Merge pull request #35 from tomaroberts/unit-tests

Adds unit tests, coverage badge and comments, and updates GHA

.github/workflows/build_and_test_cli.yml

@@ -1,4 +1,4 @@
-# Workflow to build nii2dcm and test different command line interface (CLI) options
+# Workflow to build nii2dcm, run unit tests and then execute command line interface (CLI) end-to-end
 
 name: Build nii2dcm
 
@@ -7,7 +7,7 @@ on:
 
 jobs:
   build-and-test:
-    name: Build
+    name: Build, Unit Tests & E2E
 
     runs-on: ${{ matrix.os }}
 
@@ -57,6 +57,10 @@ jobs:
         nii2dcm -h
         nii2dcm -v
 
+    - name: Run unit tests
+      run: |
+        pytest tests/
+
     - name: Test DicomMRISVR creation
       run: |
         # run nii2dcm
@@ -65,3 +69,25 @@ jobs:
         ls ./output
         # assert DICOM files exist
         [ -f "./output/IM_0001.dcm" ] && echo "Output DICOM file exists" || exit 1
+
+    - name: Build pytest coverage file
+      run: |
+        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=nii2dcm tests/ | tee pytest-coverage.txt ; echo $?
+
+    - name: Pytest coverage comment
+      id: coverageComment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: ./pytest-coverage.txt
+        junitxml-path: ./pytest.xml
+
+    - name: Update Coverage Badge
+      uses: schneegans/[email protected]
+      with:
+        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+        gistID: 57ef8057d04f67dbe6e64df410b83079
+        filename: nii2dcm-pytest-coverage-comment.json
+        label: Coverage Report
+        message: ${{ steps.coverageComment.outputs.coverage }}
+        color: ${{ steps.coverageComment.outputs.color }}
+        namedLogo: python

.gitignore

@@ -48,6 +48,8 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+pytest-coverage.txt
+pytest.xml
 
 # Sphinx documentation
 docs/_build/

README.md

@@ -20,6 +20,10 @@
     ·
     <a href="https://github.com/tomaroberts/nii2dcm/issues">Request Feature</a>
   </p>
+  <p align="center">
+    <img src="https://github.com/tomaroberts/nii2dcm/actions/workflows/build_and_test_cli.yml/badge.svg?branch=unit-tests">
+    <img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/tomaroberts/57ef8057d04f67dbe6e64df410b83079/raw/nii2dcm-pytest-coverage-comment.json"> 
+</p>
 </div>
 
 

nii2dcm/__main__.py

@@ -24,7 +24,7 @@ def cli(args=None):
     parser.add_argument("input_file", type=str, help="[.nii/.nii.gz] input NIfTI file")
     parser.add_argument("output_dir", type=str, help="[directory] output DICOM path")
     parser.add_argument(
-        "-d","--dicom_type",
+        "-d", "--dicom_type",
         type=str,
         help="[string] type of DICOM. Available types: MR, SVR."
     )

nii2dcm/_version.py

@@ -1,2 +1,2 @@
 import dunamai as _dunamai
-__version__ = _dunamai.get_version("nii2dcm", third_choice=_dunamai.Version.from_any_vcs).serialize()
+__version__ = _dunamai.get_version("nii2dcm", third_choice=_dunamai.Version.from_any_vcs).serialize()

nii2dcm/dcm.py

@@ -11,7 +11,6 @@
 import pydicom as pyd
 from pydicom.dataset import FileDataset, FileMetaDataset
 
-from nii2dcm.utils import dcm_dictionary_update
 from nii2dcm.modules.patient import Patient
 from nii2dcm.modules.general_study import GeneralStudy
 from nii2dcm.modules.patient_study import PatientStudy
@@ -67,7 +66,7 @@ def __init__(self, filename=nii2dcm_temp_filename):
 
         """
         Set Dicom Date/Time
-        Important: doing this once sets all Instances/Series/Study creation dates and times to the same values. Whereas, 
+        Important: doing this once sets all Instances/Series/Study creation dates and times to the same values. Whereas,
         doing this within the Modules would every so slightly offset the times
         """
         # TODO shift to utils.py and propagate to Modules, or, create method within this Dicom class

nii2dcm/dcm_writer.py

@@ -6,19 +6,19 @@
 import pydicom as pyd
 
 
-def write_slice(dcm, img_data, instance_index, output_dir):
+def write_slice(dcm, img_data, slice_index, output_dir):
     """
     write a single DICOM slice
 
     dcm – nii2dcm DICOM object
     img_data - [nX, nY, nSlice] image pixel data, such as from NIfTI file
-    instance_index – instance index (important: counts from 0)
+    slice_index – slice index in nibabel img_data array (important: counts from 0, whereas DICOM instances count from 1)
     output_dir – output DICOM file save location
     """
 
-    output_filename = r'IM_%04d.dcm' % (instance_index + 1)  # begin filename from 1, e.g. IM_0001.dcm
+    output_filename = r'IM_%04d.dcm' % (slice_index + 1)  # begin filename from 1, e.g. IM_0001.dcm
 
