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# -*- coding: utf-8 -*-
"""
Created on Fri Jan 25 19:56:48 2019
@author: gcg
"""
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
import numpy as np
import sys, copy
from matplotlib import cm
from numpy import ma
# Get the colormap
colormap = cm.get_cmap("nipy_spectral") # cm.get_cmap("CMRmap")
colormap._init()
lut = (colormap._lut * 255).view(np.ndarray) # Convert matplotlib colormap from 0-1 to 0 -255 for Qt
#pg.setConfigOptions(imageAxisOrder='row-major')
## Create CT image to display
nx, ny = 100, 50
structure = np.ones((nx, ny), dtype=float)
structure += np.random.normal(size=(nx,ny))
# create field image to overlay
field = np.ones((nx, ny)) * range(0, ny)
## create GUI
app = QtGui.QApplication([])
w = pg.GraphicsWindow(size=(1000,800), border=True)
w.setWindowTitle('pyqtgraph example: ROI Examples')
w1 = w.addLayout(row=0, col=0)
v1a = w1.addViewBox(row=1, col=0, lockAspect=True)
# this is the grey level CT image shwoing the structure
img1a = pg.ImageItem(structure)
v1a.addItem(img1a)
v1a.disableAutoRange('xy')
v1a.autoRange()
# this is the image that holds the transparent overlay
img2 = pg.ImageItem(pg.np.random.normal(size=(nx,ny)))
img2.setZValue(10) # make sure this image is on top
img2.setOpacity(0.6)
img2.setLookupTable(lut)
v1a.addItem(img2)
rois = []
rois.append(pg.PolyLineROI([[80, 60], [90, 30], [60, 40]], pen=(6,9), closed=True))
def show_exception_and_exit(exc_type, exc_value, tb):
import traceback
traceback.print_exception(exc_type, exc_value, tb)
raw_input("Press key to exit.")
sys.exit(-1)
sys.excepthook = show_exception_and_exit
# generate index map
def generate_idxmap():
idxmap = np.zeros((nx, ny, 2), dtype=int)
for iy in xrange(ny):
for ix in xrange(nx):
idxmap[ix, iy, 0] = ix
idxmap[ix, iy, 1] = iy
return idxmap
def update(roi):
pass
#print roi.pos(), roi.boundingRect()
rval = roi.getArrayRegion(idxmap, img1a, returnMappedCoords=False).astype(int)
print "shape of rval is", np.shape(rval)
# create an image to overlay on top of structure.
# the overlay image is a copy of the underlying image, except within the selected region
overlay_img = np.zeros((nx, ny))
overlay_img = overlay_img.view(ma.MaskedArray)
overlay_img.mask = True
sx, sy, d = np.shape(rval)
for ix in xrange(sx):
for iy in xrange(sy):
cx = rval[ix, iy, 0]
cy = rval[ix, iy, 1]
if cx and cy:
icx = int(cx)
icy = int(cy)
overlay_img[icx, icy] = field[icx, icy]
print "local bounds in ROI: ", overlay_img.min(), overlay_img.mean(), overlay_img.max()
img2.setImage(overlay_img, levels=(field.min(), field.max())) # global min/max on colormap
img2.setImage(overlay_img, levels=(overlay_img.min(), overlay_img.max())) # local min/max on colormap
idxmap = generate_idxmap()
for roi in rois:
roi.sigRegionChanged.connect(update)
v1a.addItem(roi)
update(rois[-1])
## 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_()
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