added speed and memory benchmark, and github workflow by Hendrik-code · Pull Request #128 · Hendrik-code/TPTBox

Hendrik-code · 2026-08-13T10:56:49Z

No description provided.

github-actions · 2026-08-13T11:04:52Z

Benchmark comparison

Speed (wall time per call)

baseline d8fef9f vs head d8fef9f · python 3.11.15 · 5 repeats + 1 warmup

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 ms are tagged (noise) — runner jitter on those swamps any real change.

`ct_3d` — shape (73, 47, 73)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale_seg`	3.28 ±0.03	3.37 ±0.02	+2.8%	0.002
`nii_load_img`	11.91 ±0.10	12.24 ±0.16	+2.8%	0.008
`poi_calc_centroids_nocrop`	4.89 ±0.09	5.01 ±0.02	+2.4%	0.081
`nii_rescale`	40.68 ±0.33	40.05 ±0.19	-1.5%	0.028
`nii_fill_holes`	5.00 ±0.04	5.06 ±0.06	+1.3%	0.104

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_erode_msk`	6.75 ±0.02	6.67 ±0.03	-1.3%	0.001
`nii_save`	11.96 ±0.13	12.04 ±0.07	+0.7%	0.719
`nii_dilate_msk`	119.17 ±0.48	119.73 ±0.23	+0.5%	0.021
`nii_filter_connected_components`	4.49 ±0.03	4.51 ±0.48	+0.5%	0.384
`poi_calc_poi_from_subreg_vert`	11.97 ±0.10	11.92 ±0.05	-0.4%	0.252
`nii_resample_from_to`	41.94 ±0.34	42.03 ±0.18	+0.2%	0.959
`metric_voxels`	250463.00 ±0.00	250463.00 ±0.00	+0.0%	—
`metric_labels`	3.00 ±0.00	3.00 ±0.00	+0.0%	—
`metric_foreground_pct`	14.51 ±0.00	14.51 ±0.00	+0.0%	—
`poi_load`	0.29 ±0.02	0.32 ±0.03	+8.7% (noise)	0.398
`poi_reorient`	0.46 ±0.02	0.50 ±0.03	+7.8% (noise)	0.074
`nii_apply_crop`	0.77 ±0.03	0.71 ±0.01	-7.5% (noise)	0.026
`poi_map_labels`	0.22 ±0.01	0.20 ±0.02	-6.9% (noise)	0.369
`nii_load_seg`	2.87 ±0.03	3.04 ±0.01	+5.9% (noise)	0.000
`poi_local_to_global_arr`	0.29 ±0.01	0.27 ±0.02	-5.7% (noise)	0.712
`nii_compute_crop`	0.35 ±0.01	0.37 ±0.02	+4.5% (noise)	0.514
`poi_to_global`	0.25 ±0.02	0.26 ±0.02	+4.4% (noise)	0.384
`poi_save`	0.53 ±0.02	0.51 ±0.02	-3.7% (noise)	0.058
`poi_rescale`	0.26 ±0.01	0.27 ±0.02	+2.6% (noise)	0.430
`nii_pad_to`	0.79 ±0.04	0.77 ±0.02	-2.6% (noise)	0.780
`nii_reorient`	0.88 ±0.07	0.86 ±0.02	-2.4% (noise)	0.220
`nii_set_dtype`	0.54 ±0.04	0.55 ±0.01	+2.2% (noise)	0.571
`nii_map_labels`	0.97 ±0.02	0.95 ±0.03	-2.2% (noise)	0.446
`poi_calc_centroids`	2.66 ±0.04	2.72 ±0.03	+2.1% (noise)	0.236
`nii_volumes`	1.99 ±0.02	2.01 ±0.01	+1.4% (noise)	0.097
`poi_resample_from_to`	0.72 ±0.03	0.73 ±0.02	+1.3% (noise)	0.612
`nii_get_connected_components`	2.21 ±0.04	2.18 ±0.02	-1.2% (noise)	0.085
`nii_center_of_masses`	1.89 ±0.02	1.87 ±0.01	-1.0% (noise)	0.363
`nii_unique`	0.67 ±0.01	0.68 ±0.01	+0.9% (noise)	0.282
`nii_extract_label`	0.85 ±0.03	0.85 ±0.02	-0.3% (noise)	0.318
`nii_get_array`	0.05 ±0.01	0.05 ±0.00	+0.2% (noise)	0.850