-    img_slice = img_data[:, :, instance_index]
+    img_slice = img_data[:, :, slice_index]
 
     # Instance UID – unique to current slice
     dcm.ds.SOPInstanceUID = pyd.uid.generate_uid(None)

nii2dcm/modules/mr_image.py

@@ -24,9 +24,9 @@ def __init__(self):
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.8.3.html#sect_C.8.3.1.1.1
         # For now, will omit thereby inheriting parent value
         # self.ds.ImageType = ''
-    
+
         self.ds.SamplesPerPixel = 1
-    
+
         # PhotometricInterpretation
         # TODO: decide MONOCHROME1 or MONOCHROME2 as default
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2

tests/test_dcm.py

@@ -0,0 +1,82 @@
+import pytest
+import os
+import datetime
+
+from pydicom.dataset import FileMetaDataset, FileDataset
+
+from nii2dcm.dcm import Dicom
+from nii2dcm.modules.patient import Patient
+
+
+TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1'
+DATE = datetime.datetime.now().strftime('%Y%m%d')
+PATIENT_ID = '12345678'
+PATIENT_SEX = ''
+IMAGE_TYPE = ['SECONDARY', 'DERIVED']
+CHARACTER_SET = 'ISO_IR 100'
+
+MIN_UID_LENGTH = 10  # arbitrary just to check UID has some characters
+MAX_UID_LENGTH = 64  # DICOM standard max length
+
+class TestDicom:
+    def setup_method(self):
+        self.dicom = Dicom()
+
+    def test_dicom(self):
+        """
+        Tests some metadata in basic Dicom object
+        """
+        assert self.dicom.file_meta.TransferSyntaxUID == TRANSFER_SYNTAX_UID
+        assert self.dicom.ds.ContentDate == DATE
+        assert self.dicom.ds.AcquisitionDate == DATE
+        assert self.dicom.ds.SeriesDate == DATE
+        assert self.dicom.ds.StudyDate == DATE
+
+    def test_add_module(self):
+        """
+        Tests add_module() method
+        """
+        self.dicom.add_module(Patient())
+        assert self.dicom.ds.PatientID == PATIENT_ID
+        assert self.dicom.ds.PatientSex == PATIENT_SEX
+
+    def test_add_base_modules(self):
+        """
+        Test metadata present following bulk method invocation via add_base_modules()
+        """
+        self.dicom.add_base_modules()
+        assert self.dicom.ds.SpecificCharacterSet == CHARACTER_SET
+        assert self.dicom.ds.ImageType[0] == 'SECONDARY'
+        assert self.dicom.ds.ImageType[1] == 'DERIVED'
+
+    def test_get_file_meta(self):
+        fm = self.dicom.get_file_meta()
+        assert isinstance(fm, FileMetaDataset)
+
+    def test_get_dataset(self):
+        ds = self.dicom.get_dataset()
+        assert isinstance(ds, FileDataset)
+
+    def test_save_as(self):
+        """
+        Test DICOM save (default save location: cwd)
+        """
+        self.dicom.ds.save_as(self.dicom.filename)
+        assert os.path.exists(self.dicom.filename)
+        os.remove(self.dicom.filename)
+        if os.path.exists(self.dicom.filename):
+            raise Exception("Failed to delete temporary DICOM created during pytest process.")
+
+    def test_init_study_tags(self):
+        self.dicom.init_study_tags()
+        assert isinstance(self.dicom.ds.StudyInstanceUID, str)
+        assert self.dicom.ds.StudyInstanceUID.find(".")
+        assert MIN_UID_LENGTH < len(self.dicom.ds.StudyInstanceUID) <= MAX_UID_LENGTH
+
+    def test_init_series_tags(self):
+        self.dicom.init_study_tags()
+        assert isinstance(self.dicom.ds.SeriesInstanceUID, str)
+        assert self.dicom.ds.SeriesInstanceUID.find(".")
+        assert MIN_UID_LENGTH < len(self.dicom.ds.SeriesInstanceUID) <= MAX_UID_LENGTH
+
+        assert len(str(self.dicom.ds.SeriesNumber)) == 4

