Update due to depcreation of dependency

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

Author: MMelQin

monai/deploy/operators/dicom_encapsulated_pdf_writer_operator.py

@@ -15,6 +15,11 @@
 from pathlib import Path
 from typing import Dict, Optional, Union
 
+from monai.deploy.core import ConditionType, Fragment, 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 EquipmentInfo, ModelInfo, save_dcm_file, write_common_modules
+from monai.deploy.utils.version import get_sdk_semver
 from monai.deploy.utils.importutil import optional_import
 
 dcmread, _ = optional_import("pydicom", name="dcmread")
@@ -24,13 +29,7 @@
 Dataset, _ = optional_import("pydicom.dataset", name="Dataset")
 FileDataset, _ = optional_import("pydicom.dataset", name="FileDataset")
 Sequence, _ = optional_import("pydicom.sequence", name="Sequence")
-PdfReader, _ = optional_import("PyPDF2", name="PdfReader")
-
-from monai.deploy.core import ConditionType, Fragment, 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 EquipmentInfo, ModelInfo, save_dcm_file, write_common_modules
-from monai.deploy.utils.version import get_sdk_semver
+PdfReader, _ = optional_import("pypdf", name="PdfReader")
 
 
 # @md.env(pip_packages=["pydicom >= 1.4.2", "PyPDF2 >= 2.11.1", "monai"])
@@ -58,7 +57,7 @@ def __init__(
         fragment: Fragment,
         *args,
         output_folder: Union[str, Path],
-        model_info: ModelInfo,
+        model_info: Optional[ModelInfo] = None,
         equipment_info: Optional[EquipmentInfo] = None,
         copy_tags: bool = True,
         custom_tags: Optional[Dict[str, str]] = None,
@@ -249,52 +248,51 @@ def _is_pdf_bytes(self, content: bytes):
         return True
 
 
-# Commenting out the following as pttype complains about the constructor for no reason
-# def test(test_copy_tags: bool = True):
-#     from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
-#     from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
-
-#     current_file_dir = Path(__file__).parent.resolve()
-#     dcm_folder = current_file_dir.joinpath("../../../inputs/livertumor_ct/dcm/1-CT_series_liver_tumor_from_nii014")
-#     pdf_file = current_file_dir.joinpath("../../../inputs/pdf/TestPDF.pdf")
-#     out_path = Path("output_pdf_op").absolute()
-#     pdf_bytes = b"Not PDF bytes."
-
-#     fragment = Fragment()
-#     loader = DICOMDataLoaderOperator(fragment, name="loader_op")
-#     series_selector = DICOMSeriesSelectorOperator(fragment, name="selector_op")
-#     sr_writer = DICOMEncapsulatedPDFWriterOperator(
-#         fragment,
-#         output_folder=out_path,
-#         copy_tags=test_copy_tags,
-#         model_info=None,
-#         equipment_info=EquipmentInfo(),
-#         custom_tags={"SeriesDescription": "Report from AI algorithm. Not for clinical use."},
-#         name="writer_op",
-#     )
-
-#     # Testing with the main entry functions
-#     dicom_series = None
-#     if test_copy_tags:
-#         study_list = loader.load_data_to_studies(Path(dcm_folder).absolute())
-#         study_selected_series_list = series_selector.filter(None, study_list)
-#         # Get the first DICOM Series, as for now, only expecting this.
-#         if not study_selected_series_list or len(study_selected_series_list) < 1:
-#             raise ValueError("Missing input, list of 'StudySelectedSeries'.")
-#         for study_selected_series in study_selected_series_list:
-#             if not isinstance(study_selected_series, StudySelectedSeries):
-#                 raise ValueError("Element in input is not expected type, 'StudySelectedSeries'.")
-#             for selected_series in study_selected_series.selected_series:
-#                 print(type(selected_series))
-#                 dicom_series = selected_series.series
-#                 print(type(dicom_series))
-
-#     with open(pdf_file, "rb") as f:
-#         pdf_bytes = f.read()
-
-#     sr_writer.write(pdf_bytes, dicom_series, out_path)
-
-
-# if __name__ == "__main__":
-#     test(test_copy_tags=True)
-#     test(test_copy_tags=False)
+def test(test_copy_tags: bool = True):
+    from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
+    from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
+
+    current_file_dir = Path(__file__).parent.resolve()
+    dcm_folder = current_file_dir.joinpath("../../../inputs/livertumor_ct/dcm/1-CT_series_liver_tumor_from_nii014")
+    pdf_file = current_file_dir.joinpath("../../../inputs/pdf/TestPDF.pdf")
+    out_path = Path("output_pdf_op").absolute()
+    pdf_bytes = b"Not PDF bytes."
+
+    fragment = Fragment()
+    loader = DICOMDataLoaderOperator(fragment, name="loader_op")
+    series_selector = DICOMSeriesSelectorOperator(fragment, name="selector_op")
+    sr_writer = DICOMEncapsulatedPDFWriterOperator(
+        fragment,
+        output_folder=out_path,
+        copy_tags=test_copy_tags,
+        model_info=None,
+        equipment_info=EquipmentInfo(),
+        custom_tags={"SeriesDescription": "Report from AI algorithm. Not for clinical use."},
+        name="writer_op",
+    )
+
+    # Testing with the main entry functions
+    dicom_series = None
+    if test_copy_tags:
+        study_list = loader.load_data_to_studies(Path(dcm_folder).absolute())
+        study_selected_series_list = series_selector.filter(None, study_list)
+        # Get the first DICOM Series, as for now, only expecting this.
+        if not study_selected_series_list or len(study_selected_series_list) < 1:
+            raise ValueError("Missing input, list of 'StudySelectedSeries'.")
+        for study_selected_series in study_selected_series_list:
+            if not isinstance(study_selected_series, StudySelectedSeries):
+                raise ValueError("Element in input is not expected type, 'StudySelectedSeries'.")
+            for selected_series in study_selected_series.selected_series:
+                print(type(selected_series))
+                dicom_series = selected_series.series
+                print(type(dicom_series))
+
+    with open(pdf_file, "rb") as f:
+        pdf_bytes = f.read()
+
+    sr_writer.write(pdf_bytes, dicom_series, out_path)
+
+
+if __name__ == "__main__":
+    test(test_copy_tags=True)
+    test(test_copy_tags=False)

requirements-dev.txt

@@ -24,7 +24,7 @@ cucim~=21.06; platform_system == "Linux"
 monai>=1.3.0
 docker>=5.0.0
 pydicom>=3.0.0
-PyPDF2>=2.11.1
+pypdf>=4.0.0
 highdicom>=0.18.2
 SimpleITK>=2.0.0
 Pillow>=8.0.0

requirements-examples.txt

@@ -1,6 +1,6 @@
 scikit-image>=0.17.2
 pydicom>=3.0.0
-PyPDF2>=2.11.1
+pypdf>=4.0.0
 types-pytz>=2024.1.0.20240203
 highdicom>=0.18.2
 SimpleITK>=2.0.0