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createImageFromNumpySeq handles big images #276

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createImageFromNumpySeq handles big images #276

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ef5f565
createImageFromNumpySeq handles big images
will-moore Jan 27, 2021
6a29c25
doc strings and other cleaning
will-moore Jan 27, 2021
17bf657
Fixes to creating big images from testing
will-moore Jan 28, 2021
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308 changes: 195 additions & 113 deletions src/omero/gateway/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@
from past.utils import old_div
from builtins import object
import os
import numpy
from itertools import chain

import warnings
from collections import defaultdict
Expand Down Expand Up @@ -56,6 +58,7 @@
import omero
import omero.clients
from omero.util.decorators import timeit
from omero.util.tiles import TileLoopIteration, RPSTileLoop
from omero.cmd import Chgrp2, Delete2, DoAll, SkipHead, Chown2
from omero.cmd.graphs import ChildOption
from omero.api import Save
Expand Down Expand Up @@ -3727,6 +3730,146 @@ def getAnnotationCounts(self, objDict={}):

return self.countAnnotations(obj_type, obj_ids)


def upload_tiles(self, image, zct_plane_gen, convertToType, tile_size=512):
"""
Upload numpy planes to a 'big' image as tiles.

@param image omero.model.ImageI
@param zct_plane_gen A generator of numpy 2D arrays
@param tile_size Size of tiles
"""

pixels_service = self.getPixelsService()
pixels = image.getPrimaryPixels()
tile_width = tile_height = tile_size
channelsMinMax = []
# Make a generator of all the tiles we're going to need.
# This is the SAME ORDER that RPSTileLoop will ask for them.
def tile_gen():
for theT in range(pixels.getSizeT().val):
for theC in range(pixels.getSizeC().val):
for theZ in range(pixels.getSizeZ().val):
plane = next(zct_plane_gen)
if convertToType is not None:
p = numpy.zeros(plane.shape, dtype=convertToType)
p += plane
plane = p
size_y, size_x = plane.shape
# first plane of each channel
minValue = plane.min()
maxValue = plane.max()
if len(channelsMinMax) < (theC + 1):
channelsMinMax.append([minValue, maxValue])
else:
channelsMinMax[theC][0] = min(
channelsMinMax[theC][0], minValue)
channelsMinMax[theC][1] = max(
channelsMinMax[theC][1], maxValue)
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
x2 = min(x + tile_width, size_x)
y2 = min(y + tile_height, size_y)
tile = plane[y:y2, x:x2]
byte_swapped_tile = tile.byteswap()
yield byte_swapped_tile.tostring()

tile_iter = tile_gen()

class Iteration(TileLoopIteration):

def run(self, data, z, c, t, x, y, tile_width, tile_height,
tile_count):
tile2d = next(tile_iter)
data.setTile(tile2d, z, c, t, x, y, tile_width, tile_height)

loop = RPSTileLoop(self.c.sf, omero.model.PixelsI(pixels.id.val, False))
loop.forEachTile(tile_width, tile_height, Iteration())

for theC, mm in enumerate(channelsMinMax):
pixels_service.setChannelGlobalMinMax(
pixels.id.val, theC, float(mm[0]), float(mm[1]), self.SERVICE_OPTS)
return image


def get_pixel_type(self, dtype):
# need to map numpy pixel types to omero - don't handle: bool_,
# character, int_, int64, object_
queryService = self.getQueryService()
pTypes = {'int8': PixelsTypeint8,
'int16': PixelsTypeint16,
'uint16': PixelsTypeuint16,
'int32': PixelsTypeint32,
'float_': PixelsTypefloat,
'float8': PixelsTypefloat,
'float16': PixelsTypefloat,
'float32': PixelsTypefloat,
'float64': PixelsTypedouble,
'complex_': PixelsTypecomplex,
'complex64': PixelsTypecomplex}
# try to look up any not named above
pType = pTypes.get(dtype.name, dtype.name)
# omero::model::PixelsType
return queryService.findByQuery(
"from PixelsType as p where p.value='%s'" % pType, None)

def _createImage(self, dtype, imageName, sizeX, sizeY, sizeZ=1, sizeC=1,
sizeT=1, channelList=None, sourceImageId=None,
description=None):
"""
Create a new Image according to numpy dtype or sourceImage.

