def setStrokeSettings(self, colour, width=1):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.strokeColour = rint(colour)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(width)
self.strokeWidth.setUnit(UnitsLength.POINT)
def populate_shape(o, set_unit_attributes=True):
o.fillColor = rint(0xffffffff)
o.fillRule = rstring('solid')
o.fontFamily = rstring('cursive')
if set_unit_attributes:
o.fontSize = LengthI(12, UnitsLength.POINT)
o.fontStyle = rstring('italic')
o.locked = rbool(False)
o.strokeColor = rint(0xffff0000)
o.strokeDashArray = rstring('inherit')
if SCHEMA_VERSION == '2015-01':
o.visibility = rbool(True)
o.strokeLineCap = rstring('round')
if set_unit_attributes:
o.strokeWidth = LengthI(4, UnitsLength.PIXEL)
o.textValue = rstring('the_text')
o.theC = rint(1)
o.theT = rint(2)
o.theZ = rint(3)
t = identity_transform()
if SCHEMA_VERSION == '2015-01':
o.transform = t.svg_transform
else:
o.transform = t
return o
def make_well_sample(x_pos=None, y_pos=None):
ws = WellSampleI()
image = itest.new_image(name=itest.uuid())
ws.image = image
if x_pos is not None:
ws.posX = LengthI(x_pos, UnitsLength.REFERENCEFRAME)
if y_pos is not None:
ws.posY = LengthI(y_pos, UnitsLength.REFERENCEFRAME)
return ws
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 screen_with_plates(screen):
for plate_id in range(5, 7):
o = PlateI()
o.id = rlong(plate_id)
o.name = rstring('plate_name_%d' % plate_id)
o.description = rstring('plate_description_%d' % plate_id)
o.columnNamingConvention = rstring('number')
o.rowNamingConvention = rstring('letter')
o.columns = rint(12)
o.rows = rint(8)
o.defaultSample = rint(0)
o.externalIdentifier = rstring('external_identifier_%d' % plate_id)
o.status = rstring('status_%d' % plate_id)
o.wellOriginX = LengthI(0.1, UnitsLength.REFERENCEFRAME)
o.wellOriginY = LengthI(1.1, UnitsLength.REFERENCEFRAME)
screen.linkPlate(o)
for well_id in range(7, 9):
well = WellI()
well.id = rlong(well_id)
well.column = rint(2)
well.row = rint(1)
well.externalDescription = \
rstring('external_description_%d' % well_id)
well.externalIdentifier = \
rstring('external_identifier_%d' % well_id)
well.type = rstring('the_type')
well.alpha = rint(0)
well.red = rint(255)
well.green = rint(0)
well.blue = rint(0)
well.status = rstring('the_status')
o.addWell(well)
plateacquisition = PlateAcquisitionI()
plateacquisition.id = rlong(well_id)
plateacquisition.name = rstring(
'plateacquisition_name_%d' % well_id)
plateacquisition.description = rstring(
'plateacquisition_description_%d' % well_id)
plateacquisition.maximumFieldCount = rint(1)
plateacquisition.startTime = rtime(1L)
plateacquisition.endTime = rtime(2L)
for wellsample_id in range(9, 11):
wellsample = WellSampleI()
wellsample.setPlateAcquisition(plateacquisition)
wellsample.id = rlong(wellsample_id)
wellsample.posX = LengthI(1.0, UnitsLength.REFERENCEFRAME)
wellsample.posY = LengthI(2.0, UnitsLength.REFERENCEFRAME)
wellsample.timepoint = rtime(1L)
wellsample.image = create_image(1L)
well.addWellSample(wellsample)
return screen
def addRoi(self, request, imageid):
img = self.getImage0(imageid)
if img is None:
return None
data = json.loads(request.body)
shapes = data['shapes']
x = y = l = z = t = -1
for s in shapes:
for k in s:
val = s[k]
if k == "x":
x = int(val)
elif k == "y":
y = int(val)
elif k == "width":
l = int(val)
elif k == "theZ":
z = int(val)
elif k == "theT":
t = int(val)
elif k == "fillColorAsInt":
fill = int(val)
elif k == "strokeColorAsInt":
stroke = int(val)
elif k == "strokeWidth":
strokeWidth = int(val)
if (x < 0 or y < 0 or z < 0 or t < 0 or l <= 0):
return None
