def test_load_as_matrix_channel_subselection(self):
"""
Test correctly loading image with only specific channels of what is
available.
"""
# Load image normally, assumed functional (see above)
mat_rgb = GdalImageReader().load_as_matrix(GH_FILE_ELEMENT)
mat_gb = GdalImageReader(channel_order='gb')\
.load_as_matrix(GH_FILE_ELEMENT)
numpy.testing.assert_allclose(mat_gb, mat_rgb[:, :, [1, 2]])
def test_init_channel_order_not_sequence(self):
"""
Test that ``channel_order`` sequence check catches appropriate culprits.
"""
expected_message = 'Channel order must be a sequence'
with pytest.raises(ValueError, match=expected_message):
# Sets should be invalid.
# noinspection PyTypeChecker
GdalImageReader(channel_order={1, 2, 3})
with pytest.raises(ValueError, match=expected_message):
GdalImageReader(channel_order={1: 0, 2: 3})
def test_load_as_matrix_channel_subselection_cropped(self):
"""
Same as previous test but with crop region provided.
"""
# Load image normally, assumed functional (see above)
mat_rgb = GdalImageReader().load_as_matrix(GH_CROPPED_FILE_ELEMENT)
mat_gb = GdalImageReader(channel_order='gb') \
.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=GH_CROPPED_BBOX)
assert mat_gb.ndim == 3
assert mat_gb.shape == (100, 100, 2)
numpy.testing.assert_allclose(mat_gb, mat_rgb[:, :, [1, 2]])
def test_init_channel_order_empty_sequence(self):
"""
Test that we get an error if an empty sequence is provided.
"""
expected_message = "Invalid channel order, must request at least "\
"one band"
with pytest.raises(ValueError, match=expected_message):
GdalImageReader(channel_order='')
with pytest.raises(ValueError, match=expected_message):
GdalImageReader(channel_order=[])
with pytest.raises(ValueError, match=expected_message):
GdalImageReader(channel_order=())
def test_load_as_matrix_single_channel_from_multi_cropped(self):
"""
Same as previous test but with crop region provided.
"""
# Load image normally, assumed functional (see above)
mat_rgb_cropped = GdalImageReader()\
.load_as_matrix(GH_CROPPED_FILE_ELEMENT)
mat_b_cropped = GdalImageReader(channel_order='b')\
.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=GH_CROPPED_BBOX)
assert mat_b_cropped.ndim == 2
assert mat_b_cropped.shape == (100, 100)
numpy.testing.assert_allclose(mat_b_cropped, mat_rgb_cropped[:, :, 2])
def test_load_as_matrix_single_channel_from_multi(self):
"""
Test that when requesting a single channel we get back an ndim=2 matrix
instead of a matrix with a 1-valied dimension.
"""
# Load image normally, assumed functional (see above)
mat_rgb = GdalImageReader().load_as_matrix(GH_FILE_ELEMENT)
mat_b = GdalImageReader(channel_order='b')\
.load_as_matrix(GH_FILE_ELEMENT)
assert mat_b.shape == (600, 512)
assert mat_b.ndim == 2
numpy.testing.assert_allclose(mat_b, mat_rgb[:, :, 2])
def test_load_as_matrix_with_channel_order_invalid(self):
"""
Test that we error when the requested channel order cannot be applied to
the data given.
"""
# We know that the GH_FILE_ELEMENT image is an RGB format image.
msg = "Data element did not provide channels required"
with pytest.raises(RuntimeError, match=msg):
GdalImageReader(channel_order=[gdal_io.gdal.GCI_CyanBand])\
.load_as_matrix(GH_FILE_ELEMENT)
with pytest.raises(RuntimeError, match=msg):
# Same as above, but with abbreviation
GdalImageReader(channel_order='c')\
.load_as_matrix(GH_FILE_ELEMENT)
def test_load_as_matrix_channel_reorder(self):
"""
Test correctly loading image with channels reordered as requested.
