Python NoiseEnvironment.register_plotter Examples

Example #1

#!/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()

Example #2

File: figure_grids.py Project: MattNolanLab/ei-attractor

#!/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()

Example #3

File: figure_bumps_original.py Project: MattNolanLab/ei-attractor

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)

env.plot()

Example #4

File: figure_bumps_standard_gEE_3060.py Project: lsolanka/ei-attractor

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,
                                 ],
                                 'vmin':
                                 0,
                                 'vmax':
                                 0.98,
                                 'cbar_kw':
                                 dict(ticks=ti.MultipleLocator(0.2), ),
                             },
                         })
    env.plot()

if args.rasters or args.all:
    shape = (31, 31)

Example #5

File: suppFigure_seizures.py Project: ikhaliq42/GridCellModel

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)

env.plot()

Example #6

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)

if args.diff_sweep or args.all:
    env.register_plotter(noisefigs.plotters.GridsDiffSweep)

Example #7

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)

env.plot()

Example #8

File: figure_pastoll_et_al_rasters.py Project: MattNolanLab/ei-attractor

        #         va='bottom', ha='left')
        gs.update(left=gsl, bottom=gsb, right=gsr, top=gst, hspace=.2)

        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()

Example #9

File: suppFigure_seizures.py Project: MattNolanLab/ei-attractor

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()

Example #10

File: figure_bumps.py Project: MattNolanLab/ei-attractor

from grid_cell_model.submitting import flagparse
import noisefigs
from noisefigs.env import NoiseEnvironment

import config
import nmda_0p1_config

parser = flagparse.FlagParser()
parser.add_flag('--bumpExamples')
parser.add_flag('--fracTotalSweepAnn')
parser.add_flag('--isBump')
parser.add_argument('--expScatter', action="store_true")
args = parser.parse_args()


env_0mM = NoiseEnvironment(user_config=config.get_config())
env_0p1mM = NoiseEnvironment(user_config=nmda_0p1_config.get_config())

if args.fracTotalSweepAnn or args.all:
    env_0mM.register_plotter(noisefigs.plotters.MainBumpFormationPlotter)
    env_0p1mM.register_plotter(noisefigs.plotters.MainBumpFormationPlotter)

if args.isBump or args.all:
    env_0mM.register_plotter(noisefigs.plotters.MainIsBumpPlotter)

if args.bumpExamples or args.all:
    env_0mM.register_plotter(noisefigs.plotters.BumpExamplePlotter)

env_0mM.plot()
env_0p1mM.plot()

Example #11

File: figure_bumps.py Project: MattNolanLab/ei-attractor

#!/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()

Example #12

File: figure_grids_original.py Project: MattNolanLab/ei-attractor

import noisefigs
from noisefigs.env import NoiseEnvironment

import config_original 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)

if args.diff_sweep or args.all:
    env.register_plotter(noisefigs.plotters.GridsDiffSweep)

Example #13

File: figure_grids.py Project: MattNolanLab/ei-attractor

parser = flagparse.FlagParser()
parser.add_flag('--grids')
parser.add_flag('--examplesFlag')
parser.add_flag('--examples_colorbar')
parser.add_flag('--detailed_noise')
parser.add_flag('--diff_sweep')
parser.add_flag('--conn_func')
parser.add_flag('--example_hists')
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)

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.detailed_noise or args.all:
    env.register_plotter(noisefigs.plotters.GridDetailedNoisePlotter)

if args.diff_sweep or args.all:
    env.register_plotter(noisefigs.plotters.GridsDiffSweep)

#if args.conn_func or args.all:
#    env.register_plotter(noisefigs.plotters.ConnectionFunctionPlotter)

Example #14

File: figure_drifts.py Project: MattNolanLab/ei-attractor

#!/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('--bumpDriftSweep')
parser.add_flag('--bumpDiffAtInitSweep')
#parser.add_flag('--bumpDiffResetSweep')
args = parser.parse_args()

env = NoiseEnvironment(user_config=config.get_config())

if args.bumpDriftSweep or args.all:
    env.register_plotter(noisefigs.plotters.BumpDriftAtTimePlotter)

if args.bumpDiffAtInitSweep or args.all:
    env.register_plotter(noisefigs.plotters.BumpDiffAtInitPlotter)

