Source code for libertem.viz.gms

import warnings

import numpy as np

from .base import Live2DPlot

[docs]class GMSLive2DPlot(Live2DPlot): """ Live plot for Gatan Microscopy Suite, Digital Micrograph (experimental). This works with Python scripting within GMS .. 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. """ def __init__( self, dataset, udf, roi=None, channel=None, title=None, min_delta=0.2, udfresult=None, ): super().__init__( dataset=dataset, udf=udf, roi=roi, channel=channel, title=title, min_delta=min_delta, udfresult=udfresult ) # Optional dependency, don't import top-level import DigitalMicrograph as DM self.image = DM.CreateImage( self.window = None self.disp = None self.image.SetName(self.title)
[docs] def display(self): ''' Use :meth:`DM.ShowImage` to create an image display. ''' self.window = self.image.ShowImage() self.disp = self.image.GetImageDisplay(0) self.disp.SetDoAutoSurvey(False)
[docs] def update(self, damage, force=False): if self.disp is None: assert self.window is None warnings.warn( "Plot is not displayed, not plotting. " "Call display() to display the plot." ) return valid_data =[damage] if len(valid_data) > 0: vmin = np.min(valid_data) vmax = np.max(valid_data) self.disp.SetContrastLimits(float(vmin), float(vmax)) buffer = self.image.GetNumArray() buffer[:] = self.image.UpdateImage()