savu.plugins.stats.statistics.Statistics._get_unpadded_slice_list() - Code Metrics - Inspection of "Statistics" - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed

Pull Request — master (#878)

by Daniil

created 2021-12-13 21:25 UTC

Statistics._get_unpadded_slice_list() A

↳ Parent: savu.plugins.stats.statistics

Complexity

Conditions

Size

Total Lines	14
Code Lines	12

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	4
eloc	12
nop	3
dl	0
loc	14
rs	9.8
c	0
b	0
f	0

"""
.. module:: statistics
   :platform: Unix
   :synopsis: Contains and processes statistics information for each plugin.

.. moduleauthor::Jacob Williamson <[email protected]>

"""

from savu.plugins.savers.utils.hdf5_utils import Hdf5Utils

import h5py as h5
import numpy as np
import os


class Statistics(object):
    index_dict = {"max": 0, "min": 1, "mean": 2, "mean_std_dev": 3, "median_std_dev": 4}
    key_list = ["max", "min", "mean", "mean_std_dev", "median_std_dev"]
    pattern_list = ["SINOGRAM", "PROJECTION", "VOLUME_YZ", "VOLUME_XZ", "VOLUME_XY", "VOLUME_3D", "4D_SCAN", "SINOMOVIE"]
    no_stats_plugins = ["BasicOperations", "Mipmap"]

    def __init__(self, plugin_self):
        self.plugin = plugin_self
        self.plugin_name = plugin_self.name
        self.pad_dims = []
        self.stats = {'max': [], 'min': [], 'mean': [], 'standard_deviation': []}
        self.calc_stats = False
        self._set_pattern_info()
        if self.plugin_name in Statistics.no_stats_plugins:
            self.calc_stats = False

    @classmethod
    def _setup(cls, exp):
        """Sets up the statistics class for the whole experiment (only called once)"""
        cls.count = 2
        cls.data_stats = {}
        cls.volume_stats = {}
        cls.global_stats = {}
        n_plugins = len(exp.meta_data.plugin_list.plugin_list)
        # for n in range(n_plugins):
        #    cls.data_stats[n + 1] = [None, None, None, None, None]
        #    cls.volume_stats[n + 1] = [None, None, None, None, None]
        cls.path = exp.meta_data['out_path']
        if cls.path[-1] == '/':
            cls.path = cls.path[0:-1]
        cls.path = f"{cls.path}/stats"
        if not os.path.exists(cls.path):
            os.mkdir(cls.path)

    def set_slice_stats(self, slice1):
        """Appends slice stats arrays with the stats parameters of the current slice.

        :param slice1: The slice whose stats are being calculated.
        """
        if slice1 is not None:
            slice_num = self.plugin.pcount
            slice1 = self._de_list(slice1)
            slice1 = self._unpad_slice(slice1)
            self.stats['max'].append(slice1.max())
            self.stats['min'].append(slice1.min())
            self.stats['mean'].append(np.mean(slice1))
            self.stats['standard_deviation'].append(np.std(slice1))

    def get_slice_stats(self, stat, slice_num):
        """Returns array of stats associated with the processed slices of the current plugin."""
        return self.stats[stat][slice_num]

    def set_volume_stats(self):
        """Calculates volume-wide statistics from slice stats, and updates class-wide arrays with these values.
        Links volume stats with the output dataset and writes slice stats to file.
        """
        p_num = Statistics.count
        name = self.plugin_name
        i = 2
        while name in list(Statistics.global_stats.keys()):
            name = self.plugin_name + str(i)
            i += 1
        Statistics.data_stats[p_num] = [None, None, None, None, None]
        Statistics.volume_stats[p_num] = [None, None, None, None, None]
        if len(self.stats['max']) != 0:
            if self.pattern in ['PROJECTION', 'SINOGRAM', 'TANGENTOGRAM', 'SINOMOVIE', '4D_SCAN']:
                Statistics.data_stats[p_num][0] = max(self.stats['max'])
                Statistics.data_stats[p_num][1] = min(self.stats['min'])
                Statistics.data_stats[p_num][2] = np.mean(self.stats['mean'])
                Statistics.data_stats[p_num][3] = np.mean(self.stats['standard_deviation'])
                Statistics.data_stats[p_num][4] = np.median(self.stats['standard_deviation'])
                Statistics.global_stats[p_num] = Statistics.data_stats[p_num]
                Statistics.global_stats[name] = Statistics.global_stats[p_num]
                self._link_stats_to_datasets(Statistics.global_stats[name])
            elif self.pattern in ['VOLUME_XZ', 'VOLUME_XY', 'VOLUME_YZ', 'VOLUME_3D']:
                Statistics.volume_stats[p_num][0] = max(self.stats['max'])
                Statistics.volume_stats[p_num][1] = min(self.stats['min'])
                Statistics.volume_stats[p_num][2] = np.mean(self.stats['mean'])
                Statistics.volume_stats[p_num][3] = np.mean(self.stats['standard_deviation'])
                Statistics.volume_stats[p_num][4] = np.median(self.stats['standard_deviation'])
                Statistics.global_stats[p_num] = Statistics.volume_stats[p_num]
                Statistics.global_stats[name] = Statistics.global_stats[p_num]
                self._link_stats_to_datasets(Statistics.global_stats[name])
        slice_stats = np.array([self.stats['max'], self.stats['min'], self.stats['mean'],
                                self.stats['standard_deviation']])
        self._write_stats_to_file(slice_stats, p_num)

