Fix bugs

tools/superdsm/run-superdsm.py

@@ -17,15 +17,15 @@
 
 hyperparameters = [
     ('AF_scale', float),
-    ('c2f_region_analysis/min_atom_radius', float),
-    ('c2f_region_analysis/min_norm_energy_improvement', float),
-    ('c2f_region_analysis/max_atom_norm_energy', float),
-    ('c2f_region_analysis/max_cluster_marker_irregularity', float),
+    ('c2f-region-analysis/min_atom_radius', float),
+    ('c2f-region-analysis/min_norm_energy_improvement', float),
+    ('c2f-region-analysis/max_atom_norm_energy', float),
+    ('c2f-region-analysis/max_cluster_marker_irregularity', float),
     ('dsm/alpha', float),
     ('dsm/AF_alpha', float),
-    ('global_energy_minimization/pruning', str),
-    ('global_energy_minimization/beta', float),
-    ('global_energy_minimization/AF_beta', float),
+    ('global-energy-minimization/pruning', str),
+    ('global-energy-minimization/beta', float),
+    ('global-energy-minimization/AF_beta', float),
     ('postprocess/mask_max_distance', int),
     ('postprocess/mask_stdamp', float),
     ('postprocess/max_norm_energy', float),
@@ -35,7 +35,7 @@
 
 
 def get_param_name(key):
-    return key.replace('/', '_')
+    return key.replace('/', '_').replace('-', '_')
 
 
 def create_config(args):
@@ -97,24 +97,32 @@ def flatten_dict(d, sep='/'):
         cfg = create_config(args)
         img = superdsm.io.imread(img_filepath)
 
+        # Create configuration if it is required:
+        if args.do_cfg or args.do_overlay or args.do_masks:
+            cfg, _ = superdsm.automation.create_config(pipeline, cfg, img)
+
+        # Perform segmentation if it is required:
+        if args.do_overlay or args.do_masks:
+            print('Performing segmentation')
+            data, cfg, _ = pipeline.process_image(img, cfg)
+
+        # Write configuration used for segmentation, or the automatically created one, otherwise:
         if args.do_cfg:
             print(f'Writing config to: {args.do_cfg}')
-            cfg, _ = superdsm.automation.create_config(pipeline, cfg, img)
             with open(args.do_cfg, 'w') as fp:
                 tsv_out = csv.writer(fp, delimiter='\t')
                 tsv_out.writerow(['Hyperparameter', 'Value'])
-                for key, value in flatten_dict(cfg.entries).items():
+                rows = sorted(flatten_dict(cfg.entries).items(), key=lambda item: item[0])
+                for key, value in rows:
                     tsv_out.writerow([key, value])
 
-        if args.do_overlay or args.do_masks:
-            print('Performing segmentation')
-            data, cfg, _ = pipeline.process_image(img, cfg)
-
+        # Write the overlay image:
         if args.do_overlay:
             print(f'Writing overlay to: {args.do_overlay}')
             overlay = superdsm.render.render_result_over_image(data, border_width=args.do_overlay_border, normalize_img=False)
             superdsm.io.imwrite(args.do_overlay, overlay)
 
+        # Write the label map:
         if args.do_masks:
             print(f'Writing masks to: {args.do_masks}')
             masks = superdsm.render.rasterize_labels(data)

tools/superdsm/superdsm.xml

@@ -120,7 +120,7 @@
             <option value="exact">Exact graph pruning (Kostrykin and Rohr, TPAMI 2023)</option>
             <option value="isbi24" selected="true">Robust graph pruning (Kostrykin and Rohr, ISBI 2024)</option>
         </param>
-        <param name="outputs" type="select" label="Tool outputs" multiple="true" optional="false">
+        <param name="outputs" type="select" label="Tool outputs" multiple="true" optional="false" help="Note that if neither a segmentation overlay nor a label map is created, segmentation and cluster splitting will not be performed. As a consequence, hyperparameters which are determined automatically during segmentation and cluster splitting will not be reported, even if &quot;Report all hyperparameters&quot; is selected.">
             <option value="overlay" selected="true">Create a segmentation overlay</option>
             <option value="masks">Create a label map (e.g., for further processing)</option>
             <option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option>
@@ -160,7 +160,7 @@
             <param name="global_energy_minimization_pruning" value="exact" />
             <param name="outputs" value="overlay,masks,cfg" />
             <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
-            <output name="cfg" value="cfg.tsv" ftype="tsv" compare="diff" />
+            <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" />
         </test>
         <test expect_num_outputs="1">
             <param name="dataset" value="BBBC033_C2_z28.png" />

