improved masking, now one can add or subtract with GUI; implemented also polygon
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marco cammarata
parent
33bf3384db
commit
906ec537d8
176
xray/mask.py
176
xray/mask.py
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@ -5,53 +5,91 @@ import logging
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log = logging.getLogger(__name__)
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import os
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import collections
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import numpy as np
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import matplotlib.pyplot as plt
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from matplotlib.path import Path
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maskComponent = collections.namedtuple('maskComponent',['operation','geometry','vertices'])
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def _rectangleToMask(X,Y,vertices):
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( (x1,y1), (x2,y2) ) = vertices
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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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return (X>x1) & (X<x2) & ( Y>y1) & (Y<y2)
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def _circleToMask(X,Y,vertices):
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c,p = vertices
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r = np.sqrt( (p[0]-c[0])**2 + (p[1]-c[1])**2 )
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d = np.sqrt((X-c[0])**2+(Y-c[1])**2)
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return d<r
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def _polygonToMask(X,Y,vertices):
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points = np.vstack((X.flatten(),Y.flatten())).T
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path = Path(vertices)
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grid = path.contains_points(points)
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return grid.reshape(X.shape)
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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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self._cache = None
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def _define_component(self,operation,geometry,*vertices):
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#print("define_comp",type(vertices),vertices)
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if geometry == 'circle' and len(vertices) == 3:
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xcen,ycen,radius = vertices
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vertices = ( (xcen,ycen), (xcen+radius,ycen) )
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if geometry == 'rectangle' and len(vertices) == 4:
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vertices = ( (vertices[0],vertices[1]),(vertices[2],vertices[3]) )
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# make sure vertices tuples
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if isinstance(vertices,list):
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vertices = [ (v[0],v[1]) for v in vertices ]
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vertices = tuple(vertices)
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a = dict( vertices = None )
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self.comp.append( maskComponent(operation=operation,vertices=vertices,geometry=geometry) )
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def addCircle(self,*vertices): self._define_component( 'add', 'circle', *vertices )
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def subtractCircle(self,*vertices): self._define_component( 'subtract', 'circle', *vertices )
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def addRectangle(self,*vertices): self._define_component( 'add','rectangle', *vertices)
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def subtractRectangle(self,*vertices): self._define_component( 'subtract','rectangle',*vertices)
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def addPolygon(self,*vertices): self._define_component( 'add','polygon',*vertices)
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def subtractPolygon(self,*vertices): self._define_component( 'subtract','polygon',*vertices)
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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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if shape is None and self.img is not None: shape = self.img.shape
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if shape is None and self.img is None: shape = self._cache['shape']
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if self._cache is None: self._cache = dict( shape = shape )
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# reset cache if shape does not match
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if shape != self._cache['shape']:
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self._cache = dict( shape = shape )
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X,Y = np.meshgrid ( range(shape[1]),range(shape[0]) )
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for component in self.comp:
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if component not in self._cache:
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if component.geometry == 'circle':
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mask = _circleToMask( X,Y,component.vertices )
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elif component.geometry == 'rectangle':
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mask = _rectangleToMask( X,Y,component.vertices )
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elif component.geometry == 'polygon':
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mask = _polygonToMask( X,Y,component.vertices )
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else:
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mask[m[i]] = False
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raise ValueError("Mask type %s not recongnized"%component.geometry)
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self._cache[component] = mask
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mask = np.zeros(shape,dtype=np.bool)
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for comp in self.comp:
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m = self._cache[ comp ]
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if (comp.operation == "add"):
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mask[m] = True
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else:
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mask[m] = False
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self.mask = mask
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return mask
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@ -70,25 +108,19 @@ class MyMask(object):
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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[0] > shape[1]-snapRange: snapped[0] = shape[1]
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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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if snapped[1] > shape[0]-snapRange: snapped[1] = shape[0]
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return tuple(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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def getPoints(N=1,shape=(100,100),snapRange=0):
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if N<1: print('Right click cancels last point, middle click ends the polygon')
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c = plt.ginput(N)
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c = [ snap(point,shape,snapRange=snapRange) for point in c ]
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if len(c) == 1: c = c[0]
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return c
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def makeMaskGui(img,snapRange=60):
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@ -100,20 +132,32 @@ def makeMaskGui(img,snapRange=60):
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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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ans = input("What's next p/P/c/C/r/R/done? (capitals = subtract)")
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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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print("Adding circle, click on center then another point to define radius")
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vertices = getPoints(N=2,shape=img.shape,snapRange=snapRange)
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mask.addCircle(*vertices)
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if ans == "C":
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print("Subtracting circle, click on center then another point to define radius")
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vertices = getPoints(N=2,shape=img.shape,snapRange=snapRange)
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mask.subtractCircle(*vertices)
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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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print("Adding rectangle, click on one corner and then on the opposite one")
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vertices = getPoints(N=2,shape=img.shape,snapRange=snapRange)
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mask.addRectangle(*vertices)
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if ans == "R":
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print("Subtracting rectangle, click on one corner and then on the opposite one")
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vertices = getPoints(N=2,shape=img.shape,snapRange=snapRange)
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mask.subtractRectangle(*vertices)
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if ans == 'p':
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print("Adding polygon")
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vertices = getPoints(N=-1,shape=img.shape,snapRange=snapRange)
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mask.addPolygon(*vertices)
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if ans == 'P':
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print("Subtracting polygon")
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vertices = getPoints(N=-1,shape=img.shape,snapRange=snapRange)
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mask.subtractPolygon(*vertices)
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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) if you want to save the mask (empty otherwise)")
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@ -150,6 +194,16 @@ def maskCenterLines(width,shape):
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return mask
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def test(shape=(1000,2000)):
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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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plt.imshow( mask.getMask(shape) )
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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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