savu.plugins.plugin.Plugin.get_citation_information() - Code Metrics - Inspection of "scrutinizer config" - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed

Retried Inspection

Pull Request — master (#708)

by Daniil

created 2021-02-25 17:47 UTC

Plugin.get_citation_information() A

↳ Parent: savu.plugins.plugin

Complexity

Conditions

Size

Total Lines	8
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	2
nop	1
dl	0
loc	8
rs	10
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:: plugin
   :platform: Unix
   :synopsis: Base class for all plugins used by Savu

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

"""

import ast
import copy
import logging
import inspect
import numpy as np

import savu.plugins.docstring_parser as doc
from savu.plugins.plugin_datasets import PluginDatasets


class Plugin(PluginDatasets):
    """
    The base class from which all plugins should inherit.
    :param in_datasets: Create a list of the dataset(s) to \
        process. Default: [].
    :param out_datasets: Create a list of the dataset(s) to \
        create. Default: [].
    """

    def __init__(self, name="Plugin"):
        super(Plugin, self).__init__(name)
        self.name = name
        self.parameters = {}
        self.parameters_types = {}
        self.parameters_desc = {}
        self.parameters_hide = []
        self.parameters_user = []
        self.chunk = False
        self.docstring_info = {}
        self.slice_list = None
        self.global_index = None
        self.pcount = 0
        self.exp = None
        self.check = False

    def initialise(self, params, exp, check=False):
        self.check = check
        self.exp = exp
        self._set_parameters(copy.deepcopy(params))
        self._main_setup()

    def _main_setup(self):
        """ Performs all the required plugin setup.

        It sets the experiment, then the parameters and replaces the
        in/out_dataset strings in ``self.parameters`` with the relevant data
        objects. It then creates PluginData objects for each of these datasets.
        """
        self._set_plugin_datasets()
        self._reset_process_frames_counter()
        self.setup()
        self.set_filter_padding(*(self.get_plugin_datasets()))
        self._finalise_plugin_datasets()
        self._finalise_datasets()

    def _reset_process_frames_counter(self):
        self.pcount = 0

    def get_process_frames_counter(self):
        return self.pcount

    def _set_parameters_this_instance(self, indices):
        """ Determines the parameters for this instance of the plugin, in the
        case of parameter tuning.

        param np.ndarray indices: the index of the current value in the
            parameter tuning list.
        """
        dims = set(self.multi_params_dict.keys())
        count = 0
        for dim in dims:
            info = self.multi_params_dict[dim]
            name = info['label'].split('_param')[0]
            self.parameters[name] = info['values'][indices[count]]
            count += 1

    def set_filter_padding(self, in_data, out_data):
        """
        Should be overridden to define how wide the frame should be for each
        input data set
        """
        return {}

    def setup(self):
        """
        This method is first to be called after the plugin has been created.
        It determines input/output datasets and plugin specific dataset
        information such as the pattern (e.g. sinogram/projection).
        """
        logging.error("set_up needs to be implemented")
        raise NotImplementedError("setup needs to be implemented")

    def _populate_default_parameters(self):
        """
        This method should populate all the required parameters with default
        values.  it is used for checking to see if new parameter values are
        appropriate

        It makes use of the classes including parameter information in the
        class docstring such as this

        :param error_threshold: Convergence threshold. Default: 0.001.
        """
        hidden_items = []
        user_items = []
        params = []
        not_params = []
        for clazz in inspect.getmro(self.__class__)[::-1]:
            if clazz != object:
                desc = doc.find_args(clazz, self)
                self.docstring_info['warn'] = desc['warn']
                self.docstring_info['info'] = desc['info']
                self.docstring_info['synopsis'] = desc['synopsis']
                params.extend(desc['param'])
                if desc['hide_param']:
                    hidden_items.extend(desc['hide_param'])
                if desc['user_param']:
                    user_items.extend(desc['user_param'])
                if desc['not_param']:
                    not_params.extend(desc['not_param'])
        self._add_item(params, not_params)
        user_items = [u for u in user_items if u not in not_params]
        hidden_items = [h for h in hidden_items if h not in not_params]
        user_items = list(set(user_items).difference(set(hidden_items)))
        self.parameters_hide = hidden_items
        self.parameters_user = user_items
        self.final_parameter_updates()

