Merge pull request #677 from DiamondLightSource/nics_working_branch

adds iterative plugin templates

plugin_examples/plugin_templates/iterative/testing_iterative_plugin.py

@@ -0,0 +1,97 @@
+# 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:: iterative_plugin
+   :platform: Unix
+   :synopsis: Iterative plugin example
+.. moduleauthor:: Nicola Wadeson <scientificsoftware@diamond.ac.uk>
+"""
+
+import numpy as np
+
+from savu.plugins.utils import register_plugin
+from savu.plugins.filters.base_filter import BaseFilter
+from savu.plugins.driver.iterative_plugin import IterativePlugin
+
+
+@register_plugin
+class TestingIterativePlugin(BaseFilter, IterativePlugin):
+    """
+    A plugin to test the iterative plugin driver
+    
+    :u*param nIterations: Number of iterations.  Default: 10.
+
+    """
+
+    def __init__(self):
+        super(TestingIterativePlugin, self).__init__("TestingIterativePlugin")
+
+    def pre_process(self):
+        self.set_iterations(self.parameters['nIterations'])
+
+    def process_frames(self, data):
+        # A random example function
+        if self.get_iteration() == 0:
+            return np.zeros(data[0].shape, dtype=np.float32)
+        return data[1] + np.ones(data[0].shape, dtype=np.float32)*10
+
+    def post_process(self):
+        # option here to break out of the iterations
+        #self.set_processing_complete()
+        pass
+
+    def setup(self):
+        # set up the output dataset that is created by the plugin
+        in_dataset, out_dataset = self.get_datasets()
+
+        in_pData, out_pData = self.get_plugin_datasets()
+        in_pData[0].plugin_data_setup('SINOGRAM', 'single')
+
+        # Cloned datasets are at the end of the out_dataset list
+        out_dataset[0].create_dataset(in_dataset[0])
+
+        # What is a cloned dataset?
+        # Since each dataset in Savu has its own backing hdf5 file, a dataset
+        # cannot be used for input and output at the same time.  So, in the
+        # case of iterative plugins, if a dataset is used as output and then
+        # as input on the next iteration, the subsequent output must be a
+        # different file.
+        # A cloned dataset is a copy of another dataset but with a different
+        # backing file.  It doesn't have a name, is not accessible as a dataset
+        # in the framework and is only used in alternation with another
+        # dataset to allow it to be used as both input and output
+        # simultaneously.
+
+        # This is a cloned dataset (of out_dataset[0])
+        self.create_clone(out_dataset[1], out_dataset[0])
+
+        out_pData[0].plugin_data_setup('SINOGRAM', 'single')
+        out_pData[1].plugin_data_setup('SINOGRAM', 'single')
+
+        # input and output datasets for the first iteration
+        self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]])
+        # input and output datasets for subsequent iterations
+        self.set_iteration_datasets(1, [in_dataset[0], out_dataset[0]],
+                                    [out_dataset[1]])
+        # out_dataset[0] and out_dataset[1] will continue to alternate for
+        # all remaining iterations i.e. output becomes input and input becomes
+        # output.
+
+    # total number of output datasets
+    def nOutput_datasets(self):
+        return 2
+
+    # total number of output datasets that are clones
+    def nClone_datasets(self):
+        return 1

