savu.plugins.reconstructions.base_recon.BaseRecon._get_volume_dimensions() - Code Metrics - Inspection of "forward projector using tomobar" - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed

Pull Request — master (#700)

by Daniil

created 2021-05-21 10:11 UTC

BaseRecon._get_volume_dimensions() A

↳ Parent: savu.plugins.reconstructions.base_recon

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Total Lines	2
Code Lines	2

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cc	1
eloc	2
nop	1
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# 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_recon
   :platform: Unix
   :synopsis: A base class for all reconstruction methods

.. moduleauthor:: Mark Basham <[email protected]>

"""
import math
import copy
import numpy as np
np.seterr(divide='ignore', invalid='ignore')

import savu.core.utils as cu
from savu.plugins.plugin import Plugin

MAX_OUTER_PAD = 2.1


class BaseRecon(Plugin):
    """
    A base class for reconstruction plugins

    :u*param centre_of_rotation: Centre of rotation to use for the \
    reconstruction. Default: 0.0.

    :u*param init_vol: Dataset to use as volume initialiser \
    (doesn't currently work with preview). Default: None.

    :param centre_pad: Pad the sinogram to centre it in order to fill the \
    reconstructed volume ROI for asthetic purposes.\
    NB: Only available for selected algorithms and will be ignored otherwise. \
    WARNING: This will significantly increase the size of the data and the \
    time to compute the reconstruction). Default: False.

    :param outer_pad: Pad the sinogram width to fill the reconstructed volume \
    for asthetic purposes.\
    Choose from True (defaults to sqrt(2)), False or float <= 2.1. \
    NB: Only available for selected algorithms and will be ignored otherwise.\
    WARNING: This will increase the size of the data and the \
    time to compute the reconstruction). Default: False.

    :u*param log: Take the log of the data before reconstruction \
    (True or False). Default: True.

    :u*param preview: A slice list of required frames. Default: [].

    :param force_zero: Set any values in the reconstructed image outside of \
    this range to zero. Default: [None, None].

    :param ratio: Ratio between the diameter of a circle mask and the width of\
    a reconstructed image. If passed as a list or tuple, the second value is \
    assigned to the outer mask area, e.g [0.95, 0.0]. Default: 0.95.

    :param log_func: Override the default log \
        function. Default: 'np.nan_to_num(-np.log(sino))'.

    :param vol_shape: Override the size of the reconstruction volume with an \
    integer value. Default: 'fixed'.
    """

    def __init__(self, name='BaseRecon'):
        super(BaseRecon, self).__init__(name)
        self.nOut = 1
        self.nIn = 1
        self.scan_dim = None
        self.rep_dim = None
        self.br_vol_shape = None
        self.frame_angles = None
        self.frame_cors = None
        self.frame_init_data = None
        self.centre = None
        self.base_pad_amount = None
        self.padding_alg = False
        self.cor_shift = 0
        self.init_vol = False
        self.cor_as_dataset = False

    def base_pre_process(self):
        in_data, out_data = self.get_datasets()
        in_pData, out_pData = self.get_plugin_datasets()
        self.pad_dim = \
            in_pData[0].get_data_dimension_by_axis_label('x', contains=True)
        in_meta_data = self.get_in_meta_data()[0]
        self.__set_padding_alg()

        self.exp.log(self.name + " End")
        self.br_vol_shape = out_pData[0].get_shape()
        self.set_centre_of_rotation(in_data[0], out_data[0], in_meta_data)

        self.main_dir = in_data[0].get_data_patterns()['SINOGRAM']['main_dir']
        self.angles = in_meta_data.get('rotation_angle')
        if len(self.angles.shape) != 1:
            self.scan_dim = in_data[0].get_data_dimension_by_axis_label('scan')
        self.slice_dirs = out_data[0].get_slice_dimensions()

        shape = in_pData[0].get_shape()
        factor = self.__get_outer_pad()
        self.sino_pad = int(math.ceil(factor * shape[self.pad_dim]))

        self.sino_func, self.cor_func = self.set_function(shape) if \
            self.padding_alg else self.set_function(False)

        self.range = self.parameters['force_zero']
        self.fix_sino = self.get_sino_centre_method()

    def __get_outer_pad(self):
        # length of diagonal of square is side*sqrt(2)
        factor = math.sqrt(2) - 1
        pad = self.parameters['outer_pad'] if 'outer_pad' in \
            list(self.parameters.keys()) else False

        if pad is not False and not self.padding_alg:
            msg = 'This reconstruction algorithm cannot be padded.'
            cu.user_message(msg)
            return 0

        if isinstance(pad, bool):
            return factor if pad is True else 0
        factor = float(pad)
        if factor > MAX_OUTER_PAD:
            factor = MAX_OUTER_PAD
            msg = 'Maximum outer_pad value is 2.1, using this instead'
            cu.user_message(msg)
        return float(pad)

    def __set_padding_alg(self):
        """ Determine if this is an algorithm that allows sinogram padding. """
        pad_algs = self.get_padding_algorithms()
        alg = self.parameters['algorithm'] if 'algorithm' in \
            list(self.parameters.keys()) else None
        self.padding_alg = True if alg in pad_algs else False

    def get_vol_shape(self):
        return self.br_vol_shape

    def set_centre_of_rotation(self, inData, outData, mData):
        # if cor has been passed as a dataset then do nothing
        if isinstance(self.parameters['centre_of_rotation'], str):
            return
        if 'centre_of_rotation' in list(mData.get_dictionary().keys()):
            cor = self.__set_cor_from_meta_data(mData, inData)
        else:
            val = self.parameters['centre_of_rotation']
            if isinstance(val, dict):
                cor = self.__polyfit_cor(val, inData)
            else:
                sdirs = inData.get_slice_dimensions()
                cor = np.ones(np.prod([inData.get_shape()[i] for i in sdirs]))
                # if centre of rotation has not been set then fix it in the
                # centre
                val = val if val != 0 else \
                    (self.get_vol_shape()[self._get_detX_dim()]) / 2.0
                cor *= val
                # mData.set('centre_of_rotation', cor) see Github ticket
        self.cor = cor
        outData.meta_data.set("centre_of_rotation", copy.deepcopy(self.cor))
        self.centre = self.cor[0]

    def populate_metadata_to_output(self, inData, outData, mData):
        # writing  rotation angles into the metadata associated with the output (reconstruction)
        self.angles = mData.get('rotation_angle')
        outData.meta_data.set("rotation_angle", copy.deepcopy(self.angles))
        if 'detector_x' in list(mData.get_dictionary().keys()):
            detector_x_dim = mData.get('detector_x')
        else:
            xDim = inData.get_data_dimension_by_axis_label('detector_x')
            detector_x_dim = inData.get_shape()[xDim]
        outData.meta_data.set("detector_x", copy.deepcopy(detector_x_dim))

    def __set_cor_from_meta_data(self, mData, inData):
        cor = mData.get('centre_of_rotation')
        sdirs = inData.get_slice_dimensions()
        total_frames = np.prod([inData.get_shape()[i] for i in sdirs])
        if total_frames > len(cor):
            cor = np.tile(cor, total_frames // len(cor))
        return cor

    def __polyfit_cor(self, cor_dict, inData):
        if 'detector_y' in list(inData.meta_data.get_dictionary().keys()):
            y = inData.meta_data.get('detector_y')
        else:
            yDim = inData.get_data_dimension_by_axis_label('detector_y')
            y = np.arange(inData.get_shape()[yDim])

        z = np.polyfit(list(map(int, list(cor_dict.keys()))), list(cor_dict.values()), 1)
        p = np.poly1d(z)
        cor = p(y)
        return cor

    def set_function(self, pad_shape):
        if not pad_shape:
            def cor_func(cor): return cor
            if self.parameters['log']:
                sino_func = self.__make_lambda()
            else:
                sino_func = self.__make_lambda(log=False)
        else:
            def cor_func(cor): return cor + self.sino_pad
            if self.parameters['log']:
                sino_func = self.__make_lambda(pad=pad_shape)
            else:
                sino_func = self.__make_lambda(pad=pad_shape, log=False)
        return sino_func, cor_func

    def __make_lambda(self, log=True, pad=False):
        log_func = 'np.nan_to_num(sino)' if not log else self.parameters['log_func']
        if pad:
            pad_tuples, mode = self.__get_pad_values(pad)
            log_func = log_func.replace(
                    'sino', 'np.pad(sino, %s, "%s")' % (pad_tuples, mode))
        return eval("lambda sino: " + log_func)

    def __get_pad_values(self, pad_shape):
        mode = 'edge'
        pad_tuples = [(0, 0)] * (len(pad_shape) - 1)
        pad_tuples.insert(self.pad_dim, (self.sino_pad, self.sino_pad))
        pad_tuples = tuple(pad_tuples)
        return pad_tuples, mode

    def base_process_frames_before(self, data):
        """
        Reconstruct a single sinogram with the provided centre of rotation
        """
        sl = self.get_current_slice_list()[0]
        init = data[1] if self.init_vol else None
        angles = \
            self.angles[:, sl[self.scan_dim]] if self.scan_dim else self.angles

        self.frame_angles = angles

        dim_sl = sl[self.main_dir]

        if self.cor_as_dataset:
            self.frame_cors = self.cor_func(data[len(data) - 1])
        else:
            frame_nos = \
                self.get_plugin_in_datasets()[0].get_current_frame_idx()
            a = self.cor[tuple([frame_nos])]
            self.frame_cors = self.cor_func(a)

        # for extra padded frames that make up the numbers
        if not self.frame_cors.shape:
            self.frame_cors = np.array([self.centre])

        len_data = len(np.arange(dim_sl.start, dim_sl.stop, dim_sl.step))

        missing = [self.centre] * (len(self.frame_cors) - len_data)
        self.frame_cors = np.append(self.frame_cors, missing)