    def _add_item(self, item_list, not_list):
        true_list = [i for i in item_list if i['name'] not in not_list]
        for item in true_list:
            self.parameters[item['name']] = item['default']
            self.parameters_types[item['name']] = item['dtype']
            self.parameters_desc[item['name']] = item['desc']

    def delete_parameter_entry(self, param):
        if param in list(self.parameters.keys()):
            del self.parameters[param]
            del self.parameters_types[param]
            del self.parameters_desc[param]

    def initialise_parameters(self):
        self.parameters = {}
        self.parameters_types = {}
        self._populate_default_parameters()
        self.multi_params_dict = {}
        self.extra_dims = []

    def _set_parameters(self, parameters):
        """
        This method is called after the plugin has been created by the
        pipeline framework.  It replaces ``self.parameters`` default values
        with those given in the input process list.

        :param dict parameters: A dictionary of the parameters for this \
        plugin, or None if no customisation is required.
        """
        self.initialise_parameters()
        # reverse sorting added on Python 3 conversion to make the behaviour
        # similar (hopefully the same) as on Python 2
        for key in parameters.keys():
            if key in self.parameters.keys():
                value = self.__convert_multi_params(parameters[key], key)
                self.parameters[key] = value
            else:
                error = ("Parameter '%s' is not valid for plugin %s. \nTry "
                         "opening and re-saving the process list in the "
                         "configurator to auto remove \nobsolete parameters."
                         % (key, self.name))
                raise ValueError(error)

    def __convert_multi_params(self, value, key):
        """ Set up parameter tuning.

        Convert parameter value to a list if it uses parameter tuning and set
        associated parameters, so the framework knows the new size of the data
        and which plugins to re-run.
        """
        dtype = self.parameters_types[key]
        if isinstance(value, str) and ';' in value:
            value = value.split(';')
            if ":" in value[0]:
                seq = value[0].split(':')
                seq = [eval(s) for s in seq]
                value = list(np.arange(seq[0], seq[1], seq[2]))
                if len(value) == 0:

                    raise RuntimeError(
                        'No values for tuned parameter "{}", '
                        'ensure start:stop:step; values are valid.'.format(key))
            if not isinstance(value[0], dtype):
                try:
                    value.remove('')
                except Exception:
                    pass
                if isinstance(value[0], str):
                    value = [ast.literal_eval(i) for i in value]
                value = list(map(dtype, value))
            label = key + '_params.' + type(value[0]).__name__
            self.multi_params_dict[len(self.multi_params_dict)] = \
                {'label': label, 'values': value}
            self.extra_dims.append(len(value))
        return value

    def get_parameters(self, name):
        """ Return a plugin parameter

        :params str name: parameter name (dictionary key)
        :returns: the associated value in ``self.parameters``
        :rtype: dict value
        """
        return self.parameters[name]

    def base_pre_process(self):
        """ This method is called after the plugin has been created by the
        pipeline framework as a pre-processing step.
        """
        pass

    def pre_process(self):
        """ This method is called immediately after base_pre_process(). """
        pass

    def base_process_frames_before(self, data):
        """ This method is called before each call to process frames """
        return data

    def base_process_frames_after(self, data):
        """ This method is called directly after each call to process frames \
        and before returning the data to file."""
        return data

    def plugin_process_frames(self, data):
        frames = self.base_process_frames_after(self.process_frames(
                self.base_process_frames_before(data)))
        self.pcount += 1
        return frames

    def process_frames(self, data):
        """
        This method is called after the plugin has been created by the
        pipeline framework and forms the main processing step

        :param data: A list of numpy arrays for each input dataset.
        :type data: list(np.array)
        """

        logging.error("process frames needs to be implemented")
        raise NotImplementedError("process needs to be implemented")

    def post_process(self):
        """
        This method is called after the process function in the pipeline
        framework as a post-processing step. All processes will have finished
        performing the main processing at this stage.