    def get_stats(self, plugin_name, n=None, stat=None):
        """Returns stats associated with a certain plugin.

        :param plugin_name: name of the plugin whose associated stats are being fetched.
        :param n: In a case where there are multiple instances of <plugin_name> in the process list,
            specify the nth instance. Not specifying will select the first (or only) instance.
        :param stat: Specify the stat parameter you want to fetch, i.e 'max', 'mean', 'median_std_dev'.
            If left blank will return the whole dictionary of stats:
            {'max': ,'min': ,'mean': ,'mean_std_dev': ,'median_std_dev': }
        """
        name = plugin_name
        if n is not None and n not in (0, 1):
            name = name + str(n)
        if stat is not None:
            i = Statistics.index_dict[stat]
            return Statistics.global_stats[name][i]
        else:
            stats = dict(zip(Statistics.key_list, Statistics.global_stats[name]))
            return stats

    def get_stats_from_num(self, p_num, stat=None):
        """Returns stats associated with a certain plugin, given the plugin number (its place in the process list).

        :param p_num: Plugin  number of the plugin whose associated stats are being fetched.
            If p_num <= 0, it is relative to the plugin number of the current plugin being run.
            E.g current plugin number = 5, p_num = -2 --> will return stats of the third plugin.
        :param stat: Specify the stat parameter you want to fetch, i.e 'max', 'mean', 'median_std_dev'.
            If left blank will return the whole dictionary of stats:
            {'max': ,'min': ,'mean': ,'mean_std_dev': ,'median_std_dev': }
        """
        if p_num <= 0:
            p_num = Statistics.count + p_num
        if stat is not None:
            i = Statistics.index_dict[stat]
            return Statistics.global_stats[p_num][i]
        else:
            stats = dict(zip(Statistics.key_list, Statistics.global_stats[p_num]))
            return stats

    def get_stats_from_dataset(self, dataset, stat=None, set_num=None):
        """Returns stats associated with a dataset.

        :param dataset: The dataset whose associated stats are being fetched.
        :param stat: Specify the stat parameter you want to fetch, i.e 'max', 'mean', 'median_std_dev'.
            If left blank will return the whole dictionary of stats:
            {'max': ,'min': ,'mean': ,'mean_std_dev': ,'median_std_dev': }
        :param set_num: In the (rare) case that there are multiple sets of stats associated with the dataset,
            specify which set to return.
        """
        key = "stats"
        stats = {}
        if set_num is not None:
            key = key + str(set_num)
        if key in list(dataset.meta_data.dict.keys()):
            stats = dataset.meta_data.get(key)
        if stat is not None:
            return stats[stat]
        else:
            return stats

    def get_data_stats(self):
        return Statistics.data_stats

    def get_volume_stats(self):
        return Statistics.volume_stats

    def get_global_stats(self):
        return Statistics.global_stats

    def _set_pattern_info(self):
        """Gathers information about the pattern of the data in the current plugin."""
        in_datasets, out_datasets = self.plugin.get_datasets()
        try:
            self.pattern = self.plugin.parameters['pattern']
            if self.pattern == None:
                raise KeyError
        except KeyError:
            if not out_datasets:
                self.pattern = None
            else:
                patterns = out_datasets[0].get_data_patterns()
                for pattern in patterns:
                    if 1 in patterns.get(pattern)["slice_dims"]:
                        self.pattern = pattern
                        break
        for dataset in out_datasets:
            if bool(set(Statistics.pattern_list) & set(dataset.data_info.get("data_patterns"))):
                self.calc_stats = True

