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README.md
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README.md
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# Table of Contents
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# Table of Contents
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* [Installation](#installation)
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* [Installation](#installation)
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* [Google Authentication](#google-api)
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* [Usage](#usage)
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* [Usage](#usage)
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* [Before beamtime](#usage1)
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* [Before beamtime](#usage1)
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* [During beamtime](#usage2)
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* [During beamtime](#usage2)
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* [pausing indexing](#usage2_pause)
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* [pausing indexing](#usage2_pause)
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* [After beamtime](#usage3)
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* [After beamtime](#usage3)
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* [Configuration files](#config)
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* [Configuration files](#config)
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* [Google Authentication](#google-api)
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## Description
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## Description
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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.
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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.
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gspread numpy matplotlib
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gspread numpy matplotlib
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```
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```
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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
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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
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## Google Authentication<a name="google-api"></a>
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## Google Authentication<a name="google-api"></a>
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**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
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**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
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## Google Authentication<a name="google-api"></a>
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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:
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- [enable API access for a project](https://docs.gspread.org/en/v5.10.0/oauth2.html#enable-api-access-for-a-project)
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- [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)
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## Roadmap
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## Roadmap
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## Authors and acknowledgment
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## Authors and acknowledgment
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Automatic Processing tool was made in 2018 by Karol Nass and Dmitry Ozerov.
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Automatic Processing tool was made in 2018 by Karol Nass and Dmitry Ozerov.
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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.
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