class TestAllNewContour(MacroBase):
def getName(self):
return 'Test All Contour Error Without Registration'
def run(self, window = None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.contourweigherror = WeightedContourErrorAnalysis(None)
self.areaerror = AreaIndexAnalysis(None)
self.centerlineerror = CenterlineErrorAnalysis(None)
self.savepath = 'D:/ResultData/'
self.dirs = ['icp-cen-clip-nolabel/', 'icp-cen-noclip-label/', 'icp-surface-clip-label/', 'icp-surface-noclip-nolabel/']
self.type = ['_icp_cen.mat', '_icp_cen.mat', '_icp_con.mat', '_icp_con.mat']
self.book = xlwt.Workbook()
self.sheet = self.book.add_sheet('icp_cen')
self.sheet.write(1, 0, 'MRE')
self.sheet.write(2, 0, 'AMRE')
self.sheet.write(3, 0, 'WMRE')
self.sheet.write(4, 0, 'AWMRE')
for k in range(4):
for i in range(self.cnt):
dataset = self.load(k, i)
self.process(dataset, k, i)
del dataset
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, k, i):
dataset = {'result': [], 'fix': []}
data, info, point = db.loadMatData(self.savepath + self.dirs[k]
+ self.ini.file.name_result[i] + self.type[k], None)
dataset['result'] = db.BasicData(data, info, point)
data, info, point = db.loadMatData(self.path + self.ini.file.datadir + '/Contour/'
+ self.ini.file.name_fix[i] + '.mat', None)
dataset['fix'] = db.BasicData(data, info, point)
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, k, i):
self.sheet.write(0, k * 20 + i + 1, self.ini.file.name_result[i] + str(k))
print 'Evaluation Data %s...' % self.ini.file.name_result[i]
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(dataset['result'], dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(1, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourareaerror.analysis(dataset['result'], dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(2, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourweigherror.analysis(dataset['result'], dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(3, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourweigherror.analysis(dataset['result'], dataset['fix'].getPointSet('Contour').copy(), True)
self.sheet.write(4, k * 20 + i + 1, mean_whole)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
self.book.save(self.path + self.ini.file.savedir + 'Test_weighted.xls')
class TestSegmentationRate(MacroBase):
def getName(self):
return 'Test Segmentation Distance Error'
def run(self, window=None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.savepath = self.path + self.ini.file.savedir
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.result = [{}, {}, {}]
self.resultCnt = [{}, {}, {}]
self.correct = npy.array([0.0, 0.0, 0.0])
self.count = npy.array([0, 0, 0])
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
print self.correct / self.count, npy.sum(self.correct) / npy.sum(
self.count)
'''
for cnt in range(3):
for x in self.result[cnt].keys():
self.result[cnt][x] /= self.resultCnt[cnt][x]
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA']
self.sheet = self.book.add_sheet('Distance_error')
for i in range(3):
self.sheet.write(i + 1, 0, title[i])
zmin = [0, 0, 0]
zmax = [0, 0, 0]
for cnt in range(3):
zmin[cnt] = min(self.result[cnt].keys())
zmax[cnt] = max(self.result[cnt].keys())
z1 = int(min(zmin))
z2 = int(max(zmax))
for z in range(z1, z2 + 1):
self.sheet.write(0, z - z1 + 1, z * 0.34722220897674)
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 1, int(x) - z1 + 1, self.result[cnt][x])
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 4, int(x) - z1 + 1, self.resultCnt[cnt][x])
self.book.save(self.path + self.ini.file.savedir + 'Distance_error_segmentation.xls')
'''
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': [], 'seg': []}
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + '/Contour/' +
self.ini.file.name_fix[i] + '.mat', None)
fileData = db.BasicData(data, info, point)
dataset['fix'] = fileData
data, info, point = db.loadMatData(
self.savepath + self.ini.file.name_result[i] + '_mr.mat', None)
fileData = db.BasicData(data, info, point)
dataset['seg'] = fileData
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
print 'Evaluation Data %s...' % self.ini.file.name_result[i]
