extended dixon mapping by robert-graf · Pull Request #155 · Hendrik-code/TPTBox

robert-graf · 2026-09-22T11:13:10Z

Cherry-picked content from tanja@50c8b4d without the whitespace-only reformatting noise:

Add h2d/tse2d1-4/tser2d regex to series-description → format mapping; drop the broad ".t2w?_tse." match.
Fall back to SequenceName when SeriesDescription is empty.

Cherry-picked content from tanja@50c8b4d without the whitespace-only reformatting noise: - Add h2d/tse2d1-4/tser2d regex to series-description → format mapping; drop the broad ".*t2w?_tse.*" match. - Fall back to SequenceName when SeriesDescription is empty. Co-Authored-By: Tanja Lerchl <tanja.lerchl@tum.de> Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

github-actions · 2026-09-22T11:20:31Z

Benchmark comparison

Speed (wall time per call)

baseline 33f8b5a vs head 33f8b5a · python 3.11.16 · 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_filter_connected_components`	4.16 ±0.20	5.33 ±0.56	+28.2%	0.008
`nii_fill_holes`	4.37 ±0.03	4.69 ±0.06	+7.3%	0.000
`poi_calc_centroids_nocrop`	4.16 ±0.05	4.36 ±0.04	+4.7%	0.000
`nii_erode_msk`	6.13 ±0.04	6.37 ±0.06	+4.0%	0.000
`nii_rescale_seg`	3.25 ±0.03	3.14 ±0.02	-3.1%	0.001

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`poi_calc_poi_from_subreg_vert`	12.61 ±0.20	12.90 ±0.11	+2.4%	0.167
`nii_resample_from_to`	42.36 ±0.99	41.78 ±1.54	-1.4%	0.883
`nii_load_img`	10.78 ±0.21	10.65 ±0.03	-1.2%	0.233
`nii_save`	11.79 ±0.06	11.89 ±0.10	+0.9%	0.067
`nii_dilate_msk`	124.83 ±0.61	125.83 ±0.62	+0.8%	0.017
`nii_rescale`	39.30 ±0.24	39.58 ±0.11	+0.7%	0.058
`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_reorient`	0.31 ±0.01	0.43 ±0.02	+38.9% (noise)	0.000
`poi_rescale`	0.17 ±0.02	0.23 ±0.01	+38.8% (noise)	0.001
`poi_map_labels`	0.13 ±0.01	0.18 ±0.01	+34.6% (noise)	0.000
`poi_to_global`	0.16 ±0.02	0.20 ±0.01	+29.9% (noise)	0.003
`poi_save`	0.38 ±0.01	0.49 ±0.02	+27.5% (noise)	0.000
`poi_resample_from_to`	0.58 ±0.03	0.71 ±0.02	+23.7% (noise)	0.000
`nii_get_array`	0.04 ±0.00	0.05 ±0.00	+22.6% (noise)	0.000
`nii_center_of_masses`	2.05 ±0.02	1.76 ±0.01	-14.4% (noise)	0.000
`nii_volumes`	2.14 ±0.03	1.89 ±0.02	-11.6% (noise)	0.000
`poi_load`	0.90 ±0.01	0.99 ±0.01	+10.6% (noise)	0.000
`nii_get_connected_components`	2.08 ±0.03	2.30 ±0.04	+10.6% (noise)	0.000
`nii_pad_to`	0.73 ±0.03	0.66 ±0.07	-10.0% (noise)	0.232
`poi_local_to_global_arr`	0.30 ±0.02	0.33 ±0.01	+9.6% (noise)	0.007
`nii_extract_label`	0.47 ±0.03	0.44 ±0.02	-5.9% (noise)	0.054
`nii_reorient`	0.83 ±0.04	0.79 ±0.04	-5.2% (noise)	0.506
`nii_set_dtype`	0.44 ±0.02	0.46 ±0.05	+4.0% (noise)	0.154
`nii_apply_crop`	0.73 ±0.04	0.70 ±0.06	-3.9% (noise)	0.957
`nii_map_labels`	1.07 ±0.03	1.05 ±0.01	-2.5% (noise)	0.016
`nii_unique`	0.70 ±0.02	0.68 ±0.02	-2.3% (noise)	0.042
`nii_compute_crop`	0.34 ±0.01	0.34 ±0.02	+0.5% (noise)	0.396
`poi_calc_centroids`	2.61 ±0.10	2.60 ±0.04	-0.3% (noise)	0.142
`nii_load_seg`	2.69 ±0.06	2.70 ±0.08	+0.2% (noise)	0.705