#if args.bumpDiffResetSweep or args.all:
#    env.register_plotter(noisefigs.plotters.BumpDiffResetPlotter)

env.plot()

Example #15

File: suppFigure_line_fit_error_vs_slope.py Project: lsolanka/ei-attractor

#!/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()

Example #16

File: figure_grids.py Project: MattNolanLab/ei-attractor

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),
                                 },
                             }
                         })

if args.examplesFlag or args.all:
    env.register_plotter(noisefigs.plotters.GridExamplesPlotter)

Example #17

File: suppFigure_velocity.py Project: MattNolanLab/ei-attractor

#!/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()

Example #18

#!/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()

Example #19

File: figure_seizures.py Project: lsolanka/ei-attractor

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': {
                                 'fname_prefix':
                                 'paper_',
                                 'ann':

Example #20

#!/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()

Example #21

File: suppFigure_gamma.py Project: lsolanka/ei-attractor

#!/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()

Example #22

File: figure_grids.py Project: MattNolanLab/ei-attractor

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()

Example #23

        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()

Example #24

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),
                                 },
                             }
                         })

if args.examplesFlag or args.all:
    env.register_plotter(noisefigs.plotters.GridExamplesPlotter)

Example #25

File: figure_grids.py Project: MattNolanLab/ei-attractor

#!/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/submission/single_neuron'

parser = flagparse.FlagParser()
parser.add_flag('--grids')
parser.add_flag('--Vm_examples')
parser.add_flag('--diff_sweep')
parser.add_flag('--conn_func')
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.Vm_examples or args.all:
    env.register_plotter(noisefigs.plotters.VmExamplesPlotter)

if args.conn_func or args.all:
    env.register_plotter(noisefigs.plotters.ConnectionFunctionPlotter)

env.plot()

Example #26

#!/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('--raster-examples')
args = parser.parse_args()

env = NoiseEnvironment(user_config=config.get_config())

if args.raster_examples or args.all:
    env.register_plotter(noisefigs.plotters.RasterExamplePlotter)

env.plot()

Example #27

File: figure_bumps_ratio_corrected.py Project: lsolanka/ei-attractor

 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,
             'yticks': [True, False, False],
             'ylabel':
             None,
             'bbox': (.15, .2, .85, .9),
             'ann': [
                 [
                     dict(txt='a',
                          rc=(15, 5),
                          xytext_offset=(.05, 20),
                          color='white'),
                     dict(txt='b',
                          rc=(5, 15),
                          xytext_offset=(.15, 10),
                          color='white')
                 ],
                 [
                     dict(txt='c',
                          rc=(5, 15),
                          xytext_offset=(.15, 10),
                          color='white'),
                     dict(txt='d',
                          rc=(15, 5),
                          xytext_offset=(.15, 10),
                          color='white')
                 ],
                 [
                     dict(txt='e',
                          rc=(5, 15),
                          xytext_offset=(.15, 10),
                          color='white')
                 ],
             ],
         },
     })

Example #28

File: figure_isbump_examples.py Project: lsolanka/ei-attractor

#!/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()

Example #29

File: figure_gamma.py Project: lsolanka/ei-attractor

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:
    env.register_plotter(noisefigs.plotters.GammaGridsProbabilityPlotter)
    env.register_plotter(noisefigs.plotters.GammaFreqGridsProbabilityPlotter)

Example #30

from grid_cell_model.submitting import flagparse
import noisefigs
from noisefigs.env import NoiseEnvironment

import config
import nmda_0p1_config

parser = flagparse.FlagParser()
parser.add_flag('--bumpExamples')
parser.add_flag('--fracTotalSweepAnn')
parser.add_flag('--isBump')
parser.add_argument('--expScatter', action="store_true")
args = parser.parse_args()

env_0mM = NoiseEnvironment(user_config=config.get_config())
env_0p1mM = NoiseEnvironment(user_config=nmda_0p1_config.get_config())

if args.fracTotalSweepAnn or args.all:
    env_0mM.register_plotter(noisefigs.plotters.MainBumpFormationPlotter)
    env_0p1mM.register_plotter(noisefigs.plotters.MainBumpFormationPlotter)

if args.isBump or args.all:
    env_0mM.register_plotter(noisefigs.plotters.MainIsBumpPlotter)

if args.bumpExamples or args.all:
    env_0mM.register_plotter(noisefigs.plotters.BumpExamplePlotter)

env_0mM.plot()
env_0p1mM.plot()

