from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_pastoll as config parser = flagparse.FlagParser() parser.add_flag('--velSweep') parser.add_flag('--velFitStdSweep') parser.add_flag('--velLines') parser.add_flag('--vel_slope_sweeps') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.velSweep or args.all: env.register_plotter(noisefigs.plotters.VelFitErrSweepPlotter) if args.velFitStdSweep or args.all: env.register_plotter(noisefigs.plotters.VelFitStdSweepPlotter) if args.velLines or args.all: env.register_plotter(noisefigs.plotters.VelLinesPlotter) if args.vel_slope_sweeps or args.all: env.register_plotter(noisefigs.plotters.VelSlopeSweepPlotter) env.plot()
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment singleDataRoot = "simulation_data/submission/single_neuron" parser = flagparse.FlagParser() parser.add_flag("--velSweep") parser.add_flag("--velFitStdSweep") args = parser.parse_args() # ps = ds.getDefaultParamSpaces() env = NoiseEnvironment() if args.velSweep or args.all: env.register_plotter(noisefigs.plotters.VelFitErrSweepPlotter) if args.velFitStdSweep or args.all: env.register_plotter(noisefigs.plotters.VelFitStdSweepPlotter) env.plot()
ax_theta = fig.add_axes( Bbox.from_extents(gsl, gst - .015, gsr, gst + .01)) t = np.arange(tLimits[0], tLimits[1] + self.dt, self.dt) theta = self.const + .5 * (1. + np.cos(2 * np.pi * self.freq * 1e-3 * t - np.pi)) * (1 - self.const) ax_theta.fill_between(t, theta, edgecolor='None', color=self.myc['theta_color']) ax_theta.set_xlim([tLimits[0], tLimits[1]]) ax_theta.set_ylim(-.02, 1.02) ax_theta.axis('off') plt.savefig(self.get_fname('pastoll_et_al_rasters.pdf'), dpi=300, transparent=True) plt.close(fig) parser = flagparse.FlagParser() parser.add_flag('--raster_examples') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.raster_examples or args.all: env.register_plotter(RasterExamples) env.plot()
import matplotlib.ticker as ti from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--grids') parser.add_flag('--examplesFlag') parser.add_flag('--examples_colorbar') parser.add_flag('--diff_sweep') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.grids or args.all: env.register_plotter(noisefigs.plotters.GridSweepsPlotter) env.register_plotter(noisefigs.plotters.GridSweepsPlotter, config={ 'GridSweepsPlotter': { 'population_type': 'I', 'plot_contours': [1, 1, 1], 'vmin': -0.33, 'vmax': 0.75, 'cbar_kw': { 'ticks': ti.MultipleLocator(0.2), }, } })
from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--rasters') parser.add_flag('--rastersZoom') parser.add_flag('--rates') parser.add_flag('--vel_slope_sweeps') parser.add_flag('--vel_fiterr_prob') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.rasters or args.all: env.register_plotter(noisefigs.plotters.VelocityRasterPlotter) if args.rates or args.all: env.register_plotter(noisefigs.plotters.VelocityRatePlotter) if args.rastersZoom or args.all: env.register_plotter(noisefigs.plotters.VelocityRasterZoomPlotter) if args.vel_slope_sweeps or args.all: env.register_plotter(noisefigs.plotters.VelSlopeSweepPlotter) if args.vel_fiterr_prob or args.all: env.register_plotter(noisefigs.plotters.GridsVelFitErrProbabilityPlotter)
from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_e_const_450 as config parser = flagparse.FlagParser() parser.add_flag('--theta_signal') parser.add_flag('--rastersFlag') parser.add_flag('--rates') parser.add_flag('--maxFRSweeps') parser.add_flag('--seizureProportion') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.theta_signal or args.all: env.register_plotter(noisefigs.plotters.ThetaSignalPlotter) if args.rastersFlag or args.all: env.register_plotter(noisefigs.plotters.EIRasterPlotter) if args.rates or args.all: env.register_plotter(noisefigs.plotters.EIRatePlotter) if args.maxFRSweeps or args.all: env.register_plotter(noisefigs.plotters.MaxPopulationFRSweepsPlotter) if args.seizureProportion or args.all: env.register_plotter(noisefigs.plotters.PSeizureSweepPlotter)
