def process_data(conn,script_params,file_id,coords,sr_pix_size,nm_per_pixel):
"""
Calculates the neighbour distance in all the rectangular rois
"""
image_id = script_params['ImageID']
image = conn.getObject("Image",image_id)
if not image:
message = 'Could not find specified image'
return message
imageName = image.getName()
name,ext = os.path.splitext(imageName)
if 'ome' in name:
name = name.split('.')[0]
new_name = name + '_sr_histogram.ome' + ext
else:
new_name = name + '_sr_histogram' + ext
parentDataset = image.getParent()
parentProject = parentDataset.getParent()
updateService = conn.getUpdateService()
frame_width = image.getSizeX()
print 'frame_width',frame_width
frame_height = image.getSizeY()
print 'frame_height',frame_height
sizeT = 1
sizeZ = 1
if 'czi' in ext:
num_frames = image.getSizeT()
else:
num_frames = image.getSizeZ()
if 'zeiss2d2chan' in script_params['File_Type']:
sizeC = 2
else:
sizeC = 1
binsx = (frame_width * nm_per_pixel) / sr_pix_size
binsy = (frame_height * nm_per_pixel) / sr_pix_size
hist_data = np.zeros((sizeC,binsy,binsx))
for c in range(sizeC):
hist = calc_hist('2d',coords[c,:,:],num_frames,binsy,binsx)
hist_data[c,:,:] = hist
def plane_gen():
for z in range(sizeZ):
for c in range(sizeC):
for t in range(sizeT):
plane = hist_data[c,:,:]
yield plane
description = "Created from image:\n Name: %s\n File ID: %d" % (imageName, file_id)
newImg = conn.createImageFromNumpySeq(
plane_gen(), new_name,
sizeZ=sizeZ, sizeC=sizeC, sizeT=sizeT,
description=description)
if newImg:
iid = newImg.getId()
print "New Image Id = %s" % iid
# put new images in existing dataset
dataset = None
if parentDataset is not None and parentDataset.canLink():
parentDataset = parentDataset._obj
else:
parentDataset = None
parentProject = None # don't add Dataset to parent.
if parentDataset is None:
link = None
print "No dataset created or found for new images."\
" Images will be orphans."
else:
dsLink = omero.model.DatasetImageLinkI()
dsLink.parent = omero.model.DatasetI(
parentDataset.id.val, False)
dsLink.child = omero.model.ImageI(iid, False)
updateService.saveObject(dsLink)
if parentProject and parentProject.canLink():
# and put it in the current project
projectLink = omero.model.ProjectDatasetLinkI()
projectLink.parent = omero.model.ProjectI(
parentProject.getId(), False)
projectLink.child = omero.model.DatasetI(
dataset.id.val, False)
updateService.saveAndReturnObject(projectLink)
message = 'Super resolution histogram successfully created'
else:
message = 'Something went wrong, could not make super resolution histogram'
return message