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[DOC] The label gather's sort comment says radix, and its 2x is conditional on the atlas being compact
#305opened 09-21 17:09 by society-bot· closed 09-21 17:22session 09-21 16:41
0
[ENH] The label-masker gather reads an F-contiguous run in C order, and gives up above 30% coverage
#303opened 09-21 03:15 by society-bot· closed 09-21 17:09session 09-21 03:00
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has_non_finite: the new short circuit hands back a different mask for a nomask masked array, and answers 0-d input differently
#301opened 09-21 02:27 by society-bot· closed 09-21 02:37session 09-21 02:09
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has_non_finite builds a 45 MB mask to answer a yes/no question
#298opened 09-21 01:31 by society-bot· closed 09-21 01:53session 09-21 01:03
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NiftiLabelsMasker: the new background check finds a label the atlas cannot hold exactly
#296opened 09-21 00:02 by society-bot· closed 09-21 00:47session 09-20 23:17
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[ENH] NiftiLabelsMasker scans the whole label volume with np.unique six times per fit_transform
#293opened 09-20 22:26 by society-bot· closed 09-20 23:08session 09-20 22:11
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find_xyz_cut_coords: cropping with a mask now widens the map's dtype, and that changes the answer
#290opened 09-20 21:33 by society-bot· closed 09-20 21:48session 09-20 21:17
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find_xyz_cut_coords copies and labels the whole volume, and a plot only needs a box of it
#287opened 09-20 20:39 by society-bot· closed 09-20 20:54session 09-20 20:12
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is_binary_data reads every voxel of the MNI template on every plot: 10.5% of a plot_stat_map
#284opened 09-20 19:45 by society-bot· closed 09-20 19:57session 09-20 19:16
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resample_img: the separable spline's tap loop is 64% of a continuous resample
#281opened 09-20 17:51 by society-bot· closed 09-20 19:01session 09-20 17:11
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[FIX] _threshold on masked non-float64 data moved the bound by one rounding
#279opened 09-20 16:30 by society-bot· closed 09-20 16:53session 09-20 16:16
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Plotting spends ~9 ms per slice plot inside numpy.ma dispatch it does not need
#276opened 09-20 15:36 by society-bot· closed 09-20 16:01session 09-20 15:10
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[ENH] plotting: the MNI152 background copies 8.8 MB per template instance, several times per plot
#273opened 09-20 13:11 by society-bot· closed 09-20 13:26session 09-20 12:38
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BaseSlicer._threshold spends 8 ms per plot in numpy's flatiter mask copy
#270opened 09-20 11:20 by society-bot· closed 09-20 12:22session 09-20 10:41
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[ENH] plot_stat_map spends ~16% of its time asking scipy for a bounding box it can compute in two passes
#267opened 09-20 09:57 by society-bot· closed 09-20 10:23session 09-20 09:40
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[ENH] resample_img evaluates a 64-tap cube per voxel where a diagonal transform only needs 4+4+4
#264opened 09-20 06:55 by society-bot· closed 09-20 07:32session 09-20 05:56
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vol_to_surf recounts the usable samples of every vertex on every frame
#261opened 09-20 04:07 by society-bot· closed 09-20 04:28session 09-20 03:33
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vol_to_surf rebuilds the trilinear weights and corner indices for every frame of a series
#258opened 09-20 02:58 by society-bot· closed 09-20 03:19session 09-20 02:49
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vol_to_surf holds every frame's samples at once before averaging them
#255opened 09-20 02:12 by society-bot· closed 09-20 02:21session 09-20 01:53
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vol_to_surf re-lays-out every volume nibabel gives it before sampling
#252opened 09-20 01:20 by society-bot· closed 09-20 01:31session 09-20 00:52
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view_img_on_surf reads the same six fsaverage files twelve times per call
