def testBasic_2d_Sequence(self):
data = 255 * numpy.random.random((10, 50, 100, 3))
data = data.astype(numpy.uint8)
data = vigra.taggedView(data, vigra.defaultAxistags("zyxc"))
# Must run this through an operator
# Can't use opExport.setValue() because because OpStackWriter can't work with ValueRequests
graph = Graph()
opData = OpBlockedArrayCache(graph=graph)
opData.BlockShape.setValue(data.shape)
opData.Input.setValue(data)
filepattern = self._tmpdir + "/test_export_x{x_start}-{x_stop}_y{y_start}-{y_stop}_z{slice_index}"
opExport = OpExportSlot(graph=graph)
opExport.Input.connect(opData.Output)
opExport.OutputFormat.setValue("png sequence")
opExport.OutputFilenameFormat.setValue(filepattern)
opExport.CoordinateOffset.setValue((10, 20, 30, 0))
opExport.run_export()
export_pattern = opExport.ExportPath.value
globstring = export_pattern.format(slice_index=999)
globstring = globstring.replace("999", "*")
opReader = OpStackLoader(graph=graph)
try:
opReader.globstring.setValue(globstring)
assert opReader.stack.meta.shape == data.shape, "Exported files were of the wrong shape or number."
assert (opReader.stack[:].wait() == data.view(numpy.ndarray)).all(), "Exported data was not correct"
finally:
opReader.cleanUp()
def test_Writer(self):
opData = OpArrayCache( graph=self.graph )
opData.blockShape.setValue( self.testData.shape )
opData.Input.setValue( self.testData )
opExport = OpExportMultipageTiffSequence(graph=self.graph)
opExport.FilepathPattern.setValue( self._stack_filepattern )
opExport.Input.connect( opData.Output )
opExport.SliceIndexOffset.setValue(22)
# Run the export
opExport.run_export()
globstring = self._stack_filepattern.format( slice_index=999 )
globstring = globstring.replace('999', '*')
opReader = OpStackLoader( graph=self.graph )
opReader.globstring.setValue( globstring )
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes( graph=self.graph )
opReorderAxes.AxisOrder.setValue( self._axisorder )
opReorderAxes.Input.connect( opReader.stack )
readData = opReorderAxes.Output[:].wait()
logger.debug("Expected shape={}".format( self.testData.shape ) )
logger.debug("Read shape={}".format( readData.shape ) )
assert opReorderAxes.Output.meta.shape == self.testData.shape, "Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == self.testData.view( numpy.ndarray )).all(), "Exported data was not correct"
opReorderAxes.cleanUp()
opReader.cleanUp()
def testLotsOfOptions(self):
#OLD_LAZYFLOW_STATUS_MONITOR_SECONDS = os.getenv("LAZYFLOW_STATUS_MONITOR_SECONDS", None)
#os.environ["LAZYFLOW_STATUS_MONITOR_SECONDS"] = "1"
# NOTE: In this test, cmd-line args to nosetests will also end up getting "parsed" by ilastik.
# That shouldn't be an issue, since the pixel classification workflow ignores unrecognized options.
# See if __name__ == __main__ section, below.
args = []
args.append( "--project=" + self.PROJECT_FILE )
args.append( "--headless" )
#args.append( "--sys_tmp_dir=/tmp" )
# Batch export options
args.append( '--export_source=Simple Segmentation' )
args.append( '--output_format=png sequence' ) # If we were actually launching from the command line, 'png sequence' would be in quotes...
args.append( "--output_filename_format={dataset_dir}/{nickname}_segmentation_z{slice_index}.png" )
args.append( "--export_dtype=uint8" )
args.append( "--output_axis_order=zxyc" )
args.append( "--pipeline_result_drange=(0,2)" )
args.append( "--export_drange=(0,255)" )
args.append( "--cutout_subregion=[(0,50,50,0,0), (1, 150, 150, 50, 1)]" )
args.append( self.SAMPLE_DATA )
old_sys_argv = list(sys.argv)
sys.argv = ['ilastik.py'] # Clear the existing commandline args so it looks like we're starting fresh.
