Ptychodus

ptychodus is a ptychography analysis application that supports multiple reconstruction libraries.

Standard Installation

1. Install miniforge.

2. Install ptychodus.

   • To install ptychodus with the GUI and all optional packages:

     $ conda create -c conda-forge -n ptychodus ptychodus-all

   • To install ptychodus with the GUI and no optional packages:

     $ conda create -c conda-forge -n ptychodus ptychodus

   • To install ptychodus without the GUI or optional packages:

     $ conda create -c conda-forge -n ptychodus ptychodus-core

3. Activate the ptychodus conda environment to run ptychodus.

   $ conda activate ptychodus
   $ ptychodus -h
   
   usage: ptychodus [-h] [-b {reconstruct,train}] [-f FILE_PREFIX] [-s SETTINGS_FILE] [-v] [-w OUTPUT_DIR]
   
   ptychodus is a ptychography analysis application
   
   options:
     -h, --help            show this help message and exit
     -b {reconstruct,train}, --batch {reconstruct,train}
                           run action non-interactively
     -f FILE_PREFIX, --file-prefix FILE_PREFIX
                           replace file path prefix in settings
     -s SETTINGS_FILE, --settings SETTINGS_FILE
                           use settings from file
     -v, --version         show program's version number and exit
     -w OUTPUT_DIR, --write OUTPUT_DIR
                           stage reconstruction inputs to directory
   
   $ ptychodus

Developer Installation

• For a developer installation:

$ git clone https://github.com/AdvancedPhotonSource/ptychodus.git
$ conda create -c conda-forge -n ptychodus --file ptychodus/requirements-dev.txt
$ conda activate ptychodus
$ pip install -e ./ptychodus

• To install the tike backend:

$ conda install -n ptychodus -c conda-forge tike

• To install the PtychoNN backend:

$ conda install -n ptychodus -c conda-forge ptychonn pytorch-gpu

• Launch ptychodus:

$ conda activate ptychodus
$ ptychodus

Reporting Bugs

Open a bug at https://github.com/AdvancedPhotonSource/ptychodus/issues.