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 testTicket4737WithForEachTile(self):
pix = self.pix()
class Iteration(TileLoopIteration):
def run(self, data, z, c, t, x, y, tileWidth, tileHeight, tileCount):
data.setTile([5]*tileWidth*tileHeight, z, c, t, x, y, tileWidth, tileHeight)
loop = RPSTileLoop(self.client.getSession(), pix)
loop.forEachTile(256, 256, Iteration())
pix = self.query.get("Pixels", pix.id.val)
self.check_pix(pix)
def testTicket4737WithForEachTile(self):
pix = self.pix()
class Iteration(TileLoopIteration):
def run(self, data, z, c, t, x, y, tileWidth, tileHeight,
tileCount):
data.setTile([5] * tileWidth * tileHeight, z, c, t, x, y,
tileWidth, tileHeight)
loop = RPSTileLoop(self.client.getSession(), pix)
loop.forEachTile(256, 256, Iteration())
pix = self.query.get("Pixels", pix.id.val)
self.check_pix(pix)
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 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)
