PI), (0, 0, 0), 'swapped']),
- ([[0, 0, 1, 0],
- [0, 1, 0, 0],
- [1, 0, 0, 0],
- [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, -PION2, 0), (0, 0, 0), 'swapped']),
- ([[ 0, 0, -1, 0],
- [ 0, -1, 0, 0],
- [-1, 0, 0, 0],
- [ 0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (-PI, PION2, 0), (0, 0, 0), 'preserved']),
- ([[0, 1, 0, 0],
- [1, 0, 0, 0],
- [0, 0, 1, 0],
- [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, 0, PION2), (0, 0, 0), 'swapped']),
- ([[1, 0, 0, 0],
- [0, 0, 1, 0],
- [0, 1, 0, 0],
- [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (PION2, 0, 0), (0, 0, 0), 'swapped']),
- ([[-2, 0, 0, 90],
- [ 0, 2, 0, -126],
- [ 0, 0, 2, -72],
- [ 0, 0, 0, 1]], [(2, 2, 2), (90, -126, -72), (0, 0, PI), (0, 0, 0), 'swapped']),
-
-]
-
-def read_avscale_output(output):
- lines = output.split('\n')
- # scales
- # translations
- # rotations
- # skews
- # l/r orientation (preserved or swapped)
- scales = [l for l in lines if l.startswith('Scales ')] [0]
- translations = [l for l in lines if l.startswith('Translations ')] [0]
- rotations = [l for l in lines if l.startswith('Rotation Angles')][0]
- skews = [l for l in lines if l.startswith('Skews ')] [0]
- orient = [l for l in lines if l.startswith('Left-Right ')] [0]
-
- scales = [float(s) for s in scales .split()[-3:]]
- translations = [float(s) for s in translations.split()[-3:]]
- rotations = [float(s) for s in rotations .split()[-3:]]
- skews = [float(s) for s in skews .split()[-3:]]
- orient = orient.split()[-1]
-
- return {
- 'scales' : np.array(scales),
- 'translations' : np.array(translations),
- 'rotations' : np.array(rotations),
- 'skews' : np.array(skews),
- 'orient' : orient.lower(),
- }
-
-
-def test_avscale():
-
- for affine, expected in tests:
- affine = np.array(affine)
- np.savetxt('affine.mat', affine, '%0.6f')
- print(affine)
- output = run.runfsl('avscale --allparams affine.mat')
- output = read_avscale_output(output)
-
- scales, translations, rotations, skews, orient = expected
-
- try:
- assert np.all(np.isclose(scales, output['scales']))
- assert np.all(np.isclose(translations, output['translations']))
- assert np.all(np.isclose(rotations, output['rotations']))
- assert np.all(np.isclose(skews, output['skews']))
- assert orient == output['orient']
- except AssertionError:
- print(affine)
- print(output)
- raise
-
-
-if __name__ == '__main__':
- if len(sys.argv) > 1:
- os.chdir(sys.argv[1])
- test_avscale()
--
GitLab
From 6ed1dff606f4b2d92b59851531dd75782cd03cba Mon Sep 17 00:00:00 2001
From: Taylor Hanayik <hanayik@gmail.com>
Date: Mon, 26 Jun 2023 15:23:28 +0100
Subject: [PATCH 5/6] add json tests; code cleanup;
---
fslstats.cc | 2 -
tests/fslstats/feedsRun | 113 ++++++++++++++----
tests/fslstats/test_cogMM_c.json | 15 +++
tests/fslstats/test_cogVox_C.json | 15 +++
.../test_diff_d_imageForDiff.nii.gz_m.json | 11 ++
tests/fslstats/test_entropyNonzero_E.json | 11 ++
tests/fslstats/test_entropy_e.json | 11 ++
tests/fslstats/test_histLimits_H_10_0_1.json | 22 ++++
tests/fslstats/test_hist_h_10.json | 22 ++++
tests/fslstats/test_maxCoord_x.json | 15 +++
tests/fslstats/test_meanHistCog_m_h_10_c.json | 28 +++++
tests/fslstats/test_meanHist_m_h_10.json | 23 ++++
tests/fslstats/test_meanNonzero_M.json | 11 ++
tests/fslstats/test_mean_m.json | 11 ++
tests/fslstats/test_mean_m_a.json | 11 ++
tests/fslstats/test_mean_m_a_n.json | 11 ++
tests/fslstats/test_minCoord_X.json | 15 +++
tests/fslstats/test_notRobust_R.json | 14 +++
.../fslstats/test_percentileNonzero_P_50.json | 11 ++
tests/fslstats/test_percentile_p_50.json | 11 ++
...st_preopIndexMaskMeanTimeSeries_t_K_m.json | 36 ++++++
.../fslstats/test_preopIndexMaskMean_K_m.json | 20 ++++
.../test_preopMeanTimeSeries_t_m.json | 18 +++
tests/fslstats/test_robust_r.json | 14 +++
tests/fslstats/test_roi_w.json | 20 ++++
tests/fslstats/test_stdevNonzero_S.json | 11 ++
tests/fslstats/test_stdev_s.json | 11 ++
.../test_threshold_l_0.25_u_0.75_m.json | 11 ++
tests/fslstats/test_volumeNonzero_V.json | 14 +++
tests/fslstats/test_volume_v.json | 14 +++
30 files changed, 525 insertions(+), 27 deletions(-)
create mode 100644 tests/fslstats/test_cogMM_c.json
create mode 100644 tests/fslstats/test_cogVox_C.json
create mode 100644 tests/fslstats/test_diff_d_imageForDiff.nii.gz_m.json
create mode 100644 tests/fslstats/test_entropyNonzero_E.json
create mode 100644 tests/fslstats/test_entropy_e.json
create mode 100644 tests/fslstats/test_histLimits_H_10_0_1.json
create mode 100644 tests/fslstats/test_hist_h_10.json
create mode 100644 tests/fslstats/test_maxCoord_x.json
create mode 100644 tests/fslstats/test_meanHistCog_m_h_10_c.json
create mode 100644 tests/fslstats/test_meanHist_m_h_10.json
create mode 100644 tests/fslstats/test_meanNonzero_M.json
create mode 100644 tests/fslstats/test_mean_m.json
create mode 100644 tests/fslstats/test_mean_m_a.json
create mode 100644 tests/fslstats/test_mean_m_a_n.json
create mode 100644 tests/fslstats/test_minCoord_X.json
create mode 100644 tests/fslstats/test_notRobust_R.json
create mode 100644 tests/fslstats/test_percentileNonzero_P_50.json
create mode 100644 tests/fslstats/test_percentile_p_50.json
create mode 100644 tests/fslstats/test_preopIndexMaskMeanTimeSeries_t_K_m.json
create mode 100644 tests/fslstats/test_preopIndexMaskMean_K_m.json
create mode 100644 tests/fslstats/test_preopMeanTimeSeries_t_m.json
create mode 100644 tests/fslstats/test_robust_r.json
create mode 100644 tests/fslstats/test_roi_w.json
create mode 100644 tests/fslstats/test_stdevNonzero_S.json
create mode 100644 tests/fslstats/test_stdev_s.json
create mode 100644 tests/fslstats/test_threshold_l_0.25_u_0.75_m.json
create mode 100644 tests/fslstats/test_volumeNonzero_V.json
create mode 100644 tests/fslstats/test_volume_v.json
diff --git a/fslstats.cc b/fslstats.cc
index 8e90fd2..b29d9f9 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -199,11 +199,9 @@ int fmrib_main_float(int argc, char *argv[], const bool timeseriesMode, const st
generateNonZeroMask(mask, masknz, vol);
}
int narg(2);
- bool last = false;
while (narg < argc)
{
- last = !(narg < argc - 1);
string sarg(argv[narg]);
if (sarg == "-n")
{
diff --git a/tests/fslstats/feedsRun b/tests/fslstats/feedsRun
index a007f1d..8e722db 100755
--- a/tests/fslstats/feedsRun
+++ b/tests/fslstats/feedsRun
@@ -46,31 +46,31 @@ import nibabel as nib
np.random.seed(0)
options = [
- {"option": "-r", "expected": "0.018533 0.978824"},
- {"option": "-R", "expected": "0.000546 0.999809"},
- {"option": "-e", "expected": "0.906103"},
- {"option": "-E", "expected": "0.906103"},
- {"option": "-v", "expected": "1000 1000.000000"},
- {"option": "-V", "expected": "1000 1000.000000"},
- {"option": "-m", "expected": "0.495922"},
- {"option": "-m -a", "expected": "0.495922"},
- {"option": "-m -a -n", "expected": "0.495922"},
