savu.plugins.reconstructions.astra_recons.base_astra_recon.BaseAstraRecon.setup() - Code Metrics - Inspection of "Iterative plugins API" - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed

Pull Request — master (#888)

by Daniil

created 2022-02-14 16:50 UTC

BaseAstraRecon.setup() B

↳ Parent: savu.plugins.reconstructions.astra_recons.base_astra_recon

Complexity

Conditions

Size

Total Lines	36
Code Lines	28

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	7
eloc	28
nop	1
dl	0
loc	36
rs	7.808
c	0
b	0
f	0

# Copyright 2014 Diamond Light Source Ltd.
#
# 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.

"""
.. module:: base_astra_recon
   :platform: Unix
   :synopsis: A base for all Astra toolbox reconstruction algorithms
.. moduleauthor:: Mark Basham <[email protected]>
"""

import astra
import numpy as np

from savu.plugins.reconstructions.base_recon import BaseRecon
from savu.core.iterate_plugin_group_utils import enable_iterative_loop, \
    check_if_end_plugin_in_iterate_group

class BaseAstraRecon(BaseRecon):

    def __init__(self, name='BaseAstraRecon'):
        super(BaseAstraRecon, self).__init__(name)
        self.res = False

    # total number of output datasets
    def nOutput_datasets(self):
        if check_if_end_plugin_in_iterate_group(self.exp):
            return 2
        else:
            return 1

    # total number of output datasets that are clones
    def nClone_datasets(self):
        if check_if_end_plugin_in_iterate_group(self.exp):
            return 1
        else:
            return 0

    @enable_iterative_loop
    def setup(self):
        self.alg = self.parameters['algorithm']
        self.get_max_frames = self._get_multiple if '3D' in self.alg else self._get_single

        super(BaseAstraRecon, self).setup()
        out_dataset = self.get_out_datasets()

        # if res_norm is required then setup another output dataset
        if len(out_dataset) == 3 and self.nClone_datasets() == 1:
            err_str = "The res_norm output dataset has not yet been " \
                "implemented for when AstraReconCpu is at the end of an " \
                "iterative loop"
            raise ValueError(err_str)
        elif len(out_dataset) == 2 and self.nClone_datasets() == 0:
            self.res = True
            out_pData = self.get_plugin_out_datasets()
            in_data = self.get_in_datasets()[0]
            dim_detX = \
                in_data.get_data_dimension_by_axis_label('y', contains=True)

            nIts = self.parameters['n_iterations']
            nIts = nIts if isinstance(nIts, list) else [nIts]
            self.len_res = max(nIts)
            shape = (in_data.get_shape()[dim_detX], max(nIts))

            label = ['vol_y.voxel', 'iteration.number']
            pattern = {'name': 'SINOGRAM', 'slice_dims': (0,),
                       'core_dims': (1,)}

            out_dataset[1].create_dataset(axis_labels=label, shape=shape)
            out_dataset[1].add_pattern(pattern['name'],
                                       slice_dims=pattern['slice_dims'],
                                       core_dims=pattern['core_dims'])
            out_pData[1].plugin_data_setup(
                pattern['name'], self.get_max_frames())

    def pre_process(self):
        self.alg = self.parameters['algorithm']
        self.iters = self.parameters['n_iterations']

        if '3D' in self.alg:
            self.setup_3D()
            self.process_frames = self.astra_3D_recon
        else:
            self.setup_2D()
            self.process_frames = self.astra_2D_recon

    def setup_2D(self):

        pData = self.get_plugin_in_datasets()[0]
        self.dim_detX = \
            pData.get_data_dimension_by_axis_label('x', contains=True)
        self.dim_rot = \
            pData.get_data_dimension_by_axis_label('rot', contains=True)

        self.sino_shape = pData.get_shape()
        self.nDims = len(self.sino_shape)
        self.nCols = self.sino_shape[self.dim_detX]
        self.set_mask(self.sino_shape)

