def test_screen_decoder(self, screen):
encoder = get_encoder(screen.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen)
v = decoder.decode(v)
self.assert_screen(v)
assert v.sizeOfPlateLinks() == 0
def test_roi_with_shapes_and_annotations(self,
roi_with_shapes_and_annotations):
encoder = get_encoder(roi_with_shapes_and_annotations.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi_with_shapes_and_annotations)
v = decoder.decode(v)
self.assert_roi_with_shapes(v, has_annotations=True)
def test_well_color_decoder(self, color, well):
"""Test different combinations of r, g, b, a."""
well.red = rint(color[0])
well.green = rint(color[1])
well.blue = rint(color[2])
well.alpha = rint(color[3])
encoder = get_encoder(well.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(well)
# Check we get the expected Integer
assert v.get('Color') == color[4]
v = decoder.decode(v)
# If red is None, all are None
if color[0] is None:
assert v.red is None
assert v.green is None
assert v.blue is None
assert v.alpha is None
elif color[3] is None:
# alpha None -> 255 by default
assert v.red.val == color[0]
assert v.green.val == color[1]
assert v.blue.val == color[2]
assert v.alpha.val == 255
else:
# Otherwise, all preserved
assert v.red.val == color[0]
assert v.green.val == color[1]
assert v.blue.val == color[2]
assert v.alpha.val == color[3]
def test_roi_with_shapes_and_annotations(
self, roi_with_shapes_and_annotations):
encoder = get_encoder(roi_with_shapes_and_annotations.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi_with_shapes_and_annotations)
v = decoder.decode(v)
self.assert_roi_with_shapes(v, has_annotations=True)
def test_decoder(self, mask):
encoder = get_encoder(mask.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(mask)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 8
def test_screen_decoder(self, screen):
encoder = get_encoder(screen.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen)
v = decoder.decode(v)
self.assert_screen(v)
assert v.sizeOfPlateLinks() == 0
def test_project_decoder(self, project):
encoder = get_encoder(project.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project)
v = decoder.decode(v)
self.assert_project(v)
assert v.sizeOfDatasetLinks() == 0
def test_base_decoder(self, roi):
encoder = get_encoder(roi.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi)
v = decoder.decode(v)
self.assert_roi(v)
self.assert_externalInfo(v.details.externalInfo)
def test_project_validation(self, user_A):
"""
Test to demonstrate details bug on encode->decode.
Test illustrates the ValidationException we see when
Project is encoded to dict then decoded back to Project
and saved.
No exception is seen if the original Project is simply
saved without encode & decode OR if the details are unloaded
before saving
"""
conn = get_connection(user_A)
project = ProjectI()
project.name = rstring('test_project_validation')
project = conn.getUpdateService().saveAndReturnObject(project)
# Saving original Project again is OK
conn.getUpdateService().saveObject(project)
# encode and decode before Save raises Validation Exception
project_json = get_encoder(project.__class__).encode(project)
decoder = get_decoder(project_json['@type'])
p = decoder.decode(project_json)
with pytest.raises(ValidationException):
conn.getUpdateService().saveObject(p)
p = decoder.decode(project_json)
# Unloading details allows Save without exception
p.unloadDetails()
conn.getUpdateService().saveObject(p)
def test_project_decoder(self, project):
encoder = get_encoder(project.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project)
v = decoder.decode(v)
self.assert_project(v)
assert v.sizeOfDatasetLinks() == 0
def test_base_decoder(self, roi):
encoder = get_encoder(roi.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi)
v = decoder.decode(v)
self.assert_roi(v)
self.assert_externalInfo(v.details.externalInfo)
def test_decoder(self, polygon):
encoder = get_encoder(polygon.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polygon)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 5L
assert v.points.val == '0,0 1,2 3,5'
def test_decoder(self, polygon):
encoder = get_encoder(polygon.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polygon)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 5L
assert v.points.val == '0,0 1,2 3,5'
def test_permissions_cannot_delete(self, permissions_cannot_delete):
encoder = get_encoder(permissions_cannot_delete.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(permissions_cannot_delete)
v = decoder.decode(v)
assert v.canLink()
assert v.canEdit()
assert not v.canDelete()
assert v.canAnnotate()