- {"option": "-M", "expected": "0.495922"},
- {"option": "-s", "expected": "0.290744"},
- {"option": "-S", "expected": "0.290744"},
- {"option": "-w", "expected": "0 10 0 10 0 10 0 1"},
- {"option": "-x", "expected": "9 7 4"},
- {"option": "-X", "expected": "8 2 1"},
- {"option": "-c", "expected": "4.498706 4.545873 4.613188"},
- {"option": "-C", "expected": "4.498706 4.545873 4.613188"},
- {"option": "-p 50", "expected": "0.482584"},
- {"option": "-P 50", "expected": "0.482584"},
- {"option": "-m -h 10 -c", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000 \n 4.498706 4.545873 4.613188"},
- {"option": "-m -h 10", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
- {"option": "-h 10", "expected": "101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
- {"option": "-H 10 0 1", "expected": "98.000000 \n102.000000 \n107.000000 \n108.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
- {"option": "-l 0.25 -u 0.75 -m", "expected": "0.495150"},
- {"option": "-d imageForDiff.nii.gz -m", "expected": "0.000000"},
+ {"name": "robust", "option": "-r", "expected": "0.018533 0.978824"},
+ {"name": "notRobust", "option": "-R", "expected": "0.000546 0.999809"},
+ {"name": "entropy", "option": "-e", "expected": "0.906103"},
+ {"name": "entropyNonzero", "option": "-E", "expected": "0.906103"},
+ {"name": "volume", "option": "-v", "expected": "1000 1000.000000"},
+ {"name": "volumeNonzero", "option": "-V", "expected": "1000 1000.000000"},
+ {"name": "mean", "option": "-m", "expected": "0.495922"},
+ {"name": "mean", "option": "-m -a", "expected": "0.495922"},
+ {"name": "mean", "option": "-m -a -n", "expected": "0.495922"},
+ {"name": "meanNonzero", "option": "-M", "expected": "0.495922"},
+ {"name": "stdev", "option": "-s", "expected": "0.290744"},
+ {"name": "stdevNonzero", "option": "-S", "expected": "0.290744"},
+ {"name": "roi","option": "-w", "expected": "0 10 0 10 0 10 0 1"},
+ {"name": "maxCoord", "option": "-x", "expected": "9 7 4"},
+ {"name": "minCoord", "option": "-X", "expected": "8 2 1"},
+ {"name": "cogMM", "option": "-c", "expected": "4.498706 4.545873 4.613188"},
+ {"name": "cogVox","option": "-C", "expected": "4.498706 4.545873 4.613188"},
+ {"name": "percentile", "option": "-p 50", "expected": "0.482584"},
+ {"name": "percentileNonzero","option": "-P 50", "expected": "0.482584"},
+ {"name": "meanHistCog", "option": "-m -h 10 -c", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000 \n 4.498706 4.545873 4.613188"},
+ {"name": "meanHist", "option": "-m -h 10", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+ {"name": "hist", "option": "-h 10", "expected": "101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+ {"name": "histLimits", "option": "-H 10 0 1", "expected": "98.000000 \n102.000000 \n107.000000 \n108.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+ {"name": "threshold", "option": "-l 0.25 -u 0.75 -m", "expected": "0.495150"},
+ {"name": "diff", "option": "-d imageForDiff.nii.gz -m", "expected": "0.000000"},
]
# create a list of tests and expected results
@@ -82,6 +82,7 @@ for option in options:
"mask": "",
"options": option["option"],
"expected": option["expected"],
+ "name": option["name"],
}
)
@@ -91,21 +92,49 @@ tests_with_preoptions = [
"mask": "mask.nii.gz",
"options": "-m",
"expected": "1.078044 \n1.028827 \n0.986428 \n1.020869",
+ "name": "preopIndexMaskMean",
},
{
"preoptions": "-t -K",
