Improve testing

rabies/confound_correction_pkg/confound_correction.py

@@ -316,9 +316,6 @@ def _run_interface(self, runtime):
             df.to_csv(mc_file)
 
             cleaned_file, aroma_out = exec_ICA_AROMA(inFile, mc_file, brain_mask_file, CSF_mask_file, TR, cr_opts.ica_aroma['dim'], random_seed=cr_opts.ica_aroma['random_seed'])
-            # if AROMA failed, returns empty outputs
-            if cleaned_file is None:
-                return runtime
             setattr(self, 'aroma_out', aroma_out)
 
             data_img = sitk.ReadImage(cleaned_file, sitk.sitkFloat32)

rabies/confound_correction_pkg/mod_ICA_AROMA/ICA_AROMA_functions.py

@@ -105,9 +105,8 @@ def run_ICA_AROMA(outDir,inFile,mc,TR,mask="",mask_csf="",denType="nonaggr",melD
     try:
         aromafunc.runICA(fslDir, inFile, outDir, melDir, mask, dim, TR, random_seed=random_seed)
         melIC = os.path.join(outDir, 'melodic_IC_thr.nii.gz')
-    except:
-        print('MELODIC FAILED. RETURNING EMPTY FILES.')
-        return False, False
+    except Exception as e:
+        raise ValueError(f"MELODIC FAILED DURING ICA-AROMA: {e}")
 
     print('Step 2) Automatic classification of the components')
 

scripts/error_check_rabies.py

@@ -1,20 +1,97 @@
 #! /usr/bin/env python
 
 import os
-import sys
 import tempfile
 import shutil
 import subprocess
 from rabies.utils import generate_token_data
 
-if len(sys.argv) == 2:
-    tmppath = sys.argv[1]
-else:
+import argparse
+def get_parser():
+    """Build parser object"""
+    parser = argparse.ArgumentParser(
+        description=
+            "Parser to handle testing using token data.",
+        formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument(
+        "--complete", dest='complete', action='store_true',
+        help=
+            "Run a complete testing of the pipeline."
+        )
+    parser.add_argument(
+        '--output_dir', action='store', type=str,
+        help=
+            "Provide an output directory instead of using a temporary directory.\n"
+            "This prevents the deletion of outputs.\n"
+        )
+    parser.add_argument(
+        "--custom", dest='custom', type=str, default=None,
+        help=
+            "Provide a custom command to run, without specifying input/output directories.\n "
+            "The path to token data and output folder is appended at the end of --custom, \n"
+            "then the command is run, and the script is exited. The command must be provided \n"
+            "as a string between ''.\n"
+            "If the preprocessing stage is run, the following arguments are automatically \n"
+            "provided to ensure compatibility with token data:\n"
+            "   --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \ \n"
+            "   --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz  \ \n"
+            "   --WM_mask {tmppath}/inputs/token_mask.nii.gz --CSF_mask {tmppath}/inputs/token_mask.nii.gz  \ \n"
+            "   --vascular_mask {tmppath}/inputs/token_mask.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \ \n"
+            "   --bold2anat_coreg registration=no_reg,masking=false,brain_extraction=false \ \n"
+            "   --commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16 \n"
+        )
+
+    return parser
+
+parser = get_parser()
+opts = parser.parse_args()
+
+if opts.output_dir is None:
     tmppath = tempfile.mkdtemp()
+else:
+    tmppath = opts.output_dir
 
-generate_token_data(tmppath, number_scans=1)
+generate_token_data(tmppath, number_scans=3)
 
-command = f"rabies --verbose 1 preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
+if not opts.custom is None:
+    minimal_preproc = f"rabies --inclusion_ids {tmppath}/inputs/sub-token1_bold.nii.gz --verbose 1 preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
+        --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask.nii.gz --CSF_mask {tmppath}/inputs/token_mask.nii.gz --vascular_mask {tmppath}/inputs/token_mask.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
+        --bold2anat_coreg registration=no_reg,masking=false,brain_extraction=false --commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16"
+    minimal_cc = f"rabies --verbose 1 confound_correction {tmppath}/outputs {tmppath}/outputs"
+
+    import sys
+    command = opts.custom
+    if 'preprocess' in command:
+        command += f" --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
+    --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask.nii.gz --CSF_mask {tmppath}/inputs/token_mask.nii.gz --vascular_mask {tmppath}/inputs/token_mask.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
+    --bold2anat_coreg registration=no_reg,masking=false,brain_extraction=false --commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16"
+    if 'confound_correction' in command or 'analysis' in command:
+        if not os.path.isfile(f'{tmppath}/outputs/rabies_preprocess_workflow.pkl'):
+            # provide preprocess outputs to run cc stage
+            process = subprocess.run(
+                minimal_preproc,
+                check=True,
+                shell=True,
+                )
+        if 'analysis' in command:
+            if not os.path.isfile(f'{tmppath}/outputs/rabies_confound_correction_workflow.pkl'):
+                # provide cc outputs to run analysis stage
+                process = subprocess.run(
+                    minimal_cc,
+                    check=True,
+                    shell=True,
+                    )
+
+    command += f" {tmppath}/outputs {tmppath}/outputs"
+
+    process = subprocess.run(
+        command,
+        check=True,
+        shell=True,
+        )
+    sys.exit()
+
+command = f"rabies --exclusion_ids {tmppath}/inputs/sub-token2_bold.nii.gz {tmppath}/inputs/sub-token3_bold.nii.gz --verbose 1 preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
     --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask.nii.gz --CSF_mask {tmppath}/inputs/token_mask.nii.gz --vascular_mask {tmppath}/inputs/token_mask.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
     --bold2anat_coreg registration=no_reg,masking=false,brain_extraction=false --commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16 --bold_only --detect_dummy \
     --tpattern seq-z --apply_STC --voxelwise_motion --isotropic_HMC"
@@ -24,8 +101,7 @@
     shell=True,
     )
 