updateService = self._connection.getUpdateService()
roi = RoiI()
roi.setImage(img._obj)
rect = RectangleI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(l)
rect.height = rdouble(l)
rect.theZ = rint(z)
rect.theT = rint(t)
rect.setFillColor(rint(fill))
strokeLen = LengthI()
strokeLen.setValue(strokeWidth)
strokeLen.setUnit(UnitsLength.PIXEL)
rect.setStrokeWidth(strokeLen)
rect.setStrokeColor(rint(stroke))
roi.addShape(rect)
if (updateService.saveAndReturnObject(roi) is None):
return None
return self.get_rois(imageid)
def __init__(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.WHITE = 16777215
self.BLACK = 0
self.GREY = 11184810
self.strokeColour = rint(self.GREY)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(1)
self.strokeWidth.setUnit(UnitsLength.POINT)
self.strokeDashArray = rstring('')
self.fillColour = rint(self.GREY)
self.fillRule = rstring('')
def create_plate_wells(self, user1, rows, cols, plateacquisitions=1):
"""Return Plate with Wells."""
updateService = get_update_service(user1)
plate = PlateI()
plate.name = rstring('plate')
plate = updateService.saveAndReturnObject(plate)
# PlateAcquisitions for plate
plate_acqs = []
for p in range(plateacquisitions):
plate_acq = PlateAcquisitionI()
plate_acq.name = rstring('plateacquisition_%s' % p)
plate_acq.description = rstring('plateacquisition_description')
plate_acq.maximumFieldCount = rint(3)
plate_acq.startTime = rtime(1)
plate_acq.endTime = rtime(2)
plate_acq.plate = PlateI(plate.id.val, False)
plate_acq = updateService.saveAndReturnObject(plate_acq)
plate_acqs.append(plate_acq)
# Create Wells for plate
ref_frame = UnitsLength.REFERENCEFRAME
for row in range(rows):
for col in range(cols):
# create Well
well = WellI()
well.column = rint(col)
well.row = rint(row)
well.plate = PlateI(plate.id.val, False)
# Only wells in first Column have well-samples etc.
if col == 0:
# Have 3 images/well-samples per plateacquisition
# (if no plateacquisitions, create 3 well-samples without)
for p in range(max(1, plateacquisitions)):
for i in range(3):
image = self.create_test_image(
size_x=5, size_y=5,
session=user1[0].getSession())
ws = WellSampleI()
ws.image = ImageI(image.id, False)
ws.well = well
ws.posX = LengthI(i * 10, ref_frame)
ws.posY = LengthI(i, ref_frame)
if p < len(plate_acqs):
ws.setPlateAcquisition(
PlateAcquisitionI(plate_acqs[p].id.val,
False))
well.addWellSample(ws)
updateService.saveObject(well)
return plate
def __init__(self):
self.WHITE = 16777215
self.BLACK = 0
self.GREY = 11184810
self.strokeColour = rint(self.GREY)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(1)
self.strokeWidth.setUnit(UnitsLength.POINT)
self.strokeDashArray = rstring('')
self.strokeDashOffset = rint(0)
self.strokeLineCap = rstring('')
self.strokeLineJoin = rstring('')
self.strokeMiterLimit = rint(0)
self.fillColour = rint(self.GREY)
self.fillRule = rstring('')
def populate_shape(o):
o.fillColor = rint(0xffffffff)
o.fillRule = rstring('solid')
o.fontFamily = rstring('cursive')
o.fontSize = LengthI(12, UnitsLength.POINT)
o.fontStyle = rstring('italic')
o.locked = rbool(False)
o.strokeColor = rint(0xffff0000)
o.strokeDashArray = rstring('inherit')
o.strokeLineCap = rstring('round')
o.strokeWidth = LengthI(4, UnitsLength.PIXEL)
o.textValue = rstring('the_text')
o.theC = rint(1)
o.theT = rint(2)
o.theZ = rint(3)
o.visibility = rbool(True)
return o
def _set_shape_properties(shape, name=None,
fill_color=(10, 10, 10, 255),
stroke_color=(255, 255, 255, 255),
stroke_width=1, ):
if name:
shape.setTextValue(rtypes.rstring(name))
shape.setFillColor(rtypes.rint(_rgba_to_int(*fill_color)))
