def textureFeatures(subImage):
glcmFeatures = GLCMFeatures.calcFeatures(subImage)
print(glcmFeatures)
lbpFeatures = LBPFeatures.calcFeatures(subImage, 8, 2, 'ror', 12)
print(lbpFeatures)
LoGHFeatures = LoGHistogramFeatures.calcFeatures(subImage,
numpy.array([4.0]))
print(LoGHFeatures)
gaborFeatures = GaborFeatures.calcFeatures(subImage, 2.0, 0.6)
print(gaborFeatures)
def genFeatures():
# dualRescaleOption: whether use both lesion and normal ROI for grayscale normalization
# If 'False', use only lesion image
# default value is 'True'
# Parameters and feature list of each algorithm
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPRadius = 3
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
kernel_bank = []
Gaborsigma_range = [0.6]
Gaborfreq_range = (0.1, 0.3, 0.5)
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = [
'PatientID', 'Phase', 'LesionName', 'ROI_Y', 'ROI_X', 'Width', 'Height'
]
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['LargestBox_Mean', 'LargestBox_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for casefile in os.listdir(rootDir):
if casefile.startswith('.'):
continue
if casefile.startswith('..'):
continue
if fnmatch.fnmatch(casefile, '*Icon*'):
continue
print casefile
patientid = casefile.split('_')[1] + casefile.split('_')[2]
splitlist = casefile.split('_')
phasename = ''
for item in splitlist[3:len(splitlist)]:
phasename = phasename + ' ' + item
print patientid
print phasename
phasefilepath = os.path.join(rootDir, casefile)
lesionfolder = []
for phasefile in os.listdir(phasefilepath):
if phasefile.startswith('.'):
continue
if phasefile.startswith('..'):
continue
if fnmatch.fnmatch(phasefile, '*Icon*'):
continue
if fnmatch.fnmatch(phasefile, '*Lesion*') or fnmatch.fnmatch(
phasefile, '*lesion*'):
lesionfolder.append(phasefile)
print lesionfolder
for lesionfolderfile in lesionfolder:
lesionPath = os.path.join(rootDir, casefile, lesionfolderfile)
for roifile in os.listdir(lesionPath):
if roifile.startswith('.'):
continue
if roifile.startswith('..'):
continue
if fnmatch.fnmatch(roifile, '*Icon*'):
continue
if fnmatch.fnmatch(roifile, '*rec.csv'):
lesionroiFn = roifile
# Largest rectangle file name with absolute path
lesionROIRectFn = os.path.join(lesionPath, lesionroiFn)
# DICOM file name with absolute path
lesionDicom = os.path.join(lesionPath, lesionDicomFn)
# ROI file name with absolute path
normalROICoords = os.path.join(lesionPath, roiCoordsFn)
dualROIGrayLevels = numpy.array([])
with open(normalROICoords, 'r') as roiCoordsFile:
roiCoordsList = csv.reader(roiCoordsFile, delimiter=';')
for row in roiCoordsList:
dualROIGrayLevels = numpy.append(
dualROIGrayLevels, int(row[2]))
with open(lesionROIRectFn, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
if (int(aROI['Y']) == 1) and (int(aROI['X']) == 1):
print('Invalid ROI for %s @ %s.' %
(patientid, phasename))
continue
# only normal
dicomImage = Read2DImage(lesionDicom)
subImage = dicomImage[int(aROI['Y']):(int(aROI['Y']) + int(aROI['H'])), \
int(aROI['X']):(int(aROI['X']) + int(aROI['W']))]
subImageLBP = dicomImage[int(aROI['Y']) - LBPRadius:(int(aROI['Y']) + int(aROI['H'])) + LBPRadius, \
int(aROI['X']) - LBPRadius:(int(aROI['X']) + int(aROI['W'])) + LBPRadius]
mean_LargBox, std_LargBox = Mean_Std_LargestBox2(
dicomImage, int(aROI['X']), int(aROI['Y']),
int(aROI['W']), int(aROI['H']))
subImage = GrayScaleNormalization(
subImage, dualROIGrayLevels.ptp())
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, dualROIGrayLevels.ptp())
if numpy.all(subImage == 0):
print('%s @ %s is all zero.' %
(patientid, phasename))
continue
aFeature = [
patientid, phasename, lesionfolderfile, aROI['Y'],
aROI['X'], aROI['W'], aROI['H']
]
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImage)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(
glcmFeatures[GLCMAngle][featureName])
# LBP
lbpFeatures = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius,
LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = ExtendGaborFeatures.calcFeatures(
subImage, int(aROI['W']), Gaborkernel_bank)
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox]
featureWriter.writerow(aFeature)
print('Done.')
def genTextures():
GLCMAngleList = ['Avg']
featureTitle = ['Image Contrast', 'Image Filename','X', 'Y', 'Boundary (1) or not (inside: 0), (outside:2)', 'Biopsy(1) or not (0)']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
featureTitle = featureTitle + LBPFeatureList
Gaborsigma_range = (0.6,1.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' + str(GaborFreq))
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(Gaborsigma_range, Gaborfreq_range, kernel_bank)
MeanStdfeaturelist = ['Raw_Mean','Raw_Std']
featureTitle = featureTitle + MeanStdfeaturelist
dicomnames = ['EPI', 'P', 'Q', 'RCBV', 'SPGRC', 'T2']
for texturemapfile in os.listdir(rootDir):
if texturemapfile.startswith('.'):
continue
if texturemapfile.startswith('..'):
continue
print texturemapfile
patientname = texturemapfile.split('_')[0]
if fnmatch.fnmatch(patientname, "*FSL*"):
newpatientname = patientname.replace("FSL", "")
elif fnmatch.fnmatch(patientname, "*h*"):
newpatientname = patientname.replace("h", "")
else:
newpatientname = patientname
print newpatientname
slicepathfile = os.path.join(rootDir, texturemapfile)
for slicefile in os.listdir(slicepathfile):
if slicefile.startswith('.'):
continue
if slicefile.startswith('..'):
continue
print slicefile
slicenum = slicefile.replace('slice', '')
slicenum = int(slicenum)
dcmxmlfilepath = os.path.join(slicepathfile, slicefile)
dcmfiledict = dict()
for dcmfile in os.listdir(dcmxmlfilepath):
if dcmfile.startswith('.'):
continue
if fnmatch.fnmatch(dcmfile, '*dcm*') is False:
continue
if fnmatch.fnmatch(dcmfile, '*precontrast*'):
continue
if fnmatch.fnmatch(dcmfile, '*C*SPGR*') or fnmatch.fnmatch(dcmfile, '*+C*T1*') or fnmatch.fnmatch(dcmfile,'*T1*+C*'):
SPGRCfile = dcmfile
dcmfiledict['SPGRC'] = SPGRCfile
if fnmatch.fnmatch(dcmfile, '*T2*'):
T2file = dcmfile
dcmfiledict['T2'] = T2file
if fnmatch.fnmatch(dcmfile, '*q*'):
Qfile = dcmfile
dcmfiledict['Q'] = Qfile
if fnmatch.fnmatch(dcmfile, '*p*'):
Pfile = dcmfile
dcmfiledict['P'] = Pfile
if fnmatch.fnmatch(dcmfile, '*rCBV*'):
RCBVfile = dcmfile
dcmfiledict['RCBV'] = RCBVfile
if fnmatch.fnmatch(dcmfile, '*EPI*+C*') or fnmatch.fnmatch(dcmfile, '*+C*EPI*'):
EPIfile = dcmfile
dcmfiledict['EPI'] = EPIfile
for xmlfile in os.listdir(dcmxmlfilepath):
if not fnmatch.fnmatch(xmlfile, '*.xml'):
continue
if fnmatch.fnmatch(xmlfile, '*NECROSIS*') or fnmatch.fnmatch(xmlfile,'*necrosis*'):
continue
if fnmatch.fnmatch(xmlfile, '*C*SPGR*') or fnmatch.fnmatch(xmlfile, '*+C*T1*') or fnmatch.fnmatch(
xmlfile, '*T1*+C*'):
T1xmlfile = xmlfile
if fnmatch.fnmatch(xmlfile, '*T2*'):
T2xmlfile = xmlfile
print '\n'
T1xmlfilepath = os.path.join(dcmxmlfilepath, T1xmlfile)
T2xmlfilepath = os.path.join(dcmxmlfilepath, T2xmlfile)
if slicenum not in biopsycoordinatefile[newpatientname]:
continue
else:
biopsycoordinatelist = biopsycoordinatefile[newpatientname][slicenum]
T1windowptlist = ParseXMLDrawROI(T1xmlfilepath,'T1',biopsycoordinatelist)
T2windowptlist = ParseXMLDrawROI(T2xmlfilepath,'T2',biopsycoordinatelist)
# start to do T1
featuresOutFn = 'ROI_Texture_Map.csv'
T1featuresOutFn = newpatientname + '_' + slicefile + '_' + 'T1' + '_' + featuresOutFn
