From d71da6bb6bc6fcdd23cc13dbc64440f9df77d3cd Mon Sep 17 00:00:00 2001
From: Jonathan <mail@jshimwell.com>
Date: Wed, 20 Oct 2021 01:09:51 +0100
Subject: [PATCH 1/7] adding tally accepting functions

---
 examples/plot_mesh_with_slice.py |   4 +-
 regular_mesh_plotter/__init__.py |   5 +-
 regular_mesh_plotter/core.py     | 108 +++++++++++++++++++++++++++----
 tests/test_plot_mesh.py          |   8 +--
 tests/test_slice_stl.py          |  10 +--
 5 files changed, 108 insertions(+), 27 deletions(-)

diff --git a/examples/plot_mesh_with_slice.py b/examples/plot_mesh_with_slice.py
index e40d246..3d302bb 100644
--- a/examples/plot_mesh_with_slice.py
+++ b/examples/plot_mesh_with_slice.py
@@ -1,7 +1,7 @@
 
 
-from reg
+from regular_mesh_plotter import plot_geometry_slice
 
 
-plot_stl_slice("example.stl", plane_normal=[0, 0, 1])
+plot_geometry_slice("example.stl", plane_normal=[0, 0, 1])
 
diff --git a/regular_mesh_plotter/__init__.py b/regular_mesh_plotter/__init__.py
index fe09240..12e3d54 100644
--- a/regular_mesh_plotter/__init__.py
+++ b/regular_mesh_plotter/__init__.py
@@ -1,4 +1,5 @@
 
-from .core import plot_mesh
+from .core import plot_geometry_mesh
+from .core import plot_regular_mesh_values
 from .core import get_tally_extent
-from .core import plot_stl_slice
+from .core import plot_regular_mesh_values_with_geometry
diff --git a/regular_mesh_plotter/core.py b/regular_mesh_plotter/core.py
index c233532..2742d0a 100644
--- a/regular_mesh_plotter/core.py
+++ b/regular_mesh_plotter/core.py
@@ -5,8 +5,8 @@
 import numpy as np
 from pathlib import Path
 
-def plot_stl_slice(
-    stl_or_mesh,
+def plot_geometry_mesh(
+    mesh_file_or_trimesh_object,
     plane_origin: List[float] = None,
     plane_normal: List[float] = [0, 0, 1],
     rotate_plot: float = 0,
@@ -28,12 +28,12 @@ def plot_stl_slice(
         A matplotlib.pyplot object
     """
 
-    if isinstance(stl_or_mesh, str):
-        if not Path(stl_or_mesh).is_file():
-            raise FileNotFoundError(f'file {stl_or_mesh} not found.')
-        mesh = trimesh.load_mesh(stl_or_mesh, process=False)
+    if isinstance(mesh_file_or_trimesh_object, str):
+        if not Path(mesh_file_or_trimesh_object).is_file():
+            raise FileNotFoundError(f'file {mesh_file_or_trimesh_object} not found.')
+        mesh = trimesh.load_mesh(mesh_file_or_trimesh_object, process=False)
     else:
-        mesh = stl_or_mesh
+        mesh = mesh_file_or_trimesh_object
 
     if plane_origin is None:
         plane_origin = mesh.centroid
@@ -65,7 +65,7 @@ def plot_stl_slice(
     return plt
 
 
-def plot_mesh(
+def plot_regular_mesh_values(
     values: np.ndarray,
     filename: Optional[str] = None,
     scale=None,  # LogNorm(),
@@ -100,6 +100,83 @@ def plot_mesh(
     # plt.close()
     return plt
 
+def plot_regular_mesh_values_with_geometry(
+    values: np.ndarray,
+    mesh_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_plot: float = 0,
+):
+    slice = plot_geometry_mesh(
+        mesh_file_or_trimesh_object=mesh_file_or_trimesh_object,
+        plane_origin = plane_origin,
+        plane_normal = plane_normal,
+        rotate_plot = rotate_plot
+    )
+
+    both = plot_regular_mesh_values(
+        values = values,
+        filename = filename,
+        scale=scale,  # LogNorm(),
+        vmin=vmin,
+        label=label,
+        base_plt=slice,
+        extent=extent,
+        x_label=x_label,
+        y_label=y_label,
+    )
+
+    return both
+
+def plot_regular_mesh_tally(
+    tally: np.ndarray,
+    filename: Optional[str] = None,
+    scale=None,  # LogNorm(),
+    vmin=None,
+    label="",
+    base_plt=None,
+    x_label='X [cm]',
+    y_label='Y [cm]',
+):
+
+    if base_plt:
+        plt = base_plt
+    else:
+        import matplotlib.pyplot as plt
+        plt.plot()
+
+    import openmc_post_processor as opp
+    values = statepoint.process_tally(
+        tally=my_tally_1,
+    )
+
+    extent = get_tally_extent(tally)
+
+    image_map = plt.imshow(
+        values,
+        norm=scale,
+        vmin=vmin,
+        extent=extent
+    )
+
+    plt.xlabel(x_label)
+    plt.ylabel(y_label)
+
+    # image_map = fig.imshow(values, norm=scale, vmin=vmin)
+    plt.colorbar(image_map, label=label)
+    if filename:
+        plt.savefig(filename, dpi=300)
+    # fig.clear()
+    # plt.close()
+    return plt
+
 def get_tally_extent(
     tally,
 ):
@@ -107,17 +184,20 @@ def get_tally_extent(
     for filter in tally.filters:
         if isinstance(filter, openmc.MeshFilter):
             mesh_filter = filter
-            print(mesh_filter)
-            print(mesh_filter.mesh.lower_left)
-            print(mesh_filter.mesh.upper_right)
-    
+            # print(mesh_filter)
+            # print(mesh_filter.mesh.lower_left)
+            # print(mesh_filter.mesh.upper_right)
+            # print(mesh_filter.mesh.width)
+            # print(mesh_filter.mesh.__dict__)
+            # print(mesh_filter.mesh.dimension)
+
     extent_x = (min(mesh_filter.mesh.lower_left[0],mesh_filter.mesh.upper_right[0]), max(mesh_filter.mesh.lower_left[0],mesh_filter.mesh.upper_right[0]))
     extent_y = (min(mesh_filter.mesh.lower_left[1],mesh_filter.mesh.upper_right[1]), max(mesh_filter.mesh.lower_left[1],mesh_filter.mesh.upper_right[1]))
     extent_z = (min(mesh_filter.mesh.lower_left[2],mesh_filter.mesh.upper_right[2]), max(mesh_filter.mesh.lower_left[2],mesh_filter.mesh.upper_right[2]))
     
