Reconstruct a subset of time indices #398
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@@ Coverage Diff @@
## main #398 +/- ##
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+ Coverage 7.14% 7.16% +0.02%
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Files 25 25
Lines 4435 4436 +1
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+ Hits 317 318 +1
Misses 4118 4118
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Should d2331d9 be ported into this PR? |
changed initialization
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Great call @ziw-liu. I cherry-picked that commit and modified the condition to create a new array (instead of checking if 0 is in time_indices, I'm checking if an array already exists). |
ziw-liu
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Aug 8, 2023
ziw-liu
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Aug 8, 2023
ziw-liu
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Aug 8, 2023
Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
ziw-liu
approved these changes
Aug 8, 2023
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Thanks for the improvements @ziw-liu! |
talonchandler
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Aug 9, 2023
* add `time_indices` to config file * `apply-inv-tf` for subsets of timepoints * test single time index, list of indices, and "all" * check invalid times * test time axis lengths * catch off by one errors * save to output indices * formattings * better tests * changed output shape changed initialization * create an emtpy array if one doesn't exist * fix time indexing * fix tests * Update recOrder/cli/apply_inverse_transfer_function.py Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> * remove unused lines * Update recOrder/cli/apply_inverse_transfer_function.py Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> --------- Co-authored-by: Clinton Huynh <clinton.huynh@czbiohub.org> Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
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recorder reconstructnaively loops through all time points, applying the reconstruction as it goes. This default is limiting for datasets with a large number of time points where it is more convenient to reconstruct a single time point on a single core (via multiprocessing or slurm).This PR adds a configuration-file option
time_indiceswith signature:time_indices: Union[NonNegativeInt, List[NonNegativeInt], Literal["all"]] = "all"By default
time_indices: "all"reconstructs all time point, which is backwards compatible.If
time_indices: 5, then only time-point 5 will be reconstructed.Finally, if
then the 0th, 5th, and 10th indices will be reconstructed.
@edyoshikun requested this feature for simplifying parallel reconstructions with
recOrder, and I expect we'll use a similar feature inmantis.