fix: Update to pydicom 3.0 and fixed some typos

.github/workflows/release.yml

@@ -63,15 +63,15 @@ jobs:
 
       - name: Create Release
         if: steps.check.outputs.bump == 'yes'
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ steps.bump.outputs.version }}
-          release_name: Release ${{ steps.bump.outputs.version }}
+          name: Release ${{ steps.bump.outputs.version }}
           body: ${{ steps.changelog.outputs.changelog }}
           draft: false
           prerelease: false
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Publish to PyPI
         if: steps.check.outputs.bump == 'yes'

.gitignore

@@ -160,3 +160,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+example_dir/

.pre-commit-config.yaml

@@ -26,13 +26,13 @@ repos:
       - id: check-merge-conflict
       - id: check-docstring-first
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.3
+    rev: v0.6.4
     hooks:
       - id: ruff
         args: ["--fix"]
         files: ^hooks
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.3
+    rev: v0.6.4
     hooks:
       - id: ruff-format
         files: ^hooks

.talismanrc

@@ -9,4 +9,6 @@ fileignoreconfig:
     checksum: fdb35056dbd109dbbac6fd5d3668fbff90ace8f46aa37b787eaa2572c02d0aaf
   - filename: README.md
     checksum: 4a9bf4e1400f36c5646be2b85eee66d1681d12e67bd9dce431206d21a7c85f64
+  - filename: poetry.lock
+    checksum: 868367c1e6faa49cc06eaf099af0f27c7bc2ad9eab2be84b26ae7b41a953bcf7
 version: ""

process_dcm/__init__.py

@@ -1,3 +1 @@
-"""process_dcm module."""
-
 __version__ = "0.2.0"

process_dcm/__main__.py

@@ -0,0 +1,3 @@
+from process_dcm.main import app
+
+app(prog_name="process-dcm")

process_dcm/main.py

@@ -18,7 +18,7 @@
 def print_version(value: bool) -> None:
     """Print the version of the app."""
     if value:
-        typer.echo(f"Process DCM Version: {__version__}")
+        typer.secho(f"Process DCM Version: {__version__}", fg="blue")
         raise typer.Exit()
 
 
@@ -82,18 +82,17 @@ def main(
     len_sf, base_dir, subfolders = find_dicom_folders_with_base(input_dir)
     output_dirs = []
 
-    if relative and os.path.isabs(output_dir):
-        relative = False
-        typer.secho(
-            "WARN: '--relative' x 'absolute --output_dir' are incompatible, absolute 'output_dir' takes precedence",
-            fg="yellow",
-        )
-        output_dirs = [x.replace(base_dir, output_dir) for x in subfolders]
-    elif relative and not os.path.isabs(output_dir):
-        output_dirs = [os.path.join(x, output_dir) for x in subfolders]
-    elif not relative and not os.path.isabs(output_dir):
+    if os.path.isabs(output_dir):
+        if relative:
+            typer.secho(
+                "WARN: '--relative' x 'absolute --output_dir' are incompatible, absolute 'output_dir' takes precedence",
+                fg="yellow",
+            )
+            relative = False
         output_dir = os.path.abspath(output_dir)
         output_dirs = [x.replace(base_dir, output_dir) for x in subfolders]
+    elif relative:
+        output_dirs = [os.path.join(x, output_dir) for x in subfolders]
 
     tasks = list(zip(subfolders, output_dirs))
 

process_dcm/utils.py

@@ -126,9 +126,6 @@ def meta_images(dcm_obj: FileDataset) -> dict:
     return meta
 
 
-boo = "hello"
-
-
 def process_dcm_meta(
     dcm_objs: list[FileDataset], output_dir: str, mapping: str = "", keep: str = ""
 ) -> tuple[str, str]:

pyproject.toml

@@ -20,9 +20,9 @@ classifiers = [
 [tool.poetry.dependencies]
 python = "^3.11"
 opencv-python-headless = "^4.10.0.84"
-typer = "^0.12.3"
-tqdm = "^4.66.4"
-pydicom = "^2.4.4"
+typer = "^0.12.5"
+tqdm = "^4.66.5"
+pydicom = "^3.0.0"
 natsort = "^8.4.0"
 pillow = "^10.4.0"
 python-gdcm = "^3.0.24.1"
@@ -31,32 +31,37 @@ python-gdcm = "^3.0.24.1"
 process-dcm = "process_dcm.main:cli"
 