        # fix to remove NaNs in the initialised image
        if init is not None:
            init[np.isnan(init)] == 0.0
        self.frame_init_data = init

        data[0] = self.fix_sino(self.sino_func(data[0]), self.frame_cors[0])
        return data

    def base_process_frames_after(self, data):
        lower_range, upper_range = self.range
        if lower_range is not None:
            data[data < lower_range] = 0
        if upper_range is not None:
            data[data > upper_range] = 0
        return data

    def get_padding_algorithms(self):
        """ A list of algorithms that allow the data to be padded. """
        return []

    def pad_sino(self, sino, cor):
        """  Pad the sinogram so the centre of rotation is at the centre. """
        detX = self._get_detX_dim()
        pad = self.get_centre_offset(sino, cor, detX)
        self.cor_shift = pad[0]
        pad_tuples = [(0, 0)] * (len(sino.shape) - 1)
        pad_tuples.insert(detX, tuple(pad))
        self.__set_pad_amount(max(pad))
        return np.pad(sino, tuple(pad_tuples), mode='edge')

    def _get_detX_dim(self):
        pData = self.get_plugin_in_datasets()[0]
        return pData.get_data_dimension_by_axis_label('x', contains=True)

    def get_centre_offset(self, sino, cor, detX):
        centre_pad = self.br_array_pad(cor, sino.shape[detX])
        sino_width = sino.shape[detX]
        new_width = sino_width + max(centre_pad)
        sino_pad = int(math.ceil(float(sino_width) / new_width * self.sino_pad) // 2)
        pad = np.array([sino_pad]*2) + centre_pad
        return pad

    def get_centre_shift(self, sino, cor):
        detX = self._get_detX_dim()
        return max(self.get_centre_offset(sino, self.centre, detX))

    def crop_sino(self, sino, cor):
        """  Crop the sinogram so the centre of rotation is at the centre. """
        detX = self._get_detX_dim()
        start, stop = self.br_array_pad(cor, sino.shape[detX])[::-1]
        self.cor_shift = -start
        sl = [slice(None)] * len(sino.shape)
        sl[detX] = slice(start, sino.shape[detX] - stop)
        sino = sino[tuple(sl)]
        self.set_mask(sino.shape)
        return sino

    def br_array_pad(self, ctr, nPixels):
        width = nPixels - 1.0
        alen = ctr
        blen = width - ctr
        mid = (width - 1.0) / 2.0
        shift = round(abs(blen - alen))
        p_low = 0 if (ctr > mid) else shift
        p_high = shift + 0 if (ctr > mid) else 0
        return np.array([int(p_low), int(p_high)])

    def keep_sino(self, sino, cor):
        """ No change to the sinogram """
        return sino

    def get_sino_centre_method(self):
        centre_pad = self.keep_sino
        if 'centre_pad' in list(self.parameters.keys()):
            cpad = self.parameters['centre_pad']
            if not (cpad is True or cpad is False):
                raise Exception('Unknown value for "centre_pad", please choose'
                                ' True or False.')
            centre_pad = self.pad_sino if cpad and self.padding_alg \
                else self.crop_sino
        return centre_pad

    def __set_pad_amount(self, pad_amount):
        self.base_pad_amount = pad_amount

    def get_pad_amount(self):
        return self.base_pad_amount

    def get_fov_fraction(self, sino, cor):
        """ Get the fraction of the original FOV that can be reconstructed due\
        to offset centre """
        pData = self.get_plugin_in_datasets()[0]
        detX = pData.get_data_dimension_by_axis_label('x', contains=True)
        original_length = sino.shape[detX]
        shift = self.get_centre_shift(sino, cor)
        return (original_length - shift) / float(original_length)

    def get_reconstruction_alg(self):
        return None

    def get_angles(self):
        """ Get the angles associated with the current sinogram(s).

        :returns: Angles of the current frames.
        :rtype: np.ndarray
        """
        return self.frame_angles

    def get_cors(self):
        """
        Get the centre of rotations associated with the current sinogram(s).

        :returns: Centre of rotation values for the current frames.
        :rtype: np.ndarray
        """
        return self.frame_cors + self.cor_shift

    def set_mask(self, shape):
        pass

    def get_initial_data(self):
        """
        Get the initial data (if it is exists) associated with the current \
        sinogram(s).

        :returns: The section of the initialisation data associated with the \
            current frames.
        :rtype: np.ndarray or None
        """
        return self.frame_init_data

    def get_frame_params(self):
        params = [self.get_cors(), self.get_angles(), self.get_vol_shape(),
                  self.get_initial_data()]
        return params

    def setup(self):
        in_dataset, out_dataset = self.get_datasets()
        # reduce the data as per data_subset parameter
        self.preview_flag = \
            self.set_preview(in_dataset[0], self.parameters['preview'])

        self._set_volume_dimensions(in_dataset[0])
        axis_labels = self._get_axis_labels(in_dataset[0])
        shape = self._get_shape(in_dataset[0])

        # output dataset
        out_dataset[0].create_dataset(axis_labels=axis_labels, shape=shape)
        out_dataset[0].add_volume_patterns(*self._get_volume_dimensions())

        # set information relating to the plugin data
        in_pData, out_pData = self.get_plugin_datasets()

        self.init_vol = 1 if 'init_vol' in list(self.parameters.keys()) and\
            self.parameters['init_vol'] else 0
        self.cor_as_dataset = 1 if isinstance(
            self.parameters['centre_of_rotation'], str) else 0

        for i in range(len(in_dataset) - self.init_vol - self.cor_as_dataset):
            in_pData[i].plugin_data_setup('SINOGRAM', self.get_max_frames(),
                                          slice_axis=self.get_slice_axis())
            idx = 1

