Improve conversion of DICOM-SEGs to ITK images in DICOMWeb datastore

monailabel/datastore/utils/convert.py

@@ -13,11 +13,11 @@
 import logging
 import os
 import pathlib
-import shutil
 import tempfile
 import time
 
 import numpy as np
+import pydicom
 import pydicom_seg
 import SimpleITK
 from monai.data import write_nifti
@@ -35,7 +35,7 @@ def dicom_to_nifti(series_dir, is_seg=False):
     start = time.time()
 
     if is_seg:
-        output_file = itk_dicom_seg_to_image(series_dir)
+        output_file = dicom_seg_to_itk_image(series_dir)
     else:
         # https://simpleitk.readthedocs.io/en/master/link_DicomConvert_docs.html
         if os.path.isdir(series_dir) and len(os.listdir(series_dir)) > 1:
@@ -193,30 +193,21 @@ def itk_image_to_dicom_seg(label, series_dir, template):
     return output_file
 
 
-def itk_dicom_seg_to_image(label, output_type="nifti"):
-    # TODO:: Currently supports only one file
+def dicom_seg_to_itk_image(label, output_ext=".seg.nrrd"):
     filename = label if not os.path.isdir(label) else os.path.join(label, os.listdir(label)[0])
-    with tempfile.TemporaryDirectory() as output_dir:
-        command = "segimage2itkimage"
-        args = [
-            "--inputDICOM",
-            filename,
-            "--outputType",
-            output_type,
-            "--prefix",
-            "segment",
-            "--outputDirectory",
-            output_dir,
-        ]
-        run_command(command, args)
-        output_files = [f for f in os.listdir(output_dir) if f.startswith("segment") and f.endswith(".nii.gz")]
-        if not output_files:
-            logger.warning(f"Failed to convert DICOM-SEG {label} to NIFTI")
-            return None
-
-        result_file = os.path.join(output_dir, output_files[0])
-        logger.info(f"Result/Output (NII) File: {result_file}")
 
-        output_file = tempfile.NamedTemporaryFile(suffix=".nii.gz").name
-        shutil.move(result_file, output_file)
-        return output_file
+    dcm = pydicom.dcmread(filename)
+    reader = pydicom_seg.MultiClassReader()
+    result = reader.read(dcm)
+    image = result.image
+
+    output_file = tempfile.NamedTemporaryFile(suffix=output_ext).name
+
+    SimpleITK.WriteImage(image, output_file, True)
+
+    if not os.path.exists(output_file):
+        logger.warning(f"Failed to convert DICOM-SEG {label} to ITK image")
+        return None
+
+    logger.info(f"Result/Output File: {output_file}")
+    return output_file

monailabel/interfaces/app.py

@@ -553,7 +553,7 @@ def _download_dcmqi_tools(self):
         target = os.path.join(self.app_dir, "bin")
         os.makedirs(target, exist_ok=True)
 
-        dcmqi_tools = ["segimage2itkimage", "itkimage2segimage", "segimage2itkimage.exe", "itkimage2segimage.exe"]
+        dcmqi_tools = ["itkimage2segimage", "itkimage2segimage.exe"]
         existing = [tool for tool in dcmqi_tools if shutil.which(tool) or os.path.exists(os.path.join(target, tool))]
         logger.debug(f"Existing Tools: {existing}")