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NEXUSDataWriter.py
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NEXUSDataWriter.py
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# -*- coding: utf-8 -*-
# This work is part of the Core Imaging Library (CIL) developed by CCPi
# (Collaborative Computational Project in Tomographic Imaging), with
# substantial contributions by UKRI-STFC and University of Manchester.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import numpy as np
import os
from cil.framework import AcquisitionData, AcquisitionGeometry, ImageData, ImageGeometry
import datetime
h5pyAvailable = True
try:
import h5py
except:
h5pyAvailable = False
class NEXUSDataWriter(object):
def __init__(self,
**kwargs):
self.data = kwargs.get('data', None)
self.file_name = kwargs.get('file_name', None)
if ((self.data is not None) and (self.file_name is not None)):
self.set_up(data = self.data,
file_name = self.file_name)
def set_up(self,
data = None,
file_name = None):
self.data = data
self.file_name = file_name
if not ((isinstance(self.data, ImageData)) or
(isinstance(self.data, AcquisitionData))):
raise Exception('Writer supports only following data types:\n' +
' - ImageData\n - AcquisitionData')
# check that h5py library is installed
if (h5pyAvailable == False):
raise Exception('h5py is not available, cannot load NEXUS files.')
def write(self):
# if the folder does not exist, create the folder
if not os.path.isdir(os.path.dirname(self.file_name)):
os.mkdir(os.path.dirname(self.file_name))
# create the file
with h5py.File(self.file_name, 'w') as f:
# give the file some important attributes
f.attrs['file_name'] = self.file_name
f.attrs['file_time'] = str(datetime.datetime.utcnow())
f.attrs['creator'] = np.string_('NEXUSDataWriter.py')
f.attrs['NeXus_version'] = '4.3.0'
f.attrs['HDF5_Version'] = h5py.version.hdf5_version
f.attrs['h5py_version'] = h5py.version.version
# create the NXentry group
nxentry = f.create_group('entry1/tomo_entry')
nxentry.attrs['NX_class'] = 'NXentry'
# create dataset to store data
ds_data = f.create_dataset('entry1/tomo_entry/data/data',
(self.data.as_array().shape),
dtype = 'float32',
data = self.data.as_array())
# set up dataset attributes
if (isinstance(self.data, ImageData)):
ds_data.attrs['data_type'] = 'ImageData'
else:
ds_data.attrs['data_type'] = 'AcquisitionData'
for i in range(self.data.number_of_dimensions):
ds_data.attrs['dim{}'.format(i)] = self.data.dimension_labels[i]
if (isinstance(self.data, AcquisitionData)):
# create group to store configuration
f.create_group('entry1/tomo_entry/config')
f.create_group('entry1/tomo_entry/config/source')
f.create_group('entry1/tomo_entry/config/detector')
f.create_group('entry1/tomo_entry/config/rotation_axis')
ds_data.attrs['geometry'] = self.data.geometry.config.system.geometry
ds_data.attrs['dimension'] = self.data.geometry.config.system.dimension
ds_data.attrs['num_channels'] = self.data.geometry.config.channels.num_channels
f.create_dataset('entry1/tomo_entry/config/detector/direction_x',
(self.data.geometry.config.system.detector.direction_x.shape),
dtype = 'float32',
data = self.data.geometry.config.system.detector.direction_x)
f.create_dataset('entry1/tomo_entry/config/detector/position',
(self.data.geometry.config.system.detector.position.shape),
dtype = 'float32',
data = self.data.geometry.config.system.detector.position)
if self.data.geometry.config.system.geometry == 'cone':
f.create_dataset('entry1/tomo_entry/config/source/position',
(self.data.geometry.config.system.source.position.shape),
dtype = 'float32',
data = self.data.geometry.config.system.source.position)
else:
f.create_dataset('entry1/tomo_entry/config/ray/direction',
(self.data.geometry.config.system.ray.direction.shape),
dtype = 'float32',
data = self.data.geometry.config.system.ray.direction)
f.create_dataset('entry1/tomo_entry/config/rotation_axis/position',
(self.data.geometry.config.system.rotation_axis.position.shape),
dtype = 'float32',
data = self.data.geometry.config.system.rotation_axis.position)
ds_data.attrs['num_pixels_h'] = self.data.geometry.config.panel.num_pixels[0]
ds_data.attrs['pixel_size_h'] = self.data.geometry.config.panel.pixel_size[0]
ds_data.attrs['panel_origin'] = self.data.geometry.config.panel.origin
if self.data.geometry.config.system.dimension == '3D':
f.create_dataset('entry1/tomo_entry/config/detector/direction_y',
(self.data.geometry.config.system.detector.direction_y.shape),
dtype = 'float32',
data = self.data.geometry.config.system.detector.direction_y)
f.create_dataset('entry1/tomo_entry/config/rotation_axis/direction',
(self.data.geometry.config.system.rotation_axis.direction.shape),
dtype = 'float32',
data = self.data.geometry.config.system.rotation_axis.direction)
ds_data.attrs['num_pixels_v'] = self.data.geometry.config.panel.num_pixels[1]
ds_data.attrs['pixel_size_v'] = self.data.geometry.config.panel.pixel_size[1]
angles = f.create_dataset('entry1/tomo_entry/config/angles',
(self.data.geometry.config.angles.angle_data.shape),
dtype = 'float32',
data = self.data.geometry.config.angles.angle_data)
angles.attrs['angle_unit'] = self.data.geometry.config.angles.angle_unit
angles.attrs['initial_angle'] = self.data.geometry.config.angles.initial_angle
else: # ImageData
ds_data.attrs['voxel_num_x'] = self.data.geometry.voxel_num_x
ds_data.attrs['voxel_num_y'] = self.data.geometry.voxel_num_y
ds_data.attrs['voxel_num_z'] = self.data.geometry.voxel_num_z
ds_data.attrs['voxel_size_x'] = self.data.geometry.voxel_size_x
ds_data.attrs['voxel_size_y'] = self.data.geometry.voxel_size_y
ds_data.attrs['voxel_size_z'] = self.data.geometry.voxel_size_z
ds_data.attrs['center_x'] = self.data.geometry.center_x
ds_data.attrs['center_y'] = self.data.geometry.center_y
ds_data.attrs['center_z'] = self.data.geometry.center_z
ds_data.attrs['channels'] = self.data.geometry.channels
ds_data.attrs['channel_spacing'] = self.data.geometry.channel_spacing