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Make image analysis protocols in napari from a function
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| from __future__ import annotations | |
| import inspect | |
| from typing import Callable | |
| import napari | |
| from magicgui.widgets import Label, Table, create_widget, Container | |
| import numpy as np | |
| from skimage.measure import regionprops_table | |
| # GUI class can generate image analysis protocols using decorator @gui.bind_protocol | |
| class GUI: | |
| def __init__(self, viewer:"napari.Viewer"): | |
| self.viewer = viewer | |
| self.proceed = False | |
| self._yielded_func = None | |
| def bind_protocol(self, func=None, key1:str="F1", key2:str="F2", | |
| allowed_dims:int|tuple[int, ...]=(1, 2, 3), exit_with_error:bool=False): | |
| """ | |
| Make protocol from a generator of functions. | |
| Parameters | |
| ---------- | |
| func : function generator | |
| Protocol function. This function must accept ``func(self)`` and yield functions that accept | |
| ``f(self, **kwargs)`` . Docstring of the yielded functions will be displayed on the top of the | |
| parameter container as a tooltip. Therefore it would be very useful if you write procedure of | |
| the protocol as docstrings. | |
| key1 : str, default is "F1" | |
| First key binding. When this key is pushed ``self.proceed`` will be False. | |
| key2 : str, default is "F2" | |
| Second key binding. When this key is pushed ``self.proceed`` will be True. | |
| allowed_dims : int or tuple of int, default is (1, 2, 3) | |
| Function will not be called if the number of displayed dimensions does not match it. | |
| exit_with_error :bool default is False | |
| If True, protocol will quit whenever exception is raised and key binding will be released. If | |
| False, protocol continues from the same step. | |
| """ | |
| allowed_dims = (allowed_dims,) if isinstance(allowed_dims, int) else tuple(allowed_dims) | |
| def wrapper(protocol): | |
| if not callable(protocol): | |
| raise TypeError("func must be callable.") | |
| gen = protocol(self) # prepare generator from protocol function | |
| # initialize | |
| self.proceed = False | |
| self._yielded_func = next(gen) | |
| self._add_parameter_container(self._yielded_func) | |
| def _exit(viewer:"napari.Viewer"): | |
| # delete keymap | |
| viewer.keymap.pop(key1) | |
| # delete widget | |
| viewer.window.remove_dock_widget(viewer.window._dock_widgets["Parameter Container"]) | |
| return None | |
| @self.viewer.bind_key(key1, overwrite=True) | |
| def _1(viewer:"napari.Viewer"): | |
| self.proceed = False | |
| return _base(viewer) | |
| @self.viewer.bind_key(key2, overwrite=True) | |
| def _2(viewer:"napari.Viewer"): | |
| self.proceed = True | |
| return _base(viewer) | |
| def _base(viewer:"napari.Viewer"): | |
| if not viewer.dims.ndisplay in allowed_dims: | |
| return None | |
| try: | |
| # call the current function | |
| self._yielded_func(self, **self.params) | |
| except Exception: | |
| exit_with_error and _exit(viewer) | |
| raise | |
| else: | |
| try: | |
| # get next function, update container if needed | |
| next_func = next(gen) | |
| if next_func != self._yielded_func: | |
| # This avoid container renewing | |
| self._yielded_func = next_func | |
| self._add_parameter_container(self._yielded_func) | |
| except StopIteration: | |
| _exit(viewer) | |
| # update all the layers | |
| for layer in viewer.layers: | |
| layer.refresh() | |
| return None | |
| return protocol | |
| return wrapper if func is None else wrapper(func) | |
| def _add_parameter_container(self, f:Callable): | |
| widget_name = "Parameter Container" | |
| params = inspect.signature(f).parameters | |
| if not f.__doc__ and len(params) == 1: | |