        # initial volume dataset
        if self.init_vol:
#            from savu.data.data_structures.data_types import Replicate
#            if self.rep_dim:
#                in_dataset[idx].data = Replicate(
#                    in_dataset[idx], in_dataset[0].get_shape(self.rep_dim))
            in_pData[1].plugin_data_setup('VOLUME_XZ', self.get_max_frames())
            idx += 1


        # cor dataset
        if self.cor_as_dataset:
            self.cor_as_dataset = True
            in_pData[idx].plugin_data_setup('METADATA', self.get_max_frames())

        # set pattern_name and nframes to process for all datasets
        out_pData[0].plugin_data_setup('VOLUME_XZ', self.get_max_frames())
        # metadata output populator
        in_meta_data = self.get_in_meta_data()[0]
        self.populate_metadata_to_output(in_dataset[0], out_dataset[0], in_meta_data)

    def _get_axis_labels(self, in_dataset):
        """
        Get the new axis labels for the output dataset - this is now a volume.

        Parameters
        ----------
        in_dataset : :class:`savu.data.data_structures.data.Data`
            The input dataset to the plugin.

        Returns
        -------
        labels : dict
            The axis labels for the dataset that is output from the plugin.

        """
        labels = in_dataset.data_info.get('axis_labels')[0]
        volX, volY, volZ = self._get_volume_dimensions()
        labels = [str(volX) + '.voxel_x.voxels', str(volZ) + '.voxel_z.voxels']
        if volY:
            labels.append(str(volY) + '.voxel_y.voxels')
        labels = {in_dataset: labels}
        return labels

    def _set_volume_dimensions(self, data):
        """
        Map the input dimensions to the output volume dimensions

        Parameters
        ----------
        in_dataset : :class:`savu.data.data_structures.data.Data`
            The input dataset to the plugin.
        """
        data._finalise_patterns()
        self.volX = data.get_data_dimension_by_axis_label("rotation_angle")
        self.volZ = data.get_data_dimension_by_axis_label("x", contains=True)
        self.volY = data.get_data_dimension_by_axis_label(
            "y", contains=True, exists=True)

    def _get_volume_dimensions(self):
        return self.volX, self.volY, self.volZ

    def _get_shape(self, in_dataset):
        shape = list(in_dataset.get_shape())
        volX, volY, volZ = self._get_volume_dimensions()

        if self.parameters['vol_shape'] in ('auto', 'fixed'):
            shape[volX] = shape[volZ]
        else:
            shape[volX] = self.parameters['vol_shape']
            shape[volZ] = self.parameters['vol_shape']

        if 'resolution' in self.parameters.keys():
            shape[volX] /= self.parameters['resolution']
            shape[volZ] /= self.parameters['resolution']
        return tuple(shape)

    def get_max_frames(self):
        """
        Number of data frames to pass to each instance of process_frames func

        Returns
        -------
        str or int
            "single", "multiple" or integer (only to be used if the number of
                                             frames MUST be fixed.)
        """
        return 'multiple'

    def get_slice_axis(self):
        """
        Fix the fastest changing slice dimension

        Returns
        -------
        str or None
            str should be the axis_label corresponding to the fastest changing
            dimension

        """
        return None

    def nInput_datasets(self):
        nIn = 1
        if 'init_vol' in self.parameters.keys() and \
                self.parameters['init_vol']:
            if len(self.parameters['init_vol'].split('.')) == 3:
                name, temp, self.rep_dim = self.parameters['init_vol']
                self.parameters['init_vol'] = name
            nIn += 1
            self.parameters['in_datasets'].append(self.parameters['init_vol'])
        if isinstance(self.parameters['centre_of_rotation'], str):
            self.parameters['in_datasets'].append(
                self.parameters['centre_of_rotation'])
            nIn += 1
        return nIn

    def nOutput_datasets(self):
        return self.nOut

    def reconstruct_pre_process(self):
        """
        Should be overridden to perform pre-processing in a child class
        """
        pass

    def executive_summary(self):
        summary = []
        if not self.preview_flag:
            summary.append(("WARNING: Ignoring preview parameters as a preview"
                            " has already been applied to the data."))
        if len(summary) > 0:
            return summary
        return ["Nothing to Report"]


