Merge branch 'phessey/fix-timestamps' into jaalvare/fodicom_upgrade
This commit is contained in:
Peter Hessey
Коммит
eee9876e5e
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@ -55,7 +55,7 @@ namespace Microsoft.RTConvert.MedIO.RT
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ds.Add(DicomTag.SeriesNumber, string.Empty);
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// Type 3 tags - optional but useful
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var now = DateTime.UtcNow;
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var now = DateTime.Now;
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var date = now.ToString("yyyyMMdd", CultureInfo.InvariantCulture);
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var time = now.ToString("HHmmss", CultureInfo.InvariantCulture);
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ds.Add(DicomTag.SeriesDate, date);
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@ -1,5 +1,5 @@
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dotnetcore2==2.1.23
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flake8==3.8.4
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flake8==5.0.4
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mypy==0.800
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pydicom==2.1.2
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pytest-cov==2.11.1
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@ -1,183 +1,179 @@
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# ------------------------------------------------------------------------------------------
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# Copyright (c) Microsoft Corporation. All rights reserved.
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# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
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# ------------------------------------------------------------------------------------------
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"""
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Tests for nifti_to_dicom_rt_converter.
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"""
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import logging
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from pathlib import Path
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from typing import List
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from pydicom import dcmread
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try:
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from InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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except ImportError:
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logging.info("using local src")
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from src.InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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logger = logging.getLogger('test_rtconvert')
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logger.setLevel(logging.DEBUG)
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def test_get_version() -> None:
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"""
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Test that .dotnet core can be called --info and that it is
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running version 2.1.
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"""
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(stdout, stderr) = get_version()
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert 'Microsoft.NETCore.App 2.1.' in stdout
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def test_echo() -> None:
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"""
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Test that the test Echo dll can be called and returns the test string and no error.
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"""
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test_string = "hello world2!"
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(stdout, stderr) = echo(test_string)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert stdout == test_string + '\n'
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def test_echo_err() -> None:
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"""
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Test that the test Echo dll can be called and returns the test and error strings.
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"""
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test_string = "hello world2!"
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test_error = "Test error."
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(stdout, stderr) = echo(test_string, test_error)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == test_error + '\n'
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assert stdout == test_string + '\n'
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# The directory containing this file.
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THIS_DIR: Path = Path(__file__).parent.resolve()
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# The TestData directory.
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TEST_DATA_DIR: Path = THIS_DIR / "TestData"
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# Test Nifti file.
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TestNiftiSegmentationLocation: Path = TEST_DATA_DIR / "hnsegmentation.nii.gz"
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# Test reference series.
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TestDicomVolumeLocation: Path = TEST_DATA_DIR / "HN"
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# Target test output file.
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TestOutputFile: Path = THIS_DIR / "test.dcm"
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# Test fill holes.
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FillHoles: List[bool] = \
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[
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True, True, True, True,
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False, False, True, True,
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True, True, False, True,
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True, True, True, False,
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True, False, True, True,
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False, True
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]
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# Test ROIInterpretedType.
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ROIInterpretedTypes: List[str] = \
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[
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None"
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]
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# Test structure colors.
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StructureColors: List[str] = \
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[
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"FF0001", "FF0002", "FF0003", "FF0004",
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"FF0101", "FF0102", "FF0103", "FF0103",
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"FF0201", "FF02FF", "FF0203", "FF0204",
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"FF0301", "FF0302", "01FF03", "FF0304",
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"FF0401", "00FFFF", "FF0403", "FF0404",
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"FF0501", "FF0502"
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]
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# Test structure names.
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StructureNames: List[str] = \
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[
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"External", "parotid_l", "parotid_r", "smg_l",
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"smg_r", "spinal_cord", "brainstem", "globe_l",
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"Globe_r", "mandible", "spc_muscle", "mpc_muscle",
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"Cochlea_l", "cochlea_r", "lens_l", "lens_r",
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"optic_chiasm", "optic_nerve_l", "optic_nerve_r", "pituitary_gland",
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"lacrimal_gland_l", "lacrimal_gland_r"
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]
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Manufacturer = "Contosos"
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Interpreter = "Ai"
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ModelId = "XYZ:12"
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def test_rtconvert() -> None:
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"""
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Test calling RTConvert for the test data.
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"""
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(stdout, stderr) = rtconvert(
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in_file=TestNiftiSegmentationLocation,
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reference_series=TestDicomVolumeLocation,
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out_file=TestOutputFile,
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struct_names=StructureNames,
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struct_colors=StructureColors,
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fill_holes=FillHoles,
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roi_interpreted_types=ROIInterpretedTypes,
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manufacturer=Manufacturer,
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interpreter=Interpreter,
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modelId=ModelId
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)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert "Successfully written" in stdout
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assert TestOutputFile.is_file()
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with open(TestOutputFile, 'rb') as infile:
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ds = dcmread(infile)
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assert ds is not None
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# Check the modality
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assert ds.Modality == 'RTSTRUCT'
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assert ds.Manufacturer == Manufacturer
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assert ds.SoftwareVersions == ModelId
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assert len(ds.StructureSetROISequence) == len(StructureNames)
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for i, item in enumerate(StructureNames):
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assert ds.StructureSetROISequence[i].ROINumber == i + 1
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assert ds.StructureSetROISequence[i].ROIName == item
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assert Interpreter in ds.RTROIObservationsSequence[i].ROIInterpreter
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assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == ('' if ROIInterpretedTypes[i] == 'None' else ROIInterpretedTypes[i])
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assert len(ds.ROIContourSequence) == len(StructureNames)
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for i, item in enumerate(StructureNames):
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assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
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assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(StructureColors[i])
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def _parse_rgb(rgb: str) -> List[int]:
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"""
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Convert the string representation of RGB color to an int list
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:param rgb: Color string
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:return: List of [R, G, B] components.
