def labeled_channel(image_channel_factory):
channels = list()
for index in range(2):
channel = ChannelI()
lchannel = LogicalChannelI()
lchannel.name = rstring('a channel %d' % index)
channel.logicalChannel = lchannel
channels.append(channel)
return image_channel_factory(channels)
def labeled_channel(image_channel_factory):
channels = list()
for index in range(2):
channel = ChannelI()
lchannel = LogicalChannelI()
lchannel.name = rstring('a channel %d' % index)
channel.logicalChannel = lchannel
channels.append(channel)
return image_channel_factory(channels)
def emissionWave_channel(image_channel_factory):
channels = list()
emission_waves = (LengthI(123.0, 'NANOMETER'), LengthI(456.0, 'NANOMETER'))
for emission_wave in emission_waves:
channel = ChannelI()
lchannel = LogicalChannelI()
lchannel.emissionWave = emission_wave
channel.logicalChannel = lchannel
channels.append(channel)
return image_channel_factory(channels)
def emissionWave_channel(image_channel_factory):
channels = list()
emission_waves = (LengthI(123.0, 'NANOMETER'), LengthI(456.0, 'NANOMETER'))
for emission_wave in emission_waves:
channel = ChannelI()
lchannel = LogicalChannelI()
lchannel.emissionWave = emission_wave
channel.logicalChannel = lchannel
channels.append(channel)
return image_channel_factory(channels)
def decode(self, data):
v = super(Channel201501Decoder, self).decode(data)
self.set_property(v, 'alpha', data.get('Alpha'))
self.set_property(v, 'blue', data.get('Blue'))
self.set_property(v, 'green', data.get('Green'))
self.set_property(v, 'red', data.get('Red'))
self.set_property(v, 'lookupTable', data.get('omero:lookupTable'))
logical_channel = LogicalChannelI(data.get('omero:LogicalChannelId'))
logical_channel.emissionWave = \
self.to_unit(data.get('EmissionWavelength'))
logical_channel.excitationWave = \
self.to_unit(data.get('ExcitationWavelength'))
self.set_property(logical_channel, 'fluor', data.get('Fluor'))
self.set_property(logical_channel, 'name', data.get('Name'))
self.set_property(logical_channel, 'ndFilter', data.get('NDFilter'))
logical_channel.pinHoleSize = self.to_unit(data.get('PinholeSize'))
self.set_property(
logical_channel, 'pockelCellSetting', data.get('PockelCellSetting')
)
self.set_property(
logical_channel, 'samplesPerPixel', data.get('SamplesPerPixel')
)
contrast_method = data.get('ContrastMethod')
if contrast_method is not None:
contrast_method_decoder = self.ctx.get_decoder(
contrast_method['@type']
)
logical_channel.contrastMethod = contrast_method_decoder.decode(
contrast_method
)
illumination = data.get('Illumination')
if illumination is not None:
illumination_decoder = self.ctx.get_decoder(
illumination['@type']
)
logical_channel.illumination = illumination_decoder.decode(
illumination
)
acquisition_mode = data.get('AcquisitionMode')
if acquisition_mode is not None:
acquisition_mode_decoder = self.ctx.get_decoder(
acquisition_mode['@type']
)
logical_channel.mode = acquisition_mode_decoder.decode(
acquisition_mode
)
photometric_interpretation = \
data.get('omero:photometricInterpretation')
if photometric_interpretation is not None:
photometric_interpretation_decoder = self.ctx.get_decoder(
photometric_interpretation['@type']
)
logical_channel.photometricInterpretation = \
photometric_interpretation_decoder.decode(
photometric_interpretation
)
v.logicalChannel = logical_channel
return v
def decode(self, data):
v = super(Channel201501Decoder, self).decode(data)
self.set_property(v, 'alpha', data.get('Alpha'))
self.set_property(v, 'blue', data.get('Blue'))
self.set_property(v, 'green', data.get('Green'))
self.set_property(v, 'red', data.get('Red'))
self.set_property(v, 'lookupTable', data.get('omero:lookupTable'))