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_recon
17			:platform: Unix
18			:synopsis: A base class for all reconstruction methods
19
20			.. moduleauthor:: Mark Basham <[email protected]>
21
22			"""
23			import math
24			import copy
25			import numpy as np
26			np.seterr(divide='ignore', invalid='ignore')
27
28			import savu.core.utils as cu
29			from savu.plugins.plugin import Plugin
30
31			MAX_OUTER_PAD = 2.1
32
33
34			class BaseRecon(Plugin):
35			"""
36			A base class for reconstruction plugins
37
38			:u*param centre_of_rotation: Centre of rotation to use for the \
39			reconstruction. Default: 0.0.
40
41			:u*param init_vol: Dataset to use as volume initialiser \
42			(doesn't currently work with preview). Default: None.
43
44			:param centre_pad: Pad the sinogram to centre it in order to fill the \
45			reconstructed volume ROI for asthetic purposes.\
46			NB: Only available for selected algorithms and will be ignored otherwise. \
47			WARNING: This will significantly increase the size of the data and the \
48			time to compute the reconstruction). Default: False.
49
50			:param outer_pad: Pad the sinogram width to fill the reconstructed volume \
51			for asthetic purposes.\
52			Choose from True (defaults to sqrt(2)), False or float <= 2.1. \
53			NB: Only available for selected algorithms and will be ignored otherwise.\
54			WARNING: This will increase the size of the data and the \
55			time to compute the reconstruction). Default: False.
56
57			:u*param log: Take the log of the data before reconstruction \
58			(True or False). Default: True.
59
60			:u*param preview: A slice list of required frames. Default: [].
61
62			:param force_zero: Set any values in the reconstructed image outside of \
63			this range to zero. Default: [None, None].
64
65			:param ratio: Ratio between the diameter of a circle mask and the width of\
66			a reconstructed image. If passed as a list or tuple, the second value is \
67			assigned to the outer mask area, e.g [0.95, 0.0]. Default: 0.95.
68
69			:param log_func: Override the default log \
70			function. Default: 'np.nan_to_num(-np.log(sino))'.
71
72			:param vol_shape: Override the size of the reconstruction volume with an \
73			integer value. Default: 'fixed'.
74			"""
75
76			def __init__(self, name='BaseRecon'):
77			super(BaseRecon, self).__init__(name)
78			self.nOut = 1
79			self.nIn = 1
80			self.scan_dim = None
81			self.rep_dim = None
82			self.br_vol_shape = None
83			self.frame_angles = None
84			self.frame_cors = None
85			self.frame_init_data = None
86			self.centre = None
87			self.base_pad_amount = None
88			self.padding_alg = False
89			self.cor_shift = 0
90			self.init_vol = False
91			self.cor_as_dataset = False
92
93			def base_pre_process(self):
94			in_data, out_data = self.get_datasets()
95			in_pData, out_pData = self.get_plugin_datasets()
96			self.pad_dim = \
97			in_pData[0].get_data_dimension_by_axis_label('x', contains=True)
98			in_meta_data = self.get_in_meta_data()[0]
99			self.__set_padding_alg()
100
101			self.exp.log(self.name + " End")
102			self.br_vol_shape = out_pData[0].get_shape()
103			self.set_centre_of_rotation(in_data[0], out_data[0], in_meta_data)
104
105			self.main_dir = in_data[0].get_data_patterns()['SINOGRAM']['main_dir']
106			self.angles = in_meta_data.get('rotation_angle')
107			if len(self.angles.shape) != 1:
108			self.scan_dim = in_data[0].get_data_dimension_by_axis_label('scan')
109			self.slice_dirs = out_data[0].get_slice_dimensions()
110
111			shape = in_pData[0].get_shape()
112			factor = self.__get_outer_pad()
113			self.sino_pad = int(math.ceil(factor * shape[self.pad_dim]))
114
115			self.sino_func, self.cor_func = self.set_function(shape) if \
116			self.padding_alg else self.set_function(False)
117
118			self.range = self.parameters['force_zero']
119			self.fix_sino = self.get_sino_centre_method()
120
121			def __get_outer_pad(self):
122			# length of diagonal of square is side*sqrt(2)
123			factor = math.sqrt(2) - 1
124			pad = self.parameters['outer_pad'] if 'outer_pad' in \
125			list(self.parameters.keys()) else False
126
127			if pad is not False and not self.padding_alg:
128			msg = 'This reconstruction algorithm cannot be padded.'
129			cu.user_message(msg)
130			return 0
131
132			if isinstance(pad, bool):
133			return factor if pad is True else 0
134			factor = float(pad)
135			if factor > MAX_OUTER_PAD:
136			factor = MAX_OUTER_PAD
137			msg = 'Maximum outer_pad value is 2.1, using this instead'
138			cu.user_message(msg)
139			return float(pad)
140
141			def __set_padding_alg(self):
142			""" Determine if this is an algorithm that allows sinogram padding. """
143			pad_algs = self.get_padding_algorithms()
144			alg = self.parameters['algorithm'] if 'algorithm' in \
145			list(self.parameters.keys()) else None
146			self.padding_alg = True if alg in pad_algs else False
147
148			def get_vol_shape(self):
149			return self.br_vol_shape
150
