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 d44648d vs head d44648d · python 3.11.17 · 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_load_img`	10.90 ±0.17	11.22 ±0.19	+3.0%	0.016
`nii_rescale_seg`	3.11 ±0.03	3.17 ±0.07	+2.1%	0.086
`nii_filter_connected_components`	4.70 ±0.10	4.62 ±0.05	-1.7%	0.310
`nii_fill_holes`	4.98 ±0.13	5.02 ±0.18	+1.0%	0.306
`nii_resample_from_to`	47.57 ±0.57	48.01 ±0.39	+0.9%	0.471

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_dilate_msk`	117.10 ±0.35	118.05 ±0.49	+0.8%	0.011
`nii_erode_msk`	6.60 ±0.06	6.63 ±0.16	+0.5%	0.613
`poi_calc_poi_from_subreg_vert`	11.96 ±0.07	12.01 ±0.22	+0.4%	0.140
`poi_calc_centroids_nocrop`	5.97 ±0.09	5.98 ±0.17	+0.2%	0.495
`nii_save`	10.69 ±0.11	10.70 ±0.04	+0.0%	0.996
`nii_rescale`	45.95 ±0.94	45.95 ±3.05	+0.0%	0.262
`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_set_dtype`	0.54 ±0.03	1.43 ±0.06	+164.0% (noise)	0.000
`nii_get_array`	0.07 ±0.00	0.09 ±0.06	+33.3% (noise)	0.124
`poi_reorient`	0.38 ±0.01	0.34 ±0.02	-9.7% (noise)	0.006
`nii_apply_crop`	0.64 ±0.02	0.60 ±0.03	-6.6% (noise)	0.018
`poi_resample_from_to`	0.59 ±0.01	0.61 ±0.01	+4.5% (noise)	0.001
`nii_compute_crop`	0.39 ±0.02	0.37 ±0.04	-4.4% (noise)	0.718
`nii_map_labels`	1.12 ±0.02	1.17 ±0.02	+4.3% (noise)	0.005
`nii_pad_to`	0.70 ±0.05	0.68 ±0.02	-3.3% (noise)	0.187
`nii_reorient`	0.75 ±0.04	0.77 ±0.27	+3.0% (noise)	0.333
`poi_to_global`	0.21 ±0.01	0.20 ±0.01	-2.4% (noise)	0.489
`poi_local_to_global_arr`	0.38 ±0.01	0.39 ±0.03	+2.3% (noise)	0.947
`poi_save`	0.40 ±0.02	0.41 ±0.01	+2.3% (noise)	0.495
`poi_calc_centroids`	2.33 ±0.02	2.29 ±0.03	-1.5% (noise)	0.088
`poi_rescale`	0.20 ±0.02	0.20 ±0.01	-1.5% (noise)	0.686
`nii_unique`	0.99 ±0.02	0.97 ±0.03	-1.4% (noise)	0.382
`nii_load_seg`	2.61 ±0.08	2.64 ±0.05	+1.2% (noise)	0.218
`nii_get_connected_components`	2.61 ±0.14	2.64 ±0.06	+1.2% (noise)	0.487
`nii_extract_label`	0.43 ±0.01	0.44 ±0.02	+1.1% (noise)	0.992
`nii_center_of_masses`	1.66 ±0.01	1.65 ±0.25	-0.6% (noise)	0.408
`poi_map_labels`	0.17 ±0.00	0.17 ±0.01	-0.5% (noise)	0.795
`nii_volumes`	1.79 ±0.02	1.80 ±0.04	+0.3% (noise)	0.987
`poi_load`	0.94 ±0.02	0.94 ±0.01	-0.2% (noise)	0.299

