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