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# Copyright 2008-2018 pydicom authors. See LICENSE file for details.
"""Unit tests for the JPEG-LS Pixel Data handler."""
import os
import sys
import pytest
import pydicom
from pydicom.filereader import dcmread
from pydicom.data import get_testdata_file
jpeg_ls_missing_message = ("jpeg_ls is not available "
"in this test environment")
jpeg_ls_present_message = "jpeg_ls is being tested"
from pydicom.pixel_data_handlers import numpy_handler
have_numpy_handler = numpy_handler.is_available()
from pydicom.pixel_data_handlers import jpeg_ls_handler
have_jpeg_ls_handler = jpeg_ls_handler.is_available()
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")
dir_name = os.path.dirname(sys.argv[0])
save_dir = os.getcwd()
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)
self.mr_small = dcmread(mr_name)
self.emri_jpeg_ls_lossless = dcmread(emri_jpeg_ls_lossless)
self.emri_small = dcmread(emri_name)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def test_JPEG_LS_PixelArray(self):
with pytest.raises((RuntimeError, NotImplementedError)):
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)
self.jpeg_2k_lossless = dcmread(jpeg2000_lossless_name)
self.mr_small = dcmread(mr_name)
self.emri_jpeg_2k_lossless = dcmread(emri_jpeg_2k_lossless)
self.emri_small = dcmread(emri_name)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def test_JPEG2000PixelArray(self):
"""JPEG2000: Now works"""
with pytest.raises(NotImplementedError):
self.jpeg_2k.pixel_array
def test_emri_JPEG2000PixelArray(self):
"""JPEG2000: Now works"""
with pytest.raises(NotImplementedError):
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)
self.color_3d_jpeg = dcmread(color_3d_jpeg_baseline)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def testJPEGlossy(self):
"""JPEG-lossy: Returns correct values for sample data elements"""
got = self.jpeg_lossy.DerivationCodeSequence[0].CodeMeaning
assert 'Lossy Compression' == got
def testJPEGlossyPixelArray(self):
"""JPEG-lossy: Fails gracefully when uncompressed data is asked for"""
with pytest.raises(NotImplementedError):
self.jpeg_lossy.pixel_array
def testJPEGBaselineColor3DPixelArray(self):
with pytest.raises(NotImplementedError):
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)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def testJPEGlossless(self):
"""JPEGlossless: Returns correct values for sample data elements"""
got = self.\
jpeg_lossless.\
SourceImageSequence[0].\
PurposeOfReferenceCodeSequence[0].CodeMeaning
assert 'Uncompressed predecessor' == got
def testJPEGlosslessPixelArray(self):
"""JPEGlossless: Fails gracefully when uncompressed data asked for"""
with pytest.raises(NotImplementedError):
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):
self.jpeg_ls_lossless = dcmread(jpeg_ls_lossless_name)
self.mr_small = dcmread(mr_name)
self.emri_jpeg_ls_lossless = dcmread(emri_jpeg_ls_lossless)
self.emri_small = dcmread(emri_name)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [jpeg_ls_handler, numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def test_JPEG_LS_PixelArray(self):
a = self.jpeg_ls_lossless.pixel_array
b = self.mr_small.pixel_array
assert b.mean() == a.mean()
assert a.flags.writeable
def test_emri_JPEG_LS_PixelArray(self):
a = self.emri_jpeg_ls_lossless.pixel_array
b = self.emri_small.pixel_array
assert b.mean() == a.mean()
assert a.flags.writeable
@pytest.mark.parametrize("handler_name", SUPPORTED_HANDLER_NAMES)
def test_decompress_using_handler(self, handler_name):
self.emri_jpeg_ls_lossless.decompress(handler_name=handler_name)
a = self.emri_jpeg_ls_lossless.pixel_array
b = self.emri_small.pixel_array
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):
self.jpeg_2k = dcmread(jpeg2000_name)
self.jpeg_2k_lossless = dcmread(jpeg2000_lossless_name)
self.mr_small = dcmread(mr_name)
self.emri_jpeg_2k_lossless = dcmread(emri_jpeg_2k_lossless)
self.emri_small = dcmread(emri_name)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [jpeg_ls_handler, numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def test_JPEG2000PixelArray(self):
with pytest.raises(NotImplementedError):
self.jpeg_2k.pixel_array
def test_emri_JPEG2000PixelArray(self):
with pytest.raises(NotImplementedError):
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):
self.jpeg_lossy = dcmread(jpeg_lossy_name)
self.color_3d_jpeg = dcmread(color_3d_jpeg_baseline)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [jpeg_ls_handler, numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def testJPEGlossy(self):
"""JPEG-lossy: Returns correct values for sample data elements"""
got = self.jpeg_lossy.DerivationCodeSequence[0].CodeMeaning
assert 'Lossy Compression' == got
def testJPEGlossyPixelArray(self):
with pytest.raises(NotImplementedError):
self.jpeg_lossy.pixel_array
def testJPEGBaselineColor3DPixelArray(self):
with pytest.raises(NotImplementedError):
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):
self.jpeg_lossless = dcmread(jpeg_lossless_name)
self.original_handlers = pydicom.config.pixel_data_handlers
pydicom.config.pixel_data_handlers = [jpeg_ls_handler, numpy_handler]
def teardown_method(self):
pydicom.config.pixel_data_handlers = self.original_handlers
def testJPEGlossless(self):
"""JPEGlossless: Returns correct values for sample data elements"""
got = self.\
jpeg_lossless.\
SourceImageSequence[0].\
PurposeOfReferenceCodeSequence[0].CodeMeaning
assert 'Uncompressed predecessor' == got
def testJPEGlosslessPixelArray(self):
"""JPEGlossless: Fails gracefully when uncompressed data asked for"""
with pytest.raises(NotImplementedError):
self.jpeg_lossless.pixel_array
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