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--scatterPlot') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.scatterPlot or args.all: env.register_plotter(noisefigs.plotters.ScatterGammaGridsSeparatePlotter) env.register_plotter(noisefigs.plotters.ScatterGammaFGridsSeparatePlotter) env.plot()
from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--theta_signal') parser.add_flag('--rastersFlag') parser.add_flag('--rates') parser.add_flag('--maxFRSweeps') parser.add_flag('--maxFRGridsProbability') parser.add_flag('--maxFRGridsScatter') parser.add_flag('--PSeizureGridsProbability') parser.add_flag('--PSeizureGridsScatter') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.theta_signal or args.all: env.register_plotter(noisefigs.plotters.ThetaSignalPlotter) if args.rastersFlag or args.all: env.register_plotter(noisefigs.plotters.EIRasterPlotter) if args.rates or args.all: env.register_plotter(noisefigs.plotters.EIRatePlotter) if args.maxFRSweeps or args.all: env.register_plotter(noisefigs.plotters.MaxPopulationFRSweepsPlotter) env.register_plotter(noisefigs.plotters.MaxPopulationFRSweepsPlotter, config={ 'MaxPopulationFRSweepsPlotter': {
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--bumpExamples') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.bumpExamples or args.all: env.register_plotter(noisefigs.plotters.IsBumpExamplePlotter) env.plot()
import matplotlib import matplotlib.ticker as ti from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_ratio_corrected as config parser = flagparse.FlagParser() parser.add_flag('--gamma_sweep') parser.add_flag('--examples') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.gamma_sweep or args.all: env.register_class( noisefigs.plotters.GenericGammaPlotter, config={ 'GenericGammaPlotter': { 'scale_factor': .7, 'what': 'acVal', 'fname': "gamma_sweeps{ns}.pdf", 'normalize_ticks': (True, True), # (Y, X) 'normalize_type': ('E', 'I'), 'xlabel': '', 'xticks': [False, False, False], 'ylabel': None, 'yticks': [True, False, False],
from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag("--grids") parser.add_flag("--examplesFlag") parser.add_flag("--examples_colorbar") parser.add_flag("--diff_sweep") args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.grids or args.all: env.register_plotter(noisefigs.plotters.GridSweepsPlotter) if args.examplesFlag or args.all: env.register_plotter(noisefigs.plotters.GridExamplesPlotter) if args.examples_colorbar or args.all: env.register_plotter(noisefigs.plotters.GridExampleColorbarPlotter) if args.diff_sweep or args.all: env.register_plotter(noisefigs.plotters.GridsDiffSweep) env.plot()
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config singleDataRoot = 'simulation_data/single_neuron' parser = flagparse.FlagParser() parser.add_flag('--scatter_plot') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.scatter_plot or args.all: env.register_plotter(noisefigs.plotters.GridBumpScatterPlotter) env.plot()
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--rasters') parser.add_flag('--rates') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.rasters or args.all: env.register_plotter(noisefigs.plotters.EIRasterPlotter) if args.rates or args.all: env.register_plotter(noisefigs.plotters.EIRatePlotter) env.plot()