"mask": "mask.nii.gz",
"options": "-m",
"expected": "0.526682 \n0.515652 \n0.492337 \n0.511661 \n0.551362 \n0.513176 \n0.494091 \n0.509208",
+ "name": "preopIndexMaskMeanTimeSeries",
},
{
"preoptions": "-t",
"mask": "",
"options": "-m",
"expected": "0.503236 \n0.504035",
+ "name": "preopMeanTimeSeries",
},
]
+json_tests = []
+for option in options:
+ file_string = f"test_{option['name']}_{option['option'].replace(' ', '_')}.json"
+ file_string = file_string.replace("-", "")
+ json_tests.append(
+ {
+ "preoptions": "",
+ "mask": "",
+ "options": option["option"],
+ "expected": file_string,
+ }
+ )
+
+for option in tests_with_preoptions:
+ file_string = f"test_{option['name']}_{option['preoptions'].replace(' ', '_')}_{option['options'].replace(' ', '_')}.json"
+ file_string = file_string.replace("-", "")
+ json_tests.append(
+ {
+ "preoptions": option["preoptions"],
+ "mask": option["mask"],
+ "options": option["options"],
+ "expected": file_string,
+ }
+ )
+
def test_fslstats():
imgfile = 'test.nii.gz'
@@ -121,8 +150,11 @@ def test_fslstats():
try:
assert output == test["expected"]
except AssertionError:
+ print('Failed test')
print(cmd)
+ print('Output')
print(output)
+ print('Expected')
print(test["expected"])
raise
@@ -147,6 +179,37 @@ def test_fslstats():
print(test["expected"])
raise
+ # run the json tests
+ for test in json_tests:
+ cmd = f"fslstats -json {test['preoptions']} {test['mask']} {imgfile} {test['options']}"
+ # remove any double spaces from empty test options
+ cmd = " ".join(cmd.split())
+ print(cmd, flush=True)
+ output = run.runfsl(cmd)
+
+ # try to load the expected json file
+ # if it exists, compare the output to the expected
+ try:
+ print(test["expected"])
+ with open(test["expected"], "r") as json_file:
+ # read the file as a string
+ expected = json_file.read()
+ try:
+ assert output == expected
+ except AssertionError:
+ print('Failed test')
+ print(cmd)
+ print('Output')
+ print(output)
+ print('Expected')
+ print(expected)
+ raise
+ except FileNotFoundError:
+ # if the expected json file doesn't exist, create it from the output
+ # usefull for creating new tests or the first time a test is run
+ with open(test["expected"], "w") as json_file:
+ json_file.write(output)
+
if __name__ == "__main__":
test_fslstats()
diff --git a/tests/fslstats/test_cogMM_c.json b/tests/fslstats/test_cogMM_c.json
new file mode 100644
index 0000000..758ec3c
--- /dev/null
+++ b/tests/fslstats/test_cogMM_c.json
@@ -0,0 +1,15 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-c": [
+ 4.505939956803816,
+ 4.486097425091172,
+ 4.488288600081377
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_cogVox_C.json b/tests/fslstats/test_cogVox_C.json
new file mode 100644
index 0000000..1b6b7b0
--- /dev/null
+++ b/tests/fslstats/test_cogVox_C.json
@@ -0,0 +1,15 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-C": [
+ 4.505939956803816,
+ 4.486097425091172,
+ 4.488288600081377
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_diff_d_imageForDiff.nii.gz_m.json b/tests/fslstats/test_diff_d_imageForDiff.nii.gz_m.json
new file mode 100644
index 0000000..76d250a
--- /dev/null
+++ b/tests/fslstats/test_diff_d_imageForDiff.nii.gz_m.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.0077142266542650755
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_entropyNonzero_E.json b/tests/fslstats/test_entropyNonzero_E.json
new file mode 100644