featuresCSVFn = os.path.join(outputDir, T1featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for eachdcm in dicomnames:
dicomfile = dcmfiledict[eachdcm]
dicomfilepath = os.path.join(dcmxmlfilepath, dicomfile)
dicomImage = Read2DImage(dicomfilepath)
for eachpt in T1windowptlist:
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
xcoord = int(eachpt[0])
ycoord = int(eachpt[1])
boundaryornot = int(eachpt[2])
biopsyornot = int(eachpt[3])
aFeature = [eachdcm, dicomfile, xcoord,ycoord, boundaryornot,biopsyornot]
subImage = dicomImage[ycoord - 4:ycoord + 4, xcoord - 4:xcoord + 4]
subImageGLCM = GrayScaleNormalization(subImage, subImage.max(), subImage.min())
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
GLCM.append(glcmFeatures[GLCMAngle][featureName])
# raw mean and std of subimage
Raw_mean = numpy.mean(subImage)
Raw_std = numpy.std(subImage)
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 - LBPRadius:ycoord + 4 + LBPRadius,
xcoord - 4 - LBPRadius: xcoord + 4 + LBPRadius]
extendsubImageLBP = GrayScaleNormalization(subImageLBP, subImage.max(), subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(extendsubImageLBP, LBPnPoints, LBPRadius,
LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(dicomImage, xcoord - 4, ycoord - 4, 8, 8,
Gaborkernel_bank, subImage.max(),
subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
aFeature = aFeature + GLCM + LBP + Gabor + meanstd
featureWriter.writerow(aFeature)
# start to do T2
T2featuresOutFn = newpatientname + '_' + slicefile + '_' + 'T2' + '_' + featuresOutFn
featuresCSVFn = os.path.join(outputDir, T2featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for eachdcm in dicomnames:
dicomfile = dcmfiledict[eachdcm]
dicomfilepath = os.path.join(dcmxmlfilepath, dicomfile)
dicomImage = Read2DImage(dicomfilepath)
for eachpt in T2windowptlist:
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
xcoord = int(eachpt[0])
ycoord = int(eachpt[1])
boundaryornot = int(eachpt[2])
biopsyornot = int(eachpt[3])
aFeature = [eachdcm, dicomfile, xcoord, ycoord, boundaryornot, biopsyornot]
subImage = dicomImage[ycoord - 4:ycoord + 4, xcoord - 4:xcoord + 4]
subImageGLCM = GrayScaleNormalization(subImage, subImage.max(), subImage.min())
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
GLCM.append(glcmFeatures[GLCMAngle][featureName])
# raw mean and std of subimage
Raw_mean = numpy.mean(subImage)
Raw_std = numpy.std(subImage)
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 - LBPRadius:ycoord + 4 + LBPRadius,
xcoord - 4 - LBPRadius: xcoord + 4 + LBPRadius]
extendsubImageLBP = GrayScaleNormalization(subImageLBP, subImage.max(),
subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(extendsubImageLBP, LBPnPoints, LBPRadius,
LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(dicomImage, xcoord - 4, ycoord - 4,
8, 8,
Gaborkernel_bank, subImage.max(),
subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
aFeature = aFeature + GLCM + LBP + Gabor + meanstd
featureWriter.writerow(aFeature)
def genTextures():
dicomnames = ['EPI', 'P', 'Q', 'RCBV', 'SPGRC', 'T2']
#GLCMAngleList = ['0', '45', '90', '135', 'Avg']
GLCMAngleList = ['Avg']
featureTitle = ['Patient', 'ID', 'slice number', 'X', 'Y']
for GLCMAngle in GLCMAngleList:
for dicom in dicomnames:
for featureName in haralick_labels[:-1]:
GLCMname = dicom + '-' + featureName + '_' + GLCMAngle
featureTitle.append(GLCMname)
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for dicom in dicomnames:
for x in xrange(0, LBPnPoints + 1):
LBPname = dicom + '-' +'LBP_%02d' % x
LBPFeatureList.append(LBPname)
LBPname = dicom + '-' +'LBP_Other'
LBPFeatureList.append(LBPname)
featureTitle = featureTitle + LBPFeatureList
Gaborsigma_range = (0.6,1.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
for dicom in dicomnames:
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(dicom + '-'+featureName + '_' + str(GaborSigma) + '_' + str(GaborFreq))
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(Gaborsigma_range, Gaborfreq_range, kernel_bank)
meanstdTitle = []
for dicom in dicomnames:
meanname = dicom +'-'+'Raw_Mean'
stdname = dicom + '-' + 'Raw_Std'
meanstdTitle.append(meanname)
meanstdTitle.append(stdname)
featureTitle = featureTitle + meanstdTitle
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect = 'excel')
featureWriter.writerow(featureTitle)
ptindex = 0
for pt in ptnamelist: # such as RW,JTy...according to CSV file to sort
ptslice = []
for coordtuple in ptcoordlist:
if pt in coordtuple:
ptslice.append(coordtuple[pt])
#print pt,ptslice
ptfolderpath = os.path.join(rootDir,folderdict[pt])
for slicelist in ptslice:
patientid = ptlist[ptindex]
ptindex += 1
slicenum = slicelist[2]
xcoord = slicelist[0]
ycoord = slicelist[1]
slicefolder = 'slice'+ str(slicenum)
slicefolderpath = os.path.join(ptfolderpath,slicefolder)
#print pt,slicelist, slicefolderpath
dcmfiledict = dict()
for dcmfile in os.listdir(slicefolderpath):
if dcmfile.startswith('.'):
continue
if fnmatch.fnmatch(dcmfile,'*dcm*') is False:
continue
if fnmatch.fnmatch(dcmfile,'*C*SPGR*') or fnmatch.fnmatch(dcmfile,'*+C*T1*') or fnmatch.fnmatch(dcmfile,'*T1*+C*'):
SPGRCfile = dcmfile
dcmfiledict['SPGRC']=SPGRCfile
if fnmatch.fnmatch(dcmfile,'*T2*'):
T2file = dcmfile
dcmfiledict['T2']=T2file
if fnmatch.fnmatch(dcmfile,'*q*'):
Qfile = dcmfile
dcmfiledict['Q']=Qfile
if fnmatch.fnmatch(dcmfile,'*p*'):
Pfile = dcmfile
dcmfiledict['P'] = Pfile
if fnmatch.fnmatch(dcmfile,'*rCBV*'):
# if fnmatch.fnmatch(dcmfile, '*rCBV*normalized*'):
# RCBVfile = dcmfile
# dcmfiledict['RCBVnorm'] = RCBVfile
# else:
RCBVfile = dcmfile
dcmfiledict['RCBV'] = RCBVfile
if fnmatch.fnmatch(dcmfile,'*EPI*+C*') or fnmatch.fnmatch(dcmfile,'*+C*EPI*'):
EPIfile = dcmfile
dcmfiledict['EPI'] = EPIfile
print pt,patientid,slicenum,len(dcmfiledict),dcmfiledict
aFeature = [pt, patientid, slicenum, xcoord,ycoord]
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
# start GLCM for each dicom
for GLCMAngle in GLCMAngleList:
for eachdcm in dicomnames:
dicomfile = dcmfiledict[eachdcm]
dicomfilepath = os.path.join(slicefolderpath,dicomfile)
dicomImage = Read2DImage(dicomfilepath)
subImage = dicomImage[ycoord-4:ycoord+4,xcoord-4:xcoord+4]
subImageGLCM = GrayScaleNormalization(subImage, subImage.max(),subImage.min())
if numpy.all(subImage == 0):
print('%s @ %s is all zero.' % (patientid, slicenum))
continue
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for featureName in haralick_labels[:-1]:
GLCM.append(glcmFeatures[GLCMAngle][featureName])
for eachdcm in dicomnames:
dicomfile = dcmfiledict[eachdcm]
dicomfilepath = os.path.join(slicefolderpath, dicomfile)
dicomImage = Read2DImage(dicomfilepath)
subImage = dicomImage[ycoord - 4: ycoord + 4,xcoord - 4:xcoord + 4 ]
## get normalized to 0, 255: raw mean and standard deviation
dicommean, dicomstd= Norm_Mean_Std_LargestBox(subImage,subImage.max(),subImage.min())
meanstd.append(dicommean)
meanstd.append(dicomstd)
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 - LBPRadius:ycoord + 4 + LBPRadius,
xcoord - 4 - LBPRadius: xcoord + 4 + LBPRadius]
extendsubImageLBP = GrayScaleNormalization(subImageLBP, subImage.max(),subImage.min())
# LBP
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(dicomImage, xcoord - 4, ycoord - 4, 8, 8,
Gaborkernel_bank, subImage.max(), subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
