[MAINT] rename test data dir (#988)

* fix submodules

* rename test data dir

* readd ignored folders

.gitignore

@@ -32,6 +32,8 @@ onsets*_events.mat
 ## from running tests in root dir
 */group/*
 models/*
+derivatives/models
+derivatives/options
 
 ###############################################################################
 # python

.gitmodules

@@ -2,10 +2,6 @@
 	path = lib/bids-matlab
 	url = https://github.com/bids-standard/bids-matlab.git
 	branch = dev
-[submodule "lib/spmup"]
-	path = lib/spmup
-	url = https://github.com/CPernet/spmup.git
-	branch = master
 [submodule "lib/CPP_ROI"]
 	path = lib/CPP_ROI
 	url = https://github.com/cpp-lln-lab/CPP_ROI.git

README.md

@@ -4,7 +4,7 @@
   [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/cpp-lln-lab/bidspm/main.svg)](https://results.pre-commit.ci/latest/github/cpp-lln-lab/bidspm/main)
   [![miss hit](https://img.shields.io/badge/code%20style-miss_hit-000000.svg)](https://misshit.org/)
   [![Documentation Status: main](https://readthedocs.org/projects/bidspm/badge/?version=stable)](https://bidspm.readthedocs.io/en/stable/?badge=stable)
-  [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/bidspm/dev)
+  [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/bidspm/main)
   [![tests](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests.yml)
   [![codecov](https://codecov.io/gh/cpp-lln-lab/bidspm/branch/main/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/bidspm)
   [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3554331.svg)](https://doi.org/10.5281/zenodo.3554331)

docs/source/bids_stats_model.md

@@ -462,12 +462,12 @@ their datasets.
 
 Several of the [demos](demos) have their own model and you can find several
 "dummy" models (without corresponding data) used for testing
-[in this folder](https://github.com/cpp-lln-lab/bidspm/tree/main/tests/dummyData/models).
+[in this folder](https://github.com/cpp-lln-lab/bidspm/tree/main/tests/data/models).
 
 <!-- markdown-link-check-enable -->
 
 An example of JSON file could look something like that:
 