    def set_mask(self, shape):
        l = self.get_plugin_out_datasets()[0].get_shape()[0]
        c = np.linspace(-l / 2.0, l / 2.0, l)
        x, y = np.meshgrid(c, c)

        ratio = self.parameters['ratio']
        if isinstance(ratio, list) or isinstance(ratio, tuple):
            ratio_mask = ratio[0]
            outer_mask = ratio[1]
            if isinstance(outer_mask, str):
                outer_mask = np.nan
        else:
            ratio_mask = ratio
            outer_mask = np.nan
        r = (l - 1) * ratio_mask
        outer_pad = True if self.parameters['outer_pad'] and self.padding_alg\
            else False
        if not outer_pad:
            self.manual_mask = \
                np.array((x**2 + y**2 < (r / 2.0)**2), dtype=np.float)
            self.manual_mask[self.manual_mask == 0] = outer_mask
        else:
            self.manual_mask = False

    def astra_2D_recon(self, data):
        sino = data[0]
        cor, angles, vol_shape, init = self.get_frame_params()
        angles = np.deg2rad(angles)
        if self.res:
            res = np.zeros(self.len_res)
        # create volume geom
        vol_geom = astra.create_vol_geom(vol_shape)
        # create projection geom
        det_width = sino.shape[self.dim_detX]
        proj_geom = astra.create_proj_geom('parallel', 1.0, det_width, angles)
        sino = np.transpose(sino, (self.dim_rot, self.dim_detX))

        # create sinogram id
        sino_id = astra.data2d.create("-sino", proj_geom, sino)
        # create reconstruction id
        if init is not None:
            rec_id = astra.data2d.create('-vol', vol_geom, init)
        else:
            rec_id = astra.data2d.create('-vol', vol_geom)

#        if self.mask_id:
#            self.mask_id = astra.data2d.create('-vol', vol_geom, self.mask)
        # setup configuration options
        cfg = self.set_config(rec_id, sino_id, proj_geom, vol_geom)
        # create algorithm id
        alg_id = astra.algorithm.create(cfg)
        # run algorithm
        if self.res:
            for j in range(self.iters):
                # Run a single iteration
                astra.algorithm.run(alg_id, 1)
                res[j] = astra.algorithm.get_res_norm(alg_id)
        else:
            astra.algorithm.run(alg_id, self.iters)
        # get reconstruction matrix

        if self.manual_mask is not False:
            recon = self.manual_mask * astra.data2d.get(rec_id)
        else:
            recon = astra.data2d.get(rec_id)

        # delete geometry
        self.delete(alg_id, sino_id, rec_id, False)
        return [recon, res] if self.res else recon


    def set_config(self, rec_id, sino_id, proj_geom, vol_geom):

        cfg = astra.astra_dict(self.alg)
        cfg['ReconstructionDataId'] = rec_id
        cfg['ProjectionDataId'] = sino_id
        if 'FBP' in self.alg:
            fbp_filter = self.parameters['FBP_filter'] if 'FBP_filter' in \
                list(self.parameters.keys()) else 'none'
            cfg['FilterType'] = fbp_filter
        if 'projector' in list(self.parameters.keys()):
            proj_id = astra.create_projector(
                self.parameters['projector'], proj_geom, vol_geom)
            cfg['ProjectorId'] = proj_id
        cfg = self.set_options(cfg)
        return cfg

    def delete(self, alg_id, sino_id, rec_id, proj_id):
        astra.algorithm.delete(alg_id)
        astra.data2d.delete(sino_id)
        astra.data2d.delete(rec_id)
        if proj_id:
            astra.projector.delete(proj_id)

    def _get_single(self):
        return 'single'

    def _get_multiple(self):
        return 'multiple'


