# Basic Execution

The WaveDiff pipeline is launched by the entrypoint script: `src/wf_psf/run.py`, which is referenced by the command `wavediff`.

A list of command-line arguments can be displayed using the `--help` option:

```
> wavediff --help
usage: run.py [-h] --conffile CONFFILE --outputdir OUTPUTDIR

required arguments:
  --conffile CONFFILE, -c CONFFILE
                        a configuration file containing program settings.
  --outputdir OUTPUTDIR, -o OUTPUTDIR
                        the path of the output directory.

optional arguments:
  -h, --help            show this help message and exit
```
The first argument: `--confile CONFFILE` specifies the path to the {ref}`master configuration file<master_config_file>` storing the pipeline tasks to be executed at runtime.

The second argument: `--outputdir OUTPUTDIR` is used to set the path to the main output directory, which stores the `WaveDiff` results.

To run `WaveDiff`, use the following command:

```
> wavediff -c /path/to/config/file -o /path/to/output/dir
```

## WaveDiff Output Directory Structure

WaveDiff creates an output directory at the location specified by `--outputdir` for each run. The parent directory is named with the prefix `wf-outputs-` and a timestamp accurate to the microsecond, e.g., `wf-outputs-20231119151932213823`.

Inside this directory, the following subdirectories are generated:

(wf-outputs)=
```
wf-outputs-20231119151932213823
├── checkpoint
├── config
├── log-files
├── metrics
├── optim-hist
├── plots
└── psf_model
```
A description of each subdirectory is provided in the following table.


| Sub-directory | Description |
|---------------|---------------------------------------------------|
| checkpoint    | Checkpoint weights saved during training. |
| config        | Input configuration files used for this run ([see Configuration](Configuration)). |
| log-files     | Log files generated during the run. |
| metrics       | Evaluation metrics produced by the metrics pipeline. |
| optim-hist    | Optimization history of model parameters during training. |
| plots         | Plots generated by the plotting pipeline. |
| psf_models    | Final PSF models, including full model graphs for each training cycle. |


**Notes:**
All subdirectory names are consistent across runs.
Timestamps ensure unique output directories for each execution.
This structure supports reproducibility and easy access to intermediate results.

Next, we cover how the configuration files are organized.