aFeature = aFeature + GLCM +LBP + Gabor + meanstd
featureWriter.writerow(aFeature)
def genTAfeatures(patientID, phasename, lesionDicom, lesionROIRectFn,
Gaborkernel_bank):
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
with open(lesionROIRectFn, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
if (int(aROI['Y']) == 1) and (int(aROI['X']) == 1):
print('Invalid ROI for %s @ %s.' % (patientID, phasename))
continue
dicomImage = Read2DImage(lesionDicom)
# in Python, coords should be coords(matlab)-1
# coordinates from Osirtx: 0,0 so keep it not -1
xcoord = int(aROI['X'])
ycoord = int(aROI['Y'])
width = int(aROI['W'])
height = int(aROI['H'])
subImage = dicomImage[ycoord:(ycoord + height),
xcoord:(xcoord +
width)] # errors here: before: Y + W
# if patientID == 'SHHCC_2468':
# print xcoord
# print ycoord
#
# print dicomImage
# print phasename
# print(subImage)
# print lesionDicom
# print lesionROIRectFn
subImageLBP = dicomImage[ycoord - LBPRadius:(ycoord + height) +
LBPRadius, xcoord -
LBPRadius:(xcoord + width) + LBPRadius]
## get mean and standard deviation of lesion ROI's gray level of lagest box directly from subImage
mean_LargBox = numpy.mean(subImage)
std_LargBox = numpy.std(subImage)
subImageGLCM = GrayScaleNormalization(subImage, subImage.max(),
subImage.min())
# if patientID == 'SHHCC_2468':
# print phasename
# print(subImageGLCM)
# print(numpy.shape(subImageGLCM))
# print(numpy.min(subImageGLCM))
# print (numpy.max(subImageGLCM))
# for extended LBP, we still use grayscale range of 8*8 box to normalize extended ROI 10*10 box
extendsubImageLBP = GrayScaleNormalization(subImageLBP,
subImage.max(),
subImage.min())
if numpy.all(subImage == 0):
print('%s @ %s is all zero.' % (patientID, phasename))
continue
aFeature = [
patientID, phasename, aROI['Y'], aROI['X'], aROI['W'],
aROI['H']
]
# GLCM
# dont need to extended ROI
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
# LBP
# need to use extended ROI
lbpFeatures = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord, ycoord, width, height, Gaborkernel_bank,
subImage.max(), subImage.min())
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox]
return aFeature
def genFeatures():
GLCMAngleList = ['Avg']
LBPRadius = 3
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (1.0, 3.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = ['PatientID', 'Phase', 'ROI_X', 'ROI_Y', 'Width', 'Height']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['LargestBox_Raw_Mean', 'LargestBox_Raw_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for casefile in os.listdir(rootDir):
if casefile.startswith('.'):
continue
if casefile.startswith('..'):
continue
if fnmatch.fnmatch(casefile, '*Icon*'):
continue
if fnmatch.fnmatch(casefile, '*xlsx*'):
continue
print casefile
patientID = casefile.split('_ ')[0]
print patientID
patientfilepath = os.path.join(rootDir, casefile)
phaseDir = dict()
for patientPhaseDir in os.listdir(patientfilepath):
if patientPhaseDir.startswith('.'):
continue
if patientPhaseDir.startswith('..'):
continue
if fnmatch.fnmatch(patientPhaseDir, '*Icon*'):
continue
if fnmatch.fnmatch(patientPhaseDir, '*Lesion*'):
phaseDir['lesion'] = patientPhaseDir
phasename = patientPhaseDir
print patientPhaseDir
if fnmatch.fnmatch(patientPhaseDir, '*Control*'):
phaseDir['control'] = patientPhaseDir
print patientPhaseDir
if 'lesion' not in phaseDir:
continue
lesionfile = os.path.join(patientfilepath, phaseDir['lesion'])
lesionlargestrecpath = os.path.join(lesionfile, recfile)
lesionDicom = os.path.join(lesionfile, dcmfile)
normalfile = os.path.join(patientfilepath, phaseDir['control'])
normallargestrecpath = os.path.join(normalfile, recfile)
normalDicom = os.path.join(normalfile, dcmfile)
with open(lesionlargestrecpath, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
xcoord = int(aROI['X'])
ycoord = int(aROI['Y'])
width = int(aROI['W'])
height = int(aROI['H'])
print xcoord, ycoord, width, height
lesiondicomImage = Read2DImage(lesionDicom)
normaldicomImage = Read2DImage(normalDicom)
lesionsubImage = lesiondicomImage[ycoord:(ycoord + height),
xcoord:(xcoord + width)]
normalsubImage = normaldicomImage[ycoord:(ycoord + height),
xcoord:(xcoord + width)]
mean_LargBox = numpy.mean(lesionsubImage)
std_LargBox = numpy.std(lesionsubImage)
# get max gray scale and min grayscale from both lesion and normal dicom
lesionimageMax = lesionsubImage.max()
lesionimageMin = lesionsubImage.min()
normalimageMax = normalsubImage.max()
normalimageMin = normalsubImage.min()
# compare max and min and get max / min for normalization
if lesionimageMax > normalimageMax:
subImageMax = lesionimageMax
else:
subImageMax = normalimageMax
if lesionimageMin < normalimageMin:
subImageMin = lesionimageMin
else:
subImageMin = normalimageMin
subImageGLCM = GrayScaleNormalization(lesionsubImage,
subImageMax, subImageMin)
subImageLBP = lesiondicomImage[ycoord -
LBPRadius:(ycoord + height) +
LBPRadius, xcoord -
LBPRadius:(xcoord + width) +
LBPRadius]
aFeature = [
patientID, phasename, aROI['X'], aROI['Y'], aROI['W'],
aROI['H']
]
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
# LBP
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImageMax, subImageMin)
lbpFeatures = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = ExtendGaborFeatures.calcFeatures(
lesiondicomImage, xcoord, ycoord, width, height,
Gaborkernel_bank, subImageMax, subImageMin)
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox]
featureWriter.writerow(aFeature)
def genFeatures():
# Parameters and feature list of each algorithm
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPFeatureList = ['LBP_00', 'LBP_01','LBP_02', 'LBP_03', 'LBP_04', 'LBP_05', \
'LBP_06', 'LBP_07', 'LBP_08', 'LBP_09','LBP_10', 'LBP_11']
LBPRadius = 3
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPnBins = 12
LoGHSigmaList = numpy.arange(2, 7, 2, dtype=numpy.float)
LogHFeatureList = [
'LoGH_Mean', 'LoGH_Variance', 'LoGH_Skewness', 'LoGH_Kurtosis',
'LoGH_Entropy', 'LoGH_Uniformity'
]
GaborSigmaRange = (1.0, 3.0)
GaborFreqRange = (0.6, 1)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = ['FileName', 'ROI_Y', 'ROI_X']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for LoGHSigma in LoGHSigmaList:
for featureName in LogHFeatureList:
featureTitle.append(featureName + '_' + str(LoGHSigma))
for GaborSigma in GaborSigmaRange:
for GaborFreq in GaborFreqRange:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
for dirPath, dirNames, fileNames in os.walk(rootDir):
for dicomFn in fnmatch.filter(fileNames, dicomFnMask):
dicomPath = os.path.join(dirPath, dicomFn)
roiCSVFn = os.path.join(dirPath,
os.path.splitext(dicomFn)[0] + roiExtFn)
if not os.path.isfile(roiCSVFn):
print('No ROI File for %s.' % dicomPath)
continue
featuresCSVFn = os.path.join(
dirPath,
os.path.splitext(dicomFn)[0] + featuresExtFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
with open(roiCSVFn, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
if (int(aROI['Y']) == 1) and (int(aROI['X']) == 1):
print('Invalid ROI center @ %s.' % dicomPath)
continue
#else:
#print('(%s, %s) @ %s.'%(aROI['Y'], aROI['X'], dicomPath))
dicomImage = Read2DImage(dicomPath)
subImage = dicomImage[(int(aROI['Y']) - ROI_RADIUS):(int(aROI['Y']) + ROI_RADIUS), \
(int(aROI['X']) - ROI_RADIUS):(int(aROI['X']) + ROI_RADIUS)]
