xnatqa 0.0.20__py3-none-any.whl → 0.0.23__py3-none-any.whl

xnatqa/launch.py

@@ -1,6 +1,7 @@
 import os
 import yaxil
 import argparse
+import re
 
 def main():
     # So, at this point, everything has been labeled for this session.
@@ -27,27 +28,41 @@ def main():
     # 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']
+            id = scan['ID']
+            type = scan['type']
+            SeriesDesc = scan['series_description']
+            quality = scan['quality']
 
             # if that note has a "#BOLD" tag...
             if '#BOLD' in note:
+
+                run = re.search('[0-9]{3}', note)
+                run = int(run.group())
+
+                print('')
                 print('Run BOLDQC:')
-                print(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
+                print(f'{id}\t{type}\t{SeriesDesc}\t{quality}\t{note}')
+                print(f'qsub -P cncxnat boldqc.qsub {MRsession} {run}')
+                print('')
                 if not dryrun:
-                    os.system(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
-                b+=1
+                    os.system(f'qsub -P cncxnat boldqc.qsub {MRsession} {run}')
 
             # if that note has a "#T1w" tag...
             if '#T1w' in note:
+
+                run = re.search('[0-9]{3}', note)
+                run = int(run.group())
+
+                print('')
                 print('Run ANATQC:')
-                print(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
+                print(f'{id}\t{type}\t{SeriesDesc}\t{quality}\t{note}')             
+                print(f'qsub -P cncxnat anatqc.qsub {MRsession} {run}')
+                print('')
                 if not dryrun:
-                    os.system(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
-                a+=1
+                    os.system(f'qsub -P cncxnat anatqc.qsub {MRsession} {run}')

xnatqa/tag/__init__.py

@@ -3,6 +3,7 @@ import yaml
 from glob import glob
 import re
 import xnatqa
+import shutil
 
 def extract_bids_suffix(bids_string):
         # Extract the BIDS suffix from a BIDS formatted string
@@ -18,9 +19,15 @@ def generate_tagger_config(dicom_dir, working_dir):
     # dcm2niix will also include a field called "BidsGuess" containing an "educated guess" as to what the BIDS label of this scan should be.
     # This seems to work well most of the time, with the odd hicups. I include manual code here to catch the "hicups".
 
+    # first, make sure the dcm2niix is on the searchpath. Thow an informative error if it isn't
+    if shutil.which('dcm2niix') is None:
+        raise FileNotFoundError(f'dcm2niix not found on PATH')
+
     # 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 {working_dir} -f 'output_%s_%d' -w 0 -m 1 -i y {dicom_dir} &>>{working_dir}/log.txt")
 
+def generate_tagger_yaml(working_dir):
+
     # idenfity all of these text files
     jsonFiles = glob(f'{working_dir}/output*.json')
 
@@ -29,7 +36,7 @@ def generate_tagger_config(dicom_dir, working_dir):
     jsonFiles.sort(key=lambda f: int(re.search('(?<=output_)\d+(?=_)', f).group()))
 
     # initialize a dictionary to hold xnattager data
-    tagger_data = dict(t1 = [], t1_move = [], t2 = [], t2_move = [], bold = [])
+    tagger_data = dict(t1w = [], t1w_move = [], t2w = [], t2w_move = [], bold = [])
 
     # looping over the json sidecar files...
     for f in jsonFiles:
@@ -41,13 +48,14 @@ def generate_tagger_config(dicom_dir, working_dir):
         series_description = json_data['SeriesDescription']
         series_number = json_data['SeriesNumber']
         image_type = json_data['ImageType']
-        # remove the last element of the image_type list
+        # remove the last element of the image_type list. For whatever reason
         del image_type[-1]
-        bids_guess = json_data['BidsGuess']
 
         # if there is a BidsGuess field...
         if 'BidsGuess' in json_data.keys():
 
+            bids_guess = json_data['BidsGuess']
+
             # if that guess was "func"
             if bids_guess[0] == 'func':
 
@@ -58,12 +66,12 @@ def generate_tagger_config(dicom_dir, working_dir):
                 if bids_suffix == 'bold':
 