1		# Copyright 2014 Diamond Light Source Ltd.
2		#
3		# Licensed under the Apache License, Version 2.0 (the "License");
4		# you may not use this file except in compliance with the License.
5		# You may obtain a copy of the License at
6		#
7		# http://www.apache.org/licenses/LICENSE-2.0
8		#
9		# Unless required by applicable law or agreed to in writing, software
10		# distributed under the License is distributed on an "AS IS" BASIS,
11		# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12		# See the License for the specific language governing permissions and
13		# limitations under the License.
14
15		"""
16		.. module:: base_astra_recon
17		:platform: Unix
18		:synopsis: A base for all Astra toolbox reconstruction algorithms
19		.. moduleauthor:: Mark Basham <[email protected]>
20		"""
21
22		import astra
23		import numpy as np
24
25		from savu.plugins.reconstructions.base_recon import BaseRecon
26		from savu.core.iterate_plugin_group_utils import enable_iterative_loop, \
27		check_if_end_plugin_in_iterate_group
28
29		class BaseAstraRecon(BaseRecon):
30
31		def __init__(self, name='BaseAstraRecon'):
32		super(BaseAstraRecon, self).__init__(name)
33		self.res = False
34
35		# total number of output datasets
36		def nOutput_datasets(self):
37		if check_if_end_plugin_in_iterate_group(self.exp):
38		return 2
39		else:
40		return 1
41
42		# total number of output datasets that are clones
43		def nClone_datasets(self):
44		if check_if_end_plugin_in_iterate_group(self.exp):
45		return 1
46		else:
47		return 0
48
49		@enable_iterative_loop
50		def setup(self):
51		self.alg = self.parameters['algorithm']
52		self.get_max_frames = self._get_multiple if '3D' in self.alg else self._get_single
53
54		super(BaseAstraRecon, self).setup()
55		out_dataset = self.get_out_datasets()
56
57		# if res_norm is required then setup another output dataset
58		if len(out_dataset) == 3 and self.nClone_datasets() == 1:
59		err_str = "The res_norm output dataset has not yet been " \
60		"implemented for when AstraReconCpu is at the end of an " \
61		"iterative loop"
62		raise ValueError(err_str)
63		elif len(out_dataset) == 2 and self.nClone_datasets() == 0:
64		self.res = True
65		out_pData = self.get_plugin_out_datasets()
66		in_data = self.get_in_datasets()[0]
67		dim_detX = \
68		in_data.get_data_dimension_by_axis_label('y', contains=True)
69
70		nIts = self.parameters['n_iterations']
71		nIts = nIts if isinstance(nIts, list) else [nIts]
72		self.len_res = max(nIts)
73		shape = (in_data.get_shape()[dim_detX], max(nIts))
74
75		label = ['vol_y.voxel', 'iteration.number']
76		pattern = {'name': 'SINOGRAM', 'slice_dims': (0,),
77		'core_dims': (1,)}
78
79		out_dataset[1].create_dataset(axis_labels=label, shape=shape)
80		out_dataset[1].add_pattern(pattern['name'],
81		slice_dims=pattern['slice_dims'],
82		core_dims=pattern['core_dims'])
83		out_pData[1].plugin_data_setup(
84		pattern['name'], self.get_max_frames())
85
86		def pre_process(self):
87		self.alg = self.parameters['algorithm']
88		self.iters = self.parameters['n_iterations']
89
90		if '3D' in self.alg:
91		self.setup_3D()
92		self.process_frames = self.astra_3D_recon
93		else:
94		self.setup_2D()
95		self.process_frames = self.astra_2D_recon
96
97	View Code Duplication	def setup_2D(self):
		0 ignored issues – show Duplication introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
98		pData = self.get_plugin_in_datasets()[0]
99		self.dim_detX = \
100		pData.get_data_dimension_by_axis_label('x', contains=True)
101		self.dim_rot = \
102		pData.get_data_dimension_by_axis_label('rot', contains=True)
103
104		self.sino_shape = pData.get_shape()
105		self.nDims = len(self.sino_shape)
106		self.nCols = self.sino_shape[self.dim_detX]
107		self.set_mask(self.sino_shape)