shape.setStrokeColor(rtypes.rint(_rgba_to_int(*stroke_color)))
shape.setStrokeWidth(LengthI(stroke_width, enums.UnitsLength.PIXEL))
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
# Only save theT, not theZ
rect.theT = rint(0)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
# ellipse without saving theZ & theT
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(200)
line.x2 = rdouble(300)
line.y1 = rdouble(400)
line.y2 = rdouble(500)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(1)
point.y = rdouble(1)
point.theZ = rint(1)
point.theT = rint(1)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.theZ = rint(5)
polygon.theT = rint(5)
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 200,200, 250,75"
polygon.points = rstring(points)
mask = MaskI()
mask.setTheC(rint(0))
mask.setTheZ(rint(0))
mask.setTheT(rint(0))
mask.setX(rdouble(100))
mask.setY(rdouble(100))
mask.setWidth(rdouble(500))
mask.setHeight(rdouble(500))
mask.setTextValue(rstring("test-Mask"))
mask.setBytes(None)
return [rect, ellipse, line, point, polygon, mask]
def run_processing(conn, script_params):
message = ""
image_ids = script_params['IDs']
for image in conn.getObjects("Image", image_ids):
if not image:
message = 'Could not find specified image'
return message
print 'size z:', image.getSizeZ()
physical_z = None
if (image.getSizeZ() > 1.0):
try:
physical_z = script_params['Z_Pixel_Size']
except:
message = 'Looks like you have a z-stack - you should set a non-zero value for Z_Pixel_Size'
return message
physical_x = script_params['X_Pixel_Size']
physical_y = script_params['Y_Pixel_Size']
if (physical_x == 0.0) or (physical_y == 0.0):
message = 'You should set a non-zero pixel size for both X and Y'
return message
# Get the BlitzGateway wrapped pixels and unwrap it
pixelsWrapper = image.getPrimaryPixels()
pixels = pixelsWrapper._obj
# Update and save
print "units", UnitsLength
lx = LengthI(physical_x, UnitsLength.MICROMETER)
ly = LengthI(physical_y, UnitsLength.MICROMETER)
pixels.setPhysicalSizeX(lx)
pixels.setPhysicalSizeY(ly)
if physical_z:
lz = LengthI(physical_z, UnitsLength.MICROMETER)
pixels.setPhysicalSizeZ(lz)
conn.getUpdateService().saveObject(pixels)
message += 'Successfully set pixel size on image %s' % image.getName()
return message
def addRoi(self, request, imageid):
img = self.getImage0(imageid)
if img is None:
return None
data = json.loads(request.body)
shapes = data['shapes']
x = y = l = z = t = -1
for s in shapes:
for k in s:
val = s[k]
if k == "x":
x = int(val)
elif k == "y":
y = int(val)
elif k == "width":
l = int(val)
elif k == "theZ":
z = int(val)
elif k == "theT":
t = int(val)
elif k == "fillColorAsInt":
fill = int(val)
elif k == "strokeColorAsInt":
stroke = int(val)
elif k == "strokeWidth":
strokeWidth = int(val)
if (x < 0 or y < 0 or z < 0 or t < 0 or l <= 0):
return None
updateService = self._connection.getUpdateService()
roi = RoiI()
roi.setImage(img._obj)
rect = RectangleI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(l)
rect.height = rdouble(l)
rect.theZ = rint(z)
rect.theT = rint(t)
rect.setFillColor(rint(fill))
strokeLen = LengthI()
strokeLen.setValue(strokeWidth)
strokeLen.setUnit(UnitsLength.PIXEL)
rect.setStrokeWidth(strokeLen)
rect.setStrokeColor(rint(stroke))
roi.addShape(rect)
if (updateService.saveAndReturnObject(roi) is None):
return None
return self.get_rois(imageid)
def get_length_units():
# Create a dict we can use for scalebar unit conversions
unit_symbols = {}
for name in LengthI.SYMBOLS.keys():
if name in ("PIXEL", "REFERENCEFRAME"):
continue
klass = getattr(UnitsLength, name)