"""
# Load image normally, assumed functional (see above)
mat_rgb = GdalImageReader().load_as_matrix(GH_FILE_ELEMENT)
mat_brg = GdalImageReader(channel_order='brg')\
.load_as_matrix(GH_FILE_ELEMENT)
numpy.testing.assert_allclose(mat_brg, mat_rgb[:, :, [2, 0, 1]])
# Duplicate bands? Because we can?
mat_bgrgb = GdalImageReader(channel_order='bgrbg')\
.load_as_matrix(GH_FILE_ELEMENT)
numpy.testing.assert_allclose(mat_bgrgb, mat_rgb[:, :,
[2, 1, 0, 2, 1]])
def test_init_channel_order_invalid_abbreviation_char(self):
"""
Test that exception is raise upon construction with an unknown channel
order abbreviation.
"""
msg = 'Invalid abbreviation character'
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order='!')
# Check that we catch it among other valid characters
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order='rg!')
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order='!gb')
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order='r!b')
def test_init_channel_order_invalid_gci_integer(self):
"""
Test that we catch integers that are not reported as supported constants
by inspection of GDAL module values.
"""
# We know (as of gdal 2.4.0) that 99 is not a valid GCI.
msg = "Invalid GDAL band integer values given"
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order=[99])
# Check that we catch it among other valid characters
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order=[3, 4, 99])
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order=[3, 99, 5])
with pytest.raises(ValueError, match=msg):
GdalImageReader(channel_order=[99, 4, 5])
def test_load_as_matrix_with_crop(self):
"""
Test that the image is loaded with the correct crop region.
We load two images: the original with a crop specified, and a
pre-cropped image. The results of each load should be the same,
indicating the correct region from the source image is extracted.
"""
assert \
GH_FILE_ELEMENT.get_bytes() != GH_CROPPED_FILE_ELEMENT.get_bytes()
reader = GdalImageReader(
load_method=GdalImageReader.LOAD_METHOD_TEMPFILE)
cropped_actual = reader.load_as_matrix(GH_FILE_ELEMENT,
pixel_crop=GH_CROPPED_BBOX)
cropped_expected = reader.load_as_matrix(GH_CROPPED_FILE_ELEMENT)
# noinspection PyTypeChecker
numpy.testing.assert_allclose(cropped_actual, cropped_expected)
def test_init_vsimem_req_gdal_2_pass(self, m_osgeo):
"""
Test that we do NOT get an error when using load_method='vsimem'
and GDAL reports a version greater than 2.
"""
# Mock a GDAL version greater than 2.
m_osgeo.__version__ = "2.4.0"
GdalImageReader(load_method=GdalImageReader.LOAD_METHOD_VSIMEM)
def test_load_as_matrix_empty_data(self):
"""
Test that we catch and do not load an empty data element.
"""
empty_de = DataMemoryElement(readonly=True, content_type='image/png')
assert empty_de.is_empty()
msg = "GdalImageReader cannot load 0-sized data"
with pytest.raises(ValueError, match=msg):
GdalImageReader().load_as_matrix(empty_de)
def test_serialization(self):
"""
Test that we can serialize and deserialize the algorithm, maintaining
configuration responses.
"""
expected_load_method = GdalImageReader.LOAD_METHOD_TEMPFILE
expected_channel_order = [3, 5, 4]
inst1 = GdalImageReader(load_method=expected_load_method,
channel_order=expected_channel_order)
expected_config = {'load_method': expected_load_method,
'channel_order': expected_channel_order}
assert inst1.get_config() == expected_config
buff = pickle.dumps(inst1)
#: :type: GdalImageReader
inst2 = pickle.loads(buff)
assert inst2.get_config() == expected_config
def test_GdalImageReader_usable():
"""
Test that GdalImageReader class reports as usable when GDAL is importable.
"""
# Mock module value of ``osgeo`` to something not None to simulate
# something having been imported.
with mock.patch.dict('smqtk.algorithms.image_io.gdal_io.__dict__',
{'osgeo': object()}):
assert GdalImageReader.is_usable() is True
def test_load_as_matrix_channel_reorder_cropped(self):
"""
Same as previous test but with crop region provided.
