Ecosyste.ms: Issues

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GitHub / nipy/nitransforms issues and pull requests

#221 - ENH: Implement a memory limitation mechanism in loading data

Pull Request - State: closed - Opened by oesteban 4 months ago - 1 comment

#220 - ENH: Parallelize serialized 3D+t transforms

Pull Request - State: closed - Opened by oesteban 4 months ago - 1 comment

#219 - MAINT: Update ANTs' pinnings

Pull Request - State: closed - Opened by oesteban 4 months ago

#218 - Implement "low memory" mode in ``apply()``

Issue - State: closed - Opened by oesteban 4 months ago - 1 comment

#216 - FIX: Wrong warning argument name ``level`` in ``warnings.warn``

Pull Request - State: closed - Opened by oesteban 4 months ago - 1 comment

#215 - ENH: Serialize+parallelize 4D ``apply()`` into 3D+t and add 'low memory' loading

Pull Request - State: closed - Opened by oesteban 4 months ago - 5 comments

#214 - Re-enable parallelization in ``apply()``

Issue - State: closed - Opened by oesteban 4 months ago - 2 comments

#212 - Feat: Implement a visualisation feature to NiTransforms

Pull Request - State: open - Opened by jmarabotto 5 months ago - 4 comments

#211 - FIX: Load ITK fields from H5 correctly

Pull Request - State: closed - Opened by effigies 5 months ago - 3 comments

#210 - TEST: Fix tests for Python 3.12, numpy 2.0, and pytest-xdist

Pull Request - State: closed - Opened by effigies 5 months ago - 1 comment

#208 - FIX: Forgotten test using ``xfm.apply()``

Pull Request - State: closed - Opened by oesteban 6 months ago - 2 comments

#207 - FIX: Do not transpose (see scipy.ndimage.map_coordinates docs)

Pull Request - State: closed - Opened by oesteban 6 months ago

#205 - CircleCI tests are broken

Issue - State: closed - Opened by oesteban 6 months ago

#204 - FIX: Indexing disallowed in lists introduced by bugfix

Pull Request - State: closed - Opened by oesteban 6 months ago

#203 - SurfaceTransform class

Pull Request - State: closed - Opened by feilong 6 months ago - 7 comments

#202 - Write a test for the bugfix in #188

Issue - State: open - Opened by oesteban 6 months ago

#201 - ENH: Define ``ndim`` property on nonlinear transforms

Pull Request - State: closed - Opened by oesteban 6 months ago

#200 - steps to write an itk format nifti or h5 file

Issue - State: open - Opened by mattcieslak 6 months ago - 2 comments

#199 - ENH: Enhanced #197, implementing ndim to non-linear transform

Pull Request - State: closed - Opened by jmarabotto 7 months ago

#198 - Abstract data from TransformBase saved to file

Issue - State: open - Opened by jmarabotto 7 months ago

#197 - FIX: Update implementation of ``ndim`` property of transforms

Pull Request - State: closed - Opened by jmarabotto 7 months ago

#196 - Transforms should implement an `ndim` property

Issue - State: closed - Opened by oesteban 7 months ago - 1 comment

#195 - ENH: Outsource ``apply()`` from transform objects

Pull Request - State: closed - Opened by jmarabotto 8 months ago - 2 comments

#194 - FIX _is_oblique

Pull Request - State: closed - Opened by mvdoc 8 months ago - 1 comment

#192 - Offsource `.apply()` as an independent operation

Issue - State: closed - Opened by oesteban 11 months ago

#190 - Migrate to the new pointset representation

Issue - State: open - Opened by oesteban 11 months ago

#189 - FIX: Remove unsafe cast during TransformBase.apply()

Pull Request - State: closed - Opened by effigies 12 months ago - 1 comment

#188 - FIX: Composition of deformation fields

Pull Request - State: closed - Opened by jbanusco 12 months ago

#187 - FIX: Postpone coordinate mapping on linear array transforms

Pull Request - State: closed - Opened by oesteban about 1 year ago - 2 comments

#186 - FIX: Inefficient iterative reloading of reference and moving images

Pull Request - State: closed - Opened by oesteban about 1 year ago - 1 comment

#185 - Mapping of displacement fields

Issue - State: open - Opened by jbanusco about 1 year ago - 3 comments

#183 - Is nitransforms now a full replacement for c3d_affine_tool?