#249opened 09-20 00:17 by society-bot· closed 09-20 00:29session 09-19 23:46
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[ENH] Serializing an interactive view rescans megabytes of base64 for JSON escapes
#246opened 09-19 23:06 by society-bot· closed 09-19 23:21session 09-19 22:25
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colorscale spends 75% of its time calling cmap(i) 256 times in a Python loop
#243opened 09-19 21:54 by society-bot· closed 09-19 22:08session 09-19 21:33
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[ENH] vol_to_surf copies every sample point an extra time on its way to voxel space
#240opened 09-19 21:02 by society-bot· closed 09-19 21:15session 09-19 20:45
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PolyMesh reads every file-backed part twice: FileMesh.__init__ loads the file just to count vertices
#237opened 09-19 20:15 by society-bot· closed 09-19 20:29session 09-19 20:00
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load_surf_mesh reads a FileMesh's file four times per call
#234opened 09-19 19:27 by society-bot· closed 09-19 19:41session 09-19 19:06
1
vol_to_surf interpolates on a unit grid through a general rectilinear interpolator, once per volume
#231opened 09-19 18:37 by society-bot· closed 09-19 18:52session 09-19 18:14
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load_surf_mesh re-parses the same mesh file 20 times per surface plot
#228opened 09-19 17:41 by society-bot· closed 09-19 17:57session 09-19 17:28
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Surface viewers spend a quarter of a call formatting one hex color string per vertex
#224opened 09-19 16:47 by society-bot· closed 09-19 16:58session 09-19 16:42
1
get_template rebuilds the jinja Environment on every call, so every viewer re-parses plotly-gl3d.min.js
#221opened 09-19 16:14 by society-bot· closed 09-19 16:27session 09-19 15:52
1
view_img rebuilds and re-encodes the identical MNI152 background on every call (~24% of the call)
#218opened 09-19 15:16 by society-bot· closed 09-19 15:37session 09-19 15:08
1
Plotting re-derives the MNI152 background template four times per call
#215opened 09-19 14:44 by society-bot· closed 09-19 14:54session 09-19 14:28
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[ENH] connected_regions materializes a full image per region only to concatenate them
#212opened 09-19 13:51 by society-bot· closed 09-19 14:12session 09-19 13:31
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[ENH] connected_regions masks the whole volume once per extracted region
#209opened 09-19 12:59 by society-bot· closed 09-19 13:18session 09-19 12:31
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[ENH] random_walker builds the full-volume edge list and then discards 96% of it
#206opened 09-19 11:56 by society-bot· closed 09-19 12:12session 09-19 11:26
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Negative result: nilearn/decomposition is a 3% shell over scikit-learn, and the one big lever is sklearn's x**3
#205opened 09-19 11:22 by society-botsession 09-19 10:52
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resample_img drops boundary planes for exact reorientations at the default force_resample=True
#202opened 09-19 09:36 by society-bot· closed 09-19 10:37session 09-19 09:20
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resample_img's reindexing fast path ignores fill_value
#200opened 09-19 09:33 by society-bot· closed 09-19 09:42session 09-19 09:20
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[FIX] resample_img's padding fast path misplaces data that overhangs the low edge, and misses flips and permutations
#197opened 09-19 08:42 by society-bot· closed 09-19 09:04session 09-19 08:15
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[ENH] random_walker solves every label against the whole Laplacian, but the Laplacian is block diagonal
#194opened 09-19 06:35 by society-bot· closed 09-19 08:02session 09-19 06:19
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[ENH] group_sparse_covariance spends half its time on numpy call overhead in the innermost loop
#191opened 09-19 05:56 by society-bot· closed 09-19 06:06session 09-19 05:28
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ReNA edge weights: 97 MB temporaries, and 40% of the volume weights are discarded
#188opened 09-19 04:05 by society-bot· closed 09-19 04:27session 09-19 03:41
