Update to release v2.0 that is dependent on HSDK v2 (#485)

* Update to use HSDK v2

Signed-off-by: M Q <mingmelvinq@nvidia.com>

* Supress the new Flake8 complaints

Signed-off-by: M Q <mingmelvinq@nvidia.com>

* Avoid loading DICOMDir and tested all notebooks

Signed-off-by: M Q <mingmelvinq@nvidia.com>

* fix flake8 complaint

Signed-off-by: M Q <mingmelvinq@nvidia.com>

* logging the UID, if present, of the ignored instance

Signed-off-by: M Q <mingmelvinq@nvidia.com>

---------

Signed-off-by: M Q <mingmelvinq@nvidia.com>

Author: MMelQin

monai/deploy/operators/dicom_data_loader_operator.py

@@ -42,6 +42,9 @@ class DICOMDataLoaderOperator(Operator):
 
     DEFAULT_INPUT_FOLDER = Path.cwd() / "input"
     DEFAULT_OUTPUT_NAME = "dicom_study_list"
+    SOP_CLASSES_TO_IGNORE = [
+        "1.2.840.10008.1.3.10",  # Media Storage Directory Storage, aka DICOMDIR
+    ]
 
     # For now, need to have the input folder as an instance attribute, set on init, because even there is the optional
     # named input to receive data containing the path, there might not be upstream operator to emit the data.
@@ -170,6 +173,18 @@ def _load_data(self, files: List[str]):
         for sop_instance in sop_instances:
             study_instance_uid = sop_instance[0x0020, 0x000D].value.name  # name is the UID as str
 
+            # First need to eliminate the SOP instances whose SOP Class is to be ignored.
+            if "SOPInstanceUID" not in sop_instance:
+                self._logger.warn("Instance ignored due to missing SOP instance UID tag")
+                continue
+            sop_instance_uid = sop_instance["SOPInstanceUID"].value
+            if "SOPClassUID" not in sop_instance:
+                self._logger.warn(f"Instance ignored due to missing SOP Class UID tag, {sop_instance_uid}")
+                continue
+            if sop_instance["SOPClassUID"].value in DICOMDataLoaderOperator.SOP_CLASSES_TO_IGNORE:
+                self._logger.warn(f"Instance ignored for being in the ignored class, {sop_instance_uid}")
+                continue
+
             if study_instance_uid not in study_dict:
                 study = DICOMStudy(study_instance_uid)
                 self.populate_study_attributes(study, sop_instance)

notebooks/tutorials/01_simple_app.ipynb

@@ -35,4 +35,4 @@ scikit-image>=0.17.2
 nibabel>=3.2.1
 numpy-stl>=2.12.0
 trimesh>=3.8.11
-torch~=2.0.1
+torch>=2.0.1

notebooks/tutorials/02_mednist_app-prebuilt.ipynb

@@ -4,10 +4,8 @@ PyPDF2>=2.11.1
 highdicom>=0.18.2
 SimpleITK>=2.0.0
 Pillow>=8.4.0
-numpy-stl>=2.12.0
-trimesh>=3.8.11
 nibabel>=3.2.1
 numpy-stl>=2.12.0
 trimesh>=3.8.11
-torch~=2.0.1
+torch>=2.0.1
 monai>=1.0.0

notebooks/tutorials/02_mednist_app.ipynb

@@ -1,4 +1,4 @@
-holoscan~=1.0
+holoscan~=2.0
 numpy>=1.21.6
 colorama>=0.4.1
 typeguard>=3.0.0

notebooks/tutorials/03_segmentation_app.ipynb

@@ -24,7 +24,7 @@ python_requires = >= 3.8
 #     cucim
 install_requires =
     numpy>=1.21.6
-    holoscan~=1.0
+    holoscan~=2.0
     colorama>=0.4.1
     typeguard>=3.0.0
 
@@ -51,6 +51,8 @@ ignore =
     B905,
     # B026 Star-arg unpacking after a keyword argument is strongly discouraged
     B026
+    #  B909 editing a loop's mutable iterable often leads to unexpected results/bugs
+    B909
 
 per_file_ignores =
     # e.g. F403 'from holoscan.conditions import *' used; unable to detect undefined names