def convert(nav_acq):
save_folder=nav_acq+"_8bit/"
if not os.path.isdir(save_folder):
os.makedirs(save_folder)
for dirpath, dirnames, filenames in os.walk(nav_acq):
for file_j in filenames:
print file_j
file_org = os.path.join(dirpath, file_j)
file_new = os.path.join(save_folder, file_j)
if (file_j[-3:]=='raw') and 'mask' not in file_j:
if (file_j[-4:]=='zraw'):
file_org_mhd=file_org.replace('zraw','mhd')
file_new_mhd=file_new.replace('zraw','mhd')
else:
file_org_mhd=file_org.replace('raw','mhd')
file_new_mhd=file_new.replace('raw','mhd')
org_file_mhd = open(file_org_mhd)
new_file_mhd = open(file_new_mhd,'w')
convert=False
for line in org_file_mhd:
if 'ElementNumberOfChannels = 3' in line:
newline=''
convert=True
elif 'ElementSize' in line:
newline=''
elif 'DimSize' in line:
newline=line
temp=line.split()
if len(temp) == 5:
dimSize=[int(temp[2]),int(temp[3]),int(temp[4])]
elif len(temp) == 4:
dimSize=[int(temp[2]),int(temp[3])]
else:
newline =line
new_file_mhd.write(newline)
new_file_mhd.close()
org_file_mhd.close()
dimSize=np.hstack([3,dimSize])
if convert:
raw_file = CxDataHandler.rawFileReader(file_org,dimSize)
data=raw_file.get_samples()
data=np.mean(data,axis=0)
rawWrither = CxDataHandler.rawFileWrither(file_new,data)
else:
shutil.copy2(file_org, file_new)
elif (file_j[-3:]=='mhd') and not ('mask' in file_j):
continue
else:
shutil.copy2(file_org, file_new)
def RemoveRect(nav_acq):
if nav_acq[-1]=='/':
nav_acq=nav_acq[:-1]
if os.path.isdir(nav_acq+"_removed_rect"):
print "Folder already exists"
return
shutil.copytree(nav_acq,nav_acq+"_removed_rect")
CxData=CxDataHandler.cxOpenCV.from_acq_folder(nav_acq+"_removed_rect")
for frame_no in range(0,CxData.get_no_of_frames()):
print frame_no
vtk=CxData.load_mhd(frame_no)
data=vtk.loadRawData_removeRect()
CxDataHandler.rawFileWrither(vtk.getRawFilePath(),data,True)
vtk.save_to_new_file(vtk.getFilePath(),overwrite=True)
def anonymizeFace(filePathMhd):
if RM_FACE_CUT_OFF <= 0:
return
cutOff = 0.15
mhdFile=CxDataHandler.mhdFile(filePathMhd)
if 'Modality'not in mhdFile.Params:
if not 'MR'in filePathMhd:
return
elif not mhdFile.Params['Modality'] == 'MR':
return
elif not mhdFile.get_DimSize() == 3:
pass
#return
print filePathMhd
data=mhdFile.get_samples()
X=[]
Y=[]
Z=[]
for x in range(data.shape[0]):
for y in range(data.shape[1]):
for z in range(data.shape[2]):
if data[x,y,z]>1:
X.append(x)
Y.append(y)
Z.append(z)
x_com=np.mean(X)
y_com=np.mean(Y)
z_com=np.mean(Z)
def avgElAboveLimit(plane,limit=10):
res=0
for i in range(plane.shape[0]):
for j in range(plane.shape[1]):
if plane[i,j]>limit:
res=res+1
return res/float(plane.shape[0]*plane.shape[1])
def findN(vec):
temp=None
k=0
for el in vec:
if not temp and el > 0.015:
temp=k
if temp and el >cutOff:
return k
return k-temp
k=k+1
x=[]
for i in range(data.shape[0]):
temp=avgElAboveLimit(data[i,:,:])
x.append(temp)
x1=findN(x)
x2=findN(x[::-1])
y=[]
for i in range(data.shape[1]):
temp=avgElAboveLimit(data[:,i,:])
y.append(temp)
y1=findN(y)
y2=findN(y[::-1])
z=[]
z1=None
z2=None
for i in range(data.shape[2]):