index 0000000..9573a6e
--- /dev/null
+++ b/tests/fslstats/test_entropyNonzero_E.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-E": 0.9468094676591793
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_entropy_e.json b/tests/fslstats/test_entropy_e.json
new file mode 100644
index 0000000..407d186
--- /dev/null
+++ b/tests/fslstats/test_entropy_e.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-e": 0.9468094676591793
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_histLimits_H_10_0_1.json b/tests/fslstats/test_histLimits_H_10_0_1.json
new file mode 100644
index 0000000..4ce81ec
--- /dev/null
+++ b/tests/fslstats/test_histLimits_H_10_0_1.json
@@ -0,0 +1,22 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-H": [
+ 193.0,
+ 220.0,
+ 194.0,
+ 201.0,
+ 190.0,
+ 184.0,
+ 191.0,
+ 199.0,
+ 200.0,
+ 228.0
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_hist_h_10.json b/tests/fslstats/test_hist_h_10.json
new file mode 100644
index 0000000..2e210d2
--- /dev/null
+++ b/tests/fslstats/test_hist_h_10.json
@@ -0,0 +1,22 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-h": [
+ 198.0,
+ 216.0,
+ 194.0,
+ 200.0,
+ 190.0,
+ 184.0,
+ 191.0,
+ 199.0,
+ 199.0,
+ 229.0
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_maxCoord_x.json b/tests/fslstats/test_maxCoord_x.json
new file mode 100644
index 0000000..1a20172
--- /dev/null
+++ b/tests/fslstats/test_maxCoord_x.json
@@ -0,0 +1,15 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-x": [
+ 4,
+ 8,
+ 7
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_meanHistCog_m_h_10_c.json b/tests/fslstats/test_meanHistCog_m_h_10_c.json
new file mode 100644
index 0000000..58380fd
--- /dev/null
+++ b/tests/fslstats/test_meanHistCog_m_h_10_c.json
@@ -0,0 +1,28 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-c": [
+ 4.505939956803816,
+ 4.486097425091172,
+ 4.488288600081377
+ ],
+ "-h": [
+ 198.0,
+ 216.0,
+ 194.0,
+ 200.0,
+ 190.0,
+ 184.0,
+ 191.0,
+ 199.0,
+ 199.0,
+ 229.0
+ ],
+ "-m": 0.5036357601464115
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_meanHist_m_h_10.json b/tests/fslstats/test_meanHist_m_h_10.json
new file mode 100644
index 0000000..c8316e5
--- /dev/null
+++ b/tests/fslstats/test_meanHist_m_h_10.json
@@ -0,0 +1,23 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-h": [
+ 198.0,
+ 216.0,
+ 194.0,
+ 200.0,
+ 190.0,
+ 184.0,
+ 191.0,
+ 199.0,
+ 199.0,
+ 229.0
+ ],
+ "-m": 0.5036357601464115
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_meanNonzero_M.json b/tests/fslstats/test_meanNonzero_M.json
new file mode 100644
index 0000000..e7892ba
--- /dev/null
+++ b/tests/fslstats/test_meanNonzero_M.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-M": 0.5036357601464115
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_mean_m.json b/tests/fslstats/test_mean_m.json
new file mode 100644
index 0000000..3763ba8
--- /dev/null
+++ b/tests/fslstats/test_mean_m.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.5036357601464115
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_mean_m_a.json b/tests/fslstats/test_mean_m_a.json
new file mode 100644
index 0000000..3763ba8
--- /dev/null
+++ b/tests/fslstats/test_mean_m_a.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.5036357601464115
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_mean_m_a_n.json b/tests/fslstats/test_mean_m_a_n.json
new file mode 100644
index 0000000..3763ba8
