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):
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)
