Xi-cam.NCEM

A plugin for the Xi-cam image program for electron microscopy data visualization supported by the National Center for Electron Microscopy facility of the Molecular Foundry.

This plugin is the main graphical user interface for the openNCEM ncempy package for visualizing electron microscopy data.

Supported file types are:

• Digital Micrograph version 3 and 4
• Thermo Fischer (FEI) SER files
• Thermo Fischer (FEI) EMD files written by Velox
• Berkeley EMD files
• MRC format files
• TIF files with ImageJ metadata

Components

The Xi-cam.NCEM plugin implements two types of data viewing

View

Opens and displays 2D and 3D versions of the files mentioned above.

FFTView

Shows the real space image and 'live' FFT diffractogram of a chosen region of the image.

Installation

PIP

There is now a pip installable package on pypi.org. Simply do:

pip install xicam
pip insttall xicam.NCEM

Conda

If you are using conda you can first make a new environment

conda create --name xicam python=3.8 numpy scipy dask jupyter h5py pyqtgraph matplotlib netcdf4 xarray requests astropy numcodecs pyqt intake humanize zarr
activate xicam

Then use pip to install xicam and xicam.NCEM

pip install xicam
pip insttall xicam.NCEM

From source

Here are a set of steps to install this program from source using git, conda, and pip on Windows.

1. Clone the Xicam repository from XI-CAM on github

git clone https://github.com/Xi-CAM/Xi-cam.git

2a. Get the stable Xi-cam.NCEM plugin from XI-CAM

git clone https://github.com/Xi-CAM/Xi-cam.NCEM.git

2b. OR the development version from Peter Ercius's repository

git clone https://github.com/ercius/Xi-cam.NCEM.git

3. Create and activate a new conda environment. Some dependencies are installed by pip later.

conda create --name xicam python=3.8 numpy scipy dask jupyter h5py pyqtgraph matplotlib netcdf4 xarray requests astropy numcodecs pyqt intake humanize zarr
activate xicam

4. Run the following pip commands from the parent directory of the cloned repositories above.

pip install -e Xi-cam\\
pip install -e Xi-cam.NCEM\\

• Note: Slashes (\ on windows and / on Linux or Mac) at the end of the line are important to force a local installation rather than downloading from pypi
• Note: The -e option installs the packages as 'editable' so you can update the program easily using git

Debugging

Xicam allows the user to just call the xicam executable from anywhere once the anaconda environment is activated, which is very convenient. However, there the error is captured by a logger (see below) and debugging is difficult. Debugging in QT is possible (see below).

Simple debugging

1. Open the xi-cam-unified/xicam folder. In this folder is a python file named run-xicam.py.

Run this file in the command prompt using

python run-xicam.py

The console output is shown in that console including print and error messages.

PDB debugging

To enable debugging for a pyqt program insert this code where you want to stop the program

from PyQt5.QtCore import pyqtRemoveInputHook
from pdb import set_trace
pyqtRemoveInputHook()
set_trace()

Resuming might be possible using

from PyQt5.QtCore import pyqtRestoreInputHook
pyqtRestoreInputHook()

and then pressing CTRL-C to stop the command printing. I have not tried this though.