From 3952ad03634e80b0f991ff71acf0cfac9aa9a458 Mon Sep 17 00:00:00 2001
From: David <david.boehringer@fau.de>
Date: Wed, 27 Apr 2022 16:09:58 +0200
Subject: [PATCH] Add an overlay plot of Orientation field & cell image & fiber
 image to analysis

---
 CompactionAnalyzer/CompactionFunctions.py | 17 +++++++++++++++++
 CompactionAnalyzer/plotting.py            | 20 ++++++++++++++++++++
 2 files changed, 37 insertions(+)

diff --git a/CompactionAnalyzer/CompactionFunctions.py b/CompactionAnalyzer/CompactionFunctions.py
index d7560c0..dac369a 100644
--- a/CompactionAnalyzer/CompactionFunctions.py
+++ b/CompactionAnalyzer/CompactionFunctions.py
@@ -654,6 +654,20 @@ def StuctureAnalysisMain(fiber_list,
                            path_png= os.path.join(figures,"Orientation_weighted_noquiver.png"),
                            label="Orientation",dpi=dpi) 
             plt.close("all") 
+            
+            ### more fancy overlay plot of cell & fiber & orientation (notweighted)
+            plot_fancy_overlay(im_fiber_n[edge:-edge,edge:-edge], 
+                               im_cell_n[edge:-edge,edge:-edge],
+                               orientation_dev,
+                               path_png= os.path.join(figures,"Orientation_overlay.png"),                       
+                               label="Orientation",dpi=dpi,
+                               # ,cmap_cell="Greys_r",cmap_fiber="Greys_r", ### use default values here
+                               # cmap_angle="viridis", alpha_ori =0.8,  alpha_cell = 0.4, alpha_fiber = 0.4,
+                                omin=-1, omax=1,scale=scale)
+  
+            plt.close("all") 
+        
+            
             # Polar plots        
             plot_polar(results_angle['Angles Plotting'], results_angle['Coherency (weighted by intensity)'],
                        path_png= os.path.join(figures,"polar_coherency_weighted.png"), label = "Coherency (weighted)",dpi=dpi)
@@ -698,6 +712,9 @@ def StuctureAnalysisMain(fiber_list,
                            vec1=min_evec[:,:,1], coherency_map=ori,show_n=10,
                            segmention=segmention["mask"][edge:-edge,edge:-edge], 
                            path_png=os.path.join(figures,"overlay2.png"),dpi=dpi ,scale=scale)
+            ##
+            
+            
             plt.close("all") 
             ### DISTANCE PLOTS
             # plot shells - deactived as it consumes a lot of time
diff --git a/CompactionAnalyzer/plotting.py b/CompactionAnalyzer/plotting.py
index 319b8d6..3de138b 100644
--- a/CompactionAnalyzer/plotting.py
+++ b/CompactionAnalyzer/plotting.py
@@ -140,6 +140,26 @@ def plot_coherency(coherency,path_png,label="Coherency",dpi=300):
     plt.axis('off'); cbar.set_label(label,fontsize=12)
     plt.savefig(path_png, dpi=dpi, bbox_inches='tight', pad_inches=0); plt.tight_layout()
     return fig
+
+
+def plot_fancy_overlay(fiber, cell, field,path_png,label="field",dpi=300,cmap_cell="Greys_r",cmap_fiber="Greys_r",
+                       cmap_angle="viridis", alpha_ori =0.8,  alpha_cell = 0.4, alpha_fiber = 0.4,   # example cmaps: viridis/inferno/coolwarm 
+                       omin=-1, omax=1, scale=None):                                
+    fig =plt.figure()
+    plt.imshow(field,cmap=cmap_angle,vmin=omin,vmax=omax,alpha=alpha_ori);cbar =plt.colorbar()
+    plt.imshow(fiber, cmap=cmap_fiber,alpha=alpha_fiber) 
+    plt.imshow(cell, cmap=cmap_cell,alpha=alpha_cell) 
+    plt.axis('off');
+    cbar.set_label(label,fontsize=12)
+    if scale is not None:
+        scalebar = ScaleBar(scale, "um", length_fraction=0.1, location="lower right", box_alpha=0 , 
+                    color="k")
+        plt.gca().add_artist(scalebar)    
+    plt.tight_layout()   
+    plt.savefig(path_png, dpi=dpi, bbox_inches='tight', pad_inches=0)
+    return fig
+
+
      
 def plot_polar(angle_plotting, something, path_png,label="something",dpi=300,
                something2 = None, something3 = None, label2 = None, label3 =None):