Note
Go to the end to download the full example code.
Generating sEIT forward models using a mask and a lookup tableΒΆ
import numpy as np
import reda
# used to generate a Cole-Cole response
import sip_models
import crtomo
set up plotting facilities - this will often generate better fitting plots
import crtomo.mpl
crtomo.mpl.setup()
This grid was sorted using CutMcK. The nodes were resorted!
Triangular grid found
for index, (x, z) in enumerate(tdm.grid.get_element_centroids()):
# print(index, x, z)
# depending on location assign a different pixel. This should be an integer
# that is later used to assign spectra to all pixels
tdm.parman.parsets[pid_mask][index] = int((np.abs(z) * 3))
fig, ax = tdm.show_parset(pid_mask, plot_colorbar=True, title='Mask Indices')
fig.show()
np.savetxt('mask.dat', tdm.parman.parsets[pid_mask], '%i')
mask = np.loadtxt('mask.dat').astype(int)
# generate the lookup table
lookup_table = {}
frequencies = np.logspace(-3, 3, 6)
colecole = sip_models.res.cc.cc(frequencies=frequencies)
spectrum = colecole.response([100, 0.1, 0.04, 0.6])
for index in np.unique(mask.astype(int)):
lookup_table[index] = spectrum
eit = crtomo.eitMan(grid=grid, frequencies=frequencies)
eit.assign_sip_signatures_using_mask(mask, lookup_table)
No forward models registered yet. Creating empty ones
sphinx_gallery_defer_figures
r = eit.plot_forward_models(
maglim=[80, 110],
phalim=[-30, 0],
)
r['rmag']['fig'].show()
r['rpha']['fig'].show()
fig, _ = spectrum._plot()
fig.show()
configs = reda.ConfigManager()
configs.nr_electrodes = 10
configs.gen_dipole_dipole(skipc=0)
eit.add_to_configs(configs.configs)
r = eit.measurements()
# sphinx_gallery_thumbnail_number = -1
attempting modeling
b' ######### CMod ############\nLicence:\nCopyright \xc2\xa9 1990-2020 Andreas Kemna <kemna@geo.uni-bonn.de>\nCopyright \xc2\xa9 2008-2020 CRTomo development team (see AUTHORS file)\nPermission is hereby granted, free of charge, to any person obtaining a copy of\nthis software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\nthe Software without restriction, including without limitation the rights to\nuse, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\nof the Software, and to permit persons to whom the Software is furnished to do\nso, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n \n \n CRMod Process_ID :: 4875\n OpenMP max threads: 4\n Git-Branch master\n Commit-ID cb89ccd2c4341b9b08bbe7bb08f5aea0d60916ee\n Created Mon-Mar-25-14:34:56-2024\n Compiler \n OS GNU/Linux\n\n Reading Input-Files\n++ check 1\r++ check 2 done!\n\rGetting voltage 1\rGetting voltage 2\rGetting voltage 3\rGetting voltage 4\rGetting voltage 5\rGetting voltage 6\rGetting voltage 7\rGetting voltage 8\rGetting voltage 9\rGetting voltage 10\rGetting voltage 11\rGetting voltage 12\rGetting voltage 13\rGetting voltage 14\rGetting voltage 15\rGetting voltage 16\rGetting voltage 17\rGetting voltage 18\rGetting voltage 19\rGetting voltage 20\rGetting voltage 21\rGetting voltage 22\rGetting voltage 23\rGetting voltage 24\rGetting voltage 25\rGetting voltage 26\rGetting voltage 27\rGetting voltage 28 No electrode cap file\n \n Rescheduling..\n less nodes than wavenumbers\n OpenMP threads: 3( 4)\n\n\r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 4 \r Calculating Potentials : Wavenumber 5 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 7 \r Calculating Potentials : Wavenumber 8 \r Calculating Potentials : Wavenumber 9 done, now processing\n solution time 0d/ 0h/ 0m/ 0s/ 152ms\n\n Modelling completedSTOP 0\n'
reading voltages
attempting modeling
b' ######### CMod ############\nLicence:\nCopyright \xc2\xa9 1990-2020 Andreas Kemna <kemna@geo.uni-bonn.de>\nCopyright \xc2\xa9 2008-2020 CRTomo development team (see AUTHORS file)\nPermission is hereby granted, free of charge, to any person obtaining a copy of\nthis software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\nthe Software without restriction, including without limitation the rights to\nuse, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\nof the Software, and to permit persons to whom the Software is furnished to do\nso, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n \n \n CRMod Process_ID :: 4879\n OpenMP max threads: 4\n Git-Branch master\n Commit-ID cb89ccd2c4341b9b08bbe7bb08f5aea0d60916ee\n Created Mon-Mar-25-14:34:56-2024\n Compiler \n OS GNU/Linux\n\n Reading Input-Files\n++ check 1\r++ check 2 done!