151			def set_centre_of_rotation(self, inData, outData, mData):
152			# if cor has been passed as a dataset then do nothing
153			if isinstance(self.parameters['centre_of_rotation'], str):
154			return
155			if 'centre_of_rotation' in list(mData.get_dictionary().keys()):
156			cor = self.__set_cor_from_meta_data(mData, inData)
157			else:
158			val = self.parameters['centre_of_rotation']
159			if isinstance(val, dict):
160			cor = self.__polyfit_cor(val, inData)
161			else:
162			sdirs = inData.get_slice_dimensions()
163			cor = np.ones(np.prod([inData.get_shape()[i] for i in sdirs]))
164			# if centre of rotation has not been set then fix it in the
165			# centre
166			val = val if val != 0 else \
167			(self.get_vol_shape()[self._get_detX_dim()]) / 2.0
168			cor *= val
169			# mData.set('centre_of_rotation', cor) see Github ticket
170			self.cor = cor
171			outData.meta_data.set("centre_of_rotation", copy.deepcopy(self.cor))
172			self.centre = self.cor[0]
173
174			def populate_metadata_to_output(self, inData, outData, mData):
175			# writing rotation angles into the metadata associated with the output (reconstruction)
176			self.angles = mData.get('rotation_angle')
177			outData.meta_data.set("rotation_angle", copy.deepcopy(self.angles))
178			if 'detector_x' in list(mData.get_dictionary().keys()):
179			detector_x_dim = mData.get('detector_x')
180			else:
181			xDim = inData.get_data_dimension_by_axis_label('detector_x')
182			detector_x_dim = inData.get_shape()[xDim]
183			outData.meta_data.set("detector_x", copy.deepcopy(detector_x_dim))
184
185			def __set_cor_from_meta_data(self, mData, inData):
186			cor = mData.get('centre_of_rotation')
187			sdirs = inData.get_slice_dimensions()
188			total_frames = np.prod([inData.get_shape()[i] for i in sdirs])
189			if total_frames > len(cor):
190			cor = np.tile(cor, total_frames // len(cor))
191			return cor
192
193			def __polyfit_cor(self, cor_dict, inData):
194			if 'detector_y' in list(inData.meta_data.get_dictionary().keys()):
195			y = inData.meta_data.get('detector_y')
196			else:
197			yDim = inData.get_data_dimension_by_axis_label('detector_y')
198			y = np.arange(inData.get_shape()[yDim])
199
200			z = np.polyfit(list(map(int, list(cor_dict.keys()))), list(cor_dict.values()), 1)
201			p = np.poly1d(z)
202			cor = p(y)
203			return cor
204
205			def set_function(self, pad_shape):
206			if not pad_shape:
207			def cor_func(cor): return cor
208			if self.parameters['log']:
209			sino_func = self.__make_lambda()
210			else:
211			sino_func = self.__make_lambda(log=False)
212			else:
213			def cor_func(cor): return cor + self.sino_pad
214			if self.parameters['log']:
215			sino_func = self.__make_lambda(pad=pad_shape)
216			else:
217			sino_func = self.__make_lambda(pad=pad_shape, log=False)
218			return sino_func, cor_func
219
220			def __make_lambda(self, log=True, pad=False):
221			log_func = 'np.nan_to_num(sino)' if not log else self.parameters['log_func']
222			if pad:
223			pad_tuples, mode = self.__get_pad_values(pad)
224			log_func = log_func.replace(
225			'sino', 'np.pad(sino, %s, "%s")' % (pad_tuples, mode))
226			return eval("lambda sino: " + log_func)
227
228			def __get_pad_values(self, pad_shape):
229			mode = 'edge'
230			pad_tuples = [(0, 0)] * (len(pad_shape) - 1)
231			pad_tuples.insert(self.pad_dim, (self.sino_pad, self.sino_pad))
232			pad_tuples = tuple(pad_tuples)
233			return pad_tuples, mode
234
235			def base_process_frames_before(self, data):
236			"""
237			Reconstruct a single sinogram with the provided centre of rotation
238			"""
239			sl = self.get_current_slice_list()[0]
240			init = data[1] if self.init_vol else None
241			angles = \
242			self.angles[:, sl[self.scan_dim]] if self.scan_dim else self.angles
243
244			self.frame_angles = angles
245
246			dim_sl = sl[self.main_dir]
247
248			if self.cor_as_dataset:
249			self.frame_cors = self.cor_func(data[len(data) - 1])
250			else:
251			frame_nos = \
252			self.get_plugin_in_datasets()[0].get_current_frame_idx()
253			a = self.cor[tuple([frame_nos])]
254			self.frame_cors = self.cor_func(a)
255
256			# for extra padded frames that make up the numbers
257			if not self.frame_cors.shape:
258			self.frame_cors = np.array([self.centre])
259
260			len_data = len(np.arange(dim_sl.start, dim_sl.stop, dim_sl.step))
261
262			missing = [self.centre] * (len(self.frame_cors) - len_data)
263			self.frame_cors = np.append(self.frame_cors, missing)
264
265			# fix to remove NaNs in the initialised image
266			if init is not None:
267			init[np.isnan(init)] == 0.0
268			self.frame_init_data = init
269
270			data[0] = self.fix_sino(self.sino_func(data[0]), self.frame_cors[0])
271			return data
272
273			def base_process_frames_after(self, data):
274			lower_range, upper_range = self.range
275			if lower_range is not None:
276			data[data < lower_range] = 0
277			if upper_range is not None:
278			data[data > upper_range] = 0
279			return data
280
281			def get_padding_algorithms(self):