`ct_2d` — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_dilate_msk`	13.60 ±0.08	13.82 ±0.08	+1.6%	0.007
`nii_rescale`	5.93 ±0.04	5.88 ±0.05	-0.9%	0.382
`nii_resample_from_to`	7.64 ±0.04	7.64 ±0.04	-0.0%	0.576
`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_map_labels`	0.46 ±0.01	0.43 ±0.00	-6.2% (noise)	0.000
`nii_reorient`	0.74 ±0.02	0.78 ±0.06	+4.9% (noise)	0.279
`poi_to_global`	0.22 ±0.01	0.21 ±0.01	-4.3% (noise)	0.274
`poi_save`	0.41 ±0.01	0.43 ±0.02	+4.0% (noise)	0.125
`nii_apply_crop`	0.62 ±0.02	0.60 ±0.01	-3.5% (noise)	0.011
`poi_reorient`	0.39 ±0.02	0.40 ±0.01	+3.4% (noise)	0.438
`poi_map_labels`	0.19 ±0.00	0.18 ±0.01	-3.3% (noise)	0.566
`nii_filter_connected_components`	0.75 ±0.01	0.77 ±0.02	+3.1% (noise)	0.011
`nii_pad_to`	0.52 ±0.02	0.50 ±0.02	-3.0% (noise)	0.484
`poi_rescale`	0.23 ±0.01	0.23 ±0.01	-2.8% (noise)	0.429
`nii_get_connected_components`	0.60 ±0.03	0.59 ±0.01	-2.4% (noise)	0.239
`nii_compute_crop`	0.14 ±0.00	0.14 ±0.01	+2.4% (noise)	0.567
`nii_unique`	0.12 ±0.00	0.12 ±0.01	-2.2% (noise)	0.203
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	+2.1% (noise)	0.410
`nii_set_dtype`	0.37 ±0.01	0.38 ±0.03	+2.1% (noise)	0.308
`nii_extract_label`	0.38 ±0.01	0.39 ±0.01	+2.1% (noise)	0.049
`nii_rescale_seg`	0.70 ±0.01	0.69 ±0.01	-2.0% (noise)	0.028
`poi_resample_from_to`	0.65 ±0.01	0.64 ±0.00	-1.8% (noise)	0.162
`poi_local_to_global_arr`	0.36 ±0.01	0.37 ±0.02	+1.7% (noise)	0.294
`poi_calc_centroids_nocrop`	1.01 ±0.02	0.99 ±0.00	-1.7% (noise)	0.063
`nii_load_seg`	1.45 ±0.03	1.48 ±0.06	+1.6% (noise)	0.561
`nii_load_img`	1.32 ±0.02	1.33 ±0.03	+1.5% (noise)	0.302
`nii_fill_holes`	0.76 ±0.02	0.75 ±0.03	-1.4% (noise)	0.794
`nii_volumes`	0.27 ±0.01	0.26 ±0.01	-1.0% (noise)	0.766
`poi_calc_centroids`	0.82 ±0.01	0.82 ±0.02	+0.8% (noise)	0.960
`poi_load`	0.96 ±0.01	0.97 ±0.01	+0.6% (noise)	0.344
`nii_center_of_masses`	0.20 ±0.01	0.20 ±0.01	-0.5% (noise)	0.556
`nii_save`	1.22 ±0.02	1.22 ±0.01	-0.0% (noise)	0.411
`nii_erode_msk`	0.86 ±0.01	0.86 ±0.02	+0.0% (noise)	0.595

`mri_3d` — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`poi_calc_centroids_nocrop`	12.36 ±0.04	11.37 ±0.06	-8.1%	0.000
`nii_resample_from_to`	46.30 ±0.93	44.81 ±0.35	-3.2%	0.013
`nii_erode_msk`	8.41 ±0.24	8.22 ±0.16	-2.3%	0.580
`nii_filter_connected_components`	5.04 ±0.04	4.96 ±0.06	-1.5%	0.327
`nii_rescale_seg`	3.08 ±0.02	3.11 ±0.04	+1.2%	0.482

