xnatqa 0.0.10__tar.gz → 0.0.12__tar.gz

{xnatqa-0.0.10/xnatqa.egg-info → xnatqa-0.0.12}/PKG-INFO

@@ -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-0.0.10 → xnatqa-0.0.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xnatqa"
-version = "0.0.10"
+version = "0.0.12"
 authors = [
   { name="Kyle Kurkela", email="kkurkela@bu.edu" },
 ]

{xnatqa-0.0.10 → xnatqa-0.0.12}/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-0.0.10 → xnatqa-0.0.12}/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 → xnatqa-0.0.12/xnatqa.egg-info}/PKG-INFO

@@ -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-0.0.10 → xnatqa-0.0.12}/xnatqa.egg-info/SOURCES.txt

@@ -9,5 +9,4 @@ xnatqa.egg-info/dependency_links.txt
 xnatqa.egg-info/entry_points.txt
 xnatqa.egg-info/requires.txt
 xnatqa.egg-info/top_level.txt
-xnatqa/launch/__init__.py
 xnatqa/tag/__init__.py

xnatqa-0.0.10/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