`ct_2d` — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_resample_from_to`	7.45 ±0.07	8.32 ±0.75	+11.7%	0.060
`nii_rescale`	5.26 ±0.02	5.40 ±0.08	+2.6%	0.009
`nii_dilate_msk`	14.48 ±0.08	14.81 ±0.11	+2.3%	0.000
`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%	—
`poi_to_global`	0.21 ±0.01	0.25 ±0.02	+18.4% (noise)	0.004
`nii_extract_label`	0.40 ±0.03	0.46 ±0.02	+15.2% (noise)	0.044
`poi_map_labels`	0.18 ±0.01	0.20 ±0.00	+12.3% (noise)	0.000
`nii_pad_to`	0.53 ±0.03	0.59 ±0.01	+12.1% (noise)	0.002
`nii_center_of_masses`	0.19 ±0.01	0.22 ±0.01	+11.0% (noise)	0.032
`nii_apply_crop`	0.65 ±0.02	0.72 ±0.01	+10.5% (noise)	0.002
`nii_get_connected_components`	0.61 ±0.04	0.68 ±0.02	+10.4% (noise)	0.050
`poi_load`	0.96 ±0.02	1.06 ±0.02	+10.2% (noise)	0.000
`nii_fill_holes`	0.83 ±0.04	0.90 ±0.03	+9.0% (noise)	0.049
`poi_save`	0.47 ±0.22	0.51 ±0.02	+9.0% (noise)	0.409
`nii_compute_crop`	0.14 ±0.01	0.15 ±0.01	+8.6% (noise)	0.011
`nii_save`	1.32 ±0.03	1.42 ±0.03	+7.1% (noise)	0.002
`nii_rescale_seg`	0.73 ±0.02	0.79 ±0.02	+7.1% (noise)	0.002
`nii_erode_msk`	0.95 ±0.03	1.01 ±0.01	+6.7% (noise)	0.003
`poi_calc_centroids_nocrop`	1.10 ±0.01	1.17 ±0.01	+6.3% (noise)	0.000
`nii_volumes`	0.27 ±0.01	0.29 ±0.02	+6.1% (noise)	0.042
`nii_map_labels`	0.47 ±0.01	0.50 ±0.01	+6.0% (noise)	0.005
`poi_calc_centroids`	0.91 ±0.04	0.97 ±0.02	+6.0% (noise)	0.007
`nii_filter_connected_components`	0.81 ±0.02	0.86 ±0.01	+5.6% (noise)	0.002
`poi_resample_from_to`	0.72 ±0.04	0.76 ±0.03	+5.6% (noise)	0.012
`nii_load_img`	1.50 ±0.06	1.58 ±0.06	+5.5% (noise)	0.063
`nii_load_seg`	1.70 ±0.07	1.79 ±0.03	+5.2% (noise)	0.063
`poi_rescale`	0.24 ±0.01	0.25 ±0.01	+4.5% (noise)	0.045
`nii_unique`	0.12 ±0.01	0.12 ±0.00	+4.3% (noise)	0.054
`poi_local_to_global_arr`	0.32 ±0.02	0.33 ±0.01	+4.0% (noise)	0.173
`poi_reorient`	0.42 ±0.01	0.44 ±0.01	+3.8% (noise)	0.018
`nii_set_dtype`	0.40 ±0.02	0.41 ±0.01	+3.7% (noise)	0.411
`nii_reorient`	0.81 ±0.02	0.84 ±0.02	+3.3% (noise)	0.088
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	-0.3% (noise)	0.440