282			""" A list of algorithms that allow the data to be padded. """
283			return []
284
285			def pad_sino(self, sino, cor):
286			""" Pad the sinogram so the centre of rotation is at the centre. """
287			detX = self._get_detX_dim()
288			pad = self.get_centre_offset(sino, cor, detX)
289			self.cor_shift = pad[0]
290			pad_tuples = [(0, 0)] * (len(sino.shape) - 1)
291			pad_tuples.insert(detX, tuple(pad))
292			self.__set_pad_amount(max(pad))
293			return np.pad(sino, tuple(pad_tuples), mode='edge')
294
295			def _get_detX_dim(self):
296			pData = self.get_plugin_in_datasets()[0]
297			return pData.get_data_dimension_by_axis_label('x', contains=True)
298
299			def get_centre_offset(self, sino, cor, detX):
300			centre_pad = self.br_array_pad(cor, sino.shape[detX])
301			sino_width = sino.shape[detX]
302			new_width = sino_width + max(centre_pad)
303			sino_pad = int(math.ceil(float(sino_width) / new_width * self.sino_pad) // 2)
304			pad = np.array([sino_pad]*2) + centre_pad
305			return pad
306
307			def get_centre_shift(self, sino, cor):
308			detX = self._get_detX_dim()
309			return max(self.get_centre_offset(sino, self.centre, detX))
310
311			def crop_sino(self, sino, cor):
312			""" Crop the sinogram so the centre of rotation is at the centre. """
313			detX = self._get_detX_dim()
314			start, stop = self.br_array_pad(cor, sino.shape[detX])[::-1]
315			self.cor_shift = -start
316			sl = [slice(None)] * len(sino.shape)
317			sl[detX] = slice(start, sino.shape[detX] - stop)
318			sino = sino[tuple(sl)]
319			self.set_mask(sino.shape)
320			return sino
321
322			def br_array_pad(self, ctr, nPixels):
323			width = nPixels - 1.0
324			alen = ctr
325			blen = width - ctr
326			mid = (width - 1.0) / 2.0
327			shift = round(abs(blen - alen))
328			p_low = 0 if (ctr > mid) else shift
329			p_high = shift + 0 if (ctr > mid) else 0
330			return np.array([int(p_low), int(p_high)])
331
332			def keep_sino(self, sino, cor):
333			""" No change to the sinogram """
334			return sino
335
336			def get_sino_centre_method(self):
337			centre_pad = self.keep_sino
338			if 'centre_pad' in list(self.parameters.keys()):
339			cpad = self.parameters['centre_pad']
340			if not (cpad is True or cpad is False):
341			raise Exception('Unknown value for "centre_pad", please choose'
342			' True or False.')
343			centre_pad = self.pad_sino if cpad and self.padding_alg \
344			else self.crop_sino
345			return centre_pad
346
347			def __set_pad_amount(self, pad_amount):
348			self.base_pad_amount = pad_amount
349
350			def get_pad_amount(self):
351			return self.base_pad_amount
352
353			def get_fov_fraction(self, sino, cor):
354			""" Get the fraction of the original FOV that can be reconstructed due\
355			to offset centre """
356			pData = self.get_plugin_in_datasets()[0]
357			detX = pData.get_data_dimension_by_axis_label('x', contains=True)
358			original_length = sino.shape[detX]
359			shift = self.get_centre_shift(sino, cor)
360			return (original_length - shift) / float(original_length)
361
362			def get_reconstruction_alg(self):
363			return None
364
365			def get_angles(self):
366			""" Get the angles associated with the current sinogram(s).
367
368			:returns: Angles of the current frames.
369			:rtype: np.ndarray
370			"""
371			return self.frame_angles
372
373			def get_cors(self):
374			"""
375			Get the centre of rotations associated with the current sinogram(s).
376
377			:returns: Centre of rotation values for the current frames.
378			:rtype: np.ndarray
379			"""
380			return self.frame_cors + self.cor_shift
381
382			def set_mask(self, shape):
383			pass
384
385			def get_initial_data(self):
386			"""
387			Get the initial data (if it is exists) associated with the current \
388			sinogram(s).
389
390			:returns: The section of the initialisation data associated with the \
391			current frames.
392			:rtype: np.ndarray or None
393			"""
394			return self.frame_init_data
395
396			def get_frame_params(self):
397			params = [self.get_cors(), self.get_angles(), self.get_vol_shape(),
398			self.get_initial_data()]
399			return params
400
401			def setup(self):
402			in_dataset, out_dataset = self.get_datasets()
403			# reduce the data as per data_subset parameter
404			self.preview_flag = \
405			self.set_preview(in_dataset[0], self.parameters['preview'])
406
407			self._set_volume_dimensions(in_dataset[0])
408			axis_labels = self._get_axis_labels(in_dataset[0])
409			shape = self._get_shape(in_dataset[0])
410
411			# output dataset
412			out_dataset[0].create_dataset(axis_labels=axis_labels, shape=shape)
413			out_dataset[0].add_volume_patterns(*self._get_volume_dimensions())
414
415			# set information relating to the plugin data
416			in_pData, out_pData = self.get_plugin_datasets()
417
418			self.init_vol = 1 if 'init_vol' in list(self.parameters.keys()) and\
419			self.parameters['init_vol'] else 0
420			self.cor_as_dataset = 1 if isinstance(