        :param exp: An experiment object, holding input and output datasets
        :type exp: experiment class instance
        """
        pass

    def base_post_process(self):
        """ This method is called immediately after post_process(). """
        pass

    def set_preview(self, data, params):
        if not params:
            return True
        preview = data.get_preview()
        orig_indices = preview.get_starts_stops_steps()
        nDims = len(orig_indices[0])
        no_preview = [[0]*nDims, data.get_shape(), [1]*nDims, [1]*nDims]

        # Set previewing params if previewing has not already been applied to
        # the dataset.
        if no_preview == orig_indices:
            data.get_preview().revert_shape = data.get_shape()
            data.get_preview().set_preview(params)
            return True
        return False

    def _clean_up(self):
        """ Perform necessary plugin clean up after the plugin has completed.
        """
        self._clone_datasets()
        self.__copy_meta_data()
        self.__set_previous_patterns()
        self.__clean_up_plugin_data()

    def __copy_meta_data(self):
        """
        Copy all metadata from input datasets to output datasets, except axis
        data that is no longer valid.
        """
        remove_keys = self.__remove_axis_data()
        in_meta_data, out_meta_data = self.get()
        copy_dict = {}
        for mData in in_meta_data:
            temp = copy.deepcopy(mData.get_dictionary())
            copy_dict.update(temp)

        for i in range(len(out_meta_data)):
            temp = copy_dict.copy()
            for key in remove_keys[i]:
                if temp.get(key, None) is not None:
                    del temp[key]
            temp.update(out_meta_data[i].get_dictionary())
            out_meta_data[i]._set_dictionary(temp)

    def __set_previous_patterns(self):
        for data in self.get_out_datasets():
            data._set_previous_pattern(
                copy.deepcopy(data._get_plugin_data().get_pattern()))

    def __remove_axis_data(self):
        """
        Returns a list of meta_data entries corresponding to axis labels that
        are not copied over to the output datasets
        """
        in_datasets, out_datasets = self.get_datasets()
        all_in_labels = []
        for data in in_datasets:
            axis_keys = data.get_axis_label_keys()
            all_in_labels = all_in_labels + axis_keys

        remove_keys = []
        for data in out_datasets:
            axis_keys = data.get_axis_label_keys()
            remove_keys.append(set(all_in_labels).difference(set(axis_keys)))

        return remove_keys

    def __clean_up_plugin_data(self):
        """ Remove pluginData object encapsulated in a dataset after plugin
        completion.
        """
        in_data, out_data = self.get_datasets()
        data_object_list = in_data + out_data
        for data in data_object_list:
            data._clear_plugin_data()

    def _revert_preview(self, in_data):
        """ Revert dataset back to original shape if previewing was used in a
        plugin to reduce the data shape but the original data shape should be
        used thereafter. Remove previewing if it was added in the plugin.
        """
        for data in in_data:
            if data.get_preview().revert_shape:
                data.get_preview()._unset_preview()

    def set_global_frame_index(self, frame_idx):
        self.global_index = frame_idx

    def get_global_frame_index(self):
        """ Get the global frame index. """
        return self.global_index


    def set_current_slice_list(self, sl):
        self.slice_list = sl

    def get_current_slice_list(self):
        """ Get the slice list of the current frame being processed. """
        return self.slice_list

    def get_slice_dir_reps(self, nData):
        """ Return the periodicity of the main slice direction.

