Author: Andreas Tille Last-Update: 2021-12-08 Description: Several data files need to be downloaded which is not possible at package build time Thus the downloading and the according tests are removed here --- a/pydicom/tests/test_data_manager.py +++ b/pydicom/tests/test_data_manager.py @@ -25,7 +25,7 @@ EXT_PYDICOM = False if 'pydicom-data' in external_data_sources(): EXT_PYDICOM = True - +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.fixture def download_failure(): """Simulate a download failure.""" @@ -33,7 +33,7 @@ def download_failure(): yield download._SIMULATE_NETWORK_OUTAGE = False - +@pytest.mark.skip("When building a Debian package we can not download anything") class TestGetData: def test_get_dataset(self): """Test the different functions to get lists of data files.""" @@ -113,6 +113,7 @@ class TestGetData: assert palbase in x +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not EXT_PYDICOM, reason="pydicom-data not installed") class TestExternalDataSource: """Tests for the external data sources.""" @@ -253,6 +254,7 @@ class TestExternalDataSource: assert ".pydicom/data" in fpaths[1] +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(EXT_PYDICOM, reason="pydicom-data installed") class TestDownload: """Tests for the download module.""" @@ -286,6 +288,7 @@ class TestDownload: assert [] == get_testdata_files("693_UN*") +@pytest.mark.skip("When building a Debian package we can not download anything") def test_fetch_data_files(): """Test fetch_data_files().""" # Remove a single file from the cache @@ -299,6 +302,7 @@ def test_fetch_data_files(): assert path.exists() +@pytest.mark.skip("When building a Debian package we can not download anything") def test_fetch_data_files_download_failure(download_failure): """Test fetch_data_files() with download failures.""" msg = r"An error occurred downloading the following files:" @@ -306,6 +310,7 @@ def test_fetch_data_files_download_failu fetch_data_files() +@pytest.mark.skip("When building a Debian package we can not download anything") def test_hashes(): """Test for duplicates in hashes.json.""" # We can't have case mixes because windows filenames are case insensitive @@ -316,6 +321,7 @@ def test_hashes(): assert len(set(filenames)) == len(filenames) +@pytest.mark.skip("When building a Debian package we can not download anything") def test_urls(): """Test for duplicates in urls.json.""" # We can't have case mixes because windows filenames are case insensitive --- a/pydicom/tests/test_pillow_pixel_data.py +++ b/pydicom/tests/test_pillow_pixel_data.py @@ -54,52 +54,53 @@ TEST_JPEG2K = TEST_PIL and HAVE_JPEG2K # FRAMES: NumberOfFrames # PI: PhotometricInterpretation # FMT_BA_BV_SPX_PR_FRAMESF_PI -# JPGB: 1.2.840.10008.1.2.4.50 - JPEG Baseline (8-bit only) -JPGB_08_08_3_0_1F_YBR_FULL = get_testdata_file("SC_rgb_small_odd_jpeg.dcm") -JPGB_08_08_3_0_120F_YBR_FULL_422 = get_testdata_file("color3d_jpeg_baseline.dcm") # noqa -# Different subsampling 411, 422, 444 -JPGB_08_08_3_0_1F_YBR_FULL_422_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+np.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_422_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s2.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n1.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n2.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_444 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s4.dcm") # noqa -JPGB_08_08_3_0_1F_RGB = get_testdata_file("SC_jpeg_no_color_transform.dcm") -JPGB_08_08_3_0_1F_RGB_APP14 = get_testdata_file("SC_jpeg_no_color_transform_2.dcm") # noqa -# JPGE: 1.2.840.10008.1.2.4.51 - JPEG Extended (Process 2 and 4) (8 and 12-bit) -# No supported datasets available - -# JPEG 2000 - ISO/IEC 15444 Standard -# J2KR: 1.2.840.100008.1.2.4.90 - JPEG 2000 Lossless -J2KR_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KR.dcm") -J2KR_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KR.dcm") -J2KR_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KR.dcm") -J2KR_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KR.dcm") -J2KR_16_16_1_0_10F_M2 = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") -J2KR_16_14_1_1_1F_M2 = get_testdata_file("693_J2KR.dcm") -J2KR_16_16_1_1_1F_M2 = get_testdata_file("MR_small_jp2klossless.dcm") -J2KR_16_13_1_1_1F_M2_MISMATCH = get_testdata_file("J2K_pixelrep_mismatch.dcm") -# J2KI: 1.2.840.10008.1.2.4.91 - JPEG 2000 -J2KI_08_08_3_0_1F_RGB = get_testdata_file("SC_rgb_gdcm_KY.dcm") -J2KI_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KI.dcm") -J2KI_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KI.dcm") -J2KI_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KI.dcm") -J2KI_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KI.dcm") -J2KI_16_14_1_1_1F_M2 = get_testdata_file("693_J2KI.dcm") -J2KI_16_16_1_1_1F_M2 = get_testdata_file("JPEG2000.dcm") - -# Transfer syntaxes supported by other handlers -IMPL = get_testdata_file("MR_small_implicit.dcm") -EXPL = get_testdata_file("OBXXXX1A.dcm") -EXPB = get_testdata_file("OBXXXX1A_expb.dcm") -DEFL = get_testdata_file("image_dfl.dcm") -JPEG_LS_LOSSLESS = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") -RLE = get_testdata_file("MR_small_RLE.dcm") -JPGE_16_12_1_0_1F_M2 = get_testdata_file("JPEG-lossy.dcm") -JPGL_16_16_1_1_1F_M2 = get_testdata_file("JPEG-LL.dcm") -# JPGL14: 1.2.840.10008.1.2.4.57 - JPEG Lossless P14 -# No datasets available -# JPGL: 1.2.840.10008.1.2.4.70 - JPEG Lossless, Non-hierarchical, 1st Order -JPGL_08_08_1_0_1F = get_testdata_file("JPGLosslessP14SV1_1s_1f_8b.dcm") +## JPGB: 1.2.840.10008.1.2.4.50 - JPEG Baseline (8-bit only) +#JPGB_08_08_3_0_1F_YBR_FULL = get_testdata_file("SC_rgb_small_odd_jpeg.dcm") +#JPGB_08_08_3_0_120F_YBR_FULL_422 = get_testdata_file("color3d_jpeg_baseline.dcm") # noqa +## Different subsampling 411, 422, 444 +#JPGB_08_08_3_0_1F_YBR_FULL_422_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+np.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_422_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s2.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n1.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n2.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_444 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s4.dcm") # noqa +#JPGB_08_08_3_0_1F_RGB = get_testdata_file("SC_jpeg_no_color_transform.dcm") +#JPGB_08_08_3_0_1F_RGB_APP14 = get_testdata_file("SC_jpeg_no_color_transform_2.dcm") # noqa +## JPGE: 1.2.840.10008.1.2.4.51 - JPEG Extended (Process 2 and 4) (8 and 12-bit) +## No supported datasets available +# +## JPEG 2000 - ISO/IEC 15444 Standard +## J2KR: 1.2.840.100008.1.2.4.90 - JPEG 2000 Lossless +#J2KR_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KR.dcm") +#J2KR_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KR.dcm") +#J2KR_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KR.dcm") +#J2KR_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KR.dcm") +#J2KR_16_16_1_0_10F_M2 = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") +#J2KR_16_14_1_1_1F_M2 = get_testdata_file("693_J2KR.dcm") +#J2KR_16_16_1_1_1F_M2 = get_testdata_file("MR_small_jp2klossless.dcm") +#J2KR_16_13_1_1_1F_M2_MISMATCH = get_testdata_file("J2K_pixelrep_mismatch.dcm") +## J2KI: 1.2.840.10008.1.2.4.91 - JPEG 2000 +#J2KI_08_08_3_0_1F_RGB = get_testdata_file("SC_rgb_gdcm_KY.dcm") +#J2KI_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KI.dcm") +#J2KI_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KI.dcm") +#J2KI_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KI.dcm") +#J2KI_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KI.dcm") +#J2KI_16_14_1_1_1F_M2 = get_testdata_file("693_J2KI.dcm") +#J2KI_16_16_1_1_1F_M2 = get_testdata_file("JPEG2000.dcm") +# +## Transfer syntaxes supported by other handlers +#IMPL = get_testdata_file("MR_small_implicit.dcm") +#EXPL = get_testdata_file("OBXXXX1A.dcm") +EXPL = None +#EXPB = get_testdata_file("OBXXXX1A_expb.dcm") +#DEFL = get_testdata_file("image_dfl.dcm") +#JPEG_LS_LOSSLESS = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") +#RLE = get_testdata_file("MR_small_RLE.dcm") +#JPGE_16_12_1_0_1F_M2 = get_testdata_file("JPEG-lossy.dcm") +#JPGL_16_16_1_1_1F_M2 = get_testdata_file("JPEG-LL.dcm") +## JPGL14: 1.2.840.10008.1.2.4.57 - JPEG Lossless P14 +## No datasets available +## JPGL: 1.2.840.10008.1.2.4.70 - JPEG Lossless, Non-hierarchical, 1st Order +#JPGL_08_08_1_0_1F = get_testdata_file("JPGLosslessP14SV1_1s_1f_8b.dcm") # Transfer Syntaxes (non-retired + Explicit VR Big Endian) @@ -124,13 +125,13 @@ def test_unsupported_syntaxes(): REFERENCE_DATA_UNSUPPORTED = [ - (IMPL, ('1.2.840.10008.1.2', 'CompressedSamples^MR1')), - (EXPL, ('1.2.840.10008.1.2.1', 'OB^^^^')), - (EXPB, ('1.2.840.10008.1.2.2', 'OB^^^^')), - (DEFL, ('1.2.840.10008.1.2.1.99', '^^^^')), - (JPEG_LS_LOSSLESS, ('1.2.840.10008.1.2.4.80', 'CompressedSamples^MR1')), - (JPGL_08_08_1_0_1F, ('1.2.840.10008.1.2.4.70', 'Citizen^Jan')), - (RLE, ('1.2.840.10008.1.2.5', 'CompressedSamples^MR1')), +# (IMPL, ('1.2.840.10008.1.2', 'CompressedSamples^MR1')), +# (EXPL, ('1.2.840.10008.1.2.1', 'OB^^^^')), +# (EXPB, ('1.2.840.10008.1.2.2', 'OB^^^^')), +# (DEFL, ('1.2.840.10008.1.2.1.99', '^^^^')), +# (JPEG_LS_LOSSLESS, ('1.2.840.10008.1.2.4.80', 'CompressedSamples^MR1')), +# (JPGL_08_08_1_0_1F, ('1.2.840.10008.1.2.4.70', 'Citizen^Jan')), +# (RLE, ('1.2.840.10008.1.2.5', 'CompressedSamples^MR1')), ] @@ -210,171 +211,171 @@ JPGL = JPEGLosslessSV1 J2KI = JPEG2000 J2KR = JPEG2000Lossless REFERENCE_DATA = [ - # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) - (JPGB_08_08_3_0_120F_YBR_FULL_422, (JPGB, 8, 3, 0, 120, (120, 480, 640, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_422_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_422_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_444, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_RGB, (JPGB, 8, 3, 0, 1, (256, 256, 3), 'uint8')), - (JPGB_08_08_3_0_1F_RGB_APP14, (JPGB, 8, 3, 0, 1, (256, 256, 3), 'uint8')), - (J2KR_08_08_3_0_1F_YBR_ICT, (J2KR, 8, 3, 0, 1, (480, 640, 3), 'uint8')), - (J2KR_16_10_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1760, 1760), 'uint16')), - (J2KR_16_12_1_0_1F_M2, (J2KR, 16, 1, 0, 1, (1024, 1024), 'uint16')), - (J2KR_16_15_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1955, 1841), 'uint16')), - (J2KR_16_16_1_0_10F_M2, (J2KR, 16, 1, 0, 10, (10, 64, 64), 'uint16')), - (J2KR_16_14_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (512, 512), 'int16')), - (J2KR_16_16_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (64, 64), 'int16')), - (J2KI_08_08_3_0_1F_RGB, (J2KI, 8, 3, 0, 1, (100, 100, 3), 'uint8')), - (J2KI_08_08_3_0_1F_YBR_ICT, (J2KI, 8, 3, 0, 1, (480, 640, 3), 'uint8')), - (J2KI_16_10_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1760, 1760), 'uint16')), - (J2KI_16_12_1_0_1F_M2, (J2KI, 16, 1, 0, 1, (1024, 1024), 'uint16')), - (J2KI_16_15_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1955, 1841), 'uint16')), - (J2KI_16_14_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (512, 512), 'int16')), - (J2KI_16_16_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (1024, 256), 'int16')), +# # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) +# (JPGB_08_08_3_0_120F_YBR_FULL_422, (JPGB, 8, 3, 0, 120, (120, 480, 640, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_422_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_422_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_444, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_RGB, (JPGB, 8, 3, 0, 1, (256, 256, 3), 'uint8')), +# (JPGB_08_08_3_0_1F_RGB_APP14, (JPGB, 8, 3, 0, 1, (256, 256, 3), 'uint8')), +# (J2KR_08_08_3_0_1F_YBR_ICT, (J2KR, 8, 3, 0, 1, (480, 640, 3), 'uint8')), +# (J2KR_16_10_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1760, 1760), 'uint16')), +# (J2KR_16_12_1_0_1F_M2, (J2KR, 16, 1, 0, 1, (1024, 1024), 'uint16')), +# (J2KR_16_15_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1955, 1841), 'uint16')), +# (J2KR_16_16_1_0_10F_M2, (J2KR, 16, 1, 0, 10, (10, 64, 64), 'uint16')), +# (J2KR_16_14_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (512, 512), 'int16')), +# (J2KR_16_16_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (64, 64), 'int16')), +# (J2KI_08_08_3_0_1F_RGB, (J2KI, 8, 3, 0, 1, (100, 100, 3), 'uint8')), +# (J2KI_08_08_3_0_1F_YBR_ICT, (J2KI, 8, 3, 0, 1, (480, 640, 3), 'uint8')), +# (J2KI_16_10_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1760, 1760), 'uint16')), +# (J2KI_16_12_1_0_1F_M2, (J2KI, 16, 1, 0, 1, (1024, 1024), 'uint16')), +# (J2KI_16_15_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1955, 1841), 'uint16')), +# (J2KI_16_14_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (512, 512), 'int16')), +# (J2KI_16_16_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (1024, 256), 'int16')), ] - +# JPEG_MATCHING_DATASETS = [ - # (compressed, reference, hard coded check values) - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_422_411, - get_testdata_file("SC_rgb_dcmtk_ebcynp_dcmd.dcm"), - [ - (253, 1, 0), (253, 128, 132), (0, 255, 5), (127, 255, 127), - (1, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - marks=pytest.mark.xfail(reason="Resulting image is a bad match") - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_422_422, - get_testdata_file("SC_rgb_dcmtk_ebcys2_dcmd.dcm"), - [ - (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), - (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_411, - get_testdata_file("SC_rgb_dcmtk_ebcyn1_dcmd.dcm"), - [ - (253, 1, 0), (253, 128, 132), (0, 255, 5), (127, 255, 127), - (1, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - marks=pytest.mark.xfail(reason="Resulting image is a bad match") - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_422, - get_testdata_file("SC_rgb_dcmtk_ebcyn2_dcmd.dcm"), - [ - (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), - (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_444, - get_testdata_file("SC_rgb_dcmtk_ebcys4_dcmd.dcm"), - [ - (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), - (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - ), - pytest.param( - JPGB_08_08_3_0_1F_RGB, - get_testdata_file("SC_rgb_jpeg_dcmd.dcm"), - [ - (244, 244, 244), (244, 244, 244), (244, 244, 244), (244, 244, 244), - (236, 237, 234), (244, 244, 244), (244, 244, 244), (244, 244, 244), - (244, 244, 244), (244, 244, 244), - ], - ), - pytest.param( - JPGB_08_08_3_0_1F_RGB_APP14, - get_testdata_file("SC_rgb_jpeg_app14_dcmd.dcm"), - [ - (246, 246, 246), (246, 246, 246), (246, 246, 246), (246, 246, 246), - (246, 246, 246), (244, 244, 246), (246, 246, 246), (246, 246, 246), - (246, 246, 246), (246, 246, 246), - ], - ), +# # (compressed, reference, hard coded check values) +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_422_411, +# get_testdata_file("SC_rgb_dcmtk_ebcynp_dcmd.dcm"), +# [ +# (253, 1, 0), (253, 128, 132), (0, 255, 5), (127, 255, 127), +# (1, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# marks=pytest.mark.xfail(reason="Resulting image is a bad match") +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_422_422, +# get_testdata_file("SC_rgb_dcmtk_ebcys2_dcmd.dcm"), +# [ +# (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), +# (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_411, +# get_testdata_file("SC_rgb_dcmtk_ebcyn1_dcmd.dcm"), +# [ +# (253, 1, 0), (253, 128, 132), (0, 255, 5), (127, 255, 127), +# (1, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# marks=pytest.mark.xfail(reason="Resulting image is a bad match") +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_422, +# get_testdata_file("SC_rgb_dcmtk_ebcyn2_dcmd.dcm"), +# [ +# (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), +# (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_444, +# get_testdata_file("SC_rgb_dcmtk_ebcys4_dcmd.dcm"), +# [ +# (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), +# (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_RGB, +# get_testdata_file("SC_rgb_jpeg_dcmd.dcm"), +# [ +# (244, 244, 244), (244, 244, 244), (244, 244, 244), (244, 244, 244), +# (236, 237, 234), (244, 244, 244), (244, 244, 244), (244, 244, 244), +# (244, 244, 244), (244, 244, 244), +# ], +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_RGB_APP14, +# get_testdata_file("SC_rgb_jpeg_app14_dcmd.dcm"), +# [ +# (246, 246, 246), (246, 246, 246), (246, 246, 246), (246, 246, 246), +# (246, 246, 246), (244, 244, 246), (246, 246, 246), (246, 246, 246), +# (246, 246, 246), (246, 246, 246), +# ], +# ), ] JPEG2K_MATCHING_DATASETS = [ - # (compressed, reference, fixes) - pytest.param( - J2KR_08_08_3_0_1F_YBR_ICT, - get_testdata_file("US1_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_10_1_0_1F_M1, - get_testdata_file("RG3_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_12_1_0_1F_M2, - get_testdata_file("MR2_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_15_1_0_1F_M1, - get_testdata_file("RG1_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_16_1_0_10F_M2, - get_testdata_file("emri_small.dcm"), - {'BitsStored': 16}, - ), - pytest.param( - J2KR_16_14_1_1_1F_M2, - get_testdata_file("693_UNCR.dcm"), - {'BitsStored': 14}, - ), - pytest.param( - J2KR_16_16_1_1_1F_M2, - get_testdata_file("MR_small.dcm"), - {}, - ), - pytest.param( - J2KI_08_08_3_0_1F_RGB, - get_testdata_file("SC_rgb_gdcm2k_uncompressed.dcm"), - {}, - ), - pytest.param( - J2KI_08_08_3_0_1F_YBR_ICT, - get_testdata_file("US1_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_10_1_0_1F_M1, - get_testdata_file("RG3_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_12_1_0_1F_M2, - get_testdata_file("MR2_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_15_1_0_1F_M1, - get_testdata_file("RG1_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_14_1_1_1F_M2, - get_testdata_file("693_UNCI.dcm"), - {'BitsStored': 16}, - ), - pytest.param( - J2KI_16_16_1_1_1F_M2, - get_testdata_file("JPEG2000_UNC.dcm"), - {}, - ), +# # (compressed, reference, fixes) +# pytest.param( +# J2KR_08_08_3_0_1F_YBR_ICT, +# get_testdata_file("US1_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_10_1_0_1F_M1, +# get_testdata_file("RG3_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_12_1_0_1F_M2, +# get_testdata_file("MR2_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_15_1_0_1F_M1, +# get_testdata_file("RG1_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_16_1_0_10F_M2, +# get_testdata_file("emri_small.dcm"), +# {'BitsStored': 16}, +# ), +# pytest.param( +# J2KR_16_14_1_1_1F_M2, +# get_testdata_file("693_UNCR.dcm"), +# {'BitsStored': 14}, +# ), +# pytest.param( +# J2KR_16_16_1_1_1F_M2, +# get_testdata_file("MR_small.