`ct_2d` — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_rescale`	5.85 ±0.09	5.72 ±0.08	-2.2%	0.122
`nii_resample_from_to`	7.75 ±0.09	7.77 ±0.22	+0.2%	0.910
`nii_dilate_msk`	13.79 ±0.12	13.78 ±0.20	-0.1%	0.806
`metric_voxels`	3431.00 ±0.00	3431.00 ±0.00	+0.0%	—
`metric_labels`	3.00 ±0.00	3.00 ±0.00	+0.0%	—

… 30 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`metric_foreground_pct`	37.60 ±0.00	37.60 ±0.00	+0.0%	—
`nii_erode_msk`	1.11 ±0.04	0.98 ±0.01	-12.0% (noise)	0.002
`nii_map_labels`	0.54 ±0.01	0.48 ±0.01	-10.4% (noise)	0.000
`nii_fill_holes`	0.94 ±0.05	0.85 ±0.02	-9.9% (noise)	0.014
`poi_to_global`	0.30 ±0.06	0.27 ±0.01	-9.9% (noise)	0.207
`nii_get_connected_components`	0.75 ±0.01	0.67 ±0.02	-9.5% (noise)	0.000
`nii_extract_label`	0.51 ±0.01	0.46 ±0.02	-8.7% (noise)	0.002
`nii_filter_connected_components`	0.94 ±0.02	0.86 ±0.03	-8.1% (noise)	0.011
`poi_reorient`	0.53 ±0.01	0.49 ±0.01	-7.9% (noise)	0.003
`nii_compute_crop`	0.18 ±0.02	0.17 ±0.01	-6.0% (noise)	0.276
`nii_unique`	0.17 ±0.01	0.16 ±0.01	-5.6% (noise)	0.280
`nii_load_seg`	1.82 ±0.04	1.74 ±0.03	-4.9% (noise)	0.006
`nii_center_of_masses`	0.25 ±0.01	0.24 ±0.02	-4.9% (noise)	0.177
`poi_map_labels`	0.24 ±0.01	0.23 ±0.01	-4.9% (noise)	0.151
`nii_pad_to`	0.65 ±0.02	0.62 ±0.02	-4.7% (noise)	0.047
`poi_local_to_global_arr`	0.31 ±0.00	0.30 ±0.01	-4.0% (noise)	0.062
`poi_rescale`	0.30 ±0.01	0.29 ±0.01	-3.8% (noise)	0.195
`poi_load`	0.36 ±0.01	0.35 ±0.03	-3.1% (noise)	0.369
`poi_save`	0.58 ±0.03	0.57 ±0.03	-2.6% (noise)	0.121
`poi_calc_centroids_nocrop`	1.24 ±0.01	1.21 ±0.03	-2.5% (noise)	0.027
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	+1.5% (noise)	0.562
`nii_reorient`	0.93 ±0.03	0.91 ±0.04	-1.4% (noise)	0.544
`nii_save`	1.52 ±0.03	1.50 ±0.02	-1.3% (noise)	0.142
`nii_load_img`	1.61 ±0.03	1.59 ±0.02	-1.3% (noise)	0.273
`nii_volumes`	0.33 ±0.02	0.33 ±0.01	+1.2% (noise)	0.329
`nii_rescale_seg`	0.86 ±0.03	0.87 ±0.02	+1.1% (noise)	0.568
`nii_set_dtype`	0.46 ±0.01	0.47 ±0.01	+1.0% (noise)	0.598
`poi_resample_from_to`	0.82 ±0.01	0.82 ±0.03	-0.8% (noise)	0.647
`nii_apply_crop`	0.77 ±0.01	0.77 ±0.02	+0.2% (noise)	0.533
`poi_calc_centroids`	1.04 ±0.02	1.04 ±0.11	+0.2% (noise)	0.618

`mri_3d` — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_load_seg`	3.16 ±0.02	2.85 ±0.15	-9.6%	0.018
`nii_save`	9.94 ±0.07	9.56 ±0.11	-3.9%	0.000
`poi_calc_centroids`	3.04 ±0.02	2.97 ±0.03	-2.3%	0.001
`nii_resample_from_to`	40.38 ±1.35	39.52 ±0.29	-2.1%	0.069
`poi_calc_poi_from_subreg_vert`	11.45 ±0.06	11.23 ±0.06	-1.9%	0.000

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_fill_holes`	6.03 ±0.04	5.97 ±0.03	-1.0%	0.024
`nii_rescale`	38.51 ±0.14	38.23 ±0.21	-0.7%	0.012
`nii_rescale_seg`	3.21 ±0.05	3.19 ±0.04	-0.6%	0.223
`nii_dilate_msk`	155.64 ±0.79	154.78 ±0.17	-0.6%	0.110
`poi_calc_centroids_nocrop`	9.96 ±0.04	9.91 ±0.08	-0.6%	0.350
`nii_load_img`	9.79 ±0.13	9.74 ±0.10	-0.5%	0.643
`nii_filter_connected_components`	4.74 ±0.06	4.71 ±0.06	-0.5%	0.143
`nii_erode_msk`	8.46 ±0.07	8.44 ±0.08	-0.2%	0.771
`metric_voxels`	236912.00 ±0.00	236912.00 ±0.00	+0.0%	—
`metric_labels`	8.00 ±0.00	8.00 ±0.00	+0.0%	—
`metric_foreground_pct`	18.21 ±0.00	18.21 ±0.00	+0.0%	—
`nii_get_array`	0.06 ±0.00	0.04 ±0.00	-24.5% (noise)	0.000
`nii_pad_to`	0.85 ±0.01	0.76 ±0.01	-10.8% (noise)	0.000
`nii_extract_label`	0.89 ±0.01	0.81 ±0.02	-8.2% (noise)	0.000
`nii_apply_crop`	0.84 ±0.02	0.78 ±0.04	-7.1% (noise)	0.017
`poi_local_to_global_arr`	0.31 ±0.01	0.33 ±0.02	+7.1% (noise)	0.036
`nii_compute_crop`	0.38 ±0.00	0.36 ±0.00	-6.6% (noise)	0.000
`poi_rescale`	0.34 ±0.01	0.32 ±0.01	-5.6% (noise)	0.045
`nii_map_labels`	1.03 ±0.01	0.98 ±0.03	-5.1% (noise)	0.015
`nii_unique`	0.67 ±0.01	0.65 ±0.01	-4.2% (noise)	0.011
`poi_load`	0.39 ±0.01	0.38 ±0.02	-3.6% (noise)	0.169
`poi_map_labels`	0.28 ±0.01	0.27 ±0.00	-3.5% (noise)	0.006
`nii_volumes`	2.10 ±0.01	2.04 ±0.01	-3.1% (noise)	0.000
`nii_reorient`	1.01 ±0.01	0.98 ±0.03	-2.9% (noise)	0.049
`poi_resample_from_to`	0.85 ±0.04	0.82 ±0.02	-2.8% (noise)	0.148
`nii_center_of_masses`	2.15 ±0.02	2.09 ±0.04	-2.7% (noise)	0.046
`nii_set_dtype`	0.59 ±0.01	0.58 ±0.02	-2.3% (noise)	0.434
`poi_reorient`	0.55 ±0.01	0.53 ±0.00	-2.2% (noise)	0.006
`nii_get_connected_components`	2.19 ±0.02	2.17 ±0.04	-1.2% (noise)	0.086
`poi_to_global`	0.33 ±0.01	0.33 ±0.02	+0.4% (noise)	0.525
`poi_save`	0.65 ±0.01	0.64 ±0.02	-0.4% (noise)	0.649