plugin_examples/plugin_templates/iterative/testing_iterative_plugin2.py

@@ -0,0 +1,76 @@
+# 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:: testing_iterative_plugin2
+   :platform: Unix
+   :synopsis: Iterative plugin example
+.. moduleauthor:: Nicola Wadeson <scientificsoftware@diamond.ac.uk>
+"""
+
+import numpy as np
+
+from savu.plugins.utils import register_plugin
+from savu.plugins.filters.base_filter import BaseFilter
+from savu.plugins.driver.iterative_plugin import IterativePlugin
+
+
+@register_plugin
+class TestingIterativePlugin2(BaseFilter, IterativePlugin):
+    """
+    A plugin to test the iterative plugin driver
+    """
+
+    def __init__(self):
+        super(TestingIterativePlugin2, self).\
+            __init__("TestingIterativePlugin2")
+
+    def pre_process(self):
+        self.set_iterations(3)
+
+    def process_frames(self, data):
+        if self.get_iteration() == 0:
+            return data[0]
+        return data[0]
+
+    def post_process(self):
+        # option here to break out of the iterations
+        # self.set_processing_complete()
+        pass
+
+    def setup(self):
+        self.exp.log(self.name + " Start")
+
+        # set up the output dataset that is created by the plugin
+        in_dataset, out_dataset = self.get_datasets()
+
+        in_pData, out_pData = self.get_plugin_datasets()
+        in_pData[0].plugin_data_setup('SINOGRAM', 'single')
+
+        out_dataset[0].create_dataset(in_dataset[0])
+        self.clone_dataset(out_dataset[1], out_dataset[0])
+
+        out_pData[0].plugin_data_setup('SINOGRAM', 'single')
+        out_pData[1].plugin_data_setup('SINOGRAM', 'single')
+
+        # try replacing input dataset with the output dataset
+        self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]])
+        self.set_iteration_datasets(1, [out_dataset[0]], [out_dataset[1]])
+
+        self.exp.log(self.name + " End")
+
+    def nOutput_datasets(self):
+        return 2
+
+    def nClone_datasets(self):
+        return 1

plugin_examples/plugin_templates/iterative/testing_iterative_plugin3.py

@@ -0,0 +1,87 @@
+# 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:: testing_iterative_plugin3
+   :platform: Unix
+   :synopsis: Iterative plugin example
+.. moduleauthor:: Nicola Wadeson <scientificsoftware@diamond.ac.uk>
+"""
+
+from savu.plugins.utils import register_plugin
+from savu.plugins.filters.base_filter import BaseFilter
+from savu.plugins.driver.iterative_plugin import IterativePlugin
+
+
+@register_plugin
+class TestingIterativePlugin3(BaseFilter, IterativePlugin):
+    """
+    A plugin to test the iterative plugin driver
+    """
+
+    def __init__(self):
+        super(TestingIterativePlugin3, self).\
+            __init__("TestingIterativePlugin3")
+
+    def pre_process(self):
+        self.set_iterations(3)
+
+    def process_frames(self, data):
+        return [data[0], data[0]]
+
+    def post_process(self):
+        # option here to break out of the iterations
+        # self.set_processing_complete()
+        pass
+
+    def setup(self):
+        self.exp.log(self.name + " Start")
+
+        # set up the output dataset that is created by the plugin
+        in_dataset, out_dataset = self.get_datasets()
+
+        in_pData, out_pData = self.get_plugin_datasets()
+        in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames())
+
+        # these are the datasets with names
+        out_dataset[0].create_dataset(in_dataset[0])
+        out_dataset[1].create_dataset(in_dataset[0])
+        # these are the clones
+        out_dataset[2].create_dataset(out_dataset[0])
+        out_dataset[3].create_dataset(out_dataset[1])
+
+        out_pData[0].plugin_data_setup('SINOGRAM', 'single')
+        out_pData[1].plugin_data_setup('SINOGRAM', 'single')
+        out_pData[2].plugin_data_setup('SINOGRAM', 'single')
+        out_pData[3].plugin_data_setup('SINOGRAM', 'single')
+
+        # try replacing input dataset with the output dataset
+        dIn = [in_dataset[0]]
+        dOut = [out_dataset[0], out_dataset[1]]
+        self.set_iteration_datasets(0, dIn, dOut)
+
+        dIn = [out_dataset[0], out_dataset[0], out_dataset[1]]
+        dOut = [out_dataset[2], out_dataset[3]]
+        self.set_iteration_datasets(1, dIn, dOut)
+
+        # cloned datasets used as alternating datasets?
+        self.set_alternating_datasets(out_dataset[0], out_dataset[2])
+        self.set_alternating_datasets(out_dataset[1], out_dataset[3])
+
+        self.exp.log(self.name + " End")
+
+    def nOutput_datasets(self):
+        return 4
+
+    def nClone_datasets(self):
+        return 2