def test_permissions_cannot_delete(self, permissions_cannot_delete):
encoder = get_encoder(permissions_cannot_delete.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(permissions_cannot_delete)
v = decoder.decode(v)
assert v.canLink()
assert v.canEdit()
assert not v.canDelete()
assert v.canAnnotate()
def test_decoder(self, opt_unit_label):
encoder = get_encoder(opt_unit_label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(opt_unit_label)
v = decoder.decode(v)
self.assert_shape(v, has_unit_information=False)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_project_with_datasets_and_images_decoder(
self, project_with_datasets_and_images):
encoder = get_encoder(project_with_datasets_and_images.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project_with_datasets_and_images)
v = decoder.decode(v)
assert v.id.val == 1L
assert v.name.val == 'the_name'
assert v.description.val == 'the_description'
assert v.sizeOfDatasetLinks() == 2
dataset_1, dataset_2 = v.linkedDatasetList()
assert dataset_1.id.val == 1L
assert dataset_1.name.val == 'dataset_name_1'
assert dataset_1.description.val == 'dataset_description_1'
image_1, image_2 = dataset_1.linkedImageList()
assert image_1.id.val == 1L
assert image_1.acquisitionDate.val == 1L
assert image_1.archived.val is False
assert image_1.description.val == 'image_description_1'
assert image_1.name.val == 'image_name_1'
assert image_1.partial.val is False
assert image_1.format.id.val == 1L
assert image_1.format.value.val == 'PNG'
assert image_2.id.val == 2L
assert image_2.acquisitionDate.val == 1L
assert image_2.archived.val is False
assert image_2.description.val == 'image_description_2'
assert image_2.name.val == 'image_name_2'
assert image_2.partial.val is False
assert image_2.format.id.val == 1L
assert image_2.format.value.val == 'PNG'
assert dataset_2.id.val == 2L
assert dataset_2.name.val == 'dataset_name_2'
assert dataset_2.description.val == 'dataset_description_2'
image_3, image_4 = dataset_2.linkedImageList()
assert image_3.id.val == 3L
assert image_3.acquisitionDate.val == 1L
assert image_3.archived.val is False
assert image_3.description.val == 'image_description_3'
assert image_3.name.val == 'image_name_3'
assert image_3.partial.val is False
assert image_3.format.id.val == 1L
assert image_3.format.value.val == 'PNG'
assert image_4.id.val == 4L
assert image_4.acquisitionDate.val == 1L
assert image_4.archived.val is False
assert image_4.description.val == 'image_description_4'
assert image_4.name.val == 'image_name_4'
assert image_4.partial.val is False
assert image_4.format.id.val == 1L
assert image_4.format.value.val == 'PNG'
def test_base_decoder_from_string(self):
data_as_string = """{
"@type": "http://www.openmicroscopy.org/Schemas/ROI/2015-01#ROI",
"@id": 1,
"Name": "the_name",
"Description": "the_description"
}"""
data = json.loads(data_as_string)
decoder = get_decoder(data['@type'])
v = decoder.decode(data)
self.assert_roi(v)
def test_decoder(self, polyline):
encoder = get_encoder(polyline.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polyline)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 4L
assert v.points.val == '0,0 1,2 3,5'
if SCHEMA_VERSION != '2015-01':
assert v.markerStart.val == 'Arrow'
assert v.markerEnd.val == 'Arrow'
def test_screen_with_plates_decoder(self, screen_with_plates):
encoder = get_encoder(screen_with_plates.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen_with_plates)
v = decoder.decode(v)
self.assert_screen(v)
assert v.id.val == 4L
assert v.sizeOfPlateLinks() == 2
plate_1, plate_2 = v.linkedPlateList()
self.assert_plate(plate_1, 5L)
self.assert_plate(plate_2, 6L)
def test_project_with_datasets_and_images_decoder(
self, project_with_datasets_and_images):
encoder = get_encoder(project_with_datasets_and_images.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project_with_datasets_and_images)
v = decoder.decode(v)
assert v.id.val == 1L
assert v.name.val == 'the_name'
assert v.description.val == 'the_description'
assert v.sizeOfDatasetLinks() == 2
dataset_1, dataset_2 = v.linkedDatasetList()
assert dataset_1.id.val == 1L
assert dataset_1.name.val == 'dataset_name_1'
assert dataset_1.description.val == 'dataset_description_1'
image_1, image_2 = dataset_1.linkedImageList()
assert image_1.id.val == 1L
assert image_1.acquisitionDate.val == 1L
assert image_1.archived.val is False
assert image_1.description.val == 'image_description_1'
assert image_1.name.val == 'image_name_1'
assert image_1.partial.val is False
assert image_1.format.id.val == 1L
assert image_1.format.value.val == 'PNG'
assert image_2.id.val == 2L
