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Feat: Implement a visualisation feature to NiTransforms #212

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05b61b8
feat: Implement vis
May 29, 2024
b2cac3b
enh: Update plotting
May 29, 2024
7722545
enh: Reworked figure formatting and code structure
Jun 11, 2024
227e330
enh: code structure. Plotting now a class object.
Jun 11, 2024
59104c6
fix: remove straneous spaces
Jun 11, 2024
3865b65
fix: remove straneous spaces
Jun 12, 2024
76ca16a
enh: code structure
Jun 14, 2024
3c9be6d
N/A
Jun 14, 2024
304f362
enh: update progress on vis
Jun 17, 2024
62801e5
enh: Implemented function descriptions, reworked some lines.
Jun 19, 2024
b745a9f
feat: First implementation of draft dsm plots.
Jun 19, 2024
7f96037
feat: First draft of vis.py
Jun 20, 2024
ac31803
Feat: Addition of new, improved file vis_v2.py with new developments …
Jun 24, 2024
2ffa28a
enh: 1. Implemented 3d quiver; 2. Updated formatting; 3. Updated func…
Jun 24, 2024
6bb8afd
fix: Reworked file naming and versions
Jun 26, 2024
a3cef8d
fix: Relocate draft files
Jun 26, 2024
b426904
Feat: New file version, implemented divergence of deltas field. New (…
Jun 28, 2024
f13716a
Fix: ajust location of draft files
Jun 28, 2024
8601490
enh: finalised div map, removed normalised dsm plot. Prepared V5
Jul 1, 2024
f489927
Fix: fixed jacobian calculations, implemented jacobian-mapped scatter…
Jul 3, 2024
6b86390
Feat: Created v6 and reorganised drafts
Jul 3, 2024
d560077
Feat: Created v6 and reorganised drafts
Jul 3, 2024
9d2cab8
fix: debug grid, partial fix
Jul 5, 2024
68e72ef
Feat: Finalised grid, code functional. Required: clean up files; clea…
Jul 5, 2024
ead2351
Enh: formatting
Jul 8, 2024
dc87338
Enh: Removed draft files, rename final vis.py
Jul 8, 2024
f051b7d
fix: corrected descriptions
Jul 8, 2024
bde247b
enh: code structure
Jul 9, 2024
ef53ff8
remove example
Jul 9, 2024
1507e77
Enh: New file test_vis.py for implementation of tests. Added checks f…
Jul 10, 2024
6b14738
removed draft python files
Jul 10, 2024
af24af8
enh: Further additions to test_vis, output path for figures added to …
Jul 11, 2024
ed381b3
Fix: test 3d quiver fixed, fixed identical savefig filenames
Jul 11, 2024
30e1967
fix: accidentally running examples
Jul 11, 2024
6a1eb59
Fix: pacify flake8
Jul 15, 2024
2d54dc1
Fix: pacify flake8
Jul 15, 2024
85621c1
Fix: pacify flake8
Jul 15, 2024
164372c
Fix: pacify flake8
Jul 15, 2024
c047b3c
Enh: increase CodeCov coverage
Jul 15, 2024
0aa2d08
Enh: increase CodeCov coverage, pacify flake8
Jul 15, 2024
b66fee3
Fix Pacify flake8
Jul 15, 2024
94bab2a
Fix: RGB quiver plot failing if plotting transforms independent of on…
Jul 16, 2024
138b81e
Fix: pacify flake8
Jul 16, 2024
07f94f7
Fix: pacify flake8
Jul 16, 2024
011cf30
Fix: pacify flake8
Jul 16, 2024
67da55c
Feat: creation of notebook for vis module
Jul 16, 2024
a1fcdc7
feat: plot linear, planar and spherical coefficient. Other code tidying.
Jul 19, 2024
6bef93f
pacify flake8
Jul 19, 2024
2384469
fix: mistakenly broke syntax
Jul 19, 2024
c25a501
enh: added tests for codecov
Jul 19, 2024
f51e93f
Update nitransforms/tests/test_vis.py
jmarabotto Jul 23, 2024
d44da6c
Update nitransforms/tests/test_vis.py
jmarabotto Jul 23, 2024
91191ae
Update nitransforms/vis.py
jmarabotto Jul 23, 2024
0d8d997
Update nitransforms/vis.py
jmarabotto Jul 23, 2024
c262c55
Update nitransforms/vis.py
jmarabotto Jul 23, 2024
8863189
fix: pacify flake8, updated notebook
Jul 23, 2024
664f6f5
fix? read the docs
Jul 23, 2024
36dae68
Link to notebook
effigies Sep 16, 2024
0b13408
enh: read X5 transform files
oesteban Jul 17, 2025
a22a6d0
refactor: simplify X5 loader
oesteban Jul 17, 2025
2d3ba2f
test: cover x5.from_filename
oesteban Jul 17, 2025
eeb4d5d
enh: enable loading of X5 affines
oesteban Jul 17, 2025
6b000c8
Merge pull request #244 from nipy/codex/exclude-tests-from-coverage-r…
oesteban Jul 18, 2025
8e50969
fix: process exceptions when trying to open X5
oesteban Jul 17, 2025
b02077e
tst: add round-trip test to linear mappings
oesteban Jul 18, 2025
1b544cb
move flake8 config to pyproject
oesteban Jul 18, 2025
c2f9bde
Merge pull request #245 from nipy/codex/migrate-flake8-config-to-pypr…
oesteban Jul 18, 2025
33d91ad
hotfix: make tox pickup flake8 config from ``pyproject.toml``
oesteban Jul 18, 2025
82f58c1
Merge pull request #243 from nipy/codex/add-support-for-affine-and-li…
oesteban Jul 18, 2025
55e6937
tst: refactor io/lta to reduce one partial line
oesteban Jul 18, 2025
a94e577
Merge pull request #246 from nipy/tst/one-less-partial-lta
oesteban Jul 18, 2025
987eaa8
Add failing test for serialized resampling
oesteban Jul 18, 2025
5f08a36
enh: add docstring and doctests for `nitransforms.io.get_linear_factory`
oesteban Jul 18, 2025
5da27b1
FIX: recompute targets for serialized per-volume resampling
oesteban Jul 18, 2025
b562eb3
fix: remove ``__iter__()`` as iterator protocol is not met
oesteban Jul 18, 2025
72cd04f
fix: recompute coordinates per volume in serial resampling
oesteban Jul 18, 2025
4e159c2
fix: generalize targets, test all branches
oesteban Jul 18, 2025
f1efba1
Merge pull request #247 from nipy/codex/investigate-4d-dataset-resamp…
oesteban Jul 18, 2025
a7265e4
Merge branch 'master' into tst/increase-coverage
oesteban Jul 18, 2025
6f497c0
Merge pull request #248 from nipy/tst/increase-coverage
oesteban Jul 18, 2025
4662d29
rel(25.0.0rc0): Update CHANGES [skip ci]
oesteban Jul 18, 2025
22adcfe
Merge branch 'master' into feat/vis
oesteban Jul 19, 2025
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3 changes: 2 additions & 1 deletion .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,8 @@ jobs:
-v /tmp/data/nitransforms-tests:/data -e TEST_DATA_HOME=/data \
-e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \
-v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
-v /tmp/tests:/tmp nitransforms:latest \
-v /tmp/tests:/tmp -e TEST_OUTPUT_DIR=/tmp/artifacts \
nitransforms:latest \
pytest --junit-xml=/tmp/summaries/pytest.xml \
--cov nitransforms --cov-report xml:/tmp/summaries/unittests.xml \
nitransforms/
Expand Down
18 changes: 18 additions & 0 deletions CHANGES.rst
Original file line number Diff line number Diff line change
@@ -1,3 +1,21 @@
25.0.0 (TBD)
============
A new major release with critical updates.
The new release includes a critical hotfix for 4D resamplings.
The second major improvement is the inclusion of a first implementation of the X5 format (BIDS).
The X5 implementation is currently restricted to reading/writing of linear transforms.

