From 4f4730163097457cf9ddb5674ffd158ee8fa822e Mon Sep 17 00:00:00 2001 From: Himanshu Aggarwal Date: Tue, 9 Apr 2024 10:41:29 +0200 Subject: [PATCH] REL 0.10.4 (#4354) * REL 0.10.4 * Update doc/changes/0.10.4.rst Co-authored-by: Remi Gau * add empty lines after every changelog * Update doc/changes/0.10.4.rst Co-authored-by: Remi Gau * remove dev * add more highlights --------- Co-authored-by: Remi Gau --- doc/changes/{latest.rst => 0.10.4.rst} | 47 ++++++++++++++++++++++---- doc/changes/whats_new.rst | 4 +-- nilearn/image/image.py | 4 +-- 3 files changed, 44 insertions(+), 11 deletions(-) rename doc/changes/{latest.rst => 0.10.4.rst} (79%) diff --git a/doc/changes/latest.rst b/doc/changes/0.10.4.rst similarity index 79% rename from doc/changes/latest.rst rename to doc/changes/0.10.4.rst index 823ad8cc7e..2a5c0efbc3 100644 --- a/doc/changes/latest.rst +++ b/doc/changes/0.10.4.rst @@ -2,19 +2,36 @@ .. include:: names.rst -0.10.4.dev -========== +0.10.4 +====== + +**Released April 2024** + +HIGHLIGHTS +---------- + +- :bdg-dark:`Code` Use the appropriate HTML templates for :class:`nilearn.maskers.MultiNiftiMapsMasker` and :class:`nilearn.maskers.MultiNiftiLabelsMasker` reports that would lead to empty reports for ``MultiNiftiMapsMasker`` (:gh:`4310` by `Rémi Gau`_). + +- :bdg-dark:`Code` Fix color bar handling with color map with only 1 level (:gh:`4255` by `Rémi Gau`_). + +- :bdg-dark:`Code` Improve colorbar size and labels in mosaic display (:gh:`4284` by `Rémi Gau`_). + +- :bdg-dark:`Code` Remove unused ``**kwargs`` from :func:`nilearn.plotting.view_img` and :func:`nilearn.plotting.plot_surf` (:gh:`4270` by `Rémi Gau`_). + Fixes ----- - :bdg-dark:`Code` Fix plotting of carpet plot due to a change in the coming version of matplolib (3.9.0) (:gh:`4279` by `Rémi Gau`_). + - :bdg-dark:`Code` Fix errant warning when using ``stat_type`` in :func:`nilearn.glm.compute_contrast` (:gh:`4257` by `Eric Larson`_). + - :bdg-dark:`Code` Fix when thresholding is applied to images by GLM reports (:gh:`4258` by `Rémi Gau`_). - :bdg-dark:`Code` Use the appropriate HTML templates for :class:`nilearn.maskers.MultiNiftiMapsMasker` and :class:`nilearn.maskers.MultiNiftiLabelsMasker` reports that would lead to empty reports for ``MultiNiftiMapsMasker`` (:gh:`4310` by `Rémi Gau`_). - :bdg-dark:`Code` Make masker report tables horizontally scrollable (:gh:`4308` by `Rémi Gau`_). + - :bdg-dark:`Code` Masker reports tables do not overlap with report image (:gh:`4308` by `Rémi Gau`_). - :bdg-dark:`Code` Fix color bar handling with color map with only 1 level (:gh:`4255` by `Rémi Gau`_). @@ -24,30 +41,46 @@ Fixes - :bdg-dark:`Code` Ensure that :func:`nilearn.interfaces.bids.save_glm_to_bids` serializes numpy arrays to :obj:`list` used as GLM parameters before saving them to JSON (:gh:`4325` by `Rémi Gau`_). - :bdg-dark:`Code` Check that the ``view`` parameter in surface plotting functions is a pair of ``int`` or ``float`` when it is not a ``string`` (:gh:`4297` by `Rémi Gau`_). + - :bdg-dark:`Code` Fix positions of the markers on the images on the sphere masker reports (:gh:`4285` by `Rémi Gau`_). + - :bdg-dark:`Code` Fix cut position in nifti maps maskers to match displayed map maximum (:gh:`4304` by `Rémi Gau`_). + - :bdg-dark:`Code` Make sure that :class:`nilearn.maskers.NiftiSpheresMasker` reports displays properly when it contains only 1 sphere (:gh:`4269` by `Rémi Gau`_). + - :bdg-dark:`Code` Miscellaneous fixes in GLM reports (only display FIR delay if FIR is used, display color bar "Z score" legend...) (:gh:`4266` by `Rémi Gau`_). + - :bdg-primary:`Doc` Fix minor typos in documentation (glossary and connectivity/parcellating) (:gh:`4343` by `Florent Pollet`_). +- :bdg-primary:`Doc` Update minor information on the :ref:`contributing` page (:gh:`4318` and :gh:`4320` by `Himanshu Aggarwal`_). + Enhancements ------------ - :bdg-success:`API` Add an ``avg_method`` parameter to :func:`nilearn.plotting.plot_surf_stat_map` (:gh:`4298` by `Rémi Gau`_). +- :bdg-primary:`Doc` Advertise nilearn's in built globbing capability in an example (:gh:`4334` by `Himanshu Aggarwal`_). + + Changes ------- -- :bdg-dark:`Code` Throw warnings when passing parameters to surface plotting functions that are not used by the plolty engine (:gh:`4298` by `Rémi Gau`_). -- :bdg-primary:`Doc` Render examples of GLM and masker reports as part of the documentation (:gh:`4267` and :gh:`4295` by `Rémi Gau`_). +- :bdg-dark:`Code` Throw warnings when passing parameters to surface plotting functions that are not used by the plotly engine (:gh:`4298` by `Rémi Gau`_). + - :bdg-dark:`Code` Improve colorbar size and labels in mosaic display (:gh:`4284` by `Rémi Gau`_). -- :bdg-primary:`Doc` Render the description of the templates, atlases and datasets of the :mod:`nilearn.datasets` as part of the documentation (:gh:`4232` by `Rémi Gau`_). + - :bdg-dark:`Code` Change the colormap to ``gray`` for the background image in the :class:`nilearn.maskers.NiftiSpheresMasker` (:gh:`4269` by `Rémi Gau`_). -- :bdg-dark:`Code` Remove unused ``**kwargs`` from :func:`nilearn.plotting.view_img` and :func:`nilearn.plotting.plot_surf` (:gh:`4270` by `Rémi Gau`_). -- :bdg-secondary:`Maint` HTML, CSS are now linted using prettier. (:gh:`4302`, by `Rémi Gau`_). +- :bdg-dark:`Code` Remove unused ``**kwargs`` from :func:`nilearn.plotting.view_img` and :func:`nilearn.plotting.plot_surf` (:gh:`4270` by `Rémi Gau`_). - :bdg-dark:`Code` Use red to blue color map in the GLM reports (:gh:`4266` by `Rémi Gau`_). + - :bdg-dark:`Code` :class:`nilearn.maskers.NiftiSpheresMasker` will throw warnings if the ``labels`` passed to it is not a :obj:`list` of :obj:`str`, or if the number of items in the list of labels does not match the number of regions in the label image (:gh:`4274` by `Rémi Gau`_). - :bdg-dark:`Code` Copy headers from user-specified image to the result of :func:`nilearn.image.math_img` (:gh:`4337` by `Himanshu Aggarwal`_). + +- :bdg-primary:`Doc` Render the description of the templates, atlases and datasets of the :mod:`nilearn.datasets` as part of the documentation (:gh:`4232` by `Rémi Gau`_). + +- :bdg-primary:`Doc` Render examples of GLM and masker reports as part of the documentation (:gh:`4267` and :gh:`4295` by `Rémi Gau`_). + +- :bdg-secondary:`Maint` HTML, CSS are now linted using prettier. (:gh:`4302`, by `Rémi Gau`_). diff --git a/doc/changes/whats_new.rst b/doc/changes/whats_new.rst index 8d69132a07..66b3ea48b1 100644 --- a/doc/changes/whats_new.rst +++ b/doc/changes/whats_new.rst @@ -5,8 +5,8 @@ What's new ========== -.. _latest: -.. include:: latest.rst +.. _v0.10.4: +.. include:: 0.10.4.rst .. _v0.10.3: .. include:: 0.10.3.rst .. _v0.10.2: diff --git a/nilearn/image/image.py b/nilearn/image/image.py index c42d7d0df6..c13a4b6e06 100644 --- a/nilearn/image/image.py +++ b/nilearn/image/image.py @@ -1007,7 +1007,7 @@ def math_img(formula, copy_header_from=None, **imgs): should have the same number of dimensions. If None, the default :class:`~nibabel.nifti1.Nifti1Header` is used. - .. versionadded:: 0.10.4.dev + .. versionadded:: 0.10.4 imgs : images (:class:`~nibabel.nifti1.Nifti1Image` or file names) Keyword arguments corresponding to the variables in the formula as @@ -1046,7 +1046,7 @@ def math_img(formula, copy_header_from=None, **imgs): but might have different header information, specifically the TR value, see :gh:`2645`. - .. versionadded:: 0.10.4.dev + .. versionadded:: 0.10.4 We can also copy the header from one of the input images using ``copy_header_from``::