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_08_08_3_0_1F_RGB, +# get_testdata_file("SC_rgb_gdcm2k_uncompressed.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_08_08_3_0_1F_YBR_ICT, +# get_testdata_file("US1_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_10_1_0_1F_M1, +# get_testdata_file("RG3_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_12_1_0_1F_M2, +# get_testdata_file("MR2_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_15_1_0_1F_M1, +# get_testdata_file("RG1_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_14_1_1_1F_M2, +# get_testdata_file("693_UNCI.dcm"), +# {'BitsStored': 16}, +# ), +# pytest.param( +# J2KI_16_16_1_1_1F_M2, +# get_testdata_file("JPEG2000_UNC.dcm"), +# {}, +# ), ] @@ -398,6 +399,7 @@ class TestPillowHandler_JPEG2K: assert HAVE_PIL assert PIL_HANDLER is not None + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unsupported_syntax_raises(self): """Test pixel_array raises exception for unsupported syntaxes.""" pydicom.config.pixel_data_handlers = [PIL_HANDLER] @@ -408,6 +410,7 @@ class TestPillowHandler_JPEG2K: with pytest.raises((NotImplementedError, RuntimeError)): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize("fpath, data", REFERENCE_DATA_UNSUPPORTED) def test_can_access_unsupported_dataset(self, fpath, data): """Test can read and access elements in unsupported datasets.""" @@ -415,6 +418,7 @@ class TestPillowHandler_JPEG2K: assert data[0] == ds.file_meta.TransferSyntaxUID assert data[1] == ds.PatientName + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, data', REFERENCE_DATA) def test_properties(self, fpath, data): """Test dataset and pixel array properties are as expected.""" @@ -439,6 +443,7 @@ class TestPillowHandler_JPEG2K: assert data[5] == arr.shape assert arr.dtype == data[6] + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, rpath, fixes', JPEG2K_MATCHING_DATASETS) def test_array(self, fpath, rpath, fixes): """Test pixel_array returns correct values.""" @@ -453,6 +458,7 @@ class TestPillowHandler_JPEG2K: ref = dcmread(rpath).pixel_array assert np.array_equal(arr, ref) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_warning(self): """Test that the precision warning works OK.""" ds = dcmread(J2KR_16_14_1_1_1F_M2) @@ -464,6 +470,7 @@ class TestPillowHandler_JPEG2K: with pytest.warns(UserWarning, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_decompress_using_pillow(self): """Test decompressing JPEG2K with pillow handler succeeds.""" ds = dcmread(J2KR_16_14_1_1_1F_M2) @@ -474,6 +481,8 @@ class TestPillowHandler_JPEG2K: ref = ds.pixel_array assert np.array_equal(arr, ref) + @pytest.mark.skip("When building a Debian package we can not download anything") + @pytest.mark.skip("When building a Debian package we can not download anything") def test_changing_bits_stored(self): """Test changing BitsStored affects the pixel data.""" pydicom.config.APPLY_J2K_CORRECTIONS = False @@ -486,6 +495,7 @@ class TestPillowHandler_JPEG2K: arr_14 = ds.pixel_array assert not np.array_equal(arr, arr_14) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_rep_mismatch(self): """Test mismatched j2k sign and Pixel Representation.""" ds = dcmread(J2KR_16_13_1_1_1F_M2_MISMATCH) @@ -529,6 +539,7 @@ class TestPillowHandler_JPEG: assert HAVE_PIL assert PIL_HANDLER is not None + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unsupported_syntax_raises(self): """Test pixel_array raises exception for unsupported syntaxes.""" pydicom.config.pixel_data_handlers = [PIL_HANDLER] @@ -546,6 +557,7 @@ class TestPillowHandler_JPEG: assert data[0] == ds.file_meta.TransferSyntaxUID assert data[1] == ds.PatientName + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, data', REFERENCE_DATA) def test_properties(self, fpath, data): """Test dataset and pixel array properties are as expected.""" @@ -564,6 +576,7 @@ class TestPillowHandler_JPEG: assert data[5] == arr.shape assert arr.dtype == data[6] + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, rpath, values', JPEG_MATCHING_DATASETS) def test_array(self, fpath, rpath, values): """Test pixel_array returns correct values.""" @@ -588,6 +601,7 @@ class TestPillowHandler_JPEG: assert np.array_equal(arr, ref) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_color_3d(self): """Test decoding JPEG with pillow handler succeeds.""" ds = dcmread(JPGB_08_08_3_0_120F_YBR_FULL_422) @@ -602,6 +616,7 @@ class TestPillowHandler_JPEG: assert "YBR_FULL_422" == ds.PhotometricInterpretation + @pytest.mark.skip("When building a Debian package we can not download anything") def test_JPGE_16bit_raises(self): """Test decoding JPEG lossy with pillow handler fails.""" ds = dcmread(JPGE_16_12_1_0_1F_M2) @@ -612,6 +627,7 @@ class TestPillowHandler_JPEG: with pytest.raises(NotImplementedError, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_JPGL_raises(self): """Test decoding JPEG Lossless with pillow handler fails.""" ds = dcmread(JPGL_16_16_1_1_1F_M2) @@ -619,6 +635,7 @@ class TestPillowHandler_JPEG: with pytest.raises(NotImplementedError, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_JPGB_odd_data_size(self): """Test decoding JPEG Baseline with pillow handler succeeds.""" ds = dcmread(JPGB_08_08_3_0_1F_YBR_FULL) --- a/pydicom/tests/test_pylibjpeg.py +++ b/pydicom/tests/test_pylibjpeg.py @@ -71,258 +71,258 @@ UNSUPPORTED_SYNTAXES = list( set(AllTransferSyntaxes) ^ set(SUPPORTED_SYNTAXES) ) -# Transfer syntaxes supported by other handlers -IMPL = get_testdata_file("MR_small_implicit.dcm") -EXPL = get_testdata_file("OBXXXX1A.dcm") -EXPB = get_testdata_file("OBXXXX1A_expb.dcm") -DEFL = get_testdata_file("image_dfl.dcm") - -REFERENCE_DATA_UNSUPPORTED = [ - (IMPL, ('1.2.840.10008.1.2', 'CompressedSamples^MR1')), - (EXPL, ('1.2.840.10008.1.2.1', 'OB^^^^')), - (EXPB, ('1.2.840.10008.1.2.2', 'OB^^^^')), - (DEFL, ('1.2.840.10008.1.2.1.99', '^^^^')), -] - -# RLE Lossless - PackBits algorithm -RLE_8_1_1F = get_testdata_file("OBXXXX1A_rle.dcm") -RLE_8_1_2F = get_testdata_file("OBXXXX1A_rle_2frame.dcm") -RLE_8_3_1F = get_testdata_file("SC_rgb_rle.dcm") -RLE_8_3_2F = get_testdata_file("SC_rgb_rle_2frame.dcm") -RLE_16_1_1F = get_testdata_file("MR_small_RLE.dcm") -RLE_16_1_10F = get_testdata_file("emri_small_RLE.dcm") -RLE_16_3_1F = get_testdata_file("SC_rgb_rle_16bit.dcm") -RLE_16_3_2F = get_testdata_file("SC_rgb_rle_16bit_2frame.dcm") -RLE_32_1_1F = get_testdata_file("rtdose_rle_1frame.dcm") -RLE_32_1_15F = get_testdata_file("rtdose_rle.dcm") -RLE_32_3_1F = get_testdata_file("SC_rgb_rle_32bit.dcm") -RLE_32_3_2F = get_testdata_file("SC_rgb_rle_32bit_2frame.dcm") - -# JPEG - ISO/IEC 10918 Standard -# FMT_BA_BV_SPX_PR_FRAMESF_PI -# JPGB: 1.2.840.10008.1.2.4.50 - JPEG Baseline (8-bit only) -JPGB_08_08_3_0_1F_YBR_FULL = get_testdata_file("SC_rgb_small_odd_jpeg.dcm") -JPGB_08_08_3_0_120F_YBR_FULL_422 = get_testdata_file("color3d_jpeg_baseline.dcm") # noqa -# Different subsampling 411, 422, 444 -JPGB_08_08_3_0_1F_YBR_FULL_422_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+np.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_422_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s2.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n1.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n2.dcm") # noqa -JPGB_08_08_3_0_1F_YBR_FULL_444 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s4.dcm") # noqa -JPGB_08_08_3_0_1F_RGB = get_testdata_file("SC_rgb_dcmtk_+eb+cr.dcm") -# JPGE: 1.2.840.1.2.4.51 - JPEG Extended -JPGE_BAD = get_testdata_file("JPEG-lossy.dcm") # Bad JPEG file -JPGE_16_12_1_0_1F_M2 = get_testdata_file("JPGExtended.dcm") # Fixed version -# JPGL: 1.2.840.10008.1.2.4.70 - JPEG Lossless, Non-hierarchical, 1st Order -JPGL_08_08_1_0_1F = get_testdata_file("JPGLosslessP14SV1_1s_1f_8b.dcm") -JPGL_16_16_1_1_1F_M2 = get_testdata_file("JPEG-LL.dcm") - -JPGB = JPEGBaseline8Bit -JPGE = JPEGExtended12Bit -JPGL = JPEGLosslessSV1 - +## Transfer syntaxes supported by other handlers +#IMPL = get_testdata_file("MR_small_implicit.dcm") +#EXPL = get_testdata_file("OBXXXX1A.dcm") +#EXPB = get_testdata_file("OBXXXX1A_expb.dcm") +#DEFL = get_testdata_file("image_dfl.dcm") +# +#REFERENCE_DATA_UNSUPPORTED = [ +# (IMPL, ('1.2.840.10008.1.2', 'CompressedSamples^MR1')), +# (EXPL, ('1.2.840.10008.1.2.1', 'OB^^^^')), +# (EXPB, ('1.2.840.10008.1.2.2', 'OB^^^^')), +# (DEFL, ('1.2.840.10008.1.2.1.99', '^^^^')), +#] +# +## RLE Lossless - PackBits algorithm +#RLE_8_1_1F = get_testdata_file("OBXXXX1A_rle.dcm") +#RLE_8_1_2F = get_testdata_file("OBXXXX1A_rle_2frame.dcm") +#RLE_8_3_1F = get_testdata_file("SC_rgb_rle.dcm") +#RLE_8_3_2F = get_testdata_file("SC_rgb_rle_2frame.dcm") +#RLE_16_1_1F = get_testdata_file("MR_small_RLE.dcm") +#RLE_16_1_10F = get_testdata_file("emri_small_RLE.dcm") +#RLE_16_3_1F = get_testdata_file("SC_rgb_rle_16bit.dcm") +#RLE_16_3_2F = get_testdata_file("SC_rgb_rle_16bit_2frame.dcm") +#RLE_32_1_1F = get_testdata_file("rtdose_rle_1frame.dcm") +#RLE_32_1_15F = get_testdata_file("rtdose_rle.dcm") +#RLE_32_3_1F = get_testdata_file("SC_rgb_rle_32bit.dcm") +#RLE_32_3_2F = get_testdata_file("SC_rgb_rle_32bit_2frame.dcm") +# +## JPEG - ISO/IEC 10918 Standard +## FMT_BA_BV_SPX_PR_FRAMESF_PI +## JPGB: 1.2.840.10008.1.2.4.50 - JPEG Baseline (8-bit only) +#JPGB_08_08_3_0_1F_YBR_FULL = get_testdata_file("SC_rgb_small_odd_jpeg.dcm") +#JPGB_08_08_3_0_120F_YBR_FULL_422 = get_testdata_file("color3d_jpeg_baseline.dcm") # noqa +## Different subsampling 411, 422, 444 +#JPGB_08_08_3_0_1F_YBR_FULL_422_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+np.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_422_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s2.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_411 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n1.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_422 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+n2.dcm") # noqa +#JPGB_08_08_3_0_1F_YBR_FULL_444 = get_testdata_file("SC_rgb_dcmtk_+eb+cy+s4.dcm") # noqa +#JPGB_08_08_3_0_1F_RGB = get_testdata_file("SC_rgb_dcmtk_+eb+cr.dcm") +## JPGE: 1.2.840.1.2.4.51 - JPEG Extended +#JPGE_BAD = get_testdata_file("JPEG-lossy.dcm") # Bad JPEG file +#JPGE_16_12_1_0_1F_M2 = get_testdata_file("JPGExtended.dcm") # Fixed version +## JPGL: 1.2.840.10008.1.2.4.70 - JPEG Lossless, Non-hierarchical, 1st Order +#JPGL_08_08_1_0_1F = get_testdata_file("JPGLosslessP14SV1_1s_1f_8b.dcm") +#JPGL_16_16_1_1_1F_M2 = get_testdata_file("JPEG-LL.dcm") +# +#JPGB = JPEGBaseline8Bit +#JPGE = JPEGExtended12Bit +#JPGL = JPEGLosslessSV1 +# JPG_REFERENCE_DATA = [ - # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) - (JPGB_08_08_3_0_120F_YBR_FULL_422, (JPGB, 8, 3, 0, 120, (120, 480, 640, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_422_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_422_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_YBR_FULL_444, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa - (JPGB_08_08_3_0_1F_RGB, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), - (JPGE_16_12_1_0_1F_M2, (JPGE, 16, 1, 0, 1, (1024, 256), 'uint16')), - (JPGL_08_08_1_0_1F, (JPGL, 8, 1, 0, 1, (768, 1024), 'uint8')), - (JPGL_16_16_1_1_1F_M2, (JPGL, 16, 1, 1, 1, (1024, 256), 'int16')), +# # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) +# (JPGB_08_08_3_0_120F_YBR_FULL_422, (JPGB, 8, 3, 0, 120, (120, 480, 640, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_422_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_422_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_411, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_422, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_YBR_FULL_444, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), # noqa +# (JPGB_08_08_3_0_1F_RGB, (JPGB, 8, 3, 0, 1, (100, 100, 3), 'uint8')), +# (JPGE_16_12_1_0_1F_M2, (JPGE, 16, 1, 0, 1, (1024, 256), 'uint16')), +# (JPGL_08_08_1_0_1F, (JPGL, 8, 1, 0, 1, (768, 1024), 'uint8')), +# (JPGL_16_16_1_1_1F_M2, (JPGL, 16, 1, 1, 1, (1024, 256), 'int16')), ] JPG_MATCHING_DATASETS = [ - # (compressed, reference, hard coded check values), px tolerance - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_422_411, - get_testdata_file("SC_rgb_dcmtk_ebcynp_dcmd.dcm"), - [ - (253, 1, 0), (253, 129, 131), (0, 255, 5), (127, 255, 129), - (0, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - 2 - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_422_422, - get_testdata_file("SC_rgb_dcmtk_ebcys2_dcmd.dcm"), - [ - (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), - (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - 0 - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_411, - get_testdata_file("SC_rgb_dcmtk_ebcyn1_dcmd.dcm"), - [ - (253, 1, 0), (253, 129, 131), (0, 255, 5), (127, 255, 129), - (0, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - 2 - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_422, - get_testdata_file("SC_rgb_dcmtk_ebcyn2_dcmd.dcm"), - [ - (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), - (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - 0 - ), - pytest.param( - JPGB_08_08_3_0_1F_YBR_FULL_444, - get_testdata_file("SC_rgb_dcmtk_ebcys4_dcmd.dcm"), - [ - (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), - (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - 0 - ), - pytest.param( - JPGB_08_08_3_0_1F_RGB, - get_testdata_file("SC_rgb_dcmtk_ebcr_dcmd.dcm"), - [ - (255, 0, 0), (255, 128, 128), (0, 255, 0), (128, 255, 128), - (0, 0, 255), (128, 128, 255), (0, 0, 0), (64, 64, 64), - (192, 192, 192), (255, 255, 255), - ], - 1 - ), +# # (compressed, reference, hard coded check values), px tolerance +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_422_411, +# get_testdata_file("SC_rgb_dcmtk_ebcynp_dcmd.dcm"), +# [ +# (253, 1, 0), (253, 129, 131), (0, 255, 5), (127, 255, 129), +# (0, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# 2 +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_422_422, +# get_testdata_file("SC_rgb_dcmtk_ebcys2_dcmd.dcm"), +# [ +# (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), +# (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# 0 +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_411, +# get_testdata_file("SC_rgb_dcmtk_ebcyn1_dcmd.dcm"), +# [ +# (253, 1, 0), (253, 129, 131), (0, 255, 5), (127, 255, 129), +# (0, 0, 254), (127, 128, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# 2 +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_422, +# get_testdata_file("SC_rgb_dcmtk_ebcyn2_dcmd.dcm"), +# [ +# (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), +# (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# 0 +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_YBR_FULL_444, +# get_testdata_file("SC_rgb_dcmtk_ebcys4_dcmd.dcm"), +# [ +# (254, 0, 0), (255, 127, 127), (0, 255, 5), (129, 255, 129), +# (0, 0, 254), (128, 127, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# 0 +# ), +# pytest.param( +# JPGB_08_08_3_0_1F_RGB, +# get_testdata_file("SC_rgb_dcmtk_ebcr_dcmd.dcm"), +# [ +# (255, 0, 0), (255, 128, 128), (0, 255, 0), (128, 255, 128), +# (0, 0, 255), (128, 128, 255), (0, 0, 0), (64, 64, 64), +# (192, 192, 192), (255, 255, 255), +# ], +# 1 +# ), ] - - -# JPEG-LS - ISO/IEC 14495 Standard -JLSL = JPEGLSNearLossless -JLSN = JPEGLSLossless -JPEG_LS_LOSSLESS = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") +# +# +## JPEG-LS - ISO/IEC 14495 Standard +#JLSL = JPEGLSNearLossless +#JLSN = JPEGLSLossless +#JPEG_LS_LOSSLESS = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") JLS_REFERENCE_DATA = [ - # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) - (JPEG_LS_LOSSLESS, (JLSN, 16, 1, 1, 1, (64, 64), 'int16')), +# # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) +# (JPEG_LS_LOSSLESS, (JLSN, 16, 1, 1, 1, (64, 64), 'int16')), ] # JPEG 2000 - ISO/IEC 15444 Standard J2KR = JPEG2000Lossless J2KI = JPEG2000 -# J2KR: 1.2.840.100008.1.2.4.90 - JPEG 2000 Lossless -J2KR_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KR.dcm") -J2KR_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KR.dcm") -J2KR_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KR.dcm") -J2KR_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KR.dcm") -J2KR_16_16_1_0_10F_M2 = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") -J2KR_16_14_1_1_1F_M2 = get_testdata_file("693_J2KR.dcm") -J2KR_16_16_1_1_1F_M2 = get_testdata_file("MR_small_jp2klossless.dcm") -J2KR_16_13_1_1_1F_M2_MISMATCH = get_testdata_file("J2K_pixelrep_mismatch.dcm") -# Non-conformant pixel data -> JP2 header present -J2KR_08_08_3_0_1F_YBR_RCT = get_testdata_file("GDCMJ2K_TextGBR.dcm") -# J2KI: 1.2.840.10008.1.2.4.91 - JPEG 2000 -J2KI_08_08_3_0_1F_RGB = get_testdata_file("SC_rgb_gdcm_KY.dcm") -J2KI_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KI.dcm") -J2KI_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KI.dcm") -J2KI_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KI.dcm") -J2KI_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KI.dcm") -J2KI_16_14_1_1_1F_M2 = get_testdata_file("693_J2KI.dcm") -J2KI_16_16_1_1_1F_M2 = get_testdata_file("JPEG2000.dcm") - +## J2KR: 1.2.840.100008.1.2.4.90 - JPEG 2000 Lossless +#J2KR_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KR.dcm") +#J2KR_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KR.dcm") +#J2KR_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KR.dcm") +#J2KR_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KR.dcm") +#J2KR_16_16_1_0_10F_M2 = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") +#J2KR_16_14_1_1_1F_M2 = get_testdata_file("693_J2KR.dcm") +#J2KR_16_16_1_1_1F_M2 = get_testdata_file("MR_small_jp2klossless.dcm") +#J2KR_16_13_1_1_1F_M2_MISMATCH = get_testdata_file("J2K_pixelrep_mismatch.dcm") +## Non-conformant pixel data -> JP2 header present +#J2KR_08_08_3_0_1F_YBR_RCT = get_testdata_file("GDCMJ2K_TextGBR.dcm") +## J2KI: 1.2.840.10008.1.2.4.91 - JPEG 2000 +#J2KI_08_08_3_0_1F_RGB = get_testdata_file("SC_rgb_gdcm_KY.dcm") +#J2KI_08_08_3_0_1F_YBR_ICT = get_testdata_file("US1_J2KI.dcm") +#J2KI_16_10_1_0_1F_M1 = get_testdata_file("RG3_J2KI.dcm") +#J2KI_16_12_1_0_1F_M2 = get_testdata_file("MR2_J2KI.dcm") +#J2KI_16_15_1_0_1F_M1 = get_testdata_file("RG1_J2KI.dcm") +#J2KI_16_14_1_1_1F_M2 = get_testdata_file("693_J2KI.dcm") +#J2KI_16_16_1_1_1F_M2 = get_testdata_file("JPEG2000.dcm") +# J2K_REFERENCE_DATA = [ - # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) - (J2KR_08_08_3_0_1F_YBR_ICT, (J2KR, 8, 3, 0, 1, (480, 640, 3), 'uint8')), - (J2KR_16_10_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1760, 1760), 'uint16')), - (J2KR_16_12_1_0_1F_M2, (J2KR, 16, 1, 0, 1, (1024, 1024), 'uint16')), - (J2KR_16_15_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1955, 1841), 'uint16')), - # should be Bits Stored = 12 - (J2KR_16_16_1_0_10F_M2, (J2KR, 16, 1, 0, 10, (10, 64, 64), 'uint16')), - # should be Bits Stored = 16 - (J2KR_16_14_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (512, 512), 'int16')), - (J2KR_16_16_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (64, 64), 'int16')), - (J2KI_08_08_3_0_1F_RGB, (J2KI, 8, 3, 0, 1, (100, 100, 3), 'uint8')), - (J2KI_08_08_3_0_1F_YBR_ICT, (J2KI, 8, 3, 0, 1, (480, 640, 3), 'uint8')), - (J2KI_16_10_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1760, 1760), 'uint16')), - (J2KI_16_12_1_0_1F_M2, (J2KI, 16, 1, 0, 1, (1024, 1024), 'uint16')), - (J2KI_16_15_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1955, 1841), 'uint16')), - # should be Bits Stored = 16 - (J2KI_16_14_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (512, 512), 'int16')), - (J2KI_16_16_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (1024, 256), 'int16')), +# # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) +# (J2KR_08_08_3_0_1F_YBR_ICT, (J2KR, 8, 3, 0, 1, (480, 640, 3), 'uint8')), +# (J2KR_16_10_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1760, 1760), 'uint16')), +# (J2KR_16_12_1_0_1F_M2, (J2KR, 16, 1, 0, 1, (1024, 1024), 'uint16')), +# (J2KR_16_15_1_0_1F_M1, (J2KR, 16, 1, 0, 1, (1955, 1841), 'uint16')), +# # should be Bits Stored = 12 +# (J2KR_16_16_1_0_10F_M2, (J2KR, 16, 1, 0, 10, (10, 64, 64), 'uint16')), +# # should be Bits Stored = 16 +# (J2KR_16_14_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (512, 512), 'int16')), +# (J2KR_16_16_1_1_1F_M2, (J2KR, 16, 1, 1, 1, (64, 64), 'int16')), +# (J2KI_08_08_3_0_1F_RGB, (J2KI, 8, 3, 0, 1, (100, 100, 3), 'uint8')), +# (J2KI_08_08_3_0_1F_YBR_ICT, (J2KI, 8, 3, 0, 1, (480, 640, 3), 'uint8')), +# (J2KI_16_10_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1760, 1760), 'uint16')), +# (J2KI_16_12_1_0_1F_M2, (J2KI, 16, 1, 0, 1, (1024, 1024), 'uint16')), +# (J2KI_16_15_1_0_1F_M1, (J2KI, 16, 1, 0, 1, (1955, 1841), 'uint16')), +# # should be Bits Stored = 16 +# (J2KI_16_14_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (512, 512), 'int16')), +# (J2KI_16_16_1_1_1F_M2, (J2KI, 16, 1, 1, 1, (1024, 256), 'int16')), ] J2K_MATCHING_DATASETS = [ - # (compressed, reference, fixes) - pytest.param( - J2KR_08_08_3_0_1F_YBR_ICT, - get_testdata_file("US1_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_10_1_0_1F_M1, - get_testdata_file("RG3_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_12_1_0_1F_M2, - get_testdata_file("MR2_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_15_1_0_1F_M1, - get_testdata_file("RG1_UNCR.dcm"), - {}, - ), - pytest.param( - J2KR_16_16_1_0_10F_M2, - get_testdata_file("emri_small.dcm"), - {'BitsStored': 16}, - ), - pytest.param( - J2KR_16_14_1_1_1F_M2, - get_testdata_file("693_UNCR.dcm"), - {'BitsStored': 14}, - ), - pytest.param( - J2KR_16_16_1_1_1F_M2, - get_testdata_file("MR_small.dcm"), - {}, - ), - pytest.param( - J2KI_08_08_3_0_1F_RGB, - get_testdata_file("SC_rgb_gdcm2k_uncompressed.dcm"), - {}, - ), - pytest.param( - J2KI_08_08_3_0_1F_YBR_ICT, - get_testdata_file("US1_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_10_1_0_1F_M1, - get_testdata_file("RG3_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_12_1_0_1F_M2, - get_testdata_file("MR2_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_15_1_0_1F_M1, - get_testdata_file("RG1_UNCI.dcm"), - {}, - ), - pytest.param( - J2KI_16_14_1_1_1F_M2, - get_testdata_file("693_UNCI.dcm"), - {'BitsStored': 16}, - ), - pytest.param( - J2KI_16_16_1_1_1F_M2, - get_testdata_file("JPEG2000_UNC.dcm"), - {}, - ), +# # (compressed, reference, fixes) +# pytest.param( +# J2KR_08_08_3_0_1F_YBR_ICT, +# get_testdata_file("US1_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_10_1_0_1F_M1, +# get_testdata_file("RG3_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_12_1_0_1F_M2, +# get_testdata_file("MR2_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_15_1_0_1F_M1, +# get_testdata_file("RG1_UNCR.dcm"), +# {}, +# ), +# pytest.param( +# J2KR_16_16_1_0_10F_M2, +# get_testdata_file("emri_small.dcm"), +# {'BitsStored': 16}, +# ), +# pytest.param( +# J2KR_16_14_1_1_1F_M2, +# get_testdata_file("693_UNCR.dcm"), +# {'BitsStored': 14}, +# ), +# pytest.param( +# J2KR_16_16_1_1_1F_M2, +# get_testdata_file("MR_small.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_08_08_3_0_1F_RGB, +# get_testdata_file("SC_rgb_gdcm2k_uncompressed.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_08_08_3_0_1F_YBR_ICT, +# get_testdata_file("US1_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_10_1_0_1F_M1, +# get_testdata_file("RG3_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_12_1_0_1F_M2, +# get_testdata_file("MR2_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_15_1_0_1F_M1, +# get_testdata_file("RG1_UNCI.dcm"), +# {}, +# ), +# pytest.param( +# J2KI_16_14_1_1_1F_M2, +# get_testdata_file("693_UNCI.dcm"), +# {'BitsStored': 16}, +# ), +# pytest.param( +# J2KI_16_16_1_1_1F_M2, +# get_testdata_file("JPEG2000_UNC.dcm"), +# {}, +# ), ] @@ -361,6 +361,7 @@ class TestHandler: with pytest.raises((NotImplementedError, RuntimeError)): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif( HAVE_LJ or HAVE_OJ or HAVE_RLE, reason="plugins available" ) @@ -391,6 +392,7 @@ class TestHandler: with pytest.raises(RuntimeError, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_change_photometric_interpretation(self): """Test returned value.""" ds = dcmread(J2KR_16_12_1_0_1F_M2) @@ -409,6 +411,7 @@ class TestJPEG: """Restore the environment.""" pydicom.config.pixel_data_handlers = self.original_handlers + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, data', JPG_REFERENCE_DATA) def test_properties(self, fpath, data): """Test dataset and pixel array properties are as expected.""" @@ -425,6 +428,7 @@ class TestJPEG: assert data[5] == arr.shape assert arr.dtype == data[6] + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, rpath, val, tol', JPG_MATCHING_DATASETS) def test_array(self, fpath, rpath, val, tol): """Test pixel_array returns correct values.""" @@ -450,6 +454,7 @@ class TestJPEG: # All results within `tol` intensity units of the reference assert np.allclose(arr, ref, atol=tol) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, rpath, val, tol', JPG_MATCHING_DATASETS) def test_generate_frames(self, fpath, rpath, val, tol): """Test pixel_array returns correct values.""" @@ -484,6 +489,7 @@ class TestJPEG: with pytest.raises(RuntimeError, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_element_raises(self): """Test that missing required element raises exception.""" ds = dcmread(JPGB_08_08_3_0_1F_YBR_FULL) @@ -507,6 +513,7 @@ class TestJPEGLS: """Restore the environment.""" pydicom.config.pixel_data_handlers = self.original_handlers + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, data', JLS_REFERENCE_DATA) def test_properties(self, fpath, data): """Test dataset and pixel array properties are as expected.""" @@ -523,6 +530,7 @@ class TestJPEGLS: assert data[5] == arr.shape assert arr.dtype == data[6] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_arrary(self): """Test returned array values are OK.""" ds = dcmread(JPEG_LS_LOSSLESS) @@ -546,6 +554,7 @@ class TestJPEG2K: """Restore the environment.""" pydicom.config.pixel_data_handlers = self.original_handlers + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, data', J2K_REFERENCE_DATA) def test_properties_as_array(self, fpath, data): """Test dataset, pixel_array and as_array() are as expected.""" @@ -584,6 +593,7 @@ class TestJPEG2K: assert data[5] == arr.shape assert arr.dtype == data[6] + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, rpath, fixes', J2K_MATCHING_DATASETS) def test_array(self, fpath, rpath, fixes): """Test pixel_array returns correct values.""" @@ -597,6 +607,7 @@ class TestJPEG2K: ref = dcmread(rpath).pixel_array assert np.array_equal(arr, ref) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, rpath, fixes', J2K_MATCHING_DATASETS) def test_generate_frames(self, fpath, rpath, fixes): """Test pixel_array returns correct values.""" @@ -620,6 +631,7 @@ class TestJPEG2K: with pytest.raises(StopIteration): next(frame_generator) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_warnings(self): """Test the plugin warnings work.""" # Bits Stored @@ -667,6 +679,7 @@ class TestJPEG2K: with pytest.warns(UserWarning, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_decompress_using_pylibjpeg(self): """Test decompressing JPEG2K with pylibjpeg handler succeeds.""" ds = dcmread(J2KR_16_12_1_0_1F_M2) @@ -677,6 +690,7 @@ class TestJPEG2K: ref = ds.pixel_array assert np.array_equal(arr, ref) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_rep_mismatch(self): """Test mismatched j2k sign and Pixel Representation.""" ds = dcmread(J2KR_16_13_1_1_1F_M2_MISMATCH) @@ -706,37 +720,38 @@ class TestJPEG2K: RLE_REFERENCE_DATA = [ - # fpath, (bits, nr samples, pixel repr, nr frames, shape, dtype) - (RLE_8_1_1F, (8, 1, 0, 1, (600, 800), 'uint8')), - (RLE_8_1_2F, (8, 1, 0, 2, (2, 600, 800), 'uint8')), - (RLE_8_3_1F, (8, 3, 0, 1, (100, 100, 3), 'uint8')), - (RLE_8_3_2F, (8, 3, 0, 2, (2, 100, 100, 3), 'uint8')), - (RLE_16_1_1F, (16, 1, 1, 1, (64, 64), 'int16')), - (RLE_16_1_10F, (16, 1, 0, 10, (10, 64, 64), 'uint16')), - (RLE_16_3_1F, (16, 3, 0, 1, (100, 100, 3), 'uint16')), - (RLE_16_3_2F, (16, 3, 0, 2, (2, 100, 100, 3), 'uint16')), - (RLE_32_1_1F, (32, 1, 0, 1, (10, 10), 'uint32')), - (RLE_32_1_15F, (32, 1, 0, 15, (15, 10, 10), 'uint32')), - (RLE_32_3_1F, (32, 3, 0, 1, (100, 100, 3), 'uint32')), - (RLE_32_3_2F, (32, 3, 0, 2, (2, 100, 100, 3), 'uint32')), +# # fpath, (bits, nr samples, pixel repr, nr frames, shape, dtype) +# (RLE_8_1_1F, (8, 1, 0, 1, (600, 800), 'uint8')), +# (RLE_8_1_2F, (8, 1, 0, 2, (2, 600, 800), 'uint8')), +# (RLE_8_3_1F, (8, 3, 0, 1, (100, 100, 3), 'uint8')), +# (RLE_8_3_2F, (8, 3, 0, 2, (2, 100, 100, 3), 'uint8')), +# (RLE_16_1_1F, (16, 1, 1, 1, (64, 64), 'int16')), +# (RLE_16_1_10F, (16, 1, 0, 10, (10, 64, 64), 'uint16')), +# (RLE_16_3_1F, (16, 3, 0, 1, (100, 100, 3), 'uint16')), +# (RLE_16_3_2F, (16, 3, 0, 2, (2, 100, 100, 3), 'uint16')), +# (RLE_32_1_1F, (32, 1, 0, 1, (10, 10), 'uint32')), +# (RLE_32_1_15F, (32, 1, 0, 15, (15, 10, 10), 'uint32')), +# (RLE_32_3_1F, (32, 3, 0, 1, (100, 100, 3), 'uint32')), +# (RLE_32_3_2F, (32, 3, 0, 2, (2, 100, 100, 3), 'uint32')), ] RLE_MATCHING_DATASETS = [ - # (compressed, reference) - pytest.param(RLE_8_1_1F, get_testdata_file("OBXXXX1A.dcm")), - pytest.param(RLE_8_1_2F, get_testdata_file("OBXXXX1A_2frame.dcm")), - pytest.param(RLE_8_3_1F, get_testdata_file("SC_rgb.dcm")), - pytest.param(RLE_8_3_2F, get_testdata_file("SC_rgb_2frame.dcm")), - pytest.param(RLE_16_1_1F, get_testdata_file("MR_small.dcm")), - pytest.param(RLE_16_1_10F, get_testdata_file("emri_small.dcm")), - pytest.param(RLE_16_3_1F, get_testdata_file("SC_rgb_16bit.dcm")), - pytest.param(RLE_16_3_2F, get_testdata_file("SC_rgb_16bit_2frame.dcm")), - pytest.param(RLE_32_1_1F, get_testdata_file("rtdose_1frame.dcm")), - pytest.param(RLE_32_1_15F, get_testdata_file("rtdose.dcm")), - pytest.param(RLE_32_3_1F, get_testdata_file("SC_rgb_32bit.dcm")), - pytest.param(RLE_32_3_2F, get_testdata_file("SC_rgb_32bit_2frame.dcm")), +# # (compressed, reference) +# pytest.param(RLE_8_1_1F, get_testdata_file("OBXXXX1A.dcm")), +# pytest.param(RLE_8_1_2F, get_testdata_file("OBXXXX1A_2frame.dcm")), +# pytest.param(RLE_8_3_1F, get_testdata_file("SC_rgb.dcm")), +# pytest.param(RLE_8_3_2F, get_testdata_file("SC_rgb_2frame.dcm")), +# pytest.param(RLE_16_1_1F, get_testdata_file("MR_small.dcm")), +# pytest.param(RLE_16_1_10F, get_testdata_file("emri_small.dcm")), +# pytest.param(RLE_16_3_1F, get_testdata_file("SC_rgb_16bit.dcm")), +# pytest.param(RLE_16_3_2F, get_testdata_file("SC_rgb_16bit_2frame.dcm")), +# pytest.param(RLE_32_1_1F, get_testdata_file("rtdose_1frame.dcm")), +# pytest.param(RLE_32_1_15F, get_testdata_file("rtdose.dcm")), +# pytest.param(RLE_32_3_1F, get_testdata_file("SC_rgb_32bit.dcm")), +# pytest.param(RLE_32_3_2F, get_testdata_file("SC_rgb_32bit_2frame.dcm")), ] +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not TEST_RLE, reason="no -rle plugin") class TestRLE: def test_decompress_using_pylibjpeg(self): --- a/pydicom/tests/test_JPEG_LS_transfer_syntax.py +++ b/pydicom/tests/test_JPEG_LS_transfer_syntax.py @@ -49,15 +49,16 @@ except ImportError: gdcm_handler = None HAVE_GDCM = False -mr_name = get_testdata_file("MR_small.dcm") -jpeg_ls_lossless_name = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") -emri_name = get_testdata_file("emri_small.dcm") -emri_jpeg_ls_lossless = get_testdata_file( - "emri_small_jpeg_ls_lossless.dcm") +#mr_name = get_testdata_file("MR_small.dcm") +#jpeg_ls_lossless_name = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") +#emri_name = get_testdata_file("emri_small.dcm") +#emri_jpeg_ls_lossless = get_testdata_file( +# "emri_small_jpeg_ls_lossless.dcm") dir_name = os.path.dirname(sys.argv[0]) save_dir = os.getcwd() +@pytest.mark.skip("When building a Debian package we can not download anything") class Test_JPEG_LS_Lossless_transfer_syntax(): def setup_method(self, method): self.jpeg_ls_lossless = dcmread(jpeg_ls_lossless_name) --- a/pydicom/tests/test_dataset.py +++ b/pydicom/tests/test_dataset.py @@ -20,7 +20,7 @@ except ImportError: import pydicom from pydicom import config from pydicom import dcmread -from pydicom.data import get_testdata_file +#from pydicom.data import get_testdata_file from pydicom.dataelem import DataElement, RawDataElement from pydicom.dataset import ( Dataset, FileDataset, validate_file_meta, FileMetaDataset @@ -932,6 +932,7 @@ class TestDataset: assert 'SOPInstanceUID' in group0000 assert 'SkipFrameRangeFlag' in group0000 + @pytest.mark.skip("When building a Debian package we can not download anything") def test_get_item(self): """Test Dataset.get_item""" ds = Dataset() @@ -1108,6 +1109,7 @@ class TestDataset: item = ds.get_private_item(0x0009, 0x02, 'Creator 2.0') assert 2 == item.value + @pytest.mark.skip("When building a Debian package we can not download anything") def test_private_creator_from_raw_ds(self): # regression test for #1078 ct_filename = get_testdata_file("CT_small.dcm") @@ -1119,6 +1121,7 @@ class TestDataset: ds.private_block(0x13, 'GEMS_PATI_01', create=True) assert ['GEMS_PATI_01'] == ds.private_creators(0x13) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_add_known_private_tag(self): # regression test for #1082 ds = dcmread(get_testdata_file("CT_small.dcm")) @@ -1506,6 +1509,7 @@ class TestDataset: ds.save_as(fp) assert elem.is_undefined_length + @pytest.mark.skip("When building a Debian package we can not download anything") def test_with(self): """Test Dataset.