SVSWriter reads "app_mag" from kwargs (default None).
Add shaped=False to TiffWriter context manager init (i.e. don't overwrite description with numpy style shape).
Add approximation of AppMap from MPP if only MPP given.
MPP SVS metadata is the mean of the reader mpp (falls back to SVSWriter init kwarg) or not written if None.
Set "outcolorspace" when writing SVS pages using tifffile.
Correctly filter out thumbnail warnings for approx_ok.
Change subfiletype to 0 (regular IFD) from 1 (reduced resolution).
Add docstring notes to SVSWriter:
- When writing tiled TIFF files, the tiles must all be the same size and must be written in the order left-to-right, then top-to-bottom (row-by-row). Tiles cannot be skