Copy_ROIs

util_scripts/Copy_ROIs.py

@@ -0,0 +1,167 @@
+# -*- coding: utf-8 -*-
+"""
+-----------------------------------------------------------------------------
+  Copyright (C) 2018 Glencoe Software, Inc. All rights reserved.
+  This program is free software; you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation; either version 2 of the License, or
+  (at your option) any later version.
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  You should have received a copy of the GNU General Public License along
+  with this program; if not, write to the Free Software Foundation, Inc.,
+  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+------------------------------------------------------------------------------
+"""
+
+
+import logging
+import sys
+
+LOGGER = logging.getLogger('gs_util.metadata.eSlide')
+LOGGING_FORMAT = "%(asctime)s %(levelname)-7s [%(name)16s] %(message)s"
+
+OMERO_IMPORTED = False
+try:
+    import omero
+    from omero.gateway import BlitzGateway
+    from omero.rtypes import rstring
+    import omero.scripts as scripts
+    OMERO_IMPORTED = True
+except Exception:
+    OMERO_IMPORTED = False
+    LOGGER.warn("OMERO lib not on the path.")
+
+
+# Query to retrieve the ROIs for particular image
+# externalInfo is used by PathViewer to find ROIs created in PathViewer
+# externalInfo if exists is copied to new ROI
+# this prevents the "Where was this ROI created?" dialog to pop up
+ROI_QUERY = \
+    "SELECT roi FROM Image as image " \
+    "LEFT OUTER JOIN image.rois as roi " \
+    "LEFT OUTER JOIN FETCH roi.details.externalInfo " \
+    "LEFT OUTER JOIN FETCH roi.shapes " \
+    "WHERE image.id = :id"
+
+
+def get_rois_copy(conn, source_image_id, target_image_id):
+    '''
+    This method creates copies of ROIs from the source image
+    and links them to the target image
+    '''
+    # Retrieve ROIs for source_image using ROI_QUERY
+    params = omero.sys.ParametersI()
+    params.addId(source_image_id)
+    results = conn.getQueryService().findAllByQuery(
+        ROI_QUERY, params, _ctx={'omero.group': '-1'})
+    # Check if the query result is None:
+    if len(results) == 1 and results[0] is None:
+        return []
+    LOGGER.info("Found %i ROIs to copy" % len(results))
+    # OMERO.image to link the ROIs to:
+    target_image = omero.model.ImageI(target_image_id, False)
+    # Copy ROIs in a loop:
+    for roi in results:
+        # Log ROI details:
+        roi_name = roi.name if roi.name is None else roi.name.val
+        LOGGER.info("Copying ROI name: %s, id: %i" % (roi_name, roi.id.val))
+        # Set copy ID to None - this way server knows we want to create a new
+        # ROI and not update existing one:
+        roi.id = None
+        # Get the externalInfo:
+        externalInfo = roi.details.externalInfo
+        # Unload details: ownership, groups, etc.:
+        roi.unloadDetails()
+        # Add externalInfo if exisits to inform PathViewer that it is
+        # a PathViewer created ROI (no popup):
+        if externalInfo is not None:
+            externalInfo.id = None
+            externalInfo.unloadDetails()
+            details = omero.model.DetailsI()
+            details.setExternalInfo(externalInfo)
+            roi._details = details
+        # Unload source image info:
+        roi.unloadImage()
+        # Link ROI to target image:
+        roi.setImage(target_image)
+        # Copy shapes beloning to the ROI:
+        for shape in roi.copyShapes():
+            shape.id = None
+            shape.unloadDetails()
+    return results
+
+
+def copy_rois(conn, source_image_id, target_image_id):
+    '''
+    This method asks for a copy of source image ROIs
+    and saves them to the server
+    '''
+    rois_to_copy = get_rois_copy(conn, source_image_id, target_image_id)
+    rois_to_copy = conn.getUpdateService().saveAndReturnArray(rois_to_copy)
+    return "Copied %i ROIs" % len(rois_to_copy)
+
+
+def run_as_omero_script():
+    client = scripts.client(
+        'Copy_ROIs.py',
+        """
+        This script creates map annotations.
+        """,
+        scripts.Long(
+            "Source_Image_Id", optional=False, grouping="1",
+            description="Source image Id"),
+        scripts.Long(
+            "Target_Image_Id", optional=False, grouping="2",
+            description="Source image Id"),
+        version="0.1",
+        authors=["Emil Rozbicki"],
+        institutions=["Glencoe Software Inc."],
+        contact="emil@glencoesoftware.com",
+    )
+    try:
+        # process the list of args above.
+        script_params = {}
+        for key in client.getInputKeys():
+            if client.getInput(key):
+                script_params[key.lower()] = client.getInput(key, unwrap=True)
+        # wrap client to use the Blitz Gateway
+        conn = BlitzGateway(client_obj=client)
+
+        # get image ids
+        source_image_id = script_params["source_image_id"]
+        target_image_id = script_params["target_image_id"]
+        LOGGER.info(
+            "Copying ROIs from Image %i to image %i" %
+            (source_image_id, target_image_id))
+        # copy images
+        message = copy_rois(conn, source_image_id, target_image_id)
+
+        # set ouput message in OMERO.web client
+        client.setOutput("Message", rstring(message))
+    finally:
+        client.closeSession()
+
+
+def main():
+    '''
+
+    OMERO.scripts are executed as ./script so will take advatage of that to
+    make the code usable as OMERO.script and standalone.
+
+    '''
+    level = logging.INFO
+    logging.basicConfig(level=level, format=LOGGING_FORMAT, stream=sys.stdout)
+    if not OMERO_IMPORTED:
+        LOGGER.warn("OMERO not on the path.")
+    if sys.argv[0] == './script':
+        run_as_omero_script()
+    else:
+        # Do somthing else here: parse command line args, etc.
+        pass
+
+
+if __name__ == "__main__":
+    main()