from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_pastoll as config parser = flagparse.FlagParser() parser.add_flag('--grids') parser.add_flag('--examplesFlag') parser.add_flag('--examples_colorbar') parser.add_flag('--diff_sweep') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.grids or args.all: env.register_plotter(noisefigs.plotters.GridSweepsPlotter) if args.examplesFlag or args.all: env.register_plotter(noisefigs.plotters.GridExamplesPlotter) env.register_plotter(noisefigs.plotters.GridExamplesPlotter, config={ 'GridExamplesPlotter': { 'population_type': 'I' }, }) if args.examples_colorbar or args.all: env.register_plotter(noisefigs.plotters.GridExampleColorbarPlotter)
import matplotlib.ticker as ti from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_trials as config parser = flagparse.FlagParser() #parser.add_flag('--grids') parser.add_flag('--scatter') parser.add_flag('--hist') parser.add_flag('--examples') parser.add_flag('--examples_cbar') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) #if args.grids or args.all: # env.register_plotter(noisefigs.plotters.IPCGridSweepsPlotter) # env.register_plotter(noisefigs.plotters.IPCGridSweepsPlotter, # config={ # 'IPCGridSweepsPlotter': { # 'population_type': 'I', # } # }) if args.scatter or args.all: env.register_plotter(noisefigs.plotters.IPCScatterPlotter) if args.hist or args.all: env.register_plotter(noisefigs.plotters.IPCHistogramsPlotter)
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--scatter_plot') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.scatter_plot or args.all: env.register_plotter(noisefigs.plotters.GridsLineErrScatterPlotter) env.plot()
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--isBump') parser.add_flag('--fracTotalHist') parser.add_flag('--fracTotalSweepAnn') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.fracTotalSweepAnn or args.all: env.register_plotter(noisefigs.plotters.FracTotalSweepAnnPlotter) if args.isBump or args.all: env.register_plotter(noisefigs.plotters.IsBumpPlotter) if args.fracTotalHist or args.all: env.register_plotter(noisefigs.plotters.FracTotalHistPlotter) env.plot()
if args.bumps_g_II or args.all: new_config = deepcopy(config.get_config()) new_config.update({ 'grids_data_root': None, 'bump_data_root': os.path.join('simulation_data', 'ii_connections', 'g_II_total_sweep', 'gamma_bump'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [150], 'even_shape': None, }) env = NoiseEnvironment(user_config=new_config, space_cls=JobTrialSpace1D) env.register_class( noisefigs.plotters.Generic1DPBumpPlotter, config={ 'Generic1DPBumpPlotter' : { 'fname' : 'bumps_Pbumps_g_II_{ns}.pdf', 'normalize_ticks': False, 'xlim': (-10, 410), 'ylim': (-0.05, 1.05), }, } ) env.plot()
#!/usr/bin/env python '''I-surround gamma plots with the Pastoll et al. settings.''' from __future__ import absolute_import, print_function import copy import matplotlib from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_pastoll as config parser = flagparse.FlagParser() parser.add_flag('--gamma_sweep') parser.add_flag('--examples') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.gamma_sweep or args.all: env.register_plotter(noisefigs.plotters.GammaSweepsPlotter) if args.examples or args.all: env.register_plotter(noisefigs.plotters.GammaExamplePlotter) env.plot()
None, 'bump_data_root': ('simulation_data/i_surround/' 'gamma_bump_Iext_e_theta_vs_Iext_e_const'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [0, 150, 300], 'even_shape': None, 'output_dir': 'panels', }) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.Generic2DPBumpPlotter, config={ 'Generic2DPBumpPlotter': { 'fname': "bumps_pbumps_Iext_e_theta_vs_Iext_e_const_{ns}.pdf", 'normalize_ticks': (False, False), # (Y, X) 'normalize_type': (None, None), 'xlabel': 'Constant amplitude\n(pA)', 'ylabel': '$\\theta$ amplitude (pA)', 'bbox': (.15, .2, .85, .9), 'yticks': [1, 0, 0], 'cbar': [0, 0, 1], }, }) env.plot()
