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@@ -21,26 +21,39 @@ conda develop .
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### How to run the simulation
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-The entire process is split in three main scripts. The simulation is setup and run via
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+The entire process is split in three main scripts: run, analysis and plotting. We use [pypet](https://pypet
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+.readthedocs.io/en/latest/) to organize our simulations and save intermediate results.
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+
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+#### Simulate the spatial networks
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+The simulation is setup and run via
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```bash
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-python scripts/spatial_network/perlin_map/run_simulation_perlin_map.py
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+cd scripts/spatial_network/perlin_map
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+python run_simulation_perlin_map.py
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```
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-Relevant parameters are the range of scale and seed values for the input map generation as explained in the script.
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+This script also contains the relevant parameter settings such as network size or the form of the interneuron
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+ axons. To allow exceution of the script in a reasonable time, we reduced the number of input maps that are tested
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+ . In the script, you find instructions to make the full run. After the script has successfully finished, you find
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+ the output in the `data` folder.
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+
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+#### Analysis of the network activity
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+
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A preliminary analysis of the simulated data is done by running
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```bash
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-python scripts/spatial_network/perlin_map/preliminary_analysis_perlin_map.py
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+python preliminary_analysis_perlin_map.py
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```
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-The final analysis and figure generation is done by
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+To run both simulation and preliminary analysis
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```bash
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-python scripts/spatial_network/perlin_map/final_analysis_and_plotting_perlin_map.py
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+python run_and_analyze_perlin.py
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```
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-Note, that running the simulation script will overwrite the saved data.
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-The bulk of the runtime lies within the simulation and preliminary analysis which can be executed together via
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+
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+#### Generate plots
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+
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+The final analysis and figure generation is done by
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```bash
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-python scripts/spatial_network/perlin_map/run_and_analyze_perlin.py
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+python final_analysis_and_plotting_perlin_map.py
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```
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-after which the figure script can be tweaked and executed without loss of data.
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+#### Supplemental figure
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For the supplement figure, a pinwheel map is used as an alternative input map. The run, analyse and plot scripts are
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organized in the same manner but found in the folder `scripts/spatial_network/supplement_pinwheel_map`.
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