Issue - State: closed - Opened by effigies over 1 year ago - 2 comments

#182 - FIX: Output displacement fields

Pull Request - State: closed - Opened by bpinsard over 1 year ago

#181 - MNT: Drop Python 3.7 support, test through 3.11

Pull Request - State: closed - Opened by effigies over 1 year ago - 3 comments

#180 - Fix: numpy deprecation errors after 1.22

Pull Request - State: closed - Opened by oesteban over 1 year ago

#179 - ENH: Load ITK's ``.mat`` files with ``Affine``'s loaders

Pull Request - State: closed - Opened by oesteban over 1 year ago - 1 comment

#178 - FIX: Ensure datatype of generated CIFTI2 file in ``TransformBase`` unit test

Pull Request - State: closed - Opened by oesteban over 1 year ago - 1 comment

#176 - FIX: Set x-forms on resampled images

Pull Request - State: closed - Opened by oesteban over 1 year ago - 1 comment

#175 - Resampled images do not properly set x-forms

Issue - State: closed - Opened by oesteban over 1 year ago

#174 - ENH: Read ITK's composite transforms with only affines

Pull Request - State: closed - Opened by oesteban over 1 year ago - 4 comments

#173 - Memory issues when resampling large 4D files

Issue - State: closed - Opened by oesteban almost 2 years ago - 16 comments

#172 - MAINT: Rotate CircleCI secrets and setup up org-level context

Pull Request - State: closed - Opened by oesteban almost 2 years ago - 1 comment

#171 - Incorrect dimension order with HDF5 warp field transforms

Issue - State: open - Opened by feilong almost 2 years ago

#170 - ENH: Collapse linear and nonlinear transforms chains

Pull Request - State: open - Opened by oesteban over 2 years ago - 3 comments

#168 - ENH: "Densify" voxel-wise nonlinear mappings with interpolation

Pull Request - State: closed - Opened by oesteban over 2 years ago - 1 comment

#167 - Double-check ITK's `.h5` composites

Issue - State: open - Opened by oesteban over 2 years ago

#166 - ENH: Extend the nonlinear transforms API

Pull Request - State: closed - Opened by oesteban over 2 years ago - 9 comments

#165 - ENH: API change in ``TransformChain`` - new composition convention

Pull Request - State: closed - Opened by oesteban over 2 years ago - 6 comments

#164 - MAINT: Loosen dependencies

Pull Request - State: closed - Opened by mgxd over 2 years ago - 10 comments

#163 - MAINT: Conclude migration ``poldracklab`` -> ``nipy``

Pull Request - State: closed - Opened by oesteban over 2 years ago - 1 comment

#161 - FIX: Wrong datatype used for offset when reading ITK's h5 fields.

Pull Request - State: closed - Opened by oesteban over 2 years ago

#160 - ENH: Guess open linear transform formats

Pull Request - State: closed - Opened by oesteban over 2 years ago - 7 comments

#159 - Add myself as a contributor

Pull Request - State: closed - Opened by HippocampusGirl over 2 years ago - 1 comment

#158 - Obliquity test does not capture rotations around only one axis

Issue - State: closed - Opened by oesteban over 2 years ago - 3 comments
Labels: bug

#156 - Multi-level B-Spline displacements fields

Issue - State: open - Opened by oesteban almost 3 years ago

#155 - Mapping off-grid points with the displacements field transform

Issue - State: closed - Opened by oesteban almost 3 years ago
Labels: bug

#154 - B-Spline mapping of individual points is broken

Issue - State: open - Opened by oesteban almost 3 years ago
Labels: bug

#153 - FIX: Ensure input dtype is kept after resampling

Pull Request - State: closed - Opened by oesteban almost 3 years ago

#152 - ``transform.apply()`` does not keep the dtype of the input image

Issue - State: closed - Opened by oesteban almost 3 years ago
Labels: bug

#151 - Fix #149 replace `_read_mat` with `scipy.io.loadmat`

Pull Request - State: closed - Opened by HippocampusGirl almost 3 years ago - 3 comments

