account for spaces in path when running tmi

NYU-DiffusionMRI · Dec 10, 2024 · 76ff609 · 76ff609
1 parent 2b29f22
commit 76ff609
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Showing 3 changed files with 26 additions and 19 deletions.
diff --git a/designer2/tmi.py b/designer2/tmi.py
@@ -139,6 +139,8 @@ def execute(): #pylint: disable=unused-variable
     import pandas as pd
 
     outdir = path.from_user(app.ARGS.output, True)
+    if outdir[0]=="'" and outdir[-1]=="'":
+        outdir= outdir.replace("'","")
     if not os.path.exists(outdir):
         os.makedirs(outdir)
 

diff --git a/lib/designer_fit_wrappers.py b/lib/designer_fit_wrappers.py
@@ -82,7 +82,7 @@ def save_params(paramDict, niiex, model, outdir):
 
     params = paramDict.keys()
     for key in params:
-        outpath = os.path.join(outdir, ('%s_%s.nii' % (key, model)))
+        outpath = os.path.join(r"{}".format(outdir), ("%s_%s.nii" % (key, model)))
         vol = paramDict[key]
         ndims = vol.ndim
 

diff --git a/tests/input_test_jc_docker.sh b/tests/input_test_jc_docker.sh
@@ -14,22 +14,27 @@ r_json_wrong=/Users/jc8329/Desktop/test/M0033/M0033_043YF_DIFF_meso_research_.js
 r_json=/Users/jc8329/Desktop/test/M0033/M0033_043YF_DIFF_meso_research.json
 
 #test
-root=/Users/jc8329/Desktop/test/M0033
-meso=/data/M0033_043YF_DIFF_meso.nii
-pa=/data/M0033_043YF_DIFF_meso_PA.nii
-research=/data/M0033_043YF_DIFF_meso_research.nii
-    docker run --rm -it -v ${root}:/data test_petable/designer2:main designer \
-    -eddy -rpe_pair $pa \
-    -mask -nocleanup \
-    -scratch /data/processing_json \
-    $meso,$research /data/dwi_designer_json.nii
+# root=/Users/jc8329/Desktop/test/M0033
+# meso=/data/M0033_043YF_DIFF_meso.nii
+# pa=/data/M0033_043YF_DIFF_meso_PA.nii
+# research=/data/M0033_043YF_DIFF_meso_research.nii
+#     docker run --rm -it -v ${root}:/data test_petable/designer2:main designer \
+#     -eddy -rpe_pair $pa \
+#     -mask -nocleanup \
+#     -scratch /data/processing_json \
+#     $meso,$research /data/dwi_designer_json.nii
 
-meso=/data/temp/M0033_043YF_DIFF_meso.nii
-pa=/data/temp/M0033_043YF_DIFF_meso_PA.nii
-research=/data/temp/M0033_043YF_DIFF_meso_research.nii
-    docker run --rm -it -v ${root}:/data test_petable/designer2:main designer \
-    -eddy -rpe_pair $pa_ \
-    -pf 6/8 -pe_dir j- \
-    -mask -nocleanup \
-    -scratch /data/temp/processing_nojson \
-    $meso_,$research_ /data/dwi_designer_nojson.nii
+# meso=/data/temp/M0033_043YF_DIFF_meso.nii
+# pa=/data/temp/M0033_043YF_DIFF_meso_PA.nii
+# research=/data/temp/M0033_043YF_DIFF_meso_research.nii
+#     docker run --rm -it -v ${root}:/data test_petable/designer2:main designer \
+#     -eddy -rpe_pair $pa_ \
+#     -pf 6/8 -pe_dir j- \
+#     -mask -nocleanup \
+#     -scratch /data/temp/processing_nojson \
+#     $meso_,$research_ /data/dwi_designer_nojson.nii
+
+folder=M0033
+docker run --rm --platform linux/amd64 -it -v /Users/jc8329/Desktop/test/$folder:/data test_fit/designer2:main \
+    tmi -DKI -DTI -mask /data/brain_mask.nii \
+    /data/dwi_designer.mif /data/params_test