Source code for libertem.viz.mpl

import logging
import warnings

import numpy as np
import matplotlib.pyplot as plt

from .base import Live2DPlot

logger = logging.getLogger(__name__)

[docs]class MPLLive2DPlot(Live2DPlot): """ Matplotlib-based live plot .. versionadded:: 0.7.0 Parameters ---------- dataset : DataSet The dataset on which the UDF will be run. This allows to determine the shape of the plots for initialization. udf : UDF The UDF instance this plot is associated to. This needs to be the same instance that is passed to :meth:`~libertem.api.Context.run_udf`. roi : numpy.ndarray or None Region of interest (ROI) that the UDF will be run on. This is necessary for UDFs where the `extra_shape` parameter of result buffers is a function of the ROI, such as :class:`~libertem.udf.raw.PickUDF`. channel : misc Indicate the channel to be plotted. - :code:`None`: The first plottable (2D) channel of the UDF is plotted. - :code:`str`: The UDF result buffer name that should be plotted. - :code:`tuple(str, function(ndarray) -> ndarray)`: The UDF result buffer name that should be plotted together with a function that extracts a plottable result - :code:`function(udf_result, damage) -> (ndarray, damage)`: Function that derives a plottable 2D ndarray and damage indicator from the full UDF results and the processed nav space. See :ref:`plotting` for more details! title : str The plot title. By default UDF class name and channel name. min_delta : float Minimum time span in seconds between updates to reduce overheads for slow plotting. udfresult : UDFResults, optional UDF result to initialize the plot data and determine plot shape. If None (default), this is determined using :meth:`~libertem.udf.base.UDFRunner.dry_run` on the dataset, UDF and ROI. This parameter allows re-using buffers to avoid unnecessary dry runs. **kwargs Passed on to :code:`imshow` """ def __init__( self, dataset, udf, roi=None, channel=None, title=None, min_delta=0.5, udfresult=None, **kwargs, ): super().__init__( dataset=dataset, udf=udf, roi=roi, channel=channel, title=title, min_delta=min_delta, udfresult=udfresult ) self.kwargs = kwargs self.fig = None self.axes = None self.im_obj = None
[docs] def display(self): self.fig, self.axes = plt.subplots() self.im_obj = self.axes.imshow(, **self.kwargs) # Set values compatible with log norm self.im_obj.norm.vmin = 1 self.im_obj.norm.vmax = 1 + 1e-12 self.axes.set_title(self.title)
[docs] def update(self, damage, force=False): """ Update the plot based on ``. Parameters ---------- force : bool Force an update, disabling any throttling mechanisms """ # Nothing to draw, not displayed if self.im_obj is None: assert self.fig is None assert self.axes is None warnings.warn( "Plot is not displayed, not plotting. " "Call display() to display the plot." ) return i_o = self.im_obj i_o.set_data( valid_data =[damage] valid_data = valid_data[np.isfinite(valid_data)] if len(valid_data) > 0: i_o.norm.vmin = np.min(valid_data) i_o.norm.vmax = np.max(valid_data) i_o.changed() self.fig.canvas.draw()