def getOverlapPercent(image1, image2, data):
#SET IMAGE LIMITS
gap = int(image1.shape[0] / 256.0)
xm = image1.shape[1] + gap
ym = image1.shape[0] + gap
a1 = numpy.array([
data['point1'],
[-gap, -gap],
[-gap, ym],
[xm, ym],
[xm, -gap],
])
xm = image2.shape[1] + gap
ym = image2.shape[0] + gap
a2 = numpy.array([
data['point2'],
[-gap, -gap],
[-gap, ym],
[xm, ym],
[xm, -gap],
])
#CALCULATE TRANSFORM LIMITS
a2mask = a1Toa2Data(a1, data)
a1mask = a2Toa1Data(a2, data)
#CONVERT NUMPY TO POLYGON LIST
a1masklist = []
a2masklist = []
for j in range(4):
for i in range(2):
item = int(a1mask[j + 1, i])
a1masklist.append(item)
item = int(a2mask[j + 1, i])
a2masklist.append(item)
#CREATE POLYGON MASK FROM THE LIMITS 1 -> IMAGE 2
mask2 = numpy.zeros(shape=image2.shape, dtype=numpy.bool_)
mask2b = apImage.arrayToImage(mask2, normalize=False)
mask2b = mask2b.convert("L")
draw2 = ImageDraw.Draw(mask2b)
draw2.polygon(a2masklist, fill="white")
mask2 = apImage.imageToArray(mask2b, dtype=numpy.float32)
#CREATE POLYGON MASK FROM THE LIMITS 2 -> IMAGE 1
mask1 = numpy.zeros(shape=image1.shape, dtype=numpy.bool_)
mask1b = apImage.arrayToImage(mask1, normalize=False)
mask1b = mask1b.convert("L")
draw1 = ImageDraw.Draw(mask1b)
draw1.polygon(a1masklist, fill="white")
mask1 = apImage.imageToArray(mask1b, dtype=numpy.float32)
percent1 = ndimage.sum(mask1) / (mask1.shape[0] *
mask1.shape[1]) / ndimage.maximum(mask1)
percent2 = ndimage.sum(mask2) / (mask2.shape[0] *
mask2.shape[1]) / ndimage.maximum(mask2)
return max(percent1, percent2), min(percent1, percent2)
def getOverlapPercent(image1, image2, data):
#SET IMAGE LIMITS
gap = int(image1.shape[0]/256.0)
xm = image1.shape[1]+gap
ym = image1.shape[0]+gap
a1 = numpy.array([ data['point1'], [-gap,-gap], [-gap,ym], [xm,ym], [xm,-gap], ])
xm = image2.shape[1]+gap
ym = image2.shape[0]+gap
a2 = numpy.array([ data['point2'], [-gap,-gap], [-gap,ym], [xm,ym], [xm,-gap], ])
#CALCULATE TRANSFORM LIMITS
a2mask = a1Toa2Data(a1, data)
a1mask = a2Toa1Data(a2, data)
#CONVERT NUMPY TO POLYGON LIST
a1masklist = []
a2masklist = []
for j in range(4):
for i in range(2):
item = int(a1mask[j+1,i])
a1masklist.append(item)
item = int(a2mask[j+1,i])
a2masklist.append(item)
#CREATE POLYGON MASK FROM THE LIMITS 1 -> IMAGE 2
mask2 = numpy.zeros(shape=image2.shape, dtype=numpy.bool_)
mask2b = apImage.arrayToImage(mask2, normalize=False)
mask2b = mask2b.convert("L")
draw2 = ImageDraw.Draw(mask2b)
draw2.polygon(a2masklist, fill="white")
mask2 = apImage.imageToArray(mask2b, dtype=numpy.float32)
#CREATE POLYGON MASK FROM THE LIMITS 2 -> IMAGE 1
mask1 = numpy.zeros(shape=image1.shape, dtype=numpy.bool_)
mask1b = apImage.arrayToImage(mask1, normalize=False)
mask1b = mask1b.convert("L")
draw1 = ImageDraw.Draw(mask1b)
draw1.polygon(a1masklist, fill="white")
mask1 = apImage.imageToArray(mask1b, dtype=numpy.float32)
percent1 = ndimage.sum(mask1) / (mask1.shape[0]*mask1.shape[1]) / ndimage.maximum(mask1)
percent2 = ndimage.sum(mask2) / (mask2.shape[0]*mask2.shape[1]) / ndimage.maximum(mask2)
return max(percent1,percent2), min(percent1,percent2)
def openImageFile(self, filename): self.filename = filename if filename[-4:] == '.spi': array = apImage.spiderToArray(filename, msg=False) return array elif filename[-4:] == '.mrc': array = apImage.mrcToArray(filename, msg=False) return array else: image = Image.open(filename) array = apImage.imageToArray(image, msg=False) array = array.astype(numpy.float32) return array return None