    def _link_stats_to_datasets(self, stats):
        """Links the volume wide statistics to the output dataset(s)"""
        out_datasets = self.plugin.get_out_datasets()
        n_datasets = self.plugin.nOutput_datasets()
        i = 1
        group_name = "stats"
        if n_datasets == 1:
            while group_name in list(out_datasets[0].meta_data.get_dictionary().keys()):
                group_name = f"stats{i}"
                i += 1
            out_datasets[0].data_info.set([group_name, "max"], stats[0])
            out_datasets[0].data_info.set([group_name, "min"], stats[1])
            out_datasets[0].data_info.set([group_name, "mean"], stats[2])
            out_datasets[0].data_info.set([group_name, "mean_std_dev"], stats[3])
            out_datasets[0].data_info.set([group_name, "median_std_dev"], stats[4])

    def _write_stats_to_file(self, slice_stats, p_num):
        """Writes slice statistics to a h5 file"""
        path = Statistics.path
        filename = f"{path}/stats_p{p_num}_{self.plugin_name}.h5"
        slice_stats_dim = (slice_stats.shape[1],)
        self.hdf5 = Hdf5Utils(self.plugin.exp)
        with h5.File(filename, "a") as h5file:
            i = 1
            group_name = "/stats"
            while group_name in h5file:
                group_name = f"/stats{i}"
                i += 1
            group = h5file.create_group(group_name, track_order=None)
            max_ds = self.hdf5.create_dataset_nofill(group, "max", slice_stats_dim, slice_stats.dtype)
            min_ds = self.hdf5.create_dataset_nofill(group, "min", slice_stats_dim, slice_stats.dtype)
            mean_ds = self.hdf5.create_dataset_nofill(group, "mean", slice_stats_dim, slice_stats.dtype)
            standard_deviation_ds = self.hdf5.create_dataset_nofill(group, "standard_deviation",
                                                                    slice_stats_dim, slice_stats.dtype)
            max_ds[::] = slice_stats[0]
            min_ds[::] = slice_stats[1]
            mean_ds[::] = slice_stats[2]
            standard_deviation_ds[::] = slice_stats[3]

    def _unpad_slice(self, slice1):
        """If data is padded in the slice dimension, removes this pad."""
        out_datasets = self.plugin.get_out_datasets()
        if len(out_datasets) == 1:
            out_dataset = out_datasets[0]
        else:
            for dataset in out_datasets:
                if self.pattern in list(dataset.data_info.get(["data_patterns"]).keys()):
                    out_dataset = dataset
                    break
        slice_dims = out_dataset.get_slice_dimensions()

        if self.plugin.pcount == 0:
            self.slice_list, self.pad = self._get_unpadded_slice_list(slice1, slice_dims)
        if self.pad:
            for slice_dim in slice_dims:
                temp_slice = np.swapaxes(slice1, 0, slice_dim)
                temp_slice = temp_slice[self.slice_list[slice_dim]]
                slice1 = np.swapaxes(temp_slice, 0, slice_dim)
        return slice1

    def _get_unpadded_slice_list(self, slice1, slice_dims):
        """Creates slice object(s) to un-pad slices in the slice dimension(s)."""
        slice_list = list(self.plugin.slice_list[0])
        pad = False
        if len(slice_list) == len(slice1.shape):
            for i in slice_dims:
                slice_width = self.plugin.slice_list[0][i].stop - self.plugin.slice_list[0][i].start
                if slice_width != slice1.shape[i]:
                    pad = True
                    pad_width = (slice1.shape[i] - slice_width) // 2  # Assuming symmetrical padding
                    slice_list[i] = slice(pad_width, pad_width + 1, 1)
            return tuple(slice_list), pad
        else:
            return self.plugin.slice_list[0], pad

    def _de_list(self, slice1):
        """If the slice is in a list, remove it from that list."""
        if type(slice1) == list:
            if len(slice1) != 0:
                slice1 = slice1[0]
                slice1 = self._de_list(slice1)
        return slice1

    @classmethod
    def _count(cls):
        cls.count += 1

    @classmethod
    def _post_chain(cls):
        print(cls.data_stats)
        print(cls.volume_stats)
        print(cls.global_stats)