unit = LengthI(1, klass)
to_microns = LengthI(unit, UnitsLength.MICROMETER)
unit_symbols[name] = {
'symbol': unit.getSymbol(),
'microns': to_microns.getValue()
}
return unit_symbols
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(20)
line.x2 = rdouble(30)
line.y1 = rdouble(40)
line.y2 = rdouble(50)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(50)
point.y = rdouble(50)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 100,100, 150,75"
polygon.points = rstring(points)
polyline = PolylineI()
polyline.points = rstring(points)
return [rect, ellipse, line, point, polygon, polyline]
def process_data(conn,image,file_type,ann_id,locs,nm_per_pixel,sr_pix_size,starts,stops,sizeT):
"""
Run the processing and upload the resultant image
@param conn: Blitzgateway connection
@param image: we need to get the image where the localisation data is attached --> this should be the raw timelapse data
@param file_type: the type of dataset we are dealing with (see FILE_TYPES global)
@param ann_id: the annotation id of the localisations file
@param coords: the coords being histogrammed
@param nm_per_pixel: the size of the pixel in the original image in nm (1 for Zeiss data which is already in nm)
@param sr_pix_size: the pixel size we want in the new image in nm
@param frames: the column in the dataset where we will find the first frame assignment
@param starts: a list of starting indices for the time-lapse
@param stops: a list of stopping indices for the time-lapse
@param sizeT: the number of frames in the time-lapse
"""
#set parameters
imageName = image.getName()
name,ext = os.path.splitext(imageName)
if 'ome' in name:
name = name.split('.')[0]
new_name = name + '_sr_timelapse_histogram.ome' + ext
else:
new_name = name + '_sr_timelapse_histogram' + ext
parentDataset = image.getParent()
parentProject = parentDataset.getParent()
updateService = conn.getUpdateService()
frame_width = image.getSizeX()
frame_height = image.getSizeY()
frame = file_type['frame']
print 'frame',frame
sizeZ = 1
if 'zeiss2chan2D' in file_type:
sizeC = 2
else:
sizeC = 1
#calculate histogram
rangex = frame_width * nm_per_pixel
binsx = rangex / sr_pix_size
rangey = frame_height * nm_per_pixel
binsy = rangey / sr_pix_size
hist_frames = []
for c in range(sizeC):
locs_df = locs[c]
for t in range(sizeT):
coords_in_frames = locs_df[(locs_df['time'] >= starts[t]) & (locs_df['time']<= stops[t])]
hist = calc_hist(coords_in_frames,file_type,binsy,binsx,rangey,rangex)
hist_frames.append(hist)
def plane_gen():
for z in range(sizeZ):
for c in range(sizeC):
for t in range(sizeT):
plane = hist_frames[t]
yield plane
description = "Created from image:\n Name: %s\n Annotation ID: %d\n Frame indices:\n Start:%s\n Stop:%s"\
% (imageName, ann_id, str(starts), str(stops))
newImg = conn.createImageFromNumpySeq(
plane_gen(), new_name,
sizeZ=sizeZ, sizeC=sizeC, sizeT=sizeT,
description=description)
# reload the image (also reloads pixels)
image = conn.getObject("Image", newImg.getId())
# Get the BlitzGateway wrapped pixels and unwrap it
pixelsWrapper = image.getPrimaryPixels()
pixels = pixelsWrapper._obj
# Update and save
pixSize = LengthI(float(sr_pix_size) / 1000, UnitsLength.MICROMETER)
pixels.setPhysicalSizeX( pixSize )
pixels.setPhysicalSizeY( pixSize )
updateService.saveObject(pixels)
if newImg:
iid = newImg.getId()
print "New Image Id = %s" % iid
# put new images in existing dataset
dataset = None
if parentDataset is not None and parentDataset.canLink():
parentDataset = parentDataset._obj
else:
parentDataset = None
parentProject = None # don't add Dataset to parent.