__enter__ and __exit__.""" test_file = get_testdata_file('CT_small.dcm') @@ -1537,6 +1541,7 @@ class TestDataset: with pytest.raises(ValueError, match="Random ex message!"): getattr(DSException(), 'test') + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_already_have(self): """Test Dataset._get_pixel_array when we already have the array""" # Test that _pixel_array is returned unchanged unless required @@ -1548,6 +1553,7 @@ class TestDataset: assert get_image_pixel_ids(ds) == ds._pixel_id assert 'Test Value' == ds._pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_id_changed(self): """Test that we try to get new pixel data if the id has changed.""" fpath = get_testdata_file("CT_small.dcm") @@ -1564,6 +1570,7 @@ class TestDataset: pydicom.config.pixel_data_handlers = orig_handlers + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_unknown_syntax(self): """Test that pixel_array for an unknown syntax raises exception.""" ds = dcmread(get_testdata_file("CT_small.dcm")) @@ -1603,6 +1610,7 @@ class TestDataset: ds.TransferSyntaxUID = '1.2.840.10008.1.2' assert 'Implicit VR Little Endian' in str(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_set_convert_private_elem_from_raw(self): """Test Dataset.__setitem__ with a raw private element""" test_file = get_testdata_file('CT_small.dcm') @@ -1624,6 +1632,7 @@ class TestDataset: assert "Patient's Name" in ds.top() assert "Patient ID" not in ds.top() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_trait_names(self): """Test Dataset.trait_names contains element keywords""" test_file = get_testdata_file('CT_small.dcm') @@ -1809,6 +1818,7 @@ class TestDatasetElements: assert 'ACME LTD' == file_meta.ImplementationVersionName +@pytest.mark.skip("When building a Debian package we can not download anything") class TestFileDataset: def setup_method(self): self.test_file = get_testdata_file('CT_small.dcm') @@ -1982,6 +1992,7 @@ class TestFileDataset: assert ds2.__class__ is MyDatasetSubclass +@pytest.mark.skip("When building a Debian package we can not download anything") class TestDatasetOverlayArray: """Tests for Dataset.overlay_array().""" --- a/pydicom/tests/test_gdcm_pixel_data.py +++ b/pydicom/tests/test_gdcm_pixel_data.py @@ -18,7 +18,7 @@ except ImportError: import pydicom from pydicom.filereader import dcmread -from pydicom.data import get_testdata_file +#from pydicom.data import get_testdata_file from pydicom.encaps import defragment_data from pydicom.pixel_data_handlers import numpy_handler, gdcm_handler from pydicom.pixel_data_handlers.util import ( @@ -43,59 +43,60 @@ gdcm_im_missing_message = ( ) -empty_number_tags_name = get_testdata_file( - "reportsi_with_empty_number_tags.dcm") -rtplan_name = get_testdata_file("rtplan.dcm") -rtdose_name = get_testdata_file("rtdose.dcm") -ct_name = get_testdata_file("CT_small.dcm") -mr_name = get_testdata_file("MR_small.dcm") -truncated_mr_name = get_testdata_file("MR_truncated.dcm") -jpeg2000_name = get_testdata_file("JPEG2000.dcm") -jpeg2000_lossless_name = get_testdata_file("MR_small_jp2klossless.dcm") -jpeg_ls_lossless_name = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") -jpeg_lossy_name = get_testdata_file("JPEG-lossy.dcm") -jpeg_lossless_name = get_testdata_file("JPEG-LL.dcm") -jpeg_lossless_odd_data_size_name = get_testdata_file( - 'SC_rgb_small_odd_jpeg.dcm') -deflate_name = get_testdata_file("image_dfl.dcm") -rtstruct_name = get_testdata_file("rtstruct.dcm") -priv_SQ_name = get_testdata_file("priv_SQ.dcm") -nested_priv_SQ_name = get_testdata_file("nested_priv_SQ.dcm") -meta_missing_tsyntax_name = get_testdata_file("meta_missing_tsyntax.dcm") -no_meta_group_length = get_testdata_file("no_meta_group_length.dcm") -gzip_name = get_testdata_file("zipMR.gz") -color_px_name = get_testdata_file("color-px.dcm") -color_pl_name = get_testdata_file("color-pl.dcm") -explicit_vr_le_no_meta = get_testdata_file("ExplVR_LitEndNoMeta.dcm") -explicit_vr_be_no_meta = get_testdata_file("ExplVR_BigEndNoMeta.dcm") -emri_name = get_testdata_file("emri_small.dcm") -emri_big_endian_name = get_testdata_file("emri_small_big_endian.dcm") -emri_jpeg_ls_lossless = get_testdata_file( - "emri_small_jpeg_ls_lossless.dcm") -emri_jpeg_2k_lossless = get_testdata_file( - "emri_small_jpeg_2k_lossless.dcm") -color_3d_jpeg_baseline = get_testdata_file("color3d_jpeg_baseline.dcm") -sc_rgb_jpeg_dcmtk_411_YBR_FULL_422 = get_testdata_file( - "SC_rgb_dcmtk_+eb+cy+np.dcm") -sc_rgb_jpeg_dcmtk_411_YBR_FULL = get_testdata_file( - "SC_rgb_dcmtk_+eb+cy+n1.dcm") -sc_rgb_jpeg_dcmtk_422_YBR_FULL = get_testdata_file( - "SC_rgb_dcmtk_+eb+cy+n2.dcm") -sc_rgb_jpeg_dcmtk_444_YBR_FULL = get_testdata_file( - "SC_rgb_dcmtk_+eb+cy+s4.dcm") -sc_rgb_jpeg_dcmtk_422_YBR_FULL_422 = get_testdata_file( - "SC_rgb_dcmtk_+eb+cy+s2.dcm") -sc_rgb_jpeg_dcmtk_RGB = get_testdata_file("SC_rgb_dcmtk_+eb+cr.dcm") -sc_rgb_jpeg2k_gdcm_KY = get_testdata_file("SC_rgb_gdcm_KY.dcm") -ground_truth_sc_rgb_jpeg2k_gdcm_KY_gdcm = get_testdata_file( - "SC_rgb_gdcm2k_uncompressed.dcm" -) -J2KR_16_13_1_1_1F_M2_MISMATCH = get_testdata_file("J2K_pixelrep_mismatch.dcm") +#empty_number_tags_name = get_testdata_file( +# "reportsi_with_empty_number_tags.dcm") +#rtplan_name = get_testdata_file("rtplan.dcm") +#rtdose_name = get_testdata_file("rtdose.dcm") +#ct_name = get_testdata_file("CT_small.dcm") +#mr_name = get_testdata_file("MR_small.dcm") +#truncated_mr_name = get_testdata_file("MR_truncated.dcm") +#jpeg2000_name = get_testdata_file("JPEG2000.dcm") +#jpeg2000_lossless_name = get_testdata_file("MR_small_jp2klossless.dcm") +#jpeg_ls_lossless_name = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") +#jpeg_lossy_name = get_testdata_file("JPEG-lossy.dcm") +#jpeg_lossless_name = get_testdata_file("JPEG-LL.dcm") +#jpeg_lossless_odd_data_size_name = get_testdata_file( +# 'SC_rgb_small_odd_jpeg.dcm') +#deflate_name = get_testdata_file("image_dfl.dcm") +#rtstruct_name = get_testdata_file("rtstruct.dcm") +#priv_SQ_name = get_testdata_file("priv_SQ.dcm") +#nested_priv_SQ_name = get_testdata_file("nested_priv_SQ.dcm") +#meta_missing_tsyntax_name = get_testdata_file("meta_missing_tsyntax.dcm") +#no_meta_group_length = get_testdata_file("no_meta_group_length.dcm") +#gzip_name = get_testdata_file("zipMR.gz") +#color_px_name = get_testdata_file("color-px.dcm") +#color_pl_name = get_testdata_file("color-pl.dcm") +#explicit_vr_le_no_meta = get_testdata_file("ExplVR_LitEndNoMeta.dcm") +#explicit_vr_be_no_meta = get_testdata_file("ExplVR_BigEndNoMeta.dcm") +#emri_name = get_testdata_file("emri_small.dcm") +#emri_big_endian_name = get_testdata_file("emri_small_big_endian.dcm") +#emri_jpeg_ls_lossless = get_testdata_file( +# "emri_small_jpeg_ls_lossless.dcm") +#emri_jpeg_2k_lossless = get_testdata_file( +# "emri_small_jpeg_2k_lossless.dcm") +#color_3d_jpeg_baseline = get_testdata_file("color3d_jpeg_baseline.dcm") +#sc_rgb_jpeg_dcmtk_411_YBR_FULL_422 = get_testdata_file( +# "SC_rgb_dcmtk_+eb+cy+np.dcm") +#sc_rgb_jpeg_dcmtk_411_YBR_FULL = get_testdata_file( +# "SC_rgb_dcmtk_+eb+cy+n1.dcm") +#sc_rgb_jpeg_dcmtk_422_YBR_FULL = get_testdata_file( +# "SC_rgb_dcmtk_+eb+cy+n2.dcm") +#sc_rgb_jpeg_dcmtk_444_YBR_FULL = get_testdata_file( +# "SC_rgb_dcmtk_+eb+cy+s4.dcm") +#sc_rgb_jpeg_dcmtk_422_YBR_FULL_422 = get_testdata_file( +# "SC_rgb_dcmtk_+eb+cy+s2.dcm") +#sc_rgb_jpeg_dcmtk_RGB = get_testdata_file("SC_rgb_dcmtk_+eb+cr.dcm") +#sc_rgb_jpeg2k_gdcm_KY = get_testdata_file("SC_rgb_gdcm_KY.dcm") +#ground_truth_sc_rgb_jpeg2k_gdcm_KY_gdcm = get_testdata_file( +# "SC_rgb_gdcm2k_uncompressed.dcm" +#) +#J2KR_16_13_1_1_1F_M2_MISMATCH = get_testdata_file("J2K_pixelrep_mismatch.dcm") dir_name = os.path.dirname(sys.argv[0]) save_dir = os.getcwd() +@pytest.mark.skip("When building a Debian package we can not download anything") class TestGDCM_JPEG_LS_no_gdcm: def setup_method(self): self.unicode_filename = os.path.join( @@ -121,6 +122,7 @@ class TestGDCM_JPEG_LS_no_gdcm: self.emri_jpeg_ls_lossless.pixel_array +@pytest.mark.skip("When building a Debian package we can not download anything") class TestGDCM_JPEG2000_no_gdcm: def setup_method(self): self.jpeg_2k = dcmread(jpeg2000_name) @@ -184,6 +186,7 @@ class TestGDCM_JPEGlossy_no_gdcm: self.color_3d_jpeg.pixel_array +@pytest.mark.skip("When building a Debian package we can not download anything") class TestGDCM_JPEGlossless_no_gdcm: def setup_method(self): self.jpeg_lossless = dcmread(jpeg_lossless_name) @@ -208,115 +211,6 @@ class TestGDCM_JPEGlossless_no_gdcm: self.jpeg_lossless.pixel_array -pi_rgb_test_ids = [ - "JPEG_RGB_411_AS_YBR_FULL", - "JPEG_RGB_411_AS_YBR_FULL_422", - "JPEG_RGB_422_AS_YBR_FULL", - "JPEG_RGB_422_AS_YBR_FULL_422", - "JPEG_RGB_444_AS_YBR_FULL", -] - -pi_rgb_testdata = [ - pytest.param( - sc_rgb_jpeg_dcmtk_411_YBR_FULL, - "YBR_FULL", - [ - (253, 1, 0), - (253, 128, 132), - (0, 255, 5), - (127, 255, 127), - (1, 0, 254), - (127, 128, 255), - (0, 0, 0), - (64, 64, 64), - (192, 192, 192), - (255, 255, 255), - ], - True, - ), - pytest.param( - sc_rgb_jpeg_dcmtk_411_YBR_FULL_422, - "YBR_FULL_422", - [ - (253, 1, 0), - (253, 128, 132), - (0, 255, 5), - (127, 255, 127), - (1, 0, 254), - (127, 128, 255), - (0, 0, 0), - (64, 64, 64), - (192, 192, 192), - (255, 255, 255), - ], - True, - ), - pytest.param( - sc_rgb_jpeg_dcmtk_422_YBR_FULL, - "YBR_FULL", - [ - (254, 0, 0), - (255, 127, 127), - (0, 255, 5), - (129, 255, 129), - (0, 0, 254), - (128, 127, 255), - (0, 0, 0), - (64, 64, 64), - (192, 192, 192), - (255, 255, 255), - ], - True, - ), - pytest.param( - sc_rgb_jpeg_dcmtk_422_YBR_FULL_422, - "YBR_FULL_422", - [ - (254, 0, 0), - (255, 127, 127), - (0, 255, 5), - (129, 255, 129), - (0, 0, 254), - (128, 127, 255), - (0, 0, 0), - (64, 64, 64), - (192, 192, 192), - (255, 255, 255), - ], - True, - ), - pytest.param( - sc_rgb_jpeg_dcmtk_444_YBR_FULL, - "YBR_FULL", - [ - (254, 0, 0), - (255, 127, 127), - (0, 255, 5), - (129, 255, 129), - (0, 0, 254), - (128, 127, 255), - (0, 0, 0), - (64, 64, 64), - (192, 192, 192), - (255, 255, 255), - ], - True, - ) -] - -with_gdcm_params = [ - pytest.param( - 'File', - marks=pytest.mark.skipif(not HAVE_GDCM, reason=gdcm_missing_message) - ), - pytest.param( - 'InMemory', - marks=pytest.mark.skipif( - not HAVE_GDCM_IN_MEMORY_SUPPORT, reason=gdcm_im_missing_message - ) - ) -] - class TestsWithGDCM: @pytest.fixture(params=with_gdcm_params, scope='class', autouse=True) @@ -481,9 +375,10 @@ class TestsWithGDCM: assert (57, 57, 57) == tuple(a[3, 169, 290, :]) assert "YBR_FULL_422" == color_3d_jpeg.PhotometricInterpretation - @pytest.mark.parametrize( - "image,pi,results,convert_yuv_to_rgb", - pi_rgb_testdata, ids=pi_rgb_test_ids) + @pytest.mark.skip("When building a Debian package we can not download anything") + #@pytest.mark.parametrize( + # "image,pi,results,convert_yuv_to_rgb", + # pi_rgb_testdata, ids=pi_rgb_test_ids) def test_PI_RGB(self, image, pi, results, convert_yuv_to_rgb): t = dcmread(image) assert t.PhotometricInterpretation == pi @@ -541,7 +436,7 @@ class TestsWithGDCM: arr[328:338, 106].tolist() ) - +@pytest.mark.skip("When building a Debian package we can not download anything") class TestSupportFunctions: @pytest.fixture(scope='class') def dataset_2d(self): --- a/pydicom/tests/test_jpeg_ls_pixel_data.py +++ b/pydicom/tests/test_jpeg_ls_pixel_data.py @@ -22,44 +22,44 @@ have_jpeg_ls_handler = jpeg_ls_handler.i test_jpeg_ls_decoder = have_numpy_handler and have_jpeg_ls_handler -empty_number_tags_name = get_testdata_file( - "reportsi_with_empty_number_tags.dcm") -rtplan_name = get_testdata_file("rtplan.dcm") -rtdose_name = get_testdata_file("rtdose.dcm") -ct_name = get_testdata_file("CT_small.dcm") -mr_name = get_testdata_file("MR_small.dcm") -truncated_mr_name = get_testdata_file("MR_truncated.dcm") -jpeg2000_name = get_testdata_file("JPEG2000.dcm") -jpeg2000_lossless_name = get_testdata_file( - "MR_small_jp2klossless.dcm") -jpeg_ls_lossless_name = get_testdata_file( - "MR_small_jpeg_ls_lossless.dcm") -jpeg_lossy_name = get_testdata_file("JPEG-lossy.dcm") -jpeg_lossless_name = get_testdata_file("JPEG-LL.dcm") -deflate_name = get_testdata_file("image_dfl.dcm") -rtstruct_name = get_testdata_file("rtstruct.dcm") -priv_SQ_name = get_testdata_file("priv_SQ.dcm") -nested_priv_SQ_name = get_testdata_file("nested_priv_SQ.dcm") -meta_missing_tsyntax_name = get_testdata_file( - "meta_missing_tsyntax.dcm") -no_meta_group_length = get_testdata_file( - "no_meta_group_length.dcm") -gzip_name = get_testdata_file("zipMR.gz") -color_px_name = get_testdata_file("color-px.dcm") -color_pl_name = get_testdata_file("color-pl.dcm") -explicit_vr_le_no_meta = get_testdata_file( - "ExplVR_LitEndNoMeta.dcm") -explicit_vr_be_no_meta = get_testdata_file( - "ExplVR_BigEndNoMeta.dcm") -emri_name = get_testdata_file("emri_small.dcm") -emri_big_endian_name = get_testdata_file( - "emri_small_big_endian.dcm") -emri_jpeg_ls_lossless = get_testdata_file( - "emri_small_jpeg_ls_lossless.dcm") -emri_jpeg_2k_lossless = get_testdata_file( - "emri_small_jpeg_2k_lossless.dcm") -color_3d_jpeg_baseline = get_testdata_file( - "color3d_jpeg_baseline.dcm") +#empty_number_tags_name = get_testdata_file( +# "reportsi_with_empty_number_tags.dcm") +#rtplan_name = get_testdata_file("rtplan.dcm") +#rtdose_name = get_testdata_file("rtdose.dcm") +#ct_name = get_testdata_file("CT_small.dcm") +#mr_name = get_testdata_file("MR_small.dcm") +#truncated_mr_name = get_testdata_file("MR_truncated.dcm") +#jpeg2000_name = get_testdata_file("JPEG2000.dcm") +#jpeg2000_lossless_name = get_testdata_file( +# "MR_small_jp2klossless.dcm") +#jpeg_ls_lossless_name = get_testdata_file( +# "MR_small_jpeg_ls_lossless.dcm") +#jpeg_lossy_name = get_testdata_file("JPEG-lossy.dcm") +#jpeg_lossless_name = get_testdata_file("JPEG-LL.dcm") +#deflate_name = get_testdata_file("image_dfl.dcm") +#rtstruct_name = get_testdata_file("rtstruct.dcm") +#priv_SQ_name = get_testdata_file("priv_SQ.dcm") +#nested_priv_SQ_name = get_testdata_file("nested_priv_SQ.dcm") +#meta_missing_tsyntax_name = get_testdata_file( +# "meta_missing_tsyntax.dcm") +#no_meta_group_length = get_testdata_file( +# "no_meta_group_length.dcm") +#gzip_name = get_testdata_file("zipMR.gz") +#color_px_name = get_testdata_file("color-px.dcm") +#color_pl_name = get_testdata_file("color-pl.dcm") +#explicit_vr_le_no_meta = get_testdata_file( +# "ExplVR_LitEndNoMeta.dcm") +#explicit_vr_be_no_meta = get_testdata_file( +# "ExplVR_BigEndNoMeta.dcm") +#emri_name = get_testdata_file("emri_small.dcm") +#emri_big_endian_name = get_testdata_file( +# "emri_small_big_endian.dcm") +#emri_jpeg_ls_lossless = get_testdata_file( +# "emri_small_jpeg_ls_lossless.dcm") +#emri_jpeg_2k_lossless = get_testdata_file( +# "emri_small_jpeg_2k_lossless.dcm") +#color_3d_jpeg_baseline = get_testdata_file( +# "color3d_jpeg_baseline.dcm") dir_name = os.path.dirname(sys.argv[0]) save_dir = os.getcwd() @@ -67,6 +67,7 @@ SUPPORTED_HANDLER_NAMES = ( 'jpegls', 'jpeg_ls', 'JPEG_LS', 'jpegls_handler', 'JPEG_LS_Handler' ) +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") class TestJPEGLS_no_jpeg_ls: def setup_method(self): self.jpeg_ls_lossless = dcmread(jpeg_ls_lossless_name) @@ -84,6 +85,7 @@ class TestJPEGLS_no_jpeg_ls: self.jpeg_ls_lossless.pixel_array +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") class TestJPEGLS_JPEG2000_no_jpeg_ls: def setup_method(self): self.jpeg_2k = dcmread(jpeg2000_name) @@ -108,6 +110,7 @@ class TestJPEGLS_JPEG2000_no_jpeg_ls: self.emri_jpeg_2k_lossless.pixel_array +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") class TestJPEGLS_JPEGlossy_no_jpeg_ls: def setup_method(self): self.jpeg_lossy = dcmread(jpeg_lossy_name) @@ -133,6 +136,7 @@ class TestJPEGLS_JPEGlossy_no_jpeg_ls: self.color_3d_jpeg.pixel_array +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") class TestJPEGLS_JPEGlossless_no_jpeg_ls: def setup_method(self): self.jpeg_lossless = dcmread(jpeg_lossless_name) @@ -156,6 +160,7 @@ class TestJPEGLS_JPEGlossless_no_jpeg_ls self.jpeg_lossless.pixel_array +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") @pytest.mark.skipif(not test_jpeg_ls_decoder, reason=jpeg_ls_missing_message) class TestJPEGLS_JPEG_LS_with_jpeg_ls: def setup_method(self): @@ -189,6 +194,7 @@ class TestJPEGLS_JPEG_LS_with_jpeg_ls: assert b.mean() == a.mean() +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") @pytest.mark.skipif(not test_jpeg_ls_decoder, reason=jpeg_ls_missing_message) class TestJPEGLS_JPEG2000_with_jpeg_ls: def setup_method(self): @@ -212,6 +218,7 @@ class TestJPEGLS_JPEG2000_with_jpeg_ls: self.emri_jpeg_2k_lossless.pixel_array +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") @pytest.mark.skipif(not test_jpeg_ls_decoder, reason=jpeg_ls_missing_message) class TestJPEGLS_JPEGlossy_with_jpeg_ls: def setup_method(self): @@ -237,6 +244,7 @@ class TestJPEGLS_JPEGlossy_with_jpeg_ls: self.color_3d_jpeg.pixel_array +@pytest.mark.skip("Ignore test due to wrong gdcm usage. (See https://lists.debian.org/debian-med/2021/12/msg00061.html)") @pytest.mark.skipif(not test_jpeg_ls_decoder, reason=jpeg_ls_missing_message) class TestJPEGLS_JPEGlossless_with_jpeg_ls: def setup_method(self): --- a/pydicom/tests/test_filereader.py +++ b/pydicom/tests/test_filereader.py @@ -59,45 +59,45 @@ except