`mri_3d` — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`poi_calc_centroids_nocrop`	8.67 ±0.15	9.24 ±0.06	+6.7%	0.000
`nii_filter_connected_components`	4.68 ±0.04	4.84 ±0.09	+3.4%	0.018
`nii_load_img`	8.56 ±0.41	8.84 ±0.02	+3.2%	0.853
`nii_save`	9.29 ±0.09	9.59 ±0.12	+3.2%	0.003
`nii_resample_from_to`	39.45 ±3.64	40.61 ±0.72	+2.9%	0.745

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_fill_holes`	5.42 ±0.01	5.48 ±0.09	+1.2%	0.201
`nii_erode_msk`	7.71 ±0.10	7.77 ±0.06	+0.8%	0.066
`nii_rescale`	37.58 ±0.61	37.78 ±0.35	+0.5%	0.521
`nii_dilate_msk`	162.33 ±0.82	161.55 ±0.49	-0.5%	0.088
`nii_rescale_seg`	3.06 ±0.05	3.07 ±0.07	+0.4%	0.637
`poi_calc_poi_from_subreg_vert`	11.96 ±0.39	11.92 ±0.15	-0.3%	0.199
`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`	0.05 ±0.00	0.06 ±0.00	+24.3% (noise)	0.001
`poi_rescale`	0.25 ±0.02	0.29 ±0.01	+13.5% (noise)	0.012
`poi_to_global`	0.25 ±0.01	0.28 ±0.01	+10.5% (noise)	0.002
`poi_local_to_global_arr`	0.31 ±0.01	0.34 ±0.01	+10.1% (noise)	0.002
`nii_reorient`	0.83 ±0.02	0.90 ±0.04	+8.4% (noise)	0.018
`nii_load_seg`	2.72 ±0.03	2.95 ±0.02	+8.4% (noise)	0.000
`poi_save`	0.53 ±0.02	0.57 ±0.02	+8.3% (noise)	0.021
`nii_compute_crop`	0.32 ±0.01	0.34 ±0.02	+8.0% (noise)	0.035
`nii_extract_label`	0.45 ±0.02	0.48 ±0.03	+5.8% (noise)	0.198
`poi_map_labels`	0.24 ±0.01	0.23 ±0.00	-4.2% (noise)	0.019
`nii_apply_crop`	0.71 ±0.02	0.74 ±0.04	+3.8% (noise)	0.299
`nii_set_dtype`	0.51 ±0.01	0.53 ±0.03	+3.8% (noise)	0.109
`poi_load`	2.21 ±0.06	2.29 ±0.10	+3.8% (noise)	0.399
`nii_pad_to`	0.72 ±0.02	0.75 ±0.02	+3.7% (noise)	0.021
`nii_center_of_masses`	1.96 ±0.01	2.03 ±0.02	+3.5% (noise)	0.000
`nii_map_labels`	1.00 ±0.03	1.03 ±0.01	+2.8% (noise)	0.129
`nii_get_connected_components`	2.23 ±0.04	2.28 ±0.06	+2.5% (noise)	0.165
`poi_resample_from_to`	0.81 ±0.04	0.79 ±0.02	-2.5% (noise)	0.839
`nii_volumes`	1.93 ±0.01	1.97 ±0.02	+2.3% (noise)	0.003
`nii_unique`	0.68 ±0.06	0.67 ±0.01	-1.9% (noise)	0.336
`poi_reorient`	0.46 ±0.02	0.47 ±0.01	+0.8% (noise)	0.763
`poi_calc_centroids`	2.76 ±0.10	2.78 ±0.01	+0.7% (noise)	0.482

