def testPopulateRoisPlate(self):
"""
Create a small csv file, use populate_roi.py to parse and
attach to Plate. Then query to check table has expected content.
"""
csvName = self.createCsv(colNames="Well,Field,X,Y,Type",
rowData=("A1,0,15,15,Test", ))
rowCount = 1
colCount = 1
plate = self.createPlate(rowCount, colCount)
# As opposed to the ParsingContext, here we are expected
# to link the file ourselves
ofile = self.client.upload(csvName).proxy()
ann = FileAnnotationI()
ann.file = ofile
link = PlateAnnotationLinkI()
link.parent = plate.proxy()
link.child = ann
link = self.client.sf.getUpdateService()\
.saveAndReturnObject(link)
# End linking
factory = PlateAnalysisCtxFactory(self.client.sf)
factory.implementations = (MockPlateAnalysisCtx, )
ctx = factory.get_analysis_ctx(plate.id.val)
assert 1 == ctx.get_measurement_count()
meas = ctx.get_measurement_ctx(0)
meas.parse_and_populate()
# Get file annotations
query = """select p from Plate p
left outer join fetch p.annotationLinks links
left outer join fetch links.child as ann
left outer join fetch ann.file as file
where p.id=%s""" % plate.id.val
qs = self.client.sf.getQueryService()
plate = qs.findByQuery(query, None)
anns = plate.linkedAnnotationList()
# Only expect a single annotation which is a 'bulk annotation'
# the other is the original CSV
assert len(anns) == 2
files = dict([(a.ns.val, a.file.id.val) for a in anns if a.ns])
fileid = files[NSMEASUREMENT]
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == 1
data = t.read(range(len(cols)), 0, 1)
imag = data.columns[0].values[0]
rois = self.client.sf.getRoiService()
anns = rois.getRoiMeasurements(imag, RoiOptions())
assert anns
Copyright 2009 Glencoe Software, Inc. All rights reserved.
Use is subject to license terms supplied in LICENSE.txt
"""
import omero.scripts as scripts
from omero.util.populate_roi import PlateAnalysisCtxFactory
client = scripts.client(
'Populate_ROI.py',
scripts.Long(
"Plate_ID",
optional=False,
description="ID of a valid plate with attached results files"),
version="4.2.0",
contact="*****@*****.**",
description="""Generates regions of interest from the measurement files \
associated with a plate
This script is executed by the server on initial import, and should typically\
not need to be run by users.""")
factory = PlateAnalysisCtxFactory(client.getSession())
analysis_ctx = factory.get_analysis_ctx(client.getInput("Plate_ID").val)
n_measurements = analysis_ctx.get_measurement_count()
for i in range(n_measurements):
measurement_ctx = analysis_ctx.get_measurement_ctx(i)
measurement_ctx.parse_and_populate()
Plate_ID: id of the plate which should be parsed.
Copyright 2009 Glencoe Software, Inc. All rights reserved.
Use is subject to license terms supplied in LICENSE.txt
"""
import omero.scripts as scripts
from omero.util.populate_roi import PlateAnalysisCtxFactory
client = scripts.client(
'Populate_ROI.py',
scripts.Long(
"Plate_ID", optional=False,
description="ID of a valid plate with attached results files"),
version="4.2.0",
contact="*****@*****.**",
description="""Generates regions of interest from the measurement files \
associated with a plate
This script is executed by the server on initial import, and should typically\
not need to be run by users.""")
factory = PlateAnalysisCtxFactory(client.getSession())
analysis_ctx = factory.get_analysis_ctx(client.getInput("Plate_ID").val)
n_measurements = analysis_ctx.get_measurement_count()
for i in range(n_measurements):
measurement_ctx = analysis_ctx.get_measurement_ctx(i)
measurement_ctx.parse_and_populate()
def testPopulateRoisPlate(self):
"""
Create a small csv file, use populate_roi.py to parse and
attach to Plate. Then query to check table has expected content.
"""
csvName = self.createCsv(
colNames="Well,Field,X,Y,Type",
rowData=("A1,0,15,15,Test",))
rowCount = 1
colCount = 1
plate = self.createPlate(rowCount, colCount)
# As opposed to the ParsingContext, here we are expected
# to link the file ourselves
ofile = self.client.upload(csvName).proxy()
ann = FileAnnotationI()
ann.file = ofile
link = PlateAnnotationLinkI()
link.parent = plate.proxy()
link.child = ann
link = self.client.sf.getUpdateService()\
.saveAndReturnObject(link)
# End linking
factory = PlateAnalysisCtxFactory(self.client.sf)
factory.implementations = (MockPlateAnalysisCtx,)
ctx = factory.get_analysis_ctx(plate.id.val)
assert 1 == ctx.get_measurement_count()
meas = ctx.get_measurement_ctx(0)
meas.parse_and_populate()
# Get file annotations
query = """select p from Plate p
left outer join fetch p.annotationLinks links
left outer join fetch links.child as ann
left outer join fetch ann.file as file
where p.id=%s""" % plate.id.val
qs = self.client.sf.getQueryService()
plate = qs.findByQuery(query, None)
anns = plate.linkedAnnotationList()
# Only expect a single annotation which is a 'bulk annotation'
# the other is the original CSV
assert len(anns) == 2
files = dict(
[(a.ns.val, a.file.id.val) for a in anns if a.ns])
fileid = files[NSMEASUREMENT]
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == 1
data = t.read(range(len(cols)), 0, 1)
imag = data.columns[0].values[0]
rois = self.client.sf.getRoiService()
anns = rois.getRoiMeasurements(imag, RoiOptions())
assert anns