\n\rGetting voltage 1\rGetting voltage 2\rGetting voltage 3\rGetting voltage 4\rGetting voltage 5\rGetting voltage 6\rGetting voltage 7\rGetting voltage 8\rGetting voltage 9\rGetting voltage 10\rGetting voltage 11\rGetting voltage 12\rGetting voltage 13\rGetting voltage 14\rGetting voltage 15\rGetting voltage 16\rGetting voltage 17\rGetting voltage 18\rGetting voltage 19\rGetting voltage 20\rGetting voltage 21\rGetting voltage 22\rGetting voltage 23\rGetting voltage 24\rGetting voltage 25\rGetting voltage 26\rGetting voltage 27\rGetting voltage 28 No electrode cap file\n \n Rescheduling..\n less nodes than wavenumbers\n OpenMP threads: 3( 4)\n\n\r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 4 \r Calculating Potentials : Wavenumber 5 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 7 \r Calculating Potentials : Wavenumber 9 \r Calculating Potentials : Wavenumber 9 done, now processing\n solution time 0d/ 0h/ 0m/ 0s/ 158ms\n\n Modelling completedSTOP 0\n'
reading voltages
attempting modeling
b' ######### CMod ############\nLicence:\nCopyright \xc2\xa9 1990-2020 Andreas Kemna <kemna@geo.uni-bonn.de>\nCopyright \xc2\xa9 2008-2020 CRTomo development team (see AUTHORS file)\nPermission is hereby granted, free of charge, to any person obtaining a copy of\nthis software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\nthe Software without restriction, including without limitation the rights to\nuse, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\nof the Software, and to permit persons to whom the Software is furnished to do\nso, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n \n \n CRMod Process_ID :: 4883\n OpenMP max threads: 4\n Git-Branch master\n Commit-ID cb89ccd2c4341b9b08bbe7bb08f5aea0d60916ee\n Created Mon-Mar-25-14:34:56-2024\n Compiler \n OS GNU/Linux\n\n Reading Input-Files\n++ check 1\r++ check 2 done!\n\rGetting voltage 1\rGetting voltage 2\rGetting voltage 3\rGetting voltage 4\rGetting voltage 5\rGetting voltage 6\rGetting voltage 7\rGetting voltage 8\rGetting voltage 9\rGetting voltage 10\rGetting voltage 11\rGetting voltage 12\rGetting voltage 13\rGetting voltage 14\rGetting voltage 15\rGetting voltage 16\rGetting voltage 17\rGetting voltage 18\rGetting voltage 19\rGetting voltage 20\rGetting voltage 21\rGetting voltage 22\rGetting voltage 23\rGetting voltage 24\rGetting voltage 25\rGetting voltage 26\rGetting voltage 27\rGetting voltage 28 No electrode cap file\n \n Rescheduling..\n less nodes than wavenumbers\n OpenMP threads: 3( 4)\n\n\r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 4 \r Calculating Potentials : Wavenumber 5 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 7 \r Calculating Potentials : Wavenumber 8 \r Calculating Potentials : Wavenumber 9 done, now processing\n solution time 0d/ 0h/ 0m/ 0s/ 152ms\n\n Modelling completedSTOP 0\n'
reading voltages
attempting modeling
b' ######### CMod ############\nLicence:\nCopyright \xc2\xa9 1990-2020 Andreas Kemna <kemna@geo.uni-bonn.de>\nCopyright \xc2\xa9 2008-2020 CRTomo development team (see AUTHORS file)\nPermission is hereby granted, free of charge, to any person obtaining a copy of\nthis software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\nthe Software without restriction, including without limitation the rights to\nuse, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\nof the Software, and to permit persons to whom the Software is furnished to do\nso, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n \n \n CRMod Process_ID :: 4887\n OpenMP max threads: 4\n Git-Branch master\n Commit-ID cb89ccd2c4341b9b08bbe7bb08f5aea0d60916ee\n Created Mon-Mar-25-14:34:56-2024\n Compiler \n OS GNU/Linux\n\n Reading Input-Files\n++ check 1\r++ check 2 done!\n\rGetting voltage 1\rGetting voltage 2\rGetting voltage 3\rGetting voltage 4\rGetting voltage 5\rGetting voltage 6\rGetting voltage 7\rGetting voltage 8\rGetting voltage 9\rGetting voltage 10\rGetting voltage 11\rGetting voltage 12\rGetting voltage 13\rGetting voltage 14\rGetting voltage 15\rGetting voltage 16\rGetting voltage 17\rGetting voltage 18\rGetting voltage 19\rGetting voltage 20\rGetting voltage 21\rGetting voltage 22\rGetting voltage 23\rGetting voltage 24\rGetting voltage 25\rGetting voltage 26\rGetting voltage 27\rGetting voltage 28 No electrode cap file\n \n Rescheduling..\n less nodes than wavenumbers\n OpenMP threads: 3( 4)\n\n\r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 4 \r Calculating Potentials : Wavenumber 5 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 7 \r Calculating Potentials : Wavenumber 9 \r Calculating Potentials : Wavenumber 9 done, now processing\n solution time 0d/ 0h/ 0m/ 0s/ 154ms\n\n Modelling completedSTOP 0\n'