assert image_2.acquisitionDate.val == 1L
assert image_2.archived.val is False
assert image_2.description.val == 'image_description_2'
assert image_2.name.val == 'image_name_2'
assert image_2.partial.val is False
assert image_2.format.id.val == 1L
assert image_2.format.value.val == 'PNG'
assert dataset_2.id.val == 2L
assert dataset_2.name.val == 'dataset_name_2'
assert dataset_2.description.val == 'dataset_description_2'
image_3, image_4 = dataset_2.linkedImageList()
assert image_3.id.val == 3L
assert image_3.acquisitionDate.val == 1L
assert image_3.archived.val is False
assert image_3.description.val == 'image_description_3'
assert image_3.name.val == 'image_name_3'
assert image_3.partial.val is False
assert image_3.format.id.val == 1L
assert image_3.format.value.val == 'PNG'
assert image_4.id.val == 4L
assert image_4.acquisitionDate.val == 1L
assert image_4.archived.val is False
assert image_4.description.val == 'image_description_4'
assert image_4.name.val == 'image_name_4'
assert image_4.partial.val is False
assert image_4.format.id.val == 1L
assert image_4.format.value.val == 'PNG'
def test_decoder(self, label):
encoder = get_encoder(label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(label)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_decoder(self, label):
encoder = get_encoder(label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(label)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_decoder(self, point):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(point)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 3L
assert v.cx.__class__ is RDoubleI
assert v.cx.val == 1.0
assert v.cy.__class__ is RDoubleI
assert v.cy.val == 2.0
def test_decoder(self, point):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(point)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 3L
assert v.cx.__class__ is RDoubleI
assert v.cx.val == 1.0
assert v.cy.__class__ is RDoubleI
assert v.cy.val == 2.0
def test_decoder(self, polyline):
encoder = get_encoder(polyline.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(polyline)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 4L
assert v.points.val == '0,0 1,2 3,5'
if SCHEMA_VERSION != '2015-01':
assert v.markerStart.val == 'Arrow'
assert v.markerEnd.val == 'Arrow'
def test_base_decoder_from_string(self):
data_as_string = """{
"@type": "http://www.openmicroscopy.org/Schemas/ROI/2015-01#ROI",
"@id": 1,
"Name": "the_name",
"Description": "the_description"
}"""
data = json.loads(data_as_string)
decoder = get_decoder(data['@type'])
v = decoder.decode(data)
self.assert_roi(v)
def test_screen_with_plates_decoder(self, screen_with_plates):
encoder = get_encoder(screen_with_plates.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(screen_with_plates)
v = decoder.decode(v)
self.assert_screen(v)
assert v.id.val == 4L
assert v.sizeOfPlateLinks() == 2
plate_1, plate_2 = v.linkedPlateList()
self.assert_plate(plate_1, 5L)
self.assert_plate(plate_2, 6L)
def test_decoder(self, opt_unit_label):
encoder = get_encoder(opt_unit_label.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(opt_unit_label)
v = decoder.decode(v)
self.assert_shape(v, has_unit_information=False)
assert v.id.val == 7L
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
def test_decoder(self, line):
encoder = get_encoder(line.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(line)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 6L
assert v.x1.__class__ is RDoubleI
assert v.x1.val == 0.0
assert v.y1.__class__ is RDoubleI
assert v.y1.val == 0.0
assert v.x2.__class__ is RDoubleI
assert v.x2.val == 1.0
assert v.y2.__class__ is RDoubleI
assert v.y2.val == 2.0
def test_decoder(self, line):
encoder = get_encoder(line.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(line)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 6L
assert v.x1.__class__ is RDoubleI
assert v.x1.val == 0.0
assert v.y1.__class__ is RDoubleI
assert v.y1.val == 0.0
assert v.x2.__class__ is RDoubleI
assert v.x2.val == 1.0
assert v.y2.__class__ is RDoubleI
assert v.y2.val == 2.0
def test_shape_decoder(self, point, translation_transform):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
if SCHEMA_VERSION == '2015-01':
point.transform = translation_transform.svg_transform
else:
point.transform = translation_transform
v = encoder.encode(point)
v = decoder.decode(v)
t = v.transform
if SCHEMA_VERSION == '2015-01':
assert t.val == 'matrix(1.0 0.0 0.0 1.0 3.0 4.0)'
else:
assert t.id.val == 8L
self.assert_translation_transform(t)
def _save_object(self, request, conn, object_json, **kwargs):
"""Here we handle the saving for PUT and POST."""