1			"""
2			.. module:: statistics
3			:platform: Unix
4			:synopsis: Contains and processes statistics information for each plugin.
5
6			.. moduleauthor::Jacob Williamson <[email protected]>
7
8			"""
9
10			from savu.plugins.savers.utils.hdf5_utils import Hdf5Utils
11
12			import h5py as h5
13			import numpy as np
14			import os
15
16
17			class Statistics(object):
18			index_dict = {"max": 0, "min": 1, "mean": 2, "mean_std_dev": 3, "median_std_dev": 4}
19			key_list = ["max", "min", "mean", "mean_std_dev", "median_std_dev"]
20			pattern_list = ["SINOGRAM", "PROJECTION", "VOLUME_YZ", "VOLUME_XZ", "VOLUME_XY", "VOLUME_3D", "4D_SCAN", "SINOMOVIE"]
21			no_stats_plugins = ["BasicOperations", "Mipmap"]
22
23			def __init__(self, plugin_self):
24			self.plugin = plugin_self
25			self.plugin_name = plugin_self.name
26			self.pad_dims = []
27			self.stats = {'max': [], 'min': [], 'mean': [], 'standard_deviation': []}
28			self.calc_stats = False
29			self._set_pattern_info()
30			if self.plugin_name in Statistics.no_stats_plugins:
31			self.calc_stats = False
32
33			@classmethod
34			def _setup(cls, exp):
35			"""Sets up the statistics class for the whole experiment (only called once)"""
36			cls.count = 2
37			cls.data_stats = {}
38			cls.volume_stats = {}
39			cls.global_stats = {}
40			n_plugins = len(exp.meta_data.plugin_list.plugin_list)
41			# for n in range(n_plugins):
42			# cls.data_stats[n + 1] = [None, None, None, None, None]
43			# cls.volume_stats[n + 1] = [None, None, None, None, None]
44			cls.path = exp.meta_data['out_path']
45			if cls.path[-1] == '/':
46			cls.path = cls.path[0:-1]
47			cls.path = f"{cls.path}/stats"
48			if not os.path.exists(cls.path):
49			os.mkdir(cls.path)
50
51			def set_slice_stats(self, slice1):
52			"""Appends slice stats arrays with the stats parameters of the current slice.
53
54			:param slice1: The slice whose stats are being calculated.
55			"""
56			if slice1 is not None:
57			slice_num = self.plugin.pcount
58			slice1 = self._de_list(slice1)
59			slice1 = self._unpad_slice(slice1)
60			self.stats['max'].append(slice1.max())
61			self.stats['min'].append(slice1.min())
62			self.stats['mean'].append(np.mean(slice1))
63			self.stats['standard_deviation'].append(np.std(slice1))
64
65			def get_slice_stats(self, stat, slice_num):
66			"""Returns array of stats associated with the processed slices of the current plugin."""
67			return self.stats[stat][slice_num]
68
69			def set_volume_stats(self):
70			"""Calculates volume-wide statistics from slice stats, and updates class-wide arrays with these values.
71			Links volume stats with the output dataset and writes slice stats to file.
72			"""
73			p_num = Statistics.count
74			name = self.plugin_name
75			i = 2
76			while name in list(Statistics.global_stats.keys()):
77			name = self.plugin_name + str(i)
78			i += 1
79			Statistics.data_stats[p_num] = [None, None, None, None, None]
80			Statistics.volume_stats[p_num] = [None, None, None, None, None]
81			if len(self.stats['max']) != 0:
82			if self.pattern in ['PROJECTION', 'SINOGRAM', 'TANGENTOGRAM', 'SINOMOVIE', '4D_SCAN']:
83			Statistics.data_stats[p_num][0] = max(self.stats['max'])
84			Statistics.data_stats[p_num][1] = min(self.stats['min'])
85			Statistics.data_stats[p_num][2] = np.mean(self.stats['mean'])
86			Statistics.data_stats[p_num][3] = np.mean(self.stats['standard_deviation'])
87			Statistics.data_stats[p_num][4] = np.median(self.stats['standard_deviation'])
88			Statistics.global_stats[p_num] = Statistics.data_stats[p_num]
89			Statistics.global_stats[name] = Statistics.global_stats[p_num]
90			self._link_stats_to_datasets(Statistics.global_stats[name])
91			elif self.pattern in ['VOLUME_XZ', 'VOLUME_XY', 'VOLUME_YZ', 'VOLUME_3D']:
92			Statistics.volume_stats[p_num][0] = max(self.stats['max'])
93			Statistics.volume_stats[p_num][1] = min(self.stats['min'])
94			Statistics.volume_stats[p_num][2] = np.mean(self.stats['mean'])
95			Statistics.volume_stats[p_num][3] = np.mean(self.stats['standard_deviation'])
96			Statistics.volume_stats[p_num][4] = np.median(self.stats['standard_deviation'])