-```{literalinclude} ../../tests/dummyData/models/model-vislocalizer_smdl.json
+```{literalinclude} ../../tests/data/models/model-vislocalizer_smdl.json
    :language: json
 ```

tests/.gitignore

@@ -10,19 +10,21 @@ tmp
 
 */*.json
 
-dummyData/derivatives/bidspm-*/jobs
-dummyData/derivatives/bidspm-preproc/sub*
+data/derivatives/bidspm-*/jobs
+data/derivatives/bidspm-preproc/sub*
 
-dummyData/derivatives/bidspm-preproc/desc-skullstripped.json
+data/derivatives/bidspm-preproc/desc-skullstripped.json
 
-dummyData/derivatives/bidspm-stats/sub*
-dummyData/derivatives/bidspm-stats/derivatives
-dummyData/derivatives/bidspm-stats/README
-dummyData/derivatives/bidspm-stats/CHANGES
-dummyData/derivatives/bidspm-stats/*.json
+data/derivatives/bidspm-stats/sub*
+data/derivatives/bidspm-stats/derivatives
+data/derivatives/bidspm-stats/README
+data/derivatives/bidspm-stats/CHANGES
+data/derivatives/bidspm-stats/*.json
+data/derivatives/bidspm-stats/LICENSE
+data/derivatives/bidspm-stats/.gitignore
 
-dummyData/bidspm-raw/sub*
+data/bidspm-raw/sub*
 
-dummyData/derivatives/bidspm-roi
+data/derivatives/bidspm-roi
 
 test_reports/*.md

tests/Makefile

@@ -3,20 +3,21 @@ clean: clean_local
 	mkdir bids-examples && touch bids-examples/.gitkeep
 
 clean_local:
-	rm -rf dummyData/derivatives/bidspm-preproc/sub-*
-	rm -rf dummyData/derivatives/bidspm-stats/sub-*
-	rm -rf dummyData/bidspm-raw/sub-*
-	rm -rf dummyData/derivatives/bidspm-stats/group
-	rm -rf dummyData/derivatives/bidspm-*/jobs
+	rm -rf data/derivatives/bidspm-preproc/sub-*
+	rm -rf data/derivatives/bidspm-stats/sub-*
+	rm -rf data/bidspm-raw/sub-*
+	rm -rf data/derivatives/bidspm-stats/group
+	rm -rf data/derivatives/bidspm-*/jobs
 
 data: clean
 	sh createDummyDataSet.sh
 	rm -rf bids-examples/
 	git clone https://github.com/bids-standard/bids-examples.git --depth 1
 	cp bids-examples/synthetic/dataset_description.json bids-examples/synthetic/derivatives/fmriprep
 	touch bids-examples/.gitkeep
-	wget -O moae_spm12.zip https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=
-	unzip -d ./dummyData/MoAE/derivatives/spm12 moae_spm12.zip
+	wget --quiet -O moae_spm12.zip https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=
+	mkdir -p data/MoAE/derivatives/spm12
+	unzip -d ./data/MoAE/derivatives/spm12 moae_spm12.zip
 
 clean_openneuro:
 	rm -rf openneuro/*

tests/createDummyDataSet.sh

@@ -4,10 +4,10 @@
 
 # defines where the BIDS data set will be created
 start_dir=$(pwd) # relative to starting directory
-raw_dir=${start_dir}/dummyData/bidspm-raw
-preproc_dir=${start_dir}/dummyData/derivatives/bidspm-preproc
-stats_dir=${start_dir}/dummyData/derivatives/bidspm-stats
-roi_dir=${start_dir}/dummyData/derivatives/bidspm-roi
+raw_dir=${start_dir}/data/bidspm-raw
+preproc_dir=${start_dir}/data/derivatives/bidspm-preproc
+stats_dir=${start_dir}/data/derivatives/bidspm-stats
+roi_dir=${start_dir}/data/derivatives/bidspm-roi
 
 subject_list='ctrl01 blind01 01'
 session_list='01 02'
@@ -231,8 +231,8 @@ for subject in ${subject_list}; do
 			for run in $(seq 1 2); do
 
 				filename=${this_dir}/rp_${basename}_run-${run}${suffix}.txt
-				cp dummyData/tsv_files/rp.txt "${filename}"
-				cp dummyData/tsv_files/rp.tsv ${this_dir}/${basename}_run-${run}_desc-confounds_regressors.tsv
+				cp data/tsv_files/rp.txt "${filename}"
+				cp data/tsv_files/rp.tsv ${this_dir}/${basename}_run-${run}_desc-confounds_regressors.tsv
 
 				for desc in ${desc_label_list}; do
 					touch ${this_dir}/${basename}_run-${run}_space-individual_desc-${desc}${suffix}.nii
@@ -259,8 +259,8 @@ for subject in ${subject_list}; do
 
 		### derivatives
 		filename=${this_dir}/rp_sub-${subject}_ses-${ses}_task-${task_name}${suffix}.txt
-		cp dummyData/tsv_files/rp.txt "${filename}"
-		cp dummyData/tsv_files/rp.tsv ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_desc-confounds_regressors.tsv
+		cp data/tsv_files/rp.txt "${filename}"
+		cp data/tsv_files/rp.tsv ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_desc-confounds_regressors.tsv
 
 		desc_label_list='preproc smth6'
 		for desc in ${desc_label_list}; do
@@ -333,7 +333,7 @@ for subject in ${subject_list}; do
 		this_dir=${stats_dir}/sub-${subject}/task-${task}_space-IXI549Space_FWHM-6
