Add percentile getter methods to CILViewerBase and CILViewer (#336)

* Add percentile getters

* Add CILViewerBase test

* update changelog and add skipping of tests in gh-actions

* Automated autoyapf fixes

* add hack for skipping viewer test on gh-a docker build

.github/workflows/docker_build_test_publish.yml

@@ -33,5 +33,5 @@ jobs:
       - name: Run docker container with tests
         shell: bash -l {0}
         run: |
-          docker run --rm --entrypoint /bin/bash -v /home/runner/work/CILViewer/CILViewer:/root/source_code  cil-viewer -c "source ./mambaforge/etc/profile.d/conda.sh && conda activate cilviewer_webapp && conda install cil-data pytest -c ccpi && python -m pytest /root/source_code/Wrappers/Python -k 'not test_version and not test_cli_resample'"
+          docker run --rm --entrypoint /bin/bash -v /home/runner/work/CILViewer/CILViewer:/root/source_code  cil-viewer -c "source ./mambaforge/etc/profile.d/conda.sh && conda activate cilviewer_webapp && conda install cil-data pytest -c ccpi && python -m pytest /root/source_code/Wrappers/Python -k 'not test_version and not test_cli_resample and not test_CILViewerBase and not test_CILViewer3D'"
     # TODO: publish to come later

CHANGELOG.md

@@ -7,6 +7,12 @@
   do this for some hdf5 formats.
 - Fix bug with returning HDF5 attributes from HDF5Reader
 - Move code for resetting camera out of TrameViewer3D and into CILViewer
+- Adds the following methods to CILViewer (and corresponding unit tests):
+    - getGradientOpacityPercentiles
+    - getScalarOpacityPercentiles
+    - getVolumeColorPercentiles
+- Adds to CILViewerBase (and corresponding unit tests):
+    - getSliceColorPercentiles
 - setup.py:
   - Always normalise the version from git describe to pep440
 

Wrappers/Python/ccpi/viewer/CILViewer.py

@@ -749,6 +749,21 @@ def setGradientOpacityPercentiles(self, min, max, update_pipeline=True):
         go_min, go_max = self.getImageMapRange((min, max), 'gradient')
         self.setGradientOpacityRange(go_min, go_max, update_pipeline)
 
+    def getGradientOpacityPercentiles(self):
+        '''
+        Returns
+        -----------
+        min, max: float, default: (80., 99.)
+            the percentiles on the image gradient values that the 
+            opacity will be mapped to if setVolumeRenderOpacityMethod
+            has been set to 'gradient'.
+        '''
+        go_min, go_max = self.getGradientOpacityRange()
+        value_min, value_max = self.getImageMapWholeRange('gradient')
+        min_percentage = (go_min - value_min) / (value_max - value_min) * 100
+        max_percentage = (go_max - value_min) / (value_max - value_min) * 100
+        return min_percentage, max_percentage
+
     def setScalarOpacityPercentiles(self, min, max, update_pipeline=True):
         '''
         min, max: float, default: (80., 99.)
@@ -759,14 +774,44 @@ def setScalarOpacityPercentiles(self, min, max, update_pipeline=True):
         so_min, so_max = self.getImageMapRange((min, max), 'scalar')
         self.setScalarOpacityRange(so_min, so_max, update_pipeline)
 
+    def getScalarOpacityPercentiles(self):
+        '''
+        Returns
+        -----------
+        min, max: float, default: (80., 99.)
+            the percentiles on the image values that the 
+            opacity will be mapped to if setVolumeRenderOpacityMethod
+            has been set to 'scalar'.
+        '''
+        so_min, so_max = self.getScalarOpacityRange()
+        value_min, value_max = self.getImageMapWholeRange('scalar')
+        min_percentage = (so_min - value_min) / (value_max - value_min) * 100
+        max_percentage = (so_max - value_min) / (value_max - value_min) * 100
+        return min_percentage, max_percentage
+
     def setVolumeColorPercentiles(self, min, max, update_pipeline=True):
         '''
+        Parameters
+        -----------
         min, max: int, default: (85., 95.)
             the percentiles on the image values upon which the colours will be mapped to
         '''
         cmin, cmax = self.getImageMapRange((min, max), 'scalar')
         self.setVolumeColorRange(cmin, cmax, update_pipeline)
 
+    def getVolumeColorPercentiles(self):
+        '''
+        Returns
+        -----------
+        min, max: int, default: (85., 95.)
+            the percentiles on the image values upon which the colours will be mapped to
+        '''
+        cmin, cmax = self.getVolumeColorRange()
+        value_min, value_max = self.getImageMapWholeRange('scalar')
+        min_percentage = (cmin - value_min) / (value_max - value_min) * 100
+        max_percentage = (cmax - value_min) / (value_max - value_min) * 100
+        return min_percentage, max_percentage
+
     def setGradientOpacityRange(self, min, max, update_pipeline=True):
         '''
         Parameters

Wrappers/Python/ccpi/viewer/CILViewerBase.py

@@ -266,6 +266,13 @@ def setSliceColorPercentiles(self, min_percentage, max_percentage):
         min_val, max_val = self.getSliceMapRange((min_percentage, max_percentage), 'scalar')
         self.setSliceMapRange(min_val, max_val)
 
+    def getSliceColorPercentiles(self):
+        min_val, max_val = self.getSliceMapWholeRange('scalar')
+        min_color, max_color = self.getSliceMapRange()
+        min_percentage = (min_color - min_val) / (max_val - min_val) * 100
+        max_percentage = (max_color - min_val) / (max_val - min_val) * 100
+        return min_percentage, max_percentage
+
     def setSliceColorWindow(self, window):
         '''
         Set the window for the 2D slice of the 3D image.