if parentDataset is None:
link = None
print "No dataset created or found for new images."\
" Images will be orphans."
else:
dsLink = omero.model.DatasetImageLinkI()
dsLink.parent = omero.model.DatasetI(
parentDataset.id.val, False)
dsLink.child = omero.model.ImageI(iid, False)
updateService.saveObject(dsLink)
if parentProject and parentProject.canLink():
# and put it in the current project
projectLink = omero.model.ProjectDatasetLinkI()
projectLink.parent = omero.model.ProjectI(
parentProject.getId(), False)
projectLink.child = omero.model.DatasetI(
dataset.id.val, False)
updateService.saveAndReturnObject(projectLink)
message = 'Super resolution histogram successfully created'
else:
message = 'Something went wrong, could not make super resolution histogram'
return message
def setStrokeSettings(self, colour, width=1):
self.strokeColour = rint(colour)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(width)
self.strokeWidth.setUnit(UnitsLength.POINT)
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(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
class ShapeSettingsData(object):
##
# Initialises the default values of the ShapeSettings.
# Stroke has default colour of darkGrey
# StrokeWidth defaults to 1
#
def __init__(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.WHITE = 16777215
self.BLACK = 0
self.GREY = 11184810
self.strokeColour = rint(self.GREY)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(1)
self.strokeWidth.setUnit(UnitsLength.POINT)
self.strokeDashArray = rstring('')
self.fillColour = rint(self.GREY)
self.fillRule = rstring('')
##
# Applies the settings in the ShapeSettingsData to the ROITypeI
# @param shape the omero.model.ROITypeI that these settings will
# be applied to
#
def setROIShapeSettings(self, shape):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
shape.setStrokeColor(self.strokeColour)
shape.setStrokeWidth(self.strokeWidth)
shape.setStrokeDashArray(self.strokeDashArray)
shape.setFillColor(self.fillColour)
shape.setFillRule(self.fillRule)
##
# Set the Stroke settings of the ShapeSettings.
# @param colour The colour of the stroke.
# @param width The stroke width.
#
def setStrokeSettings(self, colour, width=1):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.strokeColour = rint(colour)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(width)
self.strokeWidth.setUnit(UnitsLength.POINT)
###
# Set the Fill Settings for the ShapeSettings.
# @param colour The fill colour of the shape.
def setFillSettings(self, colour):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.fillColour = rstring(colour)
##
# Get the stroke settings as the tuple (strokeColour, strokeWidth).
# @return See above.
#
def getStrokeSettings(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
return (self.strokeColour.getValue(), self.strokeWidth.getValue())
##
# Get the fill setting as a tuple of (fillColour)
# @return See above.
#
def getFillSettings(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
return (self.fillColour.getValue())
##
# Get the tuple ((stokeColor, strokeWidth), (fillColour)).
# @return see above.
#
def getSettings(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
return (self.getStrokeSettings(), self.getFillSettings())