def openImageFile(self, filename):
self.filename = filename
if filename[-4:] == '.spi':
array = apImage.spiderToArray(filename, msg=False)
return array
elif filename[-4:] == '.mrc':
array = apImage.mrcToArray(filename, msg=False)
return array
else:
image = Image.open(filename)
array = apImage.imageToArray(image, msg=False)
array = array.astype(numpy.float32)
return array
return None
def maskOverlapRegion(image1, image2, data):
#image1 = ndimage.median_filter(image1, size=2)
#image2 = ndimage.median_filter(image2, size=2)
#SET IMAGE LIMITS
####################################
gap = int(image1.shape[0] / 256.0)
xm = image1.shape[1] + gap
ym = image1.shape[0] + gap
a1 = numpy.array([
data['point1'],
[-gap, -gap],
[-gap, ym],
[xm, ym],
[xm, -gap],
])
xm = image2.shape[1] + gap
ym = image2.shape[0] + gap
a2 = numpy.array([
data['point2'],
[-gap, -gap],
[-gap, ym],
[xm, ym],
[xm, -gap],
])
#CALCULATE TRANSFORM LIMITS
####################################
a2mask = a1Toa2Data(a1, data)
a1mask = a2Toa1Data(a2, data)
#print "a1=",a1
#print "a1mask=",a1mask
#print "a2=",a2
#print "a2mask=",a2mask
#CONVERT NUMPY TO POLYGON LIST
####################################
#maskimg2 = polygon.filledPolygon(img.shape, vert2)
a1masklist = []
a2masklist = []
for j in range(4):
for i in range(2):
item = int(a1mask[j + 1, i])
a1masklist.append(item)
item = int(a2mask[j + 1, i])
a2masklist.append(item)
#CREATE POLYGON MASK FROM THE LIMITS 1 -> IMAGE 2
####################################
#print "a2mask=",numpy.asarray(a2mask, dtype=numpy.int32)
#print "a2masklist=",a2masklist
mask2 = numpy.zeros(shape=image2.shape, dtype=numpy.bool_)
mask2b = apImage.arrayToImage(mask2, normalize=False)
mask2b = mask2b.convert("L")
draw2 = ImageDraw.Draw(mask2b)
draw2.polygon(a2masklist, fill="white")
mask2 = apImage.imageToArray(mask2b, dtype=numpy.float32)
#DRAW POLYGON ONTO IMAGE 2
####################################
mean2 = ndimage.mean(image2)
std2 = ndimage.standard_deviation(image2)
immin2 = mean2 - 2.0 * std2
#med2 = numpy.median(image2.flatten())
#print "MAX=",ndimage.maximum(image2), med2, mean2, std2
#immin2 = ndimage.minimum(image2)+1.0
image2 = (image2 - immin2) * mask2 / 255.0
#mean2 = ndimage.mean(image2)
#std2 = ndimage.standard_deviation(image2)
#med2 = numpy.median(image2.flatten())
immax2 = min(ndimage.maximum(image2), 8.0 * std2)
#print "MAX=",ndimage.maximum(image2), med2, mean2, std2
#immax2 = mean2 + 3.0 * std2
image2 = numpy.where(image2 == 0, immax2, image2)
#CREATE POLYGON MASK FROM THE LIMITS 2 -> IMAGE 1
####################################
#print "a1mask=",numpy.asarray(a1mask, dtype=numpy.int32)
#print "a1masklist=",a1masklist
mask1 = numpy.zeros(shape=image1.shape, dtype=numpy.bool_)
mask1b = apImage.arrayToImage(mask1, normalize=False)
mask1b = mask1b.convert("L")
draw1 = ImageDraw.Draw(mask1b)
draw1.polygon(a1masklist, fill="white")
mask1 = apImage.imageToArray(mask1b, dtype=numpy.float32)
#DRAW POLYGON ONTO IMAGE 1
####################################
mean1 = ndimage.mean(image1)
std1 = ndimage.standard_deviation(image1)
#med1 = numpy.median(image1.flatten())
immin1 = mean1 - 2.0 * std1
#immin1 = ndimage.minimum(image1)+1.0
#print "MAX=",ndimage.maximum(image1), med1, mean1, std1
image1 = (image1 - immin1) * mask1 / 255.0
#mean1 = ndimage.mean(image1)
#std1 = ndimage.standard_deviation(image1)