--- /dev/null
+++ b/tests/fslstats/test_mean_m_a_n.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.5036357601464115
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_minCoord_X.json b/tests/fslstats/test_minCoord_X.json
new file mode 100644
index 0000000..aa72b2e
--- /dev/null
+++ b/tests/fslstats/test_minCoord_X.json
@@ -0,0 +1,15 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-X": [
+ 8,
+ 1,
+ 6
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_notRobust_R.json b/tests/fslstats/test_notRobust_R.json
new file mode 100644
index 0000000..b5b7acd
--- /dev/null
+++ b/tests/fslstats/test_notRobust_R.json
@@ -0,0 +1,14 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-R": [
+ 0.00036734374589286745,
+ 0.9998085498809814
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_percentileNonzero_P_50.json b/tests/fslstats/test_percentileNonzero_P_50.json
new file mode 100644
index 0000000..47aeceb
--- /dev/null
+++ b/tests/fslstats/test_percentileNonzero_P_50.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-P": 0.5013243556022644
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_percentile_p_50.json b/tests/fslstats/test_percentile_p_50.json
new file mode 100644
index 0000000..a105e7c
--- /dev/null
+++ b/tests/fslstats/test_percentile_p_50.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-p": 0.5013243556022644
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_preopIndexMaskMeanTimeSeries_t_K_m.json b/tests/fslstats/test_preopIndexMaskMeanTimeSeries_t_K_m.json
new file mode 100644
index 0000000..9f0e754
--- /dev/null
+++ b/tests/fslstats/test_preopIndexMaskMeanTimeSeries_t_K_m.json
@@ -0,0 +1,36 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.5266819608311916
+ },
+ {
+ "-m": 0.5156517274568186
+ },
+ {
+ "-m": 0.49233699466459285
+ },
+ {
+ "-m": 0.5116614613561304
+ }
+ ]
+ },
+ {
+ "indices": [
+ {
+ "-m": 0.5513619920395724
+ },
+ {
+ "-m": 0.5131755568141885
+ },
+ {
+ "-m": 0.49409089087108476
+ },
+ {
+ "-m": 0.5092079986783641
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_preopIndexMaskMean_K_m.json b/tests/fslstats/test_preopIndexMaskMean_K_m.json
new file mode 100644
index 0000000..fd62a2f
--- /dev/null
+++ b/tests/fslstats/test_preopIndexMaskMean_K_m.json
@@ -0,0 +1,20 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 1.078043952870764
+ },
+ {
+ "-m": 1.0288272842710071
+ },
+ {
+ "-m": 0.9864278855356776
+ },
+ {
+ "-m": 1.0208694600344945
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_preopMeanTimeSeries_t_m.json b/tests/fslstats/test_preopMeanTimeSeries_t_m.json
new file mode 100644
index 0000000..b2b481f
--- /dev/null
+++ b/tests/fslstats/test_preopMeanTimeSeries_t_m.json
@@ -0,0 +1,18 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.503236498022452
+ }
+ ]
+ },
+ {
+ "indices": [
+ {
+ "-m": 0.504035022270371
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_robust_r.json b/tests/fslstats/test_robust_r.json
new file mode 100644
index 0000000..9810ac1
--- /dev/null
+++ b/tests/fslstats/test_robust_r.json
@@ -0,0 +1,14 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-r": [
+ 0.018357284367084503,
+ 0.982818067073822
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_roi_w.json b/tests/fslstats/test_roi_w.json
new file mode 100644
index 0000000..d023769
--- /dev/null
+++ b/tests/fslstats/test_roi_w.json
@@ -0,0 +1,20 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-w": [
