Michael Waskom mwaskom

## evc_flat_patch.ipynb

      
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                mwaskom
                / evc_flat_patch.ipynb
            
            
              Created
              April 18, 2017 15:33
            
              
                WIP notes on creating flat patches of visual cortex for Jupyter notebook visualization (and manipulation?)
              
          
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## matplotlib_surfaces.ipynb

      
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                mwaskom
                / matplotlib_surfaces.ipynb
            
            
              Created
              March 30, 2017 19:39
            
              
                Notes on cortical surface visualization without Mayavi
              
          
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## continuous_colormap.ipynb

      
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                mwaskom
                / continuous_colormap.ipynb
            
            
              Created
              March 17, 2017 17:20
            
              
                Good colormap for plotting unthresholded fMRI activations
              
          
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## find_clean_subjects.py
import numpy as np
import pandas as pd
import lyman

MOTION_THRESH = 1
ARTIFACT_THRESH = 6

if __name__ == "__main__":

    all_subjects = lyman.determine_subjects()

## read_edf.py
import os
import subprocess
import tempfile
import shutil

import numpy as np
import pandas as pd


class EyeData(object):

## pedestalelementarray.py
#!/usr/bin/env python2
"""Extend ElementArrayStim to allow nonzero pedestal values of gratings.

This adapts a prior solution for adding a non-zero pedestal value to GratingStim:
https://github.com/nwilming/PedestalGrating/blob/master/pedestal_grating.py

Covered under the PsychoPy license, as it is a simple extension of the prior code:

Copyright (C) 2015 Jonathan Peirce
Distributed under the terms of the GNU General Public License (GPL).

## run_deface.sh
#! /bin/bash

# Script for removing facial information from subject anatomical
# images before sharing the data.
# This required downloading the mri_deface binary and the face.gca and
# talairach_mixed_with_skull.gca atlas files from here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface

for s in $SUBJECTS; do
    mkdir -p $s/anat

## vernalis.py

from matplotlib.colors import ListedColormap
from numpy import nan, inf

# Used to reconstruct the colormap in viscm
parameters = {'xp': [3.559581561226338, 17.887066941343306, -44.539833643452027, -35.329307327662548, -2.5807693159666485],
              'yp': [-7.9678362573099264, -64.766081871344994, -32.529239766081844, 43.201754385964932, 6.359649122807042],
              'min_Jp': 2.08370436331,
              'max_Jp': 99.3232413179}

## bostock_rainbow.png

      
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                mwaskom
                / bostock_rainbow.png
            
            
              Last active
              April 28, 2016 22:21
            
              
                Cubehelix rainbow values from https://bl.ocks.org/mbostock/310c99e53880faec2434 as RGB lut
              
          
## bkr.py
import matplotlib as mpl

lut =[[0.97535488, 0.96717973, 0.97826556],
      [0.96210335, 0.958145, 0.96901356],
      [0.94896295, 0.94912471, 0.96025478],
      [0.93577938, 0.94018409, 0.95192643],
      [0.92251197, 0.93134405, 0.94395255],
      [0.9091769, 0.92260072, 0.93627962],
      [0.89579025, 0.91394725, 0.92888411],
      [0.88237732, 0.90537279, 0.92174829],
	import numpy as np
	import pandas as pd
	import lyman

	MOTION_THRESH = 1
	ARTIFACT_THRESH = 6

	if __name__ == "__main__":

	all_subjects = lyman.determine_subjects()
	import os
	import subprocess
	import tempfile
	import shutil

	import numpy as np
	import pandas as pd


	class EyeData(object):
	#!/usr/bin/env python2
	"""Extend ElementArrayStim to allow nonzero pedestal values of gratings.

	This adapts a prior solution for adding a non-zero pedestal value to GratingStim:
	https://github.com/nwilming/PedestalGrating/blob/master/pedestal_grating.py

	Covered under the PsychoPy license, as it is a simple extension of the prior code:

	Copyright (C) 2015 Jonathan Peirce
	Distributed under the terms of the GNU General Public License (GPL).
	#! /bin/bash

	# Script for removing facial information from subject anatomical
	# images before sharing the data.
	# This required downloading the mri_deface binary and the face.gca and
	# talairach_mixed_with_skull.gca atlas files from here:
	# https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface

	for s in $SUBJECTS; do
	mkdir -p $s/anat

	from matplotlib.colors import ListedColormap
	from numpy import nan, inf

	# Used to reconstruct the colormap in viscm
	parameters = {'xp': [3.559581561226338, 17.887066941343306, -44.539833643452027, -35.329307327662548, -2.5807693159666485],
	'yp': [-7.9678362573099264, -64.766081871344994, -32.529239766081844, 43.201754385964932, 6.359649122807042],
	'min_Jp': 2.08370436331,
	'max_Jp': 99.3232413179}
	import matplotlib as mpl

	lut =[[0.97535488, 0.96717973, 0.97826556],
	[0.96210335, 0.958145, 0.96901356],
	[0.94896295, 0.94912471, 0.96025478],
	[0.93577938, 0.94018409, 0.95192643],
	[0.92251197, 0.93134405, 0.94395255],
	[0.9091769, 0.92260072, 0.93627962],
	[0.89579025, 0.91394725, 0.92888411],
	[0.88237732, 0.90537279, 0.92174829],