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
`nii_fill_holes`	5.96 ±0.16	6.01 ±0.11	+0.7%	0.847
`nii_rescale`	44.23 ±0.62	44.55 ±0.91	+0.7%	0.985
`nii_load_img`	8.91 ±0.06	8.88 ±0.03	-0.4%	0.054
`nii_save`	8.64 ±0.06	8.60 ±0.04	-0.4%	0.433
`nii_dilate_msk`	153.10 ±0.96	153.63 ±0.32	+0.3%	0.094
`poi_calc_poi_from_subreg_vert`	11.30 ±0.95	11.32 ±0.15	+0.2%	0.421
`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%	—
`poi_map_labels`	0.24 ±0.00	0.26 ±0.01	+6.4% (noise)	0.003
`poi_reorient`	0.47 ±0.02	0.44 ±0.01	-5.7% (noise)	0.040
`poi_save`	0.52 ±0.03	0.50 ±0.03	-5.5% (noise)	0.888
`poi_local_to_global_arr`	0.44 ±0.02	0.42 ±0.03	-4.2% (noise)	0.432
`nii_set_dtype`	0.60 ±0.02	0.62 ±0.02	+3.6% (noise)	0.027
`nii_reorient`	0.84 ±0.01	0.86 ±0.02	+3.4% (noise)	0.089
`poi_to_global`	0.26 ±0.01	0.25 ±0.01	-3.2% (noise)	0.227
`nii_compute_crop`	0.38 ±0.02	0.39 ±0.02	+3.0% (noise)	0.368
`poi_rescale`	0.28 ±0.01	0.28 ±0.01	-2.9% (noise)	0.041
`nii_extract_label`	0.48 ±0.03	0.47 ±0.01	-2.7% (noise)	0.086
`poi_resample_from_to`	0.71 ±0.01	0.73 ±0.02	+2.5% (noise)	0.156
`nii_get_array`	0.08 ±0.01	0.08 ±0.01	-2.0% (noise)	0.782
`nii_map_labels`	1.17 ±0.03	1.14 ±0.03	-1.9% (noise)	0.371
`nii_get_connected_components`	2.69 ±0.02	2.64 ±0.04	-1.9% (noise)	0.066
`poi_load`	2.10 ±0.01	2.13 ±0.01	+1.5% (noise)	0.001
`nii_unique`	0.93 ±0.02	0.95 ±0.02	+1.5% (noise)	0.892
`nii_pad_to`	0.76 ±0.01	0.76 ±0.04	-0.8% (noise)	0.676
`nii_center_of_masses`	1.91 ±0.03	1.90 ±0.01	-0.8% (noise)	0.269
`nii_volumes`	1.86 ±0.02	1.87 ±0.06	+0.6% (noise)	0.314
`nii_load_seg`	2.78 ±0.02	2.77 ±0.06	-0.6% (noise)	0.513
`nii_apply_crop`	0.68 ±0.02	0.68 ±0.01	-0.5% (noise)	0.356
`poi_calc_centroids`	2.65 ±0.04	2.64 ±0.06	-0.4% (noise)	0.893

`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 ±0.14	7.96 ±0.17	+1.8%	0.150
`nii_dilate_msk`	18.16 ±0.33	18.42 ±0.20	+1.4%	0.389
`nii_rescale`	6.11 ±0.09	6.14 ±0.12	+0.6%	0.412
`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`	0.13 ±0.00	0.14 ±0.00	+11.3% (noise)	0.000
`nii_map_labels`	0.46 ±0.02	0.51 ±0.01	+10.2% (noise)	0.026
`nii_get_connected_components`	0.59 ±0.02	0.64 ±0.02	+8.7% (noise)	0.001
`poi_reorient`	0.43 ±0.01	0.46 ±0.02	+7.5% (noise)	0.035
`nii_fill_holes`	0.97 ±0.02	1.03 ±0.02	+6.7% (noise)	0.002
`nii_apply_crop`	0.62 ±0.01	0.66 ±0.02	+6.4% (noise)	0.025
`nii_filter_connected_components`	0.78 ±0.01	0.83 ±0.02	+6.3% (noise)	0.008
`poi_local_to_global_arr`	0.38 ±0.01	0.41 ±0.02	+6.2% (noise)	0.149
`poi_to_global`	0.25 ±0.01	0.27 ±0.02	+6.2% (noise)	0.109
`poi_map_labels`	0.23 ±0.00	0.24 ±0.01	+6.0% (noise)	0.001
`nii_compute_crop`	0.14 ±0.01	0.15 ±0.01	+5.1% (noise)	0.406
`nii_get_array`	0.02 ±0.00	0.02 ±0.00	-4.9% (noise)	0.148
`nii_erode_msk`	1.14 ±0.02	1.19 ±0.02	+4.8% (noise)	0.029
`poi_calc_centroids`	1.08 ±0.03	1.13 ±0.02	+4.3% (noise)	0.011
`nii_pad_to`	0.52 ±0.01	0.55 ±0.02	+4.2% (noise)	0.048
`poi_resample_from_to`	0.67 ±0.01	0.70 ±0.04	+3.8% (noise)	0.135
`poi_calc_centroids_nocrop`	1.27 ±0.05	1.31 ±0.02	+3.5% (noise)	0.615
`nii_rescale_seg`	0.73 ±0.01	0.75 ±0.02	+3.2% (noise)	0.174
`nii_save`	1.27 ±0.01	1.30 ±0.04	+2.5% (noise)	0.113
`poi_load`	1.86 ±0.01	1.90 ±0.01	+2.2% (noise)	0.000
`nii_set_dtype`	0.39 ±0.01	0.40 ±0.02	+1.9% (noise)	0.358
`nii_load_seg`	1.50 ±0.03	1.53 ±0.04	+1.9% (noise)	0.292
`poi_save`	0.48 ±0.01	0.49 ±0.01	+1.5% (noise)	0.067
`poi_rescale`	0.27 ±0.03	0.27 ±0.01	+1.4% (noise)	0.540
`nii_reorient`	0.77 ±0.01	0.76 ±0.02	-1.3% (noise)	0.614
`nii_center_of_masses`	0.43 ±0.01	0.43 ±0.02	+1.1% (noise)	0.304
`nii_load_img`	1.36 ±0.01	1.37 ±0.02	+1.1% (noise)	0.075
`nii_volumes`	0.47 ±0.02	0.48 ±0.01	+1.0% (noise)	0.715
`nii_extract_label`	0.41 ±0.02	0.40 ±0.01	-0.6% (noise)	0.799

