From b80a39b0b96c3c2956cbe73091f10617402a3724 Mon Sep 17 00:00:00 2001 From: shimoura Date: Thu, 9 Nov 2023 11:38:10 +0100 Subject: [PATCH] rename "./data/" to "./experimental_data" --- README.md | 6 +++--- {data => experimental_data}/fraction_EI/README.md | 0 .../fraction_EI/binzegger.csv | 0 .../fraction_EI/lichtman.csv | 0 .../Connectivity_Distances_HCP_DesikanKilliany.mat | Bin .../hcp_dti/DKAtlas_VolumeAndNames.mat | Bin {data => experimental_data}/hcp_dti/README.md | 0 {data => experimental_data}/macaque/.gitignore | 0 {data => experimental_data}/macaque/README.md | 0 .../macaque/preprocessing.py | 0 {data => experimental_data}/mohan/README.md | 0 {data => experimental_data}/mohan/dendriteLength.py | 0 .../mohan/morphs_atdepth_json/.gitignore | 0 .../mohan/morphs_json/.gitignore | 0 .../mohan/placeSomaAtDepth.py | 0 {data => experimental_data}/rutishauser/.gitignore | 0 {data => experimental_data}/rutishauser/README.md | 0 {data => experimental_data}/senden/README.md | 0 .../senden/rsData_7T_DKparcel/ROIs.txt | 0 .../rsData_7T_DKparcel/rsDATA_7T_DKparcel.npy | Bin .../voneconomokoskinas/README.md | 0 ...tructuralData_VonEconomoKoskinas_addedvalues.xls | Bin src/compute_scaling_experiments.py | 2 +- src/data_loader/hcp_dti.py | 2 +- src/data_loader/rutishauser.py | 2 +- src/data_loader/synapse_cellbody_probability.py | 2 +- src/data_loader/voneconomokoskinas.py | 2 +- src/figure_connectivity_construction.py | 6 +++--- src/figure_scaling_experiments.py | 2 +- 29 files changed, 12 insertions(+), 12 deletions(-) rename {data => experimental_data}/fraction_EI/README.md (100%) rename {data => experimental_data}/fraction_EI/binzegger.csv (100%) rename {data => experimental_data}/fraction_EI/lichtman.csv (100%) rename {data => experimental_data}/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat (100%) rename {data => experimental_data}/hcp_dti/DKAtlas_VolumeAndNames.mat (100%) rename {data => experimental_data}/hcp_dti/README.md (100%) rename {data => experimental_data}/macaque/.gitignore (100%) rename {data => experimental_data}/macaque/README.md (100%) rename {data => experimental_data}/macaque/preprocessing.py (100%) rename {data => experimental_data}/mohan/README.md (100%) rename {data => experimental_data}/mohan/dendriteLength.py (100%) rename {data => experimental_data}/mohan/morphs_atdepth_json/.gitignore (100%) rename {data => experimental_data}/mohan/morphs_json/.gitignore (100%) rename {data => experimental_data}/mohan/placeSomaAtDepth.py (100%) rename {data => experimental_data}/rutishauser/.gitignore (100%) rename {data => experimental_data}/rutishauser/README.md (100%) rename {data => experimental_data}/senden/README.md (100%) rename {data => experimental_data}/senden/rsData_7T_DKparcel/ROIs.txt (100%) rename {data => experimental_data}/senden/rsData_7T_DKparcel/rsDATA_7T_DKparcel.npy (100%) rename {data => experimental_data}/voneconomokoskinas/README.md (100%) rename {data => experimental_data}/voneconomokoskinas/StructuralData_VonEconomoKoskinas_addedvalues.xls (100%) diff --git a/README.md b/README.md index 921f9d8..a21987c 100644 --- a/README.md +++ b/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 diff --git a/data/fraction_EI/README.md b/experimental_data/fraction_EI/README.md similarity index 100% rename from data/fraction_EI/README.md rename to experimental_data/fraction_EI/README.md diff --git a/data/fraction_EI/binzegger.csv b/experimental_data/fraction_EI/binzegger.csv similarity index 100% rename from data/fraction_EI/binzegger.csv rename to experimental_data/fraction_EI/binzegger.csv diff --git a/data/fraction_EI/lichtman.csv b/experimental_data/fraction_EI/lichtman.csv similarity index 100% rename from data/fraction_EI/lichtman.csv rename to experimental_data/fraction_EI/lichtman.csv diff --git a/data/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat b/experimental_data/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat similarity index 100% rename from data/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat rename to experimental_data/hcp_dti/Connectivity_Distances_HCP_DesikanKilliany.mat diff --git a/data/hcp_dti/DKAtlas_VolumeAndNames.mat b/experimental_data/hcp_dti/DKAtlas_VolumeAndNames.mat similarity index 100% rename from data/hcp_dti/DKAtlas_VolumeAndNames.mat rename to experimental_data/hcp_dti/DKAtlas_VolumeAndNames.mat diff --git a/data/hcp_dti/README.md b/experimental_data/hcp_dti/README.md similarity index 100% rename from data/hcp_dti/README.md rename to experimental_data/hcp_dti/README.md diff --git a/data/macaque/.gitignore b/experimental_data/macaque/.gitignore similarity index 100% rename from data/macaque/.gitignore rename to experimental_data/macaque/.gitignore