+ 0,
+ 10,
+ 0,
+ 10,
+ 0,
+ 10,
+ 0,
+ 2
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_stdevNonzero_S.json b/tests/fslstats/test_stdevNonzero_S.json
new file mode 100644
index 0000000..cdb0547
--- /dev/null
+++ b/tests/fslstats/test_stdevNonzero_S.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-S": 0.2949828225878523
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_stdev_s.json b/tests/fslstats/test_stdev_s.json
new file mode 100644
index 0000000..b473581
--- /dev/null
+++ b/tests/fslstats/test_stdev_s.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-s": 0.29498282199940035
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_threshold_l_0.25_u_0.75_m.json b/tests/fslstats/test_threshold_l_0.25_u_0.75_m.json
new file mode 100644
index 0000000..6712e13
--- /dev/null
+++ b/tests/fslstats/test_threshold_l_0.25_u_0.75_m.json
@@ -0,0 +1,11 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-m": 0.49646345829352356
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_volumeNonzero_V.json b/tests/fslstats/test_volumeNonzero_V.json
new file mode 100644
index 0000000..9a1ed33
--- /dev/null
+++ b/tests/fslstats/test_volumeNonzero_V.json
@@ -0,0 +1,14 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-V": [
+ 2000.0,
+ 2000.0
+ ]
+ }
+ ]
+ }
+ ]
+}
diff --git a/tests/fslstats/test_volume_v.json b/tests/fslstats/test_volume_v.json
new file mode 100644
index 0000000..5e4fb29
--- /dev/null
+++ b/tests/fslstats/test_volume_v.json
@@ -0,0 +1,14 @@
+{
+ "volumes": [
+ {
+ "indices": [
+ {
+ "-v": [
+ 2000.0,
+ 2000.0
+ ]
+ }
+ ]
+ }
+ ]
+}
--
GitLab
From 2eb99bb1f2a6cce96a7b038b0053de573f8bfbac Mon Sep 17 00:00:00 2001
From: Taylor Hanayik <hanayik@gmail.com>
Date: Mon, 26 Jun 2023 17:19:04 +0100
Subject: [PATCH 6/6] update expected values for FSL 6.0.6.5
---
Makefile | 2 +-
tests/fslstats/feedsRun | 2 +-
tests/fslstats/test_preopIndexMaskMean_K_m.json | 8 ++++----
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/Makefile b/Makefile
index 29eaa0c..b1692d3 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ PROJNAME = avwutils
LIBS = -lfsl-newimage -lfsl-miscmaths -lfsl-cprob -lfsl-NewNifti -lfsl-utils -lfsl-znz
XFILES = fslorient fslstats fslmerge \
- fslpspec fslroi fslnvols fsl2ascii fslascii2img \
+ fslpspec fslroi fslnvols fsl2ascii fslascii2img \
fslsplit fslcc fslinterleave \
fslhd fslcpgeom fslcreatehd fslmaths \
fslcomplex fslfft fslmeants fslslice fslswapdim_exe \
diff --git a/tests/fslstats/feedsRun b/tests/fslstats/feedsRun
index 8e722db..6e6c725 100755
--- a/tests/fslstats/feedsRun
+++ b/tests/fslstats/feedsRun
@@ -91,7 +91,7 @@ tests_with_preoptions = [
"preoptions": "-K",
"mask": "mask.nii.gz",
"options": "-m",
- "expected": "1.078044 \n1.028827 \n0.986428 \n1.020869",
+ "expected": "0.539022 \n0.514414 \n0.493214 \n0.510435",
"name": "preopIndexMaskMean",
},
{
diff --git a/tests/fslstats/test_preopIndexMaskMean_K_m.json b/tests/fslstats/test_preopIndexMaskMean_K_m.json
index fd62a2f..13bd72e 100644
--- a/tests/fslstats/test_preopIndexMaskMean_K_m.json
+++ b/tests/fslstats/test_preopIndexMaskMean_K_m.json
@@ -3,16 +3,16 @@
{
"indices": [
{
- "-m": 1.078043952870764
+ "-m": 0.539021976435382
},
{
- "-m": 1.0288272842710071
+ "-m": 0.5144136421355036
},
{
- "-m": 0.9864278855356776
+ "-m": 0.4932139427678388
},
{
- "-m": 1.0208694600344945
+ "-m": 0.5104347300172473
}
]
}
--
GitLab