From 68087abe94b3e89ede76c3953ddb3a368434bf36 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 8 Mar 2024 14:40:46 +0000
Subject: [PATCH] gammas source working again;

---
 README.md                             | 16 ++++++++--------
 examples/example_gamma_spec_plot.py   |  3 +++
 src/openmc_source_plotter/material.py | 15 ++++++---------
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index 49d98b9..4fae8fc 100644
--- a/README.md
+++ b/README.md
@@ -14,15 +14,15 @@ pip install openmc_source_plotter
 
 # Features
 
-The package simply extends the default ```openmc.IndependentSourceBase``` and ```openmc.Model``` to provides additional functions that:
+The package provides three plotting functions that can plot source data from openmc objects.
+- ```plot_source_energy```
+- ```plot_source_position```
+- ```plot_source_direction```
+- ```plot_gamma_emission```
+ 
+Additionally the package provides a convienient method of sampling particles
+- ```sample_initial_particles```
 
-- extract the positions, directions and energy of particles
-- visualise a source with respect to:
-  - direction
-  - energy
-  - position
-
-Or just provide the initial particles with ```sample_initial_particles```
 
 # Example plots
 
diff --git a/examples/example_gamma_spec_plot.py b/examples/example_gamma_spec_plot.py
index 35177c6..4ecd5ef 100644
--- a/examples/example_gamma_spec_plot.py
+++ b/examples/example_gamma_spec_plot.py
@@ -1,6 +1,9 @@
 import openmc
 from openmc_source_plotter import plot_gamma_emission
 
+# you will need to install optional dependancies for this example
+# pip install openmc_source_plotter[gammas]
+
 # this path will need changing to point to your chain file
 # openmc.config["chain_file"] = "chain-endf.xml"
 
diff --git a/src/openmc_source_plotter/material.py b/src/openmc_source_plotter/material.py
index 58cec3c..ab9df53 100644
--- a/src/openmc_source_plotter/material.py
+++ b/src/openmc_source_plotter/material.py
@@ -3,7 +3,7 @@
 
 
 def plot_gamma_emission(
-    self,
+    material,
     label_top: int = None,
 ):
     """makes a plot of the gamma energy spectra for a material. The
@@ -26,7 +26,7 @@ def plot_gamma_emission(
         possible_energies_to_label = []
         import lineid_plot
 
-        atoms = self.get_nuclide_atoms()
+        atoms = material.get_nuclide_atoms()
         for nuc, num_atoms in atoms.items():
             dists = []
             probs = []
@@ -47,7 +47,7 @@ def plot_gamma_emission(
 
         probs = []
         en = []
-        energy_dis = self.decay_photon_energy
+        energy_dis = material.get_decay_photon_energy(clip_tolerance=0.0)
         for p in energy_dis.p:
             probs.append(0)
             probs.append(p)
@@ -60,9 +60,9 @@ def plot_gamma_emission(
         # print(probs)
         lineid_plot.plot_line_ids(
             en,
-            # self.decay_photon_energy.x,
+            # material.decay_photon_energy.x,
             probs,
-            # self.decay_photon_energy.p,
+            # material.decay_photon_energy.p,
             energies_to_label,
             labels,
         )
@@ -70,7 +70,7 @@ def plot_gamma_emission(
     else:
         probs = []
         en = []
-        energy_dis = self.decay_photon_energy
+        energy_dis = material.get_decay_photon_energy(clip_tolerance=0.0)
         for p in energy_dis.p:
             probs.append(0)
             probs.append(p)
@@ -87,6 +87,3 @@ def plot_gamma_emission(
     plt.xlabel("Energy [eV]")
     plt.ylabel("Activity [Bq/s]")
     return plt
-
-
-openmc.Material.plot_gamma_emission = plot_gamma_emission