 [tool.poetry.group.dev.dependencies]
-boto3-stubs = { extras = ["lambda", "s3"], version = "*" }
-ipdb = "*"
-ipython = "*"
-jupyterlab = "*"
-mypy = "*"
-mypy-boto3-lambda = "*"
-mypy-boto3-s3 = "*"
-pandas-stubs = "*"
-pdbpp = "*"
-pip = "*"
-pre-commit = "*"
-pytest-cov = "*"
-pytest-env = "*"
-pytest-xdist = "*"
-ruff = "*"
-typed-argument-parser = "*"
-types-pillow = "*"
-types-tqdm = "*"
-wheel = "*"
+boto3-stubs = { extras = ["lambda", "s3"], version = "1.35.14" }
+ipdb = "0.13.13"
+ipython = "8.27.0"
+jupyterlab = "4.2.5"
+mypy = "1.11.2"
+mypy-boto3-lambda = "1.35.3"
+mypy-boto3-s3 = "1.35.2"
+pandas-stubs = "2.2.2.240807"
+pdbpp = "0.10.3"
+pip = "24.2"
+pre-commit = "3.8.0"
+pytest-cov = "5.0.0"
+pytest-env = "1.1.4"
+pytest-xdist = "3.6.1"
+ruff = "0.6.4"
+typed-argument-parser = "1.10.1"
+types-pillow = "10.2.0.20240822"
+types-tqdm = "4.66.0.20240417"
+wheel = "0.44.0"
 pytest-mock = "^3.14.0"
 
 [tool.pytest.ini_options]
 addopts = "tests --cov=process_dcm/ --cov-report=term-missing:skip-covered --cov-report=xml --dist=loadgroup -n 8 --durations=5"
 
 [tool.coverage.report]
-exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"]
+exclude_lines = [
+    "no cov",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+    "app()",
+]
 
 [tool.ruff]
 target-version = "py311"
@@ -74,6 +79,9 @@ convention = "google"
 
 [tool.ruff.lint.per-file-ignores]
 "tests/*" = ["D100", "D103", "D104"]
+"__main__.py" = ["D100"]
+"__init__.py" = ["D104"]
+
 
 [tool.mypy]
 python_version = "3.11"

tests/conftest.py

@@ -1,11 +1,12 @@
+import datetime
 import os
 import tempfile
-from collections import defaultdict
 from collections.abc import Generator
 from pathlib import Path
 
+import pydicom
 import pytest
-from pydicom.dataset import Dataset, FileDataset
+from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
 from typer.testing import CliRunner
 
 from process_dcm import __version__ as version
@@ -35,7 +36,19 @@ def input_dir():
 @pytest.fixture
 def dicom_opotopol():
     """Fixture to create a mocked DICOM FileDataset for OPTOPOL."""
-    dataset = FileDataset("tests/example-dcms/bscans.dcm", {}, file_meta=defaultdict(str), preamble=b"\0" * 128)
+    # Create a FileMetaDataset instead of a defaultdict
+    file_meta = FileMetaDataset()
+    file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian  # or other appropriate UID
+
+    # Create the FileDataset object
+    dataset = FileDataset(
+        "tests/example-dcms/bscans.dcm",
+        {},
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+        is_implicit_VR=False,
+        is_little_endian=True,
+    )
 
     # Mock setting relevant fields to simulate OPTOPOL DICOM
     dataset.Modality = "OPT"
@@ -51,13 +64,30 @@ def dicom_opotopol():
 
     dataset.PerFrameFunctionalGroupsSequence = [functional_group]
 
+    # Optionally set the current date and time for the dataset
+    dt = datetime.datetime.now()
+    dataset.ContentDate = dt.strftime("%Y%m%d")
+    dataset.ContentTime = dt.strftime("%H%M%S.%f")  # fractional seconds
+
     return dataset
 