                     # there are a couple of common problems with the BidsGuess feature. One is that it does NOT properly identify "SBREF" scans. Make sure this is not an "SBREF" scan. Here I search for the keyword "SBREF" to be somewhere within the study description name.
-                    sbref_keywords = ['sbref']
+                    sbref_keywords = ['sbref'] # 'localizer'
 
                     if any(kw in series_description.lower() for kw in sbref_keywords):
 
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f"Bids Guess: {json_data['BidsGuess']}")
                         print('Is an SBREF scan. Ignoring...')
@@ -76,36 +84,40 @@ def generate_tagger_config(dicom_dir, working_dir):
                     if any(kw in series_description.lower() for kw in exclude_keywords):
 
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f"Bids Guess: {bids_guess}")
                         print('Relableing to T1...')
                         print()
 
-                        tagger_data['t1'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T1w'})
+                        tagger_data['t1w'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T1w'})
                         continue
 
                     exclude_keywords = ['t2']
                     if any(kw in series_description.lower() for kw in exclude_keywords):
 
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f'Bids Guess: {bids_guess}')
                         print('Relableing to T2...')
                         print()
 
-                        tagger_data['t2'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T2w'})
+                        #tagger_data['t2w'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T2w'})
                         continue
 
                     print()
-                    print(f'Series Number: {series_number}')    
+                    print(f'Series Number: {series_number}')
                     print(f'Series Description: {series_description}')
                     print(f'Bids Guess: {bids_guess}')
                     print('Labeling as BOLD...')
                     print()
 
-                    tagger_data['bold'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#BOLD'})
+                    entry = {'series_description': series_description, 'image_type': image_type, 'tag': '#BOLD'}
+
+                    if entry not in tagger_data['bold']:
+                        tagger_data['bold'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#BOLD'})
+
                     continue
 
             # if the BidsGuess was "anat"...
@@ -125,56 +137,56 @@ def generate_tagger_config(dicom_dir, working_dir):
                         # this is a T1w VNAV setter scan.
 
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f"Bids Guess: {bids_guess}")
                         print('Labeling as T1w_move...')
                         print()
-                        
-                        tagger_data['t1_move'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T1w_MOVE'})
+
+                        #tagger_data['t1w_move'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T1w_MOVE'})
                         continue
 
                     elif not NonlinearGradientCorrection and 'NumberOfAverages' in json_data:
-                        
+
                         # this is a T1w scan
 
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f"Bids Guess: {bids_guess}")
                         print('Labeling as T1w...')
                         print()
-                        
-                        tagger_data['t1'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T1w'})
+
+                        tagger_data['t1w'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T1w'})
                         continue
 
                 elif bids_suffix == 'T2w':
 
                     if json_data['SliceThickness'] == 8:
-                        
+
                         # this is a T2w VNAV setter scan
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f"Bids Guess: {bids_guess}")
                         print('Labeling as T2w_move...')
                         print()
 
-                        tagger_data['t2_move'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T2w_move'})
+                        #tagger_data['t2w_move'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T2w_move'})
                         continue
 
                     else:
 
                         # this is a T2w scan
                         print()
-                        print(f'Series Number: {series_number}')    
+                        print(f'Series Number: {series_number}')
                         print(f'Series Description: {series_description}')
                         print(f"Bids Guess: {bids_guess}")
-                        print('Labeling as T2w...')                        
+                        print('Labeling as T2w...')
                         print()
 
-                        tagger_data['t2'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T2w'})
-                        continue                    
+                        #tagger_data['t2w'].append({'series_description': series_description, 'image_type': image_type, 'tag': '#T2w'})
+                        continue
 
     # write tagger data to a yaml file. used by the xnattagger package for uploading tags to XNAT. See github.com/harvard-nrg/xnattager
     with open(f'{working_dir}/tagger.yaml', 'a') as file:
@@ -187,15 +199,3 @@ def update_xnat_tags(MRsession, working_dir):
 
     # run the command
     os.system(f'xnat_tagger.py --label {MRsession} --target-modality all --xnat-alias xnat --config {working_dir}/tagger.yaml')
-
-def tag_scans(dicom_dir, MRsession, working_dir, dryrun):
-    
-    this_session_working_dir=os.path.join(working_dir, MRsession)
-
-    # generate the xnattag config file
-    generate_tagger_config(dicom_dir, this_session_working_dir)
-    
-    # update the xnat tags
-    if not dryrun:
-        update_xnat_tags(MRsession, this_session_working_dir)
-

xnatqa/{xnatqa.py → tagger.py}

@@ -1,6 +1,9 @@
 import os
 import argparse
-from xnatqa.tag import tag_scans
+from xnatqa.tag import generate_tagger_config
+from xnatqa.tag import generate_tagger_yaml
+from xnatqa.tag import update_xnat_tags
+import shutil
 
 def main():
 
