def readdata():
file = h5py.File('File_Patientdata.h5', 'w')
patient = []
path = "E:/zhangjinjing/brain2D/Image_Data"
for i in os.listdir(path):
patient.append(i)
patient = np.array(patient)
for j in range(patient.shape[0]):
CH1 = util.read_mha_image_as_nuarray(path + "/" + patient[j] +
"/001/001.mha")
CH2 = util.read_mha_image_as_nuarray(path + "/" + patient[j] +
"/002/002.mha")
CH3 = util.read_mha_image_as_nuarray(path + "/" + patient[j] +
"/003/003.mha")
CH4 = util.read_mha_image_as_nuarray(path + "/" + patient[j] +
"/004/004.mha")
LABEL = util.read_mha_image_as_nuarray(path + "/" + patient[j] +
"/005/005.mha")
file.create_dataset(
'data' + str(j),
data=np.concatenate([
CH1[:, :, :, np.newaxis], CH2[:, :, :, np.newaxis],
CH3[:, :, :, np.newaxis], CH4[:, :, :, np.newaxis]
], 3))
file.create_dataset('label' + str(j), data=LABEL)
print('set data ok!')
def readDataLocal():
All_data = []
All_label = []
for zip_num in range(274):
print(zip_num)
CH1 = util.read_mha_image_as_nuarray('BrainTrain/' + str(zip_num) +
'/0001/0001.mha')
CH2 = util.read_mha_image_as_nuarray('BrainTrain/' + str(zip_num) +
'/0002/0002.mha')
CH3 = util.read_mha_image_as_nuarray('BrainTrain/' + str(zip_num) +
'/0003/0003.mha')
CH4 = util.read_mha_image_as_nuarray('BrainTrain/' + str(zip_num) +
'/0004/0004.mha')
CHLABEL = util.read_mha_image_as_nuarray('BrainTrain/' + str(zip_num) +
'/0005/0005.mha')
All_data.append(
np.concatenate([
CH1[:, :, :, np.newaxis], CH2[:, :, :, np.newaxis],
CH3[:, :, :, np.newaxis], CH4[:, :, :, np.newaxis]
], 3))
All_label.append(CHLABEL)
return All_data, All_label
def compare(path1,path2):
data1=util.read_mha_image_as_nuarray(path1)
data2=util.read_mha_image_as_nuarray(path2)
for i in range(data1.shape[0]):
for j in range(data1.shape[1]):
for k in range (data1.shape[2]):
if data1[i,j,k]==data2[i,j,k]:
data1[i,j,k]=0
return data1
def DataProcess(zip_num):
TestPath = 'E://zhangjinjing/Brain2D/BRATS_Leaderboard/' + str(zip_num + 1)
CH1 = util.read_mha_image_as_nuarray(TestPath + '/1/1.mha')
CH2 = util.read_mha_image_as_nuarray(TestPath + '/2/2.mha')
CH3 = util.read_mha_image_as_nuarray(TestPath + '/3/3.mha')
CH4 = util.read_mha_image_as_nuarray(TestPath + '/4/4.mha')
ALLtest = np.concatenate([
CH1[:, :, :, np.newaxis], CH2[:, :, :, np.newaxis],
CH3[:, :, :, np.newaxis], CH4[:, :, :, np.newaxis]
], 3)
del CH1, CH2, CH3, CH4
gc.collect()
return ALLtest
def image_getindex():
index1 = []
index2 = []
index3 = []
index4 = []
patient = []
patch = 65
path = "E:/zhangjinjing/brain2D/Image_Data"
for i in os.listdir(path):
patient.append(i)
patient = np.array(patient)
for j in range(patient.shape[0]):
label = util.read_mha_image_as_nuarray(path + "/" + patient[j] +
'/005/005.mha')
for x in range(label.shape[0]):
for y in range(label.shape[1] - patch):
y = y + int(patch / 2)
for z in range(label.shape[2] - patch):
z = z + int(patch / 2)
pixel = label[x, y, z]
if pixel == 1:
index1.append([j, x, y, z])
print('j,x,y,z:', j, x, y, z)
if pixel == 2:
index2.append([j, x, y, z])
print('j,x,y,z:', j, x, y, z)
if pixel == 3:
index3.append([j, x, y, z])
print('j,x,y,z:', j, x, y, z)
if pixel == 4:
index4.append([j, x, y, z])
print('j,x,y,z:', j, x, y, z)
return np.array(index1), np.array(index2), np.array(index3), np.array(
index4)
def load_patient_files(self):
self.file_T1 = self._find_file("T1.*\.mha")
self.file_T1c = self._find_file("T1c.*\.mha")
self.file_T2 = self._find_file("T2.*\.mha")
self.file_FLAIR = self._find_file("Flair.*\.mha")