subImage = GrayScaleNormalization(subImage)
if numpy.all(subImage == 0):
print('(%s, %s) @ %s is all zero.' %
(dicomFn, aROI['Y'], aROI['X']))
continue
aFeature = [dicomFn, aROI['Y'], aROI['X']]
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImage)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(
glcmFeatures[GLCMAngle][featureName])
# LBP
lbpFeatures = LBPFeatures.calcFeatures(
subImage, LBPnPoints, LBPRadius, LBPMethod,
LBPnBins)
aFeature = aFeature + lbpFeatures.tolist()
# LoGH
LoGHFeatures = LoGHistogramFeatures.calcFeatures(
subImage, LoGHSigmaList)
for LoGHFeaturePerSimga in LoGHFeatures:
aFeature = aFeature + LoGHFeaturePerSimga.tolist()
# Gabor
for GaborSigma in GaborSigmaRange:
for GaborFreq in GaborFreqRange:
gaborFeatures = GaborFeatures.calcFeatures(
subImage, GaborSigma, GaborFreq)
aFeature = aFeature + gaborFeatures.tolist()
featureWriter.writerow(aFeature)
def genTextures():
GLCMAngleList = ['Avg']
featureTitle = ['X', 'Y']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
featureTitle = featureTitle + LBPFeatureList
Gaborsigma_range = (0.6, 1.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
MeanStdfeaturelist = ['Raw_Mean', 'Raw_Std']
featureTitle = featureTitle + MeanStdfeaturelist
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
meanstd = list()
# GLCM = list()
# LBP = list()
# Gabor = list()
xcoord = 151
ycoord = 83
dicomImage = Read2DImage(rootDir)
aFeature = [xcoord, ycoord]
subImage = dicomImage[ycoord - 4:ycoord + 4, xcoord - 4:xcoord + 4]
subImageGLCM = GrayScaleNormalization(subImage, subImage.max(),
subImage.min())
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
# raw mean and std of subimage
Raw_mean = numpy.mean(subImage)
Raw_std = numpy.std(subImage)
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 - LBPRadius:ycoord + 4 + LBPRadius,
xcoord - 4 - LBPRadius:xcoord + 4 + LBPRadius]
extendsubImageLBP = GrayScaleNormalization(subImageLBP, subImage.max(),
subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(extendsubImageLBP, LBPnPoints,
LBPRadius, LBPMethod)
aFeature = aFeature + LBPs.tolist()
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord - 4, ycoord - 4, 8, 8, Gaborkernel_bank,
subImage.max(), subImage.min())
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + meanstd
featureWriter.writerow(aFeature)
def genFeatures():
# Parameters and feature list of each algorithm
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (0.6, 1.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = [
'PatientID', 'Dicom Image Filename', 'Xml Filename', 'Phase Name', 'X',
'Y'
]
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['Raw_Mean', 'Raw_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
#casenum = 0
# for twofolder in os.listdir(rootDir):
# if twofolder.startswith('.'):
# continue
# if twofolder.startswith('..'):
# continue
# if fnmatch.fnmatch(twofolder, '*Icon*'):
# continue
twofolder = 'malignant'
# print twofolder
rootDir2 = os.path.join(rootDir, twofolder)
casefile = 'Pt9'
# for casefile in os.listdir(rootDir2):
# if casefile.startswith('.'):
# continue
# if casefile.startswith('..'):
# continue
# if fnmatch.fnmatch(casefile, '*Icon*'):
# continue
# casefile = 'Pt36'
# casenum += 1
# print casefile
roiDicomfile = dict()
roiCCxmlfile = list()
roiMLOxmlfile = list()
lesionpath = os.path.join(rootDir2, casefile)
for lesionfile in os.listdir(lesionpath):
if lesionfile.startswith('.'):
continue
if lesionfile.startswith('..'):
continue
if fnmatch.fnmatch(lesionfile, '*Icon*'):
continue
if fnmatch.fnmatch(lesionfile, '*texture*'):
continue
if fnmatch.fnmatch(lesionfile, '*DES*CC*dcm'):
roiDicomfile['DES-CC'] = lesionfile
if fnmatch.fnmatch(lesionfile, '*LE*CC*dcm'):
roiDicomfile['LE-CC'] = lesionfile
if fnmatch.fnmatch(lesionfile, '*DES*MLO*dcm'):
roiDicomfile['DES-MLO'] = lesionfile
if fnmatch.fnmatch(lesionfile, '*LE*MLO*dcm'):
roiDicomfile['LE-MLO'] = lesionfile
if fnmatch.fnmatch(lesionfile, '*CC*xml'):
roiCCxmlfile.append(lesionfile)
if fnmatch.fnmatch(lesionfile, '*MLO*xml'):
roiMLOxmlfile.append(lesionfile)
# print roiCCxmlfile
# print roiMLOxmlfile
# print roiDicomfile
patientID = casefile
phasenames = ['DES-CC', 'LE-CC', 'DES-MLO', 'LE-MLO']
if casefile == 'Pt45':
roiccxml = roiCCxmlfile[0]
roimloxml = roiMLOxmlfile[1]
else:
# for Pt45 and Pt48, all use this setting for only getting first 2 files from list
roiccxml = roiCCxmlfile[0]
roimloxml = roiMLOxmlfile[0]
roiccxmlpath = os.path.join(lesionpath, roiccxml)
roimloxmlpath = os.path.join(lesionpath, roimloxml)
CCxmin, CCxmax, CCymin, CCymax, CCxycoord = ParseXMLDrawROI(roiccxmlpath)
MLOxmin, MLOxmax, MLOymin, MLOymax, MLOxycoord = ParseXMLDrawROI(
roimloxmlpath)
# check if coords inside boundary or outside boundary
CCwindowptlist = chooseinoutcoord(CCxmin, CCxmax, CCymin, CCymax,
CCxycoord)
MLOwindowptlist = chooseinoutcoord(MLOxmin, MLOxmax, MLOymin, MLOymax,
MLOxycoord)
featuresOutFn = 'ROI_Texture_Map.csv'
# start to do T2
featuresOutFn = patientID + '_' + twofolder + '_' + featuresOutFn
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for phase in phasenames:
print phase
lesionDicomFn = roiDicomfile[phase]
dicomfilepath = os.path.join(lesionpath, lesionDicomFn)
dicomImage = Read2DImage(dicomfilepath)
if fnmatch.fnmatch(phase, '*CC'):
for eachpt in CCwindowptlist:
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
xcoord = int(eachpt[0])
ycoord = int(eachpt[1])
# boundaryornot = int(eachpt[2])
aFeature = [
patientID, lesionDicomFn, roiccxml, phase, xcoord,
ycoord
]
subImage = dicomImage[ycoord - 4:ycoord + 4,
xcoord - 4:xcoord + 4]
subshape = numpy.shape(subImage)
if subshape[0] != 8 or subshape[1] != 8:
continue
subImageGLCM = GrayScaleNormalization(
subImage, subImage.max(), subImage.min())
# get normalized to 0, 255: raw mean and standard deviation
Raw_mean, Raw_std = Norm_Mean_Std_LargestBox(
subImage, subImage.max(), subImage.min())
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
GLCM.append(glcmFeatures[GLCMAngle][featureName])
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 - LBPRadius:ycoord +
4 + LBPRadius, xcoord - 4 -
LBPRadius:xcoord + 4 + LBPRadius]
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImage.max(), subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord - 4, ycoord - 4, 8, 8,
Gaborkernel_bank, subImage.max(), subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
TAfeatures = GLCM + LBP + Gabor + meanstd
if TAfeatures == None:
continue
aFeature = aFeature + TAfeatures
featureWriter.writerow(aFeature)
else:
for eachpt in MLOwindowptlist:
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
xcoord = int(eachpt[0])
ycoord = int(eachpt[1])
#boundaryornot = int(eachpt[2])
aFeature = [
patientID, lesionDicomFn, roimloxml, phase, xcoord,
ycoord
]
subImage = dicomImage[ycoord - 4:ycoord + 4,
xcoord - 4:xcoord + 4]
subshape = numpy.shape(subImage)
# print subshape
# for some box, it is nearly boundary of image, like Pt36, it cannot generate 8*8 box
if subshape[0] != 8 or subshape[1] != 8:
continue
subImageGLCM = GrayScaleNormalization(
subImage, subImage.max(), subImage.min())
# get normalized to 0, 255: raw mean and standard deviation
Raw_mean, Raw_std = Norm_Mean_Std_LargestBox(
subImage, subImage.max(), subImage.min())
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