-    if 1 in mesh_filter.mesh.width:
+    if 1 in mesh_filter.mesh.dimension.tolist():
         print('2d mesh tally')
-        index_of_1d = mesh_filter.mesh.width.tolist().index(1)
+        index_of_1d = mesh_filter.mesh.dimension.tolist().index(1)
         print('index', index_of_1d)
         if index_of_1d == 0:
             return extent_y + extent_z
diff --git a/tests/test_plot_mesh.py b/tests/test_plot_mesh.py
index 6584e6d..d3ac81a 100644
--- a/tests/test_plot_mesh.py
+++ b/tests/test_plot_mesh.py
@@ -1,10 +1,10 @@
 import unittest
-from regular_mesh_plotter import plot_mesh
+from regular_mesh_plotter import plot_regular_mesh_tally
 import numpy as np
 import matplotlib
 
 
-class TestPlotSpectra(unittest.TestCase):
+class TestPlotRegularMeshTally(unittest.TestCase):
     def setUp(self):
 
         self.values = np.array(
@@ -72,8 +72,8 @@ def setUp(self):
             ]
         )
 
-    def test_plot_mesh(self):
+    def test_plot_regular_mesh_tally(self):
 
-        test_plot = plot_mesh(values=self.values, filename='test.png')
+        test_plot = plot_regular_mesh_tally(values=self.values, filename='test.png')
 
         assert isinstance(test_plot, type(matplotlib.pyplot))
diff --git a/tests/test_slice_stl.py b/tests/test_slice_stl.py
index e6480d9..43ad022 100644
--- a/tests/test_slice_stl.py
+++ b/tests/test_slice_stl.py
@@ -1,7 +1,7 @@
 import unittest
 
 import trimesh
-from regular_mesh_plotter import plot_stl_slice
+from regular_mesh_plotter import plot_geometry_mesh
 
 
 class TestShape(unittest.TestCase):
@@ -11,16 +11,16 @@ def setUp(self):
 
     def test_z_axis_slice(self):
 
-        plot_stl_slice(self.mesh, plane_normal=[0, 0, 1])
+        plot_geometry_mesh(self.mesh, plane_normal=[0, 0, 1])
 
     def test_offset_z_axis_slice(self):
 
-        plot_stl_slice(self.mesh, plane_origin=[0, 0, 10], plane_normal=[0, 0, 1])
+        plot_geometry_mesh(self.mesh, plane_origin=[0, 0, 10], plane_normal=[0, 0, 1])
 
     def test_x_axis_slice(self):
 
-        plot_stl_slice(self.mesh, plane_normal=[1, 0, 0])
+        plot_geometry_mesh(self.mesh, plane_normal=[1, 0, 0])
 
     def test_offset_x_axis_slice(self):
 
-        plot_stl_slice(self.mesh, plane_origin=[10, 0, 0], plane_normal=[1, 0, 0])
+        plot_geometry_mesh(self.mesh, plane_origin=[10, 0, 0], plane_normal=[1, 0, 0])

From 31055b8775137f9287daff8c9a241afda80cc46c Mon Sep 17 00:00:00 2001
From: Jonathan <mail@jshimwell.com>
Date: Wed, 20 Oct 2021 23:48:25 +0100
Subject: [PATCH 2/7] started new test strategy