`mri_2d` — shape (68, 52, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_resample_from_to`	7.82 ±0.13	7.56 ±0.07	-3.3%	0.006
`nii_rescale`	5.89 ±0.08	5.81 ±0.07	-1.4%	0.026
`nii_dilate_msk`	18.50 ±0.13	18.29 ±0.04	-1.1%	0.079
`metric_voxels`	3536.00 ±0.00	3536.00 ±0.00	+0.0%	—
`metric_labels`	7.00 ±0.00	7.00 ±0.00	+0.0%	—

… 30 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`metric_foreground_pct`	50.17 ±0.00	50.17 ±0.00	+0.0%	—
`nii_unique`	0.17 ±0.01	0.15 ±0.01	-11.3% (noise)	0.025
`nii_apply_crop`	0.81 ±0.02	0.73 ±0.03	-9.2% (noise)	0.002
`nii_compute_crop`	0.18 ±0.01	0.17 ±0.01	-7.1% (noise)	0.076
`poi_save`	0.64 ±0.02	0.60 ±0.03	-6.4% (noise)	0.289
`nii_load_img`	1.63 ±0.04	1.54 ±0.03	-5.6% (noise)	0.002
`poi_local_to_global_arr`	0.32 ±0.01	0.30 ±0.01	-5.3% (noise)	0.167
`poi_reorient`	0.50 ±0.01	0.53 ±0.01	+5.1% (noise)	0.001
`nii_pad_to`	0.66 ±0.01	0.63 ±0.03	-5.0% (noise)	0.204
`poi_load`	0.39 ±0.02	0.38 ±0.02	-4.3% (noise)	0.247
`poi_calc_centroids`	1.15 ±0.04	1.19 ±0.02	+4.3% (noise)	0.188
`nii_extract_label`	0.48 ±0.01	0.50 ±0.02	+4.3% (noise)	0.273
`nii_rescale_seg`	0.88 ±0.03	0.85 ±0.02	-4.0% (noise)	0.021
`nii_erode_msk`	1.33 ±0.05	1.29 ±0.02	-3.4% (noise)	0.043
`nii_get_connected_components`	0.74 ±0.02	0.72 ±0.02	-3.3% (noise)	0.066
`nii_fill_holes`	1.16 ±0.02	1.12 ±0.01	-3.0% (noise)	0.032
`nii_load_seg`	1.79 ±0.05	1.74 ±0.03	-2.8% (noise)	0.071
`nii_map_labels`	0.54 ±0.02	0.53 ±0.01	-2.6% (noise)	0.125
`poi_map_labels`	0.27 ±0.01	0.27 ±0.01	-2.3% (noise)	0.241
`nii_set_dtype`	0.47 ±0.01	0.47 ±0.01	-1.5% (noise)	0.087
`poi_resample_from_to`	0.84 ±0.01	0.83 ±0.02	-1.4% (noise)	0.076
`nii_reorient`	0.91 ±0.01	0.92 ±0.03	+1.3% (noise)	0.675
`nii_volumes`	0.49 ±0.01	0.50 ±0.02	+1.2% (noise)	0.268
`nii_center_of_masses`	0.43 ±0.01	0.43 ±0.01	-0.7% (noise)	0.928
`poi_calc_centroids_nocrop`	1.44 ±0.03	1.43 ±0.02	-0.6% (noise)	0.510
`nii_filter_connected_components`	0.92 ±0.02	0.93 ±0.02	+0.5% (noise)	0.349
`poi_to_global`	0.32 ±0.02	0.31 ±0.02	-0.4% (noise)	0.934
`nii_save`	1.53 ±0.03	1.53 ±0.06	-0.4% (noise)	0.872
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	-0.1% (noise)	0.790
`poi_rescale`	0.32 ±0.01	0.32 ±0.01	+0.1% (noise)	0.671

