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Merge pull request #677 from DiamondLightSource/nics_working_branch
adds iterative plugin templates
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‎plugin_examples/plugin_templates/iterative/testing_iterative_plugin.py‎

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# Copyright 2014 Diamond Light Source Ltd.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""
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.. module:: iterative_plugin
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:platform: Unix
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:synopsis: Iterative plugin example
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.. moduleauthor:: Nicola Wadeson <[email protected]>
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"""
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import numpy as np
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from savu.plugins.utils import register_plugin
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from savu.plugins.filters.base_filter import BaseFilter
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from savu.plugins.driver.iterative_plugin import IterativePlugin
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@register_plugin
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class TestingIterativePlugin(BaseFilter, IterativePlugin):
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"""
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A plugin to test the iterative plugin driver
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:u*param nIterations: Number of iterations. Default: 10.
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"""
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def __init__(self):
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super(TestingIterativePlugin, self).__init__("TestingIterativePlugin")
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def pre_process(self):
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self.set_iterations(self.parameters['nIterations'])
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def process_frames(self, data):
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# A random example function
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if self.get_iteration() == 0:
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return np.zeros(data[0].shape, dtype=np.float32)
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return data[1] + np.ones(data[0].shape, dtype=np.float32)*10
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def post_process(self):
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# option here to break out of the iterations
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#self.set_processing_complete()
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pass
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def setup(self):
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# set up the output dataset that is created by the plugin
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in_dataset, out_dataset = self.get_datasets()
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in_pData, out_pData = self.get_plugin_datasets()
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in_pData[0].plugin_data_setup('SINOGRAM', 'single')
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# Cloned datasets are at the end of the out_dataset list
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out_dataset[0].create_dataset(in_dataset[0])
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# What is a cloned dataset?
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# Since each dataset in Savu has its own backing hdf5 file, a dataset
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# cannot be used for input and output at the same time. So, in the
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# case of iterative plugins, if a dataset is used as output and then
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# as input on the next iteration, the subsequent output must be a
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# different file.
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# A cloned dataset is a copy of another dataset but with a different
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# backing file. It doesn't have a name, is not accessible as a dataset
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# in the framework and is only used in alternation with another
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# dataset to allow it to be used as both input and output
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# simultaneously.
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# This is a cloned dataset (of out_dataset[0])
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self.create_clone(out_dataset[1], out_dataset[0])
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out_pData[0].plugin_data_setup('SINOGRAM', 'single')
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out_pData[1].plugin_data_setup('SINOGRAM', 'single')
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# input and output datasets for the first iteration
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self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]])
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# input and output datasets for subsequent iterations
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self.set_iteration_datasets(1, [in_dataset[0], out_dataset[0]],
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[out_dataset[1]])
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# out_dataset[0] and out_dataset[1] will continue to alternate for
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# all remaining iterations i.e. output becomes input and input becomes
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# output.
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# total number of output datasets
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def nOutput_datasets(self):
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return 2
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# total number of output datasets that are clones
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def nClone_datasets(self):
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return 1

‎plugin_examples/plugin_templates/iterative/testing_iterative_plugin2.py‎

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# Copyright 2014 Diamond Light Source Ltd.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""
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.. module:: testing_iterative_plugin2
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:platform: Unix
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:synopsis: Iterative plugin example
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.. moduleauthor:: Nicola Wadeson <[email protected]>
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"""
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import numpy as np
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from savu.plugins.utils import register_plugin
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from savu.plugins.filters.base_filter import BaseFilter
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from savu.plugins.driver.iterative_plugin import IterativePlugin
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@register_plugin
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class TestingIterativePlugin2(BaseFilter, IterativePlugin):
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"""
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A plugin to test the iterative plugin driver
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"""
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def __init__(self):
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super(TestingIterativePlugin2, self).\
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__init__("TestingIterativePlugin2")
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def pre_process(self):
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self.set_iterations(3)
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def process_frames(self, data):
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if self.get_iteration() == 0:
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return data[0]
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return data[0]
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def post_process(self):
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# option here to break out of the iterations
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# self.set_processing_complete()
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pass
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def setup(self):
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self.exp.log(self.name + " Start")
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# set up the output dataset that is created by the plugin
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in_dataset, out_dataset = self.get_datasets()
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in_pData, out_pData = self.get_plugin_datasets()
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in_pData[0].plugin_data_setup('SINOGRAM', 'single')
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out_dataset[0].create_dataset(in_dataset[0])
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self.clone_dataset(out_dataset[1], out_dataset[0])
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out_pData[0].plugin_data_setup('SINOGRAM', 'single')
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out_pData[1].plugin_data_setup('SINOGRAM', 'single')
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# try replacing input dataset with the output dataset
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self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]])
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self.set_iteration_datasets(1, [out_dataset[0]], [out_dataset[1]])
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self.exp.log(self.name + " End")
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def nOutput_datasets(self):
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return 2
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def nClone_datasets(self):
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return 1

