Maintenance to clip and threshold application arguments #44
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rossbar
approved these changes
Feb 14, 2023
| considered as a spot. | ||
| spots_clip (bool): Determines if pixel values will be clipped by percentile. | ||
| clip (bool): Determines if pixel values will be clipped by percentile. |
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IIUC the line below should be updated to Defaults to true. Same with the instance above in the _predict_spots_image docstring (I think)
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This PR addresses a naming discrepancy between the
SpotDetectionandPolarisapplications for theclipandthresholdparameters. The default value forclipinSpotDetectionandPolarishave now been set toTrue, because this setting gives better spot detection results on a wider range of images.It also removes a line passing a
thresholdargument into theSpotDetectionapplication inside thePolarisapplication. There are two reasons for this: (1) theSpotDetectionapplication inPolarisis instantiated withpostprocessing_fn=None, so thethresholdargument would not be used, and (2) the default value forthresholdin theSpotDetectionapplication prevents an error from being raised about its value.