Gate: a measurement fails when the baseline is ≥ 1 ms, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

Memory (peak RSS growth per call)

baseline d8fef9f vs head d8fef9f · python 3.11.15 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.90 MiB

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 MiB are tagged (noise) — runner jitter on those swamps any real change.

`ct_3d` — shape (73, 47, 73)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.21 ±0.00	5.27 ±0.00	+1.1%	—
`nii_dilate_msk`	5.87 ±0.00	5.93 ±0.00	+1.1%	—
`nii_set_dtype`	5.22 ±0.00	5.27 ±0.00	+1.0%	—
`nii_pad_to`	5.40 ±0.00	5.46 ±0.00	+1.0%	—
`nii_extract_label`	5.41 ±0.00	5.46 ±0.00	+1.0%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_map_labels`	5.47 ±0.00	5.52 ±0.00	+1.0%	—
`nii_erode_msk`	5.95 ±0.00	6.01 ±0.00	+1.0%	—
`nii_reorient`	5.84 ±0.00	5.90 ±0.00	+0.9%	—
`nii_apply_crop`	5.84 ±0.00	5.90 ±0.00	+0.9%	—
`poi_calc_centroids_nocrop`	5.90 ±0.00	5.96 ±0.00	+0.9%	—
`nii_load_seg`	5.95 ±0.00	6.00 ±0.00	+0.9%	—
`poi_calc_centroids`	6.03 ±0.00	6.09 ±0.00	+0.9%	—
`nii_rescale`	6.11 ±0.00	6.16 ±0.00	+0.8%	0.000
`nii_get_connected_components`	6.59 ±0.00	6.65 ±0.00	+0.8%	—
`poi_calc_poi_from_subreg_vert`	7.09 ±0.00	7.15 ±0.00	+0.8%	—
`nii_fill_holes`	6.39 ±0.00	6.44 ±0.00	+0.8%	—
`nii_filter_connected_components`	6.91 ±0.00	6.96 ±0.00	+0.8%	—
`nii_rescale_seg`	5.92 ±0.00	5.97 ±0.00	+0.8%	—
`nii_resample_from_to`	6.23 ±0.00	6.28 ±0.00	+0.8%	0.000
`poi_to_global`	3.09 ±0.00	3.08 ±0.00	-0.1%	—
`nii_unique`	3.15 ±0.00	3.15 ±0.00	-0.1%	—
`nii_center_of_masses`	3.28 ±0.00	3.27 ±0.00	-0.1%	—
`nii_volumes`	3.53 ±0.00	3.52 ±0.00	-0.1%	—
`nii_save`	3.71 ±0.00	3.71 ±0.00	-0.1%	—
`poi_reorient`	3.84 ±0.00	3.83 ±0.00	-0.1%	—
`nii_load_img`	3.53 ±0.00	3.53 ±0.00	+0.0%	0.178
`metric_voxels`	250463.00 ±0.00	250463.00 ±0.00	+0.0%	—
`metric_labels`	3.00 ±0.00	3.00 ±0.00	+0.0%	—
`metric_foreground_pct`	14.51 ±0.00	14.51 ±0.00	+0.0%	—
`nii_get_array`	1.65 ±0.00	1.65 ±0.00	-0.2% (noise)	—
`poi_rescale`	2.61 ±0.00	2.61 ±0.00	-0.1% (noise)	—
`nii_compute_crop`	2.90 ±0.00	2.90 ±0.00	-0.1% (noise)	—
`poi_local_to_global_arr`	2.96 ±0.00	2.96 ±0.00	-0.1% (noise)	—
`poi_save`	1.40 ±0.00	1.40 ±0.00	+0.0% (noise)	—
`poi_map_labels`	1.77 ±0.00	1.77 ±0.00	+0.0% (noise)	—
`poi_load`	1.68 ±0.00	1.68 ±0.00	+0.0% (noise)	—