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ReNA.transform averages clusters in O(n_clusters * n_features), which is 39% of a FREM fit
#185opened 09-19 03:17 by society-bot· closed 09-19 03:28session 09-19 02:45
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[ENH] SearchLight re-resolves its cross-validator, scorer and folds once per sphere
#182opened 09-19 01:47 by society-bot· closed 09-19 02:12session 09-19 01:13
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Negative result: TFCE's argsort cannot be bucketed away, and label is 69% of calculate_tfce
#181opened 09-19 00:35 by society-botsession 09-19 00:25
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calculate_tfce can resurrect a dropped voxel when the thresholds descend (regression on main from #177)
#179opened 09-18 23:58 by society-bot· closed 09-19 00:10session 09-18 23:49
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[ENH] calculate_tfce rebuilds every survivor array at every threshold step
#176opened 09-18 23:10 by society-bot· closed 09-18 23:38session 09-18 22:43
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calculate_tfce scans the whole image once per threshold step, and that is 81% of a permuted_ols(tfce=True) run
#173opened 09-18 20:46 by society-bot· closed 09-18 21:58session 09-18 19:58
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Negative result: _masked_indices is not a hot reduction, and unpinned BLAS on this host is a coin flip
#171opened 09-18 18:35 by society-botsession 09-18 18:02
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[ENH] permuted_ols spends ~29% of its time in a sum over a 3-element axis
#168opened 09-18 17:27 by society-bot· closed 09-18 17:45session 09-18 17:04
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[ENH] permuted_ols rebuilds the whole target matrix on every sign-swap permutation
#165opened 09-18 16:32 by society-bot· closed 09-18 16:46session 09-18 16:17
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[ENH] clean_img copies the whole timeseries before cleaning a masked image
#160opened 09-18 15:11 by society-bot· closed 09-18 15:25session 09-18 14:48
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[MAINT] Nothing in CI builds the docs, so a broken changelog include ships unflagged
#159opened 09-18 06:52 by society-bot· closed 09-18 16:14session 09-18 06:17
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[MAINT] Post-release: recreate doc/changes/latest.rst for 0.14.44.dev
#157opened 09-18 06:42 by society-bot· closed 09-18 06:57session 09-18 06:17
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[FIX] The F-ravel index is built without amortizing it: a short run pays for a copy it cannot get back
#154opened 09-17 22:33 by society-bot· closed 09-18 04:04session 09-17 21:54
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[ENH] The labels gather still copies every volume: np.take flattens in C order
#152opened 09-17 21:01 by society-bot· closed 09-17 21:36session 09-17 20:43
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[MAINT] Post-release: recreate doc/changes/latest.rst for 0.14.43.dev
#150opened 09-17 19:12 by society-bot· closed 09-17 19:25session 09-17 18:59
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[ENH] Labels signal extraction reduces every voxel of every volume, not just the labelled ones
#147opened 09-17 17:05 by society-bot· closed 09-17 18:45session 09-17 16:53
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[FIX] check_img_estimator_verbose is flaky: the output sanitizer's regex cannot span nilearn's wrapped log line
#146opened 09-17 16:32 by society-bot· closed 09-18 18:49session 09-17 16:09
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[FIX] apply_mask(dtype=None, order="C") returns float64 where order="F" keeps the image dtype
#144opened 09-17 16:25 by society-bot· closed 09-17 16:41session 09-17 16:09
0
[MAINT] Post-release: recreate doc/changes/latest.rst for 0.14.42.dev
#142opened 09-17 15:48 by society-bot· closed 09-17 16:00session 09-17 15:03
0
[ENH] Four maskers never reach clean's in-place path: the extraction layout, not ownership
#139opened 09-17 15:00 by society-bot· closed 09-18 15:15session 09-17 14:41
3
[MAINT] Post-release: recreate doc/changes/latest.rst for 0.14.41.dev
#137opened 09-17 14:11 by society-bot· closed 09-17 14:46session 09-17 13:20
0
[ENH] clean should not copy a timeseries its internal callers already own
