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@ -31,25 +31,6 @@ $ source /sf/jungfrau/applications/miniconda3/etc/profile.d/conda.sh
$ conda activate ap
```
### Installation from source
Automatic Processing tool can also be installed from scratch (put this to the place which is accessible from online computing nodes. res/ directory of corresponding pgroup is perfect place for this):
```
$ git clone https://gitlab.psi.ch/sf-daq/ap.git # or via ssh with
# git clone git@gitlab.psi.ch:sf-daq/ap.git
```
Needed conda environment can be sourced/used from the common place. In case new conda environment is needed, please install following packages in that environment:
```
gspread numpy matplotlib
```
In case of installation from source, so different location of the code or conda environment - change correspondingly lines in [env_setup.sh](#config_env_setup) file
## Google Authentication<a name="google-api"></a>
ap can fill automatically google spreadsheet with different information. This is done using google-api and one need to have api-keys created and allowed for the corresponding spreadsheet (logbook). To create keys, few steps needs to be done first:
- [enable API access for a project](https://docs.gspread.org/en/v5.10.0/oauth2.html#enable-api-access-for-a-project)
- [create (*hint* - do several for same project) service accounts](https://docs.gspread.org/en/v5.10.0/oauth2.html#for-bots-using-service-account) (steps 1-4)
## Usage<a name="usage"></a>
### Before beamtime<a name="usage1"></a>
@ -214,13 +195,27 @@ this file contains indexing parameters used by crystfel.
- [enable API access for a project](https://docs.gspread.org/en/v5.10.0/oauth2.html#enable-api-access-for-a-project)
- [create (*hint* - do several for same project) service accounts](https://docs.gspread.org/en/v5.10.0/oauth2.html#for-bots-using-service-account) (steps 1-4)
## Installation from source
Automatic Processing tool can also be installed from scratch (put this to the place which is accessible from online computing nodes and accesible by other people, who will run ap tool):
```
$ git clone https://gitlab.psi.ch/sf-daq/ap.git # or via ssh with
# git clone git@gitlab.psi.ch:sf-daq/ap.git
```
In case new conda environment is needed, please install following packages in that environment:
```
gspread numpy matplotlib
```
In case of such installation from source, change correspondingly lines(at the end of the file) in [env_setup.sh](#config_env_setup) file
## Roadmap
For all SFX experiments at SwissFEL (Alvra, Bernina(SwissMX and pure Bernina one) and Cristallina) this service was used in years 2018-2023 and were running by authors of the code, which helped to make a fast changes and integration with other components as well as successful tuning this product to users needs. In 2013 successful steps were made to split tool to config and executable parts and beamtimes in June at Cristallina were running with config part fully under control of beamline people, in July - executable part was tested to be running under control of beamtime people of Alvra. That opens a possibility to start a migration of this service to tool.
Till now Automatic Processing were used for SFX experiments only, since they were a more demanding for this tool. But enhancement of tool to other types of experiments at SwissFEL is certainly possible.
## Authors and acknowledgment
## Authors and reference
Automatic Processing tool was made in 2018 by Karol Nass and Dmitry Ozerov.
Automatic processing pipeline is described in "*Nass, K. et al. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCrJ 8, 905–920 (2021).*" This paper can be referenced in case usage of automatic pipeline was helpful in beamtime.