GLCM.append(glcmFeatures[GLCMAngle][featureName])
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 - LBPRadius:ycoord +
4 + LBPRadius, xcoord - 4 -
LBPRadius:xcoord + 4 + LBPRadius]
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImage.max(), subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord - 4, ycoord - 4, 8, 8,
Gaborkernel_bank, subImage.max(), subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
TAfeatures = GLCM + LBP + Gabor + meanstd
if TAfeatures == None:
continue
aFeature = aFeature + TAfeatures
featureWriter.writerow(aFeature)
def genTextures():
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (1.0, 2.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = ['PatientID']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['Raw_Mean', 'Raw_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
featuresCSVFn = os.path.join(outputDir, filename)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for casefile in os.listdir(rootDir):
if casefile.startswith('.'):
continue
if casefile.startswith('..'):
continue
if fnmatch.fnmatch(casefile, '*Icon*'):
continue
# casefile = '20586908_0.jpg'
casename = casefile.split('.')[0]
print casename
casefilepath = os.path.join(rootDir, casefile)
subImage = Read2DImage(casefilepath)
# height = subImage.shape[1]
# width = subImage.shape[0]
#
# xcoord = 5
# ycoord = 5
# subImage = dicomImage[ycoord:(ycoord + height), xcoord:(xcoord + width)] # errors here: before: Y + W
#
# subImageLBP = dicomImage[ycoord - LBPRadius:(ycoord + height) + LBPRadius,
# xcoord - LBPRadius:(xcoord + width) + LBPRadius]
# subImageGLCM = GrayScaleNormalization(subImage, subImage.max(), subImage.min())
# for extended LBP, we still use grayscale range of 8*8 box to normalize extended ROI 10*10 box
# extendsubImageLBP = GrayScaleNormalization(subImage, subImage.max(), subImage.min())
aFeature = [casename]
## get mean and standard deviation of lesion ROI's gray level of lagest box directly from subImage
Raw_mean = numpy.mean(subImage)
Raw_std = numpy.std(subImage)
# SubImagelist = list()
# SubImageArraylist = subImage.tolist()
# for smalllist in SubImageArraylist:
# SubImagelist += smalllist
#
# Raw_kurtosis = kurtosis(SubImagelist)
# Raw_skewness = skew(SubImagelist)
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImage)
# print glcmFeatures
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
# LBP
lbpFeatures = ExtendLBPFeatures.calcFeatures(
subImage, LBPnPoints, LBPRadius, LBPMethod)
# print lbpFeatures
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = KRAS_GaborFeatures.calcFeatures(
subImage, Gaborkernel_bank)
# GaborFeatures = GB.calcFeatures(subImage,Gaborsigma_range,Gaborfreq_range)
#
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
#
aFeature = aFeature + [Raw_mean, Raw_std]
featureWriter.writerow(aFeature)
def genFeatures(dualRescaleOption=True):
# dualRescaleOption: whether use both lesion and normal ROI for grayscale normalization
# If 'False', use only lesion image
# default value is 'True'
# Parameters and feature list of each algorithm
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
# LoGHSigmaList = numpy.arange(2, 7, 2, dtype=numpy.float)
# LogHFeatureList = ['LoGH_Mean', 'LoGH_Variance', 'LoGH_Skewness', 'LoGH_Kurtosis', 'LoGH_Entropy',
# 'LoGH_Uniformity']
# Gaborsigma_range = numpy.arange(1, 6, 2)
# Gaborfreq_range = numpy.round(numpy.arange(0.1, 0.6, 0.2), 2)
#kernel_bank = []
#Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(Gaborsigma_range, Gaborfreq_range, kernel_bank)
# GaborSigmaRange = (1.0, 3.0)
# GaborFreqRange = (0.1, 0.3, 0.5)
#GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = ['PatientID', 'Phase', 'ROI_Y', 'ROI_X', 'Width', 'Height']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
# for GaborSigma in Gaborsigma_range:
# for GaborFreq in Gaborfreq_range:
# for featureName in GaborFeatureList:
# featureTitle.append(featureName + '_' + str(GaborSigma) + '_' + str(GaborFreq))
MeanStdLBfeaturelist = ['LargestBox_Mean', 'LargestBox_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for patientPhaseDir in os.listdir(rootDir):
if patientPhaseDir.startswith('.') or \
os.path.isfile(os.path.join(rootDir, patientPhaseDir)):
continue
print patientPhaseDir
if fnmatch.fnmatch(patientPhaseDir, '*20160212*'):
patientID = '20160212'
else:
patientID = patientPhaseDir.split('_')[2]
if fnmatch.fnmatch(patientPhaseDir, '*ADC*'):
phasename = 'ADC'
elif fnmatch.fnmatch(patientPhaseDir, '*TRACEW*'):
phasename = 'TRACEW'
else:
phasename = 'FOV'
#print('Processing %s @ %s ...' % (patientID, phaseName))
lesionPath = os.path.join(rootDir, patientPhaseDir, lesionFolder)
normalPath = os.path.join(rootDir, patientPhaseDir, normalFolder)
# DICOM file name with absolute path
lesionDicom = os.path.join(lesionPath, lesionDicomFn)
normalDicom = os.path.join(normalPath, normalDicomFn)
# ROI file name with absolute path
lesionROICoords = os.path.join(lesionPath, roiCoordsFn)
normalROICoords = os.path.join(normalPath, roiCoordsFn)
# Largest rectangle file name with absolute path
lesionROIRectFn = os.path.join(lesionPath, lesionroiFn)
if (not os.path.isfile(lesionDicom)) or \
(not os.path.isfile(normalDicom)) or \
(not os.path.isfile(lesionROICoords)) or \
(not os.path.isfile(normalROICoords)) or \
(not os.path.isfile(normalROICoords)): # If any of the file is missing, skip
print('Missing File for %s @ %s.' % (patientID, phasename))
continue
dualROIGrayLevels = numpy.array([])
with open(lesionROICoords, 'r') as roiCoordsFile:
roiCoordsList = csv.reader(roiCoordsFile, delimiter=';')
for row in roiCoordsList:
dualROIGrayLevels = numpy.append(dualROIGrayLevels, int(row[2]))
if (dualRescaleOption):
with open(normalROICoords, 'r') as roiCoordsFile:
roiCoordsList = csv.reader(roiCoordsFile, delimiter=';')
for row in roiCoordsList:
dualROIGrayLevels = numpy.append(dualROIGrayLevels, int(row[2]))
with open(lesionROIRectFn, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
if (int(aROI['Y']) == 1) and (int(aROI['X']) == 1):
print('Invalid ROI for %s @ %s.' % (patientID, phasename))
continue
dicomImage = Read2DImage(lesionDicom)
subImage = dicomImage[int(aROI['Y']):(int(aROI['Y']) + int(aROI['H'])), \
int(aROI['X']):(int(aROI['X']) + int(aROI['W']))]
subImageLBP = dicomImage[int(aROI['Y']) - LBPRadius:(int(aROI['Y']) + int(aROI['H'])) + LBPRadius, \
int(aROI['X']) - LBPRadius:(int(aROI['X']) + int(aROI['W'])) + LBPRadius]
mean_LargBox, std_LargBox = Mean_Std_LargestBox2(dicomImage, int(aROI['X']), int(aROI['Y']),
int(aROI['W']), int(aROI['H']))
subImage = GrayScaleNormalization(subImage, dualROIGrayLevels.ptp())
extendsubImageLBP = GrayScaleNormalization(subImageLBP,dualROIGrayLevels.ptp())
if numpy.all(subImage == 0):
print('%s @ %s is all zero.' % (patientID, phasename))
continue
aFeature = [patientID, phasename, aROI['Y'], aROI['X'], aROI['W'], aROI['H']]
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImage)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
# LBP
lbpFeatures = ExtendLBPFeatures.calcFeatures(extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
# GaborFeatures = ExtendGaborFeatures.calcFeatures(subImage, int(aROI['W']), Gaborkernel_bank)
#
# for gaborfeature in GaborFeatures:
# aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox]
featureWriter.writerow(aFeature)
print('Done.')