diff --git a/data/macaque/README.md b/experimental_data/macaque/README.md similarity index 100% rename from data/macaque/README.md rename to experimental_data/macaque/README.md diff --git a/data/macaque/preprocessing.py b/experimental_data/macaque/preprocessing.py similarity index 100% rename from data/macaque/preprocessing.py rename to experimental_data/macaque/preprocessing.py diff --git a/data/mohan/README.md b/experimental_data/mohan/README.md similarity index 100% rename from data/mohan/README.md rename to experimental_data/mohan/README.md diff --git a/data/mohan/dendriteLength.py b/experimental_data/mohan/dendriteLength.py similarity index 100% rename from data/mohan/dendriteLength.py rename to experimental_data/mohan/dendriteLength.py diff --git a/data/mohan/morphs_atdepth_json/.gitignore b/experimental_data/mohan/morphs_atdepth_json/.gitignore similarity index 100% rename from data/mohan/morphs_atdepth_json/.gitignore rename to experimental_data/mohan/morphs_atdepth_json/.gitignore diff --git a/data/mohan/morphs_json/.gitignore b/experimental_data/mohan/morphs_json/.gitignore similarity index 100% rename from data/mohan/morphs_json/.gitignore rename to experimental_data/mohan/morphs_json/.gitignore diff --git a/data/mohan/placeSomaAtDepth.py b/experimental_data/mohan/placeSomaAtDepth.py similarity index 100% rename from data/mohan/placeSomaAtDepth.py rename to experimental_data/mohan/placeSomaAtDepth.py diff --git a/data/rutishauser/.gitignore b/experimental_data/rutishauser/.gitignore similarity index 100% rename from data/rutishauser/.gitignore rename to experimental_data/rutishauser/.gitignore diff --git a/data/rutishauser/README.md b/experimental_data/rutishauser/README.md similarity index 100% rename from data/rutishauser/README.md rename to experimental_data/rutishauser/README.md diff --git a/data/senden/README.md b/experimental_data/senden/README.md similarity index 100% rename from data/senden/README.md rename to experimental_data/senden/README.md diff --git a/data/senden/rsData_7T_DKparcel/ROIs.txt b/experimental_data/senden/rsData_7T_DKparcel/ROIs.txt similarity index 100% rename from data/senden/rsData_7T_DKparcel/ROIs.txt rename to experimental_data/senden/rsData_7T_DKparcel/ROIs.txt diff --git a/data/senden/rsData_7T_DKparcel/rsDATA_7T_DKparcel.npy b/experimental_data/senden/rsData_7T_DKparcel/rsDATA_7T_DKparcel.npy similarity index 100% rename from data/senden/rsData_7T_DKparcel/rsDATA_7T_DKparcel.npy rename to experimental_data/senden/rsData_7T_DKparcel/rsDATA_7T_DKparcel.npy diff --git a/data/voneconomokoskinas/README.md b/experimental_data/voneconomokoskinas/README.md similarity index 100% rename from data/voneconomokoskinas/README.md rename to experimental_data/voneconomokoskinas/README.md diff --git a/data/voneconomokoskinas/StructuralData_VonEconomoKoskinas_addedvalues.xls b/experimental_data/voneconomokoskinas/StructuralData_VonEconomoKoskinas_addedvalues.xls similarity index 100% rename from data/voneconomokoskinas/StructuralData_VonEconomoKoskinas_addedvalues.xls rename to experimental_data/voneconomokoskinas/StructuralData_VonEconomoKoskinas_addedvalues.xls diff --git a/src/compute_scaling_experiments.py b/src/compute_scaling_experiments.py index daef1ad..a7b3f6e 100644 --- a/src/compute_scaling_experiments.py +++ b/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)) diff --git a/src/data_loader/hcp_dti.py b/src/data_loader/hcp_dti.py index 0c3b9d7..cfe62c8 100644 --- a/src/data_loader/hcp_dti.py +++ b/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') diff --git a/src/data_loader/rutishauser.py b/src/data_loader/rutishauser.py index 5e61ed5..67cd7cc 100644 --- a/src/data_loader/rutishauser.py +++ b/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)) diff --git a/src/data_loader/synapse_cellbody_probability.py b/src/data_loader/synapse_cellbody_probability.py index 1d95c7d..51817a3 100644 --- a/src/data_loader/synapse_cellbody_probability.py +++ b/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=[ diff --git a/src/data_loader/voneconomokoskinas.py b/src/data_loader/voneconomokoskinas.py index a0c32da..7773a21 100644 --- a/src/data_loader/voneconomokoskinas.py +++ b/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()) diff --git a/src/figure_connectivity_construction.py b/src/figure_connectivity_construction.py index facf184..834003e 100644 --- a/src/figure_connectivity_construction.py +++ b/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/')) diff --git a/src/figure_scaling_experiments.py b/src/figure_scaling_experiments.py index a243f9e..29dfe46 100644 --- a/src/figure_scaling_experiments.py +++ b/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))