Added pg.gaussianFilter, removed all dependency on gaussian_filter
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@ -11,7 +11,6 @@ a 2D plane and interpolate data along that plane to generate a slice image
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import initExample
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import numpy as np
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import scipy
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from pyqtgraph.Qt import QtCore, QtGui
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import pyqtgraph as pg
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@ -12,7 +12,6 @@ from pyqtgraph.flowchart.library.common import CtrlNode
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from pyqtgraph.Qt import QtGui, QtCore
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import pyqtgraph as pg
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import numpy as np
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import scipy.ndimage
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app = QtGui.QApplication([])
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@ -44,7 +43,7 @@ win.show()
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## generate random input data
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data = np.random.normal(size=(100,100))
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data = 25 * scipy.ndimage.gaussian_filter(data, (5,5))
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data = 25 * pg.gaussianFilter(data, (5,5))
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data += np.random.normal(size=(100,100))
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data[40:60, 40:60] += 15.0
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data[30:50, 30:50] += 15.0
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@ -90,7 +89,7 @@ class ImageViewNode(Node):
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## CtrlNode is just a convenience class that automatically creates its
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## control widget based on a simple data structure.
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class UnsharpMaskNode(CtrlNode):
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"""Return the input data passed through scipy.ndimage.gaussian_filter."""
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"""Return the input data passed through pg.gaussianFilter."""
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nodeName = "UnsharpMask"
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uiTemplate = [
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('sigma', 'spin', {'value': 1.0, 'step': 1.0, 'range': [0.0, None]}),
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@ -110,7 +109,7 @@ class UnsharpMaskNode(CtrlNode):
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# CtrlNode has created self.ctrls, which is a dict containing {ctrlName: widget}
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sigma = self.ctrls['sigma'].value()
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strength = self.ctrls['strength'].value()
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output = dataIn - (strength * scipy.ndimage.gaussian_filter(dataIn, (sigma,sigma)))
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output = dataIn - (strength * pg.gaussianFilter(dataIn, (sigma,sigma)))
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return {'dataOut': output}
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@ -12,7 +12,6 @@ from pyqtgraph.Qt import QtCore, QtGui
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import pyqtgraph.opengl as gl
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import pyqtgraph as pg
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import numpy as np
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import scipy.ndimage as ndi
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app = QtGui.QApplication([])
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w = gl.GLViewWidget()
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@ -22,8 +21,8 @@ w.setWindowTitle('pyqtgraph example: GLImageItem')
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## create volume data set to slice three images from
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shape = (100,100,70)
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data = ndi.gaussian_filter(np.random.normal(size=shape), (4,4,4))
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data += ndi.gaussian_filter(np.random.normal(size=shape), (15,15,15))*15
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data = pg.gaussianFilter(np.random.normal(size=shape), (4,4,4))
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data += pg.gaussianFilter(np.random.normal(size=shape), (15,15,15))*15
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## slice out three planes, convert to RGBA for OpenGL texture
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levels = (-0.08, 0.08)
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@ -10,7 +10,6 @@ import initExample
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from pyqtgraph.Qt import QtCore, QtGui
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import pyqtgraph as pg
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import pyqtgraph.opengl as gl
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import scipy.ndimage as ndi
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import numpy as np
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## Create a GL View widget to display data
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@ -29,7 +28,7 @@ w.addItem(g)
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## Simple surface plot example
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## x, y values are not specified, so assumed to be 0:50
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z = ndi.gaussian_filter(np.random.normal(size=(50,50)), (1,1))
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z = pg.gaussianFilter(np.random.normal(size=(50,50)), (1,1))
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p1 = gl.GLSurfacePlotItem(z=z, shader='shaded', color=(0.5, 0.5, 1, 1))
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p1.scale(16./49., 16./49., 1.0)
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p1.translate(-18, 2, 0)
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@ -46,7 +45,7 @@ w.addItem(p2)
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## Manually specified colors
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z = ndi.gaussian_filter(np.random.normal(size=(50,50)), (1,1))
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z = pg.gaussianFilter(np.random.normal(size=(50,50)), (1,1))
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x = np.linspace(-12, 12, 50)
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y = np.linspace(-12, 12, 50)
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colors = np.ones((50,50,4), dtype=float)
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@ -7,7 +7,6 @@ Use a HistogramLUTWidget to control the contrast / coloration of an image.
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import initExample
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import numpy as np
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import scipy.ndimage as ndi
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from pyqtgraph.Qt import QtGui, QtCore
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import pyqtgraph as pg
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@ -34,7 +33,7 @@ l.addWidget(v, 0, 0)
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w = pg.HistogramLUTWidget()
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l.addWidget(w, 0, 1)
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data = ndi.gaussian_filter(np.random.normal(size=(256, 256)), (20, 20))
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data = pg.gaussianFilter(np.random.normal(size=(256, 256)), (20, 20))
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for i in range(32):
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for j in range(32):
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data[i*8, j*8] += .1
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@ -14,7 +14,6 @@ displaying and analyzing 2D and 3D data. ImageView provides:
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import initExample
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import numpy as np
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import scipy.ndimage
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from pyqtgraph.Qt import QtCore, QtGui
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import pyqtgraph as pg
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@ -29,7 +28,7 @@ win.show()
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win.setWindowTitle('pyqtgraph example: ImageView')
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## Create random 3D data set with noisy signals
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img = scipy.ndimage.gaussian_filter(np.random.normal(size=(200, 200)), (5, 5)) * 20 + 100
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img = pg.gaussianFilter(np.random.normal(size=(200, 200)), (5, 5)) * 20 + 100
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img = img[np.newaxis,:,:]
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decay = np.exp(-np.linspace(0,0.3,100))[:,np.newaxis,np.newaxis]
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data = np.random.normal(size=(100, 200, 200))
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@ -13,7 +13,6 @@ import initExample ## Add path to library (just for examples; you do not need th
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from pyqtgraph.Qt import QtGui, QtCore, USE_PYSIDE
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import numpy as np
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import pyqtgraph as pg
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import scipy.ndimage as ndi
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import pyqtgraph.ptime as ptime
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if USE_PYSIDE:
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@ -95,10 +94,13 @@ def mkData():
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if ui.rgbCheck.isChecked():
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data = np.random.normal(size=(frames,width,height,3), loc=loc, scale=scale)
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data = ndi.gaussian_filter(data, (0, 6, 6, 0))
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data = pg.gaussianFilter(data, (0, 6, 6, 0))
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else:
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data = np.random.normal(size=(frames,width,height), loc=loc, scale=scale)
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data = ndi.gaussian_filter(data, (0, 6, 6))
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print frames, width, height, loc, scale
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data = pg.gaussianFilter(data, (0, 6, 6))
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print data[0]
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pg.image(data)
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if dtype[0] != 'float':
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data = np.clip(data, 0, mx)
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data = data.astype(dt)
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@ -7,7 +7,6 @@ the mouse.
