def downloadImage(queryService, rawPixelStore, imageId, imageName):
"""
This method downloads the first (only?) plane of the OMERO image and saves it as a local image.
@param session The OMERO session
@param imageId The ID of the image to download
@param imageName The name of the image to write. If no path, saved in the current directory.
"""
# 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)
theX = pixels.getSizeX().getValue()
theY = pixels.getSizeY().getValue()
# get the plane
theZ, theC, theT = (0,0,0)
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
array2spider(plane2D, imageName)
import numpy
from Spider.Spiderarray import array2spider
size = 65
I = numpy.zeros((size,size)) # create a blank array
for j in range(size):
for i in range(size):
I[j][i] = i # Array[row][column]
array2spider(I, 'tmp001.dat')
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)
import numpy
from Spider.Spiderarray import array2spider
size = 65
I = numpy.zeros((size, size)) # create a blank array
for j in range(size):
for i in range(size):
I[j][i] = i # Array[row][column]
array2spider(I, 'tmp001.dat')
