def prepocess(self,
img,
rootCrown,
scale=1.0,
nrExRoot=1,
marker=True,
stemCorrection=False):
print 'starting to segment'
rIdx = -1
self.__io.setServerPath('./')
circleIdx = circleRatio = circleWidth = circleHeight = imgCircle = 0
Failed = False
orig = img.copy()
mask = Masking.Masking(scale=scale)
imgGrey = img.astype(np.uint8)
print 'make mask'
imgBinary = mask.calculateMask(imgGrey)
print 'saving binary mask'
scipy.misc.imsave(
self.__io.getHomePath() + '/Mask/' + self.__io.getFileName() +
'.png', imgBinary)
pathold = os.getcwd()
os.chdir(self.__io.getHomePath())
self.__io.writeServerFile(
'dirt_out.csv',
self.__io.getHomePath() + '/Mask/' + self.__io.getFileName() +
'.png,' + str(self.__io.getID()) + ',0')
os.chdir(pathold)
imgLabel = self.calculateLabelHist(imgBinary)
if marker == True:
print 'Marker is True'
circleIdx, circleRatio, circleWidth, circleHeight, imgCircle = self.findCircle(
imgLabel.copy())
else:
print 'Marker is False'
circleIdx, circleRatio, circleWidth, circleHeight, imgCircle = -1, 1, 1, 1, None
rectIdx, _, _, _, imgTag, tagText = self.findTag(imgLabel.copy(),
imgBinary,
orig,
rect_ratio=5.)
if rectIdx >= 0:
print 'tagIdx' + str(rectIdx)
try:
self.__labelHist[rectIdx] = 0
except:
pass
if circleIdx >= 0 and marker == True:
try:
self.__labelHist[circleIdx] = 0
except:
pass
'''
These two functions belong together and have to be called right after each other. I know, that is bad.
'''
if rootCrown == True:
rIdx, rIdxList, crownMin, crownMax, crownBottom, crownTop = self.findRoot(
imgLabel.copy())
if stemCorrection == True:
print 'Stem reconstruction is active '
imgRoot = self.correctForStem(imgLabel.copy(),
[circleIdx, rectIdx, rIdx],
crownMin, crownMax, crownBottom,
crownTop, rIdx, rIdxList)
else:
print 'No stem reconstruction active'
imgReturn = np.zeros_like(imgLabel)
imgReturn[rIdxList] = 1
imgRoot = imgReturn[crownMax:crownMin, crownBottom:crownTop]
if nrExRoot > 1 and rootCrown == True:
for i in range(nrExRoot):
exRIdx, imgExRoot, centerPtx, centerPty = self.findExcisedRoot(
imgLabel.copy(), [circleIdx, rectIdx, rIdx], crownMin,
crownMax)
if exRIdx != -1:
print 'found excised root ' + str(i)
try:
scipy.misc.imsave(
self.__io.getHomePath() + '/Lateral/' +
self.__io.getFileName() + '_' + str(centerPtx) +
'_' + str(centerPty) + '.png', imgExRoot)
print 'excised root ' + str(i) + 'saved'
except:
print 'NOT SAVED !!!'
raise
try:
pathold = os.getcwd()
os.chdir(self.__io.getHomePath())
self.__io.writeServerFile(
'dirt_out.csv',
self.__io.getHomePath() + '/Lateral/' +
self.__io.getFileName() + '_' + str(centerPtx) +
'_' + str(centerPty) + '.png,' +
str(self.__io.getID()) + ',0')
print 'excised root ' + str(i) + 'saved Server'
os.chdir(pathold)
except:
print 'NOT SAVED !!!!'
raise
elif nrExRoot == 1 and rootCrown == True:
exRIdx, imgExRoot, centerPtx, centerPty = self.findExcisedRoot(
imgLabel.copy(), [circleIdx, rectIdx, rIdx], crownMin,
crownMax)
if exRIdx != -1:
print 'found the excised root '
try:
pathold = os.getcwd()
os.chdir(self.__io.getHomePath())
scipy.misc.imsave(
self.__io.getHomePath() + '/Lateral/' +
self.__io.getFileName() + '_' + str(centerPtx) + '_' +
str(centerPty) + '.png', imgExRoot)
print 'excised root saved'
self.__io.writeServerFile(
'dirt_out.csv',
self.__io.getHomePath() + '/Lateral/' +
self.__io.getFileName() + '_' + str(centerPtx) + '_' +
str(centerPty) + '.png,' + str(self.__io.getID()) +
',0')
print 'excised root saved Server'
os.chdir(pathold)
except:
print 'NOT SAVED !!!!'
elif nrExRoot == 1 and rootCrown == False:
exRIdx, imgExRoot, centerPtx, centerPty = self.findExcisedRoot(
imgLabel.copy(), [circleIdx, rectIdx], 0, 1)
if exRIdx != -1:
print 'found the excised root '
rIdx = -1
try:
pathold = os.getcwd()
os.chdir(self.__io.getHomePath())
scipy.misc.imsave(
self.__io.getHomePath() + '/Lateral/' +
self.__io.getFileName() + '_' + str(centerPtx) + '_' +
str(centerPty) + '.png', imgExRoot)
print 'excised root saved'
self.__io.writeServerFile(
'dirt_out.csv',
self.__io.getHomePath() + '/Lateral/' +
self.__io.getFileName() + '_' + str(centerPtx) + '_' +
str(centerPty) + '.png,' + str(self.__io.getID()) +
',0')
print 'excised root saved Server'
os.chdir(pathold)
except:
print 'NOT SAVED !!!!'
if marker == True:
scipy.misc.imsave(
self.__io.getHomePath() + '/Mask/' + self.__io.getFileName() +
'Circle.png', imgCircle)
scipy.misc.imsave(
self.__io.getHomePath() + '/Mask/' + self.__io.getFileName() +
'Tag.png', imgTag)
#pathold=os.getcwd()
#os.chdir(self.__io.getHomePath())
if marker == True:
self.__io.writeServerFile(
'dirt_out.csv',
self.__io.getHomePath() + '/Mask/' + self.__io.getFileName() +
'Circle.png,' + str(self.__io.getID()) + ',0')
#os.chdir(pathold)
if rIdx != -1:
'''
If image is usable, then it gets segmented and copied. Otherwise we ignore it
'''
try:
print 'root image to be saved'
scipy.misc.imsave(
self.__io.getHomePath() + '/Crown/' +
self.__io.getFileName() + '.png', imgRoot)
except:
print 'CROWN NOT SAVED'
raise
try:
pathold = os.getcwd()
os.chdir(self.__io.getHomePath())
self.__io.writeServerFile(
'dirt_out.csv',
self.__io.getHomePath() + '/Crown/' +
self.__io.getFileName() + '.png,' +
str(self.__io.getID()) + ',0')
os.chdir(pathold)
except:
print 'MASK NOT WRITTEN TO SERVER FILE'
elif rIdx == -1 and exRIdx != -1:
print "Only excised roots computed"
else:
Failed = True
print "old path: " + pathold
return Failed, tagText, circleRatio, circleWidth, circleHeight