# Try to get group from request, OR from details below...
group = getIntOrDefault(request, 'group', None)
decoder = None
objType = object_json['@type']
decoder = get_decoder(objType)
# If we are passed incomplete object, or decoder couldn't be found...
if decoder is None:
raise BadRequestError('No decoder found for type: %s' % objType)
# Any marshal errors most likely due to invalid input. status=400
try:
obj = decoder.decode(object_json)
except Exception:
msg = 'Error in decode of json data by omero_marshal'
raise BadRequestError(msg, traceback.format_exc())
if group is None:
try:
# group might be None or unloaded
group = obj.getDetails().group.id.val
except AttributeError:
# Instead of default stack trace, give nicer message:
msg = ("Specify Group in omero:details or "
"query parameters ?group=:id")
raise BadRequestError(msg)
# If owner was unloaded (E.g. from get() above) or if missing
# ome.model.meta.Experimenter.ldap (not supported by omero_marshal)
# then saveObject() will give ValidationException.
# Therefore we ignore any details for now:
obj.unloadDetails()
# TODO: Unlink children for Projects, Datasets and Screens to avoid
# breaking links. See PR #4930
if hasattr(obj, 'unloadDatasetLinks'):
obj.unloadDatasetLinks()
if hasattr(obj, 'unloadImageLinks'):
obj.unloadImageLinks()
if hasattr(obj, 'unloadPlateLinks'):
obj.unloadPlateLinks()
conn.SERVICE_OPTS.setOmeroGroup(group)
obj = conn.getUpdateService().saveAndReturnObject(
obj, conn.SERVICE_OPTS)
encoder = get_encoder(obj.__class__)
return {'data': encoder.encode(obj)}
def test_project_with_datasets_decoder(self, project_with_datasets):
encoder = get_encoder(project_with_datasets.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project_with_datasets)
v = decoder.decode(v)
assert v.id.val == 1L
assert v.name.val == 'the_name'
assert v.description.val == 'the_description'
assert v.sizeOfDatasetLinks() == 2
dataset_1, dataset_2 = v.linkedDatasetList()
assert dataset_1.id.val == 1L
assert dataset_1.name.val == 'dataset_name_1'
assert dataset_1.description.val == 'dataset_description_1'
assert dataset_2.id.val == 2L
assert dataset_2.name.val == 'dataset_name_2'
assert dataset_2.description.val == 'dataset_description_2'
def test_project_with_datasets_decoder(self, project_with_datasets):
encoder = get_encoder(project_with_datasets.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(project_with_datasets)
v = decoder.decode(v)
assert v.id.val == 1L
assert v.name.val == 'the_name'
assert v.description.val == 'the_description'
assert v.sizeOfDatasetLinks() == 2
dataset_1, dataset_2 = v.linkedDatasetList()
assert dataset_1.id.val == 1L
assert dataset_1.name.val == 'dataset_name_1'
assert dataset_1.description.val == 'dataset_description_1'
assert dataset_2.id.val == 2L
assert dataset_2.name.val == 'dataset_name_2'
assert dataset_2.description.val == 'dataset_description_2'
def test_shape_decoder(self, point, rotation_transform):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
if SCHEMA_VERSION == '2015-01':
point.transform = rotation_transform.svg_transform
else:
point.transform = rotation_transform
v = encoder.encode(point)
v = decoder.decode(v)
t = v.transform
if SCHEMA_VERSION == '2015-01':
assert t.val == (
'matrix(0.707106781187 0.707106781187 -0.707106781187 '
'0.707106781187 85.3553390593 -6.06601717798)')
else:
assert t.id.val == 8L
self.assert_rotation_transform(t)
def test_decoder(self, point):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(point)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 3L
if SCHEMA_VERSION == '2016-06':