@@ -18,7 +21,21 @@ def main():
     dryrun      = args.dryrun
 
     # tag all scans in this session
-    tag_scans(dicom_dir, experiment, working_dir, dryrun)
+     # create a working directory to write temporary files
+    this_session_working_dir = os.path.join(working_dir, 'xnattager', experiment)
+    if os.path.isdir(this_session_working_dir):
+        shutil.rmtree(this_session_working_dir)
+    os.makedirs(this_session_working_dir)
+
+    # generate the xnattag config file
+    generate_tagger_config(dicom_dir, this_session_working_dir)
+    
+    # general the yaml
+    generate_tagger_yaml(this_session_working_dir)
+
+    # update the xnat tags
+    if not dryrun:
+        update_xnat_tags(experiment, this_session_working_dir)
 
 if __name__ == "__main__":
     main()

{xnatqa-0.0.20.dist-info → xnatqa-0.0.23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.20
+Version: 0.0.23
 Summary: A workflow for automatically tagging MRI scans within XNAT
 Author-email: Kyle Kurkela <kkurkela@bu.edu>
 License-Expression: MIT

xnatqa-0.0.23.dist-info/RECORD

@@ -0,0 +1,10 @@
+xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
+xnatqa/launch.py,sha256=k8e2_7XBIhJlJkTNQuTXVcPGnnkb_sbdp7jMIEjyTA8,2505
+xnatqa/tagger.py,sha256=YmjtjZRtwOgXHVYrz1FcppgdjYoXl6u3Ln7v1WdKkOo,1540
+xnatqa/tag/__init__.py,sha256=Sv1YUK0RdjkwZePlbZHpStM3nfFNpAczovwGXL9ZKkQ,9140
+xnatqa-0.0.23.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xnatqa-0.0.23.dist-info/METADATA,sha256=orWZW2DRO3PxWkiG1xXLH4IsY3w0t7DmHbsF7iiwx8E,1187
+xnatqa-0.0.23.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+xnatqa-0.0.23.dist-info/entry_points.txt,sha256=ueAa8JobR7U4C8T4CszGxy2TQVp-2cK4OMMOBUbIYYw,74
+xnatqa-0.0.23.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
+xnatqa-0.0.23.dist-info/RECORD,,

{xnatqa-0.0.20.dist-info → xnatqa-0.0.23.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.3.1)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{xnatqa-0.0.20.dist-info → xnatqa-0.0.23.dist-info}/entry_points.txt

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

xnatqa-0.0.20.dist-info/RECORD

@@ -1,10 +0,0 @@
-xnatqa/__init__.py,sha256=RIG_ihjfFD1upKlhlxI-9Fs4ISf0lIW4Zg7CaFirV4A,644
-xnatqa/launch.py,sha256=QWqLdwfbq28cmeJd4XQcV2wxs2ZGRX85uzFmxHydmfg,1963
-xnatqa/xnatqa.py,sha256=PEAe3LGFKZ2KSVO4Bd5vAGuMeaFkXCg5GVY1sCr8K-E,915
-xnatqa/tag/__init__.py,sha256=dmreB5C3_GqL6v3JIfUai59NeUtBQy6xSTb2UilcREM,9175
-xnatqa-0.0.20.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xnatqa-0.0.20.dist-info/METADATA,sha256=TVvwxvUXdB2mQSGJlCGEctq_BtjA30mqomn1jn1Kwa4,1187
-xnatqa-0.0.20.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
-xnatqa-0.0.20.dist-info/entry_points.txt,sha256=g5CvKDfx6vIIp76wdB1aiWe1SkBORj2S8gFReBBxBws,74
-xnatqa-0.0.20.dist-info/top_level.txt,sha256=FmRWgO6ww0FwyNs5ccyhP9FcAxI129qSJqLs2OKOxJw,7
-xnatqa-0.0.20.dist-info/RECORD,,