##
# Set the current shapeSettings from the ROI roi.
# @param roi see above.
#
def getShapeSettingsFromROI(self, roi):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.strokeColour = roi.getStrokeColor()
self.strokeWidth = roi.getStrokeWidth()
self.strokeDashArray = roi.getStrokeDashArray()
self.fillColour = roi.getFillColor()
self.fillRule = roi.getFillRule()
class ShapeSettingsData:
##
# Initialises the default values of the ShapeSettings.
# Stroke has default colour of darkGrey
# StrokeWidth defaults to 1
#
def __init__(self):
self.WHITE = 16777215
self.BLACK = 0
self.GREY = 11184810
self.strokeColour = rint(self.GREY)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(1)
self.strokeWidth.setUnit(UnitsLength.POINT)
self.strokeDashArray = rstring('')
self.strokeDashOffset = rint(0)
self.strokeLineCap = rstring('')
self.strokeLineJoin = rstring('')
self.strokeMiterLimit = rint(0)
self.fillColour = rint(self.GREY)
self.fillRule = rstring('')
##
# Applies the settings in the ShapeSettingsData to the ROITypeI
# @param shape the omero.model.ROITypeI that these settings will
# be applied to
#
def setROIShapeSettings(self, shape):
shape.setStrokeColor(self.strokeColour)
shape.setStrokeWidth(self.strokeWidth)
shape.setStrokeDashArray(self.strokeDashArray)
shape.setStrokeDashOffset(self.strokeDashOffset)
shape.setStrokeLineCap(self.strokeLineCap)
shape.setStrokeLineJoin(self.strokeLineJoin)
shape.setStrokeMiterLimit(self.strokeMiterLimit)
shape.setFillColor(self.fillColour)
shape.setFillRule(self.fillRule)
##
# Set the Stroke settings of the ShapeSettings.
# @param colour The colour of the stroke.
# @param width The stroke width.
#
def setStrokeSettings(self, colour, width=1):
self.strokeColour = rint(colour)
self.strokeWidth = LengthI()
self.strokeWidth.setValue(width)
self.strokeWidth.setUnit(UnitsLength.POINT)
###
# Set the Fill Settings for the ShapeSettings.
# @param colour The fill colour of the shape.
def setFillSettings(self, colour):
self.fillColour = rstring(colour)
##
# Get the stroke settings as the tuple (strokeColour, strokeWidth).
# @return See above.
#
def getStrokeSettings(self):
return (self.strokeColour.getValue(), self.strokeWidth.getValue())
##
# Get the fill setting as a tuple of (fillColour)
# @return See above.
#
def getFillSettings(self):
return (self.fillColour.getValue())
##
# Get the tuple ((stokeColor, strokeWidth), (fillColour)).
# @return see above.
#
def getSettings(self):
return (self.getStrokeSettings(), self.getFillSettings())