`ct_2d` — shape (73, 47, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.15 ±0.00	5.21 ±0.00	+1.1%	—
`nii_set_dtype`	5.15 ±0.00	5.21 ±0.00	+1.1%	—
`nii_pad_to`	5.34 ±0.00	5.39 ±0.00	+1.1%	—
`nii_extract_label`	5.34 ±0.00	5.40 ±0.00	+1.1%	—
`nii_map_labels`	5.40 ±0.00	5.46 ±0.00	+1.1%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_dilate_msk`	5.80 ±0.00	5.87 ±0.00	+1.1%	—
`nii_erode_msk`	5.88 ±0.00	5.95 ±0.00	+1.1%	—
`nii_reorient`	5.78 ±0.00	5.84 ±0.00	+1.0%	—
`nii_apply_crop`	5.78 ±0.00	5.84 ±0.00	+1.0%	—
`nii_load_seg`	5.88 ±0.00	5.94 ±0.00	+1.0%	—
`poi_calc_centroids_nocrop`	5.90 ±0.00	5.96 ±0.00	+1.0%	—
`poi_calc_centroids`	5.96 ±0.00	6.02 ±0.00	+1.0%	—
`nii_get_connected_components`	6.53 ±0.00	6.59 ±0.00	+0.9%	—
`nii_rescale_seg`	5.86 ±0.00	5.91 ±0.00	+0.9%	—
`nii_fill_holes`	6.32 ±0.00	6.38 ±0.00	+0.9%	—
`nii_filter_connected_components`	6.84 ±0.00	6.90 ±0.00	+0.9%	—
`nii_rescale`	6.04 ±0.00	6.09 ±0.00	+0.8%	—
`nii_resample_from_to`	6.17 ±0.00	6.22 ±0.00	+0.8%	—
`nii_load_img`	3.46 ±0.00	3.46 ±0.00	+0.0%	—
`nii_save`	3.65 ±0.00	3.65 ±0.00	+0.0%	—
`nii_unique`	3.09 ±0.00	3.09 ±0.00	+0.0%	—
`nii_volumes`	3.46 ±0.00	3.46 ±0.00	+0.0%	—
`nii_center_of_masses`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`poi_reorient`	3.77 ±0.00	3.77 ±0.00	+0.0%	—
`poi_to_global`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`metric_voxels`	3431.00 ±0.00	3431.00 ±0.00	+0.0%	—
`metric_labels`	3.00 ±0.00	3.00 ±0.00	+0.0%	—
`metric_foreground_pct`	37.60 ±0.00	37.60 ±0.00	+0.0%	—
`nii_get_array`	1.59 ±0.00	1.59 ±0.00	+0.0% (noise)	—
`nii_compute_crop`	2.84 ±0.00	2.84 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.54 ±0.00	2.54 ±0.00	+0.0% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.89 ±0.00	+0.0% (noise)	—
`poi_save`	1.34 ±0.00	1.34 ±0.00	+0.0% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
`poi_load`	1.61 ±0.00	1.61 ±0.00	+0.0% (noise)	—