---
 examples/plot_mesh_with_geometry_slice.py     | 18 +++++++
 examples/plot_mesh_with_slice.py              |  7 ---
 regular_mesh_plotter/__init__.py              |  5 +-
 regular_mesh_plotter/core.py                  | 49 ++++++++++++++++---
 ...lice_stl.py => test_plot_geometry_mesh.py} |  0
 tests/test_plot_regular_mesh_tally.py         |  2 +
 ...t_plot_regular_mesh_tally_with_geometry.py |  2 +
 ...sh.py => test_plot_regular_mesh_values.py} |  4 +-
 ...plot_regular_mesh_values_with_geometry.py} |  2 +-
 9 files changed, 72 insertions(+), 17 deletions(-)
 create mode 100644 examples/plot_mesh_with_geometry_slice.py
 delete mode 100644 examples/plot_mesh_with_slice.py
 rename tests/{test_slice_stl.py => test_plot_geometry_mesh.py} (100%)
 create mode 100644 tests/test_plot_regular_mesh_tally.py
 create mode 100644 tests/test_plot_regular_mesh_tally_with_geometry.py
 rename tests/{test_plot_mesh.py => test_plot_regular_mesh_values.py} (93%)
 rename tests/{test_plot_mesh_with_slice.py => test_plot_regular_mesh_values_with_geometry.py} (92%)

diff --git a/examples/plot_mesh_with_geometry_slice.py b/examples/plot_mesh_with_geometry_slice.py
new file mode 100644
index 0000000..eca6fc9
--- /dev/null
+++ b/examples/plot_mesh_with_geometry_slice.py
@@ -0,0 +1,18 @@
+
+
+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()
\ No newline at end of file
diff --git a/examples/plot_mesh_with_slice.py b/examples/plot_mesh_with_slice.py
deleted file mode 100644
index 3d302bb..0000000
--- a/examples/plot_mesh_with_slice.py
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
-from regular_mesh_plotter import plot_geometry_slice
-
-
-plot_geometry_slice("example.stl", plane_normal=[0, 0, 1])
-
diff --git a/regular_mesh_plotter/__init__.py b/regular_mesh_plotter/__init__.py
index 12e3d54..fbb3b8d 100644
--- a/regular_mesh_plotter/__init__.py
+++ b/regular_mesh_plotter/__init__.py
@@ -1,5 +1,8 @@
 
 from .core import plot_geometry_mesh
 from .core import plot_regular_mesh_values
-from .core import get_tally_extent
 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
+
diff --git a/regular_mesh_plotter/core.py b/regular_mesh_plotter/core.py
index 2742d0a..ad7470e 100644
--- a/regular_mesh_plotter/core.py
+++ b/regular_mesh_plotter/core.py
@@ -5,6 +5,9 @@
 import numpy as np
 from pathlib import Path
 
+import openmc_post_processor as opp
+import openmc
+
 def plot_geometry_mesh(
     mesh_file_or_trimesh_object,
     plane_origin: List[float] = None,
@@ -64,7 +67,6 @@ def plot_geometry_mesh(
         plt.savefig(filename, dpi=300)
     return plt
 
-
 def plot_regular_mesh_values(
     values: np.ndarray,
     filename: Optional[str] = None,
@@ -135,8 +137,42 @@ def plot_regular_mesh_values_with_geometry(
 
     return both
 
+def plot_regular_mesh_tally_with_geometry(
+    tally,
+    mesh_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_plot: float = 0,
+):
+
+    slice = plot_geometry_mesh(
+        mesh_file_or_trimesh_object=mesh_file_or_trimesh_object,
+        plane_origin = plane_origin,
+        plane_normal = plane_normal,
+        rotate_plot = rotate_plot
+    )
+
+    both = plot_regular_mesh_tally(
+        tally=tally,
+        filename=filename,
+        scale=scale,  # LogNorm(),
+        vmin=vmin,
+        label=label,
+        base_plt=slice,
+        x_label=x_label,
+        y_label=y_label,
+    )
+
+    return both
+
 def plot_regular_mesh_tally(
-    tally: np.ndarray,
+    tally,
     filename: Optional[str] = None,
     scale=None,  # LogNorm(),
     vmin=None,
@@ -152,13 +188,14 @@ def plot_regular_mesh_tally(
         import matplotlib.pyplot as plt
         plt.plot()
 
-    import openmc_post_processor as opp
-    values = statepoint.process_tally(
-        tally=my_tally_1,
+    values = opp.process_dose_tally(
+        tally=tally,
     )
 
     extent = get_tally_extent(tally)
 
+    print('extent', extent)
+
     image_map = plt.imshow(
         values,
         norm=scale,
@@ -180,7 +217,7 @@ def plot_regular_mesh_tally(
 def get_tally_extent(
     tally,
 ):
-    import openmc
+
     for filter in tally.filters:
         if isinstance(filter, openmc.MeshFilter):
             mesh_filter = filter
diff --git a/tests/test_slice_stl.py b/tests/test_plot_geometry_mesh.py
similarity index 100%
rename from tests/test_slice_stl.py
rename to tests/test_plot_geometry_mesh.py
diff --git a/tests/test_plot_regular_mesh_tally.py b/tests/test_plot_regular_mesh_tally.py
new file mode 100644
index 0000000..23d44aa
--- /dev/null
+++ b/tests/test_plot_regular_mesh_tally.py
@@ -0,0 +1,2 @@
+
+g
\ No newline at end of file
diff --git a/tests/test_plot_regular_mesh_tally_with_geometry.py b/tests/test_plot_regular_mesh_tally_with_geometry.py
new file mode 100644
index 0000000..23d44aa
--- /dev/null
+++ b/tests/test_plot_regular_mesh_tally_with_geometry.py
@@ -0,0 +1,2 @@
+
+g
\ No newline at end of file
diff --git a/tests/test_plot_mesh.py b/tests/test_plot_regular_mesh_values.py
similarity index 93%
rename from tests/test_plot_mesh.py
rename to tests/test_plot_regular_mesh_values.py
index d3ac81a..e02bb29 100644
--- a/tests/test_plot_mesh.py
+++ b/tests/test_plot_regular_mesh_values.py
@@ -1,5 +1,5 @@
 import unittest
-from regular_mesh_plotter import plot_regular_mesh_tally
+from regular_mesh_plotter import plot_regular_mesh_values
 import numpy as np
 import matplotlib
 