parser = flagparse.FlagParser() parser.add_flag('--grids') parser.add_flag('--spatial_info') parser.add_flag('--sparsity') parser.add_flag('--spatial_info_stats') parser.add_flag('--examplesFlag') parser.add_flag('--examples_colorbar') parser.add_flag('--correlation_angles') parser.add_flag('--detailed_noise') parser.add_flag('--diff_sweep') parser.add_flag('--grids_pbumps_prob') parser.add_flag('--high_gscore_frac') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.grids or args.all: env.register_plotter(noisefigs.plotters.GridSweepsPlotter) env.register_plotter(noisefigs.plotters.GridSweepsPlotter, config={ 'GridSweepsPlotter': { 'population_type': 'I', 'plot_contours': [1, 1, 1], 'vmin': -0.32, 'vmax': 0.774, 'cbar_kw': { 'ticks': ti.MultipleLocator(0.2), }, 'ann': None, }
new_config = deepcopy(config_pastoll.get_config()) new_config.update({ 'bump_data_root': None, 'grids_data_root': os.path.join('simulation_data', 'i_surround', 'pastoll_et_al', 'grids_pc_weight_3'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [150], 'even_shape': None, 'output_dir': 'panels', }) env = NoiseEnvironment(user_config=new_config) env.register_class(noisefigs.plotters.GridSweepsPlotter, config={ 'GridSweepsPlotter': { 'fname_prefix': "pastoll_pc_weight_3_", 'vmin': -0.4286, 'vmax': 0.8582, 'ann': None, }, }) env.plot() if args.grids_pastoll_pc_weight or args.all: new_config = deepcopy(config.get_config())
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--scatter_grids_fracTotal') parser.add_flag('--fracTotalSweepAnn') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.fracTotalSweepAnn or args.all: env.register_plotter(noisefigs.plotters.MainBumpFormationPlotter) if args.scatter_grids_fracTotal or args.all: env.register_plotter(noisefigs.plotters.MainScatterGridsBumpsPlotter) env.plot()
import config singleDataRoot = 'simulation_data/submission/single_neuron' parser = flagparse.FlagParser() parser.add_flag('--maxThetaFRSweeps') parser.add_flag('--maxThetaFRSweeps_median') parser.add_flag('--maxThetaFRSweeps_std') parser.add_flag('--maxThetaFRHist') parser.add_flag('--seizureProportion') args = parser.parse_args() #ps = ds.getDefaultParamSpaces() env = NoiseEnvironment(user_config=config.get_config()) if args.maxThetaFRSweeps or args.all: env.register_plotter(noisefigs.plotters.MaxMeanThetaFRSweepPlotter) if args.seizureProportion or args.all: env.register_plotter(noisefigs.plotters.PSeizureSweepPlotter) if args.maxThetaFRSweeps_std or args.all: env.register_plotter(noisefigs.plotters.MaxStdThetaFRSweepPlotter) if args.maxThetaFRSweeps_median or args.all: env.register_plotter(noisefigs.plotters.MaxMedianThetaFRSweepPlotter) if args.maxThetaFRHist or args.all: env.register_plotter(noisefigs.plotters.MaxThetaFRHistPlotter)
import copy import matplotlib import matplotlib.ticker as ti from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_ratio_corrected as config parser = flagparse.FlagParser() parser.add_flag('--gamma_sweep') parser.add_flag('--examples') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.gamma_sweep or args.all: env.register_class( noisefigs.plotters.GenericGammaPlotter, config={ 'GenericGammaPlotter': { 'scale_factor': .7, 'what': 'acVal', 'fname': "gamma_sweeps{ns}.pdf", 'normalize_ticks': (True, True), # (Y, X) 'normalize_type': ('E', 'I'), 'xlabel':
args = parser.parse_args() if args.gamma_gEE_EE_sigma or args.all: new_config = deepcopy(config.get_config()) new_config.update({ 'grids_data_root': None, 'bump_data_root': ('simulation_data/ee_connections_ei_flat/g_EE_total_vs_pEE_sigma/' 'gamma_bump'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [150], 'even_shape': None, }) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.GenericGammaPlotter, config={ 'GenericGammaPlotter': { 'what': 'acVal', 'fname': "gamma_power_gEE_pEE_sigma_{ns}.pdf", 'normalize_ticks': (True, False), # (Y, X) 'normalize_type': ('E', None), 'xlabel': '$\sigma_{E{\\rightarrow}E}$', 'ylabel': '$g_{E{\\rightarrow}E}$', 'bbox': (.2, .17, .85, .9), 'vmin': .0, 'vmax': .505, 'cbar_kw': dict( ticks = ti.MultipleLocator(0.1),
if args.pbumps_gEE_EE_sigma or args.all: new_config = deepcopy(config.get_config()) new_config.update( { "grids_data_root": None, "bump_data_root": join( "simulation_data", "ee_connections_ei_flat", "g_EE_total_vs_pEE_sigma", "gamma_bump" ), "vel_data_root": None, "const_pos_data_root": None, "singleDataRoot": None, "noise_sigmas": [0, 150, 300], "even_shape": None, } ) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.Generic2DPBumpPlotter, config={ "Generic2DPBumpPlotter": { "fname": "bumps_Pbumps_gEE_pEE_sigma_{ns}.pdf", "normalize_ticks": (True, False), # (Y, X) "normalize_type": ("E", None), "xlabel": "$\sigma_{E{\\rightarrow}E}$", "ylabel": "$g_{E{\\rightarrow}E}$", "bbox": (0.2, 0.17, 0.85, 0.9), "cbar": [0, 0, 1], "ann": [None, [dict(txt="", rc=(20, 5), xytext_offset=(0.03, 1.5), color="black")], None], "vmin": 0, "vmax": 0.959, "cbar_kw": dict(ticks=ti.MultipleLocator(0.2)),
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() #parser.add_flag('--scatterPlot') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) #if args.scatterPlot or args.all: # env.register_plotter(noisefigs.plotters.ScatterGammaGridsSeparatePlotter) # env.register_plotter(noisefigs.plotters.ScatterGammaFGridsSeparatePlotter) env.plot()
#!/usr/bin/env python from __future__ import absolute_import, print_function import copy import matplotlib from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--gammaSweep') parser.add_flag('--examples') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.gammaSweep or args.all: env.register_plotter(noisefigs.plotters.GammaSweepsPlotter) if args.examples or args.all: env.register_plotter(noisefigs.plotters.GammaExamplePlotter) env.plot()
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--rasters') parser.add_flag('--rates') parser.add_flag('--seizureProportion') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.rasters or args.all: env.register_plotter(noisefigs.plotters.EIRasterPlotter) if args.rates or args.all: env.register_plotter(noisefigs.plotters.EIRatePlotter) if args.seizureProportion or args.all: env.register_plotter(noisefigs.plotters.PSeizureSweepPlotter) env.plot()
None, 'bump_data_root': ('simulation_data/submission/i_surround/' 'gamma_bump_Iext_e_theta_vs_Iext_e_const'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [0, 150, 300], 'even_shape': None, 'output_dir': 'panels', }) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.GenericGammaPlotter, config={ 'GenericGammaPlotter': { 'what': 'acVal', 'fname': "gamma_power_Iext_e_theta_vs_Iext_e_const_{ns}.pdf", 'normalize_ticks': (False, False), # (Y, X) 'normalize_type': (None, None), 'xlabel': '', 'ylabel': '$\\theta$ amplitude (pA)', 'xticks': [0, 0, 0],
from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--theta_signal') parser.add_flag('--rastersFlag') parser.add_flag('--rates') parser.add_flag('--maxFRSweeps') parser.add_flag('--maxFRGridsProbability') parser.add_flag('--maxFRGridsScatter') parser.add_flag('--PSeizureGridsProbability') parser.add_flag('--PSeizureGridsScatter') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.theta_signal or args.all: env.register_plotter(noisefigs.plotters.ThetaSignalPlotter) if args.rastersFlag or args.all: env.register_plotter(noisefigs.plotters.EIRasterPlotter) if args.rates or args.all: env.register_plotter(noisefigs.plotters.EIRatePlotter) if args.maxFRSweeps or args.all: env.register_plotter(noisefigs.plotters.MaxPopulationFRSweepsPlotter) if args.maxFRGridsProbability or args.all: env.register_plotter(noisefigs.plotters.MaxFRGridsProbabilityPlotter)