temp=avgElAboveLimit(data[:,:,i])
z.append(temp)
z1=findN(z)
z2=findN(z[::-1])
import matplotlib.pyplot as plt
plt.plot(x)
plt.show()
print x1,x2
plt.plot(y)
plt.show()
print y1,y2
plt.plot(z)
plt.show()
print z1,z2
print
print x_com
print y_com
print z_com
I00=0
I11=0
I22=0
I01=0
I12=0
I02=0
Ixx=0
Iyy=0
Izz=0
for i in range(len(X)):
I00=I00+(Y[i]-y_com)**2+(Z[i]-z_com)**2
I11=I11+(X[i]-x_com)**2+(Z[i]-z_com)**2
I22=I22+(X[i]-x_com)**2+(Y[i]-y_com)**2
I01=I01+(X[i]-x_com)*(Y[i]-y_com)
I12=I12+(Y[i]-y_com)*(Z[i]-z_com)
I02=I02+(X[i]-x_com)*(Z[i]-z_com)
Ixx=Ixx+(X[i]-x_com)*(X[i]-x_com)
Iyy=Iyy+(Y[i]-y_com)*(Y[i]-y_com)
Izz=Izz+(Z[i]-z_com)*(Z[i]-z_com)
I00=I00/len(X)
I11=I11/len(X)
I22=I22/len(X)
I01=I01/len(X)
I12=I12/len(X)
I02=I02/len(X)
Ixx=Ixx/len(X)
Iyy=Iyy/len(X)
Izz=Izz/len(X)
print
print Ixx
print Iyy
print Izz
print
print I00
print I11
print I22
print
print I01
print I12
print I02
return
if idx==0 and lvec(idx)>0:
N=int(RM_FACE_CUT_OFF/mhdFile.get_spacing()[0])
data[0:N,:,:]=0
if idx==0 and lvec(idx)<0:
N=int(RM_FACE_CUT_OFF/mhdFile.get_spacing()[0])
data[-N:,:,:]=0
if idx==1 and lvec(idx)>0:
N=int(RM_FACE_CUT_OFF/mhdFile.get_spacing()[1])
data[:,0:N,:]=0
if idx==1 and lvec(idx)<0:
N=int(RM_FACE_CUT_OFF/mhdFile.get_spacing()[1])
data[:,-N:,:]=0
if idx==2 and lvec(idx)>0:
N=int(RM_FACE_CUT_OFF/mhdFile.get_spacing()[2])
data[:,:,0:N]=0
if idx==2 and lvec(idx)<0:
N=int(RM_FACE_CUT_OFF/mhdFile.get_spacing()[2])
data[:,:,-N:]=0
CxDataHandler.rawFileWrither(mhdFile.getRawFilePath(),data,color=False,ElementType=mhdFile.get_ElementType())
def convert(nav_acq):
save_folder = nav_acq + "_8bit/"
if not os.path.isdir(save_folder):
os.makedirs(save_folder)
for dirpath, dirnames, filenames in os.walk(nav_acq):
for file_j in filenames:
print file_j
file_org = os.path.join(dirpath, file_j)
file_new = os.path.join(save_folder, file_j)
if (file_j[-3:] == 'raw') and 'mask' not in file_j:
if (file_j[-4:] == 'zraw'):
file_org_mhd = file_org.replace('zraw', 'mhd')
file_new_mhd = file_new.replace('zraw', 'mhd')
else:
file_org_mhd = file_org.replace('raw', 'mhd')
file_new_mhd = file_new.replace('raw', 'mhd')
org_file_mhd = open(file_org_mhd)
new_file_mhd = open(file_new_mhd, 'w')
convert = False
for line in org_file_mhd:
if 'ElementNumberOfChannels = 3' in line:
newline = ''
convert = True
elif 'ElementSize' in line:
newline = ''
elif 'DimSize' in line:
newline = line
temp = line.split()
if len(temp) == 5:
dimSize = [
int(temp[2]),
int(temp[3]),
int(temp[4])
]
elif len(temp) == 4:
dimSize = [int(temp[2]), int(temp[3])]
else:
newline = line
new_file_mhd.write(newline)
new_file_mhd.close()
org_file_mhd.close()
dimSize = np.hstack([3, dimSize])
if convert:
raw_file = CxDataHandler.rawFileReader(file_org, dimSize)
data = raw_file.get_samples()
data = np.mean(data, axis=0)
rawWrither = CxDataHandler.rawFileWrither(file_new, data)
else:
shutil.copy2(file_org, file_new)
elif (file_j[-3:] == 'mhd') and not ('mask' in file_j):
continue
else:
shutil.copy2(file_org, file_new)
def convert(nav_acq):
if nav_acq[-1] == '/':
