# Copyright 2021 United Kingdom Research and Innovation
# Copyright 2021 The 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.
#
# Authors:
# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
from cil.framework import ImageGeometry, AcquisitionGeometry
from cil.framework import ImageData, AcquisitionData, DataOrder
import tomophantom
from tomophantom import TomoP2D, TomoP3D
import os
import numpy as np
import ctypes, platform
from ctypes import util
# check for the extension
if platform.system() == 'Linux':
dll = 'libctomophantom.so'
elif platform.system() == 'Windows':
dll_file = 'ctomophantom.dll'
dll = util.find_library(dll_file)
elif platform.system() == 'Darwin':
dll = 'libctomophantom.dylib'
else:
raise ValueError('Not supported platform, ', platform.system())
libtomophantom = ctypes.cdll.LoadLibrary(dll)
path = os.path.dirname(tomophantom.__file__)
path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
path_library3D = os.path.join(path, "Phantom3DLibrary.dat")
def is_model_temporal(num_model, num_dims=2):
'''Returns whether a model in the TomoPhantom library is temporal
This will go to check the installed library files from TomoPhantom
https://github.com/dkazanc/TomoPhantom/tree/master/PhantomLibrary/models
:param num_model: model number
:type num_model: int
:param num_dims: dimensionality of the phantom, 2D or 3D
:type num_dims: int, default 2
'''
return get_model_num_channels(num_model, num_dims) > 1
def get_model_num_channels(num_model, num_dims=2):
'''Returns number of temporal steps (channels) the model has
This will go to check the installed library files from TomoPhantom
https://github.com/dkazanc/TomoPhantom/tree/master/PhantomLibrary/models
https://github.com/dkazanc/TomoPhantom/blob/v1.4.9/Core/utils.c#L27
https://github.com/dkazanc/TomoPhantom/blob/v1.4.9/Core/utils.c#L269
:param num_model: model number
:type num_model: int
:param num_dims: dimensionality of the phantom, 2D or 3D
:type num_dims: int, default 2
'''
return check_model_params(num_model, num_dims=num_dims)[3]
def check_model_params(num_model, num_dims=2):
'''Returns params_switch array from the C TomoPhantom library in function checkParams2D or checkParams3D
This will go to check the installed library files from TomoPhantom
https://github.com/dkazanc/TomoPhantom/tree/master/PhantomLibrary/models
https://github.com/dkazanc/TomoPhantom/blob/v1.4.9/Core/utils.c#L27
https://github.com/dkazanc/TomoPhantom/blob/v1.4.9/Core/utils.c#L269
:param num_model: model number
:type num_model: int
:param num_dims: dimensionality of the phantom, 2D or 3D
:type num_dims: int, default 2
'''
if num_dims == 2:
libtomophantom.checkParams2D.argtypes = [ctypes.POINTER(ctypes.c_int), # pointer to the params array
ctypes.c_int, # model number selector (int)
ctypes.c_char_p] # string to the library file
params = np.zeros([10], dtype=np.int32)
params_p = params.ctypes.data_as(ctypes.POINTER(ctypes.c_int))
lib2d_p = str(path_library2D).encode('utf-8')
libtomophantom.checkParams2D(params_p, num_model, lib2d_p)
return params
elif num_dims == 3:
libtomophantom.checkParams3D.argtypes = [ctypes.POINTER(ctypes.c_int), # pointer to the params array
ctypes.c_int, # model number selector (int)
ctypes.c_char_p] # string to the library file
params = np.zeros([11], dtype=np.int32)
params_p = params.ctypes.data_as(ctypes.POINTER(ctypes.c_int))
lib2d_p = str(path_library3D).encode('utf-8')
libtomophantom.checkParams3D(params_p, num_model, lib2d_p)
return params
else:
raise ValueError('Unsupported dimensionality. Expected 2 or 3, got {}'.format(dims))
[docs]def get_ImageData(num_model, geometry):
'''Returns an ImageData relative to geometry with the model num_model from tomophantom
:param num_model: model number
:type num_model: int
:param geometry: geometrical info that describes the phantom
:type geometry: ImageGeometry
Example usage:
.. code-block:: python
ndim = 2
N=128
angles = np.linspace(0, 360, 50, True, dtype=np.float32)
offset = 0.4
channels = 3
if ndim == 2:
ag = AcquisitionGeometry.create_Cone2D((offset,-100), (offset,100))
ag.set_panel(N)
else:
ag = AcquisitionGeometry.create_Cone3D((offset,-100, 0), (offset,100,0))
ag.set_panel((N,N-2))
ag.set_channels(channels)
ag.set_angles(angles, angle_unit=AcquisitionGeometry.DEGREE)
ig = ag.get_ImageGeometry()
num_model = 1
phantom = TomoPhantom.get_ImageData(num_model=num_model, geometry=ig)
'''
ig = geometry.copy()
ig.set_labels(DataOrder.TOMOPHANTOM_IG_LABELS)
num_dims = len(ig.dimension_labels)
if ImageGeometry.CHANNEL in ig.dimension_labels:
if not is_model_temporal(num_model):
raise ValueError('Selected model {} is not a temporal model, please change your selection'.format(num_model))
if num_dims == 4:
# 3D+time for tomophantom
# output dimensions channel and then spatial,
# e.g. [ 'channel', 'vertical', 'horizontal_y', 'horizontal_x' ]
num_model = num_model
shape = tuple(ig.shape[1:])
phantom_arr = TomoP3D.ModelTemporal(num_model, shape, path_library3D)
elif num_dims == 3:
# 2D+time for tomophantom
# output dimensions channel and then spatial,
# e.g. [ 'channel', 'horizontal_y', 'horizontal_x' ]
N = ig.shape[1]
num_model = num_model
phantom_arr = TomoP2D.ModelTemporal(num_model, ig.shape[1], path_library2D)
else:
raise ValueError('Wrong ImageGeometry')
if ig.channels != phantom_arr.shape[0]:
raise ValueError('The required model {} has {} channels. The ImageGeometry you passed has {}. Please update your ImageGeometry.'\
.format(num_model, ig.channels, phantom_arr.shape[0]))
else:
if num_dims == 3:
# 3D
num_model = num_model
phantom_arr = TomoP3D.Model(num_model, ig.shape, path_library3D)
elif num_dims == 2:
# 2D
if ig.shape[0] != ig.shape[1]:
raise ValueError('Can only handle square ImageData, got shape'.format(ig.shape))
N = ig.shape[0]
num_model = num_model
phantom_arr = TomoP2D.Model(num_model, N, path_library2D)
else:
raise ValueError('Wrong ImageGeometry')
im_data = ImageData(phantom_arr, geometry=ig, suppress_warning=True)
im_data.reorder(list(geometry.dimension_labels))
return im_data