@@ -74,6 +74,6 @@ def setUp(self):
 
     def test_plot_regular_mesh_tally(self):
 
-        test_plot = plot_regular_mesh_tally(values=self.values, filename='test.png')
+        test_plot = plot_regular_mesh_values(values=self.values, filename='test.png')
 
         assert isinstance(test_plot, type(matplotlib.pyplot))
diff --git a/tests/test_plot_mesh_with_slice.py b/tests/test_plot_regular_mesh_values_with_geometry.py
similarity index 92%
rename from tests/test_plot_mesh_with_slice.py
rename to tests/test_plot_regular_mesh_values_with_geometry.py
index 6d310db..8108b4b 100644
--- a/tests/test_plot_mesh_with_slice.py
+++ b/tests/test_plot_regular_mesh_values_with_geometry.py
@@ -1,4 +1,4 @@
-
+# plot_regular_mesh_values_with_geometry
 # todo test the combination of mesh and stl slice
 # stl_slice = plot_stl_slice(
 #     stl_or_mesh='steel.stl',

From 89f3b60a62b92b3d2de886bf033ed1d627de8b1e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 21 Oct 2021 17:52:35 +0100
Subject: [PATCH 3/7] making use of dagmc_geometry_slice_plotter

---
 examples/examples_from_readme.py              |  77 +++++++++
 regular_mesh_plotter/__init__.py              |   1 -
 regular_mesh_plotter/core.py                  | 147 ++++++------------
 setup.py                                      |   3 +-
 tests/test_plot_geometry_mesh.py              |  26 ----
 tests/test_plot_regular_mesh_tally.py         |   2 -
 ...t_plot_regular_mesh_tally_with_geometry.py |   2 -
 tests/test_plot_regular_mesh_values.py        |  21 ++-
 ..._plot_regular_mesh_values_with_geometry.py | 118 +++++++++++---
 9 files changed, 239 insertions(+), 158 deletions(-)
 create mode 100644 examples/examples_from_readme.py
 delete mode 100644 tests/test_plot_geometry_mesh.py

diff --git a/examples/examples_from_readme.py b/examples/examples_from_readme.py
new file mode 100644
index 0000000..3c23db6
--- /dev/null
+++ b/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",
+)
diff --git a/regular_mesh_plotter/__init__.py b/regular_mesh_plotter/__init__.py
index fbb3b8d..49becfc 100644
--- a/regular_mesh_plotter/__init__.py
+++ b/regular_mesh_plotter/__init__.py
@@ -1,5 +1,4 @@
 
-from .core import plot_geometry_mesh
 from .core import plot_regular_mesh_values
 from .core import plot_regular_mesh_values_with_geometry
 from .core import plot_regular_mesh_tally
diff --git a/regular_mesh_plotter/core.py b/regular_mesh_plotter/core.py
index ad7470e..2e510b2 100644
--- a/regular_mesh_plotter/core.py
+++ b/regular_mesh_plotter/core.py
@@ -4,68 +4,11 @@
 from typing import List, Optional
 import numpy as np
 from pathlib import Path
+import dagmc_geometry_slice_plotter as dgsp
 
 import openmc_post_processor as opp
 import openmc
 
-def plot_geometry_mesh(
-    mesh_file_or_trimesh_object,
-    plane_origin: List[float] = None,
-    plane_normal: List[float] = [0, 0, 1],
-    rotate_plot: float = 0,
-    filename: Optional[str] = None,
-) -> plt:
-    """Slices through a 3D geometry in STL file format and extracts a slice of
-    the geometry at the provided plane and origin
-
-    Args:
-        plane_origin: the origin of the plain, if None then the mesh.centroid
-            will be used.
-        plane_normal: the plane to slice the geometry on. Defaults to slicing
-         along the Z plane which is input as [0, 0, 1].
-        rotate_plot: the angle in degrees to rotate the plot by. Useful when
-            used in conjunction with changing plane_normal to orientate the
-            plot correctly.
-
-    Return:
-        A matplotlib.pyplot object
-    """
-
-    if isinstance(mesh_file_or_trimesh_object, str):
-        if not Path(mesh_file_or_trimesh_object).is_file():
-            raise FileNotFoundError(f'file {mesh_file_or_trimesh_object} not found.')
-        mesh = trimesh.load_mesh(mesh_file_or_trimesh_object, process=False)
-    else:
-        mesh = mesh_file_or_trimesh_object
-
-    if plane_origin is None:
-        plane_origin = mesh.centroid
-    slice = mesh.section(
-        plane_origin=plane_origin,
-        plane_normal=plane_normal,
-    )
-
-    slice_2D, to_3D = slice.to_planar()
-
-    # keep plot axis scaled the same
-    plt.axes().set_aspect("equal", "datalim")
-
-    if rotate_plot != 0:
-        base = plt.gca().transData
-        rot = transforms.Affine2D().rotate_deg(rotate_plot)
-
-    for entity in slice_2D.entities:
-
-        discrete = entity.discrete(slice_2D.vertices)
-
-        if rotate_plot != 0:
-            plt.plot(*discrete.T, color="black", linewidth=1, transform=rot + base)
-        else:
-            plt.plot(*discrete.T, color="black", linewidth=1)
-
-    if filename:
-        plt.savefig(filename, dpi=300)
-    return plt
 