logical_channel = LogicalChannelI(data.get('omero:LogicalChannelId'))
logical_channel.emissionWave = \
self.to_unit(data.get('EmissionWavelength'))
logical_channel.excitationWave = \
self.to_unit(data.get('ExcitationWavelength'))
self.set_property(logical_channel, 'fluor', data.get('Fluor'))
self.set_property(logical_channel, 'name', data.get('Name'))
self.set_property(logical_channel, 'ndFilter', data.get('NDFilter'))
logical_channel.pinHoleSize = self.to_unit(data.get('PinholeSize'))
self.set_property(
logical_channel, 'pockelCellSetting', data.get('PockelCellSetting')
)
self.set_property(
logical_channel, 'samplesPerPixel', data.get('SamplesPerPixel')
)
contrast_method = data.get('ContrastMethod')
if contrast_method is not None:
contrast_method_decoder = self.ctx.get_decoder(
contrast_method['@type']
)
logical_channel.contrastMethod = contrast_method_decoder.decode(
contrast_method
)
illumination = data.get('Illumination')
if illumination is not None:
illumination_decoder = self.ctx.get_decoder(
illumination['@type']
)
logical_channel.illumination = illumination_decoder.decode(
illumination
)
acquisition_mode = data.get('AcquisitionMode')
if acquisition_mode is not None:
acquisition_mode_decoder = self.ctx.get_decoder(
acquisition_mode['@type']
)
logical_channel.mode = acquisition_mode_decoder.decode(
acquisition_mode
)
photometric_interpretation = \
data.get('omero:photometricInterpretation')
if photometric_interpretation is not None:
photometric_interpretation_decoder = self.ctx.get_decoder(
photometric_interpretation['@type']
)
logical_channel.photometricInterpretation = \
photometric_interpretation_decoder.decode(
photometric_interpretation
)
v.logicalChannel = logical_channel
return v
def unlabeled_channel(image_channel_factory):
channels = list()
for index in range(2):
channel = ChannelI()
lchannel = LogicalChannelI()
channel.logicalChannel = lchannel
channels.append(channel)
return image_channel_factory(channels)
def create_image(image_id, with_pixels=False):
image_format = FormatI(1L)
image_format.value = rstring("PNG")
image = ImageI()
image.id = rlong(image_id)
image.acquisitionDate = rtime(1L)
image.archived = rbool(False)
image.description = rstring("image_description_%d" % image_id)
image.name = rstring("image_name_%d" % image_id)
image.partial = rbool(False)
image.series = rint(0)
image.format = image_format
if not with_pixels:
return image
dimension_order = DimensionOrderI(1L)
dimension_order.value = rstring("XYZCT")
pixels_type = PixelsTypeI(1L)
pixels_type.value = "bit"
pixels = PixelsI(1L)
pixels.methodology = rstring("methodology")
pixels.physicalSizeX = LengthI(1.0, UnitsLength.MICROMETER)
pixels.physicalSizeY = LengthI(2.0, UnitsLength.MICROMETER)
pixels.physicalSizeZ = LengthI(3.0, UnitsLength.MICROMETER)
pixels.sha1 = rstring("61ee8b5601a84d5154387578466c8998848ba089")
pixels.significantBits = rint(16)
pixels.sizeX = rint(1)
pixels.sizeY = rint(2)
pixels.sizeZ = rint(3)
pixels.sizeC = rint(4)
pixels.sizeT = rint(5)
pixels.timeIncrement = TimeI(1.0, UnitsTime.MILLISECOND)
pixels.waveIncrement = rdouble(2.0)
pixels.waveStart = rint(1)
pixels.dimensionOrder = dimension_order
pixels.pixelsType = pixels_type
image.addPixels(pixels)
contrast_method = ContrastMethodI(8L)
contrast_method.value = rstring("Fluorescence")
illumination = IlluminationI(1L)
illumination.value = rstring("Transmitted")
acquisition_mode = AcquisitionModeI(1L)
acquisition_mode.value = rstring("WideField")
photometric_interpretation = PhotometricInterpretationI(1L)
photometric_interpretation.value = rstring("RGB")
channel_1 = ChannelI(1L)
channel_1.alpha = rint(255)
channel_1.blue = rint(0)