If sourceImageId is not None, the new image will be derived from
the source image, sharing some channel metadata.
"""
pixelsService = self.getPixelsService()
containerService = self.getContainerService()
convertToType = dtype
if sourceImageId is not None:
if channelList is None:
channelList = list(range(sizeC))
iId = pixelsService.copyAndResizeImage(
sourceImageId, rint(sizeX), rint(sizeY), rint(sizeZ),
rint(sizeT), channelList, None, False, self.SERVICE_OPTS)
# need to ensure that the plane dtype matches the pixels type
# of our new image
img = self.getObject("Image", iId.getValue())
newPtype = img.getPrimaryPixels().getPixelsType().getValue()
omeroToNumpy = {PixelsTypeint8: 'int8',
PixelsTypeuint8: 'uint8',
PixelsTypeint16: 'int16',
PixelsTypeuint16: 'uint16',
PixelsTypeint32: 'int32',
PixelsTypeuint32: 'uint32',
PixelsTypefloat: 'float32',
PixelsTypedouble: 'double'}
if omeroToNumpy[newPtype] != dtype.name:
convertToType = getattr(numpy, omeroToNumpy[newPtype])
img._obj.setName(rstring(imageName))
if description is not None:
img._obj.setDescription(rstring(description))
img._obj.setSeries(rint(0))
self.getUpdateService().saveObject(img._obj, self.SERVICE_OPTS)
else:
pixelsType = self.get_pixel_type(dtype)
if pixelsType is None:
raise Exception(
"Cannot create an image in omero from numpy array "
"with dtype: %s" % dType)
channelList = list(range(sizeC))
iId = pixelsService.createImage(
sizeX, sizeY, sizeZ, sizeT, channelList, pixelsType,
imageName, description, self.SERVICE_OPTS)

imageId = iId.getValue()
return (containerService.getImages(
"Image", [imageId], None, self.SERVICE_OPTS)[0], convertToType)


def createImageFromNumpySeq(self, zctPlanes, imageName, sizeZ=1, sizeC=1,
sizeT=1, description=None, dataset=None,
sourceImageId=None, channelList=None):
Expand Down Expand Up @@ -3759,7 +3902,7 @@ def planeGen():
:param session: An OMERO service factory or equivalent
with getQueryService() etc.
:param zctPlanes: A generator of numpy 2D arrays,
corresponding to Z-planes of new image.
corresponding to Z, C, T planes of new image.
:param imageName: Name of new image
:param description: Description for the new image
:param dataset: If specified, put the image in this dataset.
Expand All @@ -3770,76 +3913,16 @@ def planeGen():
source image (if specified). E.g. [0,2]
:return: The new OMERO image: omero.model.ImageI
"""
queryService = self.getQueryService()
pixelsService = self.getPixelsService()
# Make sure we don't get an existing rpStore
rawPixelsStore = self.c.sf.createRawPixelsStore()
containerService = self.getContainerService()
updateService = self.getUpdateService()

import numpy

def createImage(firstPlane, channelList):
""" Create our new Image once we have the first plane in hand """
convertToType = None
sizeY, sizeX = firstPlane.shape
if sourceImageId is not None:
if channelList is None:
channelList = list(range(sizeC))
iId = pixelsService.copyAndResizeImage(
sourceImageId, rint(sizeX), rint(sizeY), rint(sizeZ),
rint(sizeT), channelList, None, False, self.SERVICE_OPTS)
# need to ensure that the plane dtype matches the pixels type
# of our new image
img = self.getObject("Image", iId.getValue())
newPtype = img.getPrimaryPixels().getPixelsType().getValue()
omeroToNumpy = {PixelsTypeint8: 'int8',
PixelsTypeuint8: 'uint8',
PixelsTypeint16: 'int16',
PixelsTypeuint16: 'uint16',
PixelsTypeint32: 'int32',
PixelsTypeuint32: 'uint32',
PixelsTypefloat: 'float32',
PixelsTypedouble: 'double'}
if omeroToNumpy[newPtype] != firstPlane.dtype.name:
convertToType = getattr(numpy, omeroToNumpy[newPtype])
img._obj.setName(rstring(imageName))
img._obj.setSeries(rint(0))
updateService.saveObject(img._obj, self.SERVICE_OPTS)
else:
# need to map numpy pixel types to omero - don't handle: bool_,
# character, int_, int64, object_
pTypes = {'int8': PixelsTypeint8,
'int16': PixelsTypeint16,
'uint16': PixelsTypeuint16,
'int32': PixelsTypeint32,
'float_': PixelsTypefloat,
'float8': PixelsTypefloat,
'float16': PixelsTypefloat,
'float32': PixelsTypefloat,
'float64': PixelsTypedouble,
'complex_': PixelsTypecomplex,
'complex64': PixelsTypecomplex}
dType = firstPlane.dtype.name
if dType not in pTypes: # try to look up any not named above
pType = dType
else:
pType = pTypes[dType]
# omero::model::PixelsType
pixelsType = queryService.findByQuery(
"from PixelsType as p where p.value='%s'" % pType, None)
if pixelsType is None:
raise Exception(
"Cannot create an image in omero from numpy array "
"with dtype: %s" % dType)
channelList = list(range(sizeC))
iId = pixelsService.createImage(
sizeX, sizeY, sizeZ, sizeT, channelList, pixelsType,
imageName, description, self.SERVICE_OPTS)