mean_dis, mean_whole, max_dis, max_whole, result = self.contourerror.analysis(
dataset['seg'], dataset['fix'].getPointSet('Contour').copy(), True)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
for cnt in range(3):
for x in result[cnt].keys():
#self.result[cnt][x] = self.result[cnt].get(x, 0) + result[cnt][x]
#self.resultCnt[cnt][x] = self.resultCnt[cnt].get(x, 0) + 1
self.count[cnt] += 1
if result[cnt][x] <= 1.50:
self.correct[cnt] += 1
class TestAllNewContourReg(MacroBase):
def getName(self):
return 'Test All Contour Error With Registration'
def run(self, window = None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.icp = IcpPointsetRegistration(None)
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.contourweigherror = WeightedContourErrorAnalysis(None)
self.areaerror = AreaIndexAnalysis(None)
self.centerlineerror = CenterlineErrorAnalysis(None)
self.savepath = 'D:/ResultData/'
self.dirs = ['icp-cen-clip-nolabel/', 'icp-cen-noclip-label/', 'icp-surface-clip-label/', 'icp-surface-noclip-nolabel/']
self.type = ['_icp_cen.mat', '_icp_cen.mat', '_icp_con.mat', '_icp_con.mat']
self.book = xlwt.Workbook()
self.sheet = self.book.add_sheet('icp_cen')
self.sheet.write(1, 0, 'MRE')
self.sheet.write(2, 0, 'AMRE')
self.sheet.write(3, 0, 'WMRE')
self.sheet.write(4, 0, 'AWMRE')
for k in range(4):
for i in range(self.cnt):
dataset = self.load(k, i)
self.process(dataset, k, i)
del dataset
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, k, i):
dataset = {'mov': [], 'fix': []}
data, info, point = db.loadMatData(self.path + self.ini.file.datadir + '/Contour/'
+ self.ini.file.name_fix[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['fix'] = fileData
data, info, point = db.loadMatData(self.path + self.ini.file.datadir + '/Contour/'
+ self.ini.file.name_mov[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['mov'] = fileData
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, k, i):
self.sheet.write(0, k * 20 + i + 1, self.ini.file.name_result[i] + str(k))
print 'Register Data %s...' % self.ini.file.name_result[i]
if k == 0:
data, point, para = self.icp.register(dataset['fix'], dataset['mov'], 1, op = True)
elif k == 1:
data, point, para = self.icp.register(dataset['fix'], dataset['mov'], 1)
elif k == 2:
data, point, para = self.icp.register(dataset['fix'], dataset['mov'], 0, op = True)
else:
data, point, para = self.icp.register(dataset['fix'], dataset['mov'], 0)
resultData = db.ResultData(data, db.ImageInfo(dataset['fix'].info.data), point)
resultData.info.addData('fix', 1)
resultData.info.addData('move', 2)
resultData.info.addData('transform', para)
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(resultData, dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(1, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourareaerror.analysis(resultData, dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(2, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourweigherror.analysis(resultData, dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(3, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourweigherror.analysis(resultData, dataset['fix'].getPointSet('Contour').copy(), True)
self.sheet.write(4, k * 20 + i + 1, mean_whole)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
self.book.save(self.path + self.ini.file.savedir + 'AllTest.xls')
del data, point, resultData, para
class TestAllNewContour(MacroBase):
def getName(self):
return 'Test All Contour Error Without Registration'
def run(self, window=None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.contourweigherror = WeightedContourErrorAnalysis(None)
self.areaerror = AreaIndexAnalysis(None)
self.centerlineerror = CenterlineErrorAnalysis(None)
self.savepath = 'D:/ResultData/'
self.dirs = [
'icp-cen-clip-nolabel/', 'icp-cen-noclip-label/',
'icp-surface-clip-label/', 'icp-surface-noclip-nolabel/'
]
self.type = [
'_icp_cen.mat', '_icp_cen.mat', '_icp_con.mat', '_icp_con.mat'
]
self.book = xlwt.Workbook()
self.sheet = self.book.add_sheet('icp_cen')
self.sheet.write(1, 0, 'MRE')
self.sheet.write(2, 0, 'AMRE')
self.sheet.write(3, 0, 'WMRE')
self.sheet.write(4, 0, 'AWMRE')
for k in range(4):