save_folder = nav_acq[0:-1] + "_png/"
else:
save_folder = nav_acq + "_png/"
print save_folder
if not os.path.isdir(save_folder):
os.makedirs(save_folder)
just_positive = True
for dirpath, dirnames, filenames in os.walk(nav_acq):
for file_j in filenames:
if "Velocity" not in file_j:
continue
print file_j
file_org = os.path.join(dirpath, file_j)
file_new = os.path.join(save_folder,
file_j.replace('.zraw', '.raw'))
if (file_j[-4:] == 'zraw') and 'mask' not in file_j:
file_org_mhd = file_org[0:-4] + 'mhd'
org_file_mhd = open(file_org_mhd)
convert = False
channels = 1
for line in org_file_mhd:
if 'ElementNumberOfChannels = 3' in line:
channels = 3
elif 'ElementType' in line:
temp = line.split()
ElementType = temp[-1]
elif 'DimSize' in line:
temp = line.split()
if len(temp) == 5:
dimSize = [
int(temp[2]),
int(temp[3]),
int(temp[4])
]
elif len(temp) == 4:
dimSize = [int(temp[2]), int(temp[3])]
org_file_mhd.close()
if channels == 3:
dimSize = np.hstack([3, dimSize])
raw_file = CxDataHandler.rawFileReader(file_org,
dimSize,
ElementType=ElementType)
data = raw_file.get_samples()
idx_n = data < 0
if sum(sum(data < 0)) == 0:
just_positive = False
idx_p = data > 0
data = data * 0 + 125
data[idx_n] = 0
data[idx_p] = 255
# rawWrither = CxDataHandler.rawFileWrither(file_new,data,ElementType=ElementType)
print data.shape
if just_positive:
print("Only positive values")
def convert(nav_acq):
if nav_acq[-1] == '/':
save_folder=nav_acq[0:-1]+"_raw/"
else:
save_folder=nav_acq+"_raw/"
print save_folder
if not os.path.isdir(save_folder):
os.makedirs(save_folder)
for dirpath, dirnames, filenames in os.walk(nav_acq):
for file_j in filenames:
print file_j
file_org = os.path.join(dirpath, file_j)
file_new = os.path.join(save_folder, file_j.replace('.zraw','.raw'))
if (file_j[-4:]=='zraw') and 'mask' not in file_j:
file_org_mhd=file_org[0:-4] + 'mhd'
file_new_mhd=file_new[0:-3] + 'mhd'
org_file_mhd = open(file_org_mhd)
new_file_mhd = open(file_new_mhd,'w')
convert=False
channels=1
for line in org_file_mhd:
if 'ElementNumberOfChannels = 3' in line:
newline=line
channels=3
elif 'CompressedData ' in line:
newline='CompressedData = False\n'
elif 'CompressedDataSize' in line:
newline=''
elif '.raw' in line:
newline=line.replace('zraw','raw')
elif 'ElementType' in line:
temp=line.split()
ElementType=temp[-1]
newline=line
elif 'DimSize' in line:
newline=line
temp=line.split()
if len(temp) == 5:
dimSize=[int(temp[2]),int(temp[3]),int(temp[4])]
elif len(temp) == 4:
dimSize=[int(temp[2]),int(temp[3])]
elif 'ElementDataFile' in line:
newline = 'ElementDataFile = ' + file_j.replace('.zraw','.raw')
else:
newline =line
new_file_mhd.write(newline)
new_file_mhd.close()
org_file_mhd.close()
if channels == 3:
dimSize=np.hstack([3,dimSize])
raw_file = CxDataHandler.rawFileReader(file_org,dimSize,ElementType=ElementType)
data=raw_file.get_samples()
rawWrither = CxDataHandler.rawFileWrither(file_new,data,ElementType=ElementType)
elif (file_j[-3:]=='mhd') and not ('mask' in file_j):
continue
else:
shutil.copy2(file_org, file_new)
def convert(nav_acq):
