def pix(self, x=10, y=10, z=10, c=3, t=50, client=None):
"""
Creates an int8 pixel of the given size in the database.
No data is written.
"""
image = self.new_image()
pixels = PixelsI()
pixels.sizeX = rint(x)
pixels.sizeY = rint(y)
pixels.sizeZ = rint(z)
pixels.sizeC = rint(c)
pixels.sizeT = rint(t)
pixels.sha1 = rstring("")
pixels.pixelsType = PixelsTypeI()
pixels.pixelsType.value = rstring("int8")
pixels.dimensionOrder = DimensionOrderI()
pixels.dimensionOrder.value = rstring("XYZCT")
image.addPixels(pixels)
if client is None:
client = self.client
update = client.sf.getUpdateService()
image = update.saveAndReturnObject(image)
pixels = image.getPrimaryPixels()
return pixels
def test_simple_marshal_tiled(self, wrapped_image):
image = wrapped_image._obj
pixels = PixelsI()
pixels.sizeX = rint(65)
pixels.sizeY = rint(65)
image.addPixels(pixels)
data = wrapped_image.simpleMarshal(xtra={'tiled': True})
self.assert_data(data)
assert data['tiled'] is True
def test_simple_marshal_tiled(self, wrapped_image):
image = wrapped_image._obj
pixels = PixelsI()
pixels.sizeX = rint(65)
pixels.sizeY = rint(65)
image.addPixels(pixels)
data = wrapped_image.simpleMarshal(xtra={'tiled': True})
self.assert_data(data)
assert data['tiled'] is True
def pix(self, x=10, y=10, z=10, c=3, t=50, client=None):
"""
Creates an int8 pixel of the given size in the database.
No data is written.
"""
image = self.new_image()
pixels = PixelsI()
pixels.sizeX = rint(x)
pixels.sizeY = rint(y)
pixels.sizeZ = rint(z)
pixels.sizeC = rint(c)
pixels.sizeT = rint(t)
pixels.sha1 = rstring("")
pixels.pixelsType = PixelsTypeI()
pixels.pixelsType.value = rstring("int8")
pixels.dimensionOrder = DimensionOrderI()
pixels.dimensionOrder.value = rstring("XYZCT")
image.addPixels(pixels)
if client is None:
client = self.client
update = client.sf.getUpdateService()
image = update.saveAndReturnObject(image)
pixels = image.getPrimaryPixels()
return pixels
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 testTiles(self):
from omero.model import PixelsI
from omero.sys import ParametersI
from omero.util.tiles import RPSTileLoop
from omero.util.tiles import TileLoopIteration
from numpy import fromfunction
sizeX = 4096
sizeY = 4096
sizeZ = 1
sizeC = 1
sizeT = 1
tileWidth = 1024
tileHeight = 1024
imageName = "testStitchBig4K-1Ktiles"
description = None
tile_max = float(255)
pixelsService = self.client.sf.getPixelsService()
queryService = self.client.sf.getQueryService()
query = "from PixelsType as p where p.value='int8'"
pixelsType = queryService.findByQuery(query, None)
channelList = range(sizeC)
iId = pixelsService.createImage(sizeX, sizeY, sizeZ, sizeT,
channelList, pixelsType, imageName,
description)
image = queryService.findByQuery(
"select i from Image i join fetch i.pixels where i.id = :id",
ParametersI().addId(iId))
pid = image.getPrimaryPixels().getId().getValue()
def f(x, y):
"""
create some fake pixel data tile (2D numpy array)
"""
return (x * y) / (1 + x + y)
def mktile(w, h):
tile = fromfunction(f, (w, h))
tile = tile.astype(int)
tile[tile > tile_max] = tile_max
return list(tile.flatten())
tile = fromfunction(f, (tileWidth, tileHeight)).astype(int)
tile_min = float(tile.min())
tile_max = min(tile_max, float(tile.max()))
class Iteration(TileLoopIteration):
def run(self, data, z, c, t, x, y, tileWidth, tileHeight,
tileCount):
tile2d = mktile(tileWidth, tileHeight)
data.setTile(tile2d, z, c, t, x, y, tileWidth, tileHeight)
loop = RPSTileLoop(self.client.sf, PixelsI(pid, False))
loop.forEachTile(256, 256, Iteration())
c = 0
pixelsService.setChannelGlobalMinMax(pid, c, tile_min, tile_max)
def import_pyramid_pre_fs(self, tmpdir):
name = "test&sizeX=4000&sizeY=4000.fake"
fakefile = tmpdir.join(name)
fakefile.write('')
pixels = self.import_image(filename=str(fakefile), skip="checksum")[0]
id = long(float(pixels))
# wait for the pyramid to be generated
self.wait_for_pyramid(id)
query_service = self.client.sf.getQueryService()
pixels_service = self.client.sf.getPixelsService()
orig_pix = query_service.findByQuery(
"select p from Pixels p where p.id = :id",
ParametersI().addId(id))
orig_fs = query_service.findByQuery(
"select f from Image i join i.fileset f where i.id = :id",
ParametersI().addId(orig_pix.image.id.val))
try:
new_img = pixels_service.copyAndResizeImage(
orig_pix.image.id.val, rint(4000), rint(4000), rint(1),
rint(1), [0], None, True).val
pix_id = unwrap(
query_service.projection(
"select p.id from Image i join i.pixels p where i.id = :id",
ParametersI().addId(new_img)))[0][0]
# This won't work but it but we then have a pyramid without fileset
self.copyPixels(orig_pix, PixelsI(pix_id, False))
except omero.InternalException:
print "Cannot copy pixels for image %s" % orig_pix.image.id.val
finally:
