Source code for nanomesh.image._utils

import time

import matplotlib.pyplot as plt
import numpy as np
from ipywidgets import IntSlider, RadioButtons, interact

[docs]class SliceViewer: """Simple slice viewer for volumes using :mod:`matplotlib`. Parameters ---------- data : (i,j,k) numpy.ndarray Volume to display. update_delay : int Minimum delay between events in milliseconds. Reduces lag by limiting the Limit update rate. **kwargs These parametes are passed to first call of :meth:`SliceViewer.update`. """ def __init__( self, data: np.ndarray, update_delay: int = 50, **kwargs, ): self.fig, = plt.subplots() = data self.update_delay = update_delay / 1000 self.max_vals = dict(zip('zyx', np.array(data.shape) - 1)) self.labels = { 'x': ('y', 'z'), 'y': ('x', 'z'), 'z': ('x', 'y'), } self.last_update = 0.0 # Enable direct specification of slice, i.e. x=123 for along in 'xyz': if along in kwargs: kwargs['along'] = along kwargs['index'] = kwargs[along] break along = kwargs.get('along', 'x') init_max_val = self.max_vals[along] init_val = kwargs.get('index', int(init_max_val / 2)) self.int_slider = IntSlider(value=init_val, min=0, max=init_max_val) self.radio_buttons = RadioButtons(options=('x', 'y', 'z'), value=along) =[0], interpolation=None), vmax=data.max()) self.update(index=init_val, along=along)
[docs] def get_slice(self, *, index: int, along: str): """Get slice associated with index along given axes.""" if along == 'x': return[:, :, index] elif along == 'y': return[:, index, :] elif along == 'z': return[index, ...] else: raise ValueError('`along` must be one of `x`,`y`,`z`')
[docs] def update(self, index: int, along: str): """Update the image in place.""" now = time.time() diff = now - self.last_update if diff < self.update_delay: return max_val = self.max_vals[along] xlabel, ylabel = self.labels[along] index = min(index, max_val) self.int_slider.max = max_val slice = self.get_slice(along=along, index=index) top, right = slice.shape, right, 0, top))'slice {index} along {along}') self.fig.canvas.draw() self.last_update = time.time()
[docs] def interact(self): """Call interactive `ipywidgets` widget.""" interact(self.update, index=self.int_slider, along=self.radio_buttons)
[docs]def show_image(image, *, ax: plt.Axes = None, title: str = None, **kwargs) -> 'plt.Axes': """Simple function to plot an image using :mod:`matplotlib`. Parameters ---------- image : (i,j) numpy.ndarray Image to display. ax : matplotlib.axes.Axes, optional Axes to use for plotting. title : str, optional Title for the plot. **kwargs These parameters are passed to `plt.imshow`. Returns ------- ax : matplotlib.axes.Axes """ kwargs.setdefault('interpolation', None) if not ax: fig, ax = plt.subplots() ax.imshow(image, **kwargs) if title: plt.title(title) ax.set_xlabel('x') ax.set_ylabel('y') return ax