Crysalis-PEAKS2IMAGE

Jupyter notebook working in a tandem with Crysalis - software used for single crystal data processing. Can be used for single crystal data obtained at conventional and high pressure experiments.

Files are uploaded into the notebook using an upload button. The code displays information regarding lattice parameters, volume for constrained and unconstraned unit cell, orientation matrix.

Operation

The notebook works under windows. It can be simplified to the procedure:

• Start with the Jupyter-Notebook
• Load a .tif file (fabio library)
• Adjust the presentation (palette, etc)
• Open the Crysalis session
  • Open peak table pt e command of Crysalis
  • Adjust the peaks as integrated as you see fit. It would be advised to show the peaks which are presented on an oscillation image. Cleaning/Filtering of the peaks is advisable
  • Select Coordinates->detector radio button as indicated in the dialog window below
  • Push Copy to clip button
• Switch back to the Jupyter-Notebook
• Press Clipboard polling->ON
• The data should be loaded

Since the Windows system clipboard is accessed via pywin32 module, it is suggested to avoid keeping clipboard polling for a long time.

Installation

Installation under Anaconda:

conda install bokeh numpy pywin32 --yes
conda install -c conda-forge fabio ipywidgets --yes

# Jupyter Notebook
jupyter nbextension enable --py widgetsnbextension

# JupyterLab 1/2
conda install -c conda-forge nodejs --yes
jupyter labextension install @jupyter-widgets/jupyterlab-manager

#JupyterLab 3
conda install -n base -c conda-forge jupyterlab_widgets

There are some steps which are required for additional configuration of Jupyter. These steps enable upload of larger files. I found the original discussion here.

# under conda base or specific environment run
jupyter notebook --generate-config

# under windows this will generate a config file in:
%userprofile%\.jupyter\jupyter_notebook_config.py

# open this file with your favorite editor
notepad++ %userprofile%\.jupyter\jupyter_notebook_config.py

Then uncomment the parameters string:

# c.NotebookApp.tornado_settings = {}

Finally change the parameter string to:

c.NotebookApp.tornado_settings = {"websocket_max_message_size": 100 * 1024 * 1024}

Saving the Jupyter configuration file will finish the job.

I suggest restarting Jupyter lab after installation of all packages as well after the change of the configuration file. If something does not work - let me know.

Example