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some docu changes

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Jan Grewe 2020-07-22 10:30:18 +02:00
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README.md
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Database of data recorded in the group. Database of data recorded in the group.
## Assumptions & Caveats
## Assumptions & Caveats:
* there is only a single subject in each dataset * there is only a single subject in each dataset
* each recording contains a single cell * each recording contains a single cell
* RePro links to Cell and not to Dataset * RePro links to Cell and not to Dataset
* Question: should we store the sampling rate and hardware info in the database? * Question: should we store the sampling rate and hardware info in the database?
* ID card for each cell
## FIXMEs ## FIXMEs
* repro must have foreign keys to dataset **and** subject * repro must have foreign keys to dataset **and** subject
* Dataset finding samplerate in stimuli.dat can be improved * Dataset finding samplerate in stimuli.dat can be improved
* Reading fi data from old-style directories * Reading fi data from old-style directories
* maybe delegate this to Stimulus? * maybe delegate this to Stimulus?
* implement alternative dataSources, somehow * implement alternative dataSources, somehow
* stimulus contrast is not read from nix file (e.g. filestimulus) maybe a problem with all mutables? * stimulus contrast is not read from nix file (e.g. filestimulus) maybe a problem with all mutables?
* Add relacs_nix_version to dataset, could be used to decide how to read stuff, in particular, we will switch to DataFrames for most features after nixio version 1.5 * Add relacs_nix_version to dataset, could be used to decide how to read stuff, in particular, we will switch to DataFrames for most features after nixio version 1.5

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# How to use the fish book # How to use the fish book
## Requirements ## Requirements
* Python 3.5+ only, **no** python 2 * Python 3.5+ only, **no** python 2
* [datajoint](https://datajoint.io) to connect to the database and to map python objects to table entries. * [datajoint](https://datajoint.io) to connect to the database and to map python objects to table entries.
* [nixio](https://github.com/g-node/nixpy) to read the relacs-flavored nix files during import or later during data retrieval. * [nixio](https://github.com/g-node/nixpy) to read the relacs-flavored nix files during import or later during data retrieval.
## Installation ## Installation
1) clone the repository ### 1) Clone the repository
```bash
>> git clone https://whale.am28.uni-tuebingen.de/git/jgrewe/fishbook.git
```
``` ### 2) Installation
>> git clone https://whale.am28.uni-tuebingen.de/git/jgrewe/fishbook.git
```
2. installation
When installing for development: install for the current user, install as "editable": When installing for development: install for the current user, install as "editable":
``` ```bash
>> cd fishbook >> cd fishbook
>> pip3 install fishbook -e --user >> pip3 install -e fishbook --user
``` ```
When installing for use: When installing for use:
``` ```bash
>> pip3 install fishbook --user >> pip3 install fishbook --user
# or # or, for system-wide installation
>> sudo pip3 install fishbook >> sudo pip3 install fishbook
``` ```
3. connecting to the database ## Getting started
Suppose that you intend to work on a project named `foo` use the terminal to navigate to the project directory: `cd foo` ### 3) Connecting to the database
Suppose that you intend to work on a project named `foo` use the terminal to navigate to the project directory: `cd foo`