"""
# Load image normally, assumed functional (see above)
mat_rgb = GdalImageReader().load_as_matrix(GH_CROPPED_FILE_ELEMENT)
mat_brg = GdalImageReader(channel_order='brg') \
.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=GH_CROPPED_BBOX)
assert mat_brg.ndim == 3
assert mat_brg.shape == (100, 100, 3)
numpy.testing.assert_allclose(mat_brg, mat_rgb[:, :, [2, 0, 1]])
# Duplicate bands? Because we can?
mat_bgrggb = GdalImageReader(channel_order='bgrggb') \
.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=GH_CROPPED_BBOX)
assert mat_bgrggb.ndim == 3
assert mat_bgrggb.shape == (100, 100, 6)
numpy.testing.assert_allclose(mat_bgrggb, mat_rgb[:, :,
[2, 1, 0, 1, 1, 2]])
def test_init_bad_load_method(self):
"""
Test that passing a load_method string that is not one of the
expected values raises a ValueError.
"""
with pytest.raises(ValueError, match=r"Load method provided not a "
r"valid value \(given 'not a "
r"valid method'\)\. Must be one "
r"of: "):
GdalImageReader(load_method="not a valid method")
def test_load_as_matrix_tempfile(self):
"""
Test that whole image is loaded successfully using tempfile loader.
"""
wrapped_temp_loader = mock.MagicMock(wraps=load_dataset_tempfile)
wrapped_vsimem_loader = mock.MagicMock(wraps=load_dataset_vsimem)
with mock.patch.dict(GdalImageReader.LOAD_METHOD_CONTEXTMANAGERS, {
GdalImageReader.LOAD_METHOD_TEMPFILE: wrapped_temp_loader,
GdalImageReader.LOAD_METHOD_VSIMEM: wrapped_vsimem_loader
}):
# Using tempfile load method
reader = GdalImageReader(
load_method=GdalImageReader.LOAD_METHOD_TEMPFILE
)
mat = reader._load_as_matrix(GH_FILE_ELEMENT)
assert mat.shape == (600, 512, 3)
wrapped_temp_loader.assert_called_once_with(GH_FILE_ELEMENT)
wrapped_vsimem_loader.assert_not_called()
def test_configuration(self):
"""
Test configuration using helper
"""
expected_load_method = GdalImageReader.LOAD_METHOD_TEMPFILE
expected_channel_order = [3, 5, 4]
i = GdalImageReader(load_method=expected_load_method,
channel_order=expected_channel_order)
for inst in configuration_test_helper(i): # type: GdalImageReader
assert inst._load_method == expected_load_method
assert inst._channel_order == expected_channel_order
def test_init_vsimem_req_gdal_2_fail(self, m_osgeo):
"""
Test that we get a RuntimeError when using load_method='vsimem' and
the current GDAL wrapper version is < 2.
"""
# Mock a GDAL version less than 2.
m_osgeo.__version__ = "1.11.0"
with pytest.raises(RuntimeError,
match=r"Load method '{}' was specified, "
r"but required GDAL version of 2 is not "
r"satisfied \(imported version: {}\)\.".format(
GdalImageReader.LOAD_METHOD_VSIMEM, "1.11.0")):
GdalImageReader(load_method=GdalImageReader.LOAD_METHOD_VSIMEM)
def test_GdalImageReader_not_usable_missing_osgeo():
"""
Test that class reports as not usable when GDAL is not importable (set
to None in module).
"""
# Catch expected warnings to not pollute output.
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=UserWarning)
# Mock module value of ``osgeo`` to None.
with mock.patch.dict('smqtk.algorithms.image_io.gdal_io.__dict__',
{'osgeo': None}):
assert GdalImageReader.is_usable() is False
def test_load_as_matrix_vsimem(self):
"""
Test that whole image is loaded successfully using vsimem loader.
"""
if LooseVersion(osgeo.__version__).version[0] < 2:
pytest.skip("Skipping VSIMEM test because GDAL version < 2")
wrapped_temp_loader = mock.MagicMock(wraps=load_dataset_tempfile)
wrapped_vsimem_loader = mock.MagicMock(wraps=load_dataset_vsimem)
with mock.patch.dict(GdalImageReader.LOAD_METHOD_CONTEXTMANAGERS, {
GdalImageReader.LOAD_METHOD_TEMPFILE: wrapped_temp_loader,
GdalImageReader.LOAD_METHOD_VSIMEM: wrapped_vsimem_loader
}):
# Using VSIMEM load method
reader = GdalImageReader(
load_method=GdalImageReader.LOAD_METHOD_VSIMEM
)
mat = reader._load_as_matrix(GH_FILE_ELEMENT)
assert mat.shape == (600, 512, 3)
wrapped_temp_loader.assert_not_called()
wrapped_vsimem_loader.assert_called_once_with(GH_FILE_ELEMENT)
def test_valid_content_types(self, m_ggdsm):
"""
Test that valid_content_types refers to the helper method and
returns the same thing.
Mocking (wrapping) `get_gdal_driver_supported_mimetypes` in order check
that it is being called under the hood.
"""
expected_content_types = get_gdal_driver_supported_mimetypes()
actual_content_types = GdalImageReader().valid_content_types()
m_ggdsm.assert_called_once_with()
assert actual_content_types == expected_content_types
def test_GdalImageReader_not_usable_missing_osgeo():
"""
Test that class reports as not usable when GDAL is not importable (set
to None in module).
"""
# Catch expected warnings to not pollute output.
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=UserWarning)
# Mock module value of ``osgeo`` to None.
with mock.patch.dict('smqtk.algorithms.image_io.gdal_io.__dict__',
{'osgeo': None}):
assert GdalImageReader.is_usable() is False
@pytest.mark.skipif(not GdalImageReader.is_usable(),
reason="GdalImageReader implementation is not usable in "
"the current environment.")
class TestGdalImageReader (unittest.TestCase):
"""
Tests for ``GdalImageReader`` class.
If this was not skipped, ``osgeo`` must have been importable.
"""
def test_init_default(self):
"""
Test that construction with default parameters works.
"""
GdalImageReader()
def test_load_as_matrix_with_crop_not_in_bounds(self):
"""
Test that error is raised when crop bbox is not fully within the image
bounds.
"""
inst = GdalImageReader()
# Nowhere close
bb = AxisAlignedBoundingBox([5000, 6000], [7000, 8000])
with pytest.raises(RuntimeError,
match=r"Crop provided not within input image\. "
r"Image shape: \(512, 600\), crop: "):
inst.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=bb)
# Outside left side
bb = AxisAlignedBoundingBox([-1, 1], [2, 2])
with pytest.raises(RuntimeError,
match=r"Crop provided not within input image\. "
r"Image shape: \(512, 600\), crop: "):
inst.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=bb)
# Outside top side
bb = AxisAlignedBoundingBox([1, -1], [2, 2])
with pytest.raises(RuntimeError,
match=r"Crop provided not within input image\. "
r"Image shape: \(512, 600\), crop: "):
inst.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=bb)
# Outside right side
bb = AxisAlignedBoundingBox([400, 400], [513, 600])
with pytest.raises(RuntimeError,
match=r"Crop provided not within input image\. "
r"Image shape: \(512, 600\), crop: "):
inst.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=bb)
# Outside bottom side
bb = AxisAlignedBoundingBox([400, 400], [512, 601])
with pytest.raises(RuntimeError,
match=r"Crop provided not within input image\. "
r"Image shape: \(512, 600\), crop: "):
inst.load_as_matrix(GH_FILE_ELEMENT, pixel_crop=bb)
def test_init_channel_order_lower_case(self):
"""
Test that channel order if provided as string is cast to lower case.
"""
assert GdalImageReader(channel_order='rGB')._channel_order == \
"rgb"
def test_init_default(self):
"""
Test that construction with default parameters works.
"""
GdalImageReader()