140 lines
4.0 KiB
Python
140 lines
4.0 KiB
Python
from __future__ import print_function
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import sys
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if sys.version_info.major == 2: input=raw_input
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import logging
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log = logging.getLogger(__name__)
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import os
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import numpy as np
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import matplotlib.pyplot as plt
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class MyMask(object):
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def __init__(self,img=None):
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self.comp = []
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self.img = img
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self.mask = None
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def addCircle(self,xcen,ycen,radius):
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self.comp.append( ["add","circle", [xcen,ycen,radius] ] )
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def subtractCircle(self,xcen,ycen,radius):
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self.comp.append( ["subtract","circle", [xcen,ycen,radius] ] )
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def addRectangle(self,x1,y1,x2,y2):
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if x1>x2: x1,x2=x2,x1
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if y1>y2: y1,y2=y2,y1
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self.comp.append( ["add","rectangle", [x1,y1,x2,y2] ])
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def subtractRectangle(self,x1,y1,x2,y2):
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if x1>x2: x1,x2=x2,x1
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if y1>y2: y1,y2=y2,y1
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self.comp.append( ["subtract","rectangle", [x1,y1,x2,y2] ])
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def getMask(self,shape=None):
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if shape is None: shape = self.img.shape
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m = []
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X,Y = np.meshgrid ( range(shape[0]),range(shape[1]) )
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for o in self.comp:
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whattodo = o[0]
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kind=o[1]
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pars=o[2]
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if kind == "circle":
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(xc,yc,r) = pars
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d = np.sqrt((X-xc)**2+(Y-yc)**2)
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#plt.imshow(d<r)
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#raw_input()
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m.append( d<r )
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if kind == "rectangle":
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(x1,y1,x2,y2) = pars
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temp = (X>x1) & (X<x2) & ( Y>y1) & (Y<y2)
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m.append( temp )
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mask = np.zeros(shape,dtype=np.bool)
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for i in range(len(m)):
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whattodo = self.comp[i][0]
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if (whattodo == "add"):
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mask[m[i]] = True
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else:
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mask[m[i]] = False
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self.mask = mask
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return mask
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def getMatplotlibMask(self,shape=None):
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mask = self.getMask(shape=shape)
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# convert
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mpl_mask = np.zeros( (mask.shape[0],mask.shape[1],4) )
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mpl_mask[:,:,:3] = 0.5; # gray color
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mpl_mask[:,:,3] = mask/2; # give some transparency
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return mpl_mask
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def save(self,fname,inverted=False):
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import fabio
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mask = self.mask
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if (inverted): mask = ~mask
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i=fabio.edfimage.edfimage(mask.astype(np.uint8)); # edf does not support bool
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i.save(fname)
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def test():
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mask = MyMask()
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mask.addCircle(400,300,250)
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mask.subtractCircle(400,300,150)
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mask.addRectangle(350,250,1500,700)
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mask.show()
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return mask
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def snap(point,shape,snapRange=20):
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snapped = list(point)
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if snapped[0] < snapRange: snapped[0] = 0
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if snapped[0] > shape[0]-snapRange: snapped[0] = shape[0]
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if snapped[1] < snapRange: snapped[1] = 0
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if snapped[1] > shape[1]-snapRange: snapped[1] = shape[1]
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return snapped
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def getPoint(shape,snapRange):
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c = plt.ginput()[0]
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c = snap(c,shape,snapRange=snapRange)
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return c
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def makeMaskGui(img,snapRange=60):
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""" snapRange controls border snapping (in pixels, use <= 0 to disable """
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mask = MyMask(img)
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ans='ok'
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while (ans != 'done'):
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plt.imshow(img)
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plt.clim(np.percentile(img,(2,98)))
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plt.imshow(mask.getMatplotlibMask())
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plt.pause(0.01)
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ans = input("What's next c/r/done? ")
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if ans == "c":
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print("Adding circle, click on center")
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c = getPoint(img.shape,snapRange)
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print("Adding circle, click on another point to define radius")
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p = getPoint(img.shape,snapRange)
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r = np.sqrt( (p[0]-c[0])**2 + (p[1]-c[1])**2 )
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mask.addCircle(c[0],c[1],r)
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if ans == "r":
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print("Adding rectangle, click on one corner")
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c1 = getPoint(img.shape,snapRange)
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print("Adding rectangle, click on opposite corner")
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c2 = getPoint(img.shape,snapRange)
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mask.addRectangle(c1[0],c1[1],c2[0],c2[1])
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plt.imshow(mask.getMatplotlibMask())
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plt.pause(0.01)
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fname = input("Enter a valid filename (ext .edf or .npy) to save the mask")
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try:
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if fname != '':
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ext = os.path.splitext(fname)[1]
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if ext == '.edf':
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mask.save(fname)
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elif ext == '.npy':
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np.save(fname,mask.getMask())
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except Exception as e:
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log.error("Error in saving mask")
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log.error(e)
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finally:
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return mask
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if __name__ == "__main__":
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test()
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plt.show()
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ans=input("Enter to finish")
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