#med1 = numpy.median(image1.flatten())
immax1 = min(ndimage.maximum(image1), 8.0 * std1)
#print "MAX=",ndimage.maximum(image1), med1, mean1, std1
#immax1 = mean1 + 3.0 * std1
image1 = numpy.where(image1 == 0, immax1, image1)
return (image1, image2)
def maskOverlapRegion(image1, image2, data):
#image1 = ndimage.median_filter(image1, size=2)
#image2 = ndimage.median_filter(image2, size=2)
#SET IMAGE LIMITS
####################################
gap = int(image1.shape[0]/256.0)
xm = image1.shape[1]+gap
ym = image1.shape[0]+gap
a1 = numpy.array([ data['point1'], [-gap,-gap], [-gap,ym], [xm,ym], [xm,-gap], ])
xm = image2.shape[1]+gap
ym = image2.shape[0]+gap
a2 = numpy.array([ data['point2'], [-gap,-gap], [-gap,ym], [xm,ym], [xm,-gap], ])
#CALCULATE TRANSFORM LIMITS
####################################
a2mask = a1Toa2Data(a1, data)
a1mask = a2Toa1Data(a2, data)
#print "a1=",a1
#print "a1mask=",a1mask
#print "a2=",a2
#print "a2mask=",a2mask
#CONVERT NUMPY TO POLYGON LIST
####################################
#maskimg2 = polygon.filledPolygon(img.shape, vert2)
a1masklist = []
a2masklist = []
for j in range(4):
for i in range(2):
item = int(a1mask[j+1,i])
a1masklist.append(item)
item = int(a2mask[j+1,i])
a2masklist.append(item)
#CREATE POLYGON MASK FROM THE LIMITS 1 -> IMAGE 2
####################################
#print "a2mask=",numpy.asarray(a2mask, dtype=numpy.int32)
#print "a2masklist=",a2masklist
mask2 = numpy.zeros(shape=image2.shape, dtype=numpy.bool_)
mask2b = apImage.arrayToImage(mask2, normalize=False)
mask2b = mask2b.convert("L")
draw2 = ImageDraw.Draw(mask2b)
draw2.polygon(a2masklist, fill="white")
mask2 = apImage.imageToArray(mask2b, dtype=numpy.float32)
#DRAW POLYGON ONTO IMAGE 2
####################################
mean2 = ndimage.mean(image2)
std2 = ndimage.standard_deviation(image2)
immin2 = mean2 - 2.0*std2
#med2 = numpy.median(image2.flatten())
#print "MAX=",ndimage.maximum(image2), med2, mean2, std2
#immin2 = ndimage.minimum(image2)+1.0
image2 = (image2-immin2)*mask2/255.0
#mean2 = ndimage.mean(image2)
#std2 = ndimage.standard_deviation(image2)
#med2 = numpy.median(image2.flatten())
immax2 = min(ndimage.maximum(image2), 8.0*std2)
#print "MAX=",ndimage.maximum(image2), med2, mean2, std2
#immax2 = mean2 + 3.0 * std2
image2 = numpy.where(image2==0, immax2, image2)
#CREATE POLYGON MASK FROM THE LIMITS 2 -> IMAGE 1
####################################
#print "a1mask=",numpy.asarray(a1mask, dtype=numpy.int32)
#print "a1masklist=",a1masklist
mask1 = numpy.zeros(shape=image1.shape, dtype=numpy.bool_)
mask1b = apImage.arrayToImage(mask1, normalize=False)
mask1b = mask1b.convert("L")
draw1 = ImageDraw.Draw(mask1b)
draw1.polygon(a1masklist, fill="white")
mask1 = apImage.imageToArray(mask1b, dtype=numpy.float32)
#DRAW POLYGON ONTO IMAGE 1
####################################
mean1 = ndimage.mean(image1)
std1 = ndimage.standard_deviation(image1)
#med1 = numpy.median(image1.flatten())
immin1 = mean1 - 2.0 * std1
#immin1 = ndimage.minimum(image1)+1.0
#print "MAX=",ndimage.maximum(image1), med1, mean1, std1
image1 = (image1-immin1)*mask1/255.0
#mean1 = ndimage.mean(image1)
#std1 = ndimage.standard_deviation(image1)
#med1 = numpy.median(image1.flatten())
immax1 = min(ndimage.maximum(image1), 8.0*std1)
#print "MAX=",ndimage.maximum(image1), med1, mean1, std1
#immax1 = mean1 + 3.0 * std1
image1 = numpy.where(image1==0, immax1, image1)
return (image1, image2)