`mri_2d` — shape (68, 52, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_resample_from_to`	7.38 ±0.04	7.56 ±0.10	+2.4%	0.010
`nii_rescale`	5.38 ±0.14	5.29 ±0.05	-1.6%	0.886
`nii_dilate_msk`	19.53 ±0.10	19.53 ±0.09	+0.0%	0.571
`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%	—
`poi_map_labels`	0.21 ±0.01	0.24 ±0.01	+11.3% (noise)	0.042
`poi_local_to_global_arr`	0.30 ±0.01	0.33 ±0.02	+10.5% (noise)	0.007
`nii_set_dtype`	0.38 ±0.02	0.42 ±0.01	+10.4% (noise)	0.080
`poi_resample_from_to`	0.70 ±0.03	0.76 ±0.03	+9.3% (noise)	0.036
`nii_extract_label`	0.38 ±0.01	0.41 ±0.01	+8.4% (noise)	0.002
`poi_load`	1.90 ±0.04	2.06 ±0.14	+8.2% (noise)	0.043
`poi_save`	0.49 ±0.03	0.52 ±0.03	+8.0% (noise)	0.291
`nii_volumes`	0.43 ±0.02	0.46 ±0.02	+7.3% (noise)	0.019
`nii_map_labels`	0.46 ±0.02	0.49 ±0.01	+6.9% (noise)	0.008
`poi_to_global`	0.25 ±0.02	0.27 ±0.01	+6.6% (noise)	0.098
`nii_get_connected_components`	0.62 ±0.03	0.66 ±0.02	+5.9% (noise)	0.077
`nii_compute_crop`	0.14 ±0.00	0.14 ±0.01	+5.8% (noise)	0.107
`nii_fill_holes`	1.10 ±0.02	1.16 ±0.10	+5.7% (noise)	0.068
`poi_rescale`	0.27 ±0.02	0.28 ±0.01	+5.4% (noise)	0.566
`poi_reorient`	0.47 ±0.02	0.49 ±0.01	+5.2% (noise)	0.016
`nii_unique`	0.12 ±0.02	0.12 ±0.00	-4.6% (noise)	0.520
`nii_filter_connected_components`	0.85 ±0.02	0.89 ±0.03	+4.2% (noise)	0.378
`poi_calc_centroids_nocrop`	1.45 ±0.03	1.50 ±0.03	+3.6% (noise)	0.012
`nii_reorient`	0.84 ±0.02	0.82 ±0.03	-2.3% (noise)	0.518
`nii_center_of_masses`	0.40 ±0.02	0.40 ±0.01	+2.2% (noise)	0.178
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	-1.8% (noise)	0.572
`nii_rescale_seg`	0.76 ±0.01	0.77 ±0.05	+1.8% (noise)	0.808
`nii_erode_msk`	1.30 ±0.05	1.32 ±0.04	+1.5% (noise)	0.230
`poi_calc_centroids`	1.14 ±0.03	1.16 ±0.06	+1.5% (noise)	0.438
`nii_save`	1.32 ±0.01	1.33 ±0.03	+1.1% (noise)	0.780
`nii_apply_crop`	0.67 ±0.02	0.68 ±0.02	+1.0% (noise)	0.777
`nii_load_seg`	1.68 ±0.03	1.67 ±0.05	-0.6% (noise)	0.627
`nii_load_img`	1.49 ±0.03	1.49 ±0.03	-0.5% (noise)	0.436
`nii_pad_to`	0.53 ±0.03	0.53 ±0.03	+0.3% (noise)	0.998

