Closed talonchandler closed 3 months ago
Attention: Patch coverage is 8.51064%
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Project coverage is 9.54%. Comparing base (
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Files | Patch % | Lines |
---|---|---|
recOrder/io/visualization.py | 0.00% | 41 Missing :warning: |
recOrder/plugin/main_widget.py | 0.00% | 2 Missing :warning: |
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Paired with
https://github.com/czbiohub-sf/shrimPy/pull/141
, which will close without merging.This PR merges @edyoshikun's color overlays from shrimpy into
recOrder
while making necessary changes to both sets of functions:czyx
-shaped arrays as a single input for compatibility with our parallelization strategy. This required a fairly significant change torecOrder
's handling of dask arrays.channel_order
parameter.The new function signatures are:
det ret_ori_overlay(czyx, ret_max: Union[float, Literal["auto"]] = 10, cmap: Literal["JCh", "HSV"] = "JCh"):
def ret_ori_phase_overlay(czyx, max_val_V: float = 1.0, max_val_S: float = 1.0):
I have tested the new
ret_ori_overlay
on the example datasets (to check the lazy-computed dask arrays), and I've tested both new functions in CI.Notes:
ret_ori_phase_overlay
withJCh
, but I now think that this case is covered byret_ori_overlay
with theJCh
option.recOrder.io.visualization
, and I anticipate this code will move toiphub
.