Address a removed monai function, fix CUDA 11 runtime lib, and resurrect option to omit or not DICOM SEG empty frame (Project-MONAI#471)

* Updated the code where a deprecated monai core function is used.

Signed-off-by: M Q <[email protected]>

* Add back the option for if omitting DICOM SEG empty frames, defaults to true.

Signed-off-by: M Q <[email protected]>

* Pin torch to ~=2.0.1 for libcudart.11.0

Signed-off-by: M Q <[email protected]>

* Test packages

Signed-off-by: M Q <[email protected]>

---------

Signed-off-by: M Q <[email protected]>
Signed-off-by: Simone Bendazzoli <[email protected]>

Author: MMelQin

.github/workflows/pr.yml

@@ -30,8 +30,9 @@ jobs:
           python3 -c 'import sys; print(sys.executable)'
           python3 -c 'import site; print(site.getsitepackages())'
           python3 -m pip freeze
+          export LD_LIBRARY_PATH=`pwd`/.venv/lib/python3.8/site-packages/nvidia/cuda_runtime/lib:$LD_LIBRARY_PATH
           python3 -c 'from holoscan.core import *'
-          ./run check -f          
+          ./run check -f
       - name: Run Unit tests
         run: |
           source .venv/bin/activate

monai/deploy/operators/dicom_seg_writer_operator.py

@@ -1,4 +1,4 @@
-# Copyright 2021-2025 MONAI Consortium
+# Copyright 2021-2023 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -27,7 +27,6 @@
 ImplicitVRLittleEndian, _ = optional_import("pydicom.uid", name="ImplicitVRLittleEndian")
 Dataset, _ = optional_import("pydicom.dataset", name="Dataset")
 FileDataset, _ = optional_import("pydicom.dataset", name="FileDataset")
-PyDicomSequence, _ = optional_import("pydicom.sequence", name="Sequence")
 sitk, _ = optional_import("SimpleITK")
 codes, _ = optional_import("pydicom.sr.codedict", name="codes")
 if TYPE_CHECKING:
@@ -40,7 +39,6 @@
 from monai.deploy.core import ConditionType, Fragment, Image, Operator, OperatorSpec
 from monai.deploy.core.domain.dicom_series import DICOMSeries
 from monai.deploy.core.domain.dicom_series_selection import StudySelectedSeries
-from monai.deploy.operators.dicom_utils import ModelInfo
 
 
 class SegmentDescription:
@@ -185,7 +183,6 @@ def __init__(
         *args,
         segment_descriptions: List[SegmentDescription],
         output_folder: Path,
-        model_info: Optional[ModelInfo] = None,
         custom_tags: Optional[Dict[str, str]] = None,
         omit_empty_frames: bool = True,
         **kwargs,
@@ -209,8 +206,7 @@ def __init__(
                 Object encapsulating the description of each segment present in the segmentation.
             output_folder: Folder for file output, overridden by named input on compute.
                            Defaults to current working dir's child folder, output.
-            model_info (ModelInfo, optional): Object encapsulating model creator, name, version and UID.
-            custom_tags: Optional[Dict[str, str]], optional
+            custom_tags: Optonal[Dict[str, str]], optional
                 Dictionary for setting custom DICOM tags using Keywords and str values only
             omit_empty_frames: bool, optional
                 Whether to omit frames that contain no segmented pixels from the output segmentation.
@@ -221,7 +217,6 @@ def __init__(
         self._custom_tags = custom_tags
         self._omit_empty_frames = omit_empty_frames
         self.output_folder = output_folder if output_folder else DICOMSegmentationWriterOperator.DEFAULT_OUTPUT_FOLDER
-        self.model_info = model_info if model_info else ModelInfo()
 
         self.input_name_seg = "seg_image"
         self.input_name_series = "study_selected_series_list"
@@ -293,10 +288,8 @@ def process_images(
             seg_image_numpy = image.asnumpy()
         elif isinstance(image, (Path, str)):
             seg_image_numpy = self._image_file_to_numpy(str(image))
-        else:
-            if not isinstance(image, np.ndarray):
-                raise ValueError("'image' is not a numpy array, Image object, or supported image file.")
-            seg_image_numpy = image
+        elif not isinstance(image, np.ndarray):
+            raise ValueError("'image' is not a numpy array, Image object, or supported image file.")
 
         # Pick DICOM Series that was used as input for getting the seg image.
         # For now, first one in the list.
@@ -361,41 +354,6 @@ def create_dicom_seg(self, image: np.ndarray, dicom_series: DICOMSeries, output_
                         # Best effort for now.
                         logging.warning(f"Tag {k} was not written, due to {ex}")
 
-        # write model info
-        # code copied from write_common_modules method in monai.deploy.operators.dicom_utils
-
-        # Contributing Equipment Sequence
-        # The Creator shall describe each algorithm that was used to generate the results in the
-        # Contributing Equipment Sequence (0018,A001). Multiple items may be included. The Creator
-        # shall encode the following details in the Contributing Equipment Sequence:
-        #  • Purpose of Reference Code Sequence (0040,A170) shall be (Newcode1, 99IHE, 1630 "Processing Algorithm")
-        #  • Manufacturer (0008,0070)
-        #  • Manufacturer’s Model Name (0008,1090)
-        #  • Software Versions (0018,1020)
-        #  • Device UID (0018,1002)
-
-        if self.model_info:
-            # First create the Purpose of Reference Code Sequence
-            seq_purpose_of_reference_code = PyDicomSequence()
-            seg_purpose_of_reference_code = Dataset()
-            seg_purpose_of_reference_code.CodeValue = "Newcode1"
-            seg_purpose_of_reference_code.CodingSchemeDesignator = "99IHE"
-            seg_purpose_of_reference_code.CodeMeaning = '"Processing Algorithm'
-            seq_purpose_of_reference_code.append(seg_purpose_of_reference_code)
-
-            seq_contributing_equipment = PyDicomSequence()
-            seg_contributing_equipment = Dataset()
-            seg_contributing_equipment.PurposeOfReferenceCodeSequence = seq_purpose_of_reference_code
-            # '(121014, DCM, “Device Observer Manufacturer")'
-            seg_contributing_equipment.Manufacturer = self.model_info.creator
-            # u'(121015, DCM, “Device Observer Model Name")'
-            seg_contributing_equipment.ManufacturerModelName = self.model_info.name
-            # u'(111003, DCM, “Algorithm Version")'
-            seg_contributing_equipment.SoftwareVersions = self.model_info.version
-            seg_contributing_equipment.DeviceUID = self.model_info.uid  # u'(121012, DCM, “Device Observer UID")'
-            seq_contributing_equipment.append(seg_contributing_equipment)
-            seg.ContributingEquipmentSequence = seq_contributing_equipment
-
         seg.save_as(output_path)
 
         try: