def testStyleAutoMinMax():
imagePath = datastore.fetch('DDX58_AXL_EGFR_well2_XY01.ome.tif')
source = large_image_source_ometiff.open(imagePath)
image, _ = source.getRegion(output={
'maxWidth': 256,
'maxHeight': 256
},
format=TILE_FORMAT_NUMPY,
frame=1)
sourceB = large_image_source_ometiff.open(imagePath,
style={
'min': 'auto',
'max': 'auto'
})
imageB, _ = sourceB.getRegion(output={
'maxWidth': 256,
'maxHeight': 256
},
format=TILE_FORMAT_NUMPY,
frame=1)
imageB = imageB[:, :, :1]
assert numpy.any(image != imageB)
assert image.shape == imageB.shape
assert image[128][128][0] < imageB[128][128][0]
assert image[0][128][0] < imageB[0][128][0]
assert image[240][128][0] < imageB[240][128][0]
def testStyleFrameDelta():
imagePath = datastore.fetch('sample.ome.tif')
source = large_image_source_ometiff.open(imagePath,
style=json.dumps({
'bands': [{
'palette':
['#000000', '#0000ff'],
}, {
'palette':
['#000000', '#00ff00'],
}]
}))
image, _ = source.getRegion(output={
'maxWidth': 256,
'maxHeight': 256
},
format=TILE_FORMAT_NUMPY,
frame=1)
sourceB = large_image_source_ometiff.open(imagePath,
style=json.dumps({
'bands': [{
'palette':
['#000000', '#0000ff'],
}, {
'framedelta':
1,
'palette':
['#000000', '#00ff00'],
}]
}))
imageB, _ = sourceB.getRegion(output={
'maxWidth': 256,
'maxHeight': 256
},
format=TILE_FORMAT_NUMPY,
frame=1)
assert numpy.any(image != imageB)
assert image.shape == imageB.shape
sourceC = large_image_source_ometiff.open(imagePath,
style=json.dumps({
'bands': [{
'framedelta':
-1,
'palette':
['#000000', '#0000ff'],
}, {
'palette':
['#000000', '#00ff00'],
}]
}))
imageC, _ = sourceC.getRegion(output={
'maxWidth': 256,
'maxHeight': 256
},
format=TILE_FORMAT_NUMPY,
frame=2)
assert numpy.all(imageB == imageC)
assert imageB.shape == imageC.shape
def testXMLParsing():
samples = [{
'xml': """<?xml version='1.0' encoding='utf-8'?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:1ae9b229-162c-4431-8be0-1833b52302e5" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" PhysicalSizeX="0.32499998807907104" PhysicalSizeXUnit="µm" PhysicalSizeY="0.32499998807907104" PhysicalSizeYUnit="µm" SizeC="3" SizeT="1" SizeX="57346" SizeY="54325" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" Name="Red" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:1" Name="Green" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:2" Name="Blue" SamplesPerPixel="1"><LightPath /></Channel><TiffData IFD="0" PlaneCount="3" /><Plane TheC="0" TheT="0" TheZ="0" /><Plane TheC="1" TheT="0" TheZ="0" /><Plane TheC="2" TheT="0" TheZ="0" /></Pixels></Image></OME>""", # noqa
'checks': {
'frames': 3,
'IndexRange': {
'IndexC': 3
},
'IndexStride': {
'IndexC': 1
},
'channelmap': {
'Blue': 2,
'Green': 1,
'Red': 0
},
'channels': ['Red', 'Green', 'Blue'],
}
}]
# Create a source so we can use internal functions for testing
imagePath = datastore.fetch('sample.ome.tif')
source = large_image_source_ometiff.open(imagePath)
for sample in samples:
xml = ElementTree.fromstring(sample['xml'])
info = etreeToDict(xml)
assert etreeToDict(dictToEtree(info)) == info
source._omeinfo = info['OME']
source._parseOMEInfo()
metadata = source.getMetadata()
for key, value in sample['checks'].items():
if key in {'frames'}:
assert len(metadata[key]) == value
else:
assert metadata[key] == value
def testOMETiffAre16Bit():
imagePath = datastore.fetch('DDX58_AXL_EGFR_well2_XY01.ome.tif')
source = large_image_source_ometiff.open(imagePath)
tile = next(source.tileIterator(format=TILE_FORMAT_NUMPY))['tile']
assert tile.dtype == numpy.uint16
assert tile[15][15][0] == 17852
region, _ = source.getRegion(format=TILE_FORMAT_NUMPY)
assert region.dtype == numpy.uint16
assert region[300][300][0] == 17816
def testTilesFromOMETiffWithSubIFD():
imagePath = datastore.fetch('sample.subifd.ome.tif')
source = large_image_source_ometiff.open(imagePath, frame=1)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 256
assert tileMetadata['tileHeight'] == 256
assert tileMetadata['sizeX'] == 2106
assert tileMetadata['sizeY'] == 2016
assert tileMetadata['levels'] == 5
assert len(tileMetadata['frames']) == 3
assert tileMetadata['frames'][1]['Frame'] == 1
assert tileMetadata['frames'][1]['Index'] == 0
assert tileMetadata['frames'][1]['IndexC'] == 1
assert tileMetadata['IndexRange'] == {'IndexC': 3}
utilities.checkTilesZXY(source, tileMetadata)
def testTilesFromStripOMETiff():
imagePath = datastore.fetch('DDX58_AXL_EGFR_well2_XY01.ome.tif')
source = large_image_source_ometiff.open(imagePath)
tileMetadata = source.getMetadata()
assert tileMetadata['tileWidth'] == 1024
assert tileMetadata['tileHeight'] == 256
assert tileMetadata['sizeX'] == 1024
assert tileMetadata['sizeY'] == 1022
assert tileMetadata['levels'] == 3
assert len(tileMetadata['frames']) == 145
assert tileMetadata['frames'][101]['Frame'] == 101
assert tileMetadata['frames'][101]['Index'] == 20
assert tileMetadata['frames'][101]['IndexC'] == 1
assert tileMetadata['frames'][101]['IndexZ'] == 20
assert tileMetadata['channels'] == [
'Brightfield', 'CY3', 'A594', 'CY5', 'DAPI'
]
assert tileMetadata['IndexRange'] == {'IndexC': 5, 'IndexZ': 29}
utilities.checkTilesZXY(source, tileMetadata)
def testInternalMetadata():
imagePath = datastore.fetch('sample.ome.tif')
source = large_image_source_ometiff.open(imagePath)
metadata = source.getInternalMetadata()
assert 'omeinfo' in metadata