pyqtgraph/examples/imageAnalysis.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.setConfigOptions(imageAxisOrder='normal')
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=(200, 100))
data[20:80, 20:80] += 2.
data = pg.gaussianFilter(data, (3, 3))
data += np.random.normal(size=(200, 100)) * 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=0), 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_()