xnatqa 0.0.19__py3-none-any.whl → 0.0.21__py3-none-any.whl

xnatqa/tag/__init__.py

@@ -11,7 +11,7 @@ def extract_bids_suffix(bids_string):
         bids_suffix = match.group(1)
         return bids_suffix
 
-def generate_tagger_config(dicom_dir):
+def generate_tagger_config(dicom_dir, working_dir):
 
     # This calls the latest version of dcm2niix WITHOUT creating the *.nii.gz files, only the BIDS metadata *.json sidecars.
     # dcm2niix automatically skips scans that it has identified as being non-BIDS (i.e., localizers, scouts)
@@ -19,10 +19,10 @@ def generate_tagger_config(dicom_dir):
     # This seems to work well most of the time, with the odd hicups. I include manual code here to catch the "hicups".
 
     # call to dcm2niix. generates a bunch of *.json text files in the current working directory.
-    os.system(f"dcm2niix -s y -a y -b o -o $PWD -f 'output_%s_%d' -w 0 -m 1 -i y {dicom_dir} &>>log.txt")
+    os.system(f"dcm2niix -s y -a y -b o -o {working_dir} -f 'output_%s_%d' -w 0 -m 1 -i y {dicom_dir} &>>{working_dir}/log.txt")
 
     # idenfity all of these text files
-    jsonFiles = glob(os.path.abspath('./output*.json'))
+    jsonFiles = glob(f'{working_dir}/output*.json')
 
     # sort the found files so that they are in decensing order by series_number
     # this is probably unnecssary
@@ -177,23 +177,27 @@ def generate_tagger_config(dicom_dir):
                         continue                    
 
     # write tagger data to a yaml file. used by the xnattagger package for uploading tags to XNAT. See github.com/harvard-nrg/xnattager
-    with open('tagger.yaml', 'a') as file:
+    with open(f'{working_dir}/tagger.yaml', 'a') as file:
         yaml.dump(tagger_data, file)
 
-def update_xnat_tags(MRsession):
+def update_xnat_tags(MRsession, working_dir):
 
-    # make sure an xnat authentication files has already been created. See YXAIL documentation.
+    # make sure an xnat authentication files has already been created. See YAXIL documentation.
     assert os.path.exists(os.path.expanduser('~/.xnat_auth')), 'xnat authentication needs to be run'
 
     # run the command
-    os.system(f'xnat_tagger.py --label {MRsession} --target-modality all --xnat-alias xnat --config tagger.yaml')
+    os.system(f'xnat_tagger.py --label {MRsession} --target-modality all --xnat-alias xnat --config {working_dir}/tagger.yaml')
 
-def tag_scans(dicom_dir, MRsession, dryrun):
+def tag_scans(dicom_dir, MRsession, working_dir, dryrun):
     
+    this_session_working_dir=os.path.join(working_dir, MRsession)
+
+    os.mkdir(this_session_working_dir)
+
     # generate the xnattag config file
-    generate_tagger_config(dicom_dir)
+    generate_tagger_config(dicom_dir, this_session_working_dir)
     
     # update the xnat tags
     if not dryrun:
-        update_xnat_tags(MRsession)
+        update_xnat_tags(MRsession, this_session_working_dir)
 

xnatqa/xnatqa.py

@@ -8,15 +8,17 @@ def main():
     parser = argparse.ArgumentParser(description="XNAT QA Workflow")
     parser.add_argument("--dicom_dir", default="/input", help = "where the DICOMs are located", required=True)
     parser.add_argument("--experiment", default = "", required=True)
+    parser.add_argument("--working_dir", default = '/tmp', help="Where should intermediate files get written?")
     parser.add_argument("--dryrun", default = "", action='store_true', help="Run in dry run mode: No upload to XNAT")
 
     args, unknown_args = parser.parse_known_args()
-    dicom_dir  = os.path.join(args.dicom_dir)
-    experiment = args.experiment
-    dryrun     = args.dryrun
+    dicom_dir   = os.path.join(args.dicom_dir)
+    experiment  = args.experiment
+    working_dir = args.working_dir    
+    dryrun      = args.dryrun
 
     # tag all scans in this session
-    tag_scans(dicom_dir, experiment, dryrun)
+    tag_scans(dicom_dir, experiment, working_dir, dryrun)
 
 if __name__ == "__main__":
     main()

{xnatqa-0.0.19.dist-info → xnatqa-0.0.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.19
+Version: 0.0.21
 Summary: A workflow for automatically tagging MRI scans within XNAT
 Author-email: Kyle Kurkela <kkurkela@bu.edu>
 License-Expression: MIT

xnatqa-0.0.21.dist-info/RECORD

@@ -0,0 +1,10 @@
+xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
+xnatqa/launch.py,sha256=QWqLdwfbq28cmeJd4XQcV2wxs2ZGRX85uzFmxHydmfg,1963
+xnatqa/xnatqa.py,sha256=PEAe3LGFKZ2KSVO4Bd5vAGuMeaFkXCg5GVY1sCr8K-E,915
+xnatqa/tag/__init__.py,sha256=Yioqr-MPvxVtiWT3r1CPwz1UXnV0253owG57QaF2D2k,9215
+xnatqa-0.0.21.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xnatqa-0.0.21.dist-info/METADATA,sha256=8ZyM8p0vuknR0buL1RJ3QZKJmdFBjEtcLMJAH11bmjk,1187
+xnatqa-0.0.21.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+xnatqa-0.0.21.dist-info/entry_points.txt,sha256=g5CvKDfx6vIIp76wdB1aiWe1SkBORj2S8gFReBBxBws,74
+xnatqa-0.0.21.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
+xnatqa-0.0.21.dist-info/RECORD,,

xnatqa-0.0.19.dist-info/RECORD

@@ -1,10 +0,0 @@
-xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
-xnatqa/launch.py,sha256=QWqLdwfbq28cmeJd4XQcV2wxs2ZGRX85uzFmxHydmfg,1963
-xnatqa/xnatqa.py,sha256=lWNFbtJPvM-0DuUV3pjL_xfPnBxEZqGK8PIdlBaxJWE,748
-xnatqa/tag/__init__.py,sha256=wXPBIbHucCqITYVZ4V5bt3VJWq8svyrJoBjbrpH1bNE,8969
-xnatqa-0.0.19.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xnatqa-0.0.19.dist-info/METADATA,sha256=Ze37T8xBNT1oigywvb7XA-b1nvUe6DDJeRewPXHcrj0,1187
-xnatqa-0.0.19.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
-xnatqa-0.0.19.dist-info/entry_points.txt,sha256=g5CvKDfx6vIIp76wdB1aiWe1SkBORj2S8gFReBBxBws,74
-xnatqa-0.0.19.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
-xnatqa-0.0.19.dist-info/RECORD,,