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@@ -2,33 +2,33 @@
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This repository contains raw data of neuronal activity in P-type electroreceptors of the electric fish *Apteronotus leptorhynchus*, derived data i.e. analysis results, the python scripts running the analyses, simulations and the plotting.
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-## ``raw_data``
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+## ``raw_data`` folder
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This folder contains the raw datasets. Data and metadata are stored in the open [NIX](https://github.com/g-node/nix) container format. To read these data files you need the [``nixio``](https://github.com/g-node/nixpy) python library. For a more comfortable approach use the [``rlxnix``](https://github.com/relacs/relacsed_nix) python package.
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Usually, the files contain the raw membrane potential recording, the detected action potentials, the animal's electric organ discharge (EOD) together with the respective metadata. *Note:* Some datasets are older and have been used in previously analyses. The dataset structure deviates a bit from newer files.
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-## ``derived_data``
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+## ``derived_data`` folder
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-This folder contains the analysis results. The contained files will be overwritten when re-running the analysis script. *csv-*files are written with ``pandas`` using the semicolon as delimiter to read them use ``df = pd.read_csv(filename, sep=";", index_col=0)``.
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-*npz-*files are compressed ``numpy`` files.
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+This folder contains the analysis results. The contained files will be overwritten when re-running the analysis scripts. *csv-files are written with ``pandas`` using the semicolon as delimiter. To read them use something like the following pattern ``df = pd.read_csv(filename, sep=";", index_col=0)``.
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+*npz-files are compressed ``numpy`` files.
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-## ``stimuli``
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+## ``stimuli`` folder
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Contains a single file, which is the white noise stimulus waveform.
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-## ``file_lists``
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+## ``file_lists`` folder
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-Two simple text files:
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+Two simple text files that are used by the analysis scripts:
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1. listing the datasets in which the receptive field was measured, and from which we extract the baseline response properties.
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2. The datasets in which white-noise responses were measured.
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-## ``figures``
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+## ``figures`` folder
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-Contains some png files which will be embedded into the final figures. The folder is the default output folder for created figures.
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+Contains some png-files which will be embedded into the final figures. The folder is the default output folder for created figures.
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## ``code`` package
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-Three sub-packages:
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+python files performing the analyses, simulations and plotting. Three sub-packages:
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1. ``analyses``: The data analysis scripts working on the raw data
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2. ``plots``: Plotting scripts
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@@ -36,22 +36,22 @@ Three sub-packages:
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## Scripts
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-To run the analyses, simulations, or plot the figures, you can use one of the three scripts"
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+To run the analyses, simulations, or plot the figures, you can use one of the three scripts
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-1. ``run_analyses.py`` command line tool for running the all data analyses. (**Note!** analysis of the heterogeneous populations will take a while)
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-2. ``run_simulations.py`` command line tool to run the LIF simulations. (**Note!** This will take a while)
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+1. ``run_analyses.py`` command line tool for running all data analyses. (**Note: analysis of the heterogeneous populations will take a while!**)
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+2. ``run_simulations.py`` command line tool to run the LIF simulations. (**Note: This will take a while!**)
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3. ``plot_figures.py`` command line script that allows to plot the figures of the publication.
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-The first two have only a single argument which is the number of parallel processes that should be spawned for the respective task. E.g.
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+The first two take only a single optional argument which is the number of parallel processes that should be spawned for the respective task. E.g.
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```
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python3 run_simulations.py --help # to show the help text
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python3 run_simulations.py -j 12 # run the simulations using 12 parallel processes
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```
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-The plot tool takes that defines which sub command (i.e. figure) will be run. Each of these take a few more arguments that allow to select which figure should be plotted.
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+The plot tool expects as a first argument the sub command (i.e. figure) that will be run. Each of these sub-commands define a few more arguments. Using the default arguments should work.
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```
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-python3 plot_figures.py --help # to show list of all subcommands
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+python3 plot_figures.py --help # to list all available subcommands
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```
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For example:
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@@ -71,7 +71,7 @@ The scripts depend on the following packages (installed version):
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* pandas (1.1.0)
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* scipy (1.7.0)
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* nixio (1.5.2)
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-* rlxnix (0.6.10)
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+* rlxnix (0.6.10, for [installation options see](https://github.com/relacs/relacsed_nix))
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* joblib (0.16.0)
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* sklearn (0.23.1)
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* matplotlib (3.4.2)
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Jan Grewe