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 33f8b5a vs head 33f8b5a · python 3.11.16 · 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
`nii_set_dtype`	5.21 ±0.00	5.23 ±0.00	+0.3%	—
`poi_resample_from_to`	5.25 ±0.00	5.26 ±0.00	+0.3%	—
`nii_extract_label`	5.34 ±0.00	5.35 ±0.00	+0.3%	—
`nii_pad_to`	5.39 ±0.00	5.41 ±0.00	+0.3%	—
`nii_map_labels`	5.46 ±0.00	5.48 ±0.00	+0.3%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_apply_crop`	5.83 ±0.00	5.85 ±0.00	+0.3%	—
`nii_reorient`	5.88 ±0.00	5.89 ±0.00	+0.3%	—
`poi_calc_centroids_nocrop`	5.89 ±0.00	5.91 ±0.00	+0.3%	—
`nii_dilate_msk`	5.90 ±0.00	5.91 ±0.00	+0.3%	—
`nii_erode_msk`	5.91 ±0.00	5.93 ±0.00	+0.3%	—
`nii_rescale_seg`	5.94 ±0.00	5.93 ±0.00	-0.3%	—
`nii_load_seg`	5.97 ±0.00	5.99 ±0.00	+0.3%	—
`poi_calc_centroids`	6.02 ±0.00	6.04 ±0.00	+0.3%	—
`nii_rescale`	6.17 ±0.00	6.15 ±0.00	-0.3%	—
`nii_resample_from_to`	6.29 ±0.00	6.28 ±0.00	-0.2%	—
`nii_get_connected_components`	6.59 ±0.00	6.60 ±0.00	+0.2%	—
`nii_filter_connected_components`	6.84 ±0.00	6.85 ±0.00	+0.2%	—
`poi_calc_poi_from_subreg_vert`	7.08 ±0.00	7.09 ±0.00	+0.2%	—
`nii_fill_holes`	6.25 ±0.00	6.27 ±0.00	+0.2%	—
`nii_load_img`	3.56 ±0.00	3.56 ±0.00	+0.0%	—
`nii_save`	3.71 ±0.00	3.71 ±0.00	+0.0%	—
`nii_volumes`	3.52 ±0.00	3.52 ±0.00	+0.0%	—
`nii_center_of_masses`	3.27 ±0.00	3.27 ±0.00	+0.0%	—
`poi_reorient`	3.83 ±0.00	3.83 ±0.00	+0.0%	—
`poi_to_global`	3.08 ±0.00	3.08 ±0.00	+0.0%	—
`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	+0.0% (noise)	—
`nii_compute_crop`	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
`nii_unique`	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.61 ±0.00	2.61 ±0.00	+0.0% (noise)	—
`poi_local_to_global_arr`	2.96 ±0.00	2.96 ±0.00	+0.0% (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`	1.61 ±0.00	1.61 ±0.00	+0.0% (noise)	—