 def plot_regular_mesh_values(
     values: np.ndarray,
@@ -75,21 +18,17 @@ def plot_regular_mesh_values(
     label="",
     base_plt=None,
     extent=None,
-    x_label='X [cm]',
-    y_label='Y [cm]',
+    x_label="X [cm]",
+    y_label="Y [cm]",
 ):
 
     if base_plt:
         plt = base_plt
     else:
         import matplotlib.pyplot as plt
+
         plt.plot()
-    image_map = plt.imshow(
-        values,
-        norm=scale,
-        vmin=vmin,
-        extent=extent
-    )
+    image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent)
 
     plt.xlabel(x_label)
     plt.ylabel(y_label)
@@ -102,30 +41,32 @@ def plot_regular_mesh_values(
     # plt.close()
     return plt
 
+
 def plot_regular_mesh_values_with_geometry(
     values: np.ndarray,
-    mesh_file_or_trimesh_object,
+    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]',
+    x_label="X [cm]",
+    y_label="Y [cm]",
     plane_origin: List[float] = None,
     plane_normal: List[float] = [0, 0, 1],
     rotate_plot: float = 0,
 ):
-    slice = plot_geometry_mesh(
-        mesh_file_or_trimesh_object=mesh_file_or_trimesh_object,
-        plane_origin = plane_origin,
-        plane_normal = plane_normal,
-        rotate_plot = rotate_plot
+
+    slice = dgsp.plot_slice_of_dagmc_geometry(
+        dagmc_file_or_trimesh_object=dagmc_file_or_trimesh_object,
+        plane_origin=plane_origin,
+        plane_normal=plane_normal,
+        rotate_plot=rotate_plot,
     )
 
     both = plot_regular_mesh_values(
-        values = values,
-        filename = filename,
+        values=values,
+        filename=filename,
         scale=scale,  # LogNorm(),
         vmin=vmin,
         label=label,
@@ -137,25 +78,26 @@ def plot_regular_mesh_values_with_geometry(
 
     return both
 
+
 def plot_regular_mesh_tally_with_geometry(
     tally,
-    mesh_file_or_trimesh_object,
+    dagmc_file_or_trimesh_object,
     filename: Optional[str] = None,
     scale=None,  # LogNorm(),
     vmin=None,
     label="",
-    x_label='X [cm]',
-    y_label='Y [cm]',
+    x_label="X [cm]",
+    y_label="Y [cm]",
     plane_origin: List[float] = None,
     plane_normal: List[float] = [0, 0, 1],
     rotate_plot: float = 0,
 ):
 
-    slice = plot_geometry_mesh(
-        mesh_file_or_trimesh_object=mesh_file_or_trimesh_object,
-        plane_origin = plane_origin,
-        plane_normal = plane_normal,
-        rotate_plot = rotate_plot
+    slice = dgsp.plot_slice_of_dagmc_geometry(
+        dagmc_file_or_trimesh_object=dagmc_file_or_trimesh_object,
+        plane_origin=plane_origin,
+        plane_normal=plane_normal,
+        rotate_plot=rotate_plot,
     )
 
     both = plot_regular_mesh_tally(
@@ -171,6 +113,7 @@ def plot_regular_mesh_tally_with_geometry(
 
     return both
 
+
 def plot_regular_mesh_tally(
     tally,
     filename: Optional[str] = None,
@@ -178,14 +121,15 @@ def plot_regular_mesh_tally(
     vmin=None,
     label="",
     base_plt=None,
-    x_label='X [cm]',
-    y_label='Y [cm]',
+    x_label="X [cm]",
+    y_label="Y [cm]",
 ):
 
     if base_plt:
         plt = base_plt
     else:
         import matplotlib.pyplot as plt
+
         plt.plot()
 
     values = opp.process_dose_tally(
@@ -194,14 +138,9 @@ def plot_regular_mesh_tally(
 
     extent = get_tally_extent(tally)
 
-    print('extent', extent)
+    print("extent", extent)
 
-    image_map = plt.imshow(
-        values,
-        norm=scale,
-        vmin=vmin,
-        extent=extent
-    )
+    image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent)
 
     plt.xlabel(x_label)
     plt.ylabel(y_label)
@@ -214,6 +153,7 @@ def plot_regular_mesh_tally(
     # plt.close()
     return plt
 
+
 def get_tally_extent(
     tally,
 ):
@@ -228,14 +168,23 @@ def get_tally_extent(
             # print(mesh_filter.mesh.__dict__)
             # print(mesh_filter.mesh.dimension)
 
