Container for MIB conversion

This repository contains scripts to build a container for MIB conversion at ePSIC by using Podman and/or Buildah. You can use podman --version and buildah --version to see if they are installed.

Build with Podman and Buildah

By using the build.sh script, it uses Podman to first build the required packages and then uses Buildah to copy only the necessary packages from the builder image to a very small image, which does not contain a package manager. This requires the host to have dnf installed, the package manager.

It is recommended to use this approach as it produces (almost) the smallest image possible:

buildah unshare ./build.sh

Build with Podman only

You can also use Podman only to build the container. The image will be slightly larger as the final base image has the package manager installed. This uses the Dockerfile to build the image:

podman build --format docker -t mib2x .

Launch the container

You can find the container by

podman images

To have an interactive shell of the container, you can do

podman run --rm -it localhost/mib2x:latest sh

Perform MIB conversion

To perform the MIB conversion, you can do

podman run --rm -v <VISIT>:<VISIT> localhost/mib2x python mib_convert.py
--mib-path <MIB_FILE> --auto-reshape --ibf --create-json

The -v flag mounts the visit on the container. For example if you want to convert .mib file in /dls/e02/data/2024/cm37231-4/:

podman run --rm -v /dls/e02/data/2024/cm37231-4/:/dls/e02/data/2024/cm37231-4/
localhost/mib2x python mib_convert.py --mib-path
'/dls/e02/data/2024/cm37231-4/Merlin/WS2_n_fred_40um/20240821_150039/20240821_150035_data.mib'
--auto-reshape --ibf --create-json

If you want to run in debug mode, you can set the environment variable M2X_DEBUG to 1 by using -e 'M2X_DEBUG=1' when you use podman run. This will save the output file under <VISIT>/processing/debug/ instead of <VISIT>/processing.

For a full list of options, please refer to

podman run --rm localhost/mib2x python mib_convert.py --help

usage: mib_arg_parser.py [-h] --mib-path MIB_PATH [--auto-reshape | --no-reshaping | --use-fly-back | --known-shape] [--scan-x SCAN_X] [--scan-y SCAN_Y] [--ibf]
                         [--bin-sig-factor BIN_SIG_FACTOR] [--bin-nav-factor BIN_NAV_FACTOR] [--create-json] [--ptycho-config PTYCHO_CONFIG]
                         [--ptycho-template PTYCHO_TEMPLATE]

Convert MIB files to hdf5

options:
  -h, --help            show this help message and exit
  --mib-path MIB_PATH   path to the MIB file
  --auto-reshape        enable auto reshaping (default: True)
  --no-reshaping        disable reshaping (default: False)
  --use-fly-back        use fly-back method to reshape (default: False)
  --known-shape         use a known scan shape to reshape (default: False)
  --scan-x SCAN_X       number of pixels in x (columns) (default: 256)
  --scan-y SCAN_Y       number of pixels in y (rows) (default: 256)
  --ibf                 save integrated bright-field image
  --bin-sig-factor BIN_SIG_FACTOR
                        the pixel binning factor in the signal dimensions, 0 for no binning (default: 4)
  --bin-nav-factor BIN_NAV_FACTOR
                        the pixel binning factor in the navigation dimensions, 0 for no binning (default: 4)
  --create-json         create a PtyREX JSON config file
  --ptycho-config PTYCHO_CONFIG
                        the name of the PtyREX JSON config file (default: 'pty_recon')
  --ptycho-template PTYCHO_TEMPLATE
                        the path of the template PtyREX JSON config file (default: './UserExampleJson.json')