Commit ba4f4e51 authored by Luke Campagnola's avatar Luke Campagnola
Browse files

Added image analysis example

parent 04f1b0e6
......@@ -26,6 +26,7 @@ examples = OrderedDict([
('Crosshair / Mouse interaction', 'crosshair.py'),
('Data Slicing', 'DataSlicing.py'),
('Plot Customization', 'customPlot.py'),
('Image Analysis', 'imageAnalysis.py'),
('Dock widgets', 'dockarea.py'),
('Console', 'ConsoleWidget.py'),
('Histograms', 'histogram.py'),
......
# -*- coding: utf-8 -*-
"""
Demonstrates common image analysis tools.
Many of the features demonstrated here are already provided by the ImageView
widget, but here we present a lower-level approach that provides finer control
over the user interface.
"""
import initExample ## Add path to library (just for examples; you do not need this)
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
import numpy as np
pg.mkQApp()
win = pg.GraphicsLayoutWidget()
win.setWindowTitle('pyqtgraph example: Image Analysis')
# A plot area (ViewBox + axes) for displaying the image
p1 = win.addPlot()
# Item for displaying image data
img = pg.ImageItem()
p1.addItem(img)
# Custom ROI for selecting an image region
roi = pg.ROI([-8, 14], [6, 5])
roi.addScaleHandle([0.5, 1], [0.5, 0.5])
roi.addScaleHandle([0, 0.5], [0.5, 0.5])
p1.addItem(roi)
roi.setZValue(10) # make sure ROI is drawn above image
# Isocurve drawing
iso = pg.IsocurveItem(level=0.8, pen='g')
iso.setParentItem(img)
iso.setZValue(5)
# Contrast/color control
hist = pg.HistogramLUTItem()
hist.setImageItem(img)
win.addItem(hist)
# Draggable line for setting isocurve level
isoLine = pg.InfiniteLine(angle=0, movable=True, pen='g')
hist.vb.addItem(isoLine)
hist.vb.setMouseEnabled(y=False) # makes user interaction a little easier
isoLine.setValue(0.8)
isoLine.setZValue(1000) # bring iso line above contrast controls
# Another plot area for displaying ROI data
win.nextRow()
p2 = win.addPlot(colspan=2)
p2.setMaximumHeight(250)
win.resize(800, 800)
win.show()
# Generate image data
data = np.random.normal(size=(100, 200))
data[20:80, 20:80] += 2.
data = pg.gaussianFilter(data, (3, 3))
data += np.random.normal(size=(100, 200)) * 0.1
img.setImage(data)
hist.setLevels(data.min(), data.max())
# build isocurves from smoothed data
iso.setData(pg.gaussianFilter(data, (2, 2)))
# set position and scale of image
img.scale(0.2, 0.2)
img.translate(-50, 0)
# zoom to fit imageo
p1.autoRange()
# Callbacks for handling user interaction
def updatePlot():
global img, roi, data, p2
selected = roi.getArrayRegion(data, img)
p2.plot(selected.mean(axis=1), clear=True)
roi.sigRegionChanged.connect(updatePlot)
updatePlot()
def updateIsocurve():
global isoLine, iso
iso.setLevel(isoLine.value())
isoLine.sigDragged.connect(updateIsocurve)
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
......@@ -35,11 +35,6 @@ class IsocurveItem(GraphicsObject):
self.setPen(pen)
self.setData(data, level)
#if data is not None and level is not None:
#self.updateLines(data, level)
def setData(self, data, level=None):
"""
......@@ -65,6 +60,7 @@ class IsocurveItem(GraphicsObject):
"""Set the level at which the isocurve is drawn."""
self.level = level
self.path = None
self.prepareGeometryChange()
self.update()
......
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