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Fixes adding of multiple Images to a new Well. #1

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Merged
dsudar merged 1 commit into from
Nov 4, 2016
Merged

Fixes adding of multiple Images to a new Well. #1

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52 changes: 27 additions & 25 deletions Dataset_To_Well.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
components/tools/OmeroPy/scripts/omero/util_scripts/Dataset_To_Well.py

-----------------------------------------------------------------------------
Copyright (C) 2006-2014 University of Dundee. All rights reserved.
Copyright (C) 2006-2016 University of Dundee. All rights reserved.


This program is free software; you can redistribute it and/or modify
Expand Down Expand Up @@ -35,33 +35,42 @@
import omero

from omero.rtypes import rint, rlong, rstring, robject, unwrap
from omero.model.enums import UnitsLength

from random import random

def addImageToWell(conn, image, well, removeFrom=None):
def addImagesToWell(conn, images, plateId, row, col, removeFrom=None):
"""
Add the Image to a Plate, creating a new well at the specified column and
row
NB - This will fail if there is already a well at that point
Add Images to a New well, creating a new wellSample for each
"""
updateService = conn.getUpdateService()

well = omero.model.WellI()
well.plate = omero.model.PlateI(plateId, False)
well.column = rint(col-1)
well.row = rint(row-1)

try:
ws = omero.model.WellSampleI()
ws.image = omero.model.ImageI(image.id, False)
ws.well = well
well.addWellSample(ws)
updateService.saveObject(ws)
for image in images:
ws = omero.model.WellSampleI()
ws.image = omero.model.ImageI(image.id, False)
ws.well = well
# Optional, add position X and Y
ws.posX = omero.model.LengthI(random() * 100, UnitsLength.REFERENCEFRAME)
ws.posY = omero.model.LengthI(random() * 100, UnitsLength.REFERENCEFRAME)
well.addWellSample(ws)
updateService.saveObject(well)
except:
print "Failed to add image to well sample"
return False

# remove from Datast
if removeFrom is not None:
links = list(image.getParentLinks(removeFrom.id))
print " Removing image from Dataset: %s" \
% removeFrom.id
for l in links:
conn.deleteObjectDirect(l._obj)
for image in images:
for l in image.getParentLinks(removeFrom.id):
print " Removing image from Dataset: %s" \
% removeFrom.id
conn.deleteObjectDirect(l._obj)
return True


Expand All @@ -74,8 +83,8 @@ def dataset_to_well(conn, scriptParams, datasetId, plateId):

updateService = conn.getUpdateService()

row = scriptParams["Well_Column"]
col = scriptParams["Well_Row"]
col = scriptParams["Well_Column"]
row = scriptParams["Well_Row"]

plate = conn.getObject("Plate", plateId)
if plate is None:
Expand All @@ -101,14 +110,7 @@ def dataset_to_well(conn, scriptParams, datasetId, plateId):
if removeDataset:
removeFrom = dataset

well = omero.model.WellI()
well.plate = omero.model.PlateI(plate.getId(), False)
well.column = rint(col-1)
well.row = rint(row-1)
well = updateService.saveAndReturnObject(well)

for image in images:
addedCount = addImageToWell(conn, image, well, removeFrom)
addedCount = addImagesToWell(conn, images, plate.getId(), row, col, removeFrom)

# if user wanted to delete dataset, AND it's empty we can delete dataset
deleteDataset = False # Turning this functionality off for now.
Expand Down