for i in range(self.cnt):
dataset = self.load(k, i)
self.process(dataset, k, i)
del dataset
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, k, i):
dataset = {'result': [], 'fix': []}
data, info, point = db.loadMatData(
self.savepath + self.dirs[k] + self.ini.file.name_result[i] +
self.type[k], None)
dataset['result'] = db.BasicData(data, info, point)
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + '/Contour/' +
self.ini.file.name_fix[i] + '.mat', None)
dataset['fix'] = db.BasicData(data, info, point)
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, k, i):
self.sheet.write(0, k * 20 + i + 1,
self.ini.file.name_result[i] + str(k))
print 'Evaluation Data %s...' % self.ini.file.name_result[i]
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(
dataset['result'], dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(1, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourareaerror.analysis(
dataset['result'], dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(2, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourweigherror.analysis(
dataset['result'], dataset['fix'].getPointSet('Contour').copy())
self.sheet.write(3, k * 20 + i + 1, mean_whole)
mean_dis, mean_whole, max_dis, max_whole = self.contourweigherror.analysis(
dataset['result'], dataset['fix'].getPointSet('Contour').copy(),
True)
self.sheet.write(4, k * 20 + i + 1, mean_whole)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
self.book.save(self.path + self.ini.file.savedir + 'Test_weighted.xls')
class TestMissingRobust(MacroBase):
def getName(self):
return 'Test Missing Robustness'
def run(self, window = None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
#self.ini = DictIni(self.path + '/Script/Macro/test1.ini') # Remove 56L for small FOV
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.icp = IcpPointsetRegistration(None)
self.contourerror = ContourErrorAnalysis(None)
self.error = npy.zeros([10, 4], dtype = npy.float32)
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
self.error /= self.cnt
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA', 'Overall']
self.sheet = self.book.add_sheet('Missing Slice')
for i in range(4):
self.sheet.write(i + 1, 0, title[i])
for i in range(10):
self.sheet.write(0, i + 1, i + 1)
for i in range(4):
for j in range(10):
self.sheet.write(i + 1, j + 1, float(self.error[j, i]))
self.book.save('./Result/Robust_Missing.xls')
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': []}
data, info, point = db.loadMatData(self.path + self.ini.file.datadir
+ self.ini.file.name_fix[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['fix'] = fileData
data, info, point = db.loadMatData(self.path + self.ini.file.datadir
+ self.ini.file.name_mov[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['mov'] = fileData
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
# ICP with centerline
print 'Register Data %s with ICP(centerline)...' % self.ini.file.name_result[i]
for fov in range(10):
data, point, para = self.icp.register(dataset['fix'], dataset['mov'], 1, False, 0, fov + 1)
resultData = db.ResultData(data, db.ImageInfo(dataset['fix'].info.data), point)
resultData.info.addData('fix', 1)
resultData.info.addData('move', 2)
resultData.info.addData('transform', para)
print 'FOV %dmm Done!' % (fov + 1)
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(resultData, dataset['fix'].getPointSet('Contour').copy())
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
self.error[fov, :3] += mean_dis
self.error[fov, 3] += mean_whole
del data, point, resultData
class TestDistanceError(MacroBase):
def getName(self):
return 'Test Distance Error'
def run(self, window=None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test_modal.ini')
self.cnt = len(self.ini.file.name_fix)
self.icp = IcpPointsetRegistration(None)
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.result = [{}, {}, {}]
self.resultCnt = [{}, {}, {}]
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
for cnt in range(3):
for x in self.result[cnt].keys():
self.result[cnt][x] /= self.resultCnt[cnt][x]
self.savepath = self.path + self.ini.file.savedir
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA']
