Ptychodus

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

Standard Installation

Install miniforge.
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
```

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

Launch ptychodus:

$ conda activate ptychodus
$ ptychodus

Reporting Bugs

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