PEMtk fitting setup & batch run demo

01/09/22

Outline of this notebook:

• Use setup_fit_demo.py script to load data and setup fitting environment.

• Run a batch of fits…

  • 1. run batch

    • Serial with self.fit() method.

    • Parallel fitting routine with self.multiFit() method. This uses XYZpy library for quick parallelization.

  • 2. load a batch

• Exploring the results… see the “analysis” notebook for more.

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Versions

• 06/06/21 v1

• 22/08/22 v2

• 01/09/22 v2b

v2b updated version including:

• Data IO with self.writeFitData() method.

• fitting now supports additional backends, these are set in self.fitOpts. For a list of available backends run self.backends(). Currently this implements support for AF or MF fitting routines.

Setup

# Import & set paths
import pemtk
from pemtk.fit.fitClass import pemtkFit

from pathlib import Path

# Path for demo script
demoPath = Path(pemtk.__file__).parent.parent/Path('demos','fitting')

# Run demo script to configure workspace
%run {demoPath/"setup_fit_demo.py"}

*** ePSproc installation not found, setting for local copy.

* Setting plotter defaults with epsproc.basicPlotters.setPlotters(). Run directly to modify, or change options in local env.

* Set Holoviews with bokeh.

C:\Users\femtolab\.conda\envs\ePSdev\lib\site-packages\xyzpy\plot\xyz_cmaps.py:6: MatplotlibDeprecationWarning:
The revcmap function was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use Colormap.reversed() instead.
  return LinearSegmentedColormap(name, cm.revcmap(cmap._segmentdata))

*** Setting up demo fitting workspace and main `data` class object...
For more details see https://pemtk.readthedocs.io/en/latest/fitting/PEMtk_fitting_basic_demo_030621-full.html
To use local source code, pass the parent path to this script at run time, e.g. "setup_fit_demo ~/github"


* Loading packages...