xnatqa 0.0.7__tar.gz → 0.0.9__tar.gz

{xnatqa-0.0.7/xnatqa.egg-info → xnatqa-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.7
+Version: 0.0.9
 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-0.0.7 → xnatqa-0.0.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xnatqa"
-version = "0.0.7"
+version = "0.0.9"
 authors = [
   { name="Kyle Kurkela", email="kkurkela@bu.edu" },
 ]

{xnatqa-0.0.7 → xnatqa-0.0.9}/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('./output*.json')
 
     # sort the found files so that they are in decensing order by series_number
     # this is probably unnecssary

xnatqa-0.0.9/xnatqa/xnatqa.py

@@ -0,0 +1,34 @@
+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.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}')
+
+    # 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-0.0.7 → xnatqa-0.0.9/xnatqa.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.7
+Version: 0.0.9
 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-0.0.7/xnatqa/xnatqa.py

@@ -1,29 +0,0 @@
-import os
-import argparse
-from xnatqa.tag import tag_scans
-from xnatqa.launch import launch
-
-# parse input arguments
-parser = argparse.ArgumentParser(description="Auto Labeler")
-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}')
-
-# tag all scans in this session
-tag_scans(dicom_dir, experiment)
-
-# launch all QA jobs for this session
-launch(experiment)