        :params int nData: The number of the dataset in the list.
        """
        slice_dir = \
            self.get_plugin_in_datasets()[nData].get_slice_directions()[0]
        sl = [sl[slice_dir] for sl in self.slice_list]
        reps = [i for i in range(len(sl)) if sl[i] == sl[0]]
        return np.diff(reps)[0] if len(reps) > 1 else 1

    def nInput_datasets(self):
        """
        The number of datasets required as input to the plugin

        :returns:  Number of input datasets

        """
        return 1

    def nOutput_datasets(self):
        """
        The number of datasets created by the plugin

        :returns:  Number of output datasets

        """
        return 1

    def nClone_datasets(self):
        """ The number of output datasets that have an clone - i.e. they take\
        it in turns to be used as output in an iterative plugin.
        """
        return 0

    def nFrames(self):
        """ The number of frames to process during each call to process_frames.
        """
        return 'single'

    def final_parameter_updates(self):
        """ An opportunity to update the parameters after they have been set.
        """
        pass

    def get_citation_information(self):
        """
        Gets the Citation Information for a plugin

        :returns:  A populated savu.data.plugin_info.CitationInfomration

        """
        return None

    def executive_summary(self):
        """ Provide a summary to the user for the result of the plugin.

        e.g.
         - Warning, the sample may have shifted during data collection
         - Filter operated normally