97			Statistics.global_stats[p_num] = Statistics.volume_stats[p_num]
98			Statistics.global_stats[name] = Statistics.global_stats[p_num]
99			self._link_stats_to_datasets(Statistics.global_stats[name])
100			slice_stats = np.array([self.stats['max'], self.stats['min'], self.stats['mean'],
101			self.stats['standard_deviation']])
102			self._write_stats_to_file(slice_stats, p_num)
103
104			def get_stats(self, plugin_name, n=None, stat=None):
105			"""Returns stats associated with a certain plugin.
106
107			:param plugin_name: name of the plugin whose associated stats are being fetched.
108			:param n: In a case where there are multiple instances of <plugin_name> in the process list,
109			specify the nth instance. Not specifying will select the first (or only) instance.
110			:param stat: Specify the stat parameter you want to fetch, i.e 'max', 'mean', 'median_std_dev'.
111			If left blank will return the whole dictionary of stats:
112			{'max': ,'min': ,'mean': ,'mean_std_dev': ,'median_std_dev': }
113			"""
114			name = plugin_name
115			if n is not None and n not in (0, 1):
116			name = name + str(n)
117			if stat is not None:
118			i = Statistics.index_dict[stat]
119			return Statistics.global_stats[name][i]
120			else:
121			stats = dict(zip(Statistics.key_list, Statistics.global_stats[name]))
122			return stats
123
124			def get_stats_from_num(self, p_num, stat=None):
125			"""Returns stats associated with a certain plugin, given the plugin number (its place in the process list).
126
127			:param p_num: Plugin number of the plugin whose associated stats are being fetched.
128			If p_num <= 0, it is relative to the plugin number of the current plugin being run.
129			E.g current plugin number = 5, p_num = -2 --> will return stats of the third plugin.
130			:param stat: Specify the stat parameter you want to fetch, i.e 'max', 'mean', 'median_std_dev'.
131			If left blank will return the whole dictionary of stats:
132			{'max': ,'min': ,'mean': ,'mean_std_dev': ,'median_std_dev': }
133			"""
134			if p_num <= 0:
135			p_num = Statistics.count + p_num
136			if stat is not None:
137			i = Statistics.index_dict[stat]
138			return Statistics.global_stats[p_num][i]
139			else:
140			stats = dict(zip(Statistics.key_list, Statistics.global_stats[p_num]))
141			return stats
142
143			def get_stats_from_dataset(self, dataset, stat=None, set_num=None):
144			"""Returns stats associated with a dataset.
145
146			:param dataset: The dataset whose associated stats are being fetched.
147			:param stat: Specify the stat parameter you want to fetch, i.e 'max', 'mean', 'median_std_dev'.
148			If left blank will return the whole dictionary of stats:
149			{'max': ,'min': ,'mean': ,'mean_std_dev': ,'median_std_dev': }
150			:param set_num: In the (rare) case that there are multiple sets of stats associated with the dataset,
151			specify which set to return.
152			"""
153			key = "stats"
154			stats = {}
155			if set_num is not None:
156			key = key + str(set_num)
157			if key in list(dataset.meta_data.dict.keys()):
158			stats = dataset.meta_data.get(key)
159			if stat is not None:
160			return stats[stat]
161			else:
162			return stats
163
164			def get_data_stats(self):
165			return Statistics.data_stats
166
167			def get_volume_stats(self):
168			return Statistics.volume_stats
169
170			def get_global_stats(self):
171			return Statistics.global_stats
172
173			def _set_pattern_info(self):
174			"""Gathers information about the pattern of the data in the current plugin."""
175			in_datasets, out_datasets = self.plugin.get_datasets()
176			try:
177			self.pattern = self.plugin.parameters['pattern']
178			if self.pattern == None:
179			raise KeyError
180			except KeyError:
181			if not out_datasets:
182			self.pattern = None
183			else:
184			patterns = out_datasets[0].get_data_patterns()
185			for pattern in patterns:
186			if 1 in patterns.get(pattern)["slice_dims"]:
187			self.pattern = pattern
188			break
189			for dataset in out_datasets:
190			if bool(set(Statistics.pattern_list) & set(dataset.data_info.get("data_patterns"))):
191			self.calc_stats = True
192