def genFeatures(dualRescaleOption=True):
# dualRescaleOption: whether use both lesion and normal ROI for grayscale normalization
# If 'False', use only lesion image
# default value is 'True'
# Parameters and feature list of each algorithm
#GLCMAngleList = ['0', '45', '90', '135', 'Avg']
GLCMAngleList = ['Avg']
LBPRadius = 3
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
# LBPnBins = 12
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (1.0, 3.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = ['PatientID', 'Phase', 'ROI_Y', 'ROI_X', 'Width', 'Height']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['LargestBox_Mean', 'LargestBox_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for patientPhaseDir in os.listdir(rootDir):
if patientPhaseDir.startswith('.') or \
os.path.isfile(os.path.join(rootDir, patientPhaseDir)):
continue
patientID = patientPhaseDir.split('_ ')[0]
phaseName = patientPhaseDir.split('_ ')[1].split('_')[
1] # Only a simple parser, not always precise
print('Processing %s @ %s ...' % (patientID, phaseName))
lesionPath = os.path.join(rootDir, patientPhaseDir, lesionFolder)
normalPath = os.path.join(rootDir, patientPhaseDir, normalFolder)
# DICOM file name with absolute path
lesionDicom = os.path.join(lesionPath, lesionDicomFn)
normalDicom = os.path.join(normalPath, normalDicomFn)
# ROI file name with absolute path
lesionROICoords = os.path.join(lesionPath, roiCoordsFn)
normalROICoords = os.path.join(normalPath, roiCoordsFn)
# Largest rectangle file name with absolute path
lesionROIRectFn = os.path.join(lesionPath, roiFn)
if (not os.path.isfile(lesionDicom)) or \
(not os.path.isfile(normalDicom)) or \
(not os.path.isfile(lesionROICoords)) or \
(not os.path.isfile(normalROICoords)) or \
(not os.path.isfile(normalROICoords)): # If any of the file is missing, skip,
# To do: problem here
print('Missing File for %s @ %s.' % (patientID, phaseName))
continue
with open(lesionROIRectFn, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
if (int(aROI['Y']) == 1) and (int(aROI['X']) == 1):
print('Invalid ROI for %s @ %s.' %
(patientID, phaseName))
continue
lesiondicomImage = Read2DImage(lesionDicom)
normaldicomImage = Read2DImage(normalDicom)
xcoord = int(aROI['X'])
ycoord = int(aROI['Y'])
width = int(aROI['W'])
height = int(aROI['H'])
lesionsubImage = lesiondicomImage[ycoord:(ycoord + height),
xcoord:(xcoord + width)]
normalsubImage = normaldicomImage[ycoord:(ycoord + height),
xcoord:(xcoord + width)]
mean_LargBox = numpy.mean(lesionsubImage)
std_LargBox = numpy.std(lesionsubImage)
# get max gray scale and min grayscale from both lesion and normal dicom
lesionimageMax = lesionsubImage.max()
lesionimageMin = lesionsubImage.min()
normalimageMax = normalsubImage.max()
normalimageMin = normalsubImage.min()
# compare max and min and get max / min for normalization
if lesionimageMax > normalimageMax:
subImageMax = lesionimageMax
else:
subImageMax = normalimageMax
if lesionimageMin < normalimageMin:
subImageMin = lesionimageMin
else:
subImageMin = normalimageMin
subImageLBP = lesiondicomImage[
ycoord - LBPRadius:(ycoord + height) + LBPRadius,
xcoord - LBPRadius:(xcoord + width) + LBPRadius]
subImageGLCM = GrayScaleNormalization(
lesionsubImage, subImageMax, subImageMin)
if numpy.all(lesionsubImage == 0):
print('%s @ %s is all zero.' % (patientID, phaseName))
continue
aFeature = [
patientID, phaseName, aROI['Y'], aROI['X'], aROI['W'],
aROI['H']
]
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(
glcmFeatures[GLCMAngle][featureName])
# LBP
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImageMax, subImageMin)
lbpFeatures = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = ExtendGaborFeatures.calcFeatures(
lesiondicomImage, xcoord, ycoord, width, height,
Gaborkernel_bank, subImageMax, subImageMin)
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox]
featureWriter.writerow(aFeature)
print('Done.')
def genFeatures():
# Parameters and feature list of each algorithm
GLCMAngleList = ['Avg']
LBPRadius = 3
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (0.6, 1.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = MinACRExtendGaborFeatures.genKernelBank(Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std', 'Gabor_Kurtosis', 'Gabor_Skewness']
# Generate full list of features combined with parameters
featureTitle = ['PatientID', 'ROI_Y', 'ROI_X', 'Width', 'Height']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' + str(GaborFreq))
MeanStdLBfeaturelist = ['LargestBox_Mean','LargestBox_Std','LargestBox_Kurtosis','LargestBox_Skewness']
featureTitle = featureTitle + MeanStdLBfeaturelist
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for ACRfolder in os.listdir(rootDir):
if ACRfolder.startswith('.'):
continue
if ACRfolder.startswith('..'):
continue
patientid = ACRfolder.split('_')[0] + ACRfolder.split('_')[1]
ACRpath = os.path.join(rootDir,ACRfolder)
for lesionfolder in os.listdir(ACRpath):
if lesionfolder.startswith('.'):
continue
if lesionfolder.startswith('..'):
continue
ACRlesionpath = os.path.join(ACRpath,lesionfolder)
# get timepoint folder path
timepointpath1 = os.path.join(ACRlesionpath, timepointlist[0])
timepointpath2 = os.path.join(ACRlesionpath, timepointlist[1])
timepointpath3 = os.path.join(ACRlesionpath, timepointlist[2])
timepointpath4 = os.path.join(ACRlesionpath, timepointlist[3])
# get lesion dicom file path
lesionDicom1 = os.path.join(timepointpath1, dicomfile)
lesionDicom2 = os.path.join(timepointpath2, dicomfile)
lesionDicom3 = os.path.join(timepointpath3, dicomfile)
lesionDicom4 = os.path.join(timepointpath4, dicomfile)
# get image gray scale from each dicom file
dicomImage1 = Read2DImage(lesionDicom1)
dicomImage2 = Read2DImage(lesionDicom2)
dicomImage3 = Read2DImage(lesionDicom3)
dicomImage4 = Read2DImage(lesionDicom4)
# get largest box coordinate
lesionROIRectFn1 = os.path.join(timepointpath1, largestboxfile)
lesionROIRectFn2 = os.path.join(timepointpath2, largestboxfile)
lesionROIRectFn3 = os.path.join(timepointpath3, largestboxfile)
lesionROIRectFn4 = os.path.join(timepointpath4, largestboxfile)
# get subimage and subimage LBP from dicom image of 4 time points
with open(lesionROIRectFn1, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
xcoord1 = int(aROI['X'])
ycoord1 = int(aROI['Y'])
width1 = int(aROI['W'])
height1 = int(aROI['H'])
subImage1 = dicomImage1[ycoord1:ycoord1 + height1, xcoord1:xcoord1 + width1]
subImageLBP1 = dicomImage1[ycoord1 - LBPRadius:(ycoord1 + height1) + LBPRadius, xcoord1 - LBPRadius:(xcoord1 + width1) + LBPRadius]
with open(lesionROIRectFn2, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
xcoord2 = int(aROI['X'])
ycoord2 = int(aROI['Y'])
width2 = int(aROI['W'])
height2 = int(aROI['H'])
subImage2 = dicomImage2[ycoord2:ycoord2 + height2, xcoord2:xcoord2 + width2]
subImageLBP2 = dicomImage2[ycoord2 - LBPRadius:(ycoord2 + height2) + LBPRadius, xcoord2 - LBPRadius:(xcoord2 + width2) + LBPRadius]
with open(lesionROIRectFn3, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
xcoord3 = int(aROI['X'])
ycoord3 = int(aROI['Y'])
width3 = int(aROI['W'])
height3 = int(aROI['H'])
subImage3 = dicomImage3[ycoord3:ycoord3 + height3, xcoord3:xcoord3 + width3]
subImageLBP3 = dicomImage3[ycoord3 - LBPRadius:(ycoord3 + height3) + LBPRadius, xcoord3 - LBPRadius:(xcoord3 + width3) + LBPRadius]