Wrappers/Python/test/test_CILViewer3D.py

@@ -0,0 +1,82 @@
+#   Copyright 2023 STFC, United Kingdom Research and Innovation
+#
+#   Author 2023 Laura Murgatroyd
+#
+#   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.
+#
+import os
+import unittest
+from unittest import mock
+
+from ccpi.viewer.CILViewer import CILViewer
+
+# skip the tests on GitHub actions
+if os.environ.get('CONDA_BUILD', '0') == '1':
+    skip_test = True
+else:
+    skip_test = False
+
+print("skip_test is set to ", skip_test)
+
+
+@unittest.skipIf(skip_test, "Skipping tests on GitHub Actions")
+class CILViewer3DTest(unittest.TestCase):
+
+    def setUp(self):
+        self.cil_viewer = CILViewer()
+
+    def test_getGradientOpacityPercentiles_returns_correct_percentiles_when_image_values_start_at_zero(self):
+        self.cil_viewer.gradient_opacity_limits = [40, 50]
+        self.cil_viewer.getImageMapWholeRange = mock.MagicMock(return_value=[0, 50])
+        expected_percentages = (80.0, 100.0)
+        actual_percentages = self.cil_viewer.getGradientOpacityPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+    def test_getGradientOpacityPercentiles_returns_correct_percentiles_when_image_values_start_at_non_zero(self):
+        self.cil_viewer.gradient_opacity_limits = [40, 50]
+        self.cil_viewer.getImageMapWholeRange = mock.MagicMock(return_value=[10, 50])
+        expected_percentages = (75.0, 100.0)
+        actual_percentages = self.cil_viewer.getGradientOpacityPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+    def test_getScalarOpacityPercentiles_returns_correct_percentiles_when_image_values_start_at_zero(self):
+        self.cil_viewer.scalar_opacity_limits = [40, 50]
+        self.cil_viewer.getImageMapWholeRange = mock.MagicMock(return_value=[0, 50])
+        expected_percentages = (80.0, 100.0)
+        actual_percentages = self.cil_viewer.getScalarOpacityPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+    def test_getScalarOpacityPercentiles_returns_correct_percentiles_when_image_values_start_at_non_zero(self):
+        self.cil_viewer.scalar_opacity_limits = [40, 50]
+        self.cil_viewer.getImageMapWholeRange = mock.MagicMock(return_value=[10, 50])
+        expected_percentages = (75.0, 100.0)
+        actual_percentages = self.cil_viewer.getScalarOpacityPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+    def test_getVolumeColorPercentiles_returns_correct_percentiles_when_image_values_start_at_zero(self):
+        self.cil_viewer.volume_colormap_limits = [40, 50]
+        self.cil_viewer.getImageMapWholeRange = mock.MagicMock(return_value=[0, 50])
+        expected_percentages = (80.0, 100.0)
+        actual_percentages = self.cil_viewer.getVolumeColorPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+    def test_getVolumeColorPercentiles_returns_correct_percentiles_when_image_values_start_at_non_zero(self):
+        self.cil_viewer.volume_colormap_limits = [40, 50]
+        self.cil_viewer.getImageMapWholeRange = mock.MagicMock(return_value=[10, 50])
+        expected_percentages = (75.0, 100.0)
+        actual_percentages = self.cil_viewer.getVolumeColorPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+
+if __name__ == '__main__':
+    unittest.main()

Wrappers/Python/test/test_CILViewerBase.py

@@ -0,0 +1,54 @@
+#   Copyright 2023 STFC, United Kingdom Research and Innovation
+#
+#   Author 2023 Laura Murgatroyd
+#
+#   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.
+#
+import unittest
+from unittest import mock
+import os
+
+from ccpi.viewer.CILViewer import CILViewerBase
+
+# skip the tests on GitHub actions
+if os.environ.get('CONDA_BUILD', '0') == '1':
+    skip_test = True
+else:
+    skip_test = False
+
+print("skip_test is set to ", skip_test)
+
+
+@unittest.skipIf(skip_test, "Skipping tests on GitHub Actions")
+class CILViewer3DTest(unittest.TestCase):
+
+    def setUp(self):
+        self.cil_viewer = CILViewerBase()
+
+    def test_getSliceColorPercentiles_returns_correct_percentiles_when_slice_values_start_at_zero(self):
+        self.cil_viewer.getSliceMapRange = mock.MagicMock(return_value=[40, 50])
+        self.cil_viewer.getSliceMapWholeRange = mock.MagicMock(return_value=[0, 50])
+        expected_percentages = (80.0, 100.0)
+        actual_percentages = self.cil_viewer.getSliceColorPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+    def test_getSliceColorPercentiles_returns_correct_percentiles_when_slice_values_start_at_non_zero(self):
+        self.cil_viewer.getSliceMapRange = mock.MagicMock(return_value=[40, 50])
+        self.cil_viewer.getSliceMapWholeRange = mock.MagicMock(return_value=[10, 50])
+        expected_percentages = (75.0, 100.0)
+        actual_percentages = self.cil_viewer.getSliceColorPercentiles()
+        self.assertEqual(expected_percentages, actual_percentages)
+
+
+if __name__ == '__main__':
+    unittest.main()