tools/superdsm/test-data/cfg-full.tsv

@@ -0,0 +1,68 @@
+Hyperparameter	Value
+AF_scale	
+c2f-region-analysis/AF_min_atom_radius	0.33
+c2f-region-analysis/enabled	True
+c2f-region-analysis/max_atom_norm_energy	0.05
+c2f-region-analysis/max_cluster_marker_irregularity	0.2
+c2f-region-analysis/min_atom_radius	30
+c2f-region-analysis/min_norm_energy_improvement	0.1
+c2f-region-analysis/seed_connectivity	8
+dsm/AF_alpha	0.0005
+dsm/AF_background_margin	0.4
+dsm/AF_smooth_amount	0.2
+dsm/AF_smooth_subsample	0.4
+dsm/alpha	2.116
+dsm/background_margin	26
+dsm/cachesize	1
+dsm/cachetest	
+dsm/cp_timeout	300
+dsm/enabled	True
+dsm/epsilon	1.0
+dsm/gaussian_shape_multiplier	2
+dsm/init	elliptical
+dsm/scale	1000
+dsm/smooth_amount	13
+dsm/smooth_mat_dtype	float32
+dsm/smooth_mat_max_allocations	inf
+dsm/smooth_subsample	26
+dsm/sparsity_tol	0
+global-energy-minimization/AF_beta	0.66
+global-energy-minimization/AF_max_seed_distance	inf
+global-energy-minimization/beta	2793.1200000000003
+global-energy-minimization/enabled	True
+global-energy-minimization/gamma	0.8
+global-energy-minimization/max_iter	5
+global-energy-minimization/max_seed_distance	inf
+global-energy-minimization/max_work_amount	1000000
+global-energy-minimization/pruning	exact
+histological	False
+postprocess/AF_max_object_radius	inf
+postprocess/AF_min_glare_radius	inf
+postprocess/AF_min_object_radius	0.0
+postprocess/contrast_epsilon	0.0001
+postprocess/discard_image_boundary	False
+postprocess/enabled	True
+postprocess/exterior_offset	5
+postprocess/exterior_scale	5
+postprocess/fill_holes	True
+postprocess/glare_detection_min_layer	0.5
+postprocess/glare_detection_num_layers	5
+postprocess/glare_detection_smoothness	3
+postprocess/mask_max_distance	1
+postprocess/mask_smoothness	3
+postprocess/mask_stdamp	2.0
+postprocess/max_boundary_eccentricity	inf
+postprocess/max_eccentricity	0.99
+postprocess/max_norm_energy	0.2
+postprocess/max_object_radius	inf
+postprocess/min_boundary_glare_radius	inf
+postprocess/min_boundary_obj_radius	0
+postprocess/min_contrast	1.35
+postprocess/min_glare_radius	inf
+postprocess/min_object_radius	0.0
+preprocess/AF_sigma2	1.0
+preprocess/enabled	True
+preprocess/lower_clip_mean	False
+preprocess/offset_clip	3
+preprocess/sigma1	1.4142135623730951
+preprocess/sigma2	65.05382386916237