##
# Set the current shapeSettings from the ROI roi.
# @param roi see above.
#
def getShapeSettingsFromROI(self, roi):
self.strokeColour = roi.getStrokeColor()
self.strokeWidth = roi.getStrokeWidth()
self.strokeDashArray = roi.getStrokeDashArray()
self.strokeDashOffset = roi.getStrokeDashOffset()
self.strokeLineCap = roi.getStrokeLineCap()
self.strokeLineJoin = roi.getStrokeLineJoin()
self.strokeMiterLimit = roi.getStrokeMiterLimit()
self.fillColour = roi.getFillColor()
self.fillRule = roi.getFillRule()
def process_data(conn, image, file_type, file_id, locs, sr_pix_size,
srz_pix_size, z_range, nm_per_pixel):
"""
Run the processing and upload the resultant image
@param conn: Blitzgateway connection
@param image: we need to get the image where the localisation data is attached --> this should be the raw timelapse data
@param file_type: the type of dataset we are dealing with (see FILE_TYPES global)
@param file_id: the annotation id of the localisations file
@param coords: the coords being histogrammed
@param sr_pix_size: the pixel size we want in the new image in nm
@param z_range: z range covered in one z-plane (4um for Zeiss 3D)
@param nm_per_pixel: the size of the pixel in the original image in nm (1 for Zeiss data which is already in nm)
"""
imageName = image.getName()
name, ext = os.path.splitext(imageName)
if 'ome' in name:
name = name.split('.')[0]
new_name = name + '_sr_histogram.ome' + ext
sizeZ = image.getSizeT()
else:
new_name = name + '_sr_histogram' + ext
sizeZ = image.getSizeZ()
parentDataset = image.getParent()
parentProject = parentDataset.getParent()
updateService = conn.getUpdateService()
frame_width = image.getSizeX()
print 'frame_width', frame_width
frame_height = image.getSizeY()
print 'frame_height', frame_height
stepZ = nm_per_pixel[2]
print 'sizeZ,stepZ', sizeZ, stepZ
if 'zeiss2chan2D' in file_type:
sizeC = 2
else:
sizeC = 1
sizeT = 1
rangex = frame_width * nm_per_pixel[0]
binsx = rangex / sr_pix_size
rangey = frame_height * nm_per_pixel[1]
binsy = rangey / sr_pix_size
rangez = float(z_range) + (sizeZ - 1) * stepZ
print 'rangez', rangez
binsz = int(math.ceil(rangez / srz_pix_size))
print 'sizeC,binsy,binsx,binsz', sizeC, binsy, binsx, binsz
hist_data = numpy.zeros((sizeC, binsy, binsx, binsz))
for c in range(sizeC):
hist = calc_hist(locs[c], file_type, binsy, binsx, binsz, rangey,
rangex, rangez)
hist_data[c, :, :, :] = hist
def plane_gen():
for z in range(binsz):
for c in range(sizeC):
for t in range(sizeT):
plane = hist_data[c, :, :, z]
yield plane
description = "Created from image:\n Name: %s\n File ID: %d" % (
imageName, file_id)
newImg = conn.createImageFromNumpySeq(plane_gen(),
new_name,
sizeZ=binsz,
sizeC=sizeC,
sizeT=sizeT,
description=description)
# reload the image (also reloads pixels)
image = conn.getObject("Image", newImg.getId())
# Get the BlitzGateway wrapped pixels and unwrap it
pixelsWrapper = image.getPrimaryPixels()
pixels = pixelsWrapper._obj
# Update and save
pixSize = LengthI(float(sr_pix_size) / 1000, UnitsLength.MICROMETER)
pixSizeZ = LengthI(float(srz_pix_size) / 1000, UnitsLength.MICROMETER)
pixels.setPhysicalSizeX(pixSize)
pixels.setPhysicalSizeY(pixSize)
pixels.setPhysicalSizeZ(pixSize)
updateService.saveObject(pixels)
if newImg:
iid = newImg.getId()
print "New Image Id = %s" % iid
# put new images in existing dataset
dataset = None
if parentDataset is not None and parentDataset.canLink():
parentDataset = parentDataset._obj
else:
parentDataset = None
parentProject = None # don't add Dataset to parent.
if parentDataset is None:
link = None
print "No dataset created or found for new images."\
" Images will be orphans."
else:
dsLink = omero.model.DatasetImageLinkI()
dsLink.parent = omero.model.DatasetI(parentDataset.id.val, False)
dsLink.child = omero.model.ImageI(iid, False)
updateService.saveObject(dsLink)
if parentProject and parentProject.canLink():
# and put it in the current project
projectLink = omero.model.ProjectDatasetLinkI()
projectLink.parent = omero.model.ProjectI(
parentProject.getId(), False)
projectLink.child = omero.model.DatasetI(dataset.id.val, False)
updateService.saveAndReturnObject(projectLink)
message = 'Super resolution histogram successfully created'
else:
message = 'Something went wrong, could not make super resolution histogram'
return message