if args.pbumps_Iext_e or args.all: new_config = deepcopy(config.get_config()) new_config.update({ 'grids_data_root': None, 'bump_data_root': ('simulation_data/i_surround/' 'gamma_bump_Iext_e_theta_vs_Iext_e_const'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [0, 150, 300], 'even_shape': None, 'output_dir': 'panels', }) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.Generic2DPBumpPlotter, config={ 'Generic2DPBumpPlotter': { 'fname': "bumps_pbumps_Iext_e_theta_vs_Iext_e_const_{ns}.pdf", 'normalize_ticks': (False, False), # (Y, X) 'normalize_type': (None, None), 'xlabel': 'Constant amplitude\n(pA)', 'ylabel': '$\\theta$ amplitude (pA)', 'bbox': (.15, .2, .85, .9), 'yticks': [1, 0, 0], 'cbar': [0, 0, 1], }, })
if args.gamma_Iext_e or args.all: new_config = deepcopy(config.get_config()) new_config.update({ 'grids_data_root': None, 'bump_data_root': ('simulation_data/i_surround/' 'gamma_bump_Iext_e_theta_vs_Iext_e_const'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [0, 150, 300], 'even_shape': None, 'output_dir': 'panels', }) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.GenericGammaPlotter, config={ 'GenericGammaPlotter': { 'what': 'acVal', 'fname': "gamma_power_Iext_e_theta_vs_Iext_e_const_{ns}.pdf", 'normalize_ticks': (False, False), # (Y, X) 'normalize_type': (None, None), 'xlabel': '', 'ylabel': '$\\theta$ amplitude (pA)', 'xticks': [0, 0, 0], 'bbox': (.15, .2, .85, .9), 'cbar_kw': dict( label = '$1^{st}$ autocorrelation\npeak',
from noisefigs.env import NoiseEnvironment import config singleDataRoot = 'simulation_data/submission/single_neuron' parser = flagparse.FlagParser() parser.add_flag('--grids') parser.add_flag('--examplesFlag') parser.add_flag('--Vm_examples') parser.add_flag('--conn_func') parser.add_flag('--example_hists') parser.add_flag('--theta_signal') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.grids or args.all: env.register_plotter(noisefigs.plotters.GridSweepsPlotter) if args.examplesFlag or args.all: env.register_plotter(noisefigs.plotters.GridExamplesPlotter) if args.Vm_examples or args.all: env.register_plotter(noisefigs.plotters.VmExamplesPlotter) if args.conn_func or args.all: env.register_plotter(noisefigs.plotters.ConnectionFunctionPlotter) if args.example_hists or args.all: env.register_plotter(noisefigs.plotters.WeightExamplesHists)
#!/usr/bin/env python '''Grid field figures - probabilistic connections.''' from __future__ import absolute_import, print_function import matplotlib.ticker as ti from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--grids') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.grids or args.all: env.register_plotter(noisefigs.plotters.IPCGridSweepsPlotter) env.register_plotter(noisefigs.plotters.IPCGridSweepsPlotter, config={ 'IPCGridSweepsPlotter': { 'population_type': 'I', } }) env.plot()
'grids_data_root': None, 'bump_data_root': join('simulation_data', 'ee_connections_ei_flat', 'g_EE_total_vs_pEE_sigma', 'gamma_bump'), 'vel_data_root': None, 'const_pos_data_root': None, 'singleDataRoot': None, 'noise_sigmas': [0, 150, 300], 'even_shape': None, }) env = NoiseEnvironment(user_config=new_config) env.register_class( noisefigs.plotters.Generic2DPBumpPlotter, config={ 'Generic2DPBumpPlotter': { 'fname': "bumps_Pbumps_gEE_pEE_sigma_{ns}.pdf", 'normalize_ticks': (True, False), # (Y, X) 'normalize_type': ('E', None), 'xlabel': '$\sigma_{E{\\rightarrow}E}$', 'ylabel': '$g_{E{\\rightarrow}E}$', 'bbox': (.2, .17, .85, .9), 'cbar': [0, 0, 1], 'ann': [
from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_ratio_corrected as config parser = flagparse.FlagParser() parser.add_flag('--pbumps_sweep') parser.add_flag('--pbumps_threshold_sweep') parser.add_flag('--bump_examples') parser.add_flag('--bump_examples_isbump') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.pbumps_sweep or args.all: env.register_plotter( noisefigs.plotters.Generic2DPBumpPlotter, config={ 'Generic2DPBumpPlotter': { 'scale_factor': 0.8, 'cbar': [0, 0, 1], 'fname': "bumps_mainFig_isBumpFracTotal_sweeps_annotated{ns}.pdf", 'normalize_ticks': (True, True), # (Y, X) 'normalize_type': ('E', 'I'), 'xlabel': None,