-shutil.rmtree(f'{tmppath}/outputs/')
-command = f"rabies --verbose 1 preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
+command = f"rabies --inclusion_ids {tmppath}/inputs/sub-token1_bold.nii.gz --verbose 1 --force preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
     --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask.nii.gz --CSF_mask {tmppath}/inputs/token_mask.nii.gz --vascular_mask {tmppath}/inputs/token_mask.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
     --bold2anat_coreg registration=no_reg,masking=true,brain_extraction=true --commonspace_reg masking=true,brain_extraction=true,fast_commonspace=true,template_registration=no_reg --data_type int16  \
     --HMC_option 0"
@@ -51,61 +127,48 @@
     shell=True,
     )
 
+# testing --data_diagnosis in native space
 command = f"rabies --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --data_diagnosis"
 process = subprocess.run(
     command,
     check=True,
     shell=True,
     )
 
-shutil.rmtree(f'{tmppath}/inputs/')
-generate_token_data(tmppath, number_scans=3)
-
-shutil.rmtree(f'{tmppath}/outputs/')
-command = f"rabies --verbose 1 preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
-    --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask_half.nii.gz --CSF_mask {tmppath}/inputs/token_mask_half.nii.gz --vascular_mask {tmppath}/inputs/token_mask_half.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
-    --bold2anat_coreg registration=no_reg,masking=false,brain_extraction=false --commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16  \
-    --HMC_option 0"
-process = subprocess.run(
-    command,
-    check=True,
-    shell=True,
-    )
-
-command = f"rabies --verbose 1 confound_correction --read_datasink {tmppath}/outputs {tmppath}/outputs --conf_list mot_6 --smoothing_filter 0.3"
-process = subprocess.run(
-    command,
-    check=True,
-    shell=True,
-    )
-
-command = f"rabies --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --DR_ICA --NPR_temporal_comp 1 --seed_list {tmppath}/inputs/token_mask_half.nii.gz"
-process = subprocess.run(
-    command,
-    check=True,
-    shell=True,
-    )
-
-shutil.rmtree(f'{tmppath}/outputs/confound_correction_main_wf')
-shutil.rmtree(f'{tmppath}/outputs/confound_correction_datasink')
-os.remove(f'{tmppath}/outputs/rabies_confound_correction.pkl')
-command = f"rabies --verbose 1 confound_correction {tmppath}/outputs {tmppath}/outputs"
-process = subprocess.run(
-    command,
-    check=True,
-    shell=True,
-    )
-
-shutil.rmtree(f'{tmppath}/outputs/analysis_main_wf')
-shutil.rmtree(f'{tmppath}/outputs/analysis_datasink')
-os.remove(f'{tmppath}/outputs/rabies_analysis.pkl')
-command = f"rabies --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --NPR_temporal_comp 1 --data_diagnosis --DR_ICA"
-process = subprocess.run(
-    command,
-    check=True,
-    shell=True,
-    )
-
-
-if not len(sys.argv) == 2:
+if opts.complete:
+    ###GROUP LEVEL, RUNNING ALL 3 SCANS
+    shutil.rmtree(f'{tmppath}/outputs/')
+    command = f"rabies --verbose 1 preprocess {tmppath}/inputs {tmppath}/outputs --anat_inho_cor method=disable,otsu_thresh=2,multiotsu=false --bold_inho_cor method=disable,otsu_thresh=2,multiotsu=false \
+        --anat_template {tmppath}/inputs/sub-token1_T1w.nii.gz --brain_mask {tmppath}/inputs/token_mask.nii.gz --WM_mask {tmppath}/inputs/token_mask_half.nii.gz --CSF_mask {tmppath}/inputs/token_mask_half.nii.gz --vascular_mask {tmppath}/inputs/token_mask_half.nii.gz --labels {tmppath}/inputs/token_mask.nii.gz \
+        --bold2anat_coreg registration=no_reg,masking=false,brain_extraction=false --commonspace_reg masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg --data_type int16  \
+        --HMC_option 0"
+    process = subprocess.run(
+        command,
+        check=True,
+        shell=True,
+        )
+
+    command = f"rabies --verbose 1 confound_correction --read_datasink {tmppath}/outputs {tmppath}/outputs --conf_list mot_6 --smoothing_filter 0.3"
+    process = subprocess.run(
+        command,
+        check=True,
+        shell=True,
+        )
+
+    command = f"rabies --force --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --NPR_temporal_comp 1 --data_diagnosis --DR_ICA  --seed_list {tmppath}/inputs/token_mask_half.nii.gz"
+    process = subprocess.run(
+        command,
+        check=True,
+        shell=True,
+        )
+
+    # test group ICA
+    command = f"rabies --force --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --group_ica apply=true,dim=0,random_seed=1"
+    process = subprocess.run(
+        command,
+        check=True,
+        shell=True,
+        )
+
+if opts.output_dir is None:
     shutil.rmtree(tmppath)