Merge pull request #17 from fusion-energy/develop

refactored code into core and utils, improved examples and CI

.github/workflows/ci_with_install.yml

@@ -20,7 +20,8 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     container:
-      image: continuumio/miniconda3:4.9.2
+      # image: openmc/openmc:latest-dagmc is missing the dagmc universe
+      image: openmc/openmc:develop-dagmc
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -29,17 +30,27 @@ jobs:
         run: |
           python setup.py install
 
-      - name: install openmc
-        run: |
-          conda install -c conda-forge openmc
-
       - name: install packages for tests
         run: |
           pip install -r requirements-test.txt 
 
       - name: Run test_utils
         run: |
+          cp tests/example.stl .
           pytest tests/ -v --cov=regular_mesh_plotter --cov-append --cov-report term --cov-report xml
 
       - name: Upload to codecov
         uses: codecov/codecov-action@v2
+
+      - name: Run examples
+        run: |
+          cd examples
+          python create_statepoint_file_with_meshes_openmc_dagmc.py
+          python create_statepoint_file_with_meshes_openmc.py
+          # python examples_from_readme.py  # commented out as it requires entire neutronics workflow
+          python plot_regular_mesh_dose_tally.py
+          python plot_regular_mesh_dose_tally_with_geometry.py
+          python plot_regular_mesh_tally.py
+          python plot_regular_mesh_tally_with_geometry.py
+          python plot_regular_mesh_values.py
+          python plot_regular_mesh_values_with_geometry.py

README.md

@@ -18,7 +18,7 @@ Mesh results in the form of Numpy arrays or OpenMC.tally objects can be plotted
 with a single API call.
 
 A Matplotlib.pyplot object is returned by all functions so one can make changes
-to the legend, axis, colour map etc. However some key options are accessable
+to the legend, axis, colour map etc. However some key options are accessible
 in the function call directly.
 
 There are additional options that allow
@@ -38,26 +38,129 @@ and other mesh tally results.
 
 Example 1 shows a Numpy array plotted
 ```python
-TODO
+plot_regular_mesh_values(
+    values: np.ndarray,
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    base_plt=None,
+    extent=None,
+    x_label="X [cm]",
+    y_label="Y [cm]",
+    rotate_plot: float = 0,
+)
 ```
 
 Example 2 shows a Numpy array plotted with an underlying DAGMC geometry
 ```python
-TODO
+plot_regular_mesh_values_with_geometry(
+    values: np.ndarray,
+    dagmc_file_or_trimesh_object,
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    extent=None,
+    x_label="X [cm]",
+    y_label="Y [cm]",
+    plane_origin: List[float] = None,
+    plane_normal: List[float] = [0, 0, 1],
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
+)
 ```
 
-Example 3 shows a OpenMC tally plotted with an underlying DAGMC geometry
+Example 3 shows a OpenMC tally plotted
 ```python
-TODO
+plot_regular_mesh_tally(
+    tally,
+    dagmc_file_or_trimesh_object,
+    std_dev_or_tally_value="tally_value",
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    x_label="X [cm]",
+    y_label="Y [cm]",
+    plane_origin: List[float] = None,
+    plane_normal: List[float] = [0, 0, 1],
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
+    required_units=None,
+    source_strength: float = None,
+)
 ```
 
-Example 4 shows how to rotate the underlying DAGMC geometry and mesh tally.
+Example 4 shows a OpenMC tally plotted with an underlying DAGMC geometry
+```python
+plot_regular_mesh_tally_with_geometry(
+    tally,
+    dagmc_file_or_trimesh_object,
+    std_dev_or_tally_value="tally_value",
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    x_label="X [cm]",
+    y_label="Y [cm]",
+    plane_origin: List[float] = None,
+    plane_normal: List[float] = [0, 0, 1],
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
+    required_units=None,
+    source_strength: float = None,
+)
+```
+
+Example 5 shows how to rotate the underlying DAGMC geometry and mesh tally.
 This is sometimes necessary as the slice and mesh can get out of alignment
-when changing the   
+when changing the plane normal
 ```python
-TODO
+plot_regular_mesh_tally_with_geometry(
+    tally,
+    dagmc_file_or_trimesh_object,
+    std_dev_or_tally_value="tally_value",
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    x_label="X [cm]",
+    y_label="Y [cm]",
+    plane_origin: List[float] = None,
+    plane_normal: List[float] = [0, 0, 1],
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
+    required_units=None,
+    source_strength: float = None,
+)
 ```
 