-    extent_x = (min(mesh_filter.mesh.lower_left[0],mesh_filter.mesh.upper_right[0]), max(mesh_filter.mesh.lower_left[0],mesh_filter.mesh.upper_right[0]))
-    extent_y = (min(mesh_filter.mesh.lower_left[1],mesh_filter.mesh.upper_right[1]), max(mesh_filter.mesh.lower_left[1],mesh_filter.mesh.upper_right[1]))
-    extent_z = (min(mesh_filter.mesh.lower_left[2],mesh_filter.mesh.upper_right[2]), max(mesh_filter.mesh.lower_left[2],mesh_filter.mesh.upper_right[2]))
-    
+    extent_x = (
+        min(mesh_filter.mesh.lower_left[0], mesh_filter.mesh.upper_right[0]),
+        max(mesh_filter.mesh.lower_left[0], mesh_filter.mesh.upper_right[0]),
+    )
+    extent_y = (
+        min(mesh_filter.mesh.lower_left[1], mesh_filter.mesh.upper_right[1]),
+        max(mesh_filter.mesh.lower_left[1], mesh_filter.mesh.upper_right[1]),
+    )
+    extent_z = (
+        min(mesh_filter.mesh.lower_left[2], mesh_filter.mesh.upper_right[2]),
+        max(mesh_filter.mesh.lower_left[2], mesh_filter.mesh.upper_right[2]),
+    )
+
     if 1 in mesh_filter.mesh.dimension.tolist():
-        print('2d mesh tally')
+        print("2d mesh tally")
         index_of_1d = mesh_filter.mesh.dimension.tolist().index(1)
-        print('index', index_of_1d)
+        print("index", index_of_1d)
         if index_of_1d == 0:
             return extent_y + extent_z
         if index_of_1d == 1:
diff --git a/setup.py b/setup.py
index bcd4020..42cd22d 100644
--- a/setup.py
+++ b/setup.py
@@ -37,6 +37,7 @@
         "matplotlib>=3.4.2",
         "trimesh",
         "shapely",
-        "scipy"
+        "scipy",
+        "dagmc_geometry_slice_plotter"
     ],
 )
diff --git a/tests/test_plot_geometry_mesh.py b/tests/test_plot_geometry_mesh.py
deleted file mode 100644
index 43ad022..0000000
--- a/tests/test_plot_geometry_mesh.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import unittest
-
-import trimesh
-from regular_mesh_plotter import plot_geometry_mesh
-
-
-class TestShape(unittest.TestCase):
-    def setUp(self):
-
-        self.mesh = trimesh.load_mesh("tests/example.stl", process=False)
-
-    def test_z_axis_slice(self):
-
-        plot_geometry_mesh(self.mesh, plane_normal=[0, 0, 1])
-
-    def test_offset_z_axis_slice(self):
-
-        plot_geometry_mesh(self.mesh, plane_origin=[0, 0, 10], plane_normal=[0, 0, 1])
-
-    def test_x_axis_slice(self):
-
-        plot_geometry_mesh(self.mesh, plane_normal=[1, 0, 0])
-
-    def test_offset_x_axis_slice(self):
-
-        plot_geometry_mesh(self.mesh, plane_origin=[10, 0, 0], plane_normal=[1, 0, 0])
diff --git a/tests/test_plot_regular_mesh_tally.py b/tests/test_plot_regular_mesh_tally.py
index 23d44aa..e69de29 100644
--- a/tests/test_plot_regular_mesh_tally.py
+++ b/tests/test_plot_regular_mesh_tally.py
@@ -1,2 +0,0 @@
-
-g
\ No newline at end of file
diff --git a/tests/test_plot_regular_mesh_tally_with_geometry.py b/tests/test_plot_regular_mesh_tally_with_geometry.py
index 23d44aa..e69de29 100644
--- a/tests/test_plot_regular_mesh_tally_with_geometry.py
+++ b/tests/test_plot_regular_mesh_tally_with_geometry.py
@@ -1,2 +0,0 @@
-
-g
\ No newline at end of file
diff --git a/tests/test_plot_regular_mesh_values.py b/tests/test_plot_regular_mesh_values.py
index e02bb29..834d98b 100644
--- a/tests/test_plot_regular_mesh_values.py
+++ b/tests/test_plot_regular_mesh_values.py
@@ -1,10 +1,13 @@
+import os
 import unittest
-from regular_mesh_plotter import plot_regular_mesh_values
-import numpy as np
+from pathlib import Path
+
 import matplotlib
+import numpy as np
+from regular_mesh_plotter import plot_regular_mesh_values
 
 
-class TestPlotRegularMeshTally(unittest.TestCase):
+class TestPlotRegularMeshValues(unittest.TestCase):
     def setUp(self):
 
         self.values = np.array(
@@ -72,8 +75,16 @@ def setUp(self):
             ]
         )
 
-    def test_plot_regular_mesh_tally(self):
+    def test_plot_regular_mesh_values(self):
 
-        test_plot = plot_regular_mesh_values(values=self.values, filename='test.png')
+        test_plot = plot_regular_mesh_values(values=self.values)
 
         assert isinstance(test_plot, type(matplotlib.pyplot))
+
+    def test_plot_regular_mesh_values_with_output(self):
+
+        os.system('rm test.png')
+
+        plot_regular_mesh_values(values=self.values, filename='test.png')
+
+        assert Path('test.png').is_file()
diff --git a/tests/test_plot_regular_mesh_values_with_geometry.py b/tests/test_plot_regular_mesh_values_with_geometry.py
index 8108b4b..a8c934b 100644
--- a/tests/test_plot_regular_mesh_values_with_geometry.py
+++ b/tests/test_plot_regular_mesh_values_with_geometry.py
@@ -1,22 +1,96 @@
-# plot_regular_mesh_values_with_geometry
-# todo test the combination of mesh and stl slice
-# stl_slice = plot_stl_slice(
-#     stl_or_mesh='steel.stl',
-#     plane_origin = None,
-#     plane_normal = [0, 0, 1],
-#     rotate_plot = 0,
-#     filename='slice.png'
-# )
-
-# extent = get_tally_extent(my_tally)
-# print(extent)
-# plot_mesh(
-#     extent=extent,
-#     values= result,
-#     scale=None,  # LogNorm(),
-#     vmin=None,
-#     label="picosievert / cm / pulse",
-#     base_plt=stl_slice,
-#     filename= 'test.png',
-# #     vmin=1e6,
-# )
\ No newline at end of file
+import os
+import unittest
+from pathlib import Path
+
+import matplotlib
+import numpy as np
+from regular_mesh_plotter import plot_regular_mesh_values_with_geometry
+
+
+class TestPlotRegularMeshValuesWithGeometry(unittest.TestCase):
+    def setUp(self):
+
+        self.values = np.array(
+            [
+                [
+                    1.64565869e09,
+                    2.59505642e09,
+                    3.06732422e09,
+                    2.64141597e09,
+                    1.76520128e09,
+                    2.14909584e09,
+                    3.70513916e09,
+                    4.99737560e09,
+                    3.86795536e09,
+                    2.21272467e09,
+                ],
+                [
+                    2.92406594e09,
+                    5.91396360e09,
+                    9.39595883e09,
+                    5.94102629e09,
+                    2.78174231e09,
+                    3.47563407e09,
+                    1.02570496e10,
+                    2.50416310e10,
+                    1.01248003e10,
+                    3.34937674e09,
+                ],
+                [
+                    3.99684099e09,
+                    1.72147289e10,
+                    3.68431465e11,
+                    1.64968908e10,
+                    3.74168705e09,
+                    3.90640820e09,
+                    1.65505774e10,
+                    3.66837062e11,
+                    1.65568070e10,
+                    3.65646431e09,
+                ],
+                [
+                    3.27796129e09,
+                    1.01456714e10,
+                    2.45757058e10,
+                    1.00180127e10,
+                    3.45105436e09,
+                    2.63214911e09,
+                    5.95924816e09,
+                    9.43589769e09,
+                    5.71740137e09,
+                    2.75163850e09,
+                ],
+                [
+                    2.37324680e09,
+                    3.77339226e09,
+                    5.01889988e09,
+                    3.58500172e09,
+                    2.16754228e09,
+                    1.81599509e09,
+                    2.57229036e09,
+                    3.09622197e09,
+                    2.50136006e09,
+                    1.72280196e09,
+                ],
+            ]
+        )
+
+    def test_plot_regular_mesh_values_with_geometry(self):
+
+        test_plot = plot_regular_mesh_values_with_geometry(
+            values=self.values,
+            dagmc_file_or_trimesh_object='example.stl'  # this could be a h5m file
+        )
+
+        assert isinstance(test_plot, type(matplotlib.pyplot))
+
+    def test_plot_regular_mesh_values_with_geometry(self):
+
+        test_plot = plot_regular_mesh_values_with_geometry(
+            values=self.values,
+            dagmc_file_or_trimesh_object='example.stl',  # this could be a h5m file
+            filename='test.png'
+        )
+
+        assert isinstance(test_plot, type(matplotlib.pyplot))
+        assert Path('test.png').is_file()

From aa4370684a4826d4c150bb37174676d20c423db8 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 21 Oct 2021 18:14:04 +0100
Subject: [PATCH 4/7] added openmc_post_processor

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 42cd22d..cb86a3f 100644
--- a/setup.py
+++ b/setup.py
@@ -38,6 +38,7 @@
         "trimesh",
         "shapely",
         "scipy",
-        "dagmc_geometry_slice_plotter"
+        "dagmc_geometry_slice_plotter",
+        "openmc_post_processor"
     ],
 )

From fefd700cc11b2ded20e52f1a03fc4d68b1c0ca88 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 21 Oct 2021 18:18:40 +0100
Subject: [PATCH 5/7] added openmc to ci

---
 .github/workflows/ci_with_install.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index fb7ba6c..fbc3ce0 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.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 

From 003f6fed1607863ecb9a8b5f8b55152bc1e9a3ee Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 22 Oct 2021 17:38:42 +0100
Subject: [PATCH 6/7] added ability to rotate mesh plot