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import initExample ## Add path to library (just for examples; you do not need this)
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import numpy as np
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import scipy.ndimage as ndi
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import pyqtgraph as pg
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from pyqtgraph.Qt import QtGui, QtCore
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from pyqtgraph.Point import Point
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@ -33,8 +32,8 @@ p1.setAutoVisible(y=True)
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#create numpy arrays
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#make the numbers large to show that the xrange shows data from 10000 to all the way 0
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data1 = 10000 + 15000 * ndi.gaussian_filter(np.random.random(size=10000), 10) + 3000 * np.random.random(size=10000)
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data2 = 15000 + 15000 * ndi.gaussian_filter(np.random.random(size=10000), 10) + 3000 * np.random.random(size=10000)
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data1 = 10000 + 15000 * pg.gaussianFilter(np.random.random(size=10000), 10) + 3000 * np.random.random(size=10000)
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data2 = 15000 + 15000 * pg.gaussianFilter(np.random.random(size=10000), 10) + 3000 * np.random.random(size=10000)
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p1.plot(data1, pen="r")
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p1.plot(data2, pen="g")
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@ -10,7 +10,6 @@ import initExample ## Add path to library (just for examples; you do not need th
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from pyqtgraph.Qt import QtGui, QtCore
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import numpy as np
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import pyqtgraph as pg
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import scipy.ndimage as ndi
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app = QtGui.QApplication([])
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@ -18,7 +17,7 @@ app = QtGui.QApplication([])
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frames = 200
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data = np.random.normal(size=(frames,30,30), loc=0, scale=100)
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data = np.concatenate([data, data], axis=0)
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data = ndi.gaussian_filter(data, (10, 10, 10))[frames/2:frames + frames/2]
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data = pg.gaussianFilter(data, (10, 10, 10))[frames/2:frames + frames/2]
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data[:, 15:16, 15:17] += 1
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win = pg.GraphicsWindow()
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@ -2,6 +2,7 @@
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from ...Qt import QtCore, QtGui
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from ..Node import Node
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from . import functions
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from ... import functions as pgfn
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from .common import *
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import numpy as np
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@ -161,7 +162,7 @@ class Gaussian(CtrlNode):
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import scipy.ndimage
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except ImportError:
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raise Exception("GaussianFilter node requires the package scipy.ndimage.")
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return scipy.ndimage.gaussian_filter(data, self.ctrls['sigma'].value())
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return pgfn.gaussianFilter(data, self.ctrls['sigma'].value())
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class Derivative(CtrlNode):
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@ -1120,6 +1120,45 @@ def colorToAlpha(data, color):
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#raise Exception()
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return np.clip(output, 0, 255).astype(np.ubyte)
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def gaussianFilter(data, sigma):
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"""
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Drop-in replacement for scipy.ndimage.gaussian_filter.
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(note: results are only approximately equal to the output of
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gaussian_filter)
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"""
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if np.isscalar(sigma):
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sigma = (sigma,) * data.ndim
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baseline = data.mean()
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filtered = data - baseline
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for ax in range(data.ndim):
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s = sigma[ax]
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if s == 0:
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continue
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# generate 1D gaussian kernel
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ksize = int(s * 6)
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x = np.arange(-ksize, ksize)
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kernel = np.exp(-x**2 / (2*s**2))
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kshape = [1,] * data.ndim
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kshape[ax] = len(kernel)
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kernel = kernel.reshape(kshape)
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# convolve as product of FFTs
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shape = data.shape[ax] + ksize
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scale = 1.0 / (abs(s) * (2*np.pi)**0.5)
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filtered = scale * np.fft.irfft(np.fft.rfft(filtered, shape, axis=ax) *
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np.fft.rfft(kernel, shape, axis=ax),
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axis=ax)
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# clip off extra data
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sl = [slice(None)] * data.ndim
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sl[ax] = slice(filtered.shape[ax]-data.shape[ax],None,None)
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filtered = filtered[sl]
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return filtered + baseline
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def downsample(data, n, axis=0, xvals='subsample'):
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"""Downsample by averaging points together across axis.
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@ -1556,7 +1595,7 @@ def traceImage(image, values, smooth=0.5):
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paths = []
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for i in range(diff.shape[-1]):
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d = (labels==i).astype(float)
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d = ndi.gaussian_filter(d, (smooth, smooth))
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d = gaussianFilter(d, (smooth, smooth))
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lines = isocurve(d, 0.5, connected=True, extendToEdge=True)
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path = QtGui.QPainterPath()
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for line in lines:
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