Example #31

File: figure_drifts_e_const_450.py Project: lsolanka/ei-attractor

#!/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()

Example #32

File: suppFigure_gamma.py Project: MattNolanLab/ei-attractor

#!/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()

Example #33

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()

Example #34

File: figure_grids_trials.py Project: lsolanka/ei-attractor

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)

if args.examples or args.all:
    env.register_plotter(noisefigs.plotters.IPCExamplePlotter)
    env.register_plotter(noisefigs.plotters.IPCExamplePlotter,
                         config={
                             'IPCExamplePlotter': {
                                 'population_type': 'I'
                             },
                         })

if args.examples_cbar or args.all:
    env.register_plotter(noisefigs.plotters.IPCExampleColorbarPlotter)

Example #35

File: figure_gamma.py Project: MattNolanLab/ei-attractor

#!/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()

Example #36

File: figure_isBump.py Project: lsolanka/ei-attractor

#!/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()

Example #37

File: suppFigure_grids_vs_line_fit_err.py Project: MattNolanLab/ei-attractor

#!/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()

Example #38

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,
                             }
                         })

if args.spatial_info or args.all:

Example #39

File: figure_grids.py Project: lsolanka/ei-attractor

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)

if args.theta_signal or args.all:
    env.register_plotter(noisefigs.plotters.ThetaSignalPlotter)

Example #40

File: figure_bumps.py Project: lsolanka/ei-attractor

#!/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()

Example #41

File: figure_bumps.py Project: MattNolanLab/ei-attractor

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,
                ),
                'ann': [None]*3,
            },
        })

Example #42

                'cbar': [0, 0, 1],
                'cbar_kw':
                dict(
                    label='Frequency (Hz)',
                    ticks=ti.MultipleLocator(20),
                ),
                'plot_grid_contours': [0, 0, 0],
                'ann': [
                    dict(
                        txt='b',
                        rc=(5, 15),
                        xytext_offset=(.1, 0),
                        color='white',
                    ),
                    dict(
                        txt='a',
                        rc=(15, 5),
                        xytext_offset=(-.05, 20.),
                        color='white',
                    ),
                ],
                'sigma_title':
                False,
            },
        })

if args.examples or args.all:
    env.register_plotter(noisefigs.plotters.GammaExamplePlotter)

env.plot()

Example #43

File: figure_seizures_e_const_450.py Project: lsolanka/ei-attractor

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)

env.plot()

Example #44

File: figure_grids.py Project: MattNolanLab/ei-attractor

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,
                             }
                         })

if args.spatial_info or args.all:

Example #45

File: figure_intro.py Project: MattNolanLab/ei-attractor

#!/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()

Example #46

File: figure_seizures.py Project: lsolanka/ei-attractor

#!/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()

Example #47

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)

env.plot()

Example #48

File: figure_seizures.py Project: ikhaliq42/GridCellModel

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.maxFRGridsScatter or args.all:
    env.register_plotter(noisefigs.plotters.MaxFRGridsScatterAllPlotter)

Example #49

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)

if args.bump_examples_colorbar or args.all:
    env.register_plotter(noisefigs.plotters.BumpExampleColorbarPlotter)

Example #50

File: suppFigure_firing_rates.py Project: MattNolanLab/ei-attractor

#!/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('--fr_sweep')
parser.add_flag('--scatter_grids_fr')
args = parser.parse_args()


env = NoiseEnvironment(user_config=config.get_config())

if args.fr_sweep or args.all:
    env.register_plotter(noisefigs.plotters.FRSweepPlotter)

if args.scatter_grids_fr or args.all:
    env.register_plotter(noisefigs.plotters.ScatterGridsFRAllPlotter)

env.plot()