Adding a file existence test to make sure all the

files that are supposed to be in the results are
actually there.

test/files.yaml

@@ -0,0 +1,304 @@
+
+folder_path: '/home/abdullaht/actions-runner/_work/fastsurfer_analysis/subjectx/'
+
+files:
+  - scripts/deep-seg.log
+  - scripts/build.log
+  - scripts/recon-surf.log
+  - scripts/build-stamp.txt
+  - scripts/lastcall.build-stamp.txt
+  - scripts/recon-all.cmd
+  - scripts/recon-all.log
+  - scripts/recon-all-status.log
+  - scripts/recon-all.local-copy
+  - scripts/ponscc.cut.log
+  - scripts/lh.processing.cmdf
+  - scripts/rh.processing.cmdf
+  - scripts/recon-all.env.bak
+  - scripts/defect2seg.log
+  - scripts/recon-surf_times.yaml
+  - scripts/pctsurfcon.log.old
+  - scripts/pctsurfcon.log
+  - scripts/patchdir.txt
+  - scripts/recon-config.yaml
+  - scripts/unknown-args.txt
+  - scripts/recon-all.env
+  - scripts/recon-all.done
+  - scripts/recon-surf.done
+  - mri/orig.mgz
+  - mri/aparc.DKTatlas+aseg.deep.mgz
+  - mri/mask.mgz
+  - mri/aseg.auto_noCCseg.mgz
+  - mri/orig_nu.mgz
+  - mri/cerebellum.CerebNet.nii.gz
+  - mri/aparc.DKTatlas+aseg.orig.mgz
+  - mri/rawavg.mgz
+  - mri/nu.mgz
+  - mri/norm.mgz
+  - mri/T1.mgz
+  - mri/brainmask.mgz
+  - mri/aseg.auto.mgz
+  - mri/aparc.DKTatlas+aseg.deep.withCC.mgz
+  - mri/aseg.presurf.mgz
+  - mri/brain.mgz
+  - mri/brain.finalsurfs.mgz
+  - mri/brain.finalsurfs.manedit.mgz
+  - mri/antsdn.brain.mgz
+  - mri/segment.dat
+  - mri/wm.seg.mgz
+  - mri/wm.asegedit.mgz
+  - mri/wm.mgz
+  - mri/filled.mgz
+  - mri/filled.auto.mgz
+  - mri/filled-pretess127.mgz
+  - mri/filled-pretess255.mgz
+  - mri/rh.surface.defects.mgz
+  - mri/lh.surface.defects.mgz
+  - mri/ribbon.mgz
+  - mri/lh.ribbon.mgz
+  - mri/rh.ribbon.mgz
+  - mri/aseg.presurf.hypos.mgz
+  - mri/aseg.mgz
+  - mri/aparc.DKTatlas+aseg.mapped.mgz
+  - mri/wmparc.DKTatlas.mapped.mgz
+  - mri/aparc.DKTatlas+aseg.mgz
+  - mri/aparc+aseg.mgz
+  - mri/wmparc.mgz
+  - mri/orig/001.mgz
+  - mri/transforms/talairach_avi.log
+  - mri/transforms/talairach.auto.xfm
+  - mri/transforms/talairach.auto.xfm.lta
+  - mri/transforms/talairach.xfm
+  - mri/transforms/talairach.xfm.lta
+  - mri/transforms/talairach_with_skull.lta
+  - mri/transforms/talairach.lta
+  - mri/transforms/cc_up.lta
+  - stats/aseg+DKT.stats
+  - stats/cerebellum.CerebNet.stats
+  - stats/lh.curv.stats
+  - stats/rh.curv.stats
+  - stats/lh.aparc.DKTatlas.mapped.stats
+  - stats/brainvol.stats
+  - stats/rh.aparc.DKTatlas.mapped.stats
+  - stats/lh.w-g.pct.stats
+  - stats/rh.w-g.pct.stats
+  - stats/aseg.stats
+  - stats/aseg.presurf.hypos.stats
+  - stats/wmparc.DKTatlas.mapped.stats
+  - stats/lh.BA_exvivo.stats
+  - stats/lh.BA_exvivo.thresh.stats
+  - stats/rh.BA_exvivo.stats
+  - stats/rh.BA_exvivo.thresh.stats
+  - surf/rh.orig.nofix
+  - surf/lh.orig.nofix
+  - surf/rh.smoothwm.nofix
+  - surf/lh.smoothwm.nofix
+  - surf/rh.inflated.nofix
+  - surf/lh.inflated.nofix
+  - surf/lh.qsphere.nofix
+  - surf/rh.qsphere.nofix
+  - surf/lh.defect_labels
+  - surf/lh.defect_borders
+  - surf/lh.defect_chull
+  - surf/rh.defect_labels
+  - surf/rh.defect_borders
+  - surf/rh.defect_chull
+  - surf/rh.orig.premesh
+  - surf/rh.defects.pointset
+  - surf/lh.orig.premesh
+  - surf/lh.defects.pointset
+  - surf/rh.orig
+  - surf/autodet.gw.stats.rh.dat
+  - surf/lh.orig
+  - surf/autodet.gw.stats.lh.dat
+  - surf/rh.white.preaparc
+  - surf/lh.white.preaparc