self.sheet = self.book.add_sheet('Distance_error')
for i in range(3):
self.sheet.write(i + 1, 0, title[i])
zmin = [0, 0, 0]
zmax = [0, 0, 0]
for cnt in range(3):
zmin[cnt] = min(self.result[cnt].keys())
zmax[cnt] = max(self.result[cnt].keys())
z1 = int(min(zmin))
z2 = int(max(zmax))
for z in range(z1, z2 + 1):
self.sheet.write(0, z - z1 + 1, z * 0.4)
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 1,
int(x) - z1 + 1, float(self.result[cnt][x]))
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 4,
int(x) - z1 + 1,
float(self.resultCnt[cnt][x]))
self.book.save(self.path + self.ini.file.savedir +
'Distance_error_merge.xls')
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': []}
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + '/Contour/' +
self.ini.file.name_mov[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
dataset['mov'] = db.BasicData(data, info, point)
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + '/Contour/' +
self.ini.file.name_fix[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
dataset['fix'] = db.BasicData(data, info, point)
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
print 'Register Data %s with ICP(centerline) with label...' % self.ini.file.name_result[
i]
data, point, para = self.icp.register(dataset['fix'], dataset['mov'],
1)
resultData = db.ResultData(data,
db.ImageInfo(dataset['fix'].info.data),
point)
resultData.info.addData('fix', 1)
resultData.info.addData('move', 2)
resultData.info.addData('transform', para)
print 'Done!'
print 'Evaluation Data %s...' % self.ini.file.name_result[i]
mean_dis, mean_whole, max_dis, max_whole, result = self.contourerror.analysis(
resultData, dataset['fix'].getPointSet('Contour').copy(), True)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
print result
for cnt in range(3):
for x in result[cnt].keys():
self.result[cnt][x] = self.result[cnt].get(x,
0) + result[cnt][x]
self.resultCnt[cnt][x] = self.resultCnt[cnt].get(x, 0) + 1
class TestDistanceError(MacroBase):
def getName(self):
return 'Test Distance Error'
def run(self, window = None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test_modal.ini')
self.cnt = len(self.ini.file.name_fix)
self.icp = IcpPointsetRegistration(None)
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.result = [{}, {}, {}]
self.resultCnt = [{}, {}, {}]
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
for cnt in range(3):
for x in self.result[cnt].keys():
self.result[cnt][x] /= self.resultCnt[cnt][x]
self.savepath = self.path + self.ini.file.savedir
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA']
self.sheet = self.book.add_sheet('Distance_error')
for i in range(3):
self.sheet.write(i + 1, 0, title[i])
zmin = [0, 0, 0]
zmax = [0, 0, 0]
for cnt in range(3):
zmin[cnt] = min(self.result[cnt].keys())
zmax[cnt] = max(self.result[cnt].keys())
z1 = int(min(zmin))
z2 = int(max(zmax))
for z in range(z1, z2 + 1):
self.sheet.write(0, z - z1 + 1, z * 0.4)
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 1, int(x) - z1 + 1, float(self.result[cnt][x]))
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 4, int(x) - z1 + 1, float(self.resultCnt[cnt][x]))
self.book.save(self.path + self.ini.file.savedir + 'Distance_error_merge.xls')
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': []}
data, info, point = db.loadMatData(self.path + self.ini.file.datadir + '/Contour/'
+ self.ini.file.name_mov[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
dataset['mov'] = db.BasicData(data, info, point)
data, info, point = db.loadMatData(self.path + self.ini.file.datadir + '/Contour/'
+ self.ini.file.name_fix[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
dataset['fix'] = db.BasicData(data, info, point)
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
print 'Register Data %s with ICP(centerline) with label...' % self.ini.file.name_result[i]
data, point, para = self.icp.register(dataset['fix'], dataset['mov'], 1)
resultData = db.ResultData(data, db.ImageInfo(dataset['fix'].info.data), point)
resultData.info.addData('fix', 1)
resultData.info.addData('move', 2)
resultData.info.addData('transform', para)
print 'Done!'
