diff test-data/cfg.tsv @ 4:dc5f72f6b1e9 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22

--- a/test-data/cfg.tsv	Thu Nov 16 12:29:41 2023 +0000
+++ b/test-data/cfg.tsv	Mon Feb 12 14:58:45 2024 +0000
@@ -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	
+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/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/smooth_amount	13
+dsm/smooth_subsample	26
+global-energy-minimization/AF_beta	0.66
+global-energy-minimization/AF_max_seed_distance	inf
+global-energy-minimization/beta	2793.1200000000003
+global-energy-minimization/max_seed_distance	inf
+global-energy-minimization/pruning	exact
+postprocess/AF_max_object_radius	inf
+postprocess/AF_min_glare_radius	inf
+postprocess/AF_min_object_radius	0.0
+postprocess/mask_max_distance	1
+postprocess/mask_stdamp	2.0
+postprocess/max_norm_energy	0.2
+postprocess/max_object_radius	inf
+postprocess/min_contrast	1.35
+postprocess/min_glare_radius	inf
+postprocess/min_object_radius	0.0
 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