Merge pull request #44 from fusion-energy/develop

Develop refactor

Author: shimwell

README.md

@@ -6,122 +6,34 @@
 
 [![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
+## A minimal Python package that extracts 2D mesh tally results for plotting convenience.
 
-# Installation
+This package is deployed on [xsplot.com](https://www.xsplot.com) as part of the ```openmc_plot``` suite of plotting apps
 
-```bash
-pip install regular_mesh_plotter
-```
-
-Mesh results in the form of at 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 accessible
-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.
-
-The examples below require a mesh tally that can be read in with OpenMC in the following way.
-
-```python
-import openmc
-
-# loads in the statepoint file containing tallies
-statepoint = openmc.StatePoint(filepath="statepoint.2.h5")
+# Local install
 
-# gets one tally from the available tallies
-my_tally = statepoint.get_tally(name="neutron_effective_dose_on_2D_mesh_xy")
-```
-
-Example 1 shows a OpenMC tally plotted
-```python
-
-import regular_mesh_plotter as rmp
-import matplotlib.pyplot as plt
+First you will need openmc installed, then you can install this package with pip
 
-rmp.plot_regular_mesh_tally(
-    tally=my_tally,
-    std_dev_or_tally_value="tally_value",
-    x_label="X [cm]",
-    y_label="Y [cm]",
-)
-
-plt.savefig('openmc_mesh_tally_plot.png')
+```bash
+pip install regular_mesh_plotter
 ```
+# Usage
 
-Example 4 shows a OpenMC tally plotted with an underlying DAGMC geometry
-```python
-plot_regular_mesh_tally_with_geometry(
-    tally=my_tally,
-    dagmc_file_or_trimesh_object='dagmc.h5m',
-    std_dev_or_tally_value="tally_value",
-    x_label="X [cm]",
-    y_label="Y [cm]",
-)
-```
+The package can be used from within your own python script to make plots or via a GUI that is also bundled into the package install.
 
-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 plane normal
-```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,
-)
-```
+## Python API script usage
 
-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 / source_particle",
-    source_strength: float = None,
-    std_dev_or_tally_value: str = "tally_value",
-):
-```
+See the [examples folder](https://github.com/fusion-energy/regular_mesh_plotter/tree/master/examples) for example scripts
 
-Additional examples can be found in the [examples folder in the GitHub repository](https://github.com/fusion-energy/regular_mesh_plotter/tree/main/examples)
+## Graphical User Interface (GUI) usage
 
+After installing run ```openmc_mesh_plotter``` command from the terminal and the GUI should launch in a new browser window.
 # Related packages
 
+[openmc_plot](https://github.com/fusion-energy/openmc_plot)A single package that includes all the various plotters.
+
 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
+
+If you want to plot the Native CSG geometry without a mesh tally then take a look at
+the [dagmc_geometry_slice_plotter](https://github.com/fusion-energy/openmc_geometry_plot) package