print 'Evaluation Data %s...' % self.ini.file.name_result[i]
mean_dis, mean_whole, max_dis, max_whole, result = self.contourerror.analysis(resultData, dataset['fix'].getPointSet('Contour').copy(), True)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
print result
for cnt in range(3):
for x in result[cnt].keys():
self.result[cnt][x] = self.result[cnt].get(x, 0) + result[cnt][x]
self.resultCnt[cnt][x] = self.resultCnt[cnt].get(x, 0) + 1
class TestSegmentationRate(MacroBase):
def getName(self):
return 'Test Segmentation Distance Error'
def run(self, window = None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.savepath = self.path + self.ini.file.savedir
self.contourerror = ContourErrorAnalysis(None)
self.contourareaerror = ContourErrorWithAreaAnalysis(None)
self.result = [{}, {}, {}]
self.resultCnt = [{}, {}, {}]
self.correct = npy.array([0.0, 0.0, 0.0])
self.count = npy.array([0, 0, 0])
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
print self.correct / self.count, npy.sum(self.correct) / npy.sum(self.count)
'''
for cnt in range(3):
for x in self.result[cnt].keys():
self.result[cnt][x] /= self.resultCnt[cnt][x]
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA']
self.sheet = self.book.add_sheet('Distance_error')
for i in range(3):
self.sheet.write(i + 1, 0, title[i])
zmin = [0, 0, 0]
zmax = [0, 0, 0]
for cnt in range(3):
zmin[cnt] = min(self.result[cnt].keys())
zmax[cnt] = max(self.result[cnt].keys())
z1 = int(min(zmin))
z2 = int(max(zmax))
for z in range(z1, z2 + 1):
self.sheet.write(0, z - z1 + 1, z * 0.34722220897674)
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 1, int(x) - z1 + 1, self.result[cnt][x])
for cnt in range(3):
for x in self.result[cnt].keys():
self.sheet.write(cnt + 4, int(x) - z1 + 1, self.resultCnt[cnt][x])
self.book.save(self.path + self.ini.file.savedir + 'Distance_error_segmentation.xls')
'''
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': [], 'seg': []}
data, info, point = db.loadMatData(self.path + self.ini.file.datadir + '/Contour/'
+ self.ini.file.name_fix[i] + '.mat', None)
fileData = db.BasicData(data, info, point)
dataset['fix'] = fileData
data, info, point = db.loadMatData(self.savepath + self.ini.file.name_result[i] + '_mr.mat', None)
fileData = db.BasicData(data, info, point)
dataset['seg'] = fileData
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
print 'Evaluation Data %s...' % self.ini.file.name_result[i]
mean_dis, mean_whole, max_dis, max_whole, result = self.contourerror.analysis(dataset['seg'], dataset['fix'].getPointSet('Contour').copy(), True)
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
for cnt in range(3):
for x in result[cnt].keys():
#self.result[cnt][x] = self.result[cnt].get(x, 0) + result[cnt][x]
#self.resultCnt[cnt][x] = self.resultCnt[cnt].get(x, 0) + 1
self.count[cnt] += 1
if result[cnt][x] <= 1.50:
self.correct[cnt] += 1
class TestOcclusionRobust(MacroBase):
def getName(self):
return 'Test Occlusion Robustness'
def run(self, window=None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.icp = IcpPointsetRegistration(None)
self.contourerror = ContourErrorAnalysis(None)
self.error = npy.zeros([7, 4], dtype=npy.float32)
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
self.error /= self.cnt
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA', 'Overall']
self.sheet = self.book.add_sheet('Occlusion Slice')
for i in range(4):
self.sheet.write(i + 1, 0, title[i])
for i in range(7):
self.sheet.write(0, i + 1, i + 1)
for i in range(4):
for j in range(7):
self.sheet.write(i + 1, j + 1, float(self.error[j, i]))
self.book.save('./Result/Robust_Occlusion.xls')