 		mkdir -p ${this_dir}
 
-		cp dummyData/mat_files/SPM.mat ${this_dir}/SPM.mat
+		cp data/mat_files/SPM.mat ${this_dir}/SPM.mat
 
 		touch ${this_dir}/mask.nii
 
@@ -354,7 +354,7 @@ for subject in ${subject_list}; do
 		this_dir=${stats_dir}/sub-${subject}/task-${task}_space-IXI549Space_FWHM-6_node-globalSignal
 		mkdir -p ${this_dir}
 
-		cp dummyData/mat_files/SPM.mat ${this_dir}/SPM.mat
+		cp data/mat_files/SPM.mat ${this_dir}/SPM.mat
 
 		touch ${this_dir}/mask.nii
 

tests/data/MoAE/derivatives/bidspm-preproc/desc-skullstripped.json

@@ -0,0 +1,3 @@
+{
+  "SkullStripped": true
+}

tests/data/MoAE/derivatives/bidspm-preproc/jobs/auditory/sub-01/batch_spatial_preprocessing-individual-IXI549Space_2023-04-21T10-32.json

@@ -0,0 +1,20 @@
+{
+  "GeneratedBy": {
+    "name": "bidspm",
+    "Version": "v3.0.0",
+    "Branch": "concat",
+    "Commit": "7de59742",
+    "Description": "spatial_preprocessing-individual-IXI549Space",
+    "CodeURL": "https://github.com/cpp-lln-lab/bidspm",
+    "DOI": "https://doi.org/10.5281/zenodo.3554331"
+  },
+  "OS": {
+    "name": "unix",
+    "version": "Linux version 5.19.0-40-generic (buildd@lcy02-amd64-047) (x86_64-linux-gnu-gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #41~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 31 16:00:14 UTC 2\n",
+    "platform": {
+      "name": "MATLAB",
+      "version": "9.4.0.813654 (R2018a)"
+    },
+    "spmVersion": "SPM12 - 7771"
+  }
+}

tests/data/MoAE/derivatives/bidspm-preproc/jobs/auditory/sub-01/batch_spatial_preprocessing-individual_2023-04-21T10-32.json

@@ -0,0 +1,20 @@
+{
+  "GeneratedBy": {
+    "name": "bidspm",
+    "Version": "v3.0.0",
+    "Branch": "concat",
+    "Commit": "7de59742",
+    "Description": "spatial_preprocessing-individual",
+    "CodeURL": "https://github.com/cpp-lln-lab/bidspm",
+    "DOI": "https://doi.org/10.5281/zenodo.3554331"
+  },
+  "OS": {
+    "name": "unix",
+    "version": "Linux version 5.19.0-40-generic (buildd@lcy02-amd64-047) (x86_64-linux-gnu-gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #41~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 31 16:00:14 UTC 2\n",
+    "platform": {
+      "name": "MATLAB",
+      "version": "9.4.0.813654 (R2018a)"
+    },
+    "spmVersion": "SPM12 - 7771"
+  }
+}

tests/data/MoAE/derivatives/bidspm-preproc/jobs/auditory/sub-01/batch_spatial_preprocessing_individual_2023_04_21T10_32.m

@@ -0,0 +1,65 @@
+matlabbatch{1}.cfg_basicio.cfg_named_file.name = 'Anatomical';
+matlabbatch{1}.cfg_basicio.cfg_named_file.files = {{'/home/remi/github/bidspm/tests/data/MoAE/derivatives/bidspm-preproc/sub-01/anat/sub-01_T1w.nii'}};
+matlabbatch{2}.spm.spatial.realignunwarp.eoptions.weight = {''};
+matlabbatch{2}.spm.spatial.realignunwarp.uwroptions.uwwhich = [2 1];
+matlabbatch{2}.spm.spatial.realignunwarp.data.pmscan = {''};
+matlabbatch{2}.spm.spatial.realignunwarp.data.scans = {'/home/remi/github/bidspm/tests/data/MoAE/derivatives/bidspm-preproc/sub-01/func/sub-01_task-auditory_bold.nii'};
+matlabbatch{3}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Named File Selector: Anatomical(1) - Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files', '{}',{1}));
+matlabbatch{3}.spm.spatial.coreg.estimate.source(1) = cfg_dep('Realign: Estimate & Reslice/Unwarp: Mean Image', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','meanuwr'));
+matlabbatch{3}.spm.spatial.coreg.estimate.other(1) = cfg_dep('Realign: Estimate & Reslice/Unwarp: Realigned Images (Sess 1)', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','uwrfiles'));
+matlabbatch{4}.cfg_basicio.var_ops.cfg_save_vars.name = 'sub-01_task-auditory_from-scanner_to-T1w_mode-image_xfm.mat';
+matlabbatch{4}.cfg_basicio.var_ops.cfg_save_vars.outdir = {'/home/remi/github/bidspm/tests/data/MoAE/derivatives/bidspm-preproc/sub-01/func'};
+matlabbatch{4}.cfg_basicio.var_ops.cfg_save_vars.vars.vname = 'transformationMatrix';
+matlabbatch{4}.cfg_basicio.var_ops.cfg_save_vars.vars.vcont(1) = cfg_dep('Coregister: Estimate: Coregistration Matrix', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','M'));
+matlabbatch{4}.cfg_basicio.var_ops.cfg_save_vars.saveasstruct = false;
+matlabbatch{5}.spm.spatial.preproc.channel.write = [false true];