`mri_3d` — shape (68, 52, 67)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.15 ±0.00	5.21 ±0.00	+1.1%	—
`nii_set_dtype`	5.21 ±0.00	5.27 ±0.00	+1.1%	—
`nii_pad_to`	5.34 ±0.00	5.39 ±0.00	+1.1%	—
`nii_extract_label`	5.34 ±0.00	5.40 ±0.00	+1.1%	—
`nii_map_labels`	5.40 ±0.00	5.46 ±0.00	+1.1%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_dilate_msk`	5.80 ±0.00	5.87 ±0.00	+1.1%	—
`nii_erode_msk`	5.88 ±0.00	5.95 ±0.00	+1.1%	—
`nii_reorient`	5.78 ±0.00	5.84 ±0.00	+1.0%	—
`nii_apply_crop`	5.78 ±0.00	5.84 ±0.00	+1.0%	—
`poi_calc_centroids_nocrop`	5.84 ±0.00	5.89 ±0.00	+1.0%	—
`nii_load_seg`	5.88 ±0.00	5.94 ±0.00	+1.0%	—
`poi_calc_centroids`	5.96 ±0.00	6.02 ±0.00	+1.0%	—
`nii_get_connected_components`	6.53 ±0.00	6.59 ±0.00	+0.9%	—
`nii_rescale_seg`	5.86 ±0.00	5.91 ±0.00	+0.9%	—
`nii_fill_holes`	6.32 ±0.00	6.38 ±0.00	+0.9%	—
`nii_filter_connected_components`	6.84 ±0.00	6.90 ±0.00	+0.9%	—
`nii_rescale`	6.04 ±0.00	6.09 ±0.00	+0.8%	—
`poi_calc_poi_from_subreg_vert`	7.09 ±0.00	7.14 ±0.00	+0.8%	—
`nii_resample_from_to`	6.17 ±0.00	6.22 ±0.00	+0.8%	—
`nii_load_img`	3.53 ±0.00	3.53 ±0.00	+0.0%	—
`nii_save`	3.65 ±0.00	3.65 ±0.00	+0.0%	—
`nii_unique`	3.09 ±0.00	3.09 ±0.00	+0.0%	—
`nii_volumes`	3.46 ±0.00	3.46 ±0.00	+0.0%	—
`nii_center_of_masses`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`poi_reorient`	3.77 ±0.00	3.77 ±0.00	+0.0%	—
`poi_to_global`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`metric_voxels`	236912.00 ±0.00	236912.00 ±0.00	+0.0%	—
`metric_labels`	8.00 ±0.00	8.00 ±0.00	+0.0%	—
`metric_foreground_pct`	18.21 ±0.00	18.21 ±0.00	+0.0%	—
`nii_get_array`	1.59 ±0.00	1.59 ±0.00	+0.0% (noise)	—
`nii_compute_crop`	2.84 ±0.00	2.84 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.54 ±0.00	2.54 ±0.00	+0.0% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.89 ±0.00	+0.0% (noise)	—
`poi_save`	1.40 ±0.00	1.40 ±0.00	+0.0% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
`poi_load`	1.61 ±0.00	1.61 ±0.00	+0.0% (noise)	—