sys.argv += args
# Start up the ilastik.py entry script as if we had launched it from the command line
# This will execute the batch mode script
try:
self.ilastik_startup.main()
finally:
sys.argv = old_sys_argv
# if OLD_LAZYFLOW_STATUS_MONITOR_SECONDS:
# os.environ["LAZYFLOW_STATUS_MONITOR_SECONDS"] = OLD_LAZYFLOW_STATUS_MONITOR_SECONDS
output_path = self.SAMPLE_DATA[:-4] + "_segmentation_z{slice_index}.png"
globstring = output_path.format( slice_index=999 )
globstring = globstring.replace('999', '*')
opReader = OpStackLoader( graph=Graph() )
opReader.globstring.setValue( globstring )
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes( graph=Graph() )
opReorderAxes.AxisOrder.setValue( 'tzyxc' )
opReorderAxes.Input.connect( opReader.stack )
try:
readData = opReorderAxes.Output[:].wait()
# Check basic attributes
assert readData.shape[:-1] == self.data[0:1, 50:150, 50:150, 0:50, 0:1].shape[:-1] # Assume channel is last axis
assert readData.shape[-1] == 1, "Wrong number of channels. Expected 1, got {}".format( readData.shape[-1] )
finally:
# Clean-up.
opReorderAxes.cleanUp()
opReader.cleanUp()
def test_Writer(self):
opData = OpArrayCache(graph=self.graph)
opData.blockShape.setValue(self.testData.shape)
opData.Input.setValue(self.testData)
opExport = OpExportMultipageTiffSequence(graph=self.graph)
opExport.FilepathPattern.setValue(self._stack_filepattern)
opExport.Input.connect(opData.Output)
opExport.SliceIndexOffset.setValue(22)
# Run the export
opExport.run_export()
globstring = self._stack_filepattern.format(slice_index=999)
globstring = globstring.replace('999', '*')
opReader = OpStackLoader(graph=self.graph)
opReader.globstring.setValue(globstring)
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes(graph=self.graph)
opReorderAxes.AxisOrder.setValue(self._axisorder)
opReorderAxes.Input.connect(opReader.stack)
readData = opReorderAxes.Output[:].wait()
logger.debug("Expected shape={}".format(self.testData.shape))
logger.debug("Read shape={}".format(readData.shape))
assert opReorderAxes.Output.meta.shape == self.testData.shape, "Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == self.testData.view(
numpy.ndarray)).all(), "Exported data was not correct"
opReorderAxes.cleanUp()
opReader.cleanUp()
def testLotsOfOptions(self):
# NOTE: In this test, cmd-line args to nosetests will also end up getting "parsed" by ilastik.
# That shouldn't be an issue, since the pixel classification workflow ignores unrecognized options.
# See if __name__ == __main__ section, below.
args = []
args.append("--project=" + self.PROJECT_FILE)
args.append("--headless")
#args.append( "--sys_tmp_dir=/tmp" )
# Batch export options
args.append(
'--output_format=png sequence'
) # If we were actually launching from the command line, 'png sequence' would be in quotes...
args.append(
"--output_filename_format={dataset_dir}/{nickname}_prediction_z{slice_index}.png"
)
args.append("--export_dtype=uint8")
args.append("--output_axis_order=zxyc")
args.append("--pipeline_result_drange=(0.0,1.0)")
args.append("--export_drange=(0,255)")
args.append("--cutout_subregion=[(0,50,50,0,0), (1, 150, 150, 50, 2)]")
args.append(self.SAMPLE_DATA)
sys.argv = [
'ilastik.py'
] # Clear the existing commandline args so it looks like we're starting fresh.
sys.argv += args
# Start up the ilastik.py entry script as if we had launched it from the command line
# This will execute the batch mode script
self.ilastik_startup.main()
output_path = self.SAMPLE_DATA[:-4] + "_prediction_z{slice_index}.png"
globstring = output_path.format(slice_index=999)
globstring = globstring.replace('999', '*')
opReader = OpStackLoader(graph=Graph())
opReader.globstring.setValue(globstring)
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes(graph=Graph())
opReorderAxes.AxisOrder.setValue('txyzc')
opReorderAxes.Input.connect(opReader.stack)
readData = opReorderAxes.Output[:].wait()
# Check basic attributes
assert readData.shape[:-1] == self.data[
0:1, 50:150, 50:150, 0:50,
0:2].shape[:-1] # Assume channel is last axis
assert readData.shape[
-1] == 2, "Wrong number of channels. Expected 2, got {}".format(
readData.shape[-1])
# Clean-up.
opReorderAxes.cleanUp()
opReader.cleanUp()
def testLotsOfOptions(self):