channel_1.green = rint(255)
channel_1.red = rint(0)
channel_1.lookupTable = rstring("rainbow")
logical_channel_1 = LogicalChannelI(1L)
logical_channel_1.emissionWave = LengthI(509.0, UnitsLength.NANOMETER)
logical_channel_1.excitationWave = LengthI(488.0, UnitsLength.NANOMETER)
logical_channel_1.fluor = rstring("GFP")
logical_channel_1.name = rstring("GFP/488")
logical_channel_1.ndFilter = rdouble(1.0)
logical_channel_1.pinHoleSize = LengthI(1.0, UnitsLength.NANOMETER)
logical_channel_1.pockelCellSetting = rint(0)
logical_channel_1.samplesPerPixel = rint(2)
logical_channel_1.contrastMethod = contrast_method
logical_channel_1.illumination = illumination
logical_channel_1.mode = acquisition_mode
logical_channel_1.photometricInterpretation = photometric_interpretation
channel_1.logicalChannel = logical_channel_1
channel_2 = ChannelI(2L)
channel_2.alpha = rint(255)
channel_2.blue = rint(255)
channel_2.green = rint(0)
channel_2.red = rint(0)
channel_2.lookupTable = rstring("rainbow")
logical_channel_2 = LogicalChannelI(2L)
logical_channel_2.emissionWave = LengthI(470.0, UnitsLength.NANOMETER)
logical_channel_2.excitationWave = LengthI(405.0, UnitsLength.NANOMETER)
logical_channel_2.fluor = rstring("DAPI")
logical_channel_2.name = rstring("DAPI/405")
logical_channel_2.ndFilter = rdouble(1.0)
logical_channel_2.pinHoleSize = LengthI(2.0, UnitsLength.NANOMETER)
logical_channel_2.pockelCellSetting = rint(0)
logical_channel_2.samplesPerPixel = rint(2)
logical_channel_2.contrastMethod = contrast_method
logical_channel_2.illumination = illumination
logical_channel_2.mode = acquisition_mode
logical_channel_2.photometricInterpretation = photometric_interpretation
channel_2.logicalChannel = logical_channel_2
pixels.addChannel(channel_1)
pixels.addChannel(channel_2)
return image
def test_logical_channel(self):
name = u'₩€_name_$$'
ill_val = u'πλζ.test.ζ'
fluor = u'GFP-₹₹'
binning_value = u'Φωλ'
ph_size = 1.11
ph_units = UnitsLength.MICROMETER
ex_wave = 3.34
ex_units = UnitsLength.ANGSTROM
version = 123
zoom = 100
gain = 1010.23
di_model = u'Model_ 123_àÅÉ'
obj = LogicalChannelI()
obj.name = rstring(name)
obj.pinHoleSize = LengthI(ph_size, ph_units)
illumination = IlluminationI()
illumination.value = rstring(ill_val)
obj.illumination = illumination
obj.excitationWave = LengthI(ex_wave, ex_units)
obj.setFluor(rstring(fluor))
ds = DetectorSettingsI()
ds.version = rint(version)
ds.gain = rdouble(gain)
ds.zoom = rdouble(zoom)
binning = BinningI()
binning.value = rstring(binning_value)
ds.binning = binning
obj.detectorSettings = ds
dichroic = DichroicI()
dichroic.model = rstring(di_model)
light_path = LightPathI()
light_path.dichroic = dichroic
obj.lightPath = light_path
class MockChannel(LogicalChannelWrapper):
def __loadedHotSwap__(self):
# Don't need to load data for getLightPath()
pass
channel = MockChannel(None, obj)
assert channel.getName() == name.encode('utf8')
assert channel.name == name
assert channel.getPinHoleSize().getValue() == ph_size
assert channel.getPinHoleSize().getUnit() == ph_units
assert channel.getPinHoleSize().getSymbol() == 'µm'
# Illumination is an enumeration
assert channel.getIllumination().getValue() == ill_val.encode('utf8')
assert channel.getExcitationWave().getValue() == ex_wave
assert channel.getExcitationWave().getUnit() == ex_units
assert channel.getExcitationWave().getSymbol() == 'Å'
assert channel.getFluor() == fluor
assert channel.fluor == fluor
d_settings = channel.getDetectorSettings()
assert d_settings.getVersion() == version
assert d_settings.version == version
assert d_settings.getGain() == gain
assert d_settings.gain == gain
assert d_settings.getZoom() == zoom