`mri_2d` — shape (68, 52, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`poi_resample_from_to`	5.15 ±0.00	5.21 ±0.00	+1.1%	—
`nii_set_dtype`	5.21 ±0.00	5.27 ±0.00	+1.1%	—
`nii_pad_to`	5.34 ±0.00	5.39 ±0.00	+1.1%	—
`nii_extract_label`	5.34 ±0.00	5.40 ±0.00	+1.1%	—
`nii_map_labels`	5.40 ±0.00	5.46 ±0.00	+1.1%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_dilate_msk`	5.80 ±0.00	5.87 ±0.00	+1.1%	—
`nii_erode_msk`	5.88 ±0.00	5.95 ±0.00	+1.1%	—
`nii_reorient`	5.78 ±0.00	5.84 ±0.00	+1.0%	—
`nii_apply_crop`	5.78 ±0.00	5.84 ±0.00	+1.0%	—
`nii_load_seg`	5.88 ±0.00	5.94 ±0.00	+1.0%	—
`poi_calc_centroids_nocrop`	5.90 ±0.00	5.96 ±0.00	+1.0%	—
`poi_calc_centroids`	5.96 ±0.00	6.02 ±0.00	+1.0%	—
`nii_get_connected_components`	6.53 ±0.00	6.59 ±0.00	+0.9%	—
`nii_rescale_seg`	5.86 ±0.00	5.91 ±0.00	+0.9%	—
`nii_fill_holes`	6.32 ±0.00	6.38 ±0.00	+0.9%	—
`nii_filter_connected_components`	6.84 ±0.00	6.90 ±0.00	+0.9%	—
`nii_rescale`	6.04 ±0.00	6.09 ±0.00	+0.8%	—
`nii_resample_from_to`	6.17 ±0.00	6.22 ±0.00	+0.8%	—
`nii_load_img`	3.53 ±0.00	3.53 ±0.00	+0.0%	—
`nii_save`	3.65 ±0.00	3.65 ±0.00	+0.0%	—
`nii_unique`	3.09 ±0.00	3.09 ±0.00	+0.0%	—
`nii_volumes`	3.46 ±0.00	3.46 ±0.00	+0.0%	—
`nii_center_of_masses`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`poi_reorient`	3.77 ±0.00	3.77 ±0.00	+0.0%	—
`poi_to_global`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`metric_voxels`	3536.00 ±0.00	3536.00 ±0.00	+0.0%	—
`metric_labels`	7.00 ±0.00	7.00 ±0.00	+0.0%	—
`metric_foreground_pct`	50.17 ±0.00	50.17 ±0.00	+0.0%	—
`nii_get_array`	1.59 ±0.00	1.59 ±0.00	+0.0% (noise)	—
`nii_compute_crop`	2.84 ±0.00	2.84 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.54 ±0.00	2.54 ±0.00	+0.0% (noise)	—
`poi_local_to_global_arr`	2.89 ±0.00	2.89 ±0.00	+0.0% (noise)	—
`poi_save`	1.40 ±0.00	1.40 ±0.00	+0.0% (noise)	—
`poi_map_labels`	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
`poi_load`	1.61 ±0.00	1.61 ±0.00	+0.0% (noise)	—

Gate: a measurement fails when the baseline is ≥ 1 MiB, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

Comment now shows the 5 most-changed measurements per case and folds the rest into a <details> block; rows whose baseline is below 3 ms / 3 MiB are tagged (noise) so shared-runner jitter is not mistaken for a real change. CI runs only the real CT/MRI cases with 5 repeats, dropping the synthetic 400^3/256^3 workloads that dominated wall time. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

added speed and memory benchmark, and github workflow

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Copilot AI lite review requested due to automatic review settings August 13, 2026 10:56

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Hendrik-code added the speed/mem Changes that improve speed/memory of code execution label Aug 13, 2026

Hendrik-code linked an issue Aug 13, 2026 that may be closed by this pull request

Speed+Memory Benchmark upon PR #127

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Hendrik-code merged commit 393ee15 into main Aug 13, 2026
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Hendrik-code deleted the pr_benchmark branch August 13, 2026 11:50

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added speed and memory benchmark, and github workflow - #128

added speed and memory benchmark, and github workflow#128
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Benchmark comparison

Speed (wall time per call)

ct_3d — shape (73, 47, 73)

ct_2d — shape (73, 47, 1)

mri_3d — shape (68, 52, 67)

mri_2d — shape (68, 52, 1)

Memory (peak RSS growth per call)

ct_3d — shape (73, 47, 73)

ct_2d — shape (73, 47, 1)

mri_3d — shape (68, 52, 67)

mri_2d — shape (68, 52, 1)

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github-actions Bot commented Aug 13, 2026 •

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`ct_3d` — shape (73, 47, 73)

`ct_2d` — shape (73, 47, 1)

`mri_3d` — shape (68, 52, 67)

`mri_2d` — shape (68, 52, 1)

`ct_3d` — shape (73, 47, 73)

`ct_2d` — shape (73, 47, 1)

`mri_3d` — shape (68, 52, 67)

`mri_2d` — shape (68, 52, 1)