add compatibility with windows

BIMCV-CSUSP · Aug 24, 2023 · 1c69def · 1c69def
1 parent 2239af8
commit 1c69def
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Showing 2 changed files with 29 additions and 12 deletions.
diff --git a/xnat2mids/conversion/dicom_converters.py b/xnat2mids/conversion/dicom_converters.py
@@ -4,7 +4,8 @@
 import json
 import pydicom
 import shutil
-
+import platform
+sistema = platform.system()
 # def sitk_dicom2mifti(dicom_path):
 #     reader = sitk.ImageSeriesReader()
 #     dicom_names = reader.GetGDCMSeriesFileNames(dicom_path.parent)
@@ -33,12 +34,21 @@ def dicom2niix(folder_json, str_options):
     folder_nifti = folder_json.parent.parent.joinpath("LOCAL_NIFTI", "files")
     folder_nifti.mkdir(parents=True, exist_ok=True)
     print(f"dcm2niix {str_options} -o {folder_nifti} {folder_json}")
-    subprocess.call(
-        f"dcm2niix {str_options} -o {folder_nifti} {folder_json}",
-        shell=True,
-        stdout=subprocess.DEVNULL,
-        stderr=subprocess.STDOUT
-    )
+    if sistema == "Linux":
+        subprocess.call(
+            f"dcm2niix {str_options} -o {folder_nifti} {folder_json}",
+            shell=True,
+            stdout=subprocess.DEVNULL,
+            stderr=subprocess.STDOUT
+        )
+    else:
+        print(f"dcm2niix.exe {str_options} -o {folder_nifti} {folder_json}")
+        subprocess.call(
+            f"dcm2niix.exe {str_options} -o {folder_nifti} {folder_json}",
+            shell=True,
+            stdout=subprocess.DEVNULL,
+            stderr=subprocess.STDOUT
+        )
     if len(list(folder_nifti.iterdir())) == 0:
         # folder_nifti.parent.unlink(missing_ok=True)
         return folder_nifti
@@ -62,8 +72,16 @@ def dicom2png(folder_json, str_options):
         folder_png.parent.mkdir(parents=True, exist_ok=True)
         sitk_img = sitk.ReadImage(dcm_file)
         sitk.WriteImage(sitk_img, folder_png)
-    subprocess.call(
-        f"dcm2niix {str_options} -b o -o {folder_png.parent} {dcm_files[0].parent}",
+    if sistema == "Linux":
+        subprocess.call(
+            f"dcm2niix {str_options} -b o -o {folder_png.parent} {dcm_files[0].parent}",
+            shell=True,
+            stdout=subprocess.DEVNULL,
+            stderr=subprocess.STDOUT
+        )
+    else:
+        subprocess.call(
+        f"dcm2niix.exe {str_options} -b o -o {folder_png.parent} {dcm_files[0].parent}",
         shell=True,
         stdout=subprocess.DEVNULL,
         stderr=subprocess.STDOUT
@@ -90,4 +108,3 @@ def add_dicom_metadata(
                              sort_keys=True)
     with json_filepath.open('w') as dicom_file:
         dicom_file.write(string_json)
-
diff --git a/xnat2mids/mids_conversion.py b/xnat2mids/mids_conversion.py
@@ -16,7 +16,7 @@
 from pandas.errors import EmptyDataError
 
 adquisition_date_pattern = r"(?P<year>\d+)-(?P<month>\d+)-(?P<day>\d+)T(?P<hour>\d+):(?P<minutes>\d+):(?P<seconds>\d+).(?P<ms>\d+)"
-subses_pattern = r"[A-z]+(?P<prefix_sub>\d*)?(_S)(?P<suffix_sub>\d+)/[A-z]+\-?[A-z]*(?P<prefix_ses>\d*)?(_E)(?P<suffix_ses>\d+)"
+subses_pattern = r"[A-z]+(?P<prefix_sub>\d*)?(_S)(?P<suffix_sub>\d+)(\\|/)[A-z]+\-?[A-z]*(?P<prefix_ses>\d*)?(_E)(?P<suffix_ses>\d+)"
 prostate_pattern = r"(?:(?:(?:diff?|dwi)(?:\W|_)(?:.*)(?:b\d+))|dif 2000)|(?:adc|Apparent)|prop|blade|fse|tse|^ax T2$"
 
 aquisition_date_pattern_comp = re.compile(adquisition_date_pattern)
@@ -107,7 +107,7 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part, debug_le
             if "_E" not in sessions_xnat_path.name: continue
 
 
-
+            print(sessions_xnat_path)
             findings = re.search(subses_pattern, str(sessions_xnat_path), re.X)
             #print('subject,', findings.group('prefix_sub'), findings.group('suffix_sub'))
             #print('session,', findings.group('prefix_ses'), findings.group('suffix_ses'))