self.T1 = utility.read_mha_image_as_nuarray(
self._find_file("T1.*\.mha"))
self.T1c = utility.read_mha_image_as_nuarray(
self._find_file("T1c.*\.mha"))
self.T2 = utility.read_mha_image_as_nuarray(
self._find_file("T2.*\.mha"))
self.FLAIR = utility.read_mha_image_as_nuarray(
self._find_file("Flair.*\.mha"))
self.label = utility.read_mha_image_as_nuarray(
self._find_file("OT.*\.mha"))
def readdata():
path = 'E:/zhangjinjing/brain2D/Image_Data'
patient = []
for i in os.listdir(path):
print('i', i)
patient.append(i)
patient = np.array(patient)
for i in range(patient.shape[0]):
data = util.read_mha_image_as_nuarray(path + '/' + str(patient[i]) +
'/001/001.mha')
print(data.shape)
def preprocess(self):
self.set_parent_file(self.file_parent)
if (self._find_file("back_ground") == None):
back_ground = self.BFS()
utility.save_nuarray_as_mha(
os.path.join(self.file_parent, "back_ground.mha"), back_ground)
self.set_parent_file(self.file_parent)
self.back_ground = utility.read_mha_image_as_nuarray(
self._find_file("back_ground\.mha"))
balanced_data_file = os.path.join(self.file_parent,
"balanced_data.pickle")
if (not os.path.isfile(balanced_data_file)):
self.balance_data()
ff = open(balanced_data_file, "rb")
self.balanced_data_indices = pickle.load(ff)
ff.close()
def colorize():
file = util.read_mha_image_as_nuarray(test)
newfile = np.zeros([file.shape[0], file.shape[1], file.shape[2], 3])
for i in range(file.shape[0]):
for j in range(file.shape[1]):
for k in range(file.shape[2]):
if file[i, j, k] == 1:
newfile[i, j, k] = [192, 57, 43]
elif file[i, j, k] == 2:
newfile[i, j, k] = [39, 174, 96]
elif file[i, j, k] == 3:
newfile[i, j, k] = [155, 89, 182]
elif file[i, j, k] == 4:
newfile[i, j, k] = [243, 156, 18]
else:
newfile[i, j, k] = [0, 0, 0]
for i in range(file.shape[2]):
img = Image.fromarray(
np.uint8(newfile[0:newfile.shape[0], 0:newfile.shape[1], i]))
img.save("picture/test9/green/test9-g" + str(i) + ".jpg", 'jpeg')
def patient_accuracy(patient_file):
p = Patient()
p.set_parent_file(patient_file)
p.set_window_size(0)
p.start_iteration()
print("patient accuracy")
print(p.file_parent)
for z in range(0, p.limit_z):
for y in range(0, p.limit_y):
for x in range(0, p.limit_x):
if (p.label[z][y][x] != 0):
p.label[z][y][x] = 1
a = p.label
b = utility.read_mha_image_as_nuarray(p._find_file("segmentation.mha"))
print("files load , start accuracy calculation")
P = TP(a, b, 0, a.ndim) + FP(a, b, 0, a.ndim) #total positive
T = TP(a, b, 0, a.ndim) + FN(a, b, 0, a.ndim) #total actual positive
N = TN(a, b, 0, a.ndim) + FP(a, b, 0, a.ndim) #total actual negative
dice = TP(a, b, 0, a.ndim) / float(((P + T) / 2))
sens = TP(a, b, 0, a.ndim) / float(T)
spec = TN(a, b, 0, a.ndim) / float(N)
acc = (TP(a, b, 0, a.ndim) + TN(a, b, 0, a.ndim)) / float(T + N)
error = 1.0 - acc
p.stop_iteration()
print("P %s" % P)
print("T %s" % T)
print("N %s" % N)
print("dice %s" % dice)
print("sens %s" % sens)
print("spec %s" % spec)
print("acc %s" % acc)
print("error %s" % error)
def preprocess(
self
): # creates a background.mha file ,which displays black brain part
self.set_parent_file(self.file_parent)
if (self._find_file("back_ground") == None):
back_ground = self.BFS()
utility.save_nuarray_as_mha(
os.path.join(self.file_parent, "back_ground.mha"),
back_ground) #getting image from array
self.set_parent_file(self.file_parent)
self.back_ground = utility.read_mha_image_as_nuarray(
self._find_file("back_ground\.mha")) # getting array from img