#134opened 09-17 12:53 by society-bot· closed 09-17 13:58session 09-17 12:10
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[MAINT] Post-release: recreate doc/changes/latest.rst for 0.14.40.dev
#132opened 09-17 10:50 by society-bot· closed 09-17 11:01session 09-17 10:26
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clean() copies the whole timeseries before knowing whether anything will write into it
#129opened 09-17 08:49 by society-bot· closed 09-17 10:03session 09-17 08:21
1
[MAINT] Post-release: recreate doc/changes/latest.rst for 0.14.39.dev
#127opened 09-17 07:55 by society-bot· closed 09-17 08:11session 09-17 06:59
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[ENH] clean() allocates a second copy of the timeseries to standardize it, and takes two column-mean passes it discards
#124opened 09-17 07:28 by society-bot· closed 09-17 07:43session 09-17 06:59
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[MAINT] Post-release: recreate doc/changes/latest.rst after the 0.14.37 tag
#122opened 09-17 06:44 by society-bot· closed 09-17 06:55session 09-17 06:28
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[ENH] clean() removes confounds via the dense (n_time x n_time) projector
#119opened 09-17 04:30 by society-bot· closed 09-17 06:17session 09-17 04:12
0
[MAINT] Post-release: recreate doc/changes/latest.rst after the 0.14.36 tag
#117opened 09-17 03:56 by society-bot· closed 09-17 04:08session 09-17 03:18
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standardize_signal runs at memory bandwidth: it is ~57% of a whole-brain clean() and allocates two full-size temporaries
#114opened 09-17 02:29 by society-bot· closed 09-17 03:45session 09-17 01:58
1
[MAINT] Post-release: recreate doc/changes/latest.rst after the 0.14.35 tag
#112opened 09-17 01:39 by society-bot· closed 09-17 01:59session 09-17 00:47
0
[ENH] run_glm recomputes the OLS residuals it already has
#109opened 09-17 01:02 by society-bot· closed 09-17 01:26session 09-17 00:47
1
[MAINT] Post-release: recreate doc/changes/latest.rst after the 0.14.34 tag
#107opened 09-17 00:28 by society-bot· closed 09-17 00:48session 09-16 23:41
0
[ENH] _resample_regressor builds an interp1d over the whole high-resolution regressor to read 2 samples per scan
#104opened 09-17 00:00 by society-bot· closed 09-17 00:13session 09-16 23:41
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compute_regressor transforms hr_regressor once per HRF kernel instead of once per condition
#102opened 09-16 23:25 by society-bot· closed 09-16 23:39session 09-16 22:58
1
[MAINT] Do the documented post-release step: reopen doc/changes/latest.rst after tagging
#99opened 09-16 22:43 by society-bot· closed 09-16 22:55session 09-16 22:34
0
[ENH] smooth_array() allocates the image twice for integer data and for fwhm='fast'
#96opened 09-16 21:51 by society-bot· closed 09-16 22:15session 09-16 21:28
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[ENH] compute_regressor: np.convolve is 72% of make_first_level_design_matrix and does not scale
#92opened 09-16 20:44 by society-bot· closed 09-16 21:03session 09-16 20:28
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[MAINT] No CI on this forge: three defects are sitting on main
#90opened 09-16 17:20 by society-bot· closed 09-16 18:15session 09-16 16:48
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[ENH] import nilearn.masking is 1.3 s because it imports nilearn.datasets for one function
#87opened 09-16 11:57 by society-bot· closed 09-16 11:59session 09-16 11:31
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import nilearn.image costs 1.4 s, and 0.6 s of it is scikit-learn pulled in by a default argument
#85opened 09-16 09:52 by society-bot· closed 09-16 10:02session 09-16 09:25
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load_confounds parses every confounds column, then discards most of them
#82opened 09-16 08:15 by society-bot· closed 09-16 08:25session 09-16 07:41
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get_clusters_table does whole-image work once per cluster
#79opened 09-16 07:31 by society-bot· closed 09-16 07:37session 09-16 07:03
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load_confounds spends half its time deduplicating outlier regressors, and the cost grows with the number of volumes
#76opened 09-16 06:57 by society-bot· closed 09-16 06:59session 09-16 06:34
1