+  - surf/rh.smoothwm
+  - surf/rh.inflated
+  - surf/rh.sulc
+  - surf/rh.white.preaparc.K
+  - surf/rh.white.preaparc.H
+  - surf/rh.white.H
+  - surf/rh.white.K
+  - surf/lh.smoothwm
+  - surf/lh.inflated
+  - surf/lh.sulc
+  - surf/lh.white.preaparc.K
+  - surf/lh.white.preaparc.H
+  - surf/lh.white.H
+  - surf/lh.white.K
+  - surf/rh.inflated.K
+  - surf/rh.inflated.H
+  - surf/lh.inflated.K
+  - surf/lh.inflated.H
+  - surf/lh.sphere
+  - surf/lh.angles.txt
+  - surf/rh.sphere
+  - surf/rh.angles.txt
+  - surf/lh.sphere.reg
+  - surf/rh.sphere.reg
+  - surf/lh.white
+  - surf/rh.white
+  - surf/lh.pial.T1
+  - surf/lh.pial
+  - surf/lh.jacobian_white
+  - surf/lh.curv
+  - surf/lh.area
+  - surf/lh.curv.pial
+  - surf/lh.area.pial
+  - surf/rh.pial.T1
+  - surf/rh.pial
+  - surf/rh.jacobian_white
+  - surf/rh.curv
+  - surf/rh.area
+  - surf/rh.curv.pial
+  - surf/rh.area.pial
+  - surf/lh.thickness
+  - surf/lh.area.mid
+  - surf/lh.volume
+  - surf/lh.smoothwm.K.crv
+  - surf/lh.smoothwm.H.crv
+  - surf/lh.smoothwm.K1.crv
+  - surf/lh.smoothwm.K2.crv
+  - surf/lh.smoothwm.S.crv
+  - surf/lh.smoothwm.C.crv
+  - surf/lh.smoothwm.BE.crv
+  - surf/lh.smoothwm.FI.crv
+  - surf/rh.thickness
+  - surf/rh.area.mid
+  - surf/rh.volume
+  - surf/rh.smoothwm.K.crv
+  - surf/rh.smoothwm.H.crv
+  - surf/rh.smoothwm.K1.crv
+  - surf/rh.smoothwm.K2.crv
+  - surf/rh.smoothwm.S.crv
+  - surf/rh.smoothwm.C.crv
+  - surf/rh.smoothwm.BE.crv
+  - surf/rh.smoothwm.FI.crv
+  - surf/lh.w-g.pct.mgh
+  - surf/rh.w-g.pct.mgh
+  - label/rh.nofix.cortex.label
+  - label/lh.nofix.cortex.label
+  - label/rh.cortex.label
+  - label/rh.cortex+hipamyg.label
+  - label/lh.cortex.label
+  - label/lh.cortex+hipamyg.label
+  - label/rh.aparc.DKTatlas.mapped.annot
+  - label/lh.aparc.DKTatlas.mapped.annot
+  - label/aparc.annot.mapped.ctab
+  - label/lh.aparc.DKTatlas.annot
+  - label/rh.aparc.DKTatlas.annot
+  - label/lh.BA1_exvivo.label
+  - label/lh.BA2_exvivo.label
+  - label/lh.BA3a_exvivo.label
+  - label/lh.BA3b_exvivo.label
+  - label/lh.BA4a_exvivo.label
+  - label/lh.BA4p_exvivo.label
+  - label/lh.BA6_exvivo.label
+  - label/lh.BA44_exvivo.label
+  - label/lh.BA45_exvivo.label
+  - label/lh.V1_exvivo.label
+  - label/lh.V2_exvivo.label
+  - label/lh.MT_exvivo.label
+  - label/lh.perirhinal_exvivo.label
+  - label/lh.entorhinal_exvivo.label
+  - label/lh.BA1_exvivo.thresh.label
+  - label/lh.BA2_exvivo.thresh.label
+  - label/lh.BA3a_exvivo.thresh.label
+  - label/lh.BA3b_exvivo.thresh.label
+  - label/lh.BA4a_exvivo.thresh.label
+  - label/lh.BA4p_exvivo.thresh.label
+  - label/lh.BA6_exvivo.thresh.label
+  - label/lh.BA44_exvivo.thresh.label
+  - label/lh.BA45_exvivo.thresh.label
+  - label/lh.V1_exvivo.thresh.label
+  - label/lh.V2_exvivo.thresh.label
+  - label/lh.MT_exvivo.thresh.label
+  - label/lh.perirhinal_exvivo.thresh.label
+  - label/lh.entorhinal_exvivo.thresh.label
+  - label/lh.FG1.mpm.vpnl.label
+  - label/lh.FG2.mpm.vpnl.label
+  - label/lh.FG3.mpm.vpnl.label
+  - label/lh.FG4.mpm.vpnl.label
+  - label/lh.hOc1.mpm.vpnl.label
+  - label/lh.hOc2.mpm.vpnl.label
+  - label/lh.hOc3v.mpm.vpnl.label
+  - label/lh.hOc4v.mpm.vpnl.label
+  - label/lh.BA_exvivo.annot
+  - label/BA_exvivo.ctab
+  - label/lh.BA_exvivo.thresh.annot
+  - label/BA_exvivo.thresh.ctab
+  - label/lh.mpm.vpnl.annot
+  - label/rh.BA1_exvivo.label
+  - label/rh.BA2_exvivo.label
