xnatqa 0.0.15__tar.gz → 0.0.17__tar.gz

{xnatqa-0.0.15/xnatqa.egg-info → xnatqa-0.0.17}/PKG-INFO

@@ -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-0.0.15 → xnatqa-0.0.17}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xnatqa"
-version = "0.0.15"
+version = "0.0.17"
 authors = [
   { name="Kyle Kurkela", email="kkurkela@bu.edu" },
 ]
@@ -22,6 +22,7 @@ dependencies = [
 
 [project.scripts]
 xnatqa = "xnatqa.xnatqa:main"
+launch = "xnatqa.launch:main"
 
 [project.urls]
 Homepage = "https://github.com/kakurk/auto_labeler"

xnatqa-0.0.17/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-0.0.15 → xnatqa-0.0.17}/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-0.0.15 → xnatqa-0.0.17}/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 → xnatqa-0.0.17/xnatqa.egg-info}/PKG-INFO

@@ -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-0.0.15 → xnatqa-0.0.17}/xnatqa.egg-info/SOURCES.txt

@@ -2,6 +2,7 @@ LICENSE
 README.md
 pyproject.toml
 xnatqa/__init__.py
+xnatqa/launch.py
 xnatqa/xnatqa.py
 xnatqa.egg-info/PKG-INFO
 xnatqa.egg-info/SOURCES.txt

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

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