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 d44648d vs head d44648d · python 3.11.17 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.96 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_load_img`	3.62 ±0.00	3.57 ±0.00	-1.3%	—
`nii_save`	3.89 ±0.00	3.85 ±0.00	-1.2%	—
`nii_apply_crop`	5.99 ±0.00	5.94 ±0.00	-0.8%	—
`nii_load_seg`	6.13 ±0.00	6.08 ±0.00	-0.8%	—
`nii_rescale_seg`	6.25 ±0.00	6.21 ±0.00	-0.7%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_rescale`	6.48 ±0.00	6.43 ±0.00	-0.7%	—
`nii_resample_from_to`	6.61 ±0.00	6.56 ±0.00	-0.7%	—
`nii_get_connected_components`	6.74 ±0.00	6.70 ±0.00	-0.7%	—
`nii_filter_connected_components`	7.05 ±0.00	7.01 ±0.00	-0.7%	—
`poi_calc_poi_from_subreg_vert`	7.36 ±0.00	7.32 ±0.00	-0.6%	—
`nii_erode_msk`	6.13 ±0.00	6.13 ±0.00	+0.1%	—
`nii_set_dtype`	5.43 ±0.00	5.43 ±0.00	+0.0%	—
`nii_reorient`	6.03 ±0.00	6.03 ±0.00	+0.0%	—
`nii_compute_crop`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`nii_pad_to`	5.55 ±0.00	5.55 ±0.00	+0.0%	—
`nii_volumes`	3.59 ±0.00	3.59 ±0.00	+0.0%	—
`nii_center_of_masses`	3.27 ±0.00	3.27 ±0.00	+0.0%	—
`nii_extract_label`	5.55 ±0.00	5.55 ±0.00	+0.0%	—
`nii_map_labels`	5.62 ±0.00	5.62 ±0.00	+0.0%	—
`nii_dilate_msk`	6.12 ±0.00	6.12 ±0.00	+0.0%	—
`nii_fill_holes`	6.47 ±0.00	6.47 ±0.00	+0.0%	—
`poi_calc_centroids`	6.24 ±0.00	6.24 ±0.00	+0.0%	—
`poi_calc_centroids_nocrop`	6.11 ±0.00	6.11 ±0.00	+0.0%	—
`poi_reorient`	3.96 ±0.00	3.96 ±0.00	+0.0%	—
`poi_to_global`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`poi_local_to_global_arr`	3.08 ±0.00	3.08 ±0.00	+0.0%	—
`poi_resample_from_to`	5.59 ±0.00	5.59 ±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`	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
`nii_unique`	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.67 ±0.00	2.67 ±0.00	+0.0% (noise)	—
`poi_save`	1.52 ±0.00	1.52 ±0.00	+0.0% (noise)	—
`poi_map_labels`	1.84 ±0.00	1.84 ±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
`nii_load_img`	3.56 ±0.00	3.51 ±0.00	-1.3%	—
`nii_save`	3.83 ±0.00	3.79 ±0.00	-1.2%	—
`nii_apply_crop`	5.93 ±0.00	5.88 ±0.00	-0.8%	—
`nii_load_seg`	6.07 ±0.00	6.02 ±0.00	-0.8%	—
`nii_rescale_seg`	6.19 ±0.00	6.14 ±0.00	-0.8%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_rescale`	6.42 ±0.00	6.37 ±0.00	-0.7%	—
`nii_resample_from_to`	6.54 ±0.00	6.50 ±0.00	-0.7%	—
`nii_get_connected_components`	6.68 ±0.00	6.63 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.99 ±0.00	6.95 ±0.00	-0.7%	—
`nii_erode_msk`	6.07 ±0.00	6.07 ±0.00	+0.1%	—
`nii_set_dtype`	5.37 ±0.00	5.37 ±0.00	+0.0%	—
`nii_reorient`	5.97 ±0.00	5.97 ±0.00	+0.0%	—
`nii_pad_to`	5.49 ±0.00	5.49 ±0.00	+0.0%	—
`nii_volumes`	3.52 ±0.00	3.52 ±0.00	+0.0%	—
`nii_center_of_masses`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`nii_extract_label`	5.49 ±0.00	5.49 ±0.00	+0.0%	—
`nii_map_labels`	5.55 ±0.00	5.55 ±0.00	+0.0%	—
`nii_dilate_msk`	6.05 ±0.00	6.05 ±0.00	+0.0%	—
`nii_fill_holes`	6.41 ±0.00	6.41 ±0.00	+0.0%	—
`poi_calc_centroids`	6.18 ±0.00	6.18 ±0.00	+0.0%	—
`poi_calc_centroids_nocrop`	6.11 ±0.00	6.11 ±0.00	+0.0%	—
`poi_reorient`	3.89 ±0.00	3.89 ±0.00	+0.0%	—
`poi_to_global`	3.14 ±0.00	3.14 ±0.00	+0.0%	—
`poi_local_to_global_arr`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`poi_resample_from_to`	5.53 ±0.00	5.53 ±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`	1.65 ±0.00	1.65 ±0.00	+0.0% (noise)	—
`nii_compute_crop`	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
`nii_unique`	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.61 ±0.00	2.61 ±0.00	+0.0% (noise)	—
`poi_save`	1.46 ±0.00	1.46 ±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)	—

