xnatqa 0.0.15__py3-none-any.whl → 0.0.17__py3-none-any.whl

xnatqa/launch.py

@@ -0,0 +1,50 @@
+import os
+import yaxil
+import argparse
+
+def main():
+    # 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
+
+    # parse input arguments
+    parser = argparse.ArgumentParser(description="XNAT QA Workflow")
+    parser.add_argument("--experiment", default = "", required=True)
+    parser.add_argument("--dryrun", default = "", action='store_true', help="Run in dry run mode: No launching of jobs")
+
+    args, unknown_args = parser.parse_known_args()
+    MRsession = args.experiment
+    dryrun    = args.dryrun
+
+    # 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:')
+                print(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
+                if not dryrun:
+                    os.system(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
+                b+=1
+
+            # if that note has a "#T1w" tag...
+            if '#T1w' in note:
+                print('Run ANATQC:')
+                print(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
+                if not dryrun:
+                    os.system(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
+                a+=1

xnatqa/tag/__init__.py

@@ -19,7 +19,7 @@ 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}")
+    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")
 
     # idenfity all of these text files
     jsonFiles = glob(os.path.abspath('./output*.json'))
@@ -180,8 +180,6 @@ def generate_tagger_config(dicom_dir):
     with open('tagger.yaml', 'a') as file:
         yaml.dump(tagger_data, file)
 
-    print(tagger_data)
-
 def update_xnat_tags(MRsession):
 
     # make sure an xnat authentication files has already been created. See YXAIL documentation.
@@ -190,11 +188,12 @@ def update_xnat_tags(MRsession):
     # run the command
     os.system(f'xnat_tagger.py --label {MRsession} --target-modality all --xnat-alias xnat --config tagger.yaml')
 
-def tag_scans(dicom_dir, MRsession):
+def tag_scans(dicom_dir, MRsession, dryrun):
     
     # generate the xnattag config file
     generate_tagger_config(dicom_dir)
     
     # update the xnat tags
-    update_xnat_tags(MRsession)
+    if not dryrun:
+        update_xnat_tags(MRsession)
 

xnatqa/xnatqa.py

@@ -8,17 +8,19 @@ 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("--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, 'SCANS')
     experiment = args.experiment
+    dryrun     = args.dryrun
 
     # 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 $XNAT_HOST --username $XNAT_USER --password $XNAT_PASS')
 
     # tag all scans in this session
-    tag_scans(dicom_dir, experiment)
+    tag_scans(dicom_dir, experiment, dryrun)
 
 if __name__ == "__main__":
     main()

{xnatqa-0.0.15.dist-info → xnatqa-0.0.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.15
+Version: 0.0.17
 Summary: A workflow for automatically tagging MRI scans within XNAT
 Author-email: Kyle Kurkela <kkurkela@bu.edu>
 License-Expression: MIT

xnatqa-0.0.17.dist-info/RECORD

@@ -0,0 +1,10 @@
+xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
+xnatqa/launch.py,sha256=jZTCAftrT5MBcbPKXNorFux5TkezyktJBhzJaKI4ypM,1797
+xnatqa/xnatqa.py,sha256=KUXfs6EAZX15K2s8JcsIXuUOV1swma_7gJw-IRkD1yM,1016
+xnatqa/tag/__init__.py,sha256=wXPBIbHucCqITYVZ4V5bt3VJWq8svyrJoBjbrpH1bNE,8969
+xnatqa-0.0.17.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xnatqa-0.0.17.dist-info/METADATA,sha256=NdGanatTgamPgLnL20wQHgJYdJj7eHU2ZGoNdnXs2eE,1187
+xnatqa-0.0.17.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+xnatqa-0.0.17.dist-info/entry_points.txt,sha256=g5CvKDfx6vIIp76wdB1aiWe1SkBORj2S8gFReBBxBws,74
+xnatqa-0.0.17.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
+xnatqa-0.0.17.dist-info/RECORD,,

{xnatqa-0.0.15.dist-info → xnatqa-0.0.17.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.0.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{xnatqa-0.0.15.dist-info → xnatqa-0.0.17.dist-info}/entry_points.txt

@@ -1,2 +1,3 @@
 [console_scripts]
+launch = xnatqa.launch:main
 xnatqa = xnatqa.xnatqa:main

xnatqa-0.0.15.dist-info/RECORD

@@ -1,9 +0,0 @@
-xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
-xnatqa/xnatqa.py,sha256=RJp65oIE13COs_0UG4hEku_f6YFDpoQV4JHEhtppXfs,861
-xnatqa/tag/__init__.py,sha256=7i24jiDBNJdv6VF9RzkRrprXuZKpnV63bvEXnLaDXk0,8951
-xnatqa-0.0.15.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xnatqa-0.0.15.dist-info/METADATA,sha256=Pi0vL85UOTqbwRUYFbU4obHjif3acmEAoqeBf5yhMAQ,1187
-xnatqa-0.0.15.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
-xnatqa-0.0.15.dist-info/entry_points.txt,sha256=UqPAByHiJTqwkT0UBymn6EOIGBlPsb9mEZK86HIahs8,46
-xnatqa-0.0.15.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
-xnatqa-0.0.15.dist-info/RECORD,,