+matlabbatch{5}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Named File Selector: Anatomical(1) - Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files', '{}',{1}));
+matlabbatch{5}.spm.spatial.preproc.channel.biasreg = 0.001;
+matlabbatch{5}.spm.spatial.preproc.channel.biasfwhm = 60;
+matlabbatch{5}.spm.spatial.preproc.tissue(1).tpm = {'/home/remi/github/spm12/tpm/TPM.nii,1'};
+matlabbatch{5}.spm.spatial.preproc.tissue(1).ngaus = 1;
+matlabbatch{5}.spm.spatial.preproc.tissue(1).native = [1 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(1).warped = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(2).tpm = {'/home/remi/github/spm12/tpm/TPM.nii,2'};
+matlabbatch{5}.spm.spatial.preproc.tissue(2).ngaus = 1;
+matlabbatch{5}.spm.spatial.preproc.tissue(2).native = [1 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(2).warped = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(3).tpm = {'/home/remi/github/spm12/tpm/TPM.nii,3'};
+matlabbatch{5}.spm.spatial.preproc.tissue(3).ngaus = 2;
+matlabbatch{5}.spm.spatial.preproc.tissue(3).native = [1 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(3).warped = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(4).tpm = {'/home/remi/github/spm12/tpm/TPM.nii,4'};
+matlabbatch{5}.spm.spatial.preproc.tissue(4).ngaus = 3;
+matlabbatch{5}.spm.spatial.preproc.tissue(4).native = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(4).warped = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(5).tpm = {'/home/remi/github/spm12/tpm/TPM.nii,5'};
+matlabbatch{5}.spm.spatial.preproc.tissue(5).ngaus = 4;
+matlabbatch{5}.spm.spatial.preproc.tissue(5).native = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(5).warped = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(6).tpm = {'/home/remi/github/spm12/tpm/TPM.nii,6'};
+matlabbatch{5}.spm.spatial.preproc.tissue(6).ngaus = 2;
+matlabbatch{5}.spm.spatial.preproc.tissue(6).native = [0 0];
+matlabbatch{5}.spm.spatial.preproc.tissue(6).warped = [0 0];
+matlabbatch{5}.spm.spatial.preproc.warp.mrf = 1;
+matlabbatch{5}.spm.spatial.preproc.warp.cleanup = 1;
+matlabbatch{5}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
+matlabbatch{5}.spm.spatial.preproc.warp.affreg = 'mni';
+matlabbatch{5}.spm.spatial.preproc.warp.fwhm = 0;
+matlabbatch{5}.spm.spatial.preproc.warp.samp = 3;
+matlabbatch{5}.spm.spatial.preproc.warp.write = [1 1];
+matlabbatch{6}.spm.util.imcalc.input(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));
+matlabbatch{6}.spm.util.imcalc.input(2) = cfg_dep('Segment: c1 Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','tiss', '()',{1}, '.','c', '()',{':'}));
+matlabbatch{6}.spm.util.imcalc.input(3) = cfg_dep('Segment: c2 Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','tiss', '()',{2}, '.','c', '()',{':'}));
+matlabbatch{6}.spm.util.imcalc.input(4) = cfg_dep('Segment: c3 Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','tiss', '()',{3}, '.','c', '()',{':'}));
+matlabbatch{6}.spm.util.imcalc.output = 'sub-01_space-individual_desc-skullstripped_T1w.nii';
+matlabbatch{6}.spm.util.imcalc.outdir = {'/home/remi/github/bidspm/tests/data/MoAE/derivatives/bidspm-preproc/sub-01/anat'};
+matlabbatch{6}.spm.util.imcalc.expression = 'i1.*((i2+i3+i4)>0.750000)';
+matlabbatch{6}.spm.util.imcalc.options.dtype = 16;
+matlabbatch{7}.spm.util.imcalc.input(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));
+matlabbatch{7}.spm.util.imcalc.input(2) = cfg_dep('Segment: c1 Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','tiss', '()',{1}, '.','c', '()',{':'}));
+matlabbatch{7}.spm.util.imcalc.input(3) = cfg_dep('Segment: c2 Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','tiss', '()',{2}, '.','c', '()',{':'}));
+matlabbatch{7}.spm.util.imcalc.input(4) = cfg_dep('Segment: c3 Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','tiss', '()',{3}, '.','c', '()',{':'}));
+matlabbatch{7}.spm.util.imcalc.output = 'sub-01_space-individual_desc-brain_mask.nii';
+matlabbatch{7}.spm.util.imcalc.outdir = {'/home/remi/github/bidspm/tests/data/MoAE/derivatives/bidspm-preproc/sub-01/anat'};
+matlabbatch{7}.spm.util.imcalc.expression = '(i2+i3+i4)>0.750000';
+matlabbatch{7}.spm.util.imcalc.options.dtype = 16;