io improved (#120)

bin/C2C-slurm

@@ -33,11 +33,11 @@ def python_submit(command, node="amalfi"):
             print(f'Submitted the command --- "{command}" --- to slurm.')
     except subprocess.CalledProcessError:
         if node == None:
-            command = f"sbatch -c 8 --gres=gpu:1 --output ./slurm/slurm-%j.out --time=100-00:00:00 slurm.sh "
+            command = f"sbatch -c 8 --gres=gpu:1 --output ./slurm/slurm-%j.out --mem=128000 --time=100-00:00:00 slurm.sh "
             submit_command(command)
             print(f'Submitted the command --- "{command}" --- to slurm.')
         else:
-            command = f"sbatch -c 8 --gres=gpu:1 --output ./slurm/slurm-%j.out --nodelist={node} --time=100-00:00:00 slurm.sh"
+            command = f"sbatch -c 8 --gres=gpu:1 --output ./slurm/slurm-%j.out --nodelist={node} --mem=128000 --time=100-00:00:00 slurm.sh"
             submit_command(command)
             print(f'Submitted the command --- "{command}" --- to slurm.')
     os.remove("./slurm.sh")

comp2comp/io/io.py

@@ -114,17 +114,25 @@ def __call__(self, inference_pipeline):
         return {}
 
 
+def series_selector(dicom_path):
+    ds = pydicom.filereader.dcmread(dicom_path)
+    image_type_list = list(ds.ImageType)
+    if not any("primary" in s.lower() for s in image_type_list):
+        raise ValueError("Not primary image type")
+    if not any("original" in s.lower() for s in image_type_list):
+        raise ValueError("Not original image type")
+    if any("gsi" in s.lower() for s in image_type_list):
+        raise ValueError("GSI image type")
+    if ds.ImageOrientationPatient != [1, 0, 0, 0, 1, 0]:
+        raise ValueError("Image orientation is not axial")
+    return ds
+
+
 def dicom_series_to_nifti(input_path, output_file, reorient_nifti):
     reader = sitk.ImageSeriesReader()
     dicom_names = reader.GetGDCMSeriesFileNames(str(input_path))
-    print("Reading dicoms...")
-    ds = pydicom.filereader.dcmread(dicom_names[0])
-    image_type_list = list(ds.ImageType)
-    if any("gsi" in s.lower() for s in image_type_list):
-        raise ValueError("GSI Image Type detected")
+    ds = series_selector(dicom_names[0])
     reader.SetFileNames(dicom_names)
     image = reader.Execute()
-    if image.GetDirection() != (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0):
-        raise ValueError("Image orientation is not axial")
     sitk.WriteImage(image, output_file)
     return ds

comp2comp/io/io_utils.py

@@ -52,13 +52,13 @@ def get_dicom_or_nifti_paths_and_num(path):
     dicom_nifti_paths = []
     for root, dirs, files in os.walk(path):
         if len(files) > 0:
-            if all(file.endswith(".dcm") or file.endswith(".dicom") for file in files):
-                dicom_nifti_paths.append((root, len(files)))
-            else:
-                for file in files:
-                    if file.endswith(".nii") or file.endswith(".nii.gz"):
-                        num_slices = 450
-                        dicom_nifti_paths.append((os.path.join(root, file), num_slices))
+            # if all(file.endswith(".dcm") or file.endswith(".dicom") for file in files):
+            dicom_nifti_paths.append((root, len(files)))
+            # else:
+            #     for file in files:
+            #         if file.endswith(".nii") or file.endswith(".nii.gz"):
+            #             num_slices = 450
+            #             dicom_nifti_paths.append((os.path.join(root, file), num_slices))
 
     return dicom_nifti_paths