tools/superdsm/test-data/cfg.tsv

@@ -1,78 +1,32 @@
 Hyperparameter	Value
-c2f_region_analysis_min_norm_energy_improvement	0.1
-c2f_region_analysis_max_atom_norm_energy	0.05
-c2f_region_analysis_max_cluster_marker_irregularity	0.2
-dsm_AF_alpha	0.0005
-global_energy_minimization_AF_beta	0.66
-postprocess_mask_max_distance	1
-postprocess_mask_stdamp	2.0
-postprocess_max_norm_energy	0.2
-postprocess_min_contrast	1.35
-postprocess_min_object_radius	0.0
 AF_scale	
-preprocess/AF_sigma2	1.0
-preprocess/sigma2	65.05382386916237
-preprocess/enabled	True
-preprocess/sigma1	1.4142135623730951
-preprocess/offset_clip	3
-preprocess/lower_clip_mean	False
+c2f-region-analysis/AF_min_atom_radius	0.33
+c2f-region-analysis/max_atom_norm_energy	0.05
+c2f-region-analysis/max_cluster_marker_irregularity	0.2
+c2f-region-analysis/min_atom_radius	30
+c2f-region-analysis/min_norm_energy_improvement	0.1
 dsm/AF_alpha	0.0005
-dsm/alpha	2.116
+dsm/AF_background_margin	0.4
 dsm/AF_smooth_amount	0.2
-dsm/smooth_amount	13
 dsm/AF_smooth_subsample	0.4
-dsm/smooth_subsample	26
-dsm/AF_background_margin	0.4
+dsm/alpha	2.116
 dsm/background_margin	26
-dsm/enabled	True
-dsm/cachesize	1
-dsm/cachetest	
-dsm/sparsity_tol	0
-dsm/init	elliptical
-dsm/epsilon	1.0
-dsm/scale	1000
-dsm/gaussian_shape_multiplier	2
-dsm/smooth_mat_dtype	float32
-dsm/smooth_mat_max_allocations	inf
-dsm/cp_timeout	300
-c2f-region-analysis/AF_min_atom_radius	0.33
-c2f-region-analysis/min_atom_radius	30
-c2f-region-analysis/enabled	True
-c2f-region-analysis/seed_connectivity	8
-c2f-region-analysis/max_atom_norm_energy	0.05
-c2f-region-analysis/min_norm_energy_improvement	0.1
-c2f-region-analysis/max_cluster_marker_irregularity	0.2
+dsm/smooth_amount	13
+dsm/smooth_subsample	26
 global-energy-minimization/AF_beta	0.66
-global-energy-minimization/beta	2793.1200000000003
 global-energy-minimization/AF_max_seed_distance	inf
+global-energy-minimization/beta	2793.1200000000003
 global-energy-minimization/max_seed_distance	inf
-global-energy-minimization/enabled	True
-global-energy-minimization/strict	True
-global-energy-minimization/max_iter	5
-global-energy-minimization/gamma	0.8
-global-energy-minimization/max_work_amount	1000000
-postprocess/AF_min_object_radius	0.0
-postprocess/min_object_radius	0.0
+global-energy-minimization/pruning	exact
 postprocess/AF_max_object_radius	inf
-postprocess/max_object_radius	inf
 postprocess/AF_min_glare_radius	inf
-postprocess/min_glare_radius	inf
-postprocess/enabled	True
+postprocess/AF_min_object_radius	0.0
+postprocess/mask_max_distance	1
+postprocess/mask_stdamp	2.0
 postprocess/max_norm_energy	0.2
-postprocess/discard_image_boundary	False
-postprocess/min_boundary_obj_radius	0
-postprocess/max_eccentricity	0.99
-postprocess/max_boundary_eccentricity	inf
-postprocess/exterior_scale	5
-postprocess/exterior_offset	5
+postprocess/max_object_radius	inf
 postprocess/min_contrast	1.35
-postprocess/contrast_epsilon	0.0001
-postprocess/mask_stdamp	2
-postprocess/mask_max_distance	1
-postprocess/mask_smoothness	3
-postprocess/fill_holes	True
-postprocess/glare_detection_smoothness	3
-postprocess/glare_detection_num_layers	5
-postprocess/glare_detection_min_layer	0.5
-postprocess/min_boundary_glare_radius	inf
-histological	False
+postprocess/min_glare_radius	inf
+postprocess/min_object_radius	0.0
+preprocess/AF_sigma2	1.0
+preprocess/sigma2	65.05382386916237