+  - label/rh.BA3a_exvivo.label
+  - label/rh.BA3b_exvivo.label
+  - label/rh.BA4a_exvivo.label
+  - label/rh.BA4p_exvivo.label
+  - label/rh.BA6_exvivo.label
+  - label/rh.BA44_exvivo.label
+  - label/rh.BA45_exvivo.label
+  - label/rh.V1_exvivo.label
+  - label/rh.V2_exvivo.label
+  - label/rh.MT_exvivo.label
+  - label/rh.perirhinal_exvivo.label
+  - label/rh.entorhinal_exvivo.label
+  - label/rh.BA1_exvivo.thresh.label
+  - label/rh.BA2_exvivo.thresh.label
+  - label/rh.BA3a_exvivo.thresh.label
+  - label/rh.BA3b_exvivo.thresh.label
+  - label/rh.BA4a_exvivo.thresh.label
+  - label/rh.BA4p_exvivo.thresh.label
+  - label/rh.BA6_exvivo.thresh.label
+  - label/rh.BA44_exvivo.thresh.label
+  - label/rh.BA45_exvivo.thresh.label
+  - label/rh.V1_exvivo.thresh.label
+  - label/rh.V2_exvivo.thresh.label
+  - label/rh.MT_exvivo.thresh.label
+  - label/rh.perirhinal_exvivo.thresh.label
+  - label/rh.entorhinal_exvivo.thresh.label
+  - label/rh.FG1.mpm.vpnl.label
+  - label/rh.FG2.mpm.vpnl.label
+  - label/rh.FG3.mpm.vpnl.label
+  - label/rh.FG4.mpm.vpnl.label
+  - label/rh.hOc1.mpm.vpnl.label
+  - label/rh.hOc2.mpm.vpnl.label
+  - label/rh.hOc3v.mpm.vpnl.label
+  - label/rh.hOc4v.mpm.vpnl.label
+  - label/rh.BA_exvivo.annot
+  - label/rh.BA_exvivo.thresh.annot
+  - label/rh.mpm.vpnl.annot
+  - touch/asegmerge.touch
+  - touch/inorm2.touch
+  - touch/wmsegment.touch
+  - touch/fill.touch
+  - touch/rh.inflate1.touch
+  - touch/lh.inflate1.touch
+  - touch/lh.qsphere.touch
+  - touch/rh.qsphere.touch
+  - touch/rh.topofix.touch
+  - touch/rh.autodet.gw.stats.touch
+  - touch/lh.topofix.touch
+  - touch/lh.autodet.gw.stats.touch
+  - touch/rh.white.preaparc.touch
+  - touch/rh.cortex.touch
+  - touch/lh.white.preaparc.touch
+  - touch/rh.cortex+hipamyg.touch
+  - touch/lh.cortex.touch
+  - touch/rh.smoothwm2.touch
+  - touch/rh.inflate2.touch
+  - touch/lh.cortex+hipamyg.touch
+  - touch/rh.white.H.K.touch
+  - touch/lh.smoothwm2.touch
+  - touch/lh.inflate2.touch
+  - touch/lh.white.H.K.touch
+  - touch/rh.inflate.H.K.touch
+  - touch/lh.inflate.H.K.touch
+  - touch/lh.sphmorph.touch
+  - touch/rh.sphmorph.touch
+  - touch/lh.curvstats.touch
+  - touch/rh.curvstats.touch
+  - touch/cortical_ribbon.touch
+  - touch/relabelhypos.touch
+  - touch/apas2aseg.touch
+  - touch/segstats.touch

test/test_file_existence.py

@@ -0,0 +1,29 @@
+import os
+import yaml
+import unittest
+
+class TestFileExistence(unittest.TestCase):
+    def test_file_existence(self):
+        yaml_file_path = './files.yaml'  # './' refers to the current directory
+
+        # Load the YAML file
+        with open(yaml_file_path, 'r') as file:
+            data = yaml.safe_load(file)
+
+        # Get the folder path from the YAML file
+        folder_path = data['folder_path']
+
+        # Get a list of all files in the folder recursively
+        filenames = []
+        for root, dirs, files in os.walk(folder_path):
+            for file in files:
+                # Get the relative path from the current directory to the file
+                rel_path = os.path.relpath(os.path.join(root, file), folder_path)
+                filenames.append(rel_path)
+
+        # Check if each file in the YAML file exists in the folder
+        for file_name in data['files']:
+            self.assertIn(file_name, filenames, f"File '{file_name}' does not exist in the folder.")
+
+if __name__ == '__main__':
+    unittest.main()