MarcCote’s gists

MarcCote / adjusted_score

Last active December 11, 2018 21:17

# Nothing

MarcCote / trk2tck.py

Last active June 5, 2024 08:52

Script that converts TRK to TCK using https://github.com/MarcCote/nibabel/tree/streamlines_tck

	import os
	import argparse
	import nibabel as nib


	def build_argparser():
	DESCRIPTION = "Convert tractograms (TRK -> TCK)."
	p = argparse.ArgumentParser(description=DESCRIPTION)
	p.add_argument('tractograms', metavar='bundle', nargs="+", help='list of tractograms.')
	p.add_argument('-f', '--force', action="store_true", help='overwrite existing output files.')

MarcCote / tck2trk.py

Last active June 16, 2022 07:51

Script that converts TCK to TRK using https://github.com/MarcCote/nibabel/tree/streamlines_tck

	import os
	import argparse

	import nibabel as nib
	from nibabel.streamlines import Field
	from nibabel.orientations import aff2axcodes


	def build_argparser():
	DESCRIPTION = "Convert tractograms (TCK -> TRK)."

MarcCote / sum_of_stack_bug.py

Created September 15, 2014 20:03

Unexpected behaviour when summing stacked tensors

	import theano
	import theano.tensor as T
	import numpy as np

	A = theano.shared(np.array([1, 2, 3, 4, 5]))

	print "Theano"
	print T.sum(T.stack(A, A), axis=0).eval()
	print T.sum(T.stack(A, A), axis=1).eval()

MarcCote / nstreams_bug.py

Created September 3, 2014 18:45

Shows nstreams limitation on GPU

	import theano
	import numpy as np
	from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
	theano_rng = RandomStreams(42)

	# This one works fine
	print np.sum(theano_rng.uniform(size=(10000, 784), dtype=theano.config.floatX, nstreams=10000).eval(), 1)

	# This one produces NaN at the end
	print np.sum(theano_rng.uniform(size=(10000, 784), dtype=theano.config.floatX, nstreams=10000*400).eval(), 1)

MarcCote / main.py

Created August 27, 2014 17:51

Memory leak with vector of memoryviews

MarcCote / metric.pyx

Created August 13, 2014 13:34

Problem when using fused type with class inheritance in Cython

	ctypedef float[:,:] float2d
	ctypedef double[:,:] double2d

	ctypedef fused Line:
	float2d
	double2d

	cdef class Metric:
	cdef float dist(Metric self, Line line) nogil:
	pass

MarcCote / length_per_voxel.py

Last active August 29, 2015 14:04

Measure length of streamline passing trough each voxel. Plus some utility functions to test, bench and vizualize.

	from dipy.viz import fvtk

	import numpy as np

	from numpy.testing import measure
	from nose.tools import assert_equal, assert_almost_equal
	from numpy.testing import assert_array_equal, assert_array_almost_equal

	norm = lambda x: np.sqrt(np.sum(x**2))

MarcCote / save_trk_with_color.py

Created March 14, 2014 16:06

Example of saving a trk file with color using nibabel.

	import numpy as np
	from nibabel import trackvis as tv
	from dipy.segment.quickbundles import QuickBundles
	from dipy.data import get_data

	fname = get_data('fornix')

	streams, hdr = tv.read(fname)
	streamlines = [i[0] for i in streams]
	qb = QuickBundles(streamlines, dist_thr=10., pts=12)

MarcCote / tensor_dot.py

Created February 19, 2014 19:35

Gist showing an erroneous result from tensor.dot when one of the operand is zero.

	import numpy as np
	import theano
	import theano.tensor as T
	print "Version:", theano.version.version

	print "=Theano="
	A = T.zeros((2,10))
	B = T.zeros((30, 10))

	print "Shape of A:", A.eval().shape

Marc-Alexandre Côté MarcCote