rename "./data/" to "./experimental_data"

README.md

@@ -29,8 +29,8 @@ This code implements the multi-scale, spiking network model of human cortex deve
 ## Prerequisites
 ### Data
 
-Data extracted from experimental references and necessary to run the codes can be found in [data/](./data/) folder. These files will be automatically loaded when running the simulation (check section [How to run](#how-to-run) for details).
-Please note that some data has to be manually downloaded. Specifically, the data stored in `./data/macaque/` and `./data/rutishauser/`.
+Data extracted from experimental references and necessary to run the codes can be found in [experimental_data/](./experimental_data/) folder. These files will be automatically loaded when running the simulation (check section [How to run](#how-to-run) for details).
+Please note that some data has to be manually downloaded. Specifically, the data stored in `./experimental_data/macaque/` and `./experimental_data/rutishauser/`.
 
 ### Requirements
 
@@ -64,7 +64,7 @@ The NEST installation path will have to be specified in `config.yaml` described
 Folder structure:
 | directory | description |
 | --- | --- |
-| [./data/](./data/) | contains experimental datasets used for building the network and for comparing results |
+| [./experimental_data/](./experimental_data/) | contains experimental datasets used for building the network and for comparing results |
 | [./experiments/](./experiments/) | contains python scripts which set the model parameters for different simulation experiments |
 | [./figures/](./figures/) | output directory for figures |
 | [./misc/](./misc/) | includes supplementary files such as documentation, matplotlib style files, and other experiment files

src/compute_scaling_experiments.py

@@ -139,7 +139,7 @@
 # ==============================================================================
 # ==============================================================================
 
-filename = base_path + 'data/rutishauser/spikes/'
+filename = base_path + 'experimental_data/rutishauser/spikes/'
 data = load_data(filename)
 print(f'loaded {len(data)} neurons')
 all_ids = range(len(data))

src/data_loader/hcp_dti.py

@@ -187,7 +187,7 @@ def getVolume(self):
 
 if __name__ == "__main__":
 
-    dk_path = 'data/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat'
+    dk_path = 'experimental_data/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat'
     dk = HcpDesikanKilliany(dk_path)
     print(dk)
     # dk.dump('dk_tmp.hdf')

src/data_loader/rutishauser.py

@@ -34,7 +34,7 @@ def get_neuron(data, neuron_id):
     import numpy as np
     import matplotlib.pyplot as plt
 
-    filename = 'data/rutishauser/spikes/'
+    filename = 'experimental_data/rutishauser/spikes/'
     data = load_data(filename)
     print(f'loaded {len(data)} neurons')
     all_ids = range(len(data))

src/data_loader/synapse_cellbody_probability.py

@@ -33,7 +33,7 @@
 )
 
 # Mohan data: only pyramidal cells -> dummy probability of 0 for inhibitory neurons
-# Numbers extracted from data/mohan/dendriteLength.py (see the README therein)
+# Numbers extracted from experimental_data/mohan/dendriteLength.py (see the README therein)
 # The array corresponds to `s2cb` which is plotted at the end of the script.
 mohan = pd.DataFrame(
     data=[

src/data_loader/voneconomokoskinas.py

@@ -104,7 +104,7 @@ def dump(self, file_path, key=''):
 
 if __name__ == "__main__":
 
-    vek_path = '../data/voneconomokoskinas/StructuralData_VonEconomoKoskinas.xls'
+    vek_path = '../experimental_data/voneconomokoskinas/StructuralData_VonEconomoKoskinas.xls'
     vek = VonEconomoKoskinas(vek_path)
     print(vek)
     print(vek.getNeuronDensity())

src/figure_connectivity_construction.py

@@ -13,12 +13,12 @@
 
 has_macaque_data = True
 try:
-    macaque_data = pd.read_pickle('data/macaque/macaque_data_merged.pkl')
+    macaque_data = pd.read_pickle('experimental_data/macaque/macaque_data_merged.pkl')
 except FileNotFoundError:
-    print('WARNING: Did not find data/macaque/macaque_data_merged.pkl so the
+    print('WARNING: Did not find experimental_data/macaque/macaque_data_merged.pkl so the
            data in the background of panel D will be missing in the figure. To
            include the data please check if you have the necessary files in
-           data/macaque/, then run the script data/macaque/preprocessing.py')
+           experimental_data/macaque/, then run the script experimental_data/macaque/preprocessing.py')
     has_macaque_data = False
     exit(1)
 net_dict = networkDictFromDump(os.path.join(os.getcwd(), 'out/517f98422516bbe6cb324c5436e7f66f/'))

src/figure_scaling_experiments.py

@@ -475,7 +475,7 @@
 # Plot experimental fMRI
 # ==============================================================================
 
-data_dir = os.path.join(os.getcwd(), 'data/senden/rsData_7T_DKparcel/')
+data_dir = os.path.join(os.getcwd(), 'experimental_data/senden/rsData_7T_DKparcel/')
 roi = pd.read_csv(os.path.join(data_dir, 'ROIs.txt'), header=None, names=['roi'], dtype=str, squeeze=True)
 roi = roi.apply(lambda x: x.split('-')[-1])
 roi = roi.drop(range(0, 14)).drop(range(82, 85))