imageId = iId.getValue()
return (containerService.getImages(
"Image", [imageId], None, self.SERVICE_OPTS)[0], convertToType)
# use the first plane to create image.
first_plane = next(zctPlanes)
sizeY, sizeX = first_plane.shape
image, dtype = self._createImage(first_plane.dtype, imageName, sizeX, sizeY, sizeZ, sizeC,
sizeT, channelList, sourceImageId, description)

def uploadPlane(plane, z, c, t, convertToType):
# if we're given a numpy dtype, need to convert plane to that dtype
Expand All @@ -3850,60 +3933,59 @@ def uploadPlane(plane, z, c, t, convertToType):
byteSwappedPlane = plane.byteswap()
convertedPlane = byteSwappedPlane.tostring()
rawPixelsStore.setPlane(convertedPlane, z, c, t, self.SERVICE_OPTS)
return (plane.min(), plane.max())

image = None
dtype = None
channelsMinMax = []
exc = None
try:
for theZ in range(sizeZ):
for theC in range(sizeC):
for theT in range(sizeT):
plane = next(zctPlanes)
# use the first plane to create image.
if image is None:
image, dtype = createImage(plane, channelList)
pixelsId = image.getPrimaryPixels(
).getId().getValue()
rawPixelsStore.setPixelsId(
pixelsId, True, self.SERVICE_OPTS)
uploadPlane(plane, theZ, theC, theT, dtype)
# init or update min and max for this channel
minValue = plane.min()
maxValue = plane.max()
# first plane of each channel
if len(channelsMinMax) < (theC + 1):
channelsMinMax.append([minValue, maxValue])
else:
channelsMinMax[theC][0] = min(
channelsMinMax[theC][0], minValue)
channelsMinMax[theC][1] = max(
channelsMinMax[theC][1], maxValue)
except Exception as e:
logger.error(
"Failed to setPlane() on rawPixelsStore while creating Image",
exc_info=True)
exc = e
try:
rawPixelsStore.close(self.SERVICE_OPTS)
except Exception as e:
logger.error("Failed to close rawPixelsStore", exc_info=True)
if exc is None:
exc = e
if exc is not None:
raise exc
# add the first plane back into generator
zct_plane_gen = chain([first_plane], zctPlanes)

# simply completing the generator - to avoid a GeneratorExit error.
try:
next(zctPlanes)
except StopIteration:
pass
big_image_size = self.getMaxPlaneSize()
if sizeX * sizeY > big_image_size[0] * big_image_size[1]:
# For 'big' images, need to upload tiles
self.upload_tiles(image, zct_plane_gen, dtype)
else:
pixelsId = image.getPrimaryPixels().getId().getValue()
rawPixelsStore.setPixelsId(pixelsId, True, self.SERVICE_OPTS)

exc = None
try:
for theZ in range(sizeZ):
for theC in range(sizeC):
for theT in range(sizeT):
plane = next(zct_plane_gen)
minValue, maxValue = uploadPlane(plane, theZ, theC, theT, dtype)
# init or update min and max for this channel
# first plane of each channel
if len(channelsMinMax) < (theC + 1):
channelsMinMax.append([minValue, maxValue])
else:
channelsMinMax[theC][0] = min(
channelsMinMax[theC][0], minValue)
channelsMinMax[theC][1] = max(
channelsMinMax[theC][1], maxValue)
except Exception as e:
logger.error(
"Failed to setPlane() on rawPixelsStore while creating Image",
exc_info=True)
exc = e
try:
rawPixelsStore.close(self.SERVICE_OPTS)
except Exception as e:
logger.error("Failed to close rawPixelsStore", exc_info=True)
if exc is None:
exc = e
if exc is not None:
raise exc

# simply completing the generator - to avoid a GeneratorExit error.
try:
next(zctPlanes)
except StopIteration:
pass

for theC, mm in enumerate(channelsMinMax):
pixelsService.setChannelGlobalMinMax(
pixelsId, theC, float(mm[0]), float(mm[1]), self.SERVICE_OPTS)
# resetRenderingSettings(
# renderingEngine, pixelsId, theC, mm[0], mm[1])

# put the image in dataset, if specified.
if dataset:
Expand Down