From 2f887282ea20cf2ad9c42604e2197d69ab011d19 Mon Sep 17 00:00:00 2001
From: Kartik Neralwar <87446855+Kartik-Neralwar@users.noreply.github.com>
Date: Tue, 24 Sep 2024 17:24:34 +0200
Subject: [PATCH 1/2] Added a function to get J plot and RJ plot

J_class() gives the j plot classification based on j1 and j2
get_class_j_rj() calls functions to give the classes based on j plot and rj plots
---
 RJplots.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/RJplots.py b/RJplots.py
index 0c0e270..ad5cf2c 100644
--- a/RJplots.py
+++ b/RJplots.py
@@ -5,6 +5,10 @@
 ### The following are outward facing functions which may be called
 
 ### The main function of the package, returns the RJ-values of a 2D image (2d-array) as well as the classification of the structure.
+
+
+
+
 def get_rj(image):
 
     J1,J2,com,theta = moments(image)
@@ -17,6 +21,37 @@ def get_rj(image):
 
     return RJ1,RJ2,cla
 
+
+### get_class_j_rj and J_class functions are added by Kartik Neralwar. These give the j plot class and the rj plot class for a structure
+def get_class_j_rj(image):
+
+    J1,J2,com,theta = moments(image)
+
+    RJ1 = (J1 - J2)/np.sqrt(2)
+    RJ2 = (J1 + J2)/np.sqrt(2)
+    RJ2 = RJ2/(-RJ1 + np.sqrt(2))
+
+    cla = classification(RJ1,RJ2)
+    J_cla = J_class(J1, J2)
+    return J_cla, cla
+
+### J plot class as defined in Neralwar + 2022
+### 0 - Bubble
+### 1 - Filament
+### 2 - Core
+def J_class(J1, J2):
+    if(J1<0 and J2<0):
+        struc_1 = 0
+    if(J1>0 and J2<0):
+        struc_1 = 1
+    if(J1>0 and J2>0):
+        struc_1 = 2
+    else:
+        struc_1 = 3
+    return struc_1
+
+
+
 ### Uses the classification scheme described in the accompanying paper. 
 ### 1 - Quasi-circular, centrally over-dense
 ### 2 - Quasi-circular, centrally under-dense

From ae1012f388098317c1cbd4994006d7364eb38cf1 Mon Sep 17 00:00:00 2001
From: Kartik Neralwar <87446855+Kartik-Neralwar@users.noreply.github.com>
Date: Tue, 24 Sep 2024 17:27:05 +0200
Subject: [PATCH 2/2] Added J plot class description

---
 README.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a160c9d..f683b40 100644
--- a/README.md
+++ b/README.md
@@ -24,8 +24,13 @@ An example script is provided which shows how to use the package. It calculates
 * 3 - Elongated, centrally over-dense,
 * 4 - Elongated, centrally under-dense.
 
+The J plot classification referes to the following shapes:
+* 0 - Bubbles
+* 1 - Filaments
+* 2 - Cores
+
 ## Acknowledgements 
 This code was produced with the support of the Ministry of Science and Technology (MoST) in Taiwan through grant MoST 108-2112-M-001-004-MY2
 ## Contact
 
-For up-to-date contact information see my [website](https://seamusclarke.github.io/#five)
\ No newline at end of file
+For up-to-date contact information see my [website](https://seamusclarke.github.io/#five)