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': []}
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + self.ini.file.name_fix[i] +
'.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['fix'] = fileData
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + self.ini.file.name_mov[i] +
'.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['mov'] = fileData
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
# ICP with centerline
print 'Register Data %s with ICP(centerline)...' % self.ini.file.name_result[
i]
for fov in range(7):
data, point, para = self.icp.register(dataset['fix'],
dataset['mov'], 1, False, 0,
9999.0, 1, fov + 1)
resultData = db.ResultData(data,
db.ImageInfo(dataset['fix'].info.data),
point)
resultData.info.addData('fix', 1)
resultData.info.addData('move', 2)
resultData.info.addData('transform', para)
print 'FOV %dmm Done!' % (fov + 1)
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(
resultData, dataset['fix'].getPointSet('Contour').copy())
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
self.error[fov, :3] += mean_dis
self.error[fov, 3] += mean_whole
del data, point, resultData
class TestAllSegmentation(MacroBase):
def getName(self):
return 'Test All Segmentation'
def run(self, window=None):
self.path = sys.argv[0]
if os.path.isfile(self.path):
self.path = os.path.dirname(self.path)
self.ini = DictIni(self.path + '/Script/Macro/test.ini')
self.cnt = len(self.ini.file.name_fix)
self.icp = IcpPointsetRegistration(None)
self.contourerror = ContourErrorAnalysis(None)
self.areaerror = AreaIndexAnalysis(None)
self.savepath = self.path + self.ini.file.savedir
self.book = xlwt.Workbook()
title = ['CCA', 'ECA', 'ICA', 'Overall']
self.sheet1 = self.book.add_sheet('segmentation')
self.sheet1.write(1, 0, 'MRE')
for i in range(4):
self.sheet1.write(i + 1, 1, title[i])
self.sheet1.write(5, 0, 'Time')
self.sheet2 = self.book.add_sheet('registration')
self.sheet2.write(1, 0, 'MRE')
self.sheet2.write(5, 0, 'MAXE')
self.sheet2.write(9, 0, 'Dice Index')
self.sheet2.write(13, 0, 'Time')
for j in range(3):
for i in range(4):
self.sheet2.write(j * 4 + i + 1, 1, title[i])
for i in range(self.cnt):
dataset = self.load(i)
self.process(dataset, i)
del dataset
if self.gui:
self.gui.showErrorMessage('Success', 'Test sucessfully!')
else:
print 'Test sucessfully!'
def load(self, i):
dataset = {'mov': [], 'fix': []}
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + '/Contour/' +
self.ini.file.name_fix[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['fix'] = fileData
data, info, point = db.loadMatData(
self.path + self.ini.file.datadir + '/Contour/' +
self.ini.file.name_mov[i] + '.mat', None)
point['Centerline'] = calCenterlineFromContour(point)
fileData = db.BasicData(data, info, point)
dataset['mov'] = fileData
print 'Data %s loaded!' % self.ini.file.name_result[i]
return dataset
def process(self, dataset, i):
def autoDetectContour(point, cnt, start, end, delta):
self.new_points = npy.append(self.new_points, point, 0)
points = point[:, :-2]
count = 0
for j in range(start + delta, end + delta, delta):
center = calCentroidFromContour(points).reshape(2)
image = dataset['fix'].getData()[j, :, :].transpose().copy()
image = (image - npy.min(image)) / (npy.max(image) -
npy.min(image)) * 255
result = ac_segmentation(center, image)
a1 = ac_area(points.transpose(), image.shape)
a2 = ac_area(result, image.shape)
rate = a2 * 1.0 / a1
if rate >= min(1.5 + count * 0.2, 2.1) or rate <= 0.7:
temp_array = points.copy()
if cnt != 1 and rate > 0.7:
count += 1
else:
temp_array = result.transpose().copy()
count = 0
points = temp_array.copy()
temp_array = npy.insert(temp_array, 2, [[j], [cnt]], 1)
