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@ -18,7 +18,7 @@ Runs on files produced by [sf-daq](https://github.com/paulscherrerinstitute/sf_d
* [After beamtime](#usage3)
## Description
Automatic Processing tool checks for the new files/runs produced by sf-daq and runs automatically workload (currently - indexing (from crystfel)) and fills logbook (google spreadsheet) with information with some daq parameters from the sf-daq and processing.
Automatic Processing tool checks for the new files/runs produced by sf-daq and runs automatically workload (currently - indexing (by crystfel)) and fills logbook (google spreadsheet) with information with some daq parameters from the sf-daq and processing.
## Installation<a name="installation"></a>
@ -41,7 +41,39 @@ Automatic Processing tool can also be installed from scratch with:
In case of installation from source, so different location of the code and conda environment - change correspondingly line in scripts/env_setup.sh
## Configuration files<a name="config"></a>
Here description of configuration files will be, together with format and hints of usage
### BEAM_ENERGY.txt
This file should contain a beam energy values (in eV). There must be one line with the default values and (optionally) 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 value)
### 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
During preparation [step](#usage1) this file should be filled 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 (optional)<a name="google-api"></a>
@ -79,6 +111,14 @@ Here description of configuration files will be, together with format and hints
>
> lyso.cell hewl.cell
**HINT** - in case there are several space group at which protein can be indexed, it's possible to run automatically indexing in the *alternative* space group. To do this - provide an alternative space group settings in the file <cell_name>.cell_alternative. Example:
> $ ls res/ap/CELL
>
> lyso.cell chim.cell chim.cell_alternative
runs with the <cell_name>=lyso will be indexed using lyso.cell file, while for the <cell_name>=chim - indexing will be done twice, using chim.cell and chim.cell_alternative files (and results of both indexing will be filled in logbook)
* (optional, if filling is requested)
* create (an empty) google spreadsheet
@ -141,12 +181,14 @@ in case of need to re-run indexing (new config parameters, new geometry file etc
#### pausing indexing<a name="usage2_pause"></a>
in case of unknown processing parameters (detector distance, geometry file(beam center), not yet known cell file...), it's possible to pause (not start indexing jobs) putting semaphore file NO_INDEXING in config directory
> $ touch res/ap/NO_INDEXING
once this file is removed - all not indexed runs will be processed
once this file is removed - all not indexed runs will be processed by the tool
### After Beamtime<a name="usage3"></a>
* stop automatic processing executable (Ctrl-c ap.py process) once all runs are processed for this beamtime
* stop automatic processing executable (Ctrl-c ap.py process) once all runs are processed for this beamtime (no active jobs and filling of the logbook is finished)
* remove credentials*json files and revoke api-keys in [Google Developer Console](https://console.developers.google.com/) (->"Service Accounts", for each account -> click on "Actions: ..." and choose "Manage Keys", then remove key)