def download_image(conn, image, polys):
im_name = 'Image%s.ome.tif' % (image.getId())
exporter = OMEExporter(conn, image, input_dir, im_name, ROI=polys)
exporter.generate()
im_path = os.path.join(input_dir, im_name)
return im_name, im_path
def download_tiles(conn, image, theC, theZ):
"""
Export every plane in the original image, or those
selected by the user, as OME-TIFF
:param conn: BlitzGateway connection
:param image: the omero image being downloaded
:param theC: the image channel being downloaded
:parem theZ: the z-plane being downloaded
"""
num_tiles = image.getSizeT()
image_names = []
for t in range(num_tiles):
im_name = "tile_T{}.ome.tif".format(t)
exporter = OMEExporter(conn,
image,
input_dir,
im_name,
theZ=theZ,
theC=theC,
theT=t)
exporter.generate()
image_names.append(im_name)
return image_names
def download_image(conn,image, polys):
im_name = 'Image%s.ome.tif' % (image.getId())
exporter = OMEExporter(conn,image,input_dir,im_name,ROI=polys)
exporter.generate()
im_path = os.path.join(input_dir,im_name)
return im_name,im_path
def download_tiles(conn,image,theC,theZ):
# export every plane in the original image, or those
# selected by the user, as OME-TIFF
print "theZ passed to exporter",theZ
num_tiles = image.getSizeT()
image_names = []
for t in range(num_tiles):
im_name = 'tile_T%s.ome.tif' % t
exporter = OMEExporter(conn,image,input_dir,im_name,theZ=theZ,theC=theC,theT=t)
exporter.generate()
image_names.append(im_name)
return image_names
def download_tiles(conn, image, theC, theZ):
# export every plane in the original image, or those
# selected by the user, as OME-TIFF
print "theZ passed to exporter", theZ
num_tiles = image.getSizeT()
image_names = []
for t in range(num_tiles):
im_name = 'tile_T%s.ome.tif' % t
exporter = OMEExporter(conn,
image,
input_dir,
im_name,
theZ=theZ,
theC=theC,
theT=t)
exporter.generate()
image_names.append(im_name)
return image_names
def process_image(conn, parent_id, script_params, session):
"""
Makes a new image from an ROI on a parent image. If the
ROI is a PolygonI and the user chooses to 'clear outside'
a script is run via Fiji to run the clearing. Otherwise the
new image is created from the bounding box of the PolygonI
@param conn: The BlitzGateway connection
@param parent_id: The OMERO ID of the parent image
@param script_params: The parameters required to run the script
@param session: A dictionary containing session ID and hostname
"""
global input_dir
global output_dir
input_dir = tempfile.mkdtemp(prefix='tiling_input')
output_dir = tempfile.mkdtemp(prefix='tiling_output')
def empty_dir(dir_path):
for old_file in os.listdir(dir_path):
file_path = os.path.join(dir_path, old_file)
os.unlink(file_path)
updateService = conn.getUpdateService()
parent_image = conn.getObject("Image", parent_id)
parentDataset = parent_image.getParent()
parentProject = parentDataset.getParent()
rects, polys = get_rects_from_rois(conn, parent_id)
# Get the channels
channels = None
if script_params["Select_Channels"]:
channels = script_params["Channels"]
children = []
child_ids = []
# loop over bounding rectangles -
# could have originated from a polygon ROI
for i, r in enumerate(rects):
# so check the shape
empty_dir(input_dir)
empty_dir(output_dir)
xbox, ybox, wbox, hbox, rid, shape = r
print 'shape:', shape
box = r[:-1]
child_name = 'ImageID%s_ROI%s.ome.tif' % (parent_image.getId(), rid)
child_path = os.path.join(input_dir, child_name)
if script_params['Clear_Outside_Polygon'] and ('PolygonI' in shape):
exporter = OMEExporter(conn,parent_image,input_dir,child_name,\
box,theC=channels,ROI=polys)
exporter.generate()
child_path = run_clearing(conn, session, parent_image, \
child_path, xbox, ybox)
elif ('PolygonI' in shape):
# retain the PolygonI in the metadata
exporter = OMEExporter(conn,parent_image,input_dir,child_name,\
box,theC=channels,ROI=polys)
exporter.generate()
elif ('RectI' in shape):
# do not write ROI to metadata
exporter = OMEExporter(conn,parent_image,input_dir,child_name,\
box,theC=channels)
exporter.generate()
print 'child_path:', child_path
newImg = do_import(conn, session, child_path)
children.append(newImg)
child_ids.append(newImg.getId())
if len(child_ids) == 0:
print "No new images created."
