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.data.copy())
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 = self.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.data
self.image.UpdateImage()