ImportError: have_jpeg_ls = jpeg_ls is not None have_pillow = PILImg is not None -empty_number_tags_name = get_testdata_file( - "reportsi_with_empty_number_tags.dcm" -) -rtplan_name = get_testdata_file("rtplan.dcm") -rtdose_name = get_testdata_file("rtdose.dcm") -ct_name = get_testdata_file("CT_small.dcm") -mr_name = get_testdata_file("MR_small.dcm") -truncated_mr_name = get_testdata_file("MR_truncated.dcm") -jpeg2000_name = get_testdata_file("JPEG2000.dcm") -jpeg2000_embedded_sequence_delimeter_name = get_testdata_file( - "JPEG2000-embedded-sequence-delimiter.dcm" -) -jpeg2000_lossless_name = get_testdata_file("MR_small_jp2klossless.dcm") -jpeg_ls_lossless_name = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") -jpeg_lossy_name = get_testdata_file("JPEG-lossy.dcm") -jpeg_lossless_name = get_testdata_file("JPEG-LL.dcm") -deflate_name = get_testdata_file("image_dfl.dcm") -rtstruct_name = get_testdata_file("rtstruct.dcm") -priv_SQ_name = get_testdata_file("priv_SQ.dcm") -nested_priv_SQ_name = get_testdata_file("nested_priv_SQ.dcm") -meta_missing_tsyntax_name = get_testdata_file("meta_missing_tsyntax.dcm") -no_meta_group_length = get_testdata_file("no_meta_group_length.dcm") -gzip_name = get_testdata_file("zipMR.gz") -color_px_name = get_testdata_file("color-px.dcm") -color_pl_name = get_testdata_file("color-pl.dcm") -explicit_vr_le_no_meta = get_testdata_file("ExplVR_LitEndNoMeta.dcm") -explicit_vr_be_no_meta = get_testdata_file("ExplVR_BigEndNoMeta.dcm") -emri_name = get_testdata_file("emri_small.dcm") -emri_big_endian_name = get_testdata_file("emri_small_big_endian.dcm") -emri_jpeg_ls_lossless = get_testdata_file("emri_small_jpeg_ls_lossless.dcm") -emri_jpeg_2k_lossless = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") -emri_jpeg_2k_lossless_too_short = get_testdata_file( - "emri_small_jpeg_2k_lossless_too_short.dcm" -) -color_3d_jpeg_baseline = get_testdata_file("color3d_jpeg_baseline.dcm") +#empty_number_tags_name = get_testdata_file( +# "reportsi_with_empty_number_tags.dcm" +#) +#rtplan_name = get_testdata_file("rtplan.dcm") +#rtdose_name = get_testdata_file("rtdose.dcm") +#ct_name = get_testdata_file("CT_small.dcm") +#mr_name = get_testdata_file("MR_small.dcm") +#truncated_mr_name = get_testdata_file("MR_truncated.dcm") +#jpeg2000_name = get_testdata_file("JPEG2000.dcm") +#jpeg2000_embedded_sequence_delimeter_name = get_testdata_file( +# "JPEG2000-embedded-sequence-delimiter.dcm" +#) +#jpeg2000_lossless_name = get_testdata_file("MR_small_jp2klossless.dcm") +#jpeg_ls_lossless_name = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") +#jpeg_lossy_name = get_testdata_file("JPEG-lossy.dcm") +#jpeg_lossless_name = get_testdata_file("JPEG-LL.dcm") +#deflate_name = get_testdata_file("image_dfl.dcm") +#rtstruct_name = get_testdata_file("rtstruct.dcm") +#priv_SQ_name = get_testdata_file("priv_SQ.dcm") +#nested_priv_SQ_name = get_testdata_file("nested_priv_SQ.dcm") +#meta_missing_tsyntax_name = get_testdata_file("meta_missing_tsyntax.dcm") +#no_meta_group_length = get_testdata_file("no_meta_group_length.dcm") +#gzip_name = get_testdata_file("zipMR.gz") +#color_px_name = get_testdata_file("color-px.dcm") +#color_pl_name = get_testdata_file("color-pl.dcm") +#explicit_vr_le_no_meta = get_testdata_file("ExplVR_LitEndNoMeta.dcm") +#explicit_vr_be_no_meta = get_testdata_file("ExplVR_BigEndNoMeta.dcm") +#emri_name = get_testdata_file("emri_small.dcm") +#emri_big_endian_name = get_testdata_file("emri_small_big_endian.dcm") +#emri_jpeg_ls_lossless = get_testdata_file("emri_small_jpeg_ls_lossless.dcm") +#emri_jpeg_2k_lossless = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") +#emri_jpeg_2k_lossless_too_short = get_testdata_file( +# "emri_small_jpeg_2k_lossless_too_short.dcm" +#) +#color_3d_jpeg_baseline = get_testdata_file("color3d_jpeg_baseline.dcm") dir_name = os.path.dirname(sys.argv[0]) save_dir = os.getcwd() - +@pytest.mark.skip("When building a Debian package we can not download anything") class TestReader: def test_empty_numbers_tag(self): """Test that an empty tag with a number VR (FL, UL, SL, US, @@ -1376,6 +1376,7 @@ class TestDSISnumpy: config.DS_decimal(orig_DS_decimal) config.DS_numpy(orig_DS_numpy) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(have_numpy, reason="Testing import error") def test_IS_numpy_import_error(self): config.use_IS_numpy = True @@ -1384,6 +1385,7 @@ class TestDSISnumpy: with pytest.raises(ImportError): rtss.ROIContourSequence[0].ROIDisplayColor # VR is IS + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not have_numpy, reason="Testing with numpy only") def test_IS_numpy_class(self): config.use_IS_numpy = True @@ -1396,6 +1398,7 @@ class TestDSISnumpy: roi_num = rtss.ROIContourSequence[0].ReferencedROINumber assert isinstance(roi_num, numpy.int64) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_IS_not_numpy(self): """Test class of the object matches the config, when the config is changed""" @@ -1404,6 +1407,7 @@ class TestDSISnumpy: col = rtss.ROIContourSequence[0].ROIDisplayColor # VR is IS assert isinstance(col, MultiValue) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(have_numpy, reason="Testing import error") def test_DS_numpy_import_error(self): config.use_DS_numpy = True @@ -1412,6 +1416,7 @@ class TestDSISnumpy: with pytest.raises(ImportError): rtss.ROIContourSequence[0].ContourSequence[0].ContourData + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not have_numpy, reason="Testing with numpy only") def test_DS_numpy_class(self): config.use_DS_numpy = True @@ -1425,6 +1430,7 @@ class TestDSISnumpy: roi_vol = rtss.StructureSetROISequence[0].ROIVolume assert isinstance(roi_vol, numpy.float64) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_DS_not_numpy(self): """Test class of the object matches the config.""" config.use_DS_numpy = False @@ -1468,6 +1474,7 @@ class TestDSISnumpy: values.convert_IS_string(b"123", True) +@pytest.mark.skip("When building a Debian package we can not download anything") class TestDeferredRead: """Test that deferred data element reading (for large size) works as expected @@ -1537,6 +1544,7 @@ class TestDeferredRead: assert 2068 == len(private_block[0x29].value) +@pytest.mark.skip("When building a Debian package we can not download anything") class TestReadTruncatedFile: def testReadFileWithMissingPixelData(self): mr = dcmread(truncated_mr_name) @@ -1569,6 +1577,7 @@ class TestReadTruncatedFile: mr.pixel_array +@pytest.mark.skip("When building a Debian package we can not download anything") class TestFileLike: """Test that can read DICOM files with file-like object rather than filename --- a/pydicom/tests/test_cli.py +++ b/pydicom/tests/test_cli.py @@ -31,6 +31,7 @@ bad_indexes = ( ) +@pytest.mark.skip("When building a Debian package we can not download anything") class TestFilespec: @pytest.mark.parametrize("bad_spec", bad_elem_specs) def test_syntax(self, bad_spec): @@ -76,6 +77,7 @@ class TestFilespec: assert expected == filespec_parts(filespec) +@pytest.mark.skip("When building a Debian package we can not download anything") class TestFilespecElementEval: # Load plan once plan, _ = filespec_parser("pydicom::rtplan.dcm")[0] @@ -121,6 +123,7 @@ class TestCLIcall: out, _ = capsys.readouterr() assert out.startswith("usage: pydicom [-h] {") + @pytest.mark.skip("When building a Debian package we can not download anything") def test_codify_command(self, capsys): """CLI `codify` command prints correct output""" @@ -134,6 +137,7 @@ class TestCLIcall: out, _ = capsys.readouterr() assert "add_new((0x0001, 0x0001)" not in out + @pytest.mark.skip("When building a Debian package we can not download anything") def test_codify_data_element(self, capsys): """CLI `codify` command raises error if not a Dataset""" with pytest.raises(NotImplementedError): @@ -146,6 +150,7 @@ class TestCLIcall: assert out.startswith("# -*- coding: utf-8 -*-") assert "Buc^Jérôme" in out + @pytest.mark.skip("When building a Debian package we can not download anything") def test_help(self, capsys): """CLI `help` command gives expected output""" # With subcommand @@ -164,6 +169,7 @@ class TestCLIcall: out, _ = capsys.readouterr() assert "Available subcommands:" in out + @pytest.mark.skip("When building a Debian package we can not download anything") def test_show_command(self, capsys): """CLI `show` command prints correct output""" main("show pydicom::MR_small_RLE.dcm".split()) @@ -178,6 +184,7 @@ class TestCLIcall: out, _ = capsys.readouterr() assert "4000" == out.strip() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_show_options(self, capsys): """CLI `show` command with options prints correct output""" # Quiet option, image file --- a/pydicom/tests/test_dataelem.py +++ b/pydicom/tests/test_dataelem.py @@ -404,6 +404,7 @@ class TestDataElement: assert 'PN' == ds[0x00100010].VR assert 'Dionysios=Διονυσιος' == ds[0x00100010].value + @pytest.mark.skip("When building a Debian package we can not download anything") def test_reading_ds_with_known_tags_with_UN_VR( self, replace_un_with_known_vr): """Known tags with VR UN are correctly read.""" --- a/pydicom/tests/test_encaps.py +++ b/pydicom/tests/test_encaps.py @@ -472,6 +472,7 @@ class TestGeneratePixelDataFrames: assert next(frames) == b'\x03\x00\x00\x00\x02\x04' pytest.raises(StopIteration, next, frames) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_empty_bot_multi_fragments_per_frame(self): """Test multi-frame where multiple frags per frame and no BOT.""" # Regression test for #685 @@ -541,6 +542,7 @@ class TestGeneratePixelData: with pytest.raises(ValueError, match=msg): next(generate_pixel_data(bytestream)) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_empty_bot_too_few_fragments(self): """Test parsing with too few fragments.""" ds = dcmread(JP2K_10FRAME_NOBOT) @@ -1135,6 +1137,7 @@ class TestEncapsulateFrame: pytest.raises(StopIteration, next, item_generator) +@pytest.mark.skip("When building a Debian package we can not download anything") class TestEncapsulate: """Test encaps.encapsulate.""" def test_encapsulate_single_fragment_per_frame_no_bot(self): @@ -1229,6 +1232,7 @@ class TestEncapsulate: encapsulate([frame_a, frame_b], has_bot=True) +@pytest.mark.skip("When building a Debian package we can not download anything") class TestEncapsulateExtended: """Tests for encaps.encapsulate_extended.""" def test_encapsulate(self): --- a/pydicom/tests/test_encoders_pydicom.py +++ b/pydicom/tests/test_encoders_pydicom.py @@ -28,23 +28,25 @@ from pydicom.pixel_data_handlers.util im from pydicom.uid import RLELossless -# EXPL: Explicit VR Little Endian -# RLE: RLE Lossless -# 8/8-bit, 1 sample/pixel, 1 frame -EXPL_8_1_1F = get_testdata_file("OBXXXX1A.dcm") -RLE_8_1_1F = get_testdata_file("OBXXXX1A_rle.dcm") -# 8/8-bit, 3 sample/pixel, 1 frame -EXPL_8_3_1F = get_testdata_file("SC_rgb.dcm") -# 8/8-bit, 3 sample/pixel, 2 frame -EXPL_8_3_2F = get_testdata_file("SC_rgb_2frame.dcm") -# 16/16-bit, 1 sample/pixel, 1 frame -EXPL_16_1_1F = get_testdata_file("MR_small.dcm") -# 16/16-bit, 3 sample/pixel, 1 frame -EXPL_16_3_1F = get_testdata_file("SC_rgb_16bit.dcm") -# 32/32-bit, 1 sample/pixel, 1 frame -EXPL_32_1_1F = get_testdata_file("rtdose_1frame.dcm") -# 32/32-bit, 3 sample/pixel, 1 frame -EXPL_32_3_1F = get_testdata_file("SC_rgb_32bit.dcm") +## EXPL: Explicit VR Little Endian +## RLE: RLE Lossless +## 8/8-bit, 1 sample/pixel, 1 frame +#EXPL_8_1_1F = get_testdata_file("OBXXXX1A.dcm") +#RLE_8_1_1F = get_testdata_file("OBXXXX1A_rle.dcm") +RLE_8_1_1F = None +## 8/8-bit, 3 sample/pixel, 1 frame +#EXPL_8_3_1F = get_testdata_file("SC_rgb.dcm") +## 8/8-bit, 3 sample/pixel, 2 frame +#EXPL_8_3_2F = get_testdata_file("SC_rgb_2frame.dcm") +## 16/16-bit, 1 sample/pixel, 1 frame +#EXPL_16_1_1F = get_testdata_file("MR_small.dcm") +## 16/16-bit, 3 sample/pixel, 1 frame +#EXPL_16_3_1F = get_testdata_file("SC_rgb_16bit.dcm") +EXPL_16_3_1F = None +## 32/32-bit, 1 sample/pixel, 1 frame +#EXPL_32_1_1F = get_testdata_file("rtdose_1frame.dcm") +## 32/32-bit, 3 sample/pixel, 1 frame +#EXPL_32_3_1F = get_testdata_file("SC_rgb_32bit.dcm") # Tests for RLE encoding @@ -107,6 +109,7 @@ class TestEncodeRow: assert output == _encode_row(src) +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not HAVE_NP, reason="Numpy not available") class TestEncodeFrame: """Tests for rle_handler._encode_frame.""" @@ -139,6 +142,7 @@ class TestEncodeFrame: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_8bit_3sample(self): """Test an encode/decode cycle for 8-bit 3 sample/pixel.""" ds = dcmread(EXPL_8_3_1F) @@ -176,6 +180,7 @@ class TestEncodeFrame: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_16bit_3sample(self): """Test an encode/decode cycle for 16-bit 3 sample/pixel.""" ds = dcmread(EXPL_16_3_1F) @@ -351,6 +356,7 @@ class TestEncodeFrame: class TestEncodeSegment: """Tests for rle_handler._encode_segment.""" + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not HAVE_NP, reason="Numpy not available") def test_one_row(self): """Test encoding data that contains only a single row.""" @@ -372,6 +378,7 @@ class TestEncodeSegment: assert ds.Columns == len(redecoded) assert decoded[:ds.Columns] == redecoded + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle(self): """Test the decoded data remains the same after encoding/decoding.""" ds = dcmread(RLE_8_1_1F) @@ -404,6 +411,7 @@ class TestRLEEncodeFrame: with pytest.raises(ValueError, match=msg): rle_encode_frame(arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_encoding_multiple_frames_raises(self): """Test encoding multiple framed pixel data raises exception.""" # Note: only works with multi-sample data @@ -418,6 +426,7 @@ class TestRLEEncodeFrame: with pytest.raises(ValueError, match=msg): rle_encode_frame(ds.pixel_array) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_functional(self): """Test function works OK.""" ds = dcmread(EXPL_16_3_1F) @@ -436,6 +445,7 @@ class TestRLEEncodeFrame: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_big_endian_arr(self): """Test using a big endian array works.""" ds = dcmread(EXPL_16_3_1F) --- a/pydicom/tests/test_filewriter.py +++ b/pydicom/tests/test_filewriter.py @@ -246,6 +246,7 @@ class TestWriteFile: ds = dcmread(fp, force=True) assert ds[0xFFFFFFFF].value == b'123456' + @pytest.mark.skip("When building a Debian package we can not download anything") def test_write_removes_grouplength(self): ds = dcmread(color_pl_name) assert 0x00080000 in ds @@ -1395,6 +1396,7 @@ class TestWriteToStandard: assert ds.get_item(0x300A0006).is_raw # RT Plan Date assert ds.get_item(0x300A0010).is_raw # Dose Reference Sequence + @pytest.mark.skip("When building a Debian package we can not download anything") def test_raw_elements_preserved_explicit_vr(self): """Test writing the dataset preserves raw elements.""" ds = dcmread(color_pl_name) @@ -1583,6 +1585,7 @@ class TestWriteToStandard: assert ds_expl[(0x0009, 0x10e7)].VR == 'UL' assert ds_expl[(0x0043, 0x1010)].VR == 'US' + @pytest.mark.skip("When building a Debian package we can not download anything") def test_convert_rgb_from_implicit_to_explicit_vr(self, no_numpy_use): """Test converting an RGB dataset from implicit to explicit VR and vice verse.""" --- a/pydicom/tests/test_handler_util.py +++ b/pydicom/tests/test_handler_util.py @@ -43,32 +43,32 @@ from pydicom.uid import ( ) -# PAL: PALETTE COLOR Photometric Interpretation -# SEG: Segmented Palette Color -# SUP: Supplemental Palette Color -# LE, BE: little endian, big endian encoding -# 8/8, 1 sample/pixel, 1 frame -PAL_08_256_0_16_1F = get_testdata_file("OBXXXX1A.dcm") -PAL_08_200_0_16_1F = get_testdata_file("OT-PAL-8-face.dcm") -# 8/8, 1 sample/pixel, 2 frame -PAL_08_256_0_16_2F = get_testdata_file("OBXXXX1A_2frame.dcm") -# PALETTE COLOR with 16-bit LUTs (no indirect segments) -PAL_SEG_LE_16_1F = get_testdata_file("gdcm-US-ALOKA-16.dcm") -PAL_SEG_BE_16_1F = get_testdata_file("gdcm-US-ALOKA-16_big.dcm") -# Supplemental palette colour + VOI windowing -SUP_16_16_2F = get_testdata_file("eCT_Supplemental.dcm") -# 8 bit, 3 samples/pixel, 1 and 2 frame datasets -# RGB colorspace, uncompressed -RGB_8_3_1F = get_testdata_file("SC_rgb.dcm") -RGB_8_3_2F = get_testdata_file("SC_rgb_2frame.dcm") -# MOD: Modality LUT -# SEQ: Modality LUT Sequence -MOD_16 = get_testdata_file("CT_small.dcm") -MOD_16_SEQ = get_testdata_file("mlut_18.dcm") -# VOI: VOI LUT Sequence -# WIN: Windowing operation -WIN_12_1F = get_testdata_file("MR-SIEMENS-DICOM-WithOverlays.dcm") -VOI_08_1F = get_testdata_file("vlut_04.dcm") +## PAL: PALETTE COLOR Photometric Interpretation +## SEG: Segmented Palette Color +## SUP: Supplemental Palette Color +## LE, BE: little endian, big endian encoding +## 8/8, 1 sample/pixel, 1 frame +#PAL_08_256_0_16_1F = get_testdata_file("OBXXXX1A.dcm") +#PAL_08_200_0_16_1F = get_testdata_file("OT-PAL-8-face.dcm") +## 8/8, 1 sample/pixel, 2 frame +#PAL_08_256_0_16_2F = get_testdata_file("OBXXXX1A_2frame.dcm") +## PALETTE COLOR with 16-bit LUTs (no indirect segments) +#PAL_SEG_LE_16_1F = get_testdata_file("gdcm-US-ALOKA-16.dcm") +#PAL_SEG_BE_16_1F = get_testdata_file("gdcm-US-ALOKA-16_big.dcm") +## Supplemental palette colour + VOI windowing +#SUP_16_16_2F = get_testdata_file("eCT_Supplemental.dcm") +## 8 bit, 3 samples/pixel, 1 and 2 frame datasets +## RGB colorspace, uncompressed +#RGB_8_3_1F = get_testdata_file("SC_rgb.dcm") +#RGB_8_3_2F = get_testdata_file("SC_rgb_2frame.dcm") +## MOD: Modality LUT +## SEQ: Modality LUT Sequence +#MOD_16 = get_testdata_file("CT_small.dcm") +#MOD_16_SEQ = get_testdata_file("mlut_18.dcm") +## VOI: VOI LUT Sequence +## WIN: Windowing operation +#WIN_12_1F = get_testdata_file("MR-SIEMENS-DICOM-WithOverlays.dcm") +#VOI_08_1F = get_testdata_file("vlut_04.dcm") # 1/1, 1 sample/pixel, 3 frame EXPL_1_1_3F = get_testdata_file("liver.dcm") # Uncompressed YBR_FULL_422 @@ -568,6 +568,7 @@ class TestNumpy_ConvertColourSpace: arr = np.ones((2, 3)) assert np.array_equal(arr, convert_color_space(arr, current, desired)) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_rgb_ybr_rgb_single_frame(self): """Test round trip conversion of single framed pixel data.""" ds = dcmread(RGB_8_3_1F) @@ -602,6 +603,7 @@ class TestNumpy_ConvertColourSpace: assert np.allclose(rgb, arr, atol=1) assert rgb.shape == arr.shape + @pytest.mark.skip("When building a Debian package we can not download anything") def test_rgb_ybr_rgb_multi_frame(self): """Test round trip conversion of multi-framed pixel data.""" ds = dcmread(RGB_8_3_2F) @@ -649,6 +651,7 @@ class TestNumpy_ConvertColourSpace: assert np.allclose(rgb, arr, atol=1) assert rgb.shape == arr.shape + @pytest.mark.skip("When building a Debian package we can not download anything") def test_frame_by_frame(self): """Test processing frame-by-frame.""" ds = dcmread(RGB_8_3_2F) @@ -828,6 +831,7 @@ class TestGetExpectedLength: assert length[2] == get_expected_length(ds, unit='bytes') +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not HAVE_NP, reason="Numpy is not available") class TestNumpy_ModalityLUT: """Tests for util.apply_modality_lut().""" @@ -848,6 +852,7 @@ class TestNumpy_ModalityLUT: out = apply_modality_lut(arr, ds) assert np.array_equal(arr * 2.5 - 2048, out) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_lut_sequence(self): """Test the LUT Sequence transform.""" ds = dcmread(MOD_16_SEQ) @@ -875,6 +880,7 @@ class TestNumpy_ModalityLUT: assert 52428 == out[228, 385] assert 58974 == out[291, 385] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_lut_sequence_zero_entries(self): """Test that 0 entries is interpreted correctly.""" # LUTDescriptor[0] of 0 -> 65536, but only 4096 entries so any @@ -906,6 +912,7 @@ class TestNumpy_ModalityLUT: out = apply_modality_lut(arr, ds) assert arr is out + @pytest.mark.skip("When building a Debian package we can not download anything") def test_lutdata_ow(self): """Test LUT Data with VR OW.""" ds = dcmread(MOD_16_SEQ) @@ -950,6 +957,7 @@ class TestNumpy_PaletteColor: if os.path.exists(self.n_palette): os.rename(self.n_palette, self.o_palette) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_neither_ds_nor_palette_raises(self): """Test missing `ds` and `palette` raise an exception.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -957,6 +965,7 @@ class TestNumpy_PaletteColor: with pytest.raises(ValueError, match=msg): apply_color_lut(ds.pixel_array) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_palette_unknown_raises(self, disable_value_validation): """Test using an unknown `palette` raise an exception.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -970,6 +979,7 @@ class TestNumpy_PaletteColor: with pytest.raises(ValueError, match=msg): apply_color_lut(ds.pixel_array, palette='1.2.840.10008.1.1') + @pytest.mark.skip("When building a Debian package we can not download anything") def test_palette_unavailable_raises(self, disable_value_validation): """Test using a missing `palette` raise an exception.""" os.rename(self.o_palette, self.n_palette) @@ -978,6 +988,7 @@ class TestNumpy_PaletteColor: with pytest.raises(IndexError, match=msg): apply_color_lut(ds.pixel_array, palette='PET') + @pytest.mark.skip("When building a Debian package we can not download anything") def test_supplemental_raises(self): """Test that supplemental palette color LUT raises exception.""" ds = dcmread(SUP_16_16_2F) @@ -988,6 +999,7 @@ class TestNumpy_PaletteColor: with pytest.raises(ValueError, match=msg): apply_color_lut(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_invalid_bit_depth_raises(self): """Test that an invalid bit depth raises an exception.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -996,6 +1008,7 @@ class TestNumpy_PaletteColor: with pytest.raises(TypeError, match=msg): apply_color_lut(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_invalid_lut_bit_depth_raises(self): """Test that an invalid LUT bit depth raises an exception.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -1015,6 +1028,7 @@ class TestNumpy_PaletteColor: with pytest.raises(ValueError, match=msg): apply_color_lut(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unequal_lut_length_raises(self): """Test that an unequal LUT lengths raise an exception.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -1025,6 +1039,7 @@ class TestNumpy_PaletteColor: with pytest.raises(ValueError, match=msg): apply_color_lut(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_no_palette_color(self): """Test that an unequal LUT lengths raise an exception.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -1033,6 +1048,7 @@ class TestNumpy_PaletteColor: with pytest.raises(ValueError, match=msg): apply_color_lut(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_uint08_16(self): """Test uint8 Pixel Data with 16-bit LUT entries.""" ds = dcmread(PAL_08_200_0_16_1F, force=True) @@ -1053,6 +1069,7 @@ class TestNumpy_PaletteColor: # original `arr` is unchanged assert np.array_equal(orig, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_uint08_16_2frame(self): """Test 2 frame uint8 Pixel Data with 16-bit LUT entries.""" ds = dcmread(PAL_08_256_0_16_2F) @@ -1086,6 +1103,7 @@ class TestNumpy_PaletteColor: # original `arr` is unchanged assert np.array_equal(orig, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_uint16_16_segmented_litle(self): """Test uint16 Pixel Data with 16-bit LUT entries.""" ds = dcmread(PAL_SEG_LE_16_1F) @@ -1107,6 +1125,7 @@ class TestNumpy_PaletteColor: assert (orig == arr).all() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_uint16_16_segmented_big(self): """Test big endian uint16 Pixel Data with 16-bit LUT entries.""" ds = dcmread(PAL_SEG_BE_16_1F) @@ -1126,6 +1145,7 @@ class TestNumpy_PaletteColor: assert [10280, 11565, 16705] == list(rgb[479, 320, :]) assert [10280, 11565, 16705] == list(rgb[479, 639, :]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_16_allocated_8_entries(self): """Test LUT with 8-bit entries in 16 bits allocated.""" ds = dcmread(PAL_08_200_0_16_1F, force=True) @@ -1147,6 +1167,7 @@ class TestNumpy_PaletteColor: assert np.array_equal(arr, out[:, :, 1]) assert np.array_equal(arr, out[:, :, 2]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_alpha(self): """Test applying a color palette with an alpha channel.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -1157,6 +1178,7 @@ class TestNumpy_PaletteColor: assert 32768 == rgba[:, :, 3][0, 0] assert (32768 == rgba[:, :, 3]).any() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_well_known_palette(self, disable_value_validation): """Test using a well-known palette.""" ds = dcmread(PAL_08_256_0_16_1F) @@ -1190,6 +1212,7 @@ class TestNumpy_PaletteColor: uid = apply_color_lut(arr, palette='1.2.840.10008.1.5.2') assert np.array_equal(uid, rgb) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_first_map_positive(self): """Test a positive first mapping value.""" ds = dcmread(PAL_08_200_0_16_1F, force=True) @@ -1208,6 +1231,7 @@ class TestNumpy_PaletteColor: assert [50944, 16384, 27904] == list(rgb[arr == 149][0]) assert ([50944, 16384, 27904] == rgb[arr == 149]).all() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_first_map_negative(self): """Test a negative first mapping value.""" ds = dcmread(PAL_08_200_0_16_1F, force=True) @@ -1227,6 +1251,7 @@ class TestNumpy_PaletteColor: assert [60160, 25600, 37376] == list(rgb[arr == 130][0]) assert ([60160, 25600, 37376] == rgb[arr == 130]).all() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unchanged(self): """Test dataset with no LUT is unchanged.""" # Regression test for #1068 @@ -1466,6 +1491,7 @@ class TestNumpy_ExpandSegmentedLUT: @pytest.mark.skipif(not HAVE_NP, reason="Numpy is not available") class TestNumpy_ApplyWindowing: """Tests for util.apply_windowing().""" + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_single_view(self): """Test windowing with a single view.""" # 12-bit unsigned @@ -1483,6 +1509,7 @@ class TestNumpy_ApplyWindowing: out = apply_windowing(arr, ds) assert 3046.6 == pytest.approx(out[326, 130], abs=0.1) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_multi_view(self): """Test windowing with multiple views.""" ds = dcmread(WIN_12_1F) @@ -1725,6 +1752,7 @@ class TestNumpy_ApplyWindowing: ) ) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_multi_frame(self): """Test windowing with a multiple frames.""" ds = dcmread(WIN_12_1F) @@ -1745,6 +1773,7 @@ class TestNumpy_ApplyWindowing: assert 3046.6 == pytest.approx(out[0, 326, 130], abs=0.1) assert 4095.0 == pytest.approx(out[1, 326, 130], abs=0.1) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_rescale(self): """Test windowing after a rescale operation.""" ds = dcmread(WIN_12_1F) @@ -1776,6 +1805,7 @@ class TestNumpy_ApplyWindowing: assert 4455.6 == pytest.approx(out[326, 130], abs=0.1) assert 4914.0 == pytest.approx(out[316, 481], abs=0.1) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_modality_lut(self): """Test windowing after a modality LUT operation.""" ds = dcmread(MOD_16_SEQ) @@ -1806,6 +1836,7 @@ class TestNumpy_ApplyWindowing: assert 65535 == out.max() assert 0 == out.min() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_bad_photometric_interp(self): """Test bad photometric interpretation raises exception.""" ds = dcmread(WIN_12_1F) @@ -1814,6 +1845,7 @@ class TestNumpy_ApplyWindowing: with pytest.raises(ValueError, match=msg): apply_windowing(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_bad_parameters(self): """Test bad windowing parameters raise exceptions.""" ds = dcmread(WIN_12_1F) @@ -1838,6 +1870,7 @@ class TestNumpy_ApplyWindowing: with pytest.raises(ValueError, match=msg): apply_windowing(ds.pixel_array, ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_window_bad_index(self, no_numpy_use): """Test windowing with a bad view index.""" ds = dcmread(WIN_12_1F) @@ -1860,6 +1893,7 @@ class TestNumpy_ApplyWindowing: out = apply_windowing(arr, ds) assert [-128, -127, -1, 0, 1, 126, 127] == out.tolist() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_rescale_empty(self): """Test RescaleSlope and RescaleIntercept being empty.""" ds = dcmread(WIN_12_1F) @@ -1876,6 +1910,7 @@ class TestNumpy_ApplyWindowing: assert 4095.0 == pytest.approx(out[316, 481], abs=0.1) +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not HAVE_NP, reason="Numpy is not available") class TestNumpy_ApplyVOI: """Tests for util.apply_voi().""" @@ -1905,6 +1940,7 @@ class TestNumpy_ApplyVOI: assert 45746 == out[186, 389] assert 65535 == out[129, 79] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_voi_multi_view(self): """Test VOI LUT with multiple views.""" ds = dcmread(VOI_08_1F) @@ -1936,6 +1972,7 @@ class TestNumpy_ApplyVOI: assert 19789 == out1[186, 389] assert 0 == out1[129, 79] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_voi_multi_frame(self): """Test VOI with a multiple frames.""" ds = dcmread(VOI_08_1F) @@ -1957,6 +1994,7 @@ class TestNumpy_ApplyVOI: assert 19789 == out[1, 186, 389] assert 0 == out[1, 129, 79] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_voi_zero_entries(self): """Test that 0 entries is interpreted correctly.""" ds = dcmread(VOI_08_1F) @@ -2029,6 +2067,7 @@ class TestNumpy_ApplyVOI: assert 'uint16' == out.dtype assert [0, 0, 32768, 0, 65535] == out.tolist() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_voi_bad_depth(self): """Test bad LUT depth raises exception.""" ds = dcmread(VOI_08_1F) @@ -2364,6 +2403,7 @@ class TestNumpy_PackBits: """Test packing data that isn't a full byte long.""" assert output == pack_bits(np.asarray(input), pad=False) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_functional(self): """Test against a real dataset.""" ds = dcmread(EXPL_1_1_3F) --- a/pydicom/tests/test_numpy_pixel_data.py +++ b/pydicom/tests/test_numpy_pixel_data.py @@ -66,11 +66,11 @@ except ImportError: # DEFL: Deflated Explicit VR Little Endian # EXPB: Explicit VR Big Endian # 1/1, 1 sample/pixel, 1 frame -EXPL_1_1_1F = get_testdata_file("liver_1frame.dcm") -EXPB_1_1_1F = get_testdata_file("liver_expb_1frame.dcm") +##EXPL_1_1_1F = get_testdata_file("liver_1frame.dcm") +##EXPB_1_1_1F = get_testdata_file("liver_expb_1frame.dcm") # 1/1, 1 sample/pixel, 3 frame -EXPL_1_1_3F = get_testdata_file("liver.dcm") -EXPB_1_1_3F = get_testdata_file("liver_expb.dcm") +##EXPL_1_1_3F = get_testdata_file("liver.dcm") +##EXPB_1_1_3F = get_testdata_file("liver_expb.dcm") # 1/1, 3 sample/pixel, 1 frame EXPL_1_3_1F = None EXPB_1_3_1F = None @@ -78,74 +78,74 @@ EXPB_1_3_1F = None EXPL_1_3_XF = None EXPB_1_3_XF = None # 8/8, 1 sample/pixel, 1 frame -DEFL_8_1_1F = get_testdata_file("image_dfl.dcm") -EXPL_8_1_1F = get_testdata_file("OBXXXX1A.dcm") -EXPB_8_1_1F = get_testdata_file("OBXXXX1A_expb.dcm") +##DEFL_8_1_1F = get_testdata_file("image_dfl.dcm") +##EXPL_8_1_1F = get_testdata_file("OBXXXX1A.dcm") +##EXPB_8_1_1F = get_testdata_file("OBXXXX1A_expb.dcm") # 8/8, 1 sample/pixel, 2 frame -EXPL_8_1_2F = get_testdata_file("OBXXXX1A_2frame.dcm") -EXPB_8_1_2F = get_testdata_file("OBXXXX1A_expb_2frame.dcm") +##EXPL_8_1_2F = get_testdata_file("OBXXXX1A_2frame.dcm") +##EXPB_8_1_2F = get_testdata_file("OBXXXX1A_expb_2frame.dcm") # 8/8, 3 sample/pixel, 1 frame -EXPL_8_3_1F = get_testdata_file("SC_rgb.dcm") -EXPB_8_3_1F = get_testdata_file("SC_rgb_expb.dcm") +##EXPL_8_3_1F = get_testdata_file("SC_rgb.dcm") +##EXPB_8_3_1F = get_testdata_file("SC_rgb_expb.dcm") # 8/8, 3 samples/pixel, 1 frame, 3 x 3 -EXPL_8_3_1F_ODD = get_testdata_file('SC_rgb_small_odd.dcm') -EXPL_8_3_1F_ODD_BIGE = get_testdata_file('SC_rgb_small_odd_big_endian.dcm') +##EXPL_8_3_1F_ODD = get_testdata_file('SC_rgb_small_odd.dcm') +##EXPL_8_3_1F_ODD_BIGE = get_testdata_file('SC_rgb_small_odd_big_endian.dcm') # 8/8, 3 sample/pixel, 1 frame, YBR_FULL_422 -EXPL_8_3_1F_YBR422 = get_testdata_file('SC_ybr_full_422_uncompressed.dcm') +##EXPL_8_3_1F_YBR422 = get_testdata_file('SC_ybr_full_422_uncompressed.dcm') # 8/8, 3 sample/pixel, 1 frame, YBR_FULL -EXPL_8_3_1F_YBR = get_testdata_file('SC_ybr_full_uncompressed.dcm') +##EXPL_8_3_1F_YBR = get_testdata_file('SC_ybr_full_uncompressed.dcm') # 8/8, 3 sample/pixel, 2 frame -EXPL_8_3_2F = get_testdata_file("SC_rgb_2frame.dcm") -EXPB_8_3_2F = get_testdata_file("SC_rgb_expb_2frame.dcm") +##EXPL_8_3_2F = get_testdata_file("SC_rgb_2frame.dcm") +##EXPB_8_3_2F = get_testdata_file("SC_rgb_expb_2frame.dcm") # 16/16, 1 sample/pixel, 1 frame -IMPL_16_1_1F = get_testdata_file("MR_small_implicit.dcm") -EXPL_16_1_1F = get_testdata_file("MR_small.dcm") -EXPB_16_1_1F = get_testdata_file("MR_small_expb.dcm") +##IMPL_16_1_1F = get_testdata_file("MR_small_implicit.dcm") +##EXPL_16_1_1F = get_testdata_file("MR_small.dcm") +##EXPB_16_1_1F = get_testdata_file("MR_small_expb.dcm") # Pixel Data with 128 bytes trailing padding -EXPL_16_1_1F_PAD = get_testdata_file("MR_small_padded.dcm") +##EXPL_16_1_1F_PAD = get_testdata_file("MR_small_padded.dcm") # 16/12, 1 sample/pixel, 10 frame -EXPL_16_1_10F = get_testdata_file("emri_small.dcm") -EXPB_16_1_10F = get_testdata_file("emri_small_big_endian.dcm") +##EXPL_16_1_10F = get_testdata_file("emri_small.dcm") +##EXPB_16_1_10F = get_testdata_file("emri_small_big_endian.dcm") # 16/16, 3 sample/pixel, 1 frame -EXPL_16_3_1F = get_testdata_file("SC_rgb_16bit.dcm") -EXPB_16_3_1F = get_testdata_file("SC_rgb_expb_16bit.dcm") +##EXPL_16_3_1F = get_testdata_file("SC_rgb_16bit.dcm") +##EXPB_16_3_1F = get_testdata_file("SC_rgb_expb_16bit.dcm") # 16/16, 3 sample/pixel, 2 frame -EXPL_16_3_2F = get_testdata_file("SC_rgb_16bit_2frame.dcm") -EXPB_16_3_2F = get_testdata_file("SC_rgb_expb_16bit_2frame.dcm") +##EXPL_16_3_2F = get_testdata_file("SC_rgb_16bit_2frame.dcm") +##EXPB_16_3_2F = get_testdata_file("SC_rgb_expb_16bit_2frame.dcm") # 32/32, 1 sample/pixel, 1 frame -IMPL_32_1_1F = get_testdata_file("rtdose_1frame.dcm") -EXPB_32_1_1F = get_testdata_file("rtdose_expb_1frame.dcm") +##IMPL_32_1_1F = get_testdata_file("rtdose_1frame.dcm") +##EXPB_32_1_1F = get_testdata_file("rtdose_expb_1frame.dcm") # 32/32, 1 sample/pixel, 15 frame -IMPL_32_1_15F = get_testdata_file("rtdose.dcm") -EXPB_32_1_15F = get_testdata_file("rtdose_expb.dcm") +##IMPL_32_1_15F = get_testdata_file("rtdose.dcm") +##EXPB_32_1_15F = get_testdata_file("rtdose_expb.dcm") # 32/32, 3 sample/pixel, 1 frame -EXPL_32_3_1F = get_testdata_file("SC_rgb_32bit.dcm") -EXPB_32_3_1F = get_testdata_file("SC_rgb_expb_32bit.dcm") +##EXPL_32_3_1F = get_testdata_file("SC_rgb_32bit.dcm") +##EXPB_32_3_1F = get_testdata_file("SC_rgb_expb_32bit.dcm") # 32/32, 3 sample/pixel, 2 frame -EXPL_32_3_2F = get_testdata_file("SC_rgb_32bit_2frame.dcm") -EXPB_32_3_2F = get_testdata_file("SC_rgb_expb_32bit_2frame.dcm") +##EXPL_32_3_2F = get_testdata_file("SC_rgb_32bit_2frame.dcm") +##EXPB_32_3_2F = get_testdata_file("SC_rgb_expb_32bit_2frame.dcm") # Transfer syntaxes supported by other handlers # JPEG Baseline (Process 1) -JPEG_BASELINE_1 = get_testdata_file("SC_rgb_jpeg_dcmtk.dcm") +##JPEG_BASELINE_1 = get_testdata_file("SC_rgb_jpeg_dcmtk.dcm") # JPEG Baseline (Process 2 and 4) -JPEG_EXTENDED_2 = get_testdata_file("JPEG-lossy.dcm") +##JPEG_EXTENDED_2 = get_testdata_file("JPEG-lossy.dcm") # JPEG Lossless (Process 14) JPEG_LOSSLESS_14 = None # JPEG Lossless (Process 14, Selection Value 1) -JPEG_LOSSLESS_14_1 = get_testdata_file("SC_rgb_jpeg_gdcm.dcm") +##JPEG_LOSSLESS_14_1 = get_testdata_file("SC_rgb_jpeg_gdcm.dcm") # JPEG-LS Lossless -JPEG_LS_LOSSLESS = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") +##JPEG_LS_LOSSLESS = get_testdata_file("MR_small_jpeg_ls_lossless.dcm") # JPEG-LS Lossy JPEG_LS_LOSSY = None # JPEG2k Lossless -JPEG_2K_LOSSLESS = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") +##JPEG_2K_LOSSLESS = get_testdata_file("emri_small_jpeg_2k_lossless.dcm") # JPEG2k -JPEG_2K = get_testdata_file("JPEG2000.dcm") +##JPEG_2K = get_testdata_file("JPEG2000.dcm") # RLE Lossless -RLE = get_testdata_file("MR_small_RLE.dcm") +##RLE = get_testdata_file("MR_small_RLE.dcm") # No Image Pixel module -NO_PIXEL = get_testdata_file("rtplan.dcm") +##NO_PIXEL = get_testdata_file("rtplan.dcm") # Transfer Syntaxes (non-retired + Explicit VR Big Endian) @@ -167,15 +167,15 @@ def test_unsupported_syntaxes(): REFERENCE_DATA_UNSUPPORTED = [ - (JPEG_BASELINE_1, ('1.2.840.10008.1.2.4.50', 'Lestrade^G')), - (JPEG_EXTENDED_2, ('1.2.840.10008.1.2.4.51', 'CompressedSamples^NM1')), - # (JPEG_LOSSLESS_14, ('1.2.840.10008.1.2.4.57')), # No dataset available - (JPEG_LOSSLESS_14_1, ('1.2.840.10008.1.2.4.70', 'Lestrade^G')), - (JPEG_LS_LOSSLESS, ('1.2.840.10008.1.2.4.80', 'CompressedSamples^MR1')), - # (JPEG_LS_LOSSY, ('1.2.840.10008.1.2.4.81')), # No dataset available - (JPEG_2K_LOSSLESS, ('1.2.840.10008.1.2.4.90', '')), - (JPEG_2K, ('1.2.840.10008.1.2.4.91', 'CompressedSamples^NM1')), - (RLE, ('1.2.840.10008.1.2.5', 'CompressedSamples^MR1')), +# (JPEG_BASELINE_1, ('1.2.840.10008.1.2.4.50', 'Lestrade^G')), +# (JPEG_EXTENDED_2, ('1.2.840.10008.1.2.4.51', 'CompressedSamples^NM1')), +# # (JPEG_LOSSLESS_14, ('1.2.840.10008.1.2.4.57')), # No dataset available +# (JPEG_LOSSLESS_14_1, ('1.2.840.10008.1.2.4.70', 'Lestrade^G')), +# (JPEG_LS_LOSSLESS, ('1.2.840.10008.1.2.4.80', 'CompressedSamples^MR1')), +# # (JPEG_LS_LOSSY, ('1.2.840.10008.1.2.4.81')), # No dataset available +# (JPEG_2K_LOSSLESS, ('1.2.840.10008.1.2.4.90', '')), +# (JPEG_2K, ('1.2.840.10008.1.2.4.91', 'CompressedSamples^NM1')), +# (RLE, ('1.2.840.10008.1.2.5', 'CompressedSamples^MR1')), ] SUPPORTED_HANDLER_NAMES = ( @@ -338,6 +338,7 @@ class TestNumpy_NoNumpyHandler: # We numpy handler should still be available assert NP_HANDLER is not None + @pytest.mark.skip("When building a Debian package we can not download anything") def test_can_access_supported_dataset(self): """Test that we can read and access elements in dataset.""" # Explicit little @@ -360,6 +361,7 @@ class TestNumpy_NoNumpyHandler: assert 'CompressedSamples^MR1' == ds.PatientName assert 8192 == len(ds.PixelData) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize("fpath,data", REFERENCE_DATA_UNSUPPORTED) def test_can_access_unsupported_dataset(self, fpath, data): """Test can read and access elements in unsupported datasets.""" @@ -367,6 +369,7 @@ class TestNumpy_NoNumpyHandler: assert data[0] == ds.file_meta.TransferSyntaxUID assert data[1] == ds.PatientName + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_raises(self): """Test pixel_array raises exception for all syntaxes.""" ds = dcmread(EXPL_16_1_1F) @@ -378,42 +381,42 @@ class TestNumpy_NoNumpyHandler: # Numpy and the numpy handler are available MATCHING_DATASETS = [ - (EXPL_1_1_1F, EXPB_1_1_1F), - (EXPL_1_1_3F, EXPB_1_1_3F), - (EXPL_8_1_1F, EXPB_8_1_1F), - (EXPL_8_1_2F, EXPB_8_1_2F), - (EXPL_8_3_1F, EXPB_8_3_1F), - (EXPL_8_3_2F, EXPB_8_3_2F), - (EXPL_16_1_1F, EXPB_16_1_1F), - (EXPL_16_1_10F, EXPB_16_1_10F), - (EXPL_16_3_1F, EXPB_16_3_1F), - (EXPL_16_3_2F, EXPB_16_3_2F), - (IMPL_32_1_1F, EXPB_32_1_1F), - (IMPL_32_1_15F, EXPB_32_1_15F), - (EXPL_32_3_1F, EXPB_32_3_1F), - (EXPL_32_3_2F, EXPB_32_3_2F) +# (EXPL_1_1_1F, EXPB_1_1_1F), +# (EXPL_1_1_3F, EXPB_1_1_3F), +# (EXPL_8_1_1F, EXPB_8_1_1F), +# (EXPL_8_1_2F, EXPB_8_1_2F), +# (EXPL_8_3_1F, EXPB_8_3_1F), +# (EXPL_8_3_2F, EXPB_8_3_2F), +# (EXPL_16_1_1F, EXPB_16_1_1F), +# (EXPL_16_1_10F, EXPB_16_1_10F), +# (EXPL_16_3_1F, EXPB_16_3_1F), +# (EXPL_16_3_2F, EXPB_16_3_2F), +# (IMPL_32_1_1F, EXPB_32_1_1F), +# (IMPL_32_1_15F, EXPB_32_1_15F), +# (EXPL_32_3_1F, EXPB_32_3_1F), +# (EXPL_32_3_2F, EXPB_32_3_2F) ] EXPL = ExplicitVRLittleEndian IMPL = ImplicitVRLittleEndian REFERENCE_DATA_LITTLE = [ - # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) - (EXPL_1_1_1F, (EXPL, 1, 1, 0, 1, (512, 512), 'uint8')), - (EXPL_1_1_3F, (EXPL, 1, 1, 0, 3, (3, 512, 512), 'uint8')), - (EXPL_8_1_1F, (EXPL, 8, 1, 0, 1, (600, 800), 'uint8')), - (EXPL_8_3_1F_ODD, (EXPL, 8, 3, 0, 1, (3, 3, 3), 'uint8')), - (EXPL_8_3_1F_YBR422, (EXPL, 8, 3, 0, 1, (100, 100, 3), 'uint8')), - (EXPL_8_1_2F, (EXPL, 8, 1, 0, 2, (2, 600, 800), 'uint8')), - (EXPL_8_3_1F, (EXPL, 8, 3, 0, 1, (100, 100, 3), 'uint8')), - (EXPL_8_3_2F, (EXPL, 8, 3, 0, 2, (2, 100, 100, 3), 'uint8')), - (EXPL_16_1_1F, (EXPL, 16, 1, 1, 1, (64, 64), 'int16')), - (EXPL_16_1_10F, (EXPL, 16, 1, 0, 10, (10, 64, 64), 'uint16')), - (EXPL_16_3_1F, (EXPL, 16, 3, 0, 1, (100, 100, 3), 'uint16')), - (EXPL_16_3_2F, (EXPL, 16, 3, 0, 2, (2, 100, 100, 3), 'uint16')), - (IMPL_32_1_1F, (IMPL, 32, 1, 0, 1, (10, 10), 'uint32')), - (IMPL_32_1_15F, (IMPL, 32, 1, 0, 15, (15, 10, 10), 'uint32')), - (EXPL_32_3_1F, (EXPL, 32, 3, 0, 1, (100, 100, 3), 'uint32')), - (EXPL_32_3_2F, (EXPL, 32, 3, 0, 2, (2, 100, 100, 3), 'uint32')), +# # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype) +# (EXPL_1_1_1F, (EXPL, 1, 1, 0, 1, (512, 512), 'uint8')), +# (EXPL_1_1_3F, (EXPL, 1, 1, 0, 3, (3, 512, 512), 'uint8')), +# (EXPL_8_1_1F, (EXPL, 8, 1, 0, 1, (600, 800), 'uint8')), +# (EXPL_8_3_1F_ODD, (EXPL, 8, 3, 0, 1, (3, 3, 3), 'uint8')), +# (EXPL_8_3_1F_YBR422, (EXPL, 8, 3, 0, 1, (100, 100, 3), 'uint8')), +# (EXPL_8_1_2F, (EXPL, 8, 1, 0, 2, (2, 600, 800), 'uint8')), +# (EXPL_8_3_1F, (EXPL, 8, 3, 0, 1, (100, 100, 3), 'uint8')), +# (EXPL_8_3_2F, (EXPL, 8, 3, 0, 2, (2, 100, 100, 3), 'uint8')), +# (EXPL_16_1_1F, (EXPL, 16, 1, 1, 1, (64, 64), 'int16')), +# (EXPL_16_1_10F, (EXPL, 16, 1, 0, 10, (10, 64, 64), 'uint16')), +# (EXPL_16_3_1F, (EXPL, 16, 3, 0, 1, (100, 100, 3), 'uint16')), +# (EXPL_16_3_2F, (EXPL, 16, 3, 0, 2, (2, 100, 100, 3), 'uint16')), +# (IMPL_32_1_1F, (IMPL, 32, 1, 0, 1, (10, 10), 'uint32')), +# (IMPL_32_1_15F, (IMPL, 32, 1, 0, 15, (15, 10, 10), 'uint32')), +# (EXPL_32_3_1F, (EXPL, 32, 3, 0, 1, (100, 100, 3), 'uint32')), +# (EXPL_32_3_2F, (EXPL, 32, 3, 0, 2, (2, 100, 100, 3), 'uint32')), ] @@ -435,6 +438,7 @@ class TestNumpy_NumpyHandler: assert HAVE_NP assert NP_HANDLER is not None + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unsupported_syntax_raises(self): """Test pixel_array raises exception for unsupported syntaxes.""" ds = dcmread(EXPL_16_1_1F) @@ -444,6 +448,7 @@ class TestNumpy_NumpyHandler: with pytest.raises((NotImplementedError, RuntimeError)): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_dataset_pixel_array_handler_needs_convert(self): """Test Dataset.pixel_array when converting to RGB.""" ds = dcmread(EXPL_8_3_1F) @@ -472,6 +477,7 @@ class TestNumpy_NumpyHandler: # Reset NP_HANDLER.needs_to_convert_to_RGB = orig_fn + @pytest.mark.skip("When building a Debian package we can not download anything") def test_dataset_pixel_array_no_pixels(self): """Test good exception message if no pixel data in dataset.""" ds = dcmread(NO_PIXEL) @@ -483,6 +489,7 @@ class TestNumpy_NumpyHandler: with pytest.raises(AttributeError, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize("fpath, data", REFERENCE_DATA_UNSUPPORTED) def test_can_access_unsupported_dataset(self, fpath, data): """Test can read and access elements in unsupported datasets.""" @@ -490,6 +497,7 @@ class TestNumpy_NumpyHandler: assert data[0] == ds.file_meta.TransferSyntaxUID assert data[1] == ds.PatientName + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_8bit_un_signed(self): """Test pixel_array for 8-bit unsigned -> signed data.""" ds = dcmread(EXPL_8_1_1F) @@ -505,6 +513,7 @@ class TestNumpy_NumpyHandler: assert (1, -10, 1) == tuple(arr[300, 491:494]) assert 0 == arr[-1].min() == arr[-1].max() + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize("handler_name", SUPPORTED_HANDLER_NAMES) def test_decompress_using_handler(self, handler_name): """Test different possibilities for the numpy handler name.""" @@ -515,6 +524,7 @@ class TestNumpy_NumpyHandler: assert (1, 246, 1) == tuple(ds.pixel_array[300, 491:494]) assert 0 == ds.pixel_array[-1].min() == ds.pixel_array[-1].max() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_16bit_un_signed(self): """Test pixel_array for 16-bit unsigned -> signed.""" ds = dcmread(EXPL_16_3_1F) @@ -529,6 +539,7 @@ class TestNumpy_NumpyHandler: assert -1 == arr[0, :, 0].min() == arr[0, :, 0].max() assert -32640 == arr[50, :, 0].min() == arr[50, :, 0].max() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_32bit_un_signed(self): """Test pixel_array for 32-bit unsigned -> signed.""" ds = dcmread(EXPL_32_3_1F) @@ -544,6 +555,7 @@ class TestNumpy_NumpyHandler: assert -2139062144 == arr[50, :, 0].min() == arr[50, :, 0].max() # Endian independent datasets + @pytest.mark.skip("When building a Debian package we can not download anything") def test_8bit_1sample_1frame(self): """Test pixel_array for 8-bit, 1 sample/pixel, 1 frame.""" # Check supported syntaxes @@ -559,6 +571,7 @@ class TestNumpy_NumpyHandler: assert (1, 246, 1) == tuple(arr[300, 491:494]) assert 0 == arr[-1].min() == arr[-1].max() + @pytest.mark.skip("When building a Debian package we can not download anything") def test_8bit_1sample_2frame(self): """Test pixel_array for 8-bit, 1 sample/pixel, 2 frame.""" # Check supported syntaxes @@ -577,6 +590,7 @@ class TestNumpy_NumpyHandler: # Frame 2 is frame 1 inverted assert np.array_equal((2 ** ds.BitsAllocated - 1) - arr[1], arr[0]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_8bit_3sample_1frame_odd_size(self): """Test pixel_array for odd sized (3x3) pixel data.""" # Check supported syntaxes @@ -595,6 +609,7 @@ class TestNumpy_NumpyHandler: [158, 158, 158], [158, 158, 158], [158, 158, 158] ] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_8bit_3sample_1frame_ybr422(self): """Test pixel_array for YBR_FULL_422 pixel data.""" ds = dcmread(EXPL_8_3_1F_YBR422) @@ -620,6 +635,7 @@ class TestNumpy_NumpyHandler: assert (192, 128, 128) == tuple(arr[85, 50, :]) assert (255, 128, 128) == tuple(arr[95, 50, :]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_8bit_3sample_1frame(self): """Test pixel_array for 8-bit, 3 sample/pixel, 1 frame.""" # Check supported syntaxes @@ -641,6 +657,7 @@ class TestNumpy_NumpyHandler: assert (192, 192, 192) == tuple(arr[85, 50, :]) assert (255, 255, 255) == tuple(arr[95, 50, :]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_8bit_3sample_2frame(self): """Test pixel_array for 8-bit, 3 sample/pixel, 2 frame.""" # Check supported syntaxes @@ -667,6 +684,7 @@ class TestNumpy_NumpyHandler: assert np.array_equal((2 ** ds.BitsAllocated - 1) - arr[1], arr[0]) # Little endian datasets + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize('fpath, data', REFERENCE_DATA_LITTLE) def test_properties(self, fpath, data): """Test dataset and pixel array properties are as expected.""" @@ -695,6 +713,7 @@ class TestNumpy_NumpyHandler: if size % 2: assert ds.PixelData[-1] == b'\x00'[0] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_1bit_1sample_1frame(self): """Test pixel_array for little 1-bit, 1 sample/pixel, 1 frame.""" # Check all little endian syntaxes @@ -713,6 +732,7 @@ class TestNumpy_NumpyHandler: assert (0, 1, 1) == tuple(arr[254, 78:81]) assert (1, 0, 0, 1, 1, 0) == tuple(arr[254, 304:310]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_1bit_1sample_3frame(self): """Test pixel_array for little 1-bit, 1 sample/pixel, 3 frame.""" # Check all little endian syntaxes @@ -774,6 +794,7 @@ class TestNumpy_NumpyHandler: ds.file_meta.TransferSyntaxUID = uid arr = ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_16bit_1sample_1frame(self): """Test pixel_array for little 16-bit, 1 sample/pixel, 1 frame.""" # Check all little endian syntaxes @@ -790,6 +811,7 @@ class TestNumpy_NumpyHandler: # Last pixel assert 862 == arr[-1, -1] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_16bit_1sample_1frame_padded(self): """Test with padded little 16-bit, 1 sample/pixel, 1 frame.""" ds = dcmread(EXPL_16_1_1F_PAD) @@ -824,6 +846,7 @@ class TestNumpy_NumpyHandler: # Last pixel assert 862 == arr[-1, -1] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_16bit_1sample_10frame(self): """Test pixel_array for little 16-bit, 1 sample/pixel, 10 frame.""" # Check all little endian syntaxes @@ -847,6 +870,7 @@ class TestNumpy_NumpyHandler: assert (25, 4, 9) == tuple(arr[-1, 31, :3]) assert (227, 300, 147) == tuple(arr[-1, -1, -3:]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_16bit_3sample_1frame(self): """Test pixel_array for little 16-bit, 3 sample/pixel, 1 frame.""" # Check all little endian syntaxes @@ -868,6 +892,7 @@ class TestNumpy_NumpyHandler: assert (49344, 49344, 49344) == tuple(arr[85, 50, :]) assert (65535, 65535, 65535) == tuple(arr[95, 50, :]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_16bit_3sample_2frame(self): """Test pixel_array for little 16-bit, 3 sample/pixel, 2 frame.""" # Check all little endian syntaxes @@ -892,6 +917,7 @@ class TestNumpy_NumpyHandler: # Frame 2 is frame 1 inverted assert np.array_equal((2 ** ds.BitsAllocated - 1) - arr[1], arr[0]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_32bit_1sample_1frame(self): """Test pixel_array for little 32-bit, 1 sample/pixel, 1 frame.""" # Check all little endian syntaxes @@ -906,6 +932,7 @@ class TestNumpy_NumpyHandler: assert (1031000, 1029000, 1027000) == tuple(arr[4, 3:6]) assert (803000, 801000, 798000) == tuple(arr[-1, -3:]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_32bit_1sample_15frame(self): """Test pixel_array for little 32-bit, 1 sample/pixel, 15 frame.""" # Check all little endian syntaxes @@ -929,6 +956,7 @@ class TestNumpy_NumpyHandler: assert (1031000, 1031000, 1031000) == tuple(arr[-1, 4, 3:6]) assert (801000, 800000, 799000) == tuple(arr[-1, -1, -3:]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_32bit_3sample_1frame(self): """Test pixel_array for little 32-bit, 3 sample/pixel, 1 frame.""" # Check all little endian syntaxes @@ -950,6 +978,7 @@ class TestNumpy_NumpyHandler: assert (3233857728, 3233857728, 3233857728) == tuple(ar[85, 50, :]) assert (4294967295, 4294967295, 4294967295) == tuple(ar[95, 50, :]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_32bit_3sample_2frame(self): """Test pixel_array for little 32-bit, 3 sample/pixel, 10 frame.""" # Check all little endian syntaxes @@ -986,6 +1015,7 @@ class TestNumpy_NumpyHandler: # Frame 2 is frame 1 inverted assert np.array_equal((2 ** ds.BitsAllocated - 1) - arr[1], arr[0]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_32bit_float_1frame(self): """Test pixel_array for float pixel data, 1 frame.""" ds = dcmread(IMPL_32_1_1F) @@ -1002,6 +1032,7 @@ class TestNumpy_NumpyHandler: assert 1.44e-39 == pytest.approx(arr[4, 3], abs=0.01e-39) assert 1.13e-39 == pytest.approx(arr[-1, -3], abs=0.01e-39) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_32bit_float_15frame(self): """Test pixel_array for float pixel data, 15 frames.""" ds = dcmread(IMPL_32_1_15F) @@ -1018,6 +1049,7 @@ class TestNumpy_NumpyHandler: assert 1.44e-39 == pytest.approx(arr[0, 4, 3], abs=0.01e-39) assert 1.13e-39 == pytest.approx(arr[0, -1, -3], abs=0.01e-39) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_64bit_float_1frame(self): """Test pixel_array for double float pixel data, 1 frame.""" ds = dcmread(IMPL_32_1_1F) @@ -1035,6 +1067,7 @@ class TestNumpy_NumpyHandler: assert 1.80e-308 == pytest.approx(arr[4, 3], abs=0.01e-308) assert 1.69e-308 == pytest.approx(arr[-1, -3], abs=0.01e-308) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_64bit_float_15frame(self): """Test pixel_array for double float pixel data, 15 frames.""" ds = dcmread(IMPL_32_1_15F) @@ -1080,6 +1113,7 @@ class TestNumpy_NumpyHandler: assert ds.pixel_array.max() == 1 + @pytest.mark.skip("When building a Debian package we can not download anything") def test_read_only(self): """Test for #717, returned array read-only.""" ds = dcmread(EXPL_8_1_1F) @@ -1094,6 +1128,7 @@ class TestNumpy_NumpyHandler: @pytest.mark.skipif(not HAVE_NP, reason='Numpy is not available') class TestNumpy_GetPixelData: """Tests for numpy_handler.get_pixeldata with numpy.""" + @pytest.mark.skip("When building a Debian package we can not download anything") def test_no_pixel_data_raises(self): """Test get_pixeldata raises if dataset has no PixelData.""" ds = dcmread(EXPL_16_1_1F) @@ -1109,6 +1144,7 @@ class TestNumpy_GetPixelData: with