def edf(self,
x_start=0,
x_end=0,
x_step=1,
y_start=0,
y_end=0,
y_step=1,
z_start=0,
z_end=0,
z_step=1):
"""
Read 3-D tomographic projection data from an EDF (ESRF) file.
Parameters
file_name : str
Input edf file.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
z_start, z_end, z_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
Returns
out : array
Returns the data as a matrix.
"""
# Read data from file.
f = EdfFile(self.file_name, access='r')
dic = f.GetStaticHeader(0)
tmpdata = np.empty((f.NumImages, int(dic['Dim_2']), int(dic['Dim_1'])))
for (i, ar) in enumerate(tmpdata):
tmpdata[i::] = f.GetData(i)
num_z, num_y, num_x = np.shape(tmpdata)
if x_end is 0:
x_end = num_x
if y_end is 0:
y_end = num_y
if z_end is 0:
z_end = num_z
# Construct dataset from desired y.
dataset = tmpdata[z_start:z_end:z_step, y_start:y_end:y_step,
x_start:x_end:x_step]
return dataset
def edf2(self, x_start=0, x_end=0, x_step=1, y_start=0, y_end=0, y_step=1):
"""
Read 2-D tomographic projection data from an EDF (ESRF) file.
Parameters
file_name : str
Input edf file.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
Returns
out : array
Output 2-D matrix as numpy array.
"""
try:
# Read data from file.
f = EdfFile(self.file_name, access='r')
dic = f.GetStaticHeader(0)
tmpdata = np.empty((int(dic['Dim_2']), int(dic['Dim_1'])))
tmpdata[::] = f.GetData(0)
num_y, num_x = np.shape(tmpdata)
if x_end is 0:
x_end = num_x
if y_end is 0:
y_end = num_y
array = tmpdata[y_start:y_end:y_step, x_start:x_end:x_step]
except KeyError:
self.logger.error(
"FILE DOES NOT CONTAIN A VALID TOMOGRAPHY DATA SET")
array = None
return array
def edf2(self, x_start=0, x_end=0, x_step=1, y_start=0, y_end=0, y_step=1):
"""
Read 2-D tomographic projection data from an EDF (ESRF) file.
Parameters
file_name : str
Input edf file.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
Returns
out : array
Output 2-D matrix as numpy array.
"""
# Read data from file.
f = EdfFile(self.file_name, access='r')
dic = f.GetStaticHeader(0)
tmpdata = np.empty((int(dic['Dim_2']), int(dic['Dim_1'])))
tmpdata[::] = f.GetData(0)
num_y, num_x = np.shape(tmpdata)
if x_end is 0:
x_end = num_x
if y_end is 0:
y_end = num_y
return tmpdata[y_start:y_end:y_step, x_start:x_end:x_step]
