def uploadImageToDataset(services, pixelsType, imageArray, imageName, dataset=None):
"""
Uploads a local Spider image to an OMERO dataset. Same function exists in spider2omero.py.
@param services Map of OMERO services
@param pixelsType The OMERO PixelsType object for new image.
@param imageArray Numpy array of pixel data - 2D
@param imageName The local file, for getting image header info
@param dataset Dataset to put images in, if specified. omero.model.Dataset
"""
session = services["session"]
queryService = services["queryService"]
updateService = services["updateService"]
rawFileStore = services["rawFileStore"]
namespace = omero.constants.namespaces.NSCOMPANIONFILE
fileName = omero.constants.annotation.file.ORIGINALMETADATA
print "Importing image: %s" % imageName
description = ""
if len(imageArray.shape) > 2:
plane2Dlist = imageArray # 3D array already. TODO: Need to check that volume is not mirrored (Z in correct order)
else:
plane2Dlist = [imageArray] # single plane image
name = os.path.basename(imageName)
image = scriptUtil.createNewImage(session, plane2Dlist, name, description, dataset)
# header is a list of values corresponding to attributes
header = getSpiderHeader(imageName)
# if we know the pixel size, set it in the new image
if len(header) >= 38:
physicalSizeX = header[38]
physicalSizeY = header[38]
pixels = image.getPrimaryPixels()
pixels.setPhysicalSizeX(rdouble(physicalSizeX))
pixels.setPhysicalSizeY(rdouble(physicalSizeY))
updateService.saveObject(pixels)
# make a temp text file.
f = open(fileName, 'w')
f.write("[GlobalMetadata]\n")
# now add image attributes as "Original Metadata", sorted by key.
for i, h in enumerate(header):
if i in spiderHeaderMap:
f.write("%s=%s\n" % (spiderHeaderMap[i], h))
f.close()
scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, image, fileName, "text/plain", None, namespace)
# delete temp file
os.remove(fileName)
def uploadImageToDataset(session, services, pixelsType, localImage, dataset=None, description="", imageName=None):
"""
Uploads a local Spider image to an OMERO dataset. Same function exists in spider2omero.py.
@param services Map of OMERO services
@param pixelsType The OMERO PixelsType object for new image.
@param imageName The local image path/name. Also used for new image name.
@param dataset Dataset to put images in, if specified. omero.model.Dataset
"""
renderingEngine = services["renderingEngine"]
queryService = services["queryService"]
pixelsService = services["pixelsService"]
rawPixelStore = services["rawPixelStore"]
updateService = services["updateService"]
rawFileStore = services["rawFileStore"]
namespace = omero.constants.namespaces.NSCOMPANIONFILE
fileName = omero.constants.annotation.file.ORIGINALMETADATA
if imageName == None: imageName = localImage
print "Importing image: %s" % imageName
plane2D = spider2array(localImage)
plane2Dlist = [plane2D] # single plane image
image = scriptUtil.createNewImage(session, plane2Dlist, imageName, description, dataset)
# header is a list of values corresponding to attributes
header = getSpiderHeader(localImage)
# if we know the pixel size, set it in the new image
if len(header) >= 38:
physicalSizeX = header[38]
physicalSizeY = header[38]
pixels = image.getPrimaryPixels()
pixels.setPhysicalSizeX(rdouble(physicalSizeX))
pixels.setPhysicalSizeY(rdouble(physicalSizeY))
updateService.saveObject(pixels)
# make a temp text file.
f = open(fileName, 'w')
f.write("[GlobalMetadata]\n")
# now add image attributes as "Original Metadata", sorted by key.
for i, h in enumerate(header):
if i in spiderHeaderMap:
f.write("%s=%s\n" % (spiderHeaderMap[i], h))
f.close()
scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, image, fileName, "text/plain", None, namespace)
# delete temp file
os.remove(fileName)
return image
