xnatqa 0.0.10__py3-none-any.whl → 0.0.12__py3-none-any.whl

xnatqa/tag/__init__.py

@@ -22,7 +22,7 @@ def generate_tagger_config(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('./output*.json')
+    jsonFiles = glob(os.path.abspath('./output*.json'))
 
     # sort the found files so that they are in decensing order by series_number
     # this is probably unnecssary
@@ -180,6 +180,8 @@ 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.

xnatqa/xnatqa.py

@@ -1,7 +1,6 @@
 import os
 import argparse
 from xnatqa.tag import tag_scans
-from xnatqa.launch import launch
 
 def main():
 
@@ -21,8 +20,5 @@ def main():
     # 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-0.0.10.dist-info → xnatqa-0.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.10
+Version: 0.0.12
 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-0.0.12.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=1casm1PdVZJ6PmgYYpOdWTZSTWQTMq0O6Inh9s0sqAg,8962
+xnatqa-0.0.12.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xnatqa-0.0.12.dist-info/METADATA,sha256=aBlwosLPDfIyUVjJGYJR89bRDLtSTrAOwHgLmQ-MkJ4,1200
+xnatqa-0.0.12.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
+xnatqa-0.0.12.dist-info/entry_points.txt,sha256=UqPAByHiJTqwkT0UBymn6EOIGBlPsb9mEZK86HIahs8,46
+xnatqa-0.0.12.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
+xnatqa-0.0.12.dist-info/RECORD,,

{xnatqa-0.0.10.dist-info → xnatqa-0.0.12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.0.0)
 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-0.0.10.dist-info/RECORD

@@ -1,10 +0,0 @@
-xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
-xnatqa/xnatqa.py,sha256=RuQlEAEODNWnu5gN4zcxiK59vjkANX4RG1JanvFRrfM,960
-xnatqa/launch/__init__.py,sha256=zT6XGXWBHOtHZ_TVmlN9vp3V8JqUAYscxMBUZJJBlgo,1178
-xnatqa/tag/__init__.py,sha256=kjdB9zSA_YHGOPmG_BDM0HtSK6thmBt0Awd4Zj6NN5A,8921
-xnatqa-0.0.10.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xnatqa-0.0.10.dist-info/METADATA,sha256=M8Dd-yP3hg_AhC_BT0JRG3Bkng7bdDWaqIxYql5-Qcs,1200
-xnatqa-0.0.10.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-xnatqa-0.0.10.dist-info/entry_points.txt,sha256=UqPAByHiJTqwkT0UBymn6EOIGBlPsb9mEZK86HIahs8,46
-xnatqa-0.0.10.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
-xnatqa-0.0.10.dist-info/RECORD,,