xnatqa 0.0.6__py3-none-any.whl → 0.0.8__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('./output*.json')
 
     # sort the found files so that they are in decensing order by series_number
     # this is probably unnecssary

xnatqa/xnatqa.py

@@ -0,0 +1,29 @@
+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)

{xnatqa-0.0.6.dist-info → xnatqa-0.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.6
+Version: 0.0.8
 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-0.0.8.dist-info/RECORD

@@ -0,0 +1,10 @@
+xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
+xnatqa/xnatqa.py,sha256=UoX74fhC5I3Cj4nyc1ORtH8P5sGApySvQ2UmeO2kpHM,1157
+xnatqa/launch/__init__.py,sha256=zT6XGXWBHOtHZ_TVmlN9vp3V8JqUAYscxMBUZJJBlgo,1178
+xnatqa/tag/__init__.py,sha256=kjdB9zSA_YHGOPmG_BDM0HtSK6thmBt0Awd4Zj6NN5A,8921
+xnatqa-0.0.8.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xnatqa-0.0.8.dist-info/METADATA,sha256=VrY4Obk0gvF8Ryk6gGQGL_DXv5GlIa71Itx6c0pUxSM,1199
+xnatqa-0.0.8.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+xnatqa-0.0.8.dist-info/entry_points.txt,sha256=UqPAByHiJTqwkT0UBymn6EOIGBlPsb9mEZK86HIahs8,46
+xnatqa-0.0.8.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
+xnatqa-0.0.8.dist-info/RECORD,,

xnatqa-0.0.8.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+xnatqa = xnatqa.xnatqa:main

xnatqa-0.0.6.dist-info/RECORD

@@ -1,9 +0,0 @@
-xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
-xnatqa/launch/__init__.py,sha256=zT6XGXWBHOtHZ_TVmlN9vp3V8JqUAYscxMBUZJJBlgo,1178
-xnatqa/tag/__init__.py,sha256=xo9FVN7uXk4SLo6vvk6952TMYkQxZxCxR1l_Nz6IFtU,8919
-xnatqa-0.0.6.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xnatqa-0.0.6.dist-info/METADATA,sha256=fS4mtDUVMOQW2kg7caohnIGbM_YtdxVHUzt0DFvGKlk,1199
-xnatqa-0.0.6.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-xnatqa-0.0.6.dist-info/entry_points.txt,sha256=G30HgsnWfJ_xIDqEe6A_ArQaCyautyQCvoBPYM2DlFc,47
-xnatqa-0.0.6.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
-xnatqa-0.0.6.dist-info/RECORD,,

xnatqa-0.0.6.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-xnatqa = scripts.xnatqa:main