| return None | |
| if widget_name in self.viewer.window._dock_widgets: | |
| # clear all the widgets if container already exists | |
| self._container.clear() | |
| while self._container.native.layout().count() > 0: | |
| self._container.native.layout().takeAt(0) | |
| else: | |
| # make new container | |
| self._container = Container(name=widget_name) | |
| wid = self.viewer.window.add_dock_widget(self._container, area="right", name=widget_name) | |
| wid.resize(140, 100) | |
| wid.setFloating(True) | |
| if f.__doc__: | |
| self._container.append(Label(value=f.__doc__)) | |
| for i, (name, param) in enumerate(params.items()): | |
| # make a container widget | |
| if i == 0: | |
| continue | |
| value = None if param.default is inspect._empty else param.default | |
| widget = create_widget(value=value, annotation=param.annotation, | |
| name=name, param_kind=param.kind) | |
| self._container.append(widget) | |
| self.viewer.window._dock_widgets[widget_name].show() | |
| return None | |
| @property | |
| def params(self) -> dict: | |
| """ | |
| Get parameter values from the container | |
| """ | |
| if hasattr(self, "_container"): | |
| kwargs = {wid.name: wid.value for wid in self._container if not isinstance(wid, Label)} | |
| else: | |
| kwargs = {} | |
| return kwargs | |
| # Defining a class is not a must, but it will be easier to write protocols. | |
| # Here we define Measure class for running regionprops around manually picked points. | |
| class Measure: | |
| def __init__(self): | |
| self.image_layer = None | |
| self.labels_layer = None | |
| self.points_layer = None | |
| def select_molecules(self, gui:GUI): | |
| """ | |
| Add markers with "F1". | |
| Go to next step with "F2". | |
| """ | |
| if gui.proceed: | |
| return | |
| pos = gui.viewer.cursor.position | |
| if self.points_layer is None: | |
| self.points_layer = gui.viewer.add_points(pos, | |
| face_color=[0,0,0,0], | |
| edge_color=[0,1,0,1], | |
| ) | |
| else: | |
| self.points_layer.add(pos) | |
| def select_image(self, gui:GUI): | |
| """ | |
| Select target image and push "F1". | |
| """ | |
| selected = list(gui.viewer.layers.selection)[0] | |
| if not isinstance(selected, napari.layers.Image): | |
| raise TypeError("Selected layer is not an image.") | |
| self.image_layer = selected | |
| labels = np.zeros(self.image_layer.data.shape, dtype=np.uint32) | |
| self.labels_layer = gui.viewer.add_labels(labels, opacity=0.5) | |
| def label(self, gui:GUI, radius=3): | |
| """ | |
| Set proper radius to label around markers. | |
| Push "F1" to preview. | |
| Push "F2" to apply. | |
| """ | |
| coords = self.points_layer.data.astype(np.int32) | |
| lbl = self.labels_layer.data | |
| for i, crds in enumerate(coords): | |
| y0 = max(crds[0]-radius, 0) | |
| y1 = min(crds[0]+radius, lbl.shape[0]) | |
| x0 = max(crds[1]-radius, 0) | |
| x1 = min(crds[1]+radius, lbl.shape[1]) | |
| lbl[y0:y1, x0:x1] = i+1 | |
| def measure(self, gui:GUI): | |
| d = regionprops_table(self.labels_layer.data, self.image_layer.data, properties=("mean_intensity", "area")) | |
| table = Table(d) | |
| gui.viewer.window.add_dock_widget(table.native, name="Measurement", area="right") | |
| if __name__ == "__main__": | |
| viewer = napari.Viewer() | |
| gui = GUI(viewer) | |
| # Function "func" will be converted to image analysis protocol in the viewer. | |
| @gui.bind_protocol | |
| def func(gui): | |
| measure = Measure() | |
| gui.proceed = False | |
| while not gui.proceed: | |
| yield measure.select_molecules | |
| yield measure.select_image | |
| gui.proceed = False | |
| while not gui.proceed: | |
| yield measure.label | |
| measure.measure(gui) | |
| napari.run() |
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