CHANGES
-------
* FIX: Broken 4D resampling by @oesteban in https://github.com/nipy/nitransforms/pull/247
* ENH: Loading of X5 (linear) transforms by @oesteban in https://github.com/nipy/nitransforms/pull/243
* ENH: Implement X5 representation and output to filesystem by @oesteban in https://github.com/nipy/nitransforms/pull/241
* DOC: Fix references to ``os.PathLike`` by @oesteban in https://github.com/nipy/nitransforms/pull/242
* MNT: Increase coverage by testing edge cases and adding docstrings by @oesteban in https://github.com/nipy/nitransforms/pull/248
* MNT: Refactor io/lta to reduce one partial line by @oesteban in https://github.com/nipy/nitransforms/pull/246
* MNT: Move flake8 config into ``pyproject.toml`` by @oesteban in https://github.com/nipy/nitransforms/pull/245
* MNT: Configure coverage to omit tests by @oesteban in https://github.com/nipy/nitransforms/pull/244

24.1.2 (June 02, 2025)
======================
New patch release that addresses a crash when applying a 3D transform to a 4D image.
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1 change: 1 addition & 0 deletions docs/examples.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,3 +9,4 @@ A collection of Jupyter Notebooks to serve as interactive tutorials.

notebooks/isbi2020
notebooks/Reading and Writing transforms.ipynb
notebooks/Visualizing transforms.ipynb
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