+Example 6 shows how to plot a dose tally with the underlying DAGMC geometry.
+This also includes unit conversion from the base tally units to the requested
+units.
+```python
+plot_regular_mesh_dose_tally_with_geometry(
+    tally,
+    dagmc_file_or_trimesh_object,
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    x_label="X [cm]",
+    y_label="Y [cm]",
+    plane_origin: List[float] = None,
+    plane_normal: List[float] = [0, 0, 1],
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
+    required_units="picosievert cm **2 / simulated_particle",
+    source_strength: float = None,
+    std_dev_or_tally_value: str = "tally_value",
+):
+```
+
+Additional examples can be found in the [examples folder in the GitHub repository](https://github.com/fusion-energy/regular_mesh_plotter/tree/main/examples)
+
 # Related packages
 
 If you want to plot the DAGMC geometry without a mesh tally then take a look at

examples/create_statepoint_file_with_meshes_openmc.py

@@ -81,7 +81,7 @@
 )
 
 settings = odw.FusionSettings()
-settings.batches = 2
+settings.batches = 3
 settings.particles = 1000000
 # assigns a ring source of DT energy neutrons to the source using the
 # openmc_plasma_source package

examples/create_statepoint_file_with_meshes_openmc_dagmc.py

@@ -4,15 +4,15 @@
 import openmc
 import openmc_dagmc_wrapper as odw
 import openmc_plasma_source as ops
-import paramak
 from stl_to_h5m import stl_to_h5m
 
-my_shape = paramak.ExtrudeStraightShape(
-    points=[(1, 1), (1, 200), (600, 200), (600, 1)],
-    distance=180,
-)
-
-my_shape.export_stl("example.stl")
+# code used to create example.stl
+# import paramak
+# my_shape = paramak.ExtrudeStraightShape(
+#     points=[(1, 1), (1, 200), (600, 200), (600, 1)],
+#     distance=180,
+# )
+# my_shape.export_stl("example.stl")
 
 # This script converts the CAD stl files generated into h5m files that can be
 # used in DAGMC enabled codes. h5m files created in this way are imprinted,
@@ -33,13 +33,13 @@
 )
 
 materials = odw.Materials(
-    h5m_filename="dagmc.h5m", correspondence_dict={"mat1": "eurofer"}
+    h5m_filename="dagmc.h5m", correspondence_dict={"mat1": "FLiNaK"}
 )
 
 tally1 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="xy",
-    mesh_resolution=(10, ),
+    mesh_resolution=(10, 5),
     bounding_box="dagmc.h5m",
 )
 tally2 = odw.MeshTally2D(
@@ -57,7 +57,7 @@
 tally4 = odw.MeshTally2D(
     tally_type="neutron_effective_dose",
     plane="xy",
-    mesh_resolution=(10, ),
+    mesh_resolution=(10, 10),
     bounding_box="dagmc.h5m",
 )
 tally5 = odw.MeshTally2D(

examples/example.stl

@@ -0,0 +1,86 @@
+solid 
+ facet normal -1.000000e+00  0.000000e+00 -0.000000e+00
+   outer loop
+     vertex  1.000000e+00  9.000000e+01  2.000000e+02
+     vertex  1.000000e+00  9.000000e+01  1.000000e+00
+     vertex  1.000000e+00 -9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+ facet normal -1.000000e+00  0.000000e+00  0.000000e+00
+   outer loop
+     vertex  1.000000e+00 -9.000000e+01  2.000000e+02
+     vertex  1.000000e+00  9.000000e+01  2.000000e+02
+     vertex  1.000000e+00 -9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+ facet normal  0.000000e+00  0.000000e+00 -1.000000e+00
+   outer loop
+     vertex  1.000000e+00 -9.000000e+01  1.000000e+00
+     vertex  6.000000e+02  9.000000e+01  1.000000e+00
+     vertex  6.000000e+02 -9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+ facet normal  0.000000e+00  0.000000e+00 -1.000000e+00
+   outer loop
+     vertex  1.000000e+00 -9.000000e+01  1.000000e+00
+     vertex  1.000000e+00  9.000000e+01  1.000000e+00
+     vertex  6.000000e+02  9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+ facet normal  0.000000e+00 -0.000000e+00  1.000000e+00
+   outer loop
+     vertex  6.000000e+02 -9.000000e+01  2.000000e+02
+     vertex  6.000000e+02  9.000000e+01  2.000000e+02
+     vertex  1.000000e+00  9.000000e+01  2.000000e+02
+   endloop
+ endfacet
+ facet normal  0.000000e+00  0.000000e+00  1.000000e+00
+   outer loop
+     vertex  6.000000e+02 -9.000000e+01  2.000000e+02
+     vertex  1.000000e+00  9.000000e+01  2.000000e+02
+     vertex  1.000000e+00 -9.000000e+01  2.000000e+02
+   endloop
+ endfacet
+ facet normal  0.000000e+00  1.000000e+00  0.000000e+00
+   outer loop
+     vertex  6.000000e+02  9.000000e+01  2.000000e+02
+     vertex  1.000000e+00  9.000000e+01  1.000000e+00
+     vertex  1.000000e+00  9.000000e+01  2.000000e+02
+   endloop
+ endfacet
+ facet normal  0.000000e+00  1.000000e+00  0.000000e+00
+   outer loop
+     vertex  6.000000e+02  9.000000e+01  2.000000e+02
+     vertex  6.000000e+02  9.000000e+01  1.000000e+00
+     vertex  1.000000e+00  9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+ facet normal  1.000000e+00  0.000000e+00 -0.000000e+00
+   outer loop
+     vertex  6.000000e+02  9.000000e+01  1.000000e+00
+     vertex  6.000000e+02  9.000000e+01  2.000000e+02
+     vertex  6.000000e+02 -9.000000e+01  2.000000e+02
+   endloop
+ endfacet
+ facet normal  1.000000e+00  0.000000e+00  0.000000e+00
+   outer loop
+     vertex  6.000000e+02 -9.000000e+01  1.000000e+00
+     vertex  6.000000e+02  9.000000e+01  1.000000e+00
+     vertex  6.000000e+02 -9.000000e+01  2.000000e+02
+   endloop
+ endfacet
+ facet normal -0.000000e+00 -1.000000e+00  0.000000e+00
+   outer loop
+     vertex  6.000000e+02 -9.000000e+01  2.000000e+02
+     vertex  1.000000e+00 -9.000000e+01  2.000000e+02
+     vertex  1.000000e+00 -9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+ facet normal  0.000000e+00 -1.000000e+00 -0.000000e+00
+   outer loop
+     vertex  6.000000e+02 -9.000000e+01  2.000000e+02
+     vertex  1.000000e+00 -9.000000e+01  1.000000e+00
+     vertex  6.000000e+02 -9.000000e+01  1.000000e+00
+   endloop
+ endfacet
+endsolid