with open(lesionROIRectFn4, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
xcoord4 = int(aROI['X'])
ycoord4 = int(aROI['Y'])
width4 = int(aROI['W'])
height4 = int(aROI['H'])
subImage4 = dicomImage4[ycoord4:ycoord4 + height4, xcoord4:xcoord4 + width4]
subImageLBP4 = dicomImage4[ycoord4 - LBPRadius:(ycoord4 + height4) + LBPRadius, xcoord4 - LBPRadius:(xcoord4 + width4) + LBPRadius]
# generate min/max image matrix (same width and height in 4 matrix)
MinSubImage,MaxSubImage = MinMaxSubImageGen(subImage1,subImage2,subImage3,subImage4,height1,width1)
# minsize = numpy.shape(MinImage)
# maxsize = numpy.shape(MaxImage)
# print 'original:',minsize,maxsize
# get extended LBP height, width
LBPheight = height1 + 2*LBPRadius
LBPwidth = width1 + 2*LBPRadius
# get min/ max LBP subimage from 4 LBP subimages
MinLBPSubImage,MaxLBPSubImage = MinMaxSubImageGen(subImageLBP1,subImageLBP2,subImageLBP3,subImageLBP4, LBPheight,LBPwidth)
# LBPminsize = numpy.shape(MinLBPImage)
# LBPmaxsize = numpy.shape(MaxLBPImage)
# print 'LBP:',LBPminsize,LBPmaxsize
# get raw mean/ std from min subimage
mean_LargBox = numpy.mean(MinSubImage)
std_LargBox = numpy.std(MinSubImage)
# add Kurtosis and Skewness into Raw Features
MinSubImagelist = list()
MinSubImageArraylist = MinSubImage.tolist()
for smalllist in MinSubImageArraylist:
MinSubImagelist += smalllist
Kurtosis_LargBox = kurtosis(MinSubImagelist)
Skewness_LargBox = skew(MinSubImagelist)
# normalized original subimage, GLCM can use this
subImageGLCM = GrayScaleNormalization(MinSubImage, MinSubImage.max(), MinSubImage.min())
# print subImageGLCM
# for extended LBP, we still use grayscale range of 8*8 box to normalize extended ROI 10*10 box (LBP radius = 1)
extendsubImageLBP = GrayScaleNormalization(MinLBPSubImage, MinSubImage.max(), MinSubImage.min())
if numpy.all(MinSubImage == 0):
print('%s @ %s is all zero.' % (patientid))
continue
aFeature = [patientid, ycoord1,xcoord1,width1,height1]
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
# LBP
# need to use extended ROI
lbpFeatures = ExtendLBPFeatures.calcFeatures(extendsubImageLBP, LBPnPoints, LBPRadius, LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = MinACRExtendGaborFeatures.calcFeatures(dicomImage1,dicomImage2,dicomImage3,dicomImage4, xcoord1, ycoord1, xcoord2,
ycoord2,xcoord3,ycoord3,xcoord4,ycoord4, width1, height1, Gaborkernel_bank, MinSubImage.max(), MinSubImage.min())
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox,Kurtosis_LargBox,Skewness_LargBox]
featureWriter.writerow(aFeature)
imgFilename = row[1]
print imgFilename
ycoord = int(float(row[2]))
print ycoord
xcoord = int(float(row[3]))
print xcoord
aFeature = [imgContrastname, imgFilename, ycoord, xcoord]
dicomfile = os.path.join(mapfileDir,imgFilename)
dicomImage = Read2DImage(dicomfile)
subImage = dicomImage[ycoord - 4:ycoord + 4, xcoord - 4:xcoord + 4]
subImageGLCM = GrayScaleNormalization(subImage, subImage.max(), subImage.min())
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(glcmFeatures[GLCMAngle][featureName])
featureWriter.writerow(aFeature)
def genFeatures():
# dualRescaleOption: whether use both lesion and normal ROI for grayscale normalization
# If 'False', use only lesion image
# default value is 'True'
# Parameters and feature list of each algorithm
GLCMAngleList = ['0', '45', '90', '135', 'Avg']
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (1.0, 2.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = ['PatientID', 'Phase', 'ROI_Y', 'ROI_X', 'Width', 'Height']
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['LargestBox_Mean', 'LargestBox_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist
shapetitlelist = [
'compactness', 'entropy', 'bending energy', 'ratio(min/max)'
]
featureTitle = featureTitle + shapetitlelist
# List all dicom files and generate features for each images
# Feature results stored in separate csv files for each folder
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
casefilenum = 0
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for casefile in os.listdir(rootDir):
if casefile.startswith('.'):
continue
if casefile.startswith('..'):
continue
if fnmatch.fnmatch(casefile, '*Icon*'):
continue
if casefile == 'M24 - M24':
continue
if casefile == 'M5 - M5':
continue
print '\n'
print casefile
casefilenum += 1
patientid = casefile.split('-')[0]
patientfolderpath = os.path.join(rootDir, casefile)
for patientfolder in os.listdir(patientfolderpath):
if patientfolder.startswith('.'):
continue
if patientfolder.startswith('..'):
continue
if fnmatch.fnmatch(patientfolder, '*Icon*'):
continue
if fnmatch.fnmatch(patientfolder, '*roi*'):
continue
Dfolderpath = os.path.join(patientfolderpath, patientfolder)
for phasefolder in os.listdir(Dfolderpath):
phasefolderpath = os.path.join(Dfolderpath, phasefolder)
if phasefolder.startswith('.'):
continue
if phasefolder.startswith('..'):
continue
if phasefolder.startswith('*Icon*'):
continue
if os.path.isfile(phasefolderpath):
continue
print phasefolder
phase1 = phasefolder.split('-')[0].replace(' ', '')
if fnmatch.fnmatch(phase1, '*CC*DES*'):
phasename = 'CC DES'
elif fnmatch.fnmatch(phase1, '*CC*LE*'):
phasename = 'CC LE'
elif fnmatch.fnmatch(phase1, '*MLO*DES*'):
phasename = 'MLO DES'
elif fnmatch.fnmatch(phase1, '*MLO*LE*'):
phasename = 'MLO LE'
elif fnmatch.fnmatch(phase1, '*LM*DES*'):
phasename = 'LM DES'
else:
phasename = 'LM LE'
rectfile = ''
contourfile = ''
dicomfile = ''
for file in os.listdir(phasefolderpath):
if fnmatch.fnmatch(file, '*texture*'):
continue
if fnmatch.fnmatch(file, '*(1)*'):
continue
if fnmatch.fnmatch(file, '*largest_rec*'):
rectfile = file
if fnmatch.fnmatch(file, '*csv*') or fnmatch.fnmatch(
file, '*csv*'):
if not fnmatch.fnmatch(file, '*largest_rec*'):
contourfile = file
if fnmatch.fnmatch(file, '*dcm*'):
dicomfile = file
#print rectfile,contourfile,dicomfile
recpath = os.path.join(phasefolderpath, rectfile)
contourpath = os.path.join(phasefolderpath, contourfile)
dicompath = os.path.join(phasefolderpath, dicomfile)
shapedescriptors = ROI_ShapeAnalysis_92.genShapefeatures(
contourpath)
with open(recpath, 'r') as roiFile:
roiList = csv.DictReader(roiFile, dialect='excel')
for aROI in roiList:
if (int(aROI['Y']) == 1) and (int(aROI['X']) == 1):
print('Invalid ROI for %s @ %s.' %
(patientid, phasename))
continue
xcoord = int(aROI['X'])
ycoord = int(aROI['Y'])
width = int(aROI['W'])
height = int(aROI['H'])
dicomImage = Read2DImage(dicompath)
subImage = dicomImage[ycoord:(
ycoord + height), xcoord:(
xcoord +
width)] # errors here: before: Y + W
subImageLBP = dicomImage[
ycoord - LBPRadius:(ycoord + height) +
LBPRadius, xcoord -
LBPRadius:(xcoord + width) + LBPRadius]
mean_LargBox = numpy.mean(subImage)
std_LargBox = numpy.std(subImage)
subImageGLCM = GrayScaleNormalization(
subImage, subImage.max(), subImage.min())
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImage.max(), subImage.min())
if numpy.all(subImage == 0):
print('%s @ %s is all zero.' %
(patientid, phasename))
continue
aFeature = [
patientid, phasename, aROI['Y'], aROI['X'],
aROI['W'], aROI['H']
]
# GLCM
# dont need to extended ROI
glcmFeatures = GLCMFeatures.calcFeatures(
subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
aFeature.append(
glcmFeatures[GLCMAngle][featureName])
# LBP
# need to use extended ROI
lbpFeatures = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius,