from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--bumpExamples') parser.add_flag('--scatter_grids_fracTotal') parser.add_flag('--fracTotalSweepAnn') parser.add_flag('--isBump') parser.add_argument('--expScatter', action="store_true") args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.fracTotalSweepAnn or args.all: env.register_plotter(noisefigs.plotters.MainBumpFormationPlotter) env.register_plotter( noisefigs.plotters.MainBumpFormationPlotter, config={ 'MainBumpFormationPlotter': { 'fname_prefix': 'paper_', 'sigmaTitle': False, 'cbar_kw': dict( labelpad = 8, location = 'right', fraction = .25, pad = -.05, ),
from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_original as config parser = flagparse.FlagParser() parser.add_flag('--pbumps_sweep') parser.add_flag('--pbumps_threshold_sweep') parser.add_flag('--bump_examples') parser.add_flag('--bump_examples_isbump') parser.add_flag('--bump_examples_colorbar') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.pbumps_sweep or args.all: env.register_plotter(noisefigs.plotters.MainBumpFormationPlotter) if args.pbumps_threshold_sweep or args.all: env.register_plotter(noisefigs.plotters.MainIsBumpPlotter) if args.bump_examples or args.all: env.register_plotter(noisefigs.plotters.BumpExamplePlotter) if args.bump_examples_isbump or args.all: env.register_plotter(noisefigs.plotters.IsBumpExamplePlotter) if args.bump_examples_colorbar or args.all: env.register_plotter(noisefigs.plotters.BumpExampleColorbarPlotter)
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--scatterPlot') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.scatterPlot or args.all: env.register_plotter(noisefigs.plotters.ScatterGammaGridsSeparatePlotter) env.plot()
from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--gammaSweep') parser.add_flag('--threshold') parser.add_flag('--freqHist') parser.add_flag('--detailed_noise') parser.add_flag('--examples') parser.add_flag('--scatter_all') parser.add_flag('--gamma_grids_prob') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.gammaSweep or args.all: env.register_plotter(noisefigs.plotters.GammaSweepsPlotter) if args.detailed_noise or args.all: env.register_plotter(noisefigs.plotters.GammaDetailedNoisePlotter) if args.examples or args.all: env.register_plotter(noisefigs.plotters.GammaExamplePlotter) if args.scatter_all or args.all: env.register_plotter(noisefigs.plotters.GammaScatterAllPlotter) env.register_plotter(noisefigs.plotters.GammaFreqGridsScatterAllPlotter) if args.gamma_grids_prob or args.all:
from noisefigs.env import NoiseEnvironment, MplEnvironment from noisefigs.plotters.base import SeparateMultipageSaver from grid_cell_model.parameters import JobTrialSpace2D import config_standard_gEE_3060 as config parser = flagparse.FlagParser() parser.add_flag('--pbumps_sweep') parser.add_flag('--rasters') parser.add_flag('--bump_examples') parser.add_flag('--bump_examples_colorbar') parser.add_flag('--bump_running_examples') parser.add_argument('--expScatter', action="store_true") args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.pbumps_sweep or args.all: env.register_plotter(noisefigs.plotters.MainBumpFormationPlotter, config={ 'MainBumpFormationPlotter': { 'ann': [ None, [ dict(txt='', rc=(15, 15), xytext_offset=(1.5, 1.5), color='black') ], None, ],
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--pac_example') parser.add_flag('--burak_conn_weights') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.pac_example or args.all: env.register_plotter(noisefigs.plotters.PACExamplePlotter) if args.burak_conn_weights or args.all: env.register_plotter(noisefigs.plotters.Burak2009ConnectionPlotter) env.plot()