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
else:
assert v.cx.__class__ is RDoubleI
assert v.cx.val == 1.0
assert v.cy.__class__ is RDoubleI
assert v.cy.val == 2.0
def test_decoder(self, point):
encoder = get_encoder(point.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(point)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 3L
if SCHEMA_VERSION == '2016-06':
assert v.x.__class__ is RDoubleI
assert v.x.val == 1.0
assert v.y.__class__ is RDoubleI
assert v.y.val == 2.0
else:
assert v.cx.__class__ is RDoubleI
assert v.cx.val == 1.0
assert v.cy.__class__ is RDoubleI
assert v.cy.val == 2.0
def test_decoder(self, line):
encoder = get_encoder(line.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(line)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 6L
assert v.x1.__class__ is RDoubleI
assert v.x1.val == 0.0
assert v.y1.__class__ is RDoubleI
assert v.y1.val == 0.0
assert v.x2.__class__ is RDoubleI
assert v.x2.val == 1.0
assert v.y2.__class__ is RDoubleI
assert v.y2.val == 2.0
if SCHEMA_VERSION != '2015-01':
assert v.markerStart.val == 'Arrow'
assert v.markerEnd.val == 'Arrow'
def test_decoder(self, line):
encoder = get_encoder(line.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(line)
v = decoder.decode(v)
self.assert_shape(v)
assert v.id.val == 6L
assert v.x1.__class__ is RDoubleI
assert v.x1.val == 0.0
assert v.y1.__class__ is RDoubleI
assert v.y1.val == 0.0
assert v.x2.__class__ is RDoubleI
assert v.x2.val == 1.0
assert v.y2.__class__ is RDoubleI
assert v.y2.val == 2.0
if SCHEMA_VERSION != '2015-01':
assert v.markerStart.val == 'Arrow'
assert v.markerEnd.val == 'Arrow'
def test_roi_decoder_registered(self):
decoder = get_decoder('%s#ROI' % ROI_SCHEMA_URL)
assert decoder is not None
def test_image_pixels_decoder(self, image_pixels):
encoder = get_encoder(image_pixels.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(image_pixels)
v = decoder.decode(v)
self.assert_image(v)
pixels = v.getPrimaryPixels()
assert pixels.id.val == 1L
assert pixels.methodology.val == 'methodology'
assert pixels.physicalSizeX.getUnit() == UnitsLength.MICROMETER
assert pixels.physicalSizeX.getValue() == 1.0
assert pixels.physicalSizeY.getUnit() == UnitsLength.MICROMETER
assert pixels.physicalSizeY.getValue() == 2.0
assert pixels.physicalSizeZ.getUnit() == UnitsLength.MICROMETER
assert pixels.physicalSizeZ.getValue() == 3.0
assert pixels.sha1.val == '61ee8b5601a84d5154387578466c8998848ba089'
assert pixels.significantBits.val == 16
assert pixels.sizeX.val == 1
assert pixels.sizeY.val == 2
assert pixels.sizeZ.val == 3
assert pixels.sizeC.val == 4
assert pixels.sizeT.val == 5
assert pixels.timeIncrement.getUnit() == UnitsTime.MILLISECOND
assert pixels.timeIncrement.getValue() == 1.0
assert pixels.waveIncrement.val == 2.0
assert pixels.waveStart.val == 1
assert pixels.dimensionOrder.id.val == 1L
assert pixels.dimensionOrder.value.val == 'XYZCT'
assert pixels.pixelsType.id.val == 1L
assert pixels.pixelsType.value.val == 'bit'
channel_1, channel_2 = pixels.copyChannels()
assert channel_1.id.val == 1L
assert channel_1.alpha.val == 255
assert channel_1.blue.val == 0
assert channel_1.green.val == 255
assert channel_1.red.val == 0
assert channel_1.lookupTable.val == 'rainbow'
logical_channel_1 = channel_1.logicalChannel
assert logical_channel_1.id.val == 1L
assert logical_channel_1.emissionWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_1.emissionWave.getValue() == 509.0
assert logical_channel_1.excitationWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_1.excitationWave.getValue() == 488.0
assert logical_channel_1.fluor.val == 'GFP'
