ENH: Add a memory check to dynamically limit interpolation blocksize #156
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With very dense coefficients fields, we need to allocate a sparse array of npixels x ncoefficients x 3-D x 32-bit. This allocation is short-lived and can be chunked in segments. This PR dynamically adjusts the chunk size to the actual amount of free memory.
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@@ Coverage Diff @@
## master #156 +/- ##
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+ Coverage 94.44% 94.49% +0.04%
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Files 19 19
Lines 1171 1181 +10
Branches 153 153
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+ Hits 1106 1116 +10
Misses 37 37
Partials 28 28
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2.0.0rc4 * FIX: Convert SEI fieldmaps given in rad/s into Hz (#127) * FIX: Limit ``3dQwarp`` to maximum 4 CPUs for stability reasons (#128) * ENH: Generate a simple mask after correction (#161) * ENH: Increase unit-tests coverage of ``sdcflows.fieldmaps`` (#159) * ENH: Optimize tensor-product B-Spline kernel evaluation (#157) * ENH: Add a memory check to dynamically limit interpolation blocksize (#156) * ENH: Massage TOPUP's fieldcoeff files to be compatible with ours (#154) * ENH: Add a simplistic EPI masking algorithm (#152) * ENH: Utility that returns the ``B0FieldSource`` of a given potential EPI target (#151) * ENH: Write ``fmapid-`` entity in Derivatives (#150) * ENH: Multiplex fieldmap estimation outputs into a single ``outputnode`` (#149) * ENH: Putting the new API together on a base workflow (#143) * ENH: Autogenerate ``B0FieldIdentifiers`` from ``IntendedFor`` (#142) * ENH: Finalizing the API overhaul (#132) * ENH: Keep a registry of already-used identifiers (and auto-generate new) (#130) * ENH: New objects for better representation of fieldmap estimation (#114) * ENH: Show FieldmapReportlet oriented aligned with cardinal axes (#120) * ENH: New estimation API (featuring a TOPUP implementation!) (#115) * DOC: Minor improvements to the literate workflows descriptions. (#162) * DOC: Fix typo in docstring (#155) * DOC: Enable NiPype's sphinx-extension to better render Interfaces (#131) * MAINT: Drop Python 3.6 (#160) * MAINT: Enable Git-archive protocol with setuptools-scm-archive (#153) * MAINT: Migrate TravisCI -> GH Actions (completion) (#138) * MAINT: Migrate TravisCI -> GH Actions (#137) * MAINT: Minimal unit test and refactor of pepolar workflow node (#133) * MAINT: Collect code coverage from tests on Circle (#122) * MAINT: Test minimum dependencies with TravisCI (#96) * MAINT: Add FLIRT config files to prepare for TOPUP integration (#116)
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With very dense coefficients fields, we need to allocate a sparse
array of npixels x ncoefficients x 3-D x 32-bit.
This allocation is short-lived and can be chunked in segments.
This PR dynamically adjusts the chunk size to the actual amount of
free memory.