assert d_settings.getBinning().getValue() == binning_value
assert d_settings.getBinning().value == binning_value
assert channel.getLightPath().getDichroic().getModel() == di_model
def create_image(image_id, with_pixels=False):
image_format = FormatI(1)
image_format.value = rstring('PNG')
image = ImageI()
image.id = rlong(image_id)
image.acquisitionDate = rtime(1)
image.archived = rbool(False)
image.description = rstring('image_description_%d' % image_id)
image.name = rstring('image_name_%d' % image_id)
image.partial = rbool(False)
image.series = rint(0)
image.format = image_format
if not with_pixels:
return image
dimension_order = DimensionOrderI(1)
dimension_order.value = rstring('XYZCT')
pixels_type = PixelsTypeI(1)
pixels_type.value = 'bit'
pixels = PixelsI(1)
pixels.methodology = rstring('methodology')
pixels.physicalSizeX = LengthI(1.0, UnitsLength.MICROMETER)
pixels.physicalSizeY = LengthI(2.0, UnitsLength.MICROMETER)
pixels.physicalSizeZ = LengthI(3.0, UnitsLength.MICROMETER)
pixels.sha1 = rstring('61ee8b5601a84d5154387578466c8998848ba089')
pixels.significantBits = rint(16)
pixels.sizeX = rint(1)
pixels.sizeY = rint(2)
pixels.sizeZ = rint(3)
pixels.sizeC = rint(4)
pixels.sizeT = rint(5)
pixels.timeIncrement = TimeI(1.0, UnitsTime.MILLISECOND)
pixels.waveIncrement = rdouble(2.0)
pixels.waveStart = rint(1)
pixels.dimensionOrder = dimension_order
pixels.pixelsType = pixels_type
image.addPixels(pixels)
contrast_method = ContrastMethodI(8)
contrast_method.value = rstring('Fluorescence')
illumination = IlluminationI(1)
illumination.value = rstring('Transmitted')
acquisition_mode = AcquisitionModeI(1)
acquisition_mode.value = rstring('WideField')
photometric_interpretation = PhotometricInterpretationI(1)
photometric_interpretation.value = rstring('RGB')
channel_1 = ChannelI(1)
channel_1.alpha = rint(255)
channel_1.blue = rint(255)
channel_1.green = rint(255)
channel_1.red = rint(255)
channel_1.lookupTable = rstring('rainbow')
logical_channel_1 = LogicalChannelI(1)
logical_channel_1.emissionWave = LengthI(509.0, UnitsLength.NANOMETER)
logical_channel_1.excitationWave = LengthI(488.0, UnitsLength.NANOMETER)
logical_channel_1.fluor = rstring('GFP')
logical_channel_1.name = rstring('GFP/488')
logical_channel_1.ndFilter = rdouble(1.0)
logical_channel_1.pinHoleSize = LengthI(1.0, UnitsLength.NANOMETER)
logical_channel_1.pockelCellSetting = rint(0)
logical_channel_1.samplesPerPixel = rint(2)
logical_channel_1.contrastMethod = contrast_method
logical_channel_1.illumination = illumination
logical_channel_1.mode = acquisition_mode
logical_channel_1.photometricInterpretation = photometric_interpretation
channel_1.logicalChannel = logical_channel_1
channel_2 = ChannelI(2)
channel_2.alpha = rint(255)
channel_2.blue = rint(255)
channel_2.green = rint(0)
channel_2.red = rint(255)
channel_2.lookupTable = rstring('rainbow')
logical_channel_2 = LogicalChannelI(2)
logical_channel_2.emissionWave = LengthI(470.0, UnitsLength.NANOMETER)
logical_channel_2.excitationWave = LengthI(405.0, UnitsLength.NANOMETER)
logical_channel_2.fluor = rstring('DAPI')
logical_channel_2.name = rstring('DAPI/405')
logical_channel_2.ndFilter = rdouble(1.0)
logical_channel_2.pinHoleSize = LengthI(2.0, UnitsLength.NANOMETER)
logical_channel_2.pockelCellSetting = rint(0)
logical_channel_2.samplesPerPixel = rint(2)
logical_channel_2.contrastMethod = contrast_method
logical_channel_2.illumination = illumination
logical_channel_2.mode = acquisition_mode
logical_channel_2.photometricInterpretation = photometric_interpretation
channel_2.logicalChannel = logical_channel_2
pixels.addChannel(channel_1)
pixels.addChannel(channel_2)
return image