assert logical_channel_1.name.val == 'GFP/488'
assert logical_channel_1.ndFilter.val == 1.0
assert logical_channel_1.pinHoleSize.getUnit() == UnitsLength.NANOMETER
assert logical_channel_1.pinHoleSize.getValue() == 1.0
assert logical_channel_1.pockelCellSetting.val == 0
assert logical_channel_1.samplesPerPixel.val == 2
assert logical_channel_1.contrastMethod.value.val == 'Fluorescence'
assert logical_channel_1.illumination.value.val == 'Transmitted'
assert logical_channel_1.mode.value.val == 'WideField'
assert logical_channel_1.photometricInterpretation.value.val == 'RGB'
assert channel_2.id.val == 2L
assert channel_2.alpha.val == 255
assert channel_2.blue.val == 255
assert channel_2.green.val == 0
assert channel_2.red.val == 0
assert channel_2.lookupTable.val == 'rainbow'
logical_channel_2 = channel_2.logicalChannel
assert logical_channel_2.id.val == 2L
assert logical_channel_2.emissionWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_2.emissionWave.getValue() == 470.0
assert logical_channel_2.excitationWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_2.excitationWave.getValue() == 405.0
assert logical_channel_2.fluor.val == 'DAPI'
assert logical_channel_2.name.val == 'DAPI/405'
assert logical_channel_2.ndFilter.val == 1.0
assert logical_channel_2.pinHoleSize.getUnit() == UnitsLength.NANOMETER
assert logical_channel_2.pinHoleSize.getValue() == 2.0
assert logical_channel_2.pockelCellSetting.val == 0
assert logical_channel_2.samplesPerPixel.val == 2
assert logical_channel_2.contrastMethod.value.val == 'Fluorescence'
assert logical_channel_2.illumination.value.val == 'Transmitted'
assert logical_channel_2.mode.value.val == 'WideField'
assert logical_channel_2.photometricInterpretation.value.val == 'RGB'
def test_image_decoder(self, image):
encoder = get_encoder(image.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(image)
v = decoder.decode(v)
self.assert_image(v)
def test_decoder(self, rectangle):
encoder = get_encoder(rectangle.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(rectangle)
v = decoder.decode(v)
self.assert_rectangle(v)
def test_image_decoder(self, image):
encoder = get_encoder(image.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(image)
v = decoder.decode(v)
self.assert_image(v)
def test_image_pixels_decoder(self, image_pixels):
encoder = get_encoder(image_pixels.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(image_pixels)
v = decoder.decode(v)
self.assert_image(v)
pixels = v.getPrimaryPixels()
assert pixels.id.val == 1L
assert pixels.methodology.val == 'methodology'
assert pixels.physicalSizeX.getUnit() == UnitsLength.MICROMETER
assert pixels.physicalSizeX.getValue() == 1.0
assert pixels.physicalSizeY.getUnit() == UnitsLength.MICROMETER
assert pixels.physicalSizeY.getValue() == 2.0
assert pixels.physicalSizeZ.getUnit() == UnitsLength.MICROMETER
assert pixels.physicalSizeZ.getValue() == 3.0
assert pixels.sha1.val == '61ee8b5601a84d5154387578466c8998848ba089'
assert pixels.significantBits.val == 16
assert pixels.sizeX.val == 1
assert pixels.sizeY.val == 2
assert pixels.sizeZ.val == 3
assert pixels.sizeC.val == 4
assert pixels.sizeT.val == 5
assert pixels.timeIncrement.getUnit() == UnitsTime.MILLISECOND
assert pixels.timeIncrement.getValue() == 1.0
assert pixels.waveIncrement.val == 2.0
assert pixels.waveStart.val == 1
assert pixels.dimensionOrder.id.val == 1L
assert pixels.dimensionOrder.value.val == 'XYZCT'
assert pixels.pixelsType.id.val == 1L
assert pixels.pixelsType.value.val == 'bit'
channel_1, channel_2 = pixels.copyChannels()
assert channel_1.id.val == 1L
assert channel_1.alpha.val == 255