self.new_points = npy.append(self.new_points, temp_array, 0)
sys.stdout.write(str(j) + ',')
sys.stdout.flush()
print ' '
print 'Segment Data %s...' % self.ini.file.name_result[i]
tmp = dataset['fix'].pointSet.data['Contour']
tmp = tmp[tmp[:, 0] >= 0]
self.new_points = npy.array([[-1, -1, -1, -1]], dtype=npy.float32)
time1 = time.time()
bottom = int(npy.round(npy.min(tmp[:, 2])))
bif = int(db.getBifurcation(tmp) + 0.5)
up = int(npy.round(npy.max(tmp[:, 2])))
point_vital = [0] * 3
point_vital[0] = tmp[(npy.round(tmp[:, -1]) == 0)
& (npy.round(tmp[:, 2]) == bottom)].copy()
point_vital[1] = tmp[(npy.round(tmp[:, -1]) == 1)
& (npy.round(tmp[:, 2]) == up)].copy()
point_vital[2] = tmp[(npy.round(tmp[:, -1]) == 2)
& (npy.round(tmp[:, 2]) == up)].copy()
autoDetectContour(point_vital[0], 0, bottom, bif, 1)
autoDetectContour(point_vital[1], 1, up, bif, -1)
autoDetectContour(point_vital[2], 2, up, bif, -1)
time2 = time.time()
'''
# Use centerline for contour
j = 0
for center in tmp:
image = dataset['fix'].getData()[npy.round(center[2]), :, :].transpose().copy()
image = (image - npy.min(image)) / (npy.max(image) - npy.min(image)) * 255
result = ac_segmentation(center[:2], image)
point_array = npy.insert(result.transpose(), 2, [[center[2]],[center[3]]], axis = 1)
new_points = npy.append(new_points, point_array, 0)
j += 1
if j % 10 == 0:
sys.stdout.write(str(j) + ',')
sys.stdout.flush()
'''
print ' '
print 'Done! Time for segmentation is %0.2fs' % (time2 - time1)
pointset = {'Contour': self.new_points}
pointset['Centerline'] = calCenterlineFromContour(pointset)
print 'Saving Data %s...' % self.ini.file.name_result[i]
new_data = db.BasicData(dataset['fix'].data,
db.ImageInfo(dataset['fix'].info.data),
pointset)
db.saveMatData(
self.savepath + self.ini.file.name_result[i] + '_mr.mat',
[new_data], 0)
print 'Done!'
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(
new_data, dataset['fix'].getPointSet('Contour').copy())
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
self.sheet1.write(0, i + 2, self.ini.file.name_result[i])
for j in range(3):
self.sheet1.write(j + 1, i + 2, mean_dis[j])
self.sheet1.write(4, i + 2, mean_whole)
self.sheet1.write(5, i + 2, time2 - time1)
self.book.save(self.path + self.ini.file.savedir +
'Test_segmentation_final_refined.xls')
# ICP with centerline
print 'Register Data %s with ICP(centerline)...' % self.ini.file.name_result[
i]
time1 = time.time()
data, point, para = self.icp.register(new_data, dataset['mov'], 1)
time2 = time.time()
print 'Done! Time for registration is %0.2fs' % (time2 - time1)
resultData = db.ResultData(data,
db.ImageInfo(dataset['fix'].info.data),
point)
resultData.info.addData('fix', 1)
resultData.info.addData('move', 2)
resultData.info.addData('transform', para)
mean_dis, mean_whole, max_dis, max_whole = self.contourerror.analysis(
resultData, dataset['fix'].getPointSet('Contour').copy())
print 'Contour Error Done! Whole mean is %0.2fmm.' % mean_whole
dice_index, dice_index_all = self.areaerror.analysis(
resultData, dataset['fix'].getPointSet('Contour').copy())
print 'Area Error Done! Whole Dice index is %0.3f.' % dice_index_all
self.sheet2.write(0, i + 2, self.ini.file.name_result[i])
for j in range(3):
self.sheet2.write(j + 1, i + 2, mean_dis[j])
self.sheet2.write(j + 5, i + 2, max_dis[j])
self.sheet2.write(j + 9, i + 2, dice_index[j])
self.sheet2.write(4, i + 2, mean_whole)
self.sheet2.write(8, i + 2, max_whole)
self.sheet2.write(12, i + 2, dice_index_all)
self.sheet2.write(13, i + 2, time2 - time1)
self.book.save(self.path + self.ini.file.savedir +
'Test_segmentation_final_refined2.xls')
del data, point, resultData