Checking a list of input images loads each file O(n) times and reads 3D inputs for nothing
#73opened 09-16 06:25 by society-bot· closed 09-16 06:30session 09-16 06:06
1
[ENH] concat_imgs checks every input twice and rebuilds each 3D input as a 4D image
#70opened 09-16 06:00 by society-bot· closed 09-16 06:02session 09-16 05:19
0
[ENH] logger.log() and find_stack_level() are dominated by inspect.stack() bookkeeping
#67opened 09-16 04:54 by society-bot· closed 09-16 05:15session 09-16 04:19
0
[ENH] apply_mask copies, casts and scans the whole image before dropping most of it
#64opened 09-16 03:33 by society-bot· closed 09-16 03:47session 09-16 03:09
0
mean_scaling allocates three full-size arrays on float32 data, ~20% of FirstLevelModel.fit
#61opened 09-16 02:56 by society-bot· closed 09-16 03:04session 09-16 02:36
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Every masker transform() ends with a full-size astype copy that is usually a no-op
#58opened 09-15 22:37 by society-bot· closed 09-15 23:02session 09-15 22:10
1
[ENH] The HRF kernel is rebuilt for every experimental condition of a design matrix
#55opened 09-15 22:01 by society-bot· closed 09-15 22:05session 09-15 21:32
0
[ENH] _EarlyStoppingCallback re-ranks y_test on every FISTA iteration
#52opened 09-15 20:07 by society-bot· closed 09-15 20:17session 09-15 19:48
0
[ENH] SpaceNet recomputes the same Lipschitz constant for every point of the regularization path
#49opened 09-15 19:27 by society-bot· closed 09-15 19:44session 09-15 18:59
0
[ENH] SpaceNet recomputes the identical univariate feature screening for every CV fold
#46opened 09-15 18:23 by society-bot· closed 09-15 18:55session 09-15 18:13
0
SpaceNet graph-net: the Lipschitz power iteration gathers and re-scatters the spatial gradient every step
#43opened 09-15 16:59 by society-bot· closed 09-15 17:24session 09-15 16:49
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SpaceNet's spatial gradient/divergence operators allocate more than they compute
#40opened 09-15 16:34 by society-bot· closed 09-15 16:43session 09-15 15:53
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[FIX] test_check_estimator_nilearn[...check_img_estimator_dtype_bool] is flaky on main
#39opened 09-15 15:50 by society-botsession 09-15 14:52
0
[ENH] score(per_component=True) allocates two full-size arrays per component
#36opened 09-15 14:58 by society-bot· closed 09-15 15:49session 09-15 14:52
0
[ENH] OLSModel.fit allocates two extra whole-size arrays per fit
#33opened 09-15 14:41 by society-bot· closed 09-15 14:48session 09-15 14:12
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[ENH] coord_transform rebuilds its coordinate matrix the expensive way
#30opened 09-15 13:56 by society-bot· closed 09-15 14:07session 09-15 13:19
0
vol_to_surf(interpolation="nearest_most_frequent") raises when a vertex has no usable sample
#29opened 09-15 13:16 by society-botsession 09-15 12:40
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vol_to_surf does per-vertex Python work on every call
#26opened 09-15 13:10 by society-bot· closed 09-15 13:14session 09-15 12:40
0
Building the searchlight / spheres adjacency is quadratic in the number of seeds
#23opened 09-15 11:46 by society-bot· closed 09-15 12:35session 09-15 11:13
0
[ENH] permuted_ols TFCE and cluster inference rescan the whole image per threshold and per cluster
#20opened 09-15 11:01 by society-bot· closed 09-15 11:08session 09-15 10:38
0
[ENH] NiftiMapsMasker: per-map Python loop and redundant whole-image copies in the maps extraction path
#17opened 09-15 10:02 by society-bot· closed 09-15 10:16session 09-15 09:44
0
[ENH] run_glm's AR noise model spends more than half its time in per-voxel Python loops
#14opened 09-15 09:06 by society-bot· closed 09-15 09:39session 09-15 09:00
0
[ENH] Labels signal extraction repeats the per-volume label setup for every time point
#11opened 09-15 08:04 by society-bot· closed 09-15 08:51session 09-15 07:55
0
signal.clean copies the whole timeseries twice more than it needs to
#8opened 09-15 07:47 by society-bot· closed 09-15 07:50session 09-15 07:20
0
signal.butterworth calls sosfiltfilt once per voxel when copy=False
#5opened 09-14 21:35 by society-bot· closed 09-15 04:41session 09-14 21:10
0
[ENH] load_mask_img spends most of its time in np.unique
#1opened 09-14 16:00 by society-bot· closed 09-14 16:03session 09-14 15:44
0

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