# NOTE: In this test, cmd-line args to nosetests will also end up getting "parsed" by ilastik.
# That shouldn't be an issue, since the pixel classification workflow ignores unrecognized options.
# See if __name__ == __main__ section, below.
args = []
args.append( "--project=" + self.PROJECT_FILE )
args.append( "--headless" )
args.append( "--sys_tmp_dir=/tmp" )
# Batch export options
args.append( '--output_format=png sequence' ) # If we were actually launching from the command line, 'png sequence' would be in quotes...
args.append( "--output_filename_format={dataset_dir}/{nickname}_prediction_z{slice_index}.png" )
args.append( "--export_dtype=uint8" )
args.append( "--output_axis_order=zxyc" )
args.append( "--pipeline_result_drange=(0.0,1.0)" )
args.append( "--export_drange=(0,255)" )
args.append( "--cutout_subregion=[(0,50,50,0,0), (1, 150, 150, 50, 2)]" )
args.append( self.SAMPLE_DATA )
sys.argv = ['ilastik.py'] # Clear the existing commandline args so it looks like we're starting fresh.
sys.argv += args
# Start up the ilastik.py entry script as if we had launched it from the command line
# This will execute the batch mode script
ilastik_entry_file_path = os.path.join( os.path.split( ilastik.__file__ )[0], "../ilastik.py" )
imp.load_source( 'main', ilastik_entry_file_path )
output_path = self.SAMPLE_DATA[:-4] + "_prediction_z{slice_index}.png"
globstring = output_path.format( slice_index=999 )
globstring = globstring.replace('999', '*')
opReader = OpStackLoader( graph=Graph() )
opReader.globstring.setValue( globstring )
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes( graph=Graph() )
opReorderAxes.AxisOrder.setValue( 'txyzc' )
opReorderAxes.Input.connect( opReader.stack )
readData = opReorderAxes.Output[:].wait()
# Check basic attributes
assert readData.shape[:-1] == self.data[0:1, 50:150, 50:150, 0:50, 0:2].shape[:-1] # Assume channel is last axis
assert readData.shape[-1] == 2, "Wrong number of channels. Expected 2, got {}".format( readData.shape[-1] )
# Clean-up.
opReorderAxes.cleanUp()
opReader.cleanUp()
def testBasic_MultipageTiffSequence(self):
data = 255 * numpy.random.random((5, 10, 50, 100, 3))
data = data.astype(numpy.uint8)
data = vigra.taggedView(data, vigra.defaultAxistags('tzyxc'))
# Must run this through an operator
# Can't use opExport.setValue() because because OpStackWriter can't work with ValueRequests
graph = Graph()
opData = OpArrayCache(graph=graph)
opData.blockShape.setValue(data.shape)
opData.Input.setValue(data)
filepattern = self._tmpdir + '/test_export_x{x_start}-{x_stop}_y{y_start}-{y_stop}_t{slice_index}'
opExport = OpExportSlot(graph=graph)
opExport.Input.connect(opData.Output)
opExport.OutputFormat.setValue('multipage tiff sequence')
opExport.OutputFilenameFormat.setValue(filepattern)
opExport.CoordinateOffset.setValue((7, 10, 20, 30, 0))
opExport.run_export()
export_pattern = opExport.ExportPath.value
globstring = export_pattern.format(slice_index=999)
globstring = globstring.replace('999', '*')
opReader = OpStackLoader(graph=graph)
opReader.globstring.setValue(globstring)
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes(graph=graph)
opReorderAxes.AxisOrder.setValue('tzyxc')
opReorderAxes.Input.connect(opReader.stack)
assert opReorderAxes.Output.meta.shape == data.shape, "Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == data.view(
numpy.ndarray)).all(), "Exported data was not correct"
# Cleanup
opReorderAxes.cleanUp()
opReader.cleanUp()
def testBasic_MultipageTiffSequence(self):
data = 255 * numpy.random.random( (5, 10, 50,100, 3) )
data = data.astype( numpy.uint8 )