plugin_examples/plugin_templates/iterative/testing_iterative_plugin4.py

@@ -0,0 +1,94 @@
+# 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:: testing_iterative_plugin4
+   :platform: Unix
+   :synopsis: Iterative plugin example
+.. moduleauthor:: Nicola Wadeson <scientificsoftware@diamond.ac.uk>
+"""
+
+from savu.plugins.utils import register_plugin
+from savu.plugins.filters.base_filter import BaseFilter
+from savu.plugins.driver.iterative_plugin import IterativePlugin
+
+
+@register_plugin
+class TestingIterativePlugin4(BaseFilter, IterativePlugin):
+    """
+    A plugin to test the iterative plugin driver - switching between sinograms
+    and projections on each iteration.
+    """
+
+    def __init__(self):
+        super(TestingIterativePlugin4, self).\
+            __init__("TestingIterativePlugin4")
+
+    def pre_process(self):
+        self.set_iterations(3)
+
+    def process_frames(self, data):
+        return data[0]
+
+    def post_process(self):
+        # option here to break out of the iterations
+        # self.set_processing_complete()
+        pass
+
+    def setup(self):
+        # set up the output dataset that is created by the plugin
+        in_dataset, out_dataset = self.get_datasets()
+
+        in_pData, out_pData = self.get_plugin_datasets()
+        in_pData[0].plugin_data_setup('SINOGRAM', 'single')
+
+        out_dataset[0].create_dataset(in_dataset[0])
+        # Clone and set as alternating dataset - should I actually do this here?
+        self.clone_dataset(out_dataset[1], out_dataset[0])
+
+        # HOw to set more than one pattern associated with a plugin
+        out_pData[0].plugin_data_setup('SINOGRAM', 'single') # set first pattern
+        out_pData[1].plugin_data_setup('PROJECTION', 'single') # set first pattern
+
+        # Do I need two plugin data objects?  When should I set this?
+
+        # try replacing input dataset with the output dataset *****option to change the pattern on each iteration?
+        # option to set any number of patterns one after another
+        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
+        self.set_iteration_datasets(1, [out_dataset[0]], [out_dataset[1]], pattern='PROJECTION') # PROJECTION
+        # out_dataset[0] and out_dataset[1] will continue to alternate for the
+        # remaining iterations
+        self.set_alternating_patterns(['SINOGRAM', 'PROJECTION']) # or explicitly add it as above or a combination of both
+        # it could be that the first two iterations have the same pattern and the remainder alternate
+
+        # alternatively to above you could just have
+#        self.set_iteration_datasets(0, [in_dataset[0]], [out_dataset[0]])
+#        self.set_iteration_datasets(1, [out_dataset[0]], [out_dataset[1]])
+#        self.set_alternating_patterns(['SINOGRAM', 'PROJECTION']) # what if there is more than on pattern - this should also be a dictionary
+
+        # So, to set different patterns there are two ways
+        # first way is to add 'pattern' key word to set_iteration_datasets function call
+        # second way is to pass a list of patterns to set_alternating_patterns function call
+        # in either case, each entry can be a list of a dictionary
+        # if a list apply to all datasets
+        # if a dictionary, they should be {dataset: pattern} key value pairs
+
+        # Now I just have to make this work - can I just create an extra pluginData object for each dataset and alternate between those?
+        # Or will I have to calculate mfp/mft every time?
+        # Don't forget to call "finalise_datasets" or whatever the function is (usually called after the setup method)
+
+    def nOutput_datasets(self):
+        return 2
+
+    def nClone_datasets(self):
+        return 1