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# -*- coding: utf-8 -*-
# CCP in Tomographic Imaging (CCPi) Core Imaging Library (CIL).
# Copyright 2017 UKRI-STFC
# Copyright 2017 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
import os
from ccpi.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_container = kwargs.get('data_container', None)
self.file_name = kwargs.get('file_name', None)
if ((self.data_container is not None) and (self.file_name is not None)):
self.set_up(data_container = self.data_container,
file_name = self.file_name)
def set_up(self,
data_container = None,
file_name = None):
self.data_container = data_container
self.file_name = file_name
if not ((isinstance(self.data_container, ImageData)) or
(isinstance(self.data_container, 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_file(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'] = '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_container.as_array().shape),
dtype = 'float32',
data = self.data_container.as_array())
# set up dataset attributes
if (isinstance(self.data_container, ImageData)):
ds_data.attrs['data_type'] = 'ImageData'
else:
ds_data.attrs['data_type'] = 'AcquisitionData'
for i in range(self.data_container.as_array().ndim):
ds_data.attrs['dim{}'.format(i)] = self.data_container.dimension_labels[i]
if (isinstance(self.data_container, AcquisitionData)):
ds_data.attrs['geom_type'] = self.data_container.geometry.geom_type
ds_data.attrs['dimension'] = self.data_container.geometry.dimension
if self.data_container.geometry.dist_source_center is not None:
ds_data.attrs['dist_source_center'] = self.data_container.geometry.dist_source_center
if self.data_container.geometry.dist_center_detector is not None:
ds_data.attrs['dist_center_detector'] = self.data_container.geometry.dist_center_detector
ds_data.attrs['pixel_num_h'] = self.data_container.geometry.pixel_num_h
ds_data.attrs['pixel_size_h'] = self.data_container.geometry.pixel_size_h
ds_data.attrs['pixel_num_v'] = self.data_container.geometry.pixel_num_v
ds_data.attrs['pixel_size_v'] = self.data_container.geometry.pixel_size_v
ds_data.attrs['channels'] = self.data_container.geometry.channels
ds_data.attrs['n_angles'] = self.data_container.geometry.angles.shape[0]
# create the dataset to store rotation angles
ds_angles = f.create_dataset('entry1/tomo_entry/data/rotation_angle',
(self.data_container.geometry.angles.shape),
dtype = 'float32',
data = self.data_container.geometry.angles)
#ds_angles.attrs['units'] = self.data_container.geometry.angle_unit
else: # ImageData
ds_data.attrs['voxel_num_x'] = self.data_container.geometry.voxel_num_x
ds_data.attrs['voxel_num_y'] = self.data_container.geometry.voxel_num_y
ds_data.attrs['voxel_num_z'] = self.data_container.geometry.voxel_num_z
ds_data.attrs['voxel_size_x'] = self.data_container.geometry.voxel_size_x
ds_data.attrs['voxel_size_y'] = self.data_container.geometry.voxel_size_y
ds_data.attrs['voxel_size_z'] = self.data_container.geometry.voxel_size_z
ds_data.attrs['center_x'] = self.data_container.geometry.center_x
ds_data.attrs['center_y'] = self.data_container.geometry.center_y
ds_data.attrs['center_z'] = self.data_container.geometry.center_z
ds_data.attrs['channels'] = self.data_container.geometry.channels
'''
# usage example
xtek_file = '/home/evelina/nikon_data/SophiaBeads_256_averaged.xtekct'
reader = NikonDataReader()
reader.set_up(xtek_file = xtek_file,
binning = [3, 1],
roi = [200, 500, 1500, 2000],
normalize = True)
data = reader.load_projections()
ag = reader.get_geometry()
writer = NEXUSDataWriter()
writer.set_up(file_name = '/home/evelina/test_nexus.nxs',
data_container = data)
writer.write_file()
ig = ImageGeometry(voxel_num_x = 100,
voxel_num_y = 100)
im = ImageData(array = numpy.zeros((100, 100), dtype = 'float'),
geometry = ig)
im_writer = NEXUSDataWriter()
im_writer.set_up(file_name = '/home/evelina/test_nexus_im.nxs',
data_container = im)
im_writer.write_file()
ag = AcquisitionGeometry(geom_type = 'parallel',
dimension = '2D',
angles = numpy.array([0, 1]),
pixel_num_h = 200,
pixel_size_h = 1,
pixel_num_v = 100,
pixel_size_v = 1)
ad = ag.allocate()
ag_writer = NEXUSDataWriter()
ag_writer.set_up(file_name = '/home/evelina/test_nexus_ag.nxs',
data_container = ad)
ag_writer.write_file()
'''
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