Functionalities
Collection of operations aiming to help in displaying and analyzing results, e.g. to visualize images.
- execute(anchor=None, kernel_source: str = '', kernel_name: str = '', global_size: tuple = (1, 1, 1), parameters: dict = {}, constants: dict = {}, device: pyclesperanto._pyclesperanto._Device = None)[source]
Execute a kernel from a file or a string
Call, build, and execute a kernel compatible with CLIj framework. The kernel can be called from a file or a string.
- Parameters:
anchor (str, default = 'None') – Use __file__ when calling this method and the corresponding open.cl file lies in the same folder as the python file calling it. Ignored if kernel_source is a string.
kernel_source (str) – Filename of the open.cl file to be called, or string containing the open.cl source code
kernel_name (str) – Kernel method inside the open.cl file to be called most clij/clesperanto kernel functions have the same name as the file they are in
global_size (tuple (z,y,x), default = (1, 1, 1)) – Global_size according to OpenCL definition (usually shape of the destination image).
parameters (dict(str, [Array, float, int])) – Dictionary containing parameters. Take care: They must be of the right type and in the right order as specified in the open.cl file.
constants (dict(str, int), optional) – Dictionary with names/values which will be added to the define statements. They are necessary, e.g. to create arrays of a given maximum size in OpenCL as variable array lengths are not supported.
device (Device, default = None) – The device to execute the kernel on. If None, use the current device
- imshow(image, title: str | None = None, labels: bool | None = False, min_display_intensity: float | None = None, max_display_intensity: float | None = None, color_map: str | None = None, plot=None, colorbar: bool | None = False, colormap: str | ListedColormap | None = None, alpha: float | None = None, continue_drawing: bool | None = False)[source]
Visualize an image, e.g. in Jupyter notebooks using matplotlib.
- Parameters:
image (np.ndarray) – numpy or OpenCL-backed image to visualize
title (str, optional) – Obsolete (kept for ImageJ-compatibility)
labels (bool, optional) – True: integer labels will be visualized with colors False: Specified or default colormap will be used to display intensities.
min_display_intensity (float, optional) – lower limit for display range
max_display_intensity (float, optional) – upper limit for display range
color_map (str, optional) – deprecated, use colormap instead
plot (matplotlib axis, optional) – Plot object where the image should be shown. Useful for putting multiple images in subfigures.
colorbar (bool, optional) – True puts a colorbar next to the image. Will not work with label images and when visualizing multiple images (continue_drawing=True).
colormap (str or matplotlib colormap, optional)
alpha (float, optional) – alpha blending value
continue_drawing (float) – True: the next shown image can be visualized on top of the current one, e.g. with alpha = 0.5
- native_execute(anchor=None, kernel_source: str = '', kernel_name: str = '', global_size: tuple = (1, 1, 1), local_size: tuple = (1, 1, 1), parameters: dict = {}, device: pyclesperanto._pyclesperanto._Device = None)[source]
Execute an OpenCL kernel from a file or a string
Call, build, and execute a kernel compatible with OpenCL language. The kernel can be called from a file or a string.
The parameters must still be passed as a dictionary with the correct types and order. Buffer parameters must be passed as Array objects. Scalars must be passed as Python native float or int.
Warning: Only 1D buffers are supported for now.
- Parameters:
anchor (str, default = '__file__') – Enter __file__ when calling this method and the corresponding open.cl file lies in the same folder as the python file calling it. Ignored if kernel_source is a string.
kernel_source (str) – Filename of the open.cl file to be called or string containing the open.cl source code
kernel_name (str) – Kernel method inside the open.cl file to be called most clij/clesperanto kernel functions have the same name as the file they are in
global_size (tuple (z,y,x), default = (1, 1, 1)) – Global_size according to OpenCL definition (usually shape of the destination image).
local_size (tuple (z,y,x), default = (1, 1, 1)) – Local_size according to OpenCL definition (usually default is good).
parameters (dict(str, [Array, float, int])) – Dictionary containing parameters. Take care: They must be of the right type and in the right order as specified in the open.cl file.
device (Device, default = None) – The device to execute the kernel on. If None, use the current device
- operation(name: str) Callable[source]
Returns a function from the pyclesperanto package
- Parameters:
name (str) – name of the operation
- Return type:
Callable function
- operations(must_have_categories: list = None, must_not_have_categories: list = None) dict[source]
Retrieve a dictionary of operations, which can be filtered by annotated categories.
- Parameters:
must_have_categories (list of str, optional) – if provided, the result will be filtered so that operations must contain all given categories.
must_not_have_categories (list of str, optional) – if provided, the result will be filtered so that operations must not contain all given categories.
- Returns:
dict of str
- Return type:
Callable function