193			def _link_stats_to_datasets(self, stats):
194			"""Links the volume wide statistics to the output dataset(s)"""
195			out_datasets = self.plugin.get_out_datasets()
196			n_datasets = self.plugin.nOutput_datasets()
197			i = 1
198			group_name = "stats"
199			if n_datasets == 1:
200			while group_name in list(out_datasets[0].meta_data.get_dictionary().keys()):
201			group_name = f"stats{i}"
202			i += 1
203			out_datasets[0].data_info.set([group_name, "max"], stats[0])
204			out_datasets[0].data_info.set([group_name, "min"], stats[1])
205			out_datasets[0].data_info.set([group_name, "mean"], stats[2])
206			out_datasets[0].data_info.set([group_name, "mean_std_dev"], stats[3])
207			out_datasets[0].data_info.set([group_name, "median_std_dev"], stats[4])
208
209			def _write_stats_to_file(self, slice_stats, p_num):
210			"""Writes slice statistics to a h5 file"""
211			path = Statistics.path
212			filename = f"{path}/stats_p{p_num}_{self.plugin_name}.h5"
213			slice_stats_dim = (slice_stats.shape[1],)
214			self.hdf5 = Hdf5Utils(self.plugin.exp)
215			with h5.File(filename, "a") as h5file:
216			i = 1
217			group_name = "/stats"
218			while group_name in h5file:
219			group_name = f"/stats{i}"
220			i += 1
221			group = h5file.create_group(group_name, track_order=None)
222			max_ds = self.hdf5.create_dataset_nofill(group, "max", slice_stats_dim, slice_stats.dtype)
223			min_ds = self.hdf5.create_dataset_nofill(group, "min", slice_stats_dim, slice_stats.dtype)
224			mean_ds = self.hdf5.create_dataset_nofill(group, "mean", slice_stats_dim, slice_stats.dtype)
225			standard_deviation_ds = self.hdf5.create_dataset_nofill(group, "standard_deviation",
226			slice_stats_dim, slice_stats.dtype)
227			max_ds[::] = slice_stats[0]
228			min_ds[::] = slice_stats[1]
229			mean_ds[::] = slice_stats[2]
230			standard_deviation_ds[::] = slice_stats[3]
231
232			def _unpad_slice(self, slice1):
233			"""If data is padded in the slice dimension, removes this pad."""
234			out_datasets = self.plugin.get_out_datasets()
235			if len(out_datasets) == 1:
236			out_dataset = out_datasets[0]
237			else:
238			for dataset in out_datasets:
239			if self.pattern in list(dataset.data_info.get(["data_patterns"]).keys()):
240			out_dataset = dataset
241			break
242			slice_dims = out_dataset.get_slice_dimensions()
			0 ignored issues – show introduced 2021-12-13 15:56 UTC by Report Bug Copy Issue Report The variable `out_dataset` does not seem to be defined for all execution paths. Loading history...
243			if self.plugin.pcount == 0:
244			self.slice_list, self.pad = self._get_unpadded_slice_list(slice1, slice_dims)
245			if self.pad:
246			for slice_dim in slice_dims:
247			temp_slice = np.swapaxes(slice1, 0, slice_dim)
248			temp_slice = temp_slice[self.slice_list[slice_dim]]
249			slice1 = np.swapaxes(temp_slice, 0, slice_dim)
250			return slice1
251
252			def _get_unpadded_slice_list(self, slice1, slice_dims):
253			"""Creates slice object(s) to un-pad slices in the slice dimension(s)."""
254			slice_list = list(self.plugin.slice_list[0])
255			pad = False
256			if len(slice_list) == len(slice1.shape):
257			for i in slice_dims:
258			slice_width = self.plugin.slice_list[0][i].stop - self.plugin.slice_list[0][i].start
259			if slice_width != slice1.shape[i]:
260			pad = True
261			pad_width = (slice1.shape[i] - slice_width) // 2 # Assuming symmetrical padding
262			slice_list[i] = slice(pad_width, pad_width + 1, 1)
263			return tuple(slice_list), pad
264			else:
265			return self.plugin.slice_list[0], pad
266
267			def _de_list(self, slice1):
268			"""If the slice is in a list, remove it from that list."""
269			if type(slice1) == list:
270			if len(slice1) != 0:
271			slice1 = slice1[0]
272			slice1 = self._de_list(slice1)
273			return slice1
274
275			@classmethod
276			def _count(cls):
277			cls.count += 1
278
279			@classmethod
280			def _post_chain(cls):
281			print(cls.data_stats)
282			print(cls.volume_stats)
283			print(cls.global_stats)

DiamondLightSource / Savu

Pull Request — master (#878)

Statistics._get_unpadded_slice_list() A

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