108
109		def set_mask(self, shape):
110		l = self.get_plugin_out_datasets()[0].get_shape()[0]
111		c = np.linspace(-l / 2.0, l / 2.0, l)
112		x, y = np.meshgrid(c, c)
113
114		ratio = self.parameters['ratio']
115		if isinstance(ratio, list) or isinstance(ratio, tuple):
116		ratio_mask = ratio[0]
117		outer_mask = ratio[1]
118		if isinstance(outer_mask, str):
119		outer_mask = np.nan
120		else:
121		ratio_mask = ratio
122		outer_mask = np.nan
123		r = (l - 1) * ratio_mask
124		outer_pad = True if self.parameters['outer_pad'] and self.padding_alg\
125		else False
126		if not outer_pad:
127		self.manual_mask = \
128		np.array((x2 + y2 < (r / 2.0)**2), dtype=np.float)
129		self.manual_mask[self.manual_mask == 0] = outer_mask
130		else:
131		self.manual_mask = False
132
133		def astra_2D_recon(self, data):
134		sino = data[0]
135		cor, angles, vol_shape, init = self.get_frame_params()
136		angles = np.deg2rad(angles)
137		if self.res:
138		res = np.zeros(self.len_res)
139		# create volume geom
140		vol_geom = astra.create_vol_geom(vol_shape)
141		# create projection geom
142		det_width = sino.shape[self.dim_detX]
143		proj_geom = astra.create_proj_geom('parallel', 1.0, det_width, angles)
144		sino = np.transpose(sino, (self.dim_rot, self.dim_detX))
145
146		# create sinogram id
147		sino_id = astra.data2d.create("-sino", proj_geom, sino)
148		# create reconstruction id
149		if init is not None:
150		rec_id = astra.data2d.create('-vol', vol_geom, init)
151		else:
152		rec_id = astra.data2d.create('-vol', vol_geom)
153
154		# if self.mask_id:
155		# self.mask_id = astra.data2d.create('-vol', vol_geom, self.mask)
156		# setup configuration options
157		cfg = self.set_config(rec_id, sino_id, proj_geom, vol_geom)
158		# create algorithm id
159		alg_id = astra.algorithm.create(cfg)
160		# run algorithm
161		if self.res:
162		for j in range(self.iters):
163		# Run a single iteration
164		astra.algorithm.run(alg_id, 1)
165		res[j] = astra.algorithm.get_res_norm(alg_id)
166		else:
167		astra.algorithm.run(alg_id, self.iters)
168		# get reconstruction matrix
169
170		if self.manual_mask is not False:
171		recon = self.manual_mask * astra.data2d.get(rec_id)
172		else:
173		recon = astra.data2d.get(rec_id)
174
175		# delete geometry
176		self.delete(alg_id, sino_id, rec_id, False)
177		return [recon, res] if self.res else recon
		0 ignored issues – show introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `res` does not seem to be defined in case `self.res` on line `137` is `False`. Are you sure this can never be the case? Loading history...
178
179	View Code Duplication	def set_config(self, rec_id, sino_id, proj_geom, vol_geom):
		0 ignored issues – show Duplication introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
180		cfg = astra.astra_dict(self.alg)
181		cfg['ReconstructionDataId'] = rec_id
182		cfg['ProjectionDataId'] = sino_id
183		if 'FBP' in self.alg:
184		fbp_filter = self.parameters['FBP_filter'] if 'FBP_filter' in \
185		list(self.parameters.keys()) else 'none'
186		cfg['FilterType'] = fbp_filter
187		if 'projector' in list(self.parameters.keys()):
188		proj_id = astra.create_projector(
189		self.parameters['projector'], proj_geom, vol_geom)
190		cfg['ProjectorId'] = proj_id
191		cfg = self.set_options(cfg)
192		return cfg
193
194		def delete(self, alg_id, sino_id, rec_id, proj_id):
195		astra.algorithm.delete(alg_id)
196		astra.data2d.delete(sino_id)
197		astra.data2d.delete(rec_id)
198		if proj_id:
199		astra.projector.delete(proj_id)
200
201		def _get_single(self):
202		return 'single'
203
204		def _get_multiple(self):
205		return 'multiple'
206

DiamondLightSource / Savu

Pull Request — master (#888)

BaseAstraRecon.setup() B

Complexity

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