def _projection(input1: Layer,
operation_name: str = cle.maximum_z_projection.__name__,
myself=None):
if input1 is not None:
# execute operation
cle_input1 = cle.push(input1.data)
output = None
operation = cle.operation(operation_name)
output = _call_operation_ignoring_to_many_arguments(
operation, [cle_input1, output])
output = cle.pull(output).astype(int)
# show result in napari
if not hasattr(myself, 'layer'):
if isinstance(input1, Labels):
myself.viewer.add_labels(output,
translate=input1.translate[1:3])
else:
myself.viewer.add_image(output,
translate=input1.translate[1:3])
else:
myself.layer.data = output
myself.layer.contrast_limits = input1.contrast_limits
myself.layer.name = "Result of " + operation.__name__
myself.layer.translate = input1.translate[1:3]
def _denoise(input1: Image,
operation_name: str = cle.gaussian_blur.__name__,
x: float = 1,
y: float = 1,
z: float = 0,
myself=None):
if input1:
# execute operation
cle_input = cle.push(input1.data)
output = cle.create_like(cle_input)
operation = cle.operation(operation_name)
# update GUI
label_parameters(operation, [myself.gui.x, myself.gui.y, myself.gui.z])
_call_operation_ignoring_to_many_arguments(
operation, [cle_input, output, x, y, z])
max_intensity = cle.maximum_of_all_pixels(output)
if max_intensity == 0:
max_intensity = 1 # prevent division by zero in vispy
output = cle.pull(output)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_image(output,
colormap=input1.colormap,
translate=input1.translate)
else:
myself.layer.data = output
myself.layer.name = "Result of " + operation.__name__
myself.layer.contrast_limits = (0, max_intensity)
myself.layer.translate = input1.translate
def _map(input1: Labels,
operation_name: str = cle.label_pixel_count_map.__name__,
n: float = 1,
myself=None):
if input1 is not None:
# execute operation
cle_input1 = cle.push(input1.data)
output = cle.create_like(cle_input1)
operation = cle.operation(operation_name)
# update GUI
label_parameters(operation, [myself.gui.n])
_call_operation_ignoring_to_many_arguments(operation,
[cle_input1, output, n])
max_intensity = cle.maximum_of_all_pixels(output)
if max_intensity == 0:
max_intensity = 1 # prevent division by zero in vispy
output = cle.pull(output)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_image(output,
colormap='turbo',
interpolation='nearest',
translate=input1.translate)
else:
myself.layer.data = output
myself.layer.name = "Result of " + operation.__name__
myself.layer.contrast_limits = (0, max_intensity)
myself.layer.translate = input1.translate
def _mesh(input1: Labels,
operation_name: str = cle.draw_mesh_between_touching_labels.__name__,
n: float = 1,
myself=None):
if input1 is not None:
# execute operation
cle_input1 = cle.push(input1.data)
output = cle.create_like(cle_input1)
operation = cle.operation(operation_name)
# update GUI
label_parameters(operation, [myself.gui.n])
_call_operation_ignoring_to_many_arguments(operation,
[cle_input1, output, n])
min_intensity = cle.minimum_of_all_pixels(output)
max_intensity = cle.maximum_of_all_pixels(output)
if max_intensity - min_intensity == 0:
max_intensity = min_intensity + 1 # prevent division by zero in vispy
output = cle.pull(output)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_image(output,
colormap='green',
blending='additive',
translate=input1.translate)
else:
myself.layer.data = output
myself.layer.name = "Result of " + operation.__name__
myself.layer.contrast_limits = (min_intensity, max_intensity)
myself.layer.translate = input1.translate
def _combine(input1: Layer,
input2: Layer = None,
operation_name: str = cle.binary_and.__name__,
myself=None):
if input1 is not None:
if (input2 is None):
input2 = input1
# execute operation
cle_input1 = cle.push(input1.data)
cle_input2 = cle.push(input2.data)
output = cle.create_like(cle_input1)
operation = cle.operation(operation_name)
_call_operation_ignoring_to_many_arguments(
operation, [cle_input1, cle_input2, output])
max_intensity = cle.maximum_of_all_pixels(output)
if max_intensity == 0:
max_intensity = 1 # prevent division by zero in vispy
output = cle.pull(output)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_image(output,
colormap=input1.colormap,
translate=input1.translate)
else:
myself.layer.data = output
myself.layer.name = "Result of " + operation.__name__
myself.layer.contrast_limits = (0, max_intensity)
myself.layer.translate = input1.translate
def _binarize(input1: Layer,
operation_name: str = cle.threshold_otsu.__name__,
radius_x: int = 1,
radius_y: int = 1,
radius_z: int = 0,
myself=None):
if input1 is not None:
# execute operation
cle_input1 = cle.push(input1.data)
output = cle.create_like(cle_input1)
operation = cle.operation(operation_name)
# update GUI
label_parameters(
operation,
[myself.gui.radius_x, myself.gui.radius_y, myself.gui.radius_z])
_call_operation_ignoring_to_many_arguments(
