def get_planes(session, pixels):
pixels_service = session.createRawPixelsStore()
planes = list()
dtype = toNumpy(pixels.pixelsType.value.val)
try:
ctx = {'omero.group': '-1'}
pixels_service.setPixelsId(pixels.id.val, True, ctx)
for c in xrange(pixels.sizeC.val):
plane = pixels_service.getPlane(0, c, 0)
plane = np.fromstring(plane, dtype=dtype)
plane = np.reshape(plane, (pixels.sizeY.val, -1))
if sys.byteorder == 'little':
# Data coming from OMERO is always big endian
plane = plane.byteswap()
planes.append(plane)
finally:
pixels_service.close()
return planes
def readFlimImageFile(rawPixelsStore, pixels):
"""
Read the RawImageFlimFile with fileId and return it as an array [c, x, y]
@param rawPixelsStore The rawPixelStore service to get the image.
@param pixels The pixels of the image.
@return The Contents of the image for z = 0, t = 0, all channels;
"""
from numpy import zeros
sizeC = pixels.getSizeC().getValue();
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();
id = pixels.getId().getValue();
pixelsType = pixels.getPixelsType().getValue().getValue();
rawPixelsStore.setPixelsId(id , False);
cRange = range(0, sizeC);
stack = zeros((sizeC, sizeX, sizeY),dtype=pixelstypetopython.toNumpy(pixelsType));
for c in cRange:
plane = downloadPlane(rawPixelsStore, pixels, 0, c, 0);
stack[c,:,:]=plane;
return stack;
def readFlimImageFile(rawPixelsStore, pixels):
"""
Read the RawImageFlimFile with fileId and return it as an array [c, x, y]
@param rawPixelsStore The rawPixelStore service to get the image.
@param pixels The pixels of the image.
@return The Contents of the image for z = 0, t = 0, all channels;
"""
from numpy import zeros
sizeC = pixels.getSizeC().getValue();
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();
id = pixels.getId().getValue();
pixelsType = pixels.getPixelsType().getValue().getValue();
rawPixelsStore.setPixelsId(id , False);
cRange = range(0, sizeC);
stack = zeros((sizeC, sizeX, sizeY),dtype=pixelstypetopython.toNumpy(pixelsType));
for c in cRange:
plane = downloadPlane(rawPixelsStore, pixels, 0, c, 0);
stack[c,:,:]=plane;
return stack;
def downloadPlane(rawPixelsStore, pixels, z, c, t):
"""
Download the plane [z,c,t] for image pixels. Pixels must have pixelsType loaded.
N.B. The rawPixelsStore must have already been initialised by setPixelsId()
@param rawPixelsStore The rawPixelStore service to get the image.
@param pixels The pixels of the image.
@param z The Z-Section to retrieve.
@param c The C-Section to retrieve.
@param t The T-Section to retrieve.
@return The Plane of the image for z, c, t
"""
from numpy import array
rawPlane = rawPixelsStore.getPlane(z, c, t);
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();
pixelType = pixels.getPixelsType().getValue().getValue();
convertType ='>'+str(sizeX*sizeY)+pixelstypetopython.toPython(pixelType);
convertedPlane = unpack(convertType, rawPlane);
numpyType = pixelstypetopython.toNumpy(pixelType)
remappedPlane = array(convertedPlane, numpyType);
remappedPlane.resize(sizeY, sizeX);
return remappedPlane;
def downloadPlane(rawPixelsStore, pixels, z, c, t):
"""
Download the plane [z,c,t] for image pixels. Pixels must have pixelsType loaded.
N.B. The rawPixelsStore must have already been initialised by setPixelsId()
@param rawPixelsStore The rawPixelStore service to get the image.
@param pixels The pixels of the image.
@param z The Z-Section to retrieve.
@param c The C-Section to retrieve.
@param t The T-Section to retrieve.
@return The Plane of the image for z, c, t
"""
from numpy import array
rawPlane = rawPixelsStore.getPlane(z, c, t)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
pixelType = pixels.getPixelsType().getValue().getValue()
convertType = '>' + str(
sizeX * sizeY) + pixelstypetopython.toPython(pixelType)
convertedPlane = unpack(convertType, rawPlane)
numpyType = pixelstypetopython.toNumpy(pixelType)
remappedPlane = array(convertedPlane, numpyType)
remappedPlane.resize(sizeY, sizeX)
return remappedPlane
def omeroToEm(commandArgs):
# log-in
client = omero.client(commandArgs["host"])
session = client.createSession(commandArgs["username"], commandArgs["password"])
# get the services we need
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
rawPixelStore = session.createRawPixelsStore()
containerService = session.getContainerService()
images = []
if "image" in commandArgs:
iId = long(commandArgs["image"])
i = containerService.getImages("Image", [iId], None)[0]
images.append(i)
elif "dataset" in commandArgs:
dIds = [long(commandArgs["dataset"])]
images = containerService.getImages("Dataset", dIds, None)
else:
print "No image or dataset ID given"
return
path = None
if "path" in commandArgs:
path = commandArgs["path"]
if not os.path.exists(path):
print "Given path: %s not found. Saving images in current directory." % path
path = None
extension = "dat" # default
format = None
if "extension" in commandArgs:
ext = commandArgs["extension"]
if ext in filetypes:
extension = ext
print "Saving all images as .%s files." % extension
else:
print "Invalid extension: %s (not supported by Spider). Using %s" % (ext, extension)
for image in images:
iName = image.getName().getValue()
imageName = os.path.basename(iName) # make sure no dir separators in name.
imageId = image.getId().getValue()
if not imageName.endswith(".%s" % extension):
imageName = "%s.%s" % (imageName, extension)
if path:
imageName = os.path.join(path,imageName)
i = 1 # don't overwrite. Add number before extension
dirName, ext = imageName.rsplit(".", 1)
while os.path.exists(imageName):
imageName = "%s_%s.%s" % (dirName,i,ext)
i +=1
print "Preparing to save image: %s" % imageName
figLegend = ""
# get pixels, with pixelsType
query_string = "select p from Pixels p join fetch p.image i join fetch p.pixelsType pt where i.id='%d'" % imageId
pixels = queryService.findByQuery(query_string, None)
ptype = pixels.pixelsType.getValue().getValue()
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
# prepare rawPixelStore
theC, theT = (0, 0)
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
if sizeZ == 1:
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, 0, theC, theT)
array2spider(plane2D, imageName)
else:
numpyType = pixelstypetopython.toNumpy(ptype)
array3D = zeros( (sizeZ, sizeY, sizeX), dtype=numpyType )
for z in range(sizeZ):
# get each plane and add to 3D array
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, z, theC, theT)
array3D[z] = plane2D
array2spider(array3D, imageName)