---
 regular_mesh_plotter/core.py | 63 ++++++++++++++++++++----------------
 1 file changed, 36 insertions(+), 27 deletions(-)

diff --git a/regular_mesh_plotter/core.py b/regular_mesh_plotter/core.py
index 2e510b2..2ff1f32 100644
--- a/regular_mesh_plotter/core.py
+++ b/regular_mesh_plotter/core.py
@@ -5,6 +5,7 @@
 import numpy as np
 from pathlib import Path
 import dagmc_geometry_slice_plotter as dgsp
+from matplotlib import transforms
 
 import openmc_post_processor as opp
 import openmc
@@ -20,6 +21,7 @@ def plot_regular_mesh_values(
     extent=None,
     x_label="X [cm]",
     y_label="Y [cm]",
+    rotate_plot: float = 0,
 ):
 
     if base_plt:
@@ -28,7 +30,18 @@ def plot_regular_mesh_values(
         import matplotlib.pyplot as plt
 
         plt.plot()
-    image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent)
+
+    if rotate_plot != 0:
+        x_center = sum(extent[:2]) / 2
+        y_center = sum(extent[2:]) / 2
+        base = plt.gca().transData
+        rot = transforms.Affine2D().rotate_deg_around(x_center, y_center, rotate_plot)
+
+        image_map = plt.imshow(
+            values, norm=scale, vmin=vmin, extent=extent, transform=rot + base
+        )
+    else:
+        image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent)
 
     plt.xlabel(x_label)
     plt.ylabel(y_label)
@@ -37,8 +50,6 @@ def plot_regular_mesh_values(
     plt.colorbar(image_map, label=label)
     if filename:
         plt.savefig(filename, dpi=300)
-    # fig.clear()
-    # plt.close()
     return plt
 
 
@@ -54,14 +65,15 @@ def plot_regular_mesh_values_with_geometry(
     y_label="Y [cm]",
     plane_origin: List[float] = None,
     plane_normal: List[float] = [0, 0, 1],
-    rotate_plot: float = 0,
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
 ):
 
     slice = dgsp.plot_slice_of_dagmc_geometry(
         dagmc_file_or_trimesh_object=dagmc_file_or_trimesh_object,
         plane_origin=plane_origin,
         plane_normal=plane_normal,
-        rotate_plot=rotate_plot,
+        rotate_plot=rotate_geometry,
     )
 
     both = plot_regular_mesh_values(
@@ -74,6 +86,7 @@ def plot_regular_mesh_values_with_geometry(
         extent=extent,
         x_label=x_label,
         y_label=y_label,
+        rotate_plot=rotate_mesh,
     )
 
     return both
@@ -90,14 +103,15 @@ def plot_regular_mesh_tally_with_geometry(
     y_label="Y [cm]",
     plane_origin: List[float] = None,
     plane_normal: List[float] = [0, 0, 1],
-    rotate_plot: float = 0,
+    rotate_mesh: float = 0,
+    rotate_geometry: float = 0,
 ):
 
     slice = dgsp.plot_slice_of_dagmc_geometry(
         dagmc_file_or_trimesh_object=dagmc_file_or_trimesh_object,
         plane_origin=plane_origin,
         plane_normal=plane_normal,
-        rotate_plot=rotate_plot,
+        rotate_plot=rotate_geometry,
     )
 
     both = plot_regular_mesh_tally(
@@ -109,6 +123,7 @@ def plot_regular_mesh_tally_with_geometry(
         base_plt=slice,
         x_label=x_label,
         y_label=y_label,
+        rotate_plot=rotate_mesh,
     )
 
     return both
@@ -123,35 +138,29 @@ def plot_regular_mesh_tally(
     base_plt=None,
     x_label="X [cm]",
     y_label="Y [cm]",
+    rotate_plot: float = 0,
 ):
 
-    if base_plt:
-        plt = base_plt
-    else:
-        import matplotlib.pyplot as plt
-
-        plt.plot()
-
     values = opp.process_dose_tally(
         tally=tally,
     )
 
     extent = get_tally_extent(tally)
 
-    print("extent", extent)
-
-    image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent)
-
-    plt.xlabel(x_label)
-    plt.ylabel(y_label)
+    plot = plot_regular_mesh_values(
+        values=values,
+        filename=filename,
+        scale=scale,
+        vmin=vmin,
+        label=label,
+        base_plt=base_plt,
+        extent=extent,
+        x_label=x_label,
+        y_label=y_label,
+        rotate_plot=rotate_plot,
+    )
 
-    # image_map = fig.imshow(values, norm=scale, vmin=vmin)
-    plt.colorbar(image_map, label=label)
-    if filename:
-        plt.savefig(filename, dpi=300)
-    # fig.clear()
-    # plt.close()
-    return plt
+    return plot
 
 
 def get_tally_extent(

From 2228beaffeb71db47317ea2bcf6f2d6102d4978f Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 22 Oct 2021 18:02:22 +0100
Subject: [PATCH 7/7] added rotate mesh option and started readme

---
 README.md                                 | 66 ++++++++++++++++++++++-
 examples/plot_mesh_with_geometry_slice.py |  3 +-
 2 files changed, 65 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index ba746a1..59d7134 100644
--- a/README.md
+++ b/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
diff --git a/examples/plot_mesh_with_geometry_slice.py b/examples/plot_mesh_with_geometry_slice.py
index eca6fc9..fb2622c 100644
--- a/examples/plot_mesh_with_geometry_slice.py
+++ b/examples/plot_mesh_with_geometry_slice.py
@@ -1,5 +1,4 @@
 
-
 from regular_mesh_plotter import plot_regular_mesh_tally_with_geometry
 import openmc
 
@@ -15,4 +14,4 @@
     mesh_file_or_trimesh_object="dagmc.h5m",
 )
 
-plot.show()
\ No newline at end of file
+plot.show()