xnatqa 0.0.9__py3-none-any.whl → 0.0.11__py3-none-any.whl

xnatqa/xnatqa.py

@@ -1,34 +1,24 @@
 import os
 import argparse
 from xnatqa.tag import tag_scans
-from xnatqa.launch import launch
 
 def main():
 
     # parse input arguments
-    parser = argparse.ArgumentParser(description="Auto Labeler")
+    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("--host", default="https://xnat2.bu.edu", help="BU XNAT host", required=True)
-    parser.add_argument("--user", help="BU XNAT2 username", required=True)
-    parser.add_argument("--password", help="BU XNAT2 Password", required=True)
     parser.add_argument("--experiment", default = "", required=True)
 
     args, unknown_args = parser.parse_known_args()
     dicom_dir  = os.path.join(args.dicom_dir, 'SCANS')
-    host       = args.host
-    user       = args.user
-    password   = args.password
     experiment = args.experiment
 
     # run xnat authentication for this container. writes an ~/.xnat_auth file to the home directory
     # this file is used in all subsequent calls to XNAT
-    os.system(f'xnat_auth --alias xnat --url {host} --username {user} --password {password}')
+    os.system(f'xnat_auth --alias xnat --url $XNAT_HOST --username $XNAT_USER --password $XNAT_PASS')
 
     # tag all scans in this session
     tag_scans(dicom_dir, experiment)
 
-    # launch all QA jobs for this session
-    launch(experiment)
-
 if __name__ == "__main__":
     main()

{xnatqa-0.0.9.dist-info → xnatqa-0.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.9
+Version: 0.0.11
 Summary: A workflow for automatically labeling and running QA on MRI scans within XNAT
 Author-email: Kyle Kurkela <kkurkela@bu.edu>
 License-Expression: MIT

xnatqa-0.0.11.dist-info/RECORD

@@ -0,0 +1,9 @@
+xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
+xnatqa/xnatqa.py,sha256=RJp65oIE13COs_0UG4hEku_f6YFDpoQV4JHEhtppXfs,861
+xnatqa/tag/__init__.py,sha256=kjdB9zSA_YHGOPmG_BDM0HtSK6thmBt0Awd4Zj6NN5A,8921
+xnatqa-0.0.11.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xnatqa-0.0.11.dist-info/METADATA,sha256=viecCkDxux1GEdxGxDQxetiEDoklWT9U-AyJ7ZCqDpE,1200
+xnatqa-0.0.11.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
+xnatqa-0.0.11.dist-info/entry_points.txt,sha256=UqPAByHiJTqwkT0UBymn6EOIGBlPsb9mEZK86HIahs8,46
+xnatqa-0.0.11.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
+xnatqa-0.0.11.dist-info/RECORD,,

{xnatqa-0.0.9.dist-info → xnatqa-0.0.11.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (79.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

xnatqa/launch/__init__.py

@@ -1,36 +0,0 @@
-import os
-import yaxil
-
-def launch(MRsession):
-    # So, at this point, everything has been labeled for this session.
-    # We now need to:
-
-    # Identify all of the tagged scans in this sessions
-    # For each tagged scan, launch the appropriate QA routine
-
-    # authenticate with xnat using the ~/.xnat_auth file created earlier in the workflow
-    auth = yaxil.auth(alias = 'xnat')
-
-    # open and automatically close a connection to XNAT using the auth
-    with yaxil.session(auth) as sess:
-        # keep track of the number of BOLD (b) and ANAT (a) scans idenfified
-        b = 0
-        a = 0
-
-        # for each scan in this session...
-        for scan in sess.scans(label=MRsession):
-
-            # this scan's note
-            note = scan['note']
-
-            # if that note has a "#BOLD" tag...
-            if '#BOLD' in note:
-                print('Run BOLDQC')
-                os.system(f'qsub -P drkrcs boldqc.qsub {MRsession} {b}')
-                b+=1
-
-            # if that note has a "#T1w" tag...
-            if '#T1w' in note:
-                print('Run ANATQC')
-                os.system(f'qsub -P drkrcs anatqc.qsub {MRsession} {a}')
-                a+=1

xnatqa-0.0.9.dist-info/RECORD

@@ -1,10 +0,0 @@
-xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
-xnatqa/xnatqa.py,sha256=8W4iN98gWyVD8uVcdTkF3K7pFqrm6riBQaS90pq9ohk,1289
-xnatqa/launch/__init__.py,sha256=zT6XGXWBHOtHZ_TVmlN9vp3V8JqUAYscxMBUZJJBlgo,1178
-xnatqa/tag/__init__.py,sha256=kjdB9zSA_YHGOPmG_BDM0HtSK6thmBt0Awd4Zj6NN5A,8921
-xnatqa-0.0.9.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xnatqa-0.0.9.dist-info/METADATA,sha256=3fDVZzf8u6yRY4fAlMrDuo5CsiIRWh0WILFmSRIdzX0,1199
-xnatqa-0.0.9.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-xnatqa-0.0.9.dist-info/entry_points.txt,sha256=UqPAByHiJTqwkT0UBymn6EOIGBlPsb9mEZK86HIahs8,46
-xnatqa-0.0.9.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
-xnatqa-0.0.9.dist-info/RECORD,,