`mri_3d` — shape (68, 52, 67)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_load_img`	3.62 ±0.00	3.57 ±0.00	-1.3%	—
`nii_save`	3.83 ±0.00	3.79 ±0.00	-1.2%	—
`nii_apply_crop`	5.93 ±0.00	5.88 ±0.00	-0.8%	—
`nii_load_seg`	6.07 ±0.00	6.02 ±0.00	-0.8%	—
`nii_rescale_seg`	6.19 ±0.00	6.14 ±0.00	-0.8%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_rescale`	6.42 ±0.00	6.37 ±0.00	-0.7%	—
`nii_resample_from_to`	6.54 ±0.00	6.50 ±0.00	-0.7%	—
`nii_get_connected_components`	6.68 ±0.00	6.63 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.99 ±0.00	6.95 ±0.00	-0.7%	—
`poi_calc_poi_from_subreg_vert`	7.36 ±0.00	7.31 ±0.00	-0.6%	—
`nii_erode_msk`	6.07 ±0.00	6.07 ±0.00	+0.1%	—
`nii_set_dtype`	5.43 ±0.00	5.43 ±0.00	+0.0%	—
`nii_reorient`	5.97 ±0.00	5.97 ±0.00	+0.0%	—
`nii_pad_to`	5.49 ±0.00	5.49 ±0.00	+0.0%	—
`nii_volumes`	3.52 ±0.00	3.52 ±0.00	+0.0%	—
`nii_center_of_masses`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`nii_extract_label`	5.49 ±0.00	5.49 ±0.00	+0.0%	—
`nii_map_labels`	5.55 ±0.00	5.55 ±0.00	+0.0%	—
`nii_dilate_msk`	6.05 ±0.00	6.05 ±0.00	+0.0%	—
`nii_fill_holes`	6.41 ±0.00	6.41 ±0.00	+0.0%	—
`poi_calc_centroids`	6.18 ±0.00	6.18 ±0.00	+0.0%	—
`poi_calc_centroids_nocrop`	6.05 ±0.00	6.05 ±0.00	+0.0%	—
`poi_reorient`	3.89 ±0.00	3.89 ±0.00	+0.0%	—
`poi_to_global`	3.14 ±0.00	3.14 ±0.00	+0.0%	—
`poi_local_to_global_arr`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`poi_resample_from_to`	5.53 ±0.00	5.53 ±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`	1.65 ±0.00	1.65 ±0.00	+0.0% (noise)	—
`nii_compute_crop`	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
`nii_unique`	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.61 ±0.00	2.61 ±0.00	+0.0% (noise)	—
`poi_save`	1.52 ±0.00	1.52 ±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)	—

