Merge pull request #9 from fusion-energy/develop

Develop

.github/workflows/ci_with_install.yml

@@ -29,6 +29,10 @@ 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 

README.md

@@ -1,2 +1,64 @@
-# dose_map_plotter
-A Python package for plotting neutronics dose maps
+[![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
+
+[![CI with install](https://github.com/fusion-energy/regular_mesh_plotter/actions/workflows/ci_with_install.yml/badge.svg?branch=develop)](https://github.com/fusion-energy/regular_mesh_plotter/actions/workflows/ci_with_install.yml)
+
+[![PyPI](https://img.shields.io/pypi/v/regular-mesh-plotter?color=brightgreen&label=pypi&logo=grebrightgreenen&logoColor=green)](https://pypi.org/project/regular-mesh-plotter/)
+
+[![codecov](https://codecov.io/gh/fusion-energy/regular_mesh_plotter/branch/main/graph/badge.svg)](https://codecov.io/gh/fusion-energy/regular_mesh_plotter)
+
+## A minimal Python package that plots 2D mesh tally results with the underlying DAGMC geometry
+
+# Installation
+
+```bash
+pip install regular_mesh_plotter
+```
+
+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
+in the function call directly.
+
+There are additional options that allow
+
+- rotation of the mesh tally results
+- rotation of the DAGMC geometry slice
+- saving the plot as an image file
+- specifying contour lines TODO
+- changing axis and colour bar labels
+- changing colour scale applied
+- truncation of values
+- The plane_normal of the DAGMC geometry
+
+The resulting plots can be used to show dose maps, activation, reaction rate
+and other mesh tally results.
+
+
+Example 1 shows a Numpy array plotted
+```python
+TODO
+```
+
+Example 2 shows a Numpy array plotted with an underlying DAGMC geometry
+```python
+TODO
+```
+
+Example 3 shows a OpenMC tally plotted with an underlying DAGMC geometry
+```python
+TODO
+```
+
+Example 4 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   
+```python
+TODO
+```
+
+# Related packages
+
+If you want to plot the DAGMC geometry without a mesh tally then take a look at
+the [dagmc_geometry_slice_plotter](https://github.com/fusion-energy/dagmc_geometry_slice_plotter) package

examples/examples_from_readme.py

@@ -0,0 +1,77 @@
+# this examples requires additional python packages
+
+from dagmc_geometry_slice_plotter import plot_slice_of_dagmc_geometry
+from stl_to_h5m import stl_to_h5m
+
+import paramak
+
+my_reactor = paramak.SubmersionTokamak(
+    inner_bore_radial_thickness=30,
+    inboard_tf_leg_radial_thickness=30,
+    center_column_shield_radial_thickness=30,
+    divertor_radial_thickness=80,
+    inner_plasma_gap_radial_thickness=50,
+    plasma_radial_thickness=200,
+    outer_plasma_gap_radial_thickness=50,
+    firstwall_radial_thickness=30,
+    blanket_rear_wall_radial_thickness=30,
+    number_of_tf_coils=16,
+    rotation_angle=360,
+    support_radial_thickness=90,
+    inboard_blanket_radial_thickness=30,
+    outboard_blanket_radial_thickness=30,
+    elongation=2.00,
+    triangularity=0.50,
+    pf_coil_case_thicknesses=[10, 10, 10, 10],
+    pf_coil_radial_thicknesses=[20, 50, 50, 20],
+    pf_coil_vertical_thicknesses=[20, 50, 50, 20],
+    pf_coil_radial_position=[500, 550, 550, 500],
+    pf_coil_vertical_position=[270, 100, -100, -270],
+    rear_blanket_to_tf_gap=50,
+    outboard_tf_coil_radial_thickness=30,
+    outboard_tf_coil_poloidal_thickness=30,
+)
+
+
+stl_filenames = my_reactor.export_stl()
+
+
+stl_to_h5m(
+    files_with_tags=[
+        (stl_filename, name)
+        for name, stl_filename in zip(my_reactor.name, stl_filenames)
+    ],
+    h5m_filename="dagmc.h5m",
+)
+
+
+plot = plot_slice_of_dagmc_geometry(
+    dagmc_file_or_trimesh_object="dagmc.h5m",
+    plane_normal=[0, 0, 1],
+    output_filename="my_plot1.png",
+)
+
+
+plot = plot_slice_of_dagmc_geometry(
+    dagmc_file_or_trimesh_object="dagmc.h5m",
+    plane_origin=[0, 0, 300],
+    plane_normal=[0, 0, 1],
+    output_filename="my_plot2.png",
+)
+
+
+plot = plot_slice_of_dagmc_geometry(
+    dagmc_file_or_trimesh_object="dagmc.h5m",
+    plane_normal=[0, 1, 0],
+    rotate_plot=45,
+    output_filename="my_plot3.png",
+)
+
+plot.savefig("big.png", dpi=600)
+
+plot_slice_of_dagmc_geometry(
+    dagmc_file_or_trimesh_object="dagmc.h5m",
+    plane_normal=[1, 0, 0],
+    rotate_plot=270,
+    output_filename="my_plot4.png",
+)

examples/plot_mesh_with_geometry_slice.py

@@ -0,0 +1,17 @@
+
+from regular_mesh_plotter import plot_regular_mesh_tally_with_geometry
+import openmc
+
+# loads in the statepoint file containing tallies
+statepoint = openmc.StatePoint(filepath="statepoint.3.h5")
+
+# gets one tally from the available tallies
+my_tally = statepoint.get_tally(name="neutron_effective_dose_on_2D_mesh_xy")
+
+# creates the matplotlib mesh plot with geometry
+plot = plot_regular_mesh_tally_with_geometry(
+    tally=my_tally,
+    mesh_file_or_trimesh_object="dagmc.h5m",
+)
+
+plot.show()

regular_mesh_plotter/__init__.py

@@ -1,4 +1,7 @@
 
-from .core import plot_mesh
+from .core import plot_regular_mesh_values
+from .core import plot_regular_mesh_values_with_geometry
+from .core import plot_regular_mesh_tally
+from .core import plot_regular_mesh_tally_with_geometry
 from .core import get_tally_extent
-from .core import plot_stl_slice
+