def testWeirdAxisInfos(self):
"""
If we add a dataset that has the channel axis in the wrong place,
the operator should automatically transpose it to be last.
"""
weirdAxisFilename = os.path.join(self.workingDir, "WeirdAxes.npy")
expected_data = numpy.random.random((3, 100, 100))
numpy.save(weirdAxisFilename, expected_data)
info = FilesystemDatasetInfo(filePath=weirdAxisFilename, axistags=vigra.defaultAxistags("cxy"))
op = OpDataSelectionGroup(graph=Graph(), forceAxisOrder=False)
op.WorkingDirectory.setValue(self.workingDir)
op.DatasetRoles.setValue(["RoleA"])
op.DatasetGroup.resize(1)
op.DatasetGroup[0].setValue(info)
assert op.ImageGroup[0].ready()
data_from_op = op.ImageGroup[0][:].wait()
assert data_from_op.dtype == expected_data.dtype
assert data_from_op.shape == expected_data.shape, (data_from_op.shape, expected_data.shape)
assert (data_from_op == expected_data).all()
# op.Image is a synonym for op.ImageGroup[0]
assert op.Image.ready()
assert (op.Image[:].wait() == expected_data).all()
# Ensure that files opened by the inner operators are closed before we exit.
op.DatasetGroup.resize(0)
def testNoChannelAxis(self):
"""
If we add a dataset that is missing a channel axis altogether,
the operator should automatically append a channel axis.
"""
noChannelFilename = os.path.join(self.workingDir, "NoChannelAxis.npy")
noChannelData = numpy.random.random((100, 100))
numpy.save(noChannelFilename, noChannelData)
info = FilesystemDatasetInfo(filePath=noChannelFilename, axistags=vigra.defaultAxistags("xy"))
op = OpDataSelectionGroup(graph=Graph())
op.WorkingDirectory.setValue(self.workingDir)
op.DatasetRoles.setValue(["RoleA"])
op.DatasetGroup.resize(1)
op.DatasetGroup[0].setValue(info)
assert op.ImageGroup[0].ready()
# Note that we expect a channel axis to be appended to the data.
expected_data = noChannelData[:, :, numpy.newaxis]
data_from_op = op.ImageGroup[0][:].wait()
assert data_from_op.dtype == expected_data.dtype
assert data_from_op.shape == expected_data.shape
assert (data_from_op == expected_data).all()
# op.Image is a synonym for op.ImageGroup[0]
assert op.Image.ready()
assert (op.Image[:].wait() == expected_data).all()
# Ensure that files opened by the inner operators are closed before we exit.
op.DatasetGroup.resize(0)
def create_and_modify_widget(
qtbot,
infos: List[DatasetInfo],
project_file: h5py.File,
nickname: str = None,
axiskeys: str = "",
normalizeDisplay: bool = DONT_SET_NORMALIZE,
drange: Tuple[Number, Number] = None,
display_mode: str = None,
location: type = None,
):
project_file = project_file or empty_project_file()
opDataSelectionGroup = OpDataSelectionGroup(graph=Graph())
opDataSelectionGroup.ProjectFile.setValue(project_file)
opDataSelectionGroup.ProjectDataGroup.setValue(TOP_GROUP_NAME)
serializer = DataSelectionSerializer(opDataSelectionGroup, TOP_GROUP_NAME)
widget = DatasetInfoEditorWidget(None, infos, serializer)
qtbot.addWidget(widget)
widget.show()
assert widget.multi_axes_display.text() == "Current: " + ", ".join(
info.axiskeys for info in infos)
if axiskeys:
assert widget.axesEdit.isVisible()
assert widget.axesEdit.isEnabled()
widget.axesEdit.setText(axiskeys)
if nickname:
assert widget.nicknameEdit.isEnabled()
widget.nicknameEdit.setText("SOME_NICKNAME")
if normalizeDisplay is not DONT_SET_NORMALIZE:
widget.normalizeDisplayComboBox.setCurrentIndex(
widget.normalizeDisplayComboBox.findData(normalizeDisplay))
if drange is not None:
widget.rangeMinSpinBox.setValue(drange[0])
widget.rangeMaxSpinBox.setValue(drange[1])
if display_mode is not None:
index = widget.displayModeComboBox.findData(display_mode)
widget.displayModeComboBox.setCurrentIndex(index)
if location is not None:
comboIndex = widget.storageComboBox.findData(location)
widget.storageComboBox.setCurrentIndex(comboIndex)
return widget
def test(self):
"""
Make sure that the dataset roles work the way we expect them to.