self.delete([orig_fs])
return pix_id
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 duplicateMIF(self, orig_img):
"""
Use copyAndResizeImage to create a "synthetic" image
(one without a fileset)
"""
new_img = self.pixels.copyAndResizeImage(
orig_img.id.val, rint(16), rint(16), rint(1), rint(1),
[0], None, True).val
pix_id = unwrap(self.query.projection(
"select p.id from Image i join i.pixels p where i.id = :id",
ParametersI().addId(new_img)))[0][0]
new_img = ImageI(new_img, False)
new_pix = PixelsI(pix_id, False)
return new_img, new_pix
def run(password, target, host, port):
for i in range(1, 51):
username = "******" % i
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
params = omero.sys.ParametersI()
params.addString('username', username)
query = "from Dataset where name='%s' \
AND details.owner.omeName=:username" % target
query_service = conn.getQueryService()
datasets = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(datasets) == 0:
print("No datasets with name %s found" % target)
continue
dataset_id = datasets[0].getId().getValue()
print('dataset', dataset_id)
params2 = omero.sys.ParametersI()
params2.addId(dataset_id)
query = "select l.child.id from DatasetImageLink l \
where l.parent.id = :id"
images = query_service.projection(query, params2,
conn.SERVICE_OPTS)
for k in range(0, len(images)):
image_id = images[k][0].getValue()
delta_t = 300
image = conn.getObject("Image", image_id)
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
query = "from PlaneInfo as Info where \
Info.theZ=0 and Info.theC=0 and pixels.id=:pid"
info_list = query_service.findAllByQuery(
query, params, conn.SERVICE_OPTS)
print('info_list', len(info_list))
if len(info_list) == 0:
print("Creating info...", image.getSizeT())
info_list = []
for t_index in range(image.getSizeT()):
print(' t', t_index)
info = PlaneInfoI()
info.theT = rint(t_index)
info.theZ = rint(0)
info.theC = rint(0)
info.pixels = PixelsI(image.getPixelsId(), False)
dt = t_index * delta_t
info.deltaT = TimeI(dt, UnitsTime.SECOND)
info_list.append(info)
else:
for info in info_list:
unwrap_t = unwrap(info.theT)
unwrap_z = unwrap(info.theZ)
print('theT %s, theZ %s' % (unwrap_t, unwrap_z))
t_index = info.theT.getValue()
dt = t_index * delta_t
info.deltaT = TimeI(dt, UnitsTime.SECOND)
print("Saving info_list", len(info_list))
conn.getUpdateService().saveArray(info_list)
except Exception as exc:
print("Error when setting the timestamps: %s" % str(exc))
finally:
conn.close()
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_from_tiles(conn, source, image_name, description,
box, tile_size):
pixels_service = conn.getPixelsService()
query_service = conn.getQueryService()
xbox, ybox, wbox, hbox, z1box, z2box, t1box, t2box = box
size_x = wbox
size_y = hbox
size_z = source.getSizeZ()
size_t = source.getSizeT()
size_c = source.getSizeC()
tile_width = tile_size
tile_height = tile_size
primary_pixels = source.getPrimaryPixels()
def create_image():
query = "from PixelsType as p where p.value='uint8'"
pixels_type = query_service.findByQuery(query, None)
channel_list = range(size_c)
# bytesPerPixel = pixelsType.bitSize.val / 8
iid = pixels_service.createImage(
size_x,
size_y,
size_z,
size_t,
channel_list,
pixels_type,
image_name,
description,
conn.SERVICE_OPTS)
return conn.getObject("Image", iid)
# Make a list of all the tiles we're going to need.
# This is the SAME ORDER that RPSTileLoop will ask for them.
zct_tile_list = []
for t in range(0, size_t):
for c in range(0, size_c):
for z in range(0, size_z):
for tile_offset_y in range(
0, ((size_y + tile_height - 1) / tile_height)):
for tile_offset_x in range(
0, ((size_x + tile_width - 1) / tile_width)):
x = tile_offset_x * tile_width
y = tile_offset_y * tile_height
w = tile_width
if (w + x > size_x):
w = size_x - x
h = tile_height
if (h + y > size_y):
h = size_y - y
tile_xywh = (xbox + x, ybox + y, w, h)
zct_tile_list.append((z, c, t, tile_xywh))
# This is a generator that will return tiles in the sequence above
# getTiles() only opens 1 rawPixelsStore for all the tiles
# whereas getTile() opens and closes a rawPixelsStore for each tile.
tile_gen = primary_pixels.getTiles(zct_tile_list)
def next_tile():
return tile_gen.next()
class Iteration(TileLoopIteration):
def run(self, data, z, c, t, x, y, tile_width, tile_height,
tile_count):
tile2d = next_tile()
data.setTile(tile2d, z, c, t, x, y, tile_width, tile_height)
new_image = create_image()
pid = new_image.getPixelsId()
loop = RPSTileLoop(conn.c.sf, PixelsI(pid, False))
loop.forEachTile(tile_width, tile_height, Iteration())
for the_c in range(size_c):
pixels_service.setChannelGlobalMinMax(pid, the_c, float(0),
float(255), conn.SERVICE_OPTS)
return new_image
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