balanced_data_file = os.path.join(
self.file_parent, "balanced_data.pickle") #file pickling
if (not os.path.isfile(balanced_data_file)):
self.balance_data()
ff = open(balanced_data_file, "rb")
self.balanced_data_indices = pickle.load(ff)
ff.close()
import numpy as np
import utility as util
modi210=util.read_mha_image_as_nuarray('test210.mha')
temp=np.zeros([155,240,240])
temp[:,32:207,32:207]=modi210
util.save_nuarray_as_mha('test210_2.mha', temp)
import numpy as np
import utility as util
import h5py
import gc
import tensorflow as tf
import os
os.environ['CUDA_VISIBLE_DEVICES'] = '1'
patch_size = 65
patch_size2 = 33
halfpz = int(patch_size / 2)
halfpz2 = int(patch_size2 / 2)
path = 'Testing/'
patient = '78'
CH1 = util.read_mha_image_as_nuarray(path + patient + '/0001/0001.mha')
CH2 = util.read_mha_image_as_nuarray(path + patient + '/0002/0002.mha')
CH3 = util.read_mha_image_as_nuarray(path + patient + '/0003/0003.mha')
CH4 = util.read_mha_image_as_nuarray(path + patient + '/0004/0004.mha')
#CHLABEL = util.read_mha_image_as_nuarray(path+patient+'/0005/0005.mha')
ALLtest = np.concatenate([
CH1[:, :, :, np.newaxis], CH2[:, :, :, np.newaxis],
CH3[:, :, :, np.newaxis], CH4[:, :, :, np.newaxis]
], 3)
del CH1, CH2, CH3, CH4
gc.collect()
def getBatch2D(pos_x, pos_y):
#print(index_shuffle.shape)
import gc
import tensorflow as tf
import os
os.environ['CUDA_VISIBLE_DEVICES']='1'
patch_size=65
patch_size2=33
halfpz=int(patch_size/2)
halfpz2=int(patch_size2/2)
zip_num=114
#TestPath='Testing/'+str(zip_num)
TrainPath='BrainTrain/'+str(zip_num)
CH1=util.read_mha_image_as_nuarray(TrainPath+'/0001/0001.mha')
CH2=util.read_mha_image_as_nuarray(TrainPath+'/0002/0002.mha')
CH3=util.read_mha_image_as_nuarray(TrainPath+'/0003/0003.mha')
CH4=util.read_mha_image_as_nuarray(TrainPath+'/0004/0004.mha')
CHLABEL=util.read_mha_image_as_nuarray(TrainPath+'/0005/0005.mha')
ALLtest=np.concatenate([CH1[:,:,:,np.newaxis],
CH2[:,:,:,np.newaxis],
CH3[:,:,:,np.newaxis],
CH4[:,:,:,np.newaxis]],3)
del CH1,CH2,CH3,CH4
gc.collect()
def getBatch2D(pos_x,pos_y):
Combine_conv = tf.nn.conv2d(
Combine, WCombine_conv, strides=[1, 1, 1, 1
], padding='VALID') + BCombine_conv
ReCombine_conv = tf.reshape(Combine_conv, [175, 5])
OUT = tf.nn.softmax(ReCombine_conv)
#loss=tf.reduce_mean(-tf.reduce_sum(Yp*tf.log(OUT),reduction_indices=[1]))
#correct_prediction = tf.equal(tf.argmax(OUT,1), tf.argmax(Yp,1))
#accuracy = tf.reduce_mean(tf.cast(correct_prediction, "float"))
index = readindex()
index = np.array(index)
for zip_num in range(index.shape[0]):
TestPath = 'Testing/' + str(zip_num + 1)
CH1 = util.read_mha_image_as_nuarray(TestPath + '/0001/0001.mha')
CH2 = util.read_mha_image_as_nuarray(TestPath + '/0002/0002.mha')
CH3 = util.read_mha_image_as_nuarray(TestPath + '/0003/0003.mha')
CH4 = util.read_mha_image_as_nuarray(TestPath + '/0004/0004.mha')
# CHLABEL=util.read_mha_image_as_nuarray(TestPath+'/0005/0005.mha')
ALLtest = np.concatenate([
CH1[:, :, :, np.newaxis], CH2[:, :, :, np.newaxis],
CH3[:, :, :, np.newaxis], CH4[:, :, :, np.newaxis]
], 3)
del CH1, CH2, CH3, CH4
gc.collect()
print('ALLTEST:', ALLtest.shape)
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess = tf.Session(config=config)
def adjust():
file = util.read_mha_image_as_nuarray(trainpatient)
for i in range(file.shape[1]):
img = Image.fromarray(
np.uint8(file[0:file.shape[0], 0:file.shape[2], i]))
img.save("picture/flair/green/flair" + str(i) + ".jpg", 'jpeg')