421			self.parameters['centre_of_rotation'], str) else 0
422
423			for i in range(len(in_dataset) - self.init_vol - self.cor_as_dataset):
424			in_pData[i].plugin_data_setup('SINOGRAM', self.get_max_frames(),
425			slice_axis=self.get_slice_axis())
426			idx = 1
427
428			# initial volume dataset
429			if self.init_vol:
430			# from savu.data.data_structures.data_types import Replicate
431			# if self.rep_dim:
432			# in_dataset[idx].data = Replicate(
433			# in_dataset[idx], in_dataset[0].get_shape(self.rep_dim))
434			in_pData[1].plugin_data_setup('VOLUME_XZ', self.get_max_frames())
435			idx += 1
			0 ignored issues – show introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `idx` does not seem to be defined in case the `for` loop on line `423` is not entered. Are you sure this can never be the case? Loading history...
436
437			# cor dataset
438			if self.cor_as_dataset:
439			self.cor_as_dataset = True
440			in_pData[idx].plugin_data_setup('METADATA', self.get_max_frames())
441
442			# set pattern_name and nframes to process for all datasets
443			out_pData[0].plugin_data_setup('VOLUME_XZ', self.get_max_frames())
444			# metadata output populator
445			in_meta_data = self.get_in_meta_data()[0]
446			self.populate_metadata_to_output(in_dataset[0], out_dataset[0], in_meta_data)
447
448			def _get_axis_labels(self, in_dataset):
449			"""
450			Get the new axis labels for the output dataset - this is now a volume.
451
452			Parameters
453			----------
454			in_dataset : :class:`savu.data.data_structures.data.Data`
455			The input dataset to the plugin.
456
457			Returns
458			-------
459			labels : dict
460			The axis labels for the dataset that is output from the plugin.
461
462			"""
463			labels = in_dataset.data_info.get('axis_labels')[0]
464			volX, volY, volZ = self._get_volume_dimensions()
465			labels = [str(volX) + '.voxel_x.voxels', str(volZ) + '.voxel_z.voxels']
466			if volY:
467			labels.append(str(volY) + '.voxel_y.voxels')
468			labels = {in_dataset: labels}
469			return labels
470
471			def _set_volume_dimensions(self, data):
472			"""
473			Map the input dimensions to the output volume dimensions
474
475			Parameters
476			----------
477			in_dataset : :class:`savu.data.data_structures.data.Data`
478			The input dataset to the plugin.
479			"""
480			data._finalise_patterns()
481			self.volX = data.get_data_dimension_by_axis_label("rotation_angle")
482			self.volZ = data.get_data_dimension_by_axis_label("x", contains=True)
483			self.volY = data.get_data_dimension_by_axis_label(
484			"y", contains=True, exists=True)
485
486			def _get_volume_dimensions(self):
487			return self.volX, self.volY, self.volZ
488
489			def _get_shape(self, in_dataset):
490			shape = list(in_dataset.get_shape())
491			volX, volY, volZ = self._get_volume_dimensions()
492
493			if self.parameters['vol_shape'] in ('auto', 'fixed'):
494			shape[volX] = shape[volZ]
495			else:
496			shape[volX] = self.parameters['vol_shape']
497			shape[volZ] = self.parameters['vol_shape']
498
499			if 'resolution' in self.parameters.keys():
500			shape[volX] /= self.parameters['resolution']
501			shape[volZ] /= self.parameters['resolution']
502			return tuple(shape)
503
504			def get_max_frames(self):
505			"""
506			Number of data frames to pass to each instance of process_frames func
507
508			Returns
509			-------
510			str or int
511			"single", "multiple" or integer (only to be used if the number of
512			frames MUST be fixed.)
513			"""
514			return 'multiple'
515
516			def get_slice_axis(self):
517			"""
518			Fix the fastest changing slice dimension
519
520			Returns
521			-------
522			str or None
523			str should be the axis_label corresponding to the fastest changing
524			dimension
525
526			"""
527			return None
528
529			def nInput_datasets(self):
530			nIn = 1
531			if 'init_vol' in self.parameters.keys() and \
532			self.parameters['init_vol']:
533			if len(self.parameters['init_vol'].split('.')) == 3:
534			name, temp, self.rep_dim = self.parameters['init_vol']
535			self.parameters['init_vol'] = name
536			nIn += 1
537			self.parameters['in_datasets'].append(self.parameters['init_vol'])
538			if isinstance(self.parameters['centre_of_rotation'], str):
539			self.parameters['in_datasets'].append(
540			self.parameters['centre_of_rotation'])
541			nIn += 1
542			return nIn
543
544			def nOutput_datasets(self):
545			return self.nOut
546
547			def reconstruct_pre_process(self):
548			"""
549			Should be overridden to perform pre-processing in a child class
550			"""
551			pass
552
553			def executive_summary(self):
554			summary = []
555			if not self.preview_flag:
556			summary.append(("WARNING: Ignoring preview parameters as a preview"
557			" has already been applied to the data."))
558			if len(summary) > 0:
559			return summary
560			return ["Nothing to Report"]
561

DiamondLightSource / Savu

Pull Request — master (#700)

BaseRecon._get_volume_dimensions() A

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