        :returns:  A list of string summaries
        """
        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:: plugin
17			:platform: Unix
18			:synopsis: Base class for all plugins used by Savu
19
20			.. moduleauthor:: Mark Basham <[email protected]>
21
22			"""
23
24			import ast
25			import copy
26			import logging
27			import inspect
28			import numpy as np
29
30			import savu.plugins.docstring_parser as doc
31			from savu.plugins.plugin_datasets import PluginDatasets
32
33
34			class Plugin(PluginDatasets):
35			"""
36			The base class from which all plugins should inherit.
37			:param in_datasets: Create a list of the dataset(s) to \
38			process. Default: [].
39			:param out_datasets: Create a list of the dataset(s) to \
40			create. Default: [].
41			"""
42
43			def __init__(self, name="Plugin"):
44			super(Plugin, self).__init__(name)
45			self.name = name
46			self.parameters = {}
47			self.parameters_types = {}
48			self.parameters_desc = {}
49			self.parameters_hide = []
50			self.parameters_user = []
51			self.chunk = False
52			self.docstring_info = {}
53			self.slice_list = None
54			self.global_index = None
55			self.pcount = 0
56			self.exp = None
57			self.check = False
58
59			def initialise(self, params, exp, check=False):
60			self.check = check
61			self.exp = exp
62			self._set_parameters(copy.deepcopy(params))
63			self._main_setup()
64
65			def _main_setup(self):
66			""" Performs all the required plugin setup.
67
68			It sets the experiment, then the parameters and replaces the
69			in/out_dataset strings in ``self.parameters`` with the relevant data
70			objects. It then creates PluginData objects for each of these datasets.
71			"""
72			self._set_plugin_datasets()
73			self._reset_process_frames_counter()
74			self.setup()
75			self.set_filter_padding(*(self.get_plugin_datasets()))
76			self._finalise_plugin_datasets()
77			self._finalise_datasets()
78
79			def _reset_process_frames_counter(self):
80			self.pcount = 0
81
82			def get_process_frames_counter(self):
83			return self.pcount
84
85			def _set_parameters_this_instance(self, indices):
86			""" Determines the parameters for this instance of the plugin, in the
87			case of parameter tuning.
88
89			param np.ndarray indices: the index of the current value in the
90			parameter tuning list.
91			"""
92			dims = set(self.multi_params_dict.keys())
93			count = 0
94			for dim in dims:
95			info = self.multi_params_dict[dim]
96			name = info['label'].split('_param')[0]
97			self.parameters[name] = info['values'][indices[count]]
98			count += 1
99
100			def set_filter_padding(self, in_data, out_data):
101			"""
102			Should be overridden to define how wide the frame should be for each
103			input data set
104			"""
105			return {}
106
107			def setup(self):
108			"""
109			This method is first to be called after the plugin has been created.
110			It determines input/output datasets and plugin specific dataset
111			information such as the pattern (e.g. sinogram/projection).
112			"""
113			logging.error("set_up needs to be implemented")
114			raise NotImplementedError("setup needs to be implemented")
115
116			def _populate_default_parameters(self):
117			"""
118			This method should populate all the required parameters with default
119			values. it is used for checking to see if new parameter values are
120			appropriate
121
122			It makes use of the classes including parameter information in the
123			class docstring such as this
124
125			:param error_threshold: Convergence threshold. Default: 0.001.
126			"""
127			hidden_items = []
128			user_items = []
129			params = []
130			not_params = []
131			for clazz in inspect.getmro(self.__class__)[::-1]:
132			if clazz != object:
133			desc = doc.find_args(clazz, self)
134			self.docstring_info['warn'] = desc['warn']
135			self.docstring_info['info'] = desc['info']
136			self.docstring_info['synopsis'] = desc['synopsis']
137			params.extend(desc['param'])
138			if desc['hide_param']:
139			hidden_items.extend(desc['hide_param'])
140			if desc['user_param']:
141			user_items.extend(desc['user_param'])
142			if desc['not_param']:
143			not_params.extend(desc['not_param'])
144			self._add_item(params, not_params)
145			user_items = [u for u in user_items if u not in not_params]
146			hidden_items = [h for h in hidden_items if h not in not_params]
147			user_items = list(set(user_items).difference(set(hidden_items)))
148			self.parameters_hide = hidden_items
149			self.parameters_user = user_items
150			self.final_parameter_updates()
151
152			def _add_item(self, item_list, not_list):
153			true_list = [i for i in item_list if i['name'] not in not_list]
154			for item in true_list:
155			self.parameters[item['name']] = item['default']
156			self.parameters_types[item['name']] = item['dtype']
157			self.parameters_desc[item['name']] = item['desc']
158
159			def delete_parameter_entry(self, param):
160			if param in list(self.parameters.keys()):
161			del self.parameters[param]