pytest.raises(AttributeError, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_required_elem_pixel_data_monochrome(self): """Tet get_pixeldata raises if dataset missing required element.""" required_attrs = ( @@ -1130,6 +1166,7 @@ class TestNumpy_GetPixelData: with pytest.raises(AttributeError, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_required_elem_pixel_data_color(self): """Tet get_pixeldata raises if dataset missing required element.""" ds = dcmread(EXPL_8_3_1F) @@ -1142,6 +1179,7 @@ class TestNumpy_GetPixelData: with pytest.raises(AttributeError, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_conditionally_required_elem_pixel_data_color(self): """Tet get_pixeldata raises if dataset missing required element.""" ds = dcmread(EXPL_8_3_1F) @@ -1154,6 +1192,7 @@ class TestNumpy_GetPixelData: with pytest.raises(AttributeError, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_required_elem_float_pixel_data_monochrome(self): """Tet get_pixeldata raises if dataset missing required element.""" ds = dcmread(IMPL_32_1_1F) @@ -1167,6 +1206,7 @@ class TestNumpy_GetPixelData: with pytest.raises(AttributeError, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unknown_pixel_representation_raises(self): """Test get_pixeldata raises if unsupported PixelRepresentation.""" ds = dcmread(EXPL_16_1_1F) @@ -1175,6 +1215,7 @@ class TestNumpy_GetPixelData: match=r"value of '2' for '\(0028,0103"): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_unsupported_syntaxes_raises(self): """Test get_pixeldata raises if unsupported Transfer Syntax.""" ds = dcmread(EXPL_16_1_1F) @@ -1183,6 +1224,7 @@ class TestNumpy_GetPixelData: match=' the transfer syntax is not supported'): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_bad_length_raises(self): """Test bad pixel data length raises exception.""" ds = dcmread(EXPL_8_1_1F) @@ -1197,6 +1239,7 @@ class TestNumpy_GetPixelData: with pytest.raises(ValueError, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_padding_warns(self): """A warning shall be issued if the padding for odd data is missing.""" ds = dcmread(EXPL_8_3_1F_ODD) @@ -1206,6 +1249,7 @@ class TestNumpy_GetPixelData: with pytest.warns(UserWarning, match=msg): get_pixeldata(ds) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_change_photometric_interpretation(self): """Test get_pixeldata changes PhotometricInterpretation if required.""" @@ -1229,6 +1273,7 @@ class TestNumpy_GetPixelData: NP_HANDLER.should_change_PhotometricInterpretation_to_RGB = orig_fn + @pytest.mark.skip("When building a Debian package we can not download anything") def test_array_read_only(self): """Test returning a read only array for BitsAllocated > 8.""" ds = dcmread(EXPL_8_1_1F) @@ -1243,6 +1288,7 @@ class TestNumpy_GetPixelData: with pytest.raises(ValueError, match="is read-only"): arr[10] = 0 + @pytest.mark.skip("When building a Debian package we can not download anything") def test_array_read_only_bit_packed(self): """Test returning a read only array for BitsAllocated = 1.""" ds = dcmread(EXPL_1_1_1F) @@ -1252,6 +1298,7 @@ class TestNumpy_GetPixelData: arr = get_pixeldata(ds, read_only=True) assert arr.flags.writeable + @pytest.mark.skip("When building a Debian package we can not download anything") def test_ybr422_excess_padding(self): """Test YBR data with excess padding.""" ds = dcmread(EXPL_8_3_1F_YBR422) @@ -1276,6 +1323,7 @@ class TestNumpy_GetPixelData: assert (192, 128, 128) == tuple(arr[85, 50, :]) assert (255, 128, 128) == tuple(arr[95, 50, :]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_ybr422_wrong_interpretation(self): """Test YBR data with wrong Photometric Interpretation.""" ds = dcmread(EXPL_8_3_1F_YBR) @@ -1289,6 +1337,7 @@ class TestNumpy_GetPixelData: # Resulting data will be nonsense but of correct shape assert (100, 100, 3) == arr.shape + @pytest.mark.skip("When building a Debian package we can not download anything") def test_float_pixel_data(self): """Test handling of Float Pixel Data.""" # Only 1 sample per pixel allowed @@ -1299,6 +1348,7 @@ class TestNumpy_GetPixelData: arr = get_pixeldata(ds) assert 'float32' == arr.dtype + @pytest.mark.skip("When building a Debian package we can not download anything") def test_double_float_pixel_data(self): """Test handling of Double Float Pixel Data.""" # Only 1 sample per pixel allowed @@ -1309,6 +1359,7 @@ class TestNumpy_GetPixelData: arr = get_pixeldata(ds) assert 'float64' == arr.dtype + @pytest.mark.skip("When building a Debian package we can not download anything") def test_big_endian_rgb_data(self): """RGB data encoded as OW in Big Endian transfer syntax shall yield the same data as if encoded in Little Endian.""" --- a/pydicom/tests/test_encoders.py +++ b/pydicom/tests/test_encoders.py @@ -270,6 +270,7 @@ class TestEncoder: assert 'foo - requires bar' == s[0] +@pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(not HAVE_NP, reason="Numpy not available") class TestEncoder_Encode: """Tests for Encoder.encode() and related methods.""" --- a/pydicom/tests/test_encoders_gdcm.py +++ b/pydicom/tests/test_encoders_gdcm.py @@ -21,18 +21,19 @@ except ImportError: HAVE_GDCM = False GDCM_VERSION = [0, 0, 0] -# EXPL: Explicit VR Little Endian -EXPL_8_1_1F = get_testdata_file("OBXXXX1A.dcm") -EXPL_8_3_1F = get_testdata_file("SC_rgb.dcm") -EXPL_16_1_1F = get_testdata_file("MR_small.dcm") -EXPL_16_3_1F = get_testdata_file("SC_rgb_16bit.dcm") -EXPL_32_1_1F = get_testdata_file("rtdose_1frame.dcm") -EXPL_32_3_1F = get_testdata_file("SC_rgb_32bit.dcm") +## EXPL: Explicit VR Little Endian +#EXPL_8_1_1F = get_testdata_file("OBXXXX1A.dcm") +#EXPL_8_3_1F = get_testdata_file("SC_rgb.dcm") +#EXPL_16_1_1F = get_testdata_file("MR_small.dcm") +#EXPL_16_3_1F = get_testdata_file("SC_rgb_16bit.dcm") +#EXPL_32_1_1F = get_testdata_file("rtdose_1frame.dcm") +#EXPL_32_3_1F = get_testdata_file("SC_rgb_32bit.dcm") @pytest.mark.skipif(not HAVE_GDCM, reason='GDCM plugin is not available') class TestRLELossless: """Tests for encoding RLE Lossless.""" + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_u8_1s_1f(self): """Test an encode/decode cycle for 8-bit 1 sample/pixel.""" ds = dcmread(EXPL_8_1_1F) @@ -51,6 +52,7 @@ class TestRLELossless: assert np.array_equal(ref.ravel(), arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_u8_3s_1f(self): """Test an encode/decode cycle for 8-bit 3 sample/pixel.""" ds = dcmread(EXPL_8_3_1F) @@ -73,6 +75,7 @@ class TestRLELossless: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_i16_1s_1f(self): """Test an encode/decode cycle for 16-bit 1 sample/pixel.""" ds = dcmread(EXPL_16_1_1F) @@ -93,6 +96,7 @@ class TestRLELossless: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_u16_3s_1f(self): """Test an encode/decode cycle for 16-bit 3 sample/pixel.""" ds = dcmread(EXPL_16_3_1F) @@ -115,6 +119,7 @@ class TestRLELossless: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_cycle_u32_1s_1f(self): """Test an encode/decode cycle for 32-bit 1 sample/pixel.""" ds = dcmread(EXPL_32_1_1F) @@ -135,6 +140,7 @@ class TestRLELossless: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(GDCM_VERSION < [3, 0, 10], reason="GDCM bug") def test_cycle_u32_3s_1f(self): """Test an encode/decode cycle for 32-bit 3 sample/pixel.""" @@ -159,6 +165,7 @@ class TestRLELossless: assert np.array_equal(ref, arr) + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.skipif(GDCM_VERSION >= [3, 0, 10], reason="GDCM bug fixed") def test_cycle_u32_3s_1f_raises(self): """Test that 32-bit, 3 sample/px data raises exception.""" @@ -176,6 +183,7 @@ class TestRLELossless: with pytest.raises(RuntimeError, match=msg): gdcm_rle_encode(ds.PixelData, **kwargs) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_invalid_byteorder_raises(self): """Test that big endian source raises exception.""" ds = dcmread(EXPL_8_1_1F) @@ -191,6 +199,7 @@ class TestRLELossless: ds.PixelData, encoding_plugin='gdcm', byteorder='>', **kwargs ) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_above_32bit_raises(self): """Test that > 32-bit Bits Allocated raises exception.""" ds = dcmread(EXPL_8_1_1F) @@ -206,6 +215,7 @@ class TestRLELossless: with pytest.raises(RuntimeError, match=msg): enc.encode(ds.PixelData, encoding_plugin='gdcm', **kwargs) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_encoding_failure_raises(self): """Test that a encoding failure result raises an exception""" kwargs = { @@ -226,6 +236,7 @@ class TestRLELossless: with pytest.raises(RuntimeError, match=msg): gdcm_rle_encode(b'\x00', **kwargs) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_no_sequence_raises(self): """Test that no sequence of fragments raises an exception""" kwargs = { --- a/pydicom/tests/test_overlay_np.py +++ b/pydicom/tests/test_overlay_np.py @@ -55,13 +55,13 @@ except ImportError: # Paths to the test datasets # EXPL: Explicit VR Little Endian # Overlay Data -# 1/1, 1 sample/pixel, 1 frame -EXPL_1_1_1F = get_testdata_file("MR-SIEMENS-DICOM-WithOverlays.dcm") +## 1/1, 1 sample/pixel, 1 frame +#EXPL_1_1_1F = get_testdata_file("MR-SIEMENS-DICOM-WithOverlays.dcm") # 1/1, 1 sample/pixel, N frame EXPL_1_1_3F = None # No Overlay Data -# 16/16, 1 sample/pixel, 1 frame -EXPL_16_1_1F = get_testdata_file("MR_small.dcm") +## 16/16, 1 sample/pixel, 1 frame +#EXPL_16_1_1F = get_testdata_file("MR_small.dcm") # Numpy unavailable and the numpy handler is available @@ -82,6 +82,7 @@ class TestNoNumpy_NumpyHandler: assert not HAVE_NP assert NP_HANDLER is not None + @pytest.mark.skip("When building a Debian package we can not download anything") def test_overlay_array_raises(self): """Test overlay_array raises exception""" ds = dcmread(EXPL_1_1_1F) @@ -89,6 +90,7 @@ class TestNoNumpy_NumpyHandler: with pytest.raises(RuntimeError, match=msg): ds.overlay_array(0x6000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_get_overlay_array_raises(self): """Test get_overlay_array raises exception""" ds = dcmread(EXPL_1_1_1F) @@ -110,7 +112,7 @@ IMPL = ImplicitVRLittleEndian REFERENCE_DATA_LITTLE = [ # fpath, (syntax, bits, nr samples, pixel repr, nr frames, shape, dtype, # group) - (EXPL_1_1_1F, (EXPL, 1, 1, 0, 1, (484, 484), 'uint8', 0x6000)), +# (EXPL_1_1_1F, (EXPL, 1, 1, 0, 1, (484, 484), 'uint8', 0x6000)), # (EXPL_1_1_3F, (EXPL, 1, 1, 0, 3, (3, 512, 512), 'uint8', 0x6000)), ] @@ -154,6 +156,7 @@ class TestNumpy_NumpyHandler: if size % 2: assert ds[group, 0x3000].value[-1] == b'\x00'[0] + @pytest.mark.skip("When building a Debian package we can not download anything") def test_little_1bit_1sample_1frame(self): """Test pixel_array for little 1-bit, 1 sample/pixel, 1 frame.""" ds = dcmread(EXPL_1_1_1F) @@ -170,6 +173,7 @@ class TestNumpy_NumpyHandler: ds = dcmread(EXPL_1_1_3F) arr = ds.overlay_array(0x6000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_read_only(self): """Test for #717, returned array read-only.""" ds = dcmread(EXPL_1_1_1F) @@ -179,6 +183,7 @@ class TestNumpy_NumpyHandler: assert 1 == arr[0, 0] assert arr.flags.writeable + @pytest.mark.skip("When building a Debian package we can not download anything") def test_bad_group_raises(self): """Test that using a bad group raises exception.""" ds = dcmread(EXPL_1_1_1F) @@ -191,6 +196,7 @@ class TestNumpy_NumpyHandler: with pytest.raises(ValueError, match=msg): ds.overlay_array(0x6100) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_no_frames(self): """Test handler with no NumberOfFramesInOverlay element.""" ds = dcmread(EXPL_1_1_1F) @@ -206,6 +212,7 @@ class TestNumpy_NumpyHandler: @pytest.mark.skipif(not HAVE_NP, reason='Numpy is not available') class TestNumpy_GetOverlayArray: """Tests for numpy_handler.get_overlay_array with numpy.""" + @pytest.mark.skip("When building a Debian package we can not download anything") def test_no_overlay_data_raises(self): """Test get_overlay_array raises if dataset has no OverlayData.""" ds = dcmread(EXPL_1_1_1F) @@ -214,6 +221,7 @@ class TestNumpy_GetOverlayArray: with pytest.raises(AttributeError, match=r' dataset: OverlayData'): get_overlay_array(ds, 0x6000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_bad_length_raises(self): """Test bad pixel data length raises exception.""" ds = dcmread(EXPL_1_1_1F) @@ -228,6 +236,7 @@ class TestNumpy_GetOverlayArray: with pytest.raises(ValueError, match=msg): get_overlay_array(ds, 0x6000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_missing_padding_warns(self): """A warning shall be issued if the padding for odd data is missing.""" ds = dcmread(EXPL_1_1_1F) @@ -239,6 +248,7 @@ class TestNumpy_GetOverlayArray: with pytest.warns(UserWarning, match=msg): get_overlay_array(ds, 0x6000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_excess_padding(self): """A warning shall be issued excess padding present.""" ds = dcmread(EXPL_1_1_1F) @@ -254,6 +264,7 @@ class TestNumpy_GetOverlayArray: with pytest.warns(UserWarning, match=msg): get_overlay_array(ds, 0x6000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_old_import(self): """Test that can import using the old path.""" from pydicom.overlay_data_handlers import numpy_handler as np_old --- a/pydicom/tests/test_rle_pixel_data.py +++ b/pydicom/tests/test_rle_pixel_data.py @@ -308,6 +308,7 @@ class TestNumpy_NoRLEHandler: assert ds.PatientName == 'CompressedSamples^MR1' assert len(ds.PixelData) == 6128 + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize("fpath,data", REFERENCE_DATA_UNSUPPORTED) def test_can_access_unsupported_dataset(self, fpath, data): """Test can read and access elements in unsupported datasets.""" @@ -360,6 +361,7 @@ class TestNumpy_RLEHandler: with pytest.raises(NotImplementedError, match=msg): ds.decompress(handler_name='rle') + @pytest.mark.skip("When building a Debian package we can not download anything") @pytest.mark.parametrize("fpath,data", REFERENCE_DATA_UNSUPPORTED) def test_can_access_unsupported_dataset(self, fpath, data): """Test can read and access elements in unsupported datasets.""" @@ -368,6 +370,7 @@ class TestNumpy_RLEHandler: assert ds.PatientName == data[1] assert len(ds.PixelData) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_signed(self): """Test pixel_array for unsigned -> signed data.""" ds = dcmread(RLE_8_1_1F) @@ -391,6 +394,7 @@ class TestNumpy_RLEHandler: with pytest.raises(NotImplementedError, match=msg): ds.pixel_array + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_8bit_1sample_1f(self): """Test pixel_array for 8-bit, 1 sample/pixel, 1 frame.""" ds = dcmread(RLE_8_1_1F) @@ -409,6 +413,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[300, 491:494]) == (1, 246, 1) assert arr[-1].min() == arr[-1].max() == 0 + @pytest.mark.skip("When building a Debian package we can not download anything") def test_decompress_with_handler(self): """Test that decompress works with the correct handler.""" ds = dcmread(RLE_8_1_1F) @@ -426,6 +431,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[300, 491:494]) == (1, 246, 1) assert arr[-1].min() == arr[-1].max() == 0 + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_8bit_1sample_2f(self): """Test pixel_array for 8-bit, 1 sample/pixel, 2 frame.""" ds = dcmread(RLE_8_1_2F) @@ -447,6 +453,7 @@ class TestNumpy_RLEHandler: # Frame 2 is frame 1 inverted assert np.array_equal((2**ds.BitsAllocated - 1) - arr[1], arr[0]) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_8bit_3sample_1f(self): """Test pixel_array for 8-bit, 3 sample/pixel, 1 frame.""" ds = dcmread(RLE_8_3_1F) @@ -472,6 +479,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[85, 50, :]) == (192, 192, 192) assert tuple(arr[95, 50, :]) == (255, 255, 255) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_8bit_3sample_2f(self): """Test pixel_array for 8-bit, 3 sample/pixel, 2 frame.""" ds = dcmread(RLE_8_3_2F) @@ -521,6 +529,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[31, :3]) == (366, 363, 322) assert tuple(arr[-1, -3:]) == (1369, 1129, 862) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_16bit_1sample_10f(self): """Test pixel_array for 16-bit, 1, sample/pixel, 10 frame.""" ds = dcmread(RLE_16_1_10F) @@ -552,6 +561,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[-1, 31, :3]) == (25, 4, 9) assert tuple(arr[-1, -1, -3:]) == (227, 300, 147) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_16bit_3sample_1f(self): """Test pixel_array for 16-bit, 3 sample/pixel, 1 frame.""" ds = dcmread(RLE_16_3_1F) @@ -578,6 +588,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[85, 50, :]) == (49344, 49344, 49344) assert tuple(arr[95, 50, :]) == (65535, 65535, 65535) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_16bit_3sample_2f(self): """Test pixel_array for 16-bit, 3, sample/pixel, 10 frame.""" ds = dcmread(RLE_16_3_2F) @@ -660,6 +671,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[-1, 4, 3:6]) == (1031000, 1031000, 1031000) assert tuple(arr[-1, -1, -3:]) == (801000, 800000, 799000) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_32bit_3sample_1f(self): """Test pixel_array for 32-bit, 3 sample/pixel, 1 frame.""" ds = dcmread(RLE_32_3_1F) @@ -686,6 +698,7 @@ class TestNumpy_RLEHandler: assert tuple(arr[85, 50, :]) == (3233857728, 3233857728, 3233857728) assert tuple(arr[95, 50, :]) == (4294967295, 4294967295, 4294967295) + @pytest.mark.skip("When building a Debian package we can not download anything") def test_pixel_array_32bit_3sample_2f(self): """Test pixel_array for 32-bit, 3, sample/pixel, 2 frame.""" ds = dcmread(RLE_32_3_2F)