LBPMethod)
aFeature = aFeature + lbpFeatures.tolist()
# Gabor
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord, ycoord, width,
height, Gaborkernel_bank, subImage.max(),
subImage.min())
for gaborfeature in GaborFeatures:
aFeature = aFeature + gaborfeature.tolist()
aFeature = aFeature + [mean_LargBox, std_LargBox]
aFeature = aFeature + shapedescriptors
featureWriter.writerow(aFeature)
def genFeatures():
# Parameters and feature list of each algorithm
GLCMAngleList = ['Avg']
LBPRadius = 1
LBPnPoints = 8 * LBPRadius
LBPMethod = 'uniform'
LBPFeatureList = []
for x in xrange(0, LBPnPoints + 1):
LBPFeatureList.append('LBP_%02d' % x)
LBPFeatureList.append('LBP_Other')
Gaborsigma_range = (0.6, 1.0)
Gaborfreq_range = (0.1, 0.3, 0.5)
kernel_bank = []
Gaborkernel_bank = ExtendGaborFeatures.genKernelBank(
Gaborsigma_range, Gaborfreq_range, kernel_bank)
GaborFeatureList = ['Gabor_Mean', 'Gabor_Std']
# Generate full list of features combined with parameters
featureTitle = [
'PatientID', 'Dicom Image Filename', 'Xml Filename', 'Phase Name', 'X',
'Y', 'Boundary (1) or not (inside: 0)'
]
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
featureTitle.append(featureName + '_' + GLCMAngle)
featureTitle = featureTitle + LBPFeatureList
for GaborSigma in Gaborsigma_range:
for GaborFreq in Gaborfreq_range:
for featureName in GaborFeatureList:
featureTitle.append(featureName + '_' + str(GaborSigma) + '_' +
str(GaborFreq))
MeanStdLBfeaturelist = ['Raw_Mean', 'Raw_Std']
featureTitle = featureTitle + MeanStdLBfeaturelist + ['Ylabel']
for eachptfolder in os.listdir(rootDir):
if eachptfolder.startswith('.'):
continue
if eachptfolder.startswith('..'):
continue
if fnmatch.fnmatch(eachptfolder, '*Icon*'):
continue
if eachptfolder == 'M24 - M24':
continue
if eachptfolder == 'M5 - M5':
continue
# ptnum+=1
print('\n')
# print eachptfolder
patientID = eachptfolder.split('-')[0]
print patientID
if fnmatch.fnmatch(eachptfolder, '*B*'):
twofolder = 'benign'
else:
twofolder = 'malignant'
rootDir2 = os.path.join(rootDir, eachptfolder)
for folder2 in os.listdir(rootDir2):
if folder2.startswith('.'):
continue
if folder2.startswith('..'):
continue
if fnmatch.fnmatch(folder2, '*Icon*'):
continue
if fnmatch.fnmatch(folder2, '*roi*'):
continue
# print folder2
rootDir3 = os.path.join(rootDir2, folder2)
ccxmlfile = list()
mloxmlfile = list()
roiDicomfile = dict()
roiDicomfolder = dict()
phasefolderpath = ''
for xmlcasefolder in os.listdir(rootDir3):
phasefolderpath = os.path.join(rootDir3, xmlcasefolder)
if xmlcasefolder.startswith('.'):
continue
if xmlcasefolder.startswith('..'):
continue
if fnmatch.fnmatch(xmlcasefolder, '*Icon*'):
continue
if fnmatch.fnmatch(xmlcasefolder, '*CC*xml'):
ccxmlfile.append(xmlcasefolder)
print ccxmlfile
# xmlnum+=1
if fnmatch.fnmatch(xmlcasefolder, '*MLO*xml'):
mloxmlfile.append(xmlcasefolder)
print mloxmlfile
# xmlnum+=1
if os.path.isdir(phasefolderpath):
roiDicomfile, roiDicomfolder = finddcmfile(
phasefolderpath, xmlcasefolder, roiDicomfile,
roiDicomfolder)
roiccxmlpath = os.path.join(rootDir3, ccxmlfile[0])
roimloxmlpath = os.path.join(rootDir3, mloxmlfile[0])
CCxmin, CCxmax, CCymin, CCymax, CCxycoord = ParseXMLDrawROI(
roiccxmlpath)
MLOxmin, MLOxmax, MLOymin, MLOymax, MLOxycoord = ParseXMLDrawROI(
roimloxmlpath)
# check if coords inside boundary or outside boundary
CCwindowptlist = chooseinoutcoord(CCxmin, CCxmax, CCymin, CCymax,
CCxycoord)
MLOwindowptlist = chooseinoutcoord(MLOxmin, MLOxmax, MLOymin,
MLOymax, MLOxycoord)
featuresOutFn = 'ROI_Texture_Map.csv'
# start to do T2
featuresOutFn = patientID + '_' + twofolder + '_' + featuresOutFn
featuresCSVFn = os.path.join(outputDir, featuresOutFn)
phasenames = ['DES-CC', 'LE-CC', 'DES-MLO', 'LE-MLO']
with open(featuresCSVFn, 'wb') as featureCSVFile:
featureWriter = csv.writer(featureCSVFile, dialect='excel')
featureWriter.writerow(featureTitle)
for phase in phasenames:
print phase
lesionDicomFn = roiDicomfile[phase]
lesionDicomFolder = roiDicomfolder[phase]
lesionDicomFolderpath = os.path.join(
rootDir3, lesionDicomFolder)
dicomfilepath = os.path.join(lesionDicomFolderpath,
lesionDicomFn)
dicomImage = Read2DImage(dicomfilepath)
if fnmatch.fnmatch(phase, '*CC'):
for eachpt in CCwindowptlist:
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
xcoord = int(eachpt[0])
ycoord = int(eachpt[1])
boundaryornot = int(eachpt[2])
aFeature = [
patientID, lesionDicomFn, ccxmlfile[0], phase,
xcoord, ycoord, boundaryornot
]
subImage = dicomImage[ycoord - 4:ycoord + 4,
xcoord - 4:xcoord + 4]
subshape = numpy.shape(subImage)
if subshape[0] != 8 or subshape[1] != 8:
continue
subImageGLCM = GrayScaleNormalization(
subImage, subImage.max(), subImage.min())
# get normalized to 0, 255: raw mean and standard deviation
Raw_mean, Raw_std = Norm_Mean_Std_LargestBox(
subImage, subImage.max(), subImage.min())
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(
subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
GLCM.append(
glcmFeatures[GLCMAngle][featureName])
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 -
LBPRadius:ycoord + 4 +
LBPRadius, xcoord - 4 -
LBPRadius:xcoord + 4 +
LBPRadius]
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImage.max(), subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius,
LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord - 4, ycoord - 4, 8,
8, Gaborkernel_bank, subImage.max(),
subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
TAfeatures = GLCM + LBP + Gabor + meanstd
if TAfeatures == None:
continue
aFeature = aFeature + TAfeatures
featureWriter.writerow(aFeature)
else:
for eachpt in MLOwindowptlist:
meanstd = list()
GLCM = list()
LBP = list()
Gabor = list()
xcoord = int(eachpt[0])
ycoord = int(eachpt[1])
boundaryornot = int(eachpt[2])
aFeature = [
patientID, lesionDicomFn, mloxmlfile[0], phase,
xcoord, ycoord, boundaryornot
]
subImage = dicomImage[ycoord - 4:ycoord + 4,
xcoord - 4:xcoord + 4]
subshape = numpy.shape(subImage)
# print subshape
# for some box, it is nearly boundary of image, like Pt36, it cannot generate 8*8 box
if subshape[0] != 8 or subshape[1] != 8:
continue
subImageGLCM = GrayScaleNormalization(
subImage, subImage.max(), subImage.min())
# get normalized to 0, 255: raw mean and standard deviation
Raw_mean, Raw_std = Norm_Mean_Std_LargestBox(
subImage, subImage.max(), subImage.min())
meanstd.append(Raw_mean)
meanstd.append(Raw_std)
# GLCM
glcmFeatures = GLCMFeatures.calcFeatures(
subImageGLCM)
for GLCMAngle in GLCMAngleList:
for featureName in haralick_labels[:-1]:
GLCM.append(
glcmFeatures[GLCMAngle][featureName])
# LBP subimage
subImageLBP = dicomImage[ycoord - 4 -
LBPRadius:ycoord + 4 +
LBPRadius, xcoord - 4 -
LBPRadius:xcoord + 4 +
LBPRadius]
extendsubImageLBP = GrayScaleNormalization(
subImageLBP, subImage.max(), subImage.min())
# need to use extended ROI
LBPs = ExtendLBPFeatures.calcFeatures(
extendsubImageLBP, LBPnPoints, LBPRadius,
LBPMethod)
for lbp in LBPs:
LBP.append(lbp)
# Gabor, width = 8
# use extended ROI
GaborFeatures = ExtendGaborFeatures.calcFeatures(
dicomImage, xcoord - 4, ycoord - 4, 8,
8, Gaborkernel_bank, subImage.max(),
subImage.min())
for gaborfeature in GaborFeatures:
for eachg in gaborfeature:
Gabor.append(eachg)
TAfeatures = GLCM + LBP + Gabor + meanstd
if TAfeatures == None:
continue
aFeature = aFeature + TAfeatures
featureWriter.writerow(aFeature)
