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Adding a readme for the figures
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‎figures/kCSD_properties/README.txt‎

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Instructions for the figures from kCSD paper.
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Instructions for the figures from kCSD-revisited paper.
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To create Figure 6 (figure6_kCSD2d.py) and 7 (figure7_kCSD2d.py) data available
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at Dropbox PNI folder is required (Dropbox/PNI/kCSDrev-pics/error_maps_2D).
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 1 - Schematic
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To create Figure 9 (tutorial_broken_electrodes.py) and extended version of this
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figure (tutorial_broken_electrodes_sig_err.py) download necessary data from:
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sources_electrodes.odg
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 2 - 1D spectral properties of kCSD method
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figure_eigensources_M_1D.py
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figure_eigensources_R_1D.py (another version with inset plot)
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 3 and 4 - Noise-free Electrode/Basis source placement
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figure_Tbasis.py
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 3 and 4 - Noisy electrodes / Basis source placement
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figure_Tbasis.py
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 5 - L-curve method for regularization
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 6 - L-curve versus Cross-validation
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fig2_cv_vs_lc.py
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 7 - Error propagation map
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error_propagation.py
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colorblind_friendly.py
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 8 - Reliability map
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reliability_map_2d.py
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error_maps_2D/point_error_large_100_all_ele.npy
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error_maps_2D/point_error_small_100_all_ele.npy
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 9 - Reliability map; Use case in a 2D dipolar large source
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figure7_kCSD2d.py
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error_maps_2D/point_error_large_100_all_ele.npy
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error_maps_2D/point_error_small_100_all_ele.npy
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 10 - Average Error (Diff) when broken electrode and loss in reconstruction quality
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 11 - Basic features tutorial
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You will need to run tutorial3.py first or download files from here
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https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
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tutorial_basic.py
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~~~~~~~~~~~~~~~~~~~~~~~
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Figure 12 - Noisy electrodes tutorial
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tutorial_noisy_electrodes.py
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~~~~~~~~~~~~~~~~~~~~~~~~
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Figure 13 - Broken electrodes tutorial
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Download first from
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https://www.dropbox.com/sh/6kykj4d3dx3fp5s/AAACtN49VCbAHA9otOfNXbnOa?dl=0
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(generated from tweaking tutorial3.py)
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tutorial_broken_electrodes.py
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tutorial_broken_electrodes_sig_err.py (another variant)
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~~~~~~~~~~~~~~~~~~~~~~~~
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Figure 14 - L-Curve and CV landscape
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=====================
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Supplementary Figures
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=====================
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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Figure S1 / 15 - spectral properties of kCSD method for simple 2D case
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figure_eigensources_M_2D.py
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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Figure S2 / 16 - Error propagation maps for 1D
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pots_propagation.py
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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Figure S3 / 17 - 3D source reconstruction
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tutorial_basic_3d.py
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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Figure S4 / 18 - sKCSD example
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‎figures/kCSD_properties/sources_electrodes.odg‎

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Binary file not shown.

‎figures/kCSD_properties/tutorial3.py‎

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@@ -148,8 +148,13 @@ def do_kcsd(CSD_PROFILE, csd_seed, prefix, missing_ele):
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true_csd=true_csd, pots=pots, post_cv=est_csd_post_cv, R=k.R)
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if __name__ == '__main__':
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CSD_PROFILE = CSD.gauss_2d_large #CSD.gauss_2d_small #
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prefix = '/home/chaitanya/kCSD-python/figures/kCSD_properties/large_srcs_minus_20'
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CSD_PROFILE = CSD.gauss_2d_large
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prefix = '/home/chaitanya/kCSD-python/figures/kCSD_properties/large_srcs_all_ele'
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for csd_seed in range(100):
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do_kcsd(CSD_PROFILE, csd_seed, prefix, missing_ele=20)
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do_kcsd(CSD_PROFILE, csd_seed, prefix, missing_ele=0)
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print("Done ", csd_seed)
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CSD_PROFILE = CSD.gauss_2d_small
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prefix = '/home/chaitanya/kCSD-python/figures/kCSD_properties/small_srcs_all_ele'
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for csd_seed in range(100):
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do_kcsd(CSD_PROFILE, csd_seed, prefix, missing_ele=0)
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print("Done ", csd_seed)

‎figures/kCSD_properties/tutorial_broken_electrodes.py‎

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if csd_type =='small':
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seed_list = range(100)
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else:
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seed_list = range(60)
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seed_list = range(100)
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fldrs = fetch_folder(csd_type=csd_type)
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list_dicts = load_files(fldrs, seed_list)
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errs = eval_errors(list_dicts, seed_list)

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