def image_rois(self, user1, shapes):
"""Return Image with ROIs."""
image = ImageI()
image.name = rstring('Image for ROIs')
image = get_update_service(user1).saveAndReturnObject(image)
# ROI with all but one shapes
rois = []
roi = RoiI()
for shape in shapes[:-1]:
roi.addShape(shape)
roi.setImage(image)
rois.append(roi)
# roi without shapes
roi = RoiI()
roi.setImage(image)
rois.append(roi)
# roi without image
roi = RoiI()
roi.addShape(shapes[-1])
rois.append(roi)
rois = get_update_service(user1).saveAndReturnArray(rois)
rois.sort(key=lambda x: x.id.val)
return image, rois
def image_no_acquisition_date(request, gatewaywrapper):
"""Creates an Image."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
image = ImageI()
image.name = rstring('an image')
image.acquisitionDate = rtime(0L)
image_id, = update_service.saveAndReturnIds([image])
return gw.getObject('Image', image_id)
def image_no_acquisition_date(request, gatewaywrapper):
"""Creates an Image."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
image = ImageI()
image.name = rstring('an image')
image.acquisitionDate = rtime(0L)
image_id, = update_service.saveAndReturnIds([image])
return gw.getObject('Image', image_id)
def wrapped_image():
image = ImageI()
image.id = rlong(1L)
image.description = rstring('description')
image.name = rstring('name')
image.acquisitionDate = rtime(1000) # In milliseconds
image.details.owner = ExperimenterI(1L, False)
creation_event = EventI()
creation_event.time = rtime(2000) # In milliseconds
image.details.creationEvent = creation_event
return ImageWrapper(conn=MockConnection(), obj=image)
def wrapped_image():
image = ImageI()
image.id = rlong(1L)
image.description = rstring('description')
image.name = rstring('name')
image.acquisitionDate = rtime(1000) # In milliseconds
image.details.owner = ExperimenterI(1L, False)
creation_event = EventI()
creation_event.time = rtime(2000) # In milliseconds
image.details.creationEvent = creation_event
return ImageWrapper(conn=MockConnection(), obj=image)
def image(request, gatewaywrapper):
"""Creates an Image."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
image = ImageI()
image.name = rstring('an image')
# 2015-04-21 01:15:00
image.acquisitionDate = rtime(int(1429578900000))
image_id, = update_service.saveAndReturnIds([image])
return gw.getObject('Image', image_id)
def testListOrphans(self, orphaned, load_pixels, gatewaywrapper):
# We login as 'User', since they have no other orphaned images
gatewaywrapper.loginAsUser()
conn = gatewaywrapper.gateway
eid = conn.getUserId()
# Create 5 orphaned images
iids = []
for i in range(0, 5):
img = gatewaywrapper.createTestImage(imageName=str(uuid.uuid1()))
iids.append(img.id)
# Create image in Dataset, to check this isn't found
dataset = DatasetI()
dataset.name = wrap('testListOrphans')
image = ImageI()
image.name = wrap('testListOrphans')
dataset.linkImage(image)
dataset = conn.getUpdateService().saveAndReturnObject(dataset)
try:
# Only test listOrphans() if orphaned
if orphaned:
# Pagination
params = omero.sys.ParametersI()
params.page(1, 3)
findImagesInPage = list(
conn.listOrphans("Image", eid=eid, params=params))
assert len(findImagesInPage) == 3
# No pagination (all orphans)
findImages = list(
conn.listOrphans("Image", loadPixels=load_pixels))
assert len(findImages) == 5
for p in findImages:
assert p._obj.pixelsLoaded == load_pixels
# Test getObjects() with 'orphaned' option
opts = {'orphaned': orphaned, 'load_pixels': load_pixels}
getImages = list(conn.getObjects("Image", opts=opts))
assert orphaned == (len(getImages) == 5)
for p in getImages:
assert p._obj.pixelsLoaded == load_pixels
# Simply check this doesn't fail See https://github.com/
# openmicroscopy/openmicroscopy/pull/4950#issuecomment-264142956
dsIds = [d.id for d in conn.listOrphans("Dataset")]
assert dataset.id.val in dsIds
finally:
# Cleanup - Delete what we created
conn.deleteObjects('Image', iids, deleteAnns=True, wait=True)
conn.deleteObjects('Dataset', [dataset.id.val],
deleteChildren=True,
wait=True)
def create_image(image_index):
image = ImageI()
image.name = rstring("%s_%d" % (uuid(), image_index))
image.acquisitionDate = rtime(0)
pixels = PixelsI()
pixels.sha1 = rstring("")
pixels.sizeX = rint(1)
pixels.sizeY = rint(1)
pixels.sizeZ = rint(1)
pixels.sizeC = rint(1)
pixels.sizeT = rint(1)
pixels.dimensionOrder = DimensionOrderI(1L, False) # XYZCT
pixels.pixelsType = PixelsTypeI(1L, False) # bit
image.addPixels(pixels)
return image
def create_image(image_index):
image = ImageI()
image.name = rstring('%s_%d' % (uuid(), image_index))
image.acquisitionDate = rtime(0)
pixels = PixelsI()
pixels.sha1 = rstring('')
pixels.sizeX = rint(1)
pixels.sizeY = rint(1)
pixels.sizeZ = rint(1)
pixels.sizeC = rint(1)
pixels.sizeT = rint(1)
pixels.dimensionOrder = DimensionOrderI(1L, False) # XYZCT
pixels.pixelsType = PixelsTypeI(1L, False) # bit
image.addPixels(pixels)
return image
def plate(request, gatewaywrapper):
"""Creates a Plate."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
plate = PlateI()
plate.name = rstring(uuid())
for well_index in range(3):
well = WellI()
well.row = rint(well_index**2)
well.column = rint(well_index**3)
for well_sample_index in range(2):
well_sample = WellSampleI()
image = ImageI()
image.name = rstring('%s_%d' % (uuid(), well_sample_index))
image.acquisitionDate = rtime(0)
well_sample.image = image
well.addWellSample(well_sample)
plate.addWell(well)
plate_id, = update_service.saveAndReturnIds([plate])
return gw.getObject('Plate', plate_id)
def plate(request, gatewaywrapper):
"""Creates a Plate."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
plate = PlateI()
plate.name = rstring(uuid())
for well_index in range(3):
well = WellI()
well.row = rint(well_index**2)
well.column = rint(well_index**3)
for well_sample_index in range(2):
well_sample = WellSampleI()
image = ImageI()
image.name = rstring('%s_%d' % (uuid(), well_sample_index))
image.acquisitionDate = rtime(0)
well_sample.image = image
well.addWellSample(well_sample)
plate.addWell(well)
plate_id, = update_service.saveAndReturnIds([plate])
return gw.getObject('Plate', plate_id)
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 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