data = vigra.taggedView( data, vigra.defaultAxistags('tzyxc') )
# Must run this through an operator
# Can't use opExport.setValue() because because OpStackWriter can't work with ValueRequests
graph = Graph()
opData = OpArrayCache( graph=graph )
opData.blockShape.setValue( data.shape )
opData.Input.setValue( data )
filepattern = self._tmpdir + '/test_export_x{x_start}-{x_stop}_y{y_start}-{y_stop}_t{slice_index}'
opExport = OpExportSlot(graph=graph)
opExport.Input.connect( opData.Output )
opExport.OutputFormat.setValue( 'multipage tiff sequence' )
opExport.OutputFilenameFormat.setValue( filepattern )
opExport.CoordinateOffset.setValue( (7, 10, 20, 30, 0) )
opExport.run_export()
export_pattern = opExport.ExportPath.value
globstring = export_pattern.format( slice_index=999 )
globstring = globstring.replace('999', '*')
opReader = OpStackLoader( graph=graph )
opReader.globstring.setValue( globstring )
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes( graph=graph )
opReorderAxes.AxisOrder.setValue( 'tzyxc' )
opReorderAxes.Input.connect( opReader.stack )
assert opReorderAxes.Output.meta.shape == data.shape, "Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == data.view( numpy.ndarray )).all(), "Exported data was not correct"
# Cleanup
opReorderAxes.cleanUp()
opReader.cleanUp()
def testLotsOfOptions(self):
# OLD_LAZYFLOW_STATUS_MONITOR_SECONDS = os.getenv("LAZYFLOW_STATUS_MONITOR_SECONDS", None)
# os.environ["LAZYFLOW_STATUS_MONITOR_SECONDS"] = "1"
# NOTE: In this test, cmd-line args to tests will also end up getting "parsed" by ilastik.
# That shouldn't be an issue, since the pixel classification workflow ignores unrecognized options.
# See if __name__ == __main__ section, below.
args = []
args.append("--project=" + self.PROJECT_FILE)
args.append("--headless")
# args.append( "--sys_tmp_dir=/tmp" )
# Batch export options
args.append("--export_source=Simple Segmentation")
args.append(
"--output_format=png sequence"
) # If we were actually launching from the command line, 'png sequence' would be in quotes...
args.append("--output_filename_format={dataset_dir}/{nickname}_segmentation_z{slice_index}.png")
args.append("--export_dtype=uint8")
args.append("--output_axis_order=zxyc")
args.append("--pipeline_result_drange=(0,2)")
args.append("--export_drange=(0,255)")
args.append("--cutout_subregion=[(0,10,10,0,0), (1, 20, 20, 5, 1)]")
args.append(self.SAMPLE_DATA)
old_sys_argv = list(sys.argv)
sys.argv = ["ilastik.py"] # Clear the existing commandline args so it looks like we're starting fresh.
sys.argv += args
# Start up the ilastik.py entry script as if we had launched it from the command line
# This will execute the batch mode script
try:
self.ilastik_startup.main()
finally:
sys.argv = old_sys_argv
# if OLD_LAZYFLOW_STATUS_MONITOR_SECONDS:
# os.environ["LAZYFLOW_STATUS_MONITOR_SECONDS"] = OLD_LAZYFLOW_STATUS_MONITOR_SECONDS
output_path = self.SAMPLE_DATA[:-4] + "_segmentation_z{slice_index}.png"
globstring = output_path.format(slice_index=999)
globstring = globstring.replace("999", "*")
opReader = OpStackLoader(graph=Graph())
opReader.globstring.setValue(globstring)
# (The OpStackLoader produces txyzc order.)
opReorderAxes = OpReorderAxes(graph=Graph())
opReorderAxes.AxisOrder.setValue("tzyxc")
opReorderAxes.Input.connect(opReader.stack)
try:
readData = opReorderAxes.Output[:].wait()
# Check basic attributes
assert readData.shape[:-1] == (1, 10, 10, 5), readData.shape[:-1] # Assume channel is last axis
assert readData.shape[-1] == 1, "Wrong number of channels. Expected 1, got {}".format(readData.shape[-1])
finally:
# Clean-up.
opReorderAxes.cleanUp()
opReader.cleanUp()
