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readme, moved config part down the text

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Dmitry Ozerov
2023-09-06 15:39:32 +02:00
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README.md
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@ -44,39 +44,6 @@ gspread numpy matplotlib
In case of installation from source, so different location of the code and conda environment - change correspondingly lines in [env_setup.sh](#config_env_setup) file
## Configuration files<a name="config"></a>
### BEAM_ENERGY.txt
This file should contain a beam energy values (in eV). There must be one line with the default value and it's possible to define beam energy values, different from defaults for specific runs(scans).
Example:
```
$ cat BEAM_ENERGY.txt
DEFAULT 11330.0
run9876 11001.2
run9870 12015.1
```
(for the runs 9876 and 9870 - 11001.2 and 12015.1 photon beam energy will be used, while for any other - 11330.0)
### DETECTOR_DISTANCE.txt
This file should contain a detector distance (from sample to detector) in meter. Format is similar to BEAM_ENERGY.txt file, so for example:
```
$ cat DETECTOR_DISTANCE.txt
DEFAULT 0.09369
run9988 0.09212
run9977 0.09413
```
(for runs 9988 and 9977 - 9.212cm and 9.413cm will be used as detector distance, for all other runs a default value of 9.369cm will be used)
### env_setup.sh<a name="config_env_setup"></a>
During preparation [step](#usage1) this file should be filled (manually) with the proper values for the beamline name(alvra or bernina or ..), pgroup name (p12345), DETECTOR_NAME (JF17T16V01) used in experiment, THRESHOLD_INDEXING (can be changed, adapted, in run_index.sh file, see latter) and LOGBOOK (url to google spreadsheet which will be used for automatic filling)
### run_index.sh
this file contains indexing parameters used by crystfel.
**HINT** - in case several proteins are used during expertiment, it's possible to define different indexing parameters for each of them: in case run_index.<cell_name>.sh file is present - indexing parameters from that file will be used to process <cell_name> protein sample, if not present(default) - run_index.sh parameters are used
## 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:
@ -209,6 +176,40 @@ once this file is removed - all not indexed runs will be processed by the tool
* revoke write access to to google spreadsheet to the service-accounts used by ap
## Configuration files<a name="config"></a>
### BEAM_ENERGY.txt
This file should contain a beam energy values (in eV). There must be one line with the default value and it's possible to define beam energy values, different from defaults for specific runs(scans).
Example:
```
$ cat BEAM_ENERGY.txt
DEFAULT 11330.0
run9876 11001.2
run9870 12015.1
```
(for the runs 9876 and 9870 - 11001.2 and 12015.1 photon beam energy will be used, while for any other - 11330.0)
### DETECTOR_DISTANCE.txt
This file should contain a detector distance (from sample to detector) in meter. Format is similar to BEAM_ENERGY.txt file, so for example:
```
$ cat DETECTOR_DISTANCE.txt
DEFAULT 0.09369
run9988 0.09212
run9977 0.09413
```
(for runs 9988 and 9977 - 9.212cm and 9.413cm will be used as detector distance, for all other runs a default value of 9.369cm will be used)
### env_setup.sh<a name="config_env_setup"></a>
During preparation [step](#usage1) this file should be filled (manually) with the proper values for the beamline name(alvra or bernina or ..), pgroup name (p12345), DETECTOR_NAME (JF17T16V01) used in experiment, THRESHOLD_INDEXING (can be changed, adapted, in run_index.sh file, see latter) and LOGBOOK (url to google spreadsheet which will be used for automatic filling)
### run_index.sh
this file contains indexing parameters used by crystfel.
**HINT** - in case several proteins are used during expertiment, it's possible to define different indexing parameters for each of them: in case run_index.<cell_name>.sh file is present - indexing parameters from that file will be used to process <cell_name> protein sample, if not present(default) - run_index.sh parameters are used
## 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.