return
if script_params['New_Dataset'] and \
len(script_params['Container_Name'].strip()) > 0:
# create a new dataset for new images
datasetName = script_params['Container_Name']
print "\nMaking Dataset '%s' of Images from ROIs of Image: %s" \
% (datasetName, parent_id)
dataset = omero.model.DatasetI()
dataset.name = rstring(datasetName)
desc = "Images in this Dataset are from ROIs of parent Image:\n"\
" Name: %s\n Image ID: %d" % (parent_image.getName(), parent_id)
dataset.description = rstring(desc)
dataset = updateService.saveAndReturnObject(dataset)
parentDataset = dataset
else:
# 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:
link = []
for cid in child_ids:
dsLink = omero.model.DatasetImageLinkI()
dsLink.parent = omero.model.DatasetI(parentDataset.id.val, False)
dsLink.child = omero.model.ImageI(cid, False)
updateService.saveObject(dsLink)
link.append(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)
shutil.rmtree(input_dir)
shutil.rmtree(output_dir)
return children, dataset, link, child_ids
def process_image(conn, parent_id, script_params, session):
"""
Makes a new image from an ROI on a parent image. If the
ROI is a PolygonI and the user chooses to 'clear outside'
a script is run via Fiji to run the clearing. Otherwise the
new image is created from the bounding box of the PolygonI
@param conn: The BlitzGateway connection
@param parent_id: The OMERO ID of the parent image
@param script_params: The parameters required to run the script
@param session: A dictionary containing session ID and hostname
"""
global input_dir
global output_dir
input_dir = tempfile.mkdtemp(prefix='tiling_input')
output_dir = tempfile.mkdtemp(prefix='tiling_output')
def empty_dir(dir_path):
for old_file in os.listdir(dir_path):
file_path = os.path.join(dir_path, old_file)
os.unlink(file_path)
updateService = conn.getUpdateService()
parent_image = conn.getObject("Image", parent_id)
parentDataset = parent_image.getParent()
parentProject = parentDataset.getParent()
rects,polys = get_rects_from_rois(conn, parent_id)
# Get the channels
channels = None
if script_params["Select_Channels"]:
channels = script_params["Channels"]
children = []
child_ids = []
# loop over bounding rectangles -
# could have originated from a polygon ROI
for i,r in enumerate(rects):
# so check the shape
empty_dir(input_dir)
empty_dir(output_dir)
xbox, ybox, wbox, hbox, rid, shape = r
print 'shape:',shape
box = r[:-1]
child_name ='ImageID%s_ROI%s.ome.tif'%(parent_image.getId(),rid)
child_path = os.path.join(input_dir,child_name)
if script_params['Clear_Outside_Polygon'] and ('PolygonI' in shape):
exporter = OMEExporter(conn,parent_image,input_dir,child_name,\
box,theC=channels,ROI=polys)
exporter.generate()
child_path = run_clearing(conn, session, parent_image, \
child_path, xbox, ybox)
elif ('PolygonI' in shape):
# retain the PolygonI in the metadata
exporter = OMEExporter(conn,parent_image,input_dir,child_name,\
box,theC=channels,ROI=polys)
exporter.generate()
elif ('RectI' in shape):
# do not write ROI to metadata
exporter = OMEExporter(conn,parent_image,input_dir,child_name,\
box,theC=channels)
exporter.generate()
print 'child_path:',child_path
newImg = do_import(conn,session,child_path)
children.append(newImg)
child_ids.append(newImg.getId())
if len(child_ids) == 0:
print "No new images created."
return
if script_params['New_Dataset'] and \
len(script_params['Container_Name'].strip()) > 0:
# create a new dataset for new images
datasetName = script_params['Container_Name']
print "\nMaking Dataset '%s' of Images from ROIs of Image: %s" \
% (datasetName, parent_id)
dataset = omero.model.DatasetI()
dataset.name = rstring(datasetName)
desc = "Images in this Dataset are from ROIs of parent Image:\n"\
" Name: %s\n Image ID: %d" % (parent_image.getName(), parent_id)
dataset.description = rstring(desc)
dataset = updateService.saveAndReturnObject(dataset)
parentDataset = dataset
else:
# 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:
link = []
for cid in child_ids:
dsLink = omero.model.DatasetImageLinkI()
dsLink.parent = omero.model.DatasetI(
parentDataset.id.val, False)
dsLink.child = omero.model.ImageI(cid, False)
updateService.saveObject(dsLink)
link.append(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)
shutil.rmtree(input_dir)
shutil.rmtree(output_dir)
return children, dataset, link, child_ids