"""
infoA = DatasetInfo()
infoA.filePath = self.group1Data[0][0]
infoC = DatasetInfo()
infoC.filePath = self.group1Data[1][0]
graph = Graph()
op = OpDataSelectionGroup(graph=graph)
op.WorkingDirectory.setValue(self.workingDir)
op.DatasetRoles.setValue(['RoleA', 'RoleB', 'RoleC'])
op.DatasetGroup.resize(3)
op.DatasetGroup[0].setValue(infoA)
# Leave RoleB blank -- datasets other than the first are optional
op.DatasetGroup[2].setValue(infoC)
assert op.ImageGroup[0].ready()
assert op.ImageGroup[2].ready()
expectedDataA = self.group1Data[0][1]
dataFromOpA = op.ImageGroup[0][:].wait()
assert dataFromOpA.dtype == expectedDataA.dtype
assert dataFromOpA.shape == expectedDataA.shape
assert (dataFromOpA == expectedDataA).all()
expectedDataC = self.group1Data[0][1]
dataFromOpC = op.ImageGroup[0][:].wait()
assert dataFromOpC.dtype == expectedDataC.dtype
assert dataFromOpC.shape == expectedDataC.shape
assert (dataFromOpC == expectedDataC).all()
assert op.Image.ready()
assert (op.Image[:].wait() == expectedDataA).all()
# Ensure that files opened by the inner operators are closed before we exit.
op.DatasetGroup.resize(0)
def testWeirdAxisInfos(self):
"""
If we add a dataset that has the channel axis in the wrong place,
the operator should automatically transpose it to be last.
"""
weirdAxisFilename = os.path.join(self.workingDir, 'WeirdAxes.npy')
weirdAxisData = numpy.random.random( (3,100,100) )
numpy.save(weirdAxisFilename, weirdAxisData)
info = DatasetInfo()
info.filePath = weirdAxisFilename
info.axistags = vigra.defaultAxistags('cxy')
graph = Graph()
op = OpDataSelectionGroup( graph=graph )
op.WorkingDirectory.setValue( self.workingDir )
op.DatasetRoles.setValue( ['RoleA'] )
op.DatasetGroup.resize( 1 )
op.DatasetGroup[0].setValue( info )
assert op.ImageGroup[0].ready()
# Note that we expect the channel axis to be transposed to be last.
expected_data = weirdAxisData.transpose( 1,2,0 )
data_from_op = op.ImageGroup[0][:].wait()
assert data_from_op.dtype == expected_data.dtype
assert data_from_op.shape == expected_data.shape
assert (data_from_op == expected_data).all()
# op.Image is a synonym for op.ImageGroup[0]
assert op.Image.ready()
assert (op.Image[:].wait() == expected_data).all()
# Ensure that files opened by the inner operators are closed before we exit.
op.DatasetGroup.resize(0)
def test(self):
infoA = DatasetInfo()
infoA.filePath = self.group1Data[0][0]
infoC = DatasetInfo()
infoC.filePath = self.group1Data[1][0]
graph = Graph()
op = OpDataSelectionGroup(graph=graph)
op.WorkingDirectory.setValue(self.workingDir)
op.DatasetRoles.setValue(['RoleA', 'RoleB', 'RoleC'])
op.DatasetGroup.resize(3)
op.DatasetGroup[0].setValue(infoA)
# Leave RoleB blank -- datasets other than the first are optional
op.DatasetGroup[2].setValue(infoC)
assert op.ImageGroup[0].ready()
assert op.ImageGroup[2].ready()
expectedDataA = self.group1Data[0][1]
dataFromOpA = op.ImageGroup[0][:].wait()
assert dataFromOpA.dtype == expectedDataA.dtype
assert dataFromOpA.shape == expectedDataA.shape
assert (dataFromOpA == expectedDataA).all()
expectedDataC = self.group1Data[0][1]
dataFromOpC = op.ImageGroup[0][:].wait()
assert dataFromOpC.dtype == expectedDataC.dtype
assert dataFromOpC.shape == expectedDataC.shape
assert (dataFromOpC == expectedDataC).all()
assert op.Image.ready()
assert (op.Image[:].wait() == expectedDataA).all()