if nav_acq[-1] == '/':
save_folder = nav_acq[0:-1] + "_png/"
else:
save_folder = nav_acq + "_png/"
print save_folder
if not os.path.isdir(save_folder):
os.makedirs(save_folder)
for dirpath, dirnames, filenames in os.walk(nav_acq):
for file_j in filenames:
if "Velocity" not in file_j:
continue
print file_j
file_org = os.path.join(dirpath, file_j)
file_new = os.path.join(save_folder,
file_j.replace('.zraw', '.png'))
if (file_j[-4:] == 'zraw') and 'mask' not in file_j:
file_org_mhd = file_org[0:-4] + 'mhd'
org_file_mhd = open(file_org_mhd)
convert = False
channels = 1
for line in org_file_mhd:
if 'ElementNumberOfChannels = 3' in line:
channels = 3
elif 'ElementType' in line:
temp = line.split()
ElementType = temp[-1]
elif 'DimSize' in line:
temp = line.split()
if len(temp) == 5:
dimSize = [
int(temp[2]),
int(temp[3]),
int(temp[4])
]
elif len(temp) == 4:
dimSize = [int(temp[2]), int(temp[3])]
org_file_mhd.close()
if channels == 3:
dimSize = np.hstack([3, dimSize])
raw_file = CxDataHandler.rawFileReader(file_org,
dimSize,
ElementType=ElementType)
data = raw_file.get_samples()
if channels == 3:
data = np.swapaxes(data, 0, 2)
plt.imshow(data)
else:
data = np.swapaxes(data, 0, 1)
idx_n = data < 0
idx_p = data > 0
data = data * 0 + 125
data[idx_n] = 0
data[idx_p] = 255
plt.imshow(data, cmap="gray")
print data.shape
plt.savefig(file_new)
plt.close()
def convert(nav_acq):
if nav_acq[-1] == '/':
save_folder = nav_acq[0:-1] + "_raw/"
else:
save_folder = nav_acq + "_raw/"
print save_folder
if not os.path.isdir(save_folder):
os.makedirs(save_folder)
for dirpath, dirnames, filenames in os.walk(nav_acq):
for file_j in filenames:
print file_j
file_org = os.path.join(dirpath, file_j)
file_new = os.path.join(save_folder,
file_j.replace('.zraw', '.raw'))
if (file_j[-4:] == 'zraw') and 'mask' not in file_j:
file_org_mhd = file_org[0:-4] + 'mhd'
file_new_mhd = file_new[0:-3] + 'mhd'
org_file_mhd = open(file_org_mhd)
new_file_mhd = open(file_new_mhd, 'w')
convert = False
channels = 1
for line in org_file_mhd:
if 'ElementNumberOfChannels = 3' in line:
newline = line
channels = 3
elif 'CompressedData ' in line:
newline = 'CompressedData = False\n'
elif 'CompressedDataSize' in line:
newline = ''
elif '.raw' in line:
newline = line.replace('zraw', 'raw')
elif 'ElementType' in line:
temp = line.split()
ElementType = temp[-1]
newline = line
elif 'DimSize' in line:
newline = line
temp = line.split()
if len(temp) == 5:
dimSize = [
int(temp[2]),
int(temp[3]),
int(temp[4])
]
elif len(temp) == 4:
dimSize = [int(temp[2]), int(temp[3])]
elif 'ElementDataFile' in line:
newline = 'ElementDataFile = ' + file_j.replace(
'.zraw', '.raw')
else:
newline = line
new_file_mhd.write(newline)
new_file_mhd.close()
org_file_mhd.close()
if channels == 3:
dimSize = np.hstack([3, dimSize])
raw_file = CxDataHandler.rawFileReader(file_org,
dimSize,
ElementType=ElementType)
data = raw_file.get_samples()
rawWrither = CxDataHandler.rawFileWrither(
file_new, data, ElementType=ElementType)
elif (file_j[-3:] == 'mhd') and not ('mask' in file_j):
continue
else:
shutil.copy2(file_org, file_new)
def anonymizeFace(filePathMhd):
if RM_FACE_CUT_OFF <= 0:
return
cutOff = 0.15
mhdFile = CxDataHandler.mhdFile(filePathMhd)
if 'Modality' not in mhdFile.Params:
if not 'MR' in filePathMhd:
return
elif not mhdFile.Params['Modality'] == 'MR':
return
elif not mhdFile.get_DimSize() == 3:
pass
#return
print filePathMhd
data = mhdFile.get_samples()
X = []
Y = []
Z = []
for x in range(data.shape[0]):
for y in range(data.shape[1]):
for z in range(data.shape[2]):
if data[x, y, z] > 1:
X.append(x)
Y.append(y)
Z.append(z)
x_com = np.mean(X)
y_com = np.mean(Y)
z_com = np.mean(Z)
def avgElAboveLimit(plane, limit=10):
res = 0
for i in range(plane.shape[0]):
for j in range(plane.shape[1]):
if plane[i, j] > limit:
res = res + 1
return res / float(plane.shape[0] * plane.shape[1])
def findN(vec):
temp = None
k = 0
for el in vec:
if not temp and el > 0.015:
temp = k
if temp and el > cutOff:
return k
return k - temp
k = k + 1
x = []
for i in range(data.shape[0]):
temp = avgElAboveLimit(data[i, :, :])
x.append(temp)
x1 = findN(x)
x2 = findN(x[::-1])
y = []
for i in range(data.shape[1]):
temp = avgElAboveLimit(data[:, i, :])
y.append(temp)
y1 = findN(y)
y2 = findN(y[::-1])
z = []
z1 = None
z2 = None
for i in range(data.shape[2]):
temp = avgElAboveLimit(data[:, :, i])
z.append(temp)
z1 = findN(z)
z2 = findN(z[::-1])
import matplotlib.pyplot as plt
plt.plot(x)
plt.show()
print x1, x2
plt.plot(y)
plt.show()
print y1, y2
plt.plot(z)
plt.show()
print z1, z2
print
print x_com
print y_com
print z_com
I00 = 0
I11 = 0
I22 = 0
I01 = 0
I12 = 0
I02 = 0
Ixx = 0
Iyy = 0
Izz = 0
for i in range(len(X)):
I00 = I00 + (Y[i] - y_com)**2 + (Z[i] - z_com)**2
I11 = I11 + (X[i] - x_com)**2 + (Z[i] - z_com)**2
I22 = I22 + (X[i] - x_com)**2 + (Y[i] - y_com)**2
I01 = I01 + (X[i] - x_com) * (Y[i] - y_com)
I12 = I12 + (Y[i] - y_com) * (Z[i] - z_com)
I02 = I02 + (X[i] - x_com) * (Z[i] - z_com)
Ixx = Ixx + (X[i] - x_com) * (X[i] - x_com)
Iyy = Iyy + (Y[i] - y_com) * (Y[i] - y_com)
Izz = Izz + (Z[i] - z_com) * (Z[i] - z_com)
I00 = I00 / len(X)
I11 = I11 / len(X)
I22 = I22 / len(X)
I01 = I01 / len(X)
I12 = I12 / len(X)
I02 = I02 / len(X)
Ixx = Ixx / len(X)
Iyy = Iyy / len(X)
Izz = Izz / len(X)
print
print Ixx
print Iyy
print Izz
print
print I00
print I11
print I22
print
print I01
print I12
print I02
return
if idx == 0 and lvec(idx) > 0:
N = int(RM_FACE_CUT_OFF / mhdFile.get_spacing()[0])
data[0:N, :, :] = 0
if idx == 0 and lvec(idx) < 0:
N = int(RM_FACE_CUT_OFF / mhdFile.get_spacing()[0])
data[-N:, :, :] = 0
if idx == 1 and lvec(idx) > 0:
N = int(RM_FACE_CUT_OFF / mhdFile.get_spacing()[1])
data[:, 0:N, :] = 0
if idx == 1 and lvec(idx) < 0:
N = int(RM_FACE_CUT_OFF / mhdFile.get_spacing()[1])
data[:, -N:, :] = 0
if idx == 2 and lvec(idx) > 0:
N = int(RM_FACE_CUT_OFF / mhdFile.get_spacing()[2])
data[:, :, 0:N] = 0
if idx == 2 and lvec(idx) < 0:
N = int(RM_FACE_CUT_OFF / mhdFile.get_spacing()[2])
data[:, :, -N:] = 0
CxDataHandler.rawFileWrither(mhdFile.getRawFilePath(),
data,
color=False,
ElementType=mhdFile.get_ElementType())