reading voltages
attempting modeling
b' ######### CMod ############\nLicence:\nCopyright \xc2\xa9 1990-2020 Andreas Kemna <kemna@geo.uni-bonn.de>\nCopyright \xc2\xa9 2008-2020 CRTomo development team (see AUTHORS file)\nPermission is hereby granted, free of charge, to any person obtaining a copy of\nthis software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\nthe Software without restriction, including without limitation the rights to\nuse, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\nof the Software, and to permit persons to whom the Software is furnished to do\nso, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n \n \n CRMod Process_ID :: 4891\n OpenMP max threads: 4\n Git-Branch master\n Commit-ID cb89ccd2c4341b9b08bbe7bb08f5aea0d60916ee\n Created Mon-Mar-25-14:34:56-2024\n Compiler \n OS GNU/Linux\n\n Reading Input-Files\n++ check 1\r++ check 2 done!\n\rGetting voltage 1\rGetting voltage 2\rGetting voltage 3\rGetting voltage 4\rGetting voltage 5\rGetting voltage 6\rGetting voltage 7\rGetting voltage 8\rGetting voltage 9\rGetting voltage 10\rGetting voltage 11\rGetting voltage 12\rGetting voltage 13\rGetting voltage 14\rGetting voltage 15\rGetting voltage 16\rGetting voltage 17\rGetting voltage 18\rGetting voltage 19\rGetting voltage 20\rGetting voltage 21\rGetting voltage 22\rGetting voltage 23\rGetting voltage 24\rGetting voltage 25\rGetting voltage 26\rGetting voltage 27\rGetting voltage 28 No electrode cap file\n \n Rescheduling..\n less nodes than wavenumbers\n OpenMP threads: 3( 4)\n\n\r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 4 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 7 \r Calculating Potentials : Wavenumber 8 \r Calculating Potentials : Wavenumber 9 done, now processing\n solution time 0d/ 0h/ 0m/ 0s/ 152ms\n\n Modelling completedSTOP 0\n'
reading voltages
attempting modeling
b' ######### CMod ############\nLicence:\nCopyright \xc2\xa9 1990-2020 Andreas Kemna <kemna@geo.uni-bonn.de>\nCopyright \xc2\xa9 2008-2020 CRTomo development team (see AUTHORS file)\nPermission is hereby granted, free of charge, to any person obtaining a copy of\nthis software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\nthe Software without restriction, including without limitation the rights to\nuse, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\nof the Software, and to permit persons to whom the Software is furnished to do\nso, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n \n \n CRMod Process_ID :: 4895\n OpenMP max threads: 4\n Git-Branch master\n Commit-ID cb89ccd2c4341b9b08bbe7bb08f5aea0d60916ee\n Created Mon-Mar-25-14:34:56-2024\n Compiler \n OS GNU/Linux\n\n Reading Input-Files\n++ check 1\r++ check 2 done!\n\rGetting voltage 1\rGetting voltage 2\rGetting voltage 3\rGetting voltage 4\rGetting voltage 5\rGetting voltage 6\rGetting voltage 7\rGetting voltage 8\rGetting voltage 9\rGetting voltage 10\rGetting voltage 11\rGetting voltage 12\rGetting voltage 13\rGetting voltage 14\rGetting voltage 15\rGetting voltage 16\rGetting voltage 17\rGetting voltage 18\rGetting voltage 19\rGetting voltage 20\rGetting voltage 21\rGetting voltage 22\rGetting voltage 23\rGetting voltage 24\rGetting voltage 25\rGetting voltage 26\rGetting voltage 27\rGetting voltage 28 No electrode cap file\n \n Rescheduling..\n less nodes than wavenumbers\n OpenMP threads: 3( 4)\n\n\r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 3 \r Calculating Potentials : Wavenumber 4 \r Calculating Potentials : Wavenumber 5 \r Calculating Potentials : Wavenumber 6 \r Calculating Potentials : Wavenumber 7 \r Calculating Potentials : Wavenumber 8 \r Calculating Potentials : Wavenumber 9 done, now processing\n solution time 0d/ 0h/ 0m/ 0s/ 162ms\n\n Modelling completedSTOP 0\n'
reading voltages