162			del self.parameters_types[param]
163			del self.parameters_desc[param]
164
165			def initialise_parameters(self):
166			self.parameters = {}
167			self.parameters_types = {}
168			self._populate_default_parameters()
169			self.multi_params_dict = {}
170			self.extra_dims = []
171
172			def _set_parameters(self, parameters):
173			"""
174			This method is called after the plugin has been created by the
175			pipeline framework. It replaces ``self.parameters`` default values
176			with those given in the input process list.
177
178			:param dict parameters: A dictionary of the parameters for this \
179			plugin, or None if no customisation is required.
180			"""
181			self.initialise_parameters()
182			# reverse sorting added on Python 3 conversion to make the behaviour
183			# similar (hopefully the same) as on Python 2
184			for key in parameters.keys():
185			if key in self.parameters.keys():
186			value = self.__convert_multi_params(parameters[key], key)
187			self.parameters[key] = value
188			else:
189			error = ("Parameter '%s' is not valid for plugin %s. \nTry "
190			"opening and re-saving the process list in the "
191			"configurator to auto remove \nobsolete parameters."
192			% (key, self.name))
193			raise ValueError(error)
194
195			def __convert_multi_params(self, value, key):
196			""" Set up parameter tuning.
197
198			Convert parameter value to a list if it uses parameter tuning and set
199			associated parameters, so the framework knows the new size of the data
200			and which plugins to re-run.
201			"""
202			dtype = self.parameters_types[key]
203			if isinstance(value, str) and ';' in value:
204			value = value.split(';')
205			if ":" in value[0]:
206			seq = value[0].split(':')
207			seq = [eval(s) for s in seq]
208			value = list(np.arange(seq[0], seq[1], seq[2]))
209			if len(value) == 0:
			0 ignored issues – show Comprehensibility Best Practice introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `len` does not seem to be defined. Loading history...
210			raise RuntimeError(
211			'No values for tuned parameter "{}", '
212			'ensure start:stop:step; values are valid.'.format(key))
213			if not isinstance(value[0], dtype):
214			try:
215			value.remove('')
216			except Exception:
217			pass
218			if isinstance(value[0], str):
219			value = [ast.literal_eval(i) for i in value]
220			value = list(map(dtype, value))
221			label = key + '_params.' + type(value[0]).__name__
222			self.multi_params_dict[len(self.multi_params_dict)] = \
223			{'label': label, 'values': value}
224			self.extra_dims.append(len(value))
225			return value
226
227			def get_parameters(self, name):
228			""" Return a plugin parameter
229
230			:params str name: parameter name (dictionary key)
231			:returns: the associated value in ``self.parameters``
232			:rtype: dict value
233			"""
234			return self.parameters[name]
235
236			def base_pre_process(self):
237			""" This method is called after the plugin has been created by the
238			pipeline framework as a pre-processing step.
239			"""
240			pass
241
242			def pre_process(self):
243			""" This method is called immediately after base_pre_process(). """
244			pass
245
246			def base_process_frames_before(self, data):
247			""" This method is called before each call to process frames """
248			return data
249
250			def base_process_frames_after(self, data):
251			""" This method is called directly after each call to process frames \
252			and before returning the data to file."""
253			return data
254
255			def plugin_process_frames(self, data):
256			frames = self.base_process_frames_after(self.process_frames(
257			self.base_process_frames_before(data)))
258			self.pcount += 1
259			return frames
260
261			def process_frames(self, data):
262			"""
263			This method is called after the plugin has been created by the
264			pipeline framework and forms the main processing step
265
266			:param data: A list of numpy arrays for each input dataset.
267			:type data: list(np.array)
268			"""
269
270			logging.error("process frames needs to be implemented")
271			raise NotImplementedError("process needs to be implemented")
272
273			def post_process(self):
274			"""
275			This method is called after the process function in the pipeline
276			framework as a post-processing step. All processes will have finished
277			performing the main processing at this stage.
278
279			:param exp: An experiment object, holding input and output datasets
280			:type exp: experiment class instance
281			"""
282			pass
283
284			def base_post_process(self):
285			""" This method is called immediately after post_process(). """
286			pass
287
288			def set_preview(self, data, params):
289			if not params:
290			return True
291			preview = data.get_preview()
292			orig_indices = preview.get_starts_stops_steps()
293			nDims = len(orig_indices[0])
294			no_preview = [[0]nDims, data.get_shape(), [1]nDims, [1]*nDims]
295
296			# Set previewing params if previewing has not already been applied to
