#41 Changed from clearing figures to closing them, as pyplot suggests…

… close rather than clf

src/processing_steps/0225_generate_hdf5_novisim.py

@@ -85,7 +85,7 @@
         plt.vlines([scaled_valley], 0, smoothed[valley].astype(int), color='g')
         print (f'The valley is at {scaled_valley}')
         plt.savefig(f"{plotting_dir}/histogram.pdf", bbox_inches='tight')
-        plt.clf()
+        plt.close()
 
     # Print metadata keys and attributes
     if args.verbose >= 1:

src/processing_steps/1050_compute_ridges.py

@@ -892,7 +892,7 @@ def update_config():
     else:
         # Preload pyplot, as the first figure takes around 3 seconds to compute. For timing only
         plt.figure()
-        plt.clf()
+        plt.close()
         gui()
         if not args.dry_run:
             save_config()

src/processing_steps/1550_segment_osteocyt.py

@@ -99,7 +99,7 @@
         if args.verbose >= 1: print (f'Plotting histogram of ellipsoid errors to {plotting_dir}/')
         plt.hist(errors, bins=100, log=True)
         plt.savefig(f'{plotting_dir}/{args.sample}_ellipsoid_errors.png')
-        plt.clf()
+        plt.close()
 
     # Final osteocyte segmentation
     osteocyte_segments = np.argwhere(osteocyte_sized & (~weirdly_long) & (~weirdly_shaped)).flatten().astype(np.uint64)

src/processing_steps/1600_bic.py

@@ -82,7 +82,7 @@
     if args.plotting:
         bics_path = f'{plotting_dir}/bics.pdf'
         if args.verbose >= 1: print (f'Plotting BICs to {bics_path}')
-        plt.plot(bics); plt.savefig(f"{bics_path}", bbox_inches='tight'); plt.clf()
+        plt.plot(bics); plt.savefig(f"{bics_path}", bbox_inches='tight'); plt.close()
 
     if args.verbose >= 1: print (f'Saving BICs to {output_dir}')
     np.save(f"{output_dir}/bics.npy", bics)

src/processing_steps/1800_healthy_bone.py

@@ -92,7 +92,7 @@
             plt.figure(figsize=(10,10))
             plt.imshow(plane)
             plt.savefig(f'{plotting_dir}/soft_{name}.pdf', bbox_inches='tight')
-            plt.clf()
+            plt.close()
         del soft
 
     if args.verbose >= 1: print (f'Loading the bone probabilities from {bone_path}')
@@ -110,7 +110,7 @@
             plt.figure(figsize=(10,10))
             plt.imshow(plane)
             plt.savefig(f'{plotting_dir}/bone_{name}.pdf', bbox_inches='tight')
-            plt.clf()
+            plt.close()
 
     bone_bp = bitpack_encode(bone_threshed, verbose=args.verbose)
     bone_bp_opened = open_3d(bone_bp, opening_voxels, args.verbose)
@@ -125,7 +125,7 @@
             plt.figure(figsize=(10,10))
             plt.imshow(plane)
             plt.savefig(f'{plotting_dir}/bone_opened_{name}.pdf', bbox_inches='tight')
-            plt.clf()
+            plt.close()
 
     if args.verbose >= 1: print (f'Computing the distance field')
     disted_bp = soft_bp & bone_bp_opened
@@ -139,7 +139,7 @@
             plt.figure(figsize=(10,10))
             plt.imshow(plane)
             plt.savefig(f'{plotting_dir}/dist_{name}.pdf', bbox_inches='tight')
-            plt.clf()
+            plt.close()
 
     bone_count = np.sum(bone_opened)
     dist_count = np.sum(disted)