diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000000000000000000000000000000000000..07f04632fc22dee40c5f68bde9406197619cb128
--- /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 83a987301fa76c02be5faef947a71d6acf180485..8e90fd22080a2e5a0917f1cccbf5eba447e2b46e 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 c6d130521f54644eec25efea7243e2b4c08204b4..a007f1dd74c02c6dcb61231246aa462a4af03f61 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 0000000000000000000000000000000000000000..f4d00fe3675aa6b9dd763c59d6da23ec402c2b17
--- /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 0000000000000000000000000000000000000000..3a7c1553ca342e57efe8b8ffd49bd880b6832c7f
--- /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 0000000000000000000000000000000000000000..f4d00fe3675aa6b9dd763c59d6da23ec402c2b17
--- /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 0000000000000000000000000000000000000000..247023d54a81d5c7994b0561ed2fc17768cbf514
--- /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