makes superdsm output tsv instead of csv

tools/superdsm/run-superdsm.py

@@ -12,6 +12,8 @@
 import pathlib
 import shutil
 import tempfile
+import io
+import csv
 
 
 hyperparameters = [
@@ -44,6 +46,16 @@ def create_config(args):
             cfg[key] = value
     return cfg
 
+def flatten_dict(d, sep='/'):
+    result = {}
+    for key, val in d.items():
+        if isinstance(val, dict):
+            for sub_key, sub_val in flatten_dict(val, sep=sep).items():
+                result[f'{key}{sep}{sub_key}'] = sub_val
+        else:
+            result[key] = val
+    return result
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Segmentation of cell nuclei in 2-D fluorescence microscopy images')
@@ -87,8 +99,14 @@ def create_config(args):
 
         if args.do_cfg:
             print(f'Writing config to: {args.do_cfg}')
+            #cfg_buf = io.StringIO()
+            #cfg.dump_json(cfg_buf)
+            #cfg_json = json.loads(cfg_buf.get_value())
             with open(args.do_cfg, 'w') as fp:
-                cfg.dump_json(fp)
+                tsv_out = csv.writer(fp, delimiter='\t')
+                tsv_out.writerow(['Hyperparameter', 'Value'])
+                for key, value in flatten_dict(cfg.entries).items():
+                    tsv_out.writerow([key, value])
 
         if args.do_overlay:
             print(f'Writing overlay to: {args.do_overlay}')

tools/superdsm/superdsm.xml

@@ -28,7 +28,7 @@
             --do-masks 'masks.png'
         #end if
         #if $do_cfg_enabled == 'true':
-            --do-cfg 'cfg.json'
+            --do-cfg 'cfg.tsv'
         #end if
         #if $do_overlay.do_overlay_enabled == 'true':
             --do-overlay 'overlay.png'
@@ -131,7 +131,7 @@
         <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks">
             <filter>outputs['do_masks_enabled'] == 'true'</filter>
         </data>
-        <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg">
+        <data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg">
             <filter>outputs['do_cfg_enabled'] == 'true'</filter>
         </data>
         <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay">
@@ -145,6 +145,7 @@
             <param name="do_overlay_enabled" value="true" />
             <param name="do_cfg_enabled" value="true" />
             <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
+            <output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
         </test>
         <test expect_num_outputs="1">
             <param name="dataset" value="BBBC033_C2_z28.png" />

tools/superdsm/test-data/cfg.tsv

@@ -0,0 +1,78 @@
+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
+dsm/AF_alpha	0.0005
+dsm/alpha	2.116
+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/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
+global-energy-minimization/AF_beta	0.66
+global-energy-minimization/beta	2793.1200000000003
+global-energy-minimization/AF_max_seed_distance	inf
+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
+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/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/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