Merge remote-tracking branch 'origin/Dev' into Dev

CNBP · Sep 4, 2019 · 3a06f6c · 3a06f6c
2 parents 5a2956f + ba2807f
commit 3a06f6c
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Showing 9 changed files with 10 additions and 6 deletions.
diff --git a/Python/DICOM/DICOM_universal.py b/Python/DICOM/DICOM_universal.py
@@ -30,10 +30,10 @@ def DICOM_universal_convert(input_folder, output_folder):
         else:
             os.chdir(output_folder)
 
-        DICOM_converter.raw(input_folder, output_folder)
+        #DICOM_converter.raw(input_folder, output_folder)
         DICOM_converter.raw_sorted(input_folder, output_folder)
-        DICOM_converter.raw_sorted_decompressed(input_folder, output_folder)
-        DICOM_converter.nii(input_folder, output_folder)
+        #DICOM_converter.raw_sorted_decompressed(input_folder, output_folder)
+        #DICOM_converter.nii(input_folder, output_folder)
         from pathlib import Path
 
         nii_cube = Path.joinpath(Path(output_folder), "raw_sorted_decompressed")
@@ -248,11 +248,13 @@ def DICOM_universal_convert_default(
 
     if len(sys.argv) != 3:
         input_root_folder = r"/toshiba2/Mathieus_MRI_Sab/dTGA_toConvert/dTGA_025_post_14-06-2019_FromClinicalPACs"
+        input_root_folder = (
+            r"/tmp/VXS38"
+        )
     else:
         logger.info(f"First Argument, input root folder path:{sys.argv[1]}")
         logger.info(f"Second Argument, output folder path: {sys.argv[2]}")
         input_root_folder = sys.argv[1]
         output_folder = sys.argv[2]
 
     DICOM_converter.DICOM_universal_convert_default(input_root_folder)
-    # DICOM_decompress.decompress_folder(r"/toshiba2/Mathieus_MRI_Sab/HIE_Raw/HIE_023_3226838_DICOMUniversal_2019-04-03/raw_sorted_decompressed")
diff --git a/Python/DICOM/tools.py b/Python/DICOM/tools.py
diff --git a/Python/Integration/fsm_retrospective.py b/Python/Integration/fsm_retrospective.py
@@ -109,7 +109,7 @@ def upload_retrospective_study(path_study_root_folder_path):
 
     start = time.time()
     logging.basicConfig(level=logging.INFO)
-    path_input = r"/toshiba2/Genetic_MRI_all_Sab"
+    path_input = r"/toshiba2/PRO_011_MathieuStudies/Mathieus_MRI_Sab/NewSubjects"
     upload_retrospective_study(path_input)
     end = time.time()
     print(str((end - start) / 60 / 60) + " hours")
diff --git a/Python/redcap/mysql_query.py b/Python/redcap/mysql_query.py
diff --git a/Python/redcap/test_mysql_query.py b/Python/redcap/test_mysql_query.py
diff --git a/Python/scheduler/crontab b/Python/scheduler/crontab
diff --git a/Python/scheduler/run_FSM.py b/Python/scheduler/run_FSM.py
diff --git a/Python/scheduler/run_LocalDB_dump.py b/Python/scheduler/run_LocalDB_dump.py
diff --git a/requirements.txt b/requirements.txt
@@ -13,4 +13,6 @@ flask
 transitions
 SimpleITK
 mysql-connector-python
-openpyxl
+openpyxl
+joblib
+sentry_sdk