297			# the dataset.
298			if no_preview == orig_indices:
299			data.get_preview().revert_shape = data.get_shape()
300			data.get_preview().set_preview(params)
301			return True
302			return False
303
304			def _clean_up(self):
305			""" Perform necessary plugin clean up after the plugin has completed.
306			"""
307			self._clone_datasets()
308			self.__copy_meta_data()
309			self.__set_previous_patterns()
310			self.__clean_up_plugin_data()
311
312			def __copy_meta_data(self):
313			"""
314			Copy all metadata from input datasets to output datasets, except axis
315			data that is no longer valid.
316			"""
317			remove_keys = self.__remove_axis_data()
318			in_meta_data, out_meta_data = self.get()
319			copy_dict = {}
320			for mData in in_meta_data:
321			temp = copy.deepcopy(mData.get_dictionary())
322			copy_dict.update(temp)
323
324			for i in range(len(out_meta_data)):
325			temp = copy_dict.copy()
326			for key in remove_keys[i]:
327			if temp.get(key, None) is not None:
328			del temp[key]
329			temp.update(out_meta_data[i].get_dictionary())
330			out_meta_data[i]._set_dictionary(temp)
331
332			def __set_previous_patterns(self):
333			for data in self.get_out_datasets():
334			data._set_previous_pattern(
335			copy.deepcopy(data._get_plugin_data().get_pattern()))
336
337			def __remove_axis_data(self):
338			"""
339			Returns a list of meta_data entries corresponding to axis labels that
340			are not copied over to the output datasets
341			"""
342			in_datasets, out_datasets = self.get_datasets()
343			all_in_labels = []
344			for data in in_datasets:
345			axis_keys = data.get_axis_label_keys()
346			all_in_labels = all_in_labels + axis_keys
347
348			remove_keys = []
349			for data in out_datasets:
350			axis_keys = data.get_axis_label_keys()
351			remove_keys.append(set(all_in_labels).difference(set(axis_keys)))
352
353			return remove_keys
354
355			def __clean_up_plugin_data(self):
356			""" Remove pluginData object encapsulated in a dataset after plugin
357			completion.
358			"""
359			in_data, out_data = self.get_datasets()
360			data_object_list = in_data + out_data
361			for data in data_object_list:
362			data._clear_plugin_data()
363
364			def _revert_preview(self, in_data):
365			""" Revert dataset back to original shape if previewing was used in a
366			plugin to reduce the data shape but the original data shape should be
367			used thereafter. Remove previewing if it was added in the plugin.
368			"""
369			for data in in_data:
370			if data.get_preview().revert_shape:
371			data.get_preview()._unset_preview()
372
373			def set_global_frame_index(self, frame_idx):
374			self.global_index = frame_idx
375
376			def get_global_frame_index(self):
377			""" Get the global frame index. """
378			return self.global_index
379
380
381			def set_current_slice_list(self, sl):
382			self.slice_list = sl
383
384			def get_current_slice_list(self):
385			""" Get the slice list of the current frame being processed. """
386			return self.slice_list
387
388			def get_slice_dir_reps(self, nData):
389			""" Return the periodicity of the main slice direction.
390
391			:params int nData: The number of the dataset in the list.
392			"""
393			slice_dir = \
394			self.get_plugin_in_datasets()[nData].get_slice_directions()[0]
395			sl = [sl[slice_dir] for sl in self.slice_list]
396			reps = [i for i in range(len(sl)) if sl[i] == sl[0]]
397			return np.diff(reps)[0] if len(reps) > 1 else 1
398
399			def nInput_datasets(self):
400			"""
401			The number of datasets required as input to the plugin
402
403			:returns: Number of input datasets
404
405			"""
406			return 1
407
408			def nOutput_datasets(self):
409			"""
410			The number of datasets created by the plugin
411
412			:returns: Number of output datasets
413
414			"""
415			return 1
416
417			def nClone_datasets(self):
418			""" The number of output datasets that have an clone - i.e. they take\
419			it in turns to be used as output in an iterative plugin.
420			"""
421			return 0
422
423			def nFrames(self):
424			""" The number of frames to process during each call to process_frames.
425			"""
426			return 'single'
427
428			def final_parameter_updates(self):
429			""" An opportunity to update the parameters after they have been set.
430			"""
431			pass
432
433			def get_citation_information(self):
434			"""
435			Gets the Citation Information for a plugin
436
437			:returns: A populated savu.data.plugin_info.CitationInfomration
438
439			"""
440			return None
441
442			def executive_summary(self):
443			""" Provide a summary to the user for the result of the plugin.
444
445			e.g.
446			- Warning, the sample may have shifted during data collection
447			- Filter operated normally
448
449			:returns: A list of string summaries
450			"""
451			return ["Nothing to Report"]
452

DiamondLightSource / Savu

Pull Request — master (#708)

Plugin.get_citation_information() A

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