tests/test_dcm_writer.py

@@ -0,0 +1,46 @@
+import os
+
+import pytest
+import nibabel as nib
+
+from nii2dcm import dcm_writer
+from nii2dcm.dcm import Dicom
+from nii2dcm.nii import Nifti
+
+
+NII_FILE_PATH = "tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz"
+INSTANCE_INDEX = 10  # dcm instances count from 1
+SLICE_NUMBER = INSTANCE_INDEX-1  # nibabel slice array counts from 0
+OUTPUT_DIR = "tests/data"
+OUTPUT_DCM_FILENAME = r'IM_%04d.dcm' % (INSTANCE_INDEX)
+OUTPUT_DCM_PATH = os.path.join(os.getcwd(), OUTPUT_DIR, OUTPUT_DCM_FILENAME)
+
+class TestDicomWriter:
+    def setup_method(self):
+        self.dicom = Dicom()
+        self.nii = nib.load(NII_FILE_PATH)
+        self.img_data = self.nii.get_fdata().astype("uint16")
+        self.nii2dcm_parameters = Nifti.get_nii2dcm_parameters(self.nii)
+
+    def test_write_slice(self):
+        dcm_writer.write_slice(self.dicom, self.img_data, SLICE_NUMBER, OUTPUT_DIR)
+
+        assert os.path.exists(OUTPUT_DCM_PATH)
+        os.remove(OUTPUT_DCM_PATH)
+        if os.path.exists(OUTPUT_DCM_PATH):
+            raise Exception("Failed to delete temporary DICOM created during pytest process.")
+
+    def test_transfer_nii_hdr_series_tags(self):
+        dcm_writer.transfer_nii_hdr_series_tags(self.dicom, self.nii2dcm_parameters)
+        assert self.dicom.ds.Rows == self.nii.shape[0]
+        assert self.dicom.ds.Columns == self.nii.shape[1]
+
+    def test_transfer_nii_hdr_instance_tags(self):
+        dcm_writer.transfer_nii_hdr_instance_tags(self.dicom, self.nii2dcm_parameters, SLICE_NUMBER)
+        assert self.dicom.ds.InstanceNumber == INSTANCE_INDEX
+
+    def test_transfer_ref_dicom_series_tags(self):
+        """
+        TODO: implement test
+        """
+        pass

tests/test_nii.py

@@ -0,0 +1,23 @@
+import pytest
+
+from nii2dcm.nii import Nifti
+import nibabel as nib
+
+
+NII_FILE_PATH = "tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz"
+NII_VOXEL_DIMS = (180, 221, 180)
+NII_VOXEL_SPACING = (0.5, 0.5, 0.5)
+
+class TestNifti:
+    def setup_method(self):
+        self.nii = nib.load(NII_FILE_PATH)
+
+    def test_get_nii2dcm_parameters(self):
+        nii_parameters = Nifti.get_nii2dcm_parameters(self.nii)
+        assert nii_parameters["Rows"] == NII_VOXEL_DIMS[0]
+        assert nii_parameters["Columns"] == NII_VOXEL_DIMS[1]
+        assert nii_parameters["NumberOfSlices"] == NII_VOXEL_DIMS[2]
+        assert nii_parameters["AcquisitionMatrix"] == [0, NII_VOXEL_DIMS[0], NII_VOXEL_DIMS[1], 0]
+        assert nii_parameters["dimX"] == NII_VOXEL_SPACING[0]
+        assert nii_parameters["dimY"] == NII_VOXEL_SPACING[1]
+        assert nii_parameters["SliceThickness"] == str(NII_VOXEL_SPACING[2])

tests/test_run.py

@@ -0,0 +1,55 @@
+import pytest
+import os, shutil
+import pydicom as pyd
+
+from nii2dcm.run import run_nii2dcm
+
+
+NII_FILE_PATH = "tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz"
+OUTPUT_DIR = "tests/data/tmp_dcm_dir"
+OUTPUT_DCM_PATH = os.path.join(os.getcwd(), OUTPUT_DIR)
+NUM_DICOM_FILES = 180
+SINGLE_DICOM_FILENAME = "IM_0001.dcm"
+
+class TestRun:
+    def setup_method(self):
+        os.makedirs(OUTPUT_DCM_PATH, exist_ok=True)
+
+    @pytest.mark.parametrize(
+        "TEST_DICOM_TYPE, TEST_DCM_MODALITY",
+        [
+            (None, ''),  # basic DICOM with undefined modality
+            ("MR", "MR"),  # MRI DICOM
+            ("SVR", "MR")  # SVR DICOM hence MR modality
+        ]
+    )
+    def test_run_dicom_types(self, TEST_DICOM_TYPE, TEST_DCM_MODALITY):
+        """
+        Test run_nii2dcm with different dicom_types
+        """
+        run_nii2dcm(
+            NII_FILE_PATH,
+            OUTPUT_DCM_PATH,
+            dicom_type=TEST_DICOM_TYPE
+        )
+        assert os.path.exists(os.path.join(OUTPUT_DCM_PATH, SINGLE_DICOM_FILENAME))
+        assert len(os.listdir(OUTPUT_DCM_PATH)) == NUM_DICOM_FILES
+
+        ds = pyd.dcmread(os.path.join(OUTPUT_DCM_PATH, SINGLE_DICOM_FILENAME))
+        assert ds.Modality == TEST_DCM_MODALITY
+
+        shutil.rmtree(OUTPUT_DCM_PATH)
+
+    def test_run_reference_dicom(self):
+        """
+        Test run_nii2dcm with different ref_dicom option
+        """
+        # TODO: implement - will involve adding reference DICOM test dataset
+        pass
+
+    def teardown_method(self):
+        """
+        Remove output DICOM directory in event of test failure
+        """
+        if os.path.exists(OUTPUT_DCM_PATH):
+            shutil.rmtree(OUTPUT_DCM_PATH)

tests/test_version.py

@@ -0,0 +1,9 @@
+import pytest
+from packaging import version
+
+from nii2dcm._version import __version__
+
+
+class TestVersion:
+    def test_version(self):
+        assert isinstance(version.parse(__version__), version.Version)