odebeir’s gists

odebeir / feature_wood.py

Created June 17, 2016 15:57

feature woof

	def wavelet_analysis(sig):
	""" decompose signal into wavelets
	returns the frequence of the thesholded filtered signal
	"""
	widths = np.arange(1, 100,1)
	cwtmatr = signal.cwt(sig, signal.ricker, widths)

	N = sig.size
	fsig = cwtmatr[98,:]
	detect_pos = fsig>30

odebeir / watershed_sample.py

Created July 11, 2014 14:07

	import matplotlib.pyplot as plt

	from skimage.morphology import watershed,disk
	from skimage.filter import rank
	from skimage import data

	import numpy as np

	image = data.camera()
	gradient = rank.gradient(image, disk(2))

odebeir / gist:5598052

Last active December 17, 2015 10:49

label2rgb

	label = np.asarray([[0,1],[2,3]])

	rgblabel = np.zeros([2,2,3])
	rgblabel[label==1,:]=[1,0,0]
	rgblabel[label==2,:]=[0,1,0]
	rgblabel[label==3,:]=[0,0,1]
	plt.imshow(rgblabel,interpolation='nearest')
	plt.show()

odebeir / gist:5237529

Last active November 8, 2021 12:49

Small python code for building Gabor filters

	# opencv
	import cv2.cv as cv
	import cv2

	def build_filters():
	""" returns a list of kernels in several orientations
	"""
	filters = []
	ksize = 31
	for theta in np.arange(0, np.pi, np.pi / 32):

odebeir / gist:5038467

Last active April 1, 2016 23:10

Color deconvolution for python cf : A. C. Ruifrok and D. A. Johnston, “Quantification of histochemical staining by color deconvolution.,” Analytical and quantitative cytology and histology / the International Academy of Cytology [and] American Society of Cytology, vol. 23, no. 4, pp. 291–9, Aug. 2001.

	def convert_to_optical_densities(rgb,r0,g0,b0):
	OD = rgb.astype(float)
	OD[:,:,0] /= r0
	OD[:,:,1] /= g0
	OD[:,:,2] /= b0

	return -np.log(OD)

	def color_deconvolution(rgb,r0,g0,b0,verbose=False):
	stain_OD = np.asarray([[0.18,0.20,0.08],[0.01,0.13,0.0166],[0.10,0.21,0.29]]) #hematoxylin, eosyn, DAB

odebeir / gist:3918044

Created October 19, 2012 12:38

Example of Gabor filter usage

	#opencv
	import cv2.cv as cv
	import cv2
	import numpy as np

	def build_filters():

	filters = []
	ksize = 31
	for theta in np.arange(0, np.pi, np.pi / 32):

odebeir / patissier2.py

Created May 7, 2012 13:57

BSP - Monday 7 May - some tests

	import numpy as np
	import matplotlib.pyplot as plt
	import matplotlib.cm as cm

	def create_data(n):
	data = np.reshape(range(n**2),(n,n))
	data = data[:,:,np.newaxis]
	print '-'*40
	print data[:,:,0],data.shape
	print '-'*40

odebeir / patissier.py

Created May 7, 2012 12:06

BSP - Monday 7 May

	import numpy as np


	n = 4
	data = np.reshape(range(4*4),(n,n))
	data = data[:,:,np.newaxis]

	print data[:,:,0],data.shape

	seq = [0,1,2,3]

odebeir / gist:508087

Created August 4, 2010 12:57

	from enthought.enable.api import ComponentEditor, BaseTool
	from enthought.chaco.api import ArrayPlotData, Plot, jet, gray, PlotGraphicsContext
	from enthought.traits.api import HasTraits, Instance, Enum, Range, Dict, Button, Int, Bool, Str, Property,Event, Array, DelegatesTo, on_trait_change,List, Tuple
	from enthought.traits.ui.api import Item, Group, View, InstanceEditor


	def draw_plot(filename, container,size=(800,600)):
	"""Render a plot to file"""
	container.outer_bounds = list(size)
	container.do_layout(force=True)

odebeir / gist:508082

Created August 4, 2010 12:54

	from enthought.enable.api import ComponentEditor, BaseTool
	from enthought.chaco.api import ArrayPlotData, Plot, jet, gray, PlotGraphicsContext
	from enthought.traits.api import HasTraits, Instance, Enum, Range, Dict, Button, Int, Bool, Str, Property,Event, Array, DelegatesTo, on_trait_change,List, Tuple
	from enthought.traits.ui.api import Item, Group, View, InstanceEditor

	def draw_plot(filename, container,size=(800,600)):
	"""Render a plot to file"""
	container.outer_bounds = list(size)
	container.do_layout(force=True)
	gc = PlotGraphicsContext(size, dpi=150)

Olivier Debeir odebeir