assert channel_1.blue.val == 255
assert channel_1.green.val == 255
assert channel_1.red.val == 255
assert channel_1.lookupTable.val == 'rainbow'
logical_channel_1 = channel_1.logicalChannel
assert logical_channel_1.id.val == 1L
assert logical_channel_1.emissionWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_1.emissionWave.getValue() == 509.0
assert logical_channel_1.excitationWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_1.excitationWave.getValue() == 488.0
assert logical_channel_1.fluor.val == 'GFP'
assert logical_channel_1.name.val == 'GFP/488'
assert logical_channel_1.ndFilter.val == 1.0
assert logical_channel_1.pinHoleSize.getUnit() == UnitsLength.NANOMETER
assert logical_channel_1.pinHoleSize.getValue() == 1.0
assert logical_channel_1.pockelCellSetting.val == 0
assert logical_channel_1.samplesPerPixel.val == 2
assert logical_channel_1.contrastMethod.value.val == 'Fluorescence'
assert logical_channel_1.illumination.value.val == 'Transmitted'
assert logical_channel_1.mode.value.val == 'WideField'
assert logical_channel_1.photometricInterpretation.value.val == 'RGB'
assert channel_2.id.val == 2L
assert channel_2.alpha.val == 255
assert channel_2.blue.val == 255
assert channel_2.green.val == 0
assert channel_2.red.val == 255
assert channel_2.lookupTable.val == 'rainbow'
logical_channel_2 = channel_2.logicalChannel
assert logical_channel_2.id.val == 2L
assert logical_channel_2.emissionWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_2.emissionWave.getValue() == 470.0
assert logical_channel_2.excitationWave.getUnit() \
== UnitsLength.NANOMETER
assert logical_channel_2.excitationWave.getValue() == 405.0
assert logical_channel_2.fluor.val == 'DAPI'
assert logical_channel_2.name.val == 'DAPI/405'
assert logical_channel_2.ndFilter.val == 1.0
assert logical_channel_2.pinHoleSize.getUnit() == UnitsLength.NANOMETER
assert logical_channel_2.pinHoleSize.getValue() == 2.0
assert logical_channel_2.pockelCellSetting.val == 0
assert logical_channel_2.samplesPerPixel.val == 2
assert logical_channel_2.contrastMethod.value.val == 'Fluorescence'
assert logical_channel_2.illumination.value.val == 'Transmitted'
assert logical_channel_2.mode.value.val == 'WideField'
assert logical_channel_2.photometricInterpretation.value.val == 'RGB'
def test_decoder(self, ellipse):
encoder = get_encoder(ellipse.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(ellipse)
v = decoder.decode(v)
self.assert_ellipse(v)
def test_encoder_with_annotations(self, ellipse_with_annotations):
encoder = get_encoder(ellipse_with_annotations.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(ellipse_with_annotations)
v = decoder.decode(v)
self.assert_ellipse(v, has_annotations=True)
def test_decoder(self, rectangle):
encoder = get_encoder(rectangle.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(rectangle)
v = decoder.decode(v)
self.assert_rectangle(v)
def test_encoder_with_annotations(self, ellipse_with_annotations):
encoder = get_encoder(ellipse_with_annotations.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(ellipse_with_annotations)
v = decoder.decode(v)
self.assert_ellipse(v, has_annotations=True)
def test_decoder(self, ellipse):
encoder = get_encoder(ellipse.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(ellipse)
v = decoder.decode(v)
self.assert_ellipse(v)
def persist_rois(request, conn=None, **kwargs):
if not request.method == 'POST':
return JsonResponse({"errors": ["Use HTTP POST to send data!"]})
try:
rois_dict = json.loads(request.body)
except Exception as e:
return JsonResponse({"errors": ["Failed to load json: " + repr(e)]})
