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Refactor selection workflow #17
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439ffe6
use dictionaries + introduce classes list
sophiamaedler 943cc32
ensure consistent typing, fix bug
sophiamaedler 50839f3
update docstring
sophiamaedler b38bdd1
make processes and threads consistent
sophiamaedler 670e6f1
Merge branch 'improve_selection_big_datasets' into refactor_selection…
sophiamaedler c8752d8
make typing consistent
sophiamaedler 0f907af
implement additional coordinate lookup calculation method
sophiamaedler c740a96
cleanup print statements
sophiamaedler e6ee255
improve log output
sophiamaedler e3adbef
add numba accelerated sparse coordinate calculation
sophiamaedler bc88147
fix incorrect assumption
sophiamaedler 4b954b3
add safety check to ensure that no cell_id with empty coordinates is …
sophiamaedler 639e8d0
fix typo
sophiamaedler 500fc19
cleanup log output
sophiamaedler 249f942
improve debug plot
sophiamaedler 91697f1
limit number of processes to number of cell sets that need to be proc…
sophiamaedler 8881a13
further improvements to look of debugging plot
sophiamaedler 66a6316
add possibility to return plot and improve plot look
sophiamaedler f6d64d8
perform line compression with the Ramer–Douglas–Peucker algorithm
sophiamaedler 45d5ca8
fix default parameter values for rdp_epsilon
sophiamaedler 5053a8f
update python version dependency
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One could potentially reduce code complexity by using a dictionary of typed Lists instead of numpy arrays, as lists can be quickly appended on the fly instead of extending (and resizing) the numpy arrays. To do so, the
_numba_accelerator_coord_calculation
could be modified so that it uses typed lists instead of arrays as data representation:The
_create_coord_index_sparse
function stays the same except for the added dictionary comprehension at the end to obtain numpy arrays.There was a problem hiding this comment.
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Compared to the current implementation, this leads to a slight overhead in scenarios with many cells (due to the additional dictionary comprehension at the end) in small and medium-sized images but is not noticeable for large images.
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Code for benchmarks
Benchmarking