#!/usr/bin/env python '''I-surround bump drift plots with the original E-surround settings but with an increased constant drive to E cells.''' from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_e_const_450 as config parser = flagparse.FlagParser() parser.add_flag('--drift_sweep') parser.add_flag('--theta_signal') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.drift_sweep or args.all: env.register_plotter(noisefigs.plotters.BumpDriftAtTimePlotter) if args.theta_signal or args.all: env.register_plotter(noisefigs.plotters.ThetaSignalPlotter) env.plot()
from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment import config_e_const_375 as config parser = flagparse.FlagParser() parser.add_flag('--pbumps_sweep') parser.add_flag('--pbumps_threshold_sweep') parser.add_flag('--bump_examples') parser.add_flag('--bump_examples_isbump') parser.add_flag('--bump_examples_colorbar') args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.pbumps_sweep or args.all: env.register_plotter(noisefigs.plotters.MainBumpFormationPlotter) if args.pbumps_threshold_sweep or args.all: env.register_plotter(noisefigs.plotters.MainIsBumpPlotter) if args.bump_examples or args.all: env.register_plotter(noisefigs.plotters.BumpExamplePlotter) if args.bump_examples_isbump or args.all: env.register_plotter(noisefigs.plotters.IsBumpExamplePlotter) if args.bump_examples_colorbar or args.all: env.register_plotter(noisefigs.plotters.BumpExampleColorbarPlotter)
#!/usr/bin/env python from __future__ import absolute_import, print_function from grid_cell_model.submitting import flagparse import noisefigs from noisefigs.env import NoiseEnvironment parser = flagparse.FlagParser() parser.add_flag('--scatter_plot') args = parser.parse_args() env = NoiseEnvironment() if args.scatter_plot or args.all: env.register_plotter(noisefigs.plotters.LineErrSlopeScatterPlotter) env.plot()
from noisefigs.env import NoiseEnvironment import config parser = flagparse.FlagParser() parser.add_flag('--bumpSweep') parser.add_flag('--bumpExamples') parser.add_flag('--bump_examples_colorbar') parser.add_flag('--detailed_noise') parser.add_flag('--scatter_grids_fracTotal') parser.add_flag('--fracTotalSweepAnn') parser.add_flag('--isBump') parser.add_argument('--expScatter', action="store_true") args = parser.parse_args() env = NoiseEnvironment(user_config=config.get_config()) if args.fracTotalSweepAnn or args.all: env.register_plotter(noisefigs.plotters.MainBumpFormationPlotter) if args.scatter_grids_fracTotal or args.all: env.register_plotter(noisefigs.plotters.MainScatterGridsBumpsPlotter) if args.isBump or args.all: env.register_plotter(noisefigs.plotters.MainIsBumpPlotter) if args.bumpSweep or args.all: env.register_plotter(noisefigs.plotters.BumpSigmaSweepPlotter) if args.bumpExamples or args.all: env.register_plotter(noisefigs.plotters.BumpExamplePlotter)
import noisefigs from noisefigs.env import NoiseEnvironment singleDataRoot = 'simulation_data/submission/single_neuron' parser = flagparse.FlagParser() parser.add_flag('--maxThetaFRSweeps') parser.add_flag('--maxThetaFRSweeps_median') parser.add_flag('--maxThetaFRSweeps_std') parser.add_flag('--maxThetaFRHist') parser.add_flag('--seizureProportion') args = parser.parse_args() #ps = ds.getDefaultParamSpaces() env = NoiseEnvironment() if args.maxThetaFRSweeps or args.all: env.register_plotter(noisefigs.plotters.MaxMeanThetaFRSweepPlotter) if args.maxThetaFRSweeps_std or args.all: env.register_plotter(noisefigs.plotters.MaxStdThetaFRSweepPlotter) if args.maxThetaFRSweeps_median or args.all: env.register_plotter(noisefigs.plotters.MaxMedianThetaFRSweepPlotter) if args.maxThetaFRHist or args.all: env.register_plotter(noisefigs.plotters.MaxThetaFRHistPlotter) env.plot()