 
 @pytest.fixture
 def dicom_attribute_error():
     """Fixture to create a mocked DICOM FileDataset for AttributeError simulation."""
-    dataset = FileDataset("tests/example-dcms/bscans.dcm", {}, file_meta=defaultdict(str), preamble=b"\0" * 128)
+    # Create a FileMetaDataset instead of a defaultdict
+    file_meta = FileMetaDataset()
+    file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian  # or appropriate UID
+
+    # Create the FileDataset object
+    dataset = FileDataset(
+        "tests/example-dcms/bscans.dcm",
+        {},
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+        is_implicit_VR=False,
+        is_little_endian=True,
+    )
 
     # Mock setting relevant fields to simulate a DICOM file
     dataset.Modality = "OPT"
@@ -67,18 +97,36 @@ def dicom_attribute_error():
     dataset.NumberOfFrames = 5
     dataset.AccessionNumber = 0
 
+    # Add the PerFrameFunctionalGroupsSequence
     functional_group = Dataset()
     functional_group.OphthalmicFrameLocationSequence = []
 
     dataset.PerFrameFunctionalGroupsSequence = [functional_group]
 
+    # Optionally set the current date and time for the dataset
+    dt = datetime.datetime.now()
+    dataset.ContentDate = dt.strftime("%Y%m%d")
+    dataset.ContentTime = dt.strftime("%H%M%S.%f")  # fractional seconds
+
     return dataset
 
 
 @pytest.fixture
 def dicom_with_photo_locations():
     """Fixture to create a mocked DICOM FileDataset for valid photo locations."""
-    dataset = FileDataset("tests/example-dcms/bscans.dcm", {}, file_meta=defaultdict(str), preamble=b"\0" * 128)
+    # Create a FileMetaDataset instead of a defaultdict
+    file_meta = FileMetaDataset()
+    file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian  # or appropriate UID
+
+    # Create the FileDataset object
+    dataset = FileDataset(
+        "tests/example-dcms/bscans.dcm",
+        {},
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+        is_implicit_VR=False,
+        is_little_endian=True,
+    )
 
     # Mock setting relevant fields to simulate a DICOM file
     dataset.Modality = "OPT"
@@ -92,21 +140,38 @@ def dicom_with_photo_locations():
     frame_location = Dataset()
     frame_location.OphthalmicFrameLocationSequence = [Dataset()]
     frame_location.OphthalmicFrameLocationSequence[0].ReferenceCoordinates = [0.0, 0.0, 512.0, 512.0]
+
+    # Repeat the same PerFrameFunctionalGroupsSequence for each frame
     dataset.PerFrameFunctionalGroupsSequence = [frame_location for _ in range(dataset.NumberOfFrames)]
 
+    # Optionally set the current date and time for the dataset
+    dt = datetime.datetime.now()
+    dataset.ContentDate = dt.strftime("%Y%m%d")
+    dataset.ContentTime = dt.strftime("%H%M%S.%f")  # fractional seconds
+
     return dataset
 
 
 @pytest.fixture
 def dicom_base():
     """Base fixture for creating a mocked DICOM FileDataset."""
-    dataset = FileDataset("test.dcm", {}, file_meta=defaultdict(str), preamble=b"\0" * 128)
+    # Create a FileMetaDataset instead of a defaultdict
+    file_meta = FileMetaDataset()
+    file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian  # or appropriate UID
+
+    # Create the FileDataset object
+    dataset = FileDataset(
+        "test.dcm", {}, file_meta=file_meta, preamble=b"\0" * 128, is_implicit_VR=False, is_little_endian=True
+    )
+
+    # Mock setting relevant fields to simulate a basic DICOM file
     dataset.AccessionNumber = 0
     dataset.Modality = ImageModality.OCT
     dataset.PatientBirthDate = "19020202"
     dataset.Manufacturer = ""
     dataset.SeriesDescription = ""
     dataset.PatientID = "bbff7a25-d32c-4192-9330-0bb01d49f746"
+
     return dataset