# some preliminary checks are following...
image_id = rois_dict.get('imageId', None)
if image_id is None:
return JsonResponse({"errors": ["No image id provided!"]})
rois = rois_dict.get('rois', None)
if rois is None:
return JsonResponse({"errors": ["Could not find rois object!"]})
# get the associated image and an instance of the update service
image = conn.getObject("Image", image_id, opts=conn.SERVICE_OPTS)
if image is None:
return JsonResponse({"errors": ["Could not find associated image!"]})
# prepare services
update_service = conn.getUpdateService()
if update_service is None:
return JsonResponse({"errors": ["Could not get update service!"]})
# when persisting we use the specific group context
conn.SERVICE_OPTS['omero.group'] = image.getDetails().getGroup().getId()
# for id syncing
ids_to_sync = {}
# keep track of errors
errors = []
# insert new ones
try:
new = rois.get('new', [])
new_count = len(new)
if new_count > 0:
decoded_rois = []
for n in new:
new_roi = {
"@type":
"http://www.openmicroscopy.org/Schemas/OME/2016-06#ROI",
"shapes": [n]
}
decoder = omero_marshal.get_decoder(new_roi.get("@type"))
decoded_roi = decoder.decode(new_roi)
decoded_roi.setImage(image._obj)
decoded_rois.append(decoded_roi)
decoded_rois = update_service.saveAndReturnArray(
decoded_rois, conn.SERVICE_OPTS)
# sync ids
for r in range(new_count):
ids_to_sync[new[r]['oldId']] = \
str(decoded_rois[r].getId().getValue()) + ':' + \
str(decoded_rois[r].getShape(0).getId().getValue())
except Exception as marshal_or_persistence_exception:
errors.append('Error persisting new rois: ' +
repr(marshal_or_persistence_exception))
# modify existing ones
try:
modified = rois.get('modified', [])
modified_count = len(modified)
if modified_count > 0:
decoded_shapes = []
for m in modified:
decoder = omero_marshal.get_decoder(m.get("@type"))
decoded_shapes.append(decoder.decode(m))
update_service.saveArray(decoded_shapes, conn.SERVICE_OPTS)
# set ids after successful modification
for r in range(modified_count):
ids_to_sync[modified[r]['oldId']] = modified[r]['oldId']
except Exception as marshal_or_persistence_exception:
errors.append('Error modifying rois: ' +
repr(marshal_or_persistence_exception))
# delete entire (empty) rois
try:
empty_rois = rois.get('empty_rois', {})
empty_rois_ids = [int(k) for k in list(empty_rois.keys())]
if (len(empty_rois_ids) > 0):
conn.deleteObjects("Roi", empty_rois_ids, wait=True)
# set ids after successful deletion,
for e in empty_rois:
for s in empty_rois[e]:
ids_to_sync[s] = s
except Exception as deletion_exception:
errors.append('Error deleting empty rois: ' + repr(deletion_exception))
# remove individual shapes (so as to not punch holes into shape index)
try:
deleted = rois.get('deleted', {})
deleted_rois_ids = deleted.keys()
if len(deleted_rois_ids) > 0:
rois_service = conn.getRoiService()
rois_to_be_updated = []
for d in deleted_rois_ids:
r = rois_service.findByRoi(int(d), None,
conn.SERVICE_OPTS).rois[0]
for s in r.copyShapes():
roi_shape_id = str(d) + ':' + str(s.getId().getValue())
if roi_shape_id in deleted[d]:
r.removeShape(s)
rois_to_be_updated.append(r)
update_service.saveArray(rois_to_be_updated, conn.SERVICE_OPTS)
# set ids after successful deletion,
for d in deleted:
for s in deleted[d]:
ids_to_sync[s] = s
except Exception as deletion_exception:
errors.append('Error deleting shapes: ' + repr(deletion_exception))
# prepare response
ret = {'ids': ids_to_sync}
if len(errors) > 0:
ret['errors'] = errors
return JsonResponse(ret)
def test_null_string(self):
data = json.loads(self.AS_STRING)
data['Description'] = None
decoder = get_decoder(data['@type'])
v = decoder.decode(data)
assert v.description is None
def test_roi_decoder_registered(self):
decoder = get_decoder("http://www.openmicroscopy.org/Schemas/ROI/2015-01#ROI")
assert decoder is not None
def test_base_decoder_from_string(self):
data = json.loads(self.AS_STRING)
decoder = get_decoder(data['@type'])
v = decoder.decode(data)
self.assert_roi(v)
def test_roi_with_shapes(self, roi_with_shapes):
encoder = get_encoder(roi_with_shapes.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi_with_shapes)
v = decoder.decode(v)
self.assert_roi_with_shapes(v)
def test_base_decoder(self, roi):
encoder = get_encoder(roi.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi)
v = decoder.decode(v)
self.assert_roi(v)
def test_roi_with_shapes(self, roi_with_shapes):
encoder = get_encoder(roi_with_shapes.__class__)
decoder = get_decoder(encoder.TYPE)
v = encoder.encode(roi_with_shapes)
v = decoder.decode(v)
self.assert_roi_with_shapes(v)