examples/plot_regular_mesh_dose_tally.py

@@ -10,15 +10,15 @@
 # creates a plot of the mesh tally
 my_plot = rmp.plot_regular_mesh_dose_tally(
     tally=my_tally,  # the openmc tally object to plot, must be a 2d mesh tally
-    filename='plot_regular_mesh_dose_tally.png',  # the filename of the picture file saved
+    filename="plot_regular_mesh_dose_tally.png",  # the filename of the picture file saved
     scale=None,  # LogNorm(),
     vmin=None,
     label="",
     x_label="X [cm]",
     y_label="Y [cm]",
-    rotate_plot = 0,
-    required_units='picosievert cm **2 / simulated_particle',
-    source_strength = None,
+    rotate_plot=0,
+    required_units="picosievert cm **2 / simulated_particle",
+    source_strength=None,
 )
 
 # displays the plot

examples/plot_regular_mesh_dose_tally_with_geometry.py

@@ -11,18 +11,18 @@
 my_plot = rmp.plot_regular_mesh_dose_tally_with_geometry(
     tally=my_tally,
     dagmc_file_or_trimesh_object="dagmc.h5m",
-    filename = 'plot_regular_mesh_dose_tally_with_geometry.png',
+    filename="plot_regular_mesh_dose_tally_with_geometry.png",
     scale=None,  # LogNorm(),
     vmin=None,
     label="",
     x_label="X [cm]",
     y_label="Y [cm]",
-    plane_origin = None,  # this could be skipped as it defaults to None, which uses the center of the mesh
-    plane_normal = [0, 0, 1],
-    rotate_mesh = 0,
-    rotate_geometry = 0,
-    required_units='picosievert cm **2 / simulated_particle',
-    source_strength = None,
+    plane_origin=None,  # this could be skipped as it defaults to None, which uses the center of the mesh
+    plane_normal=[0, 0, 1],
+    rotate_mesh=0,
+    rotate_geometry=0,
+    required_units="picosievert cm **2 / simulated_particle",
+    source_strength=None,
 )
 
 my_plot.show()

examples/plot_regular_mesh_tally.py

@@ -1,4 +1,3 @@
-
 import regular_mesh_plotter as rmp
 import openmc
 
@@ -11,7 +10,7 @@
 # creates a plot of the mesh
 rmp.plot_regular_mesh_tally(
     tally=my_tally,
-    filename= 'neutron_effective_dose_on_2D_mesh_xy.png',
+    filename="neutron_effective_dose_on_2D_mesh_xy.png",
     scale=None,  # LogNorm(),
     vmin=None,
     label="",
@@ -21,4 +20,4 @@
     # rotate_plot: float = 0,
     # required_units: str = None,
     # source_strength: float = None,
-)
+)