‎plugin_examples/plugin_templates/iterative/testing_iterative_plugin3.py‎

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# Copyright 2014 Diamond Light Source Ltd.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""
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.. module:: testing_iterative_plugin3
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:platform: Unix
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:synopsis: Iterative plugin example
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.. moduleauthor:: Nicola Wadeson <[email protected]>
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"""
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from savu.plugins.utils import register_plugin
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from savu.plugins.filters.base_filter import BaseFilter
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from savu.plugins.driver.iterative_plugin import IterativePlugin
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@register_plugin
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class TestingIterativePlugin3(BaseFilter, IterativePlugin):
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"""
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A plugin to test the iterative plugin driver
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"""
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def __init__(self):
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super(TestingIterativePlugin3, self).\
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__init__("TestingIterativePlugin3")
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def pre_process(self):
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self.set_iterations(3)
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def process_frames(self, data):
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return [data[0], data[0]]
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def post_process(self):
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# option here to break out of the iterations
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# self.set_processing_complete()
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pass
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def setup(self):
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self.exp.log(self.name + " Start")
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# set up the output dataset that is created by the plugin
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in_dataset, out_dataset = self.get_datasets()
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in_pData, out_pData = self.get_plugin_datasets()
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in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames())
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# these are the datasets with names
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out_dataset[0].create_dataset(in_dataset[0])
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out_dataset[1].create_dataset(in_dataset[0])
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# these are the clones
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out_dataset[2].create_dataset(out_dataset[0])
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out_dataset[3].create_dataset(out_dataset[1])
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out_pData[0].plugin_data_setup('SINOGRAM', 'single')
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out_pData[1].plugin_data_setup('SINOGRAM', 'single')
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out_pData[2].plugin_data_setup('SINOGRAM', 'single')
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out_pData[3].plugin_data_setup('SINOGRAM', 'single')
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# try replacing input dataset with the output dataset
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dIn = [in_dataset[0]]
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dOut = [out_dataset[0], out_dataset[1]]
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self.set_iteration_datasets(0, dIn, dOut)
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dIn = [out_dataset[0], out_dataset[0], out_dataset[1]]
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dOut = [out_dataset[2], out_dataset[3]]
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self.set_iteration_datasets(1, dIn, dOut)
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# cloned datasets used as alternating datasets?
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self.set_alternating_datasets(out_dataset[0], out_dataset[2])
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self.set_alternating_datasets(out_dataset[1], out_dataset[3])
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self.exp.log(self.name + " End")
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def nOutput_datasets(self):
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return 4
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def nClone_datasets(self):
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return 2

‎plugin_examples/plugin_templates/iterative/testing_iterative_plugin4.py‎

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# Copyright 2014 Diamond Light Source Ltd.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""
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.. module:: testing_iterative_plugin4
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:platform: Unix
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:synopsis: Iterative plugin example
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.. moduleauthor:: Nicola Wadeson <[email protected]>
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"""
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from savu.plugins.utils import register_plugin
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from savu.plugins.filters.base_filter import BaseFilter
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from savu.plugins.driver.iterative_plugin import IterativePlugin
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@register_plugin
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class TestingIterativePlugin4(BaseFilter, IterativePlugin):
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"""
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A plugin to test the iterative plugin driver - switching between sinograms
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and projections on each iteration.
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"""
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def __init__(self):
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super(TestingIterativePlugin4, self).\
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__init__("TestingIterativePlugin4")
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def pre_process(self):
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self.set_iterations(3)
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def process_frames(self, data):
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return data[0]
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def post_process(self):
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# option here to break out of the iterations
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# self.set_processing_complete()
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pass
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def setup(self):
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# set up the output dataset that is created by the plugin
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in_dataset, out_dataset = self.get_datasets()
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in_pData, out_pData = self.get_plugin_datasets()
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in_pData[0].plugin_data_setup('SINOGRAM', 'single')
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out_dataset[0].create_dataset(in_dataset[0])
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# Clone and set as alternating dataset - should I actually do this here?
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self.clone_dataset(out_dataset[1], out_dataset[0])
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# HOw to set more than one pattern associated with a plugin
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out_pData[0].plugin_data_setup('SINOGRAM', 'single') # set first pattern
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out_pData[1].plugin_data_setup('PROJECTION', 'single') # set first pattern
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# Do I need two plugin data objects? When should I set this?
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# try replacing input dataset with the output dataset *****option to change the pattern on each iteration?
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# option to set any number of patterns one after another
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self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]], pattern='SINOGRAM') # Add option for pattern to be a dictionary with different pattern for each dataset
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self.set_iteration_datasets(1, [out_dataset[0]], [out_dataset[1]], pattern='PROJECTION') # PROJECTION
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# out_dataset[0] and out_dataset[1] will continue to alternate for the
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# remaining iterations
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self.set_alternating_patterns(['SINOGRAM', 'PROJECTION']) # or explicitly add it as above or a combination of both
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# it could be that the first two iterations have the same pattern and the remainder alternate
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# alternatively to above you could just have
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# self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]])
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# self.set_iteration_datasets(1, [out_dataset[0]], [out_dataset[1]])
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# self.set_alternating_patterns(['SINOGRAM', 'PROJECTION']) # what if there is more than on pattern - this should also be a dictionary
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# So, to set different patterns there are two ways
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# first way is to add 'pattern' key word to set_iteration_datasets function call
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# second way is to pass a list of patterns to set_alternating_patterns function call
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# in either case, each entry can be a list of a dictionary
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# if a list apply to all datasets
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# if a dictionary, they should be {dataset: pattern} key value pairs
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# Now I just have to make this work - can I just create an extra pluginData object for each dataset and alternate between those?
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# Or will I have to calculate mfp/mft every time?
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# Don't forget to call "finalise_datasets" or whatever the function is (usually called after the setup method)
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def nOutput_datasets(self):
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return 2
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def nClone_datasets(self):
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return 1

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