def setUp(self):
AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \
FromFileOriginalFileProvider
original_files = list()
# Create our container images and an original file image map
images = list()
n_images = 0
for row in range(16):
for column in range(24):
well = WellI(n_images, True)
well.column = rint(column)
well.row = rint(row)
well_sample = WellSampleI(n_images, True)
well_sample.well = well
image = ImageI(n_images, True)
image.addWellSample(well_sample)
images.append(image)
original_file_image_map = dict()
# Our required original file format
format = rstring('Companion/InCell')
# Create original file representing the result file
o = OriginalFileI(1, True)
o.name = rstring(self.RESULT_FILE)
o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE))
o.mimetype = format
original_files.append(o) # [1] = o
original_file_image_map[1] = image
sf = TestingServiceFactory()
self.analysis_ctx = InCellPlateAnalysisCtx(images, original_files,
original_file_image_map, 1,
sf)
def setUp(self):
AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \
FromFileOriginalFileProvider
original_files = list()
# Create our container images and an original file image map
images = list()
n_images = 0
for row in range(16):
for column in range(24):
well = WellI(n_images, True)
well.column = rint(column)
well.row = rint(row)
well_sample = WellSampleI(n_images, True)
well_sample.well = well
image = ImageI(n_images, True)
image.addWellSample(well_sample)
images.append(image)
original_file_image_map = dict()
# Our required original file format
format = rstring('Companion/InCell')
# Create original file representing the result file
o = OriginalFileI(1L, True)
o.name = rstring(self.RESULT_FILE)
o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE))
o.mimetype = format
original_files.append(o) #[1L] = o
original_file_image_map[1L] = image
sf = TestingServiceFactory()
self.analysis_ctx = InCellPlateAnalysisCtx(
images, original_files, original_file_image_map, 1L, sf)
def create_fileset():
"""Creates and returns a Fileset with associated Images."""
fileset = FilesetI()
fileset.templatePrefix = rstring("")
for image_index in range(2):
image = create_image(image_index)
for fileset_index in range(2):
fileset_entry = FilesetEntryI()
fileset_entry.clientPath = rstring("/client/path/filename_%d.ext" % fileset_index)
original_file = OriginalFileI()
original_file.name = rstring("filename_%d.ext" % fileset_index)
original_file.path = rstring("/server/path/")
original_file.size = rlong(50L)
fileset_entry.originalFile = original_file
fileset.addFilesetEntry(fileset_entry)
fileset.addImage(image)
return fileset
def create_fileset():
"""Creates and returns a Fileset with associated Images."""
fileset = FilesetI()
fileset.templatePrefix = rstring('')
for image_index in range(2):
image = create_image(image_index)
for fileset_index in range(2):
fileset_entry = FilesetEntryI()
fileset_entry.clientPath = rstring('/client/path/filename_%d.ext' %
fileset_index)
original_file = OriginalFileI()
original_file.name = rstring('filename_%d.ext' % fileset_index)
original_file.path = rstring('/server/path/')
original_file.size = rlong(50L)
fileset_entry.originalFile = original_file
fileset.addFilesetEntry(fileset_entry)
fileset.addImage(image)
return fileset
def images_with_original_files(request, gatewaywrapper):
"""Creates Images with associated OriginalFiles."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
original_files = list()
for original_file_index in range(2):
original_file = OriginalFileI()
original_file.name = rstring("filename_%d.ext" % original_file_index)
original_file.path = rstring("/server/path/")
original_file.size = rlong(50L)
original_files.append(original_file)
images = list()
for image_index in range(2):
image = create_image(image_index)
for original_file in original_files:
image.getPrimaryPixels().linkOriginalFile(original_file)
images.append(image)
image_ids = update_service.saveAndReturnIds(images)
return [gw.getObject("Image", image_id) for image_id in image_ids]
def images_with_original_files(request, gatewaywrapper):
"""Creates Images with associated OriginalFiles."""
gatewaywrapper.loginAsAuthor()
gw = gatewaywrapper.gateway
update_service = gw.getUpdateService()
original_files = list()
for original_file_index in range(2):
original_file = OriginalFileI()
original_file.name = rstring('filename_%d.ext' % original_file_index)
original_file.path = rstring('/server/path/')
original_file.size = rlong(50L)
original_files.append(original_file)
images = list()
for image_index in range(2):
image = create_image(image_index)
for original_file in original_files:
image.getPrimaryPixels().linkOriginalFile(original_file)
images.append(image)
image_ids = update_service.saveAndReturnIds(images)
return [gw.getObject('Image', image_id) for image_id in image_ids]
