extraction.core.functions.cell¶
Base functions to extract information from a single cell
These functions are automatically read by extractor.py, and so can only have the cell_mask and trap_image as inputs and must return only one value.
- They assume that there are no NaNs in the image.
We use bottleneck when it performs faster than numpy:
Median
values containing NaNs (We make sure this does not happen)
Functions
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Find the area of a cell mask |
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Estimates the volume of the cell |
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Find the eccentricity using the approximate major and minor axes |
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Finds the mean of the brightest 2.5% of pixels in the cell. |
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Finds the mean of the five brightest pixels in the cell. |
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Finds the mean of the pixels in the cell. |
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Finds the median of the pixels in the cell. |
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Finds the lengths of the minor and major axes of an ellipse from a cell mask. |
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Estimates the volume of the cell assuming it is a sphere with the mask providing a cross-section through the median plane of the sphere. |
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Finds the standard deviation of the values of the pixels in the cell. |
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Estimates the volume of the cell assuming it is an ellipsoid with the mask providing a cross-section through the median plane of the ellipsoid. |