`mri_2d` — shape (68, 52, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_load_img`	3.62 ±0.00	3.57 ±0.00	-1.3%	—
`nii_save`	3.83 ±0.00	3.79 ±0.00	-1.2%	—
`nii_apply_crop`	5.93 ±0.00	5.88 ±0.00	-0.8%	—
`nii_load_seg`	6.07 ±0.00	6.02 ±0.00	-0.8%	—
`nii_rescale_seg`	6.19 ±0.00	6.14 ±0.00	-0.8%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
`nii_rescale`	6.42 ±0.00	6.37 ±0.00	-0.7%	—
`nii_resample_from_to`	6.54 ±0.00	6.50 ±0.00	-0.7%	—
`nii_get_connected_components`	6.68 ±0.00	6.63 ±0.00	-0.7%	—
`nii_filter_connected_components`	6.99 ±0.00	6.95 ±0.00	-0.7%	—
`nii_erode_msk`	6.07 ±0.00	6.07 ±0.00	+0.1%	—
`nii_set_dtype`	5.43 ±0.00	5.43 ±0.00	+0.0%	—
`nii_reorient`	5.97 ±0.00	5.97 ±0.00	+0.0%	—
`nii_pad_to`	5.49 ±0.00	5.49 ±0.00	+0.0%	—
`nii_volumes`	3.52 ±0.00	3.52 ±0.00	+0.0%	—
`nii_center_of_masses`	3.21 ±0.00	3.21 ±0.00	+0.0%	—
`nii_extract_label`	5.49 ±0.00	5.49 ±0.00	+0.0%	—
`nii_map_labels`	5.55 ±0.00	5.55 ±0.00	+0.0%	—
`nii_dilate_msk`	6.05 ±0.00	6.05 ±0.00	+0.0%	—
`nii_fill_holes`	6.41 ±0.00	6.41 ±0.00	+0.0%	—
`poi_calc_centroids`	6.18 ±0.00	6.18 ±0.00	+0.0%	—
`poi_calc_centroids_nocrop`	6.11 ±0.00	6.11 ±0.00	+0.0%	—
`poi_reorient`	3.89 ±0.00	3.89 ±0.00	+0.0%	—
`poi_to_global`	3.14 ±0.00	3.14 ±0.00	+0.0%	—
`poi_local_to_global_arr`	3.02 ±0.00	3.02 ±0.00	+0.0%	—
`poi_resample_from_to`	5.53 ±0.00	5.53 ±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`	1.65 ±0.00	1.65 ±0.00	+0.0% (noise)	—
`nii_compute_crop`	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
`nii_unique`	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
`poi_rescale`	2.61 ±0.00	2.61 ±0.00	+0.0% (noise)	—
`poi_save`	1.52 ±0.00	1.52 ±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)	—

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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robert-graf and others added 3 commits October 1, 2026 11:23

Merge branch 'main' into tanja2

e8c6775

Merge branch 'main' into tanja2

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Merge branch 'main' into tanja2

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Hendrik-code approved these changes Oct 19, 2026

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Hendrik-code merged commit 7f39708 into main Oct 19, 2026
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Hendrik-code deleted the tanja2 branch October 19, 2026 12:01

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extended dixon mapping - #155

extended dixon mapping#155
Hendrik-code merged 6 commits into
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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)