`ct_2d` — shape (73, 47, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_set_dtype`	5.15 ±0.00	5.16 ±0.00	+0.3%	—
`poi_resample_from_to`	5.18 ±0.00	5.20 ±0.00	+0.3%	—
`nii_extract_label`	5.27 ±0.00	5.29 ±0.00	+0.3%	—
`nii_pad_to`	5.33 ±0.00	5.35 ±0.00	+0.3%	—
`nii_map_labels`	5.40 ±0.00	5.41 ±0.00	+0.3%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_apply_crop`	5.77 ±0.00	5.79 ±0.00	+0.3%	—
`nii_reorient`	5.81 ±0.00	5.83 ±0.00	+0.3%	—
`nii_dilate_msk`	5.84 ±0.03	5.85 ±0.00	+0.3%	0.088
`nii_erode_msk`	5.85 ±0.00	5.87 ±0.00	+0.3%	—
`nii_rescale_seg`	5.88 ±0.00	5.86 ±0.00	-0.3%	—
`poi_calc_centroids_nocrop`	5.89 ±0.00	5.91 ±0.00	+0.3%	—
`nii_load_seg`	5.91 ±0.00	5.93 ±0.00	+0.3%	—
`poi_calc_centroids`	5.96 ±0.00	5.98 ±0.00	+0.3%	—
`nii_rescale`	6.11 ±0.00	6.09 ±0.00	-0.3%	—
`nii_resample_from_to`	6.23 ±0.00	6.21 ±0.00	-0.3%	—
`nii_get_connected_components`	6.52 ±0.00	6.54 ±0.00	+0.2%	—
`nii_filter_connected_components`	6.77 ±0.00	6.79 ±0.00	+0.2%	—
`nii_fill_holes`	6.19 ±0.00	6.20 ±0.00	+0.2%	—
`nii_load_img`	3.50 ±0.00	3.50 ±0.00	+0.0%	—
`nii_save`	3.64 ±0.00	3.64 ±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)	—
`nii_unique`	2.90 ±0.00	2.90 ±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`	1.55 ±0.00	1.55 ±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`	5.18 ±0.00	5.20 ±0.00	+0.3%	—
`nii_set_dtype`	5.21 ±0.00	5.23 ±0.00	+0.3%	—
`nii_extract_label`	5.27 ±0.00	5.29 ±0.00	+0.3%	—
`nii_pad_to`	5.33 ±0.00	5.35 ±0.00	+0.3%	—
`nii_map_labels`	5.40 ±0.00	5.41 ±0.00	+0.3%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_apply_crop`	5.77 ±0.00	5.79 ±0.00	+0.3%	—
`nii_reorient`	5.81 ±0.00	5.83 ±0.00	+0.3%	—
`poi_calc_centroids_nocrop`	5.83 ±0.00	5.85 ±0.00	+0.3%	—
`nii_dilate_msk`	5.84 ±0.00	5.85 ±0.00	+0.3%	—
`nii_erode_msk`	5.85 ±0.00	5.87 ±0.00	+0.3%	—
`nii_rescale_seg`	5.88 ±0.00	5.86 ±0.00	-0.3%	—
`nii_load_seg`	5.91 ±0.00	5.93 ±0.00	+0.3%	—
`poi_calc_centroids`	5.96 ±0.00	5.98 ±0.00	+0.3%	—
`nii_rescale`	6.11 ±0.00	6.09 ±0.00	-0.3%	—
`nii_resample_from_to`	6.23 ±0.00	6.21 ±0.00	-0.3%	—
`nii_get_connected_components`	6.52 ±0.00	6.54 ±0.00	+0.2%	—
`nii_filter_connected_components`	6.77 ±0.00	6.79 ±0.00	+0.2%	—
`poi_calc_poi_from_subreg_vert`	7.08 ±0.00	7.09 ±0.00	+0.2%	—
`nii_fill_holes`	6.19 ±0.00	6.20 ±0.00	+0.2%	—
`nii_load_img`	3.56 ±0.00	3.56 ±0.00	+0.0%	—
`nii_save`	3.64 ±0.00	3.64 ±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)	—
`nii_unique`	2.90 ±0.00	2.90 ±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`	1.55 ±0.00	1.55 ±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`	5.18 ±0.00	5.20 ±0.00	+0.3%	—
`nii_set_dtype`	5.21 ±0.00	5.23 ±0.00	+0.3%	—
`nii_extract_label`	5.27 ±0.00	5.29 ±0.00	+0.3%	—
`nii_pad_to`	5.33 ±0.00	5.35 ±0.00	+0.3%	—
`nii_map_labels`	5.40 ±0.00	5.41 ±0.00	+0.3%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_apply_crop`	5.77 ±0.00	5.79 ±0.00	+0.3%	—
`nii_reorient`	5.81 ±0.00	5.83 ±0.00	+0.3%	—
`nii_dilate_msk`	5.84 ±0.00	5.85 ±0.00	+0.3%	—
`nii_erode_msk`	5.85 ±0.00	5.87 ±0.00	+0.3%	—
`nii_rescale_seg`	5.88 ±0.00	5.86 ±0.00	-0.3%	—
`poi_calc_centroids_nocrop`	5.89 ±0.00	5.91 ±0.00	+0.3%	—
`nii_load_seg`	5.91 ±0.00	5.93 ±0.00	+0.3%	—
`poi_calc_centroids`	5.96 ±0.00	5.98 ±0.00	+0.3%	—
`nii_rescale`	6.11 ±0.00	6.09 ±0.00	-0.3%	—
`nii_resample_from_to`	6.23 ±0.00	6.21 ±0.00	-0.3%	—
`nii_get_connected_components`	6.52 ±0.00	6.54 ±0.00	+0.2%	—
`nii_filter_connected_components`	6.77 ±0.00	6.79 ±0.00	+0.2%	—
`nii_fill_holes`	6.19 ±0.00	6.20 ±0.00	+0.2%	—
`nii_load_img`	3.56 ±0.00	3.56 ±0.00	+0.0%	—
`nii_save`	3.64 ±0.00	3.64 ±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)	—
`nii_unique`	2.90 ±0.00	2.90 ±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`	1.55 ±0.00	1.55 ±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.

robert-graf and others added 2 commits September 22, 2026 11:10

style fixes by ruff

2a51ed6

robert-graf assigned robert-graf and TanjaLe and unassigned robert-graf Sep 22, 2026

robert-graf requested a review from Hendrik-code September 22, 2026 11:15

Merge branch 'main' into tanja2

3ab419b

robert-graf mentioned this pull request Sep 25, 2026

Stitching refactor + RAM-saving overlap + c_val option + trivial-memory warning #157

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Merge branch 'main' into tanja2

e8c6775

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extended dixon mapping - #155

extended dixon mapping#155
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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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`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)