operation, [cle_input1, output, radius_x, radius_y, radius_z])
output = cle.pull(output).astype(int)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_labels(output, translate=input1.translate)
else:
myself.layer.data = output
myself.layer.contrast_limits = (0, 1)
myself.layer.name = "Result of " + operation.__name__
myself.layer.translate = input1.translate
def _execute(self, layer, layer_number):
command = ""
try:
method = cle.operation(layer.metadata['dialog'].filter_gui.operation_name.value)
parameter_names = method.fullargspec.args
method_name = "cle." + method.__name__
method_name = method_name.replace("please_select", "copy")
except AttributeError:
method = layer.metadata['dialog'].filter_gui._function
# let's chat about this, probably a better way
import inspect
parameter_names = inspect.getfullargspec(method).args
method_name = method.__name__
command = command + "from " + method.__module__ + " import " + method.__qualname__ + "\n"
command = command + method_name + "("
first_image_parameter = None
put_comma = False
for i, parameter_name in enumerate([x.name for x in layer.metadata['dialog'].filter_gui]):
if (i < len(parameter_names)):
comma = ""
if put_comma:
comma = ", "
put_comma = True
widget = layer.metadata['dialog'].filter_gui[parameter_name]
value = widget.value
if isinstance(value, Image) or isinstance(value, Labels):
image_str = "image" + str(self._get_index_of_layer(value))
if first_image_parameter is None:
first_image_parameter = image_str
command = command + comma + image_str
elif isinstance(value, str):
if parameter_name != "operation_name":
command = command + comma + "'" + value + "'"
else:
command = command + comma + "image" + str(layer_number)
else:
command = command + comma + str(value)
command = command + ")\n"
if first_image_parameter is not None:
command = "image" + str(layer_number) + " = cle.create_like(" + first_image_parameter + ")\n" + \
"image" + str(layer_number) + " = " + command
command = "\n" + self._comment(" Layer " + layer.name) + "\n" + command
return command
def _transform(input1: Layer,
operation_name: str = cle.sub_stack.__name__,
a: float = 0,
b: float = 0,
c: float = 0,
d: bool = False,
e: bool = False,
myself=None):
if input1 is not None:
# determine shift; todo: to this in a generic way
import numpy as np
translate = np.copy(input1.translate)
if operation_name == cle.sub_stack.__name__:
translate[0] += a # a corresponds to start_z
elif operation_name == cle.reduce_stack.__name__:
translate[0] += b # b corresponds to offset
# execute operation
cle_input1 = cle.push(input1.data)
output = None
operation = cle.operation(operation_name)
# update GUI
label_parameters(operation, [
myself.gui.a, myself.gui.b, myself.gui.c, myself.gui.d,
myself.gui.e
])
output = _call_operation_ignoring_to_many_arguments(
operation, [cle_input1, output, a, b, c, d, e])
output = cle.pull(output).astype(int)
# show result in napari
if not hasattr(myself, 'layer'):
if isinstance(input1, Labels):
myself.viewer.add_labels(output, translate=translate)
else:
myself.viewer.add_image(output, translate=translate)
else:
myself.layer.data = output
myself.layer.contrast_limits = input1.contrast_limits
myself.layer.name = "Result of " + operation.__name__
myself.layer.translate = translate
def _label_processing(
input1: Labels,
operation_name: str = cle.exclude_labels_on_edges.__name__,
min: float = 0,
max: float = 100,
myself=None):
if input1 is not None:
# execute operation
cle_input1 = cle.push(input1.data)
output = cle.create_like(cle_input1)
operation = cle.operation(operation_name)
# update GUI
label_parameters(operation, [myself.gui.min, myself.gui.max])
_call_operation_ignoring_to_many_arguments(
operation, [cle_input1, output, min, max])
output = cle.pull(output).astype(int)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_labels(output, translate=input1.translate)
else:
myself.layer.data = output
myself.layer.name = "Result of " + operation.__name__
myself.layer.translate = input1.translate
def _label(
input1: Layer,
operation_name: str = cle.connected_components_labeling_box.__name__,
a: float = 2,
b: float = 2,
myself=None):
if input1 is not None:
# execute operation
cle_input1 = cle.push(input1.data)
operation = cle.operation(operation_name)
# update GUI
label_parameters(operation, [myself.gui.a, myself.gui.b])
output = cle.create_like(cle_input1)
_call_operation_ignoring_to_many_arguments(operation,
[cle_input1, output, a, b])
output = cle.pull(output).astype(int)
# show result in napari
if not hasattr(myself, 'layer'):
myself.viewer.add_labels(output, translate=input1.translate)
else:
myself.layer.data = output
myself.layer.name = "Result of " + operation.__name__
myself.layer.translate = input1.translate
def test_operation():
import pyclesperanto_prototype as cle
op = cle.operation("gaussian_blur")
assert op is not None