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"""
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return [int(rgb[i:i+2], 16) for i in (0, 2, 4)]
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# ------------------------------------------------------------------------------------------
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# Copyright (c) Microsoft Corporation. All rights reserved.
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# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
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# ------------------------------------------------------------------------------------------
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"""
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Tests for nifti_to_dicom_rt_converter.
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"""
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import logging
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from pathlib import Path
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from typing import List
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from pydicom import dcmread
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try:
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from InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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except ImportError:
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logging.info("using local src")
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from src.InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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logger = logging.getLogger('test_rtconvert')
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logger.setLevel(logging.DEBUG)
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def test_get_version() -> None:
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"""
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Test that .dotnet core can be called --info and that it is
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running version 2.1.
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"""
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(stdout, stderr) = get_version()
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert 'Microsoft.NETCore.App 2.1.' in stdout
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def test_echo() -> None:
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"""
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Test that the test Echo dll can be called and returns the test string and no error.
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"""
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test_string = "hello world2!"
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(stdout, stderr) = echo(test_string)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert stdout == test_string + '\n'
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def test_echo_err() -> None:
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"""
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Test that the test Echo dll can be called and returns the test and error strings.
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"""
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test_string = "hello world2!"
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test_error = "Test error."
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(stdout, stderr) = echo(test_string, test_error)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == test_error + '\n'
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assert stdout == test_string + '\n'
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# The directory containing this file.
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THIS_DIR: Path = Path(__file__).parent.resolve()
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# The TestData directory.
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TEST_DATA_DIR: Path = THIS_DIR / "TestData"
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# Test Nifti file.
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TestNiftiSegmentationLocation: Path = TEST_DATA_DIR / "hnsegmentation.nii.gz"
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# Test reference series.
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TestDicomVolumeLocation: Path = TEST_DATA_DIR / "HN"
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# Target test output file.
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TestOutputFile: Path = THIS_DIR / "test.dcm"
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# Test fill holes.
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FillHoles: List[bool] = [
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True, True, True, True,
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False, False, True, True,
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True, True, False, True,
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True, True, True, False,
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True, False, True, True,
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False, True
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]
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# Test ROIInterpretedType.
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ROIInterpretedTypes: List[str] = [
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None"
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]
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# Test structure colors.
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StructureColors: List[str] = [
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"FF0001", "FF0002", "FF0003", "FF0004",
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"FF0101", "FF0102", "FF0103", "FF0103",
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"FF0201", "FF02FF", "FF0203", "FF0204",
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"FF0301", "FF0302", "01FF03", "FF0304",
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"FF0401", "00FFFF", "FF0403", "FF0404",
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"FF0501", "FF0502"
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]
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# Test structure names.
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StructureNames: List[str] = [
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"External", "parotid_l", "parotid_r", "smg_l",
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"smg_r", "spinal_cord", "brainstem", "globe_l",
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"Globe_r", "mandible", "spc_muscle", "mpc_muscle",
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"Cochlea_l", "cochlea_r", "lens_l", "lens_r",
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"optic_chiasm", "optic_nerve_l", "optic_nerve_r", "pituitary_gland",
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"lacrimal_gland_l", "lacrimal_gland_r"
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]
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Manufacturer = "Contosos"
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Interpreter = "Ai"
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ModelId = "XYZ:12"
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def test_rtconvert() -> None:
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"""
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Test calling RTConvert for the test data.
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"""
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(stdout, stderr) = rtconvert(
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in_file=TestNiftiSegmentationLocation,
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reference_series=TestDicomVolumeLocation,
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out_file=TestOutputFile,
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struct_names=StructureNames,
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struct_colors=StructureColors,
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fill_holes=FillHoles,
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roi_interpreted_types=ROIInterpretedTypes,
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manufacturer=Manufacturer,
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interpreter=Interpreter,
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modelId=ModelId
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)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert "Successfully written" in stdout
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assert TestOutputFile.is_file()
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with open(TestOutputFile, 'rb') as infile:
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ds = dcmread(infile)
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assert ds is not None
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# Check the modality
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assert ds.Modality == 'RTSTRUCT'
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assert ds.Manufacturer == Manufacturer
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assert ds.SoftwareVersions == ModelId
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assert len(ds.StructureSetROISequence) == len(StructureNames)
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for i, item in enumerate(StructureNames):
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assert ds.StructureSetROISequence[i].ROINumber == i + 1
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assert ds.StructureSetROISequence[i].ROIName == item
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assert Interpreter in ds.RTROIObservationsSequence[i].ROIInterpreter
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assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == ('' if ROIInterpretedTypes[i] == 'None' else ROIInterpretedTypes[i])
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assert len(ds.ROIContourSequence) == len(StructureNames)
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for i, item in enumerate(StructureNames):
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assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
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assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(StructureColors[i])
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def _parse_rgb(rgb: str) -> List[int]:
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"""
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Convert the string representation of RGB color to an int list
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||||
:param rgb: Color string
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||||
:return: List of [R, G, B] components.
|
||||
"""
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return [int(rgb[i:i+2], 16) for i in (0, 2, 4)]
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|
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