aoba-ptycho

Prerequisites

• Python 3.6
• NLC 3.1.0

Installation

1. Ensure pip is up to date:

   pip3 install --user -U pip
   

2. Install the wheel file:

   pip3 install --user aoba_ptycho-0.1.0-py3-none-any.whl
   

Usage

The package provides a CLI tool named aoba-ptycho. The usage is as follows:

aoba-ptycho [-h] [--iter ITER] [--plot] [-v] input output

Positional arguments:

• input: Input file in MATLAB v7.3 format. Observations and configurations should be supplied included in this file.
• output: Output file in MATLAB v7.3 format. It includes the complex object image and R-factor history.

Optional arguments:

• -h, --help: Show help message and exit.
• --iter ITER: Override the number of ePIE iterations.
• --plot: Generate plots (object phase image and R-factor)
• -v, --version: Show version information.

Building instructions

The following commands should be executed on a front-end nodes of AOBA-S (compute nodes lack access to compilers).

1. Compile the VE library:

   aoba/ptychography/jit/compile.sh
   

2. Update packaging tools:

   pip3 install --user -U pip wheel
   

3. Build the wheel:

   pip3 wheel --no-deps .
   

Distribute the generate wheel (aoba_ptycho-x.y.z-py3-none-any.whl) to users.