#150 - Implement AFNI's "deoblique" operation

Issue - State: closed - Opened by oesteban almost 3 years ago

#149 - `DeprecationWarning` with scipy 1.8.0

Issue - State: closed - Opened by HippocampusGirl almost 3 years ago - 4 comments

#148 - MAINT: Fix path to test summaries in CircleCI

Pull Request - State: closed - Opened by oesteban almost 3 years ago

#146 - FIX: Add FSL-LTA-FSL regression tests

Pull Request - State: closed - Opened by oesteban almost 3 years ago - 1 comment

#145 - FIX: Refactor of LTA implementation

Pull Request - State: closed - Opened by oesteban almost 3 years ago - 2 comments

#144 - FIX: Increase FSL serialization precision

Pull Request - State: closed - Opened by effigies almost 3 years ago

#143 - FIX: Load arrays of linear transforms from AFNI files

Pull Request - State: closed - Opened by oesteban almost 3 years ago - 1 comment

#142 - FIX: Load arrays of linear transforms from FSL files

Pull Request - State: closed - Opened by oesteban almost 3 years ago - 2 comments

#141 - FIX: Double-check dtypes within tests and increase RMSE tolerance

Pull Request - State: closed - Opened by oesteban almost 3 years ago - 1 comment

#140 - MAINT: Move testdata on to gin.g-node.org & datalad

Pull Request - State: closed - Opened by oesteban almost 3 years ago

#139 - MAINT: scipy-1.8, numpy-1.22 require python 3.8

Pull Request - State: closed - Opened by oesteban almost 3 years ago

#138 - ENH: Base implementation of B-Spline transforms

Pull Request - State: closed - Opened by oesteban almost 3 years ago - 3 comments

#137 - Problem applying h5-files from fmriprep outputs for reproduction of normalization

Issue - State: open - Opened by m-petersen almost 3 years ago - 6 comments
Labels: bug

#136 - DOC: Add zenodo metadata record

Pull Request - State: closed - Opened by oesteban about 3 years ago

#135 - FIX: Final edits to JOSS submission

Pull Request - State: closed - Opened by oesteban about 3 years ago - 1 comment

#134 - ENH: Add more comprehensive comments to notebook

Pull Request - State: closed - Opened by oesteban about 3 years ago

#133 - DOC: Better document the ipython notebooks

Pull Request - State: closed - Opened by oesteban about 3 years ago - 2 comments

#132 - FIX: Add mention to potential alternatives in JOSS submission

Pull Request - State: closed - Opened by oesteban about 3 years ago - 1 comment

#131 - DOC: Transfer CoC from NiBabel

Pull Request - State: closed - Opened by oesteban about 3 years ago - 1 comment

#130 - DOC: Add contributing page to RTD

Pull Request - State: closed - Opened by mgxd over 3 years ago - 1 comment

#129 - FIX: Misinterpretation of voxel ordering in LTAs

Pull Request - State: closed - Opened by oesteban over 3 years ago - 4 comments

#128 - DOC: Clarify integration plans with *NiBabel* in the README

Pull Request - State: closed - Opened by oesteban over 3 years ago - 1 comment

#127 - DOC: Add CONTRIBUTING.md file pointing at NiBabel

Pull Request - State: closed - Opened by oesteban over 3 years ago - 2 comments

#126 - DOC: Add example notebooks to sphinx documentation

Pull Request - State: closed - Opened by mgxd over 3 years ago - 2 comments

#125 - BUG: Errors reading LTAs, especially interpreting VOX2VOX type

Issue - State: closed - Opened by oesteban over 3 years ago - 1 comment
Labels: bug

#124 - FIX: Invalid DOI

Pull Request - State: closed - Opened by mgxd over 3 years ago - 1 comment

#123 - JOSS review - software

Issue - State: closed - Opened by robbisg over 3 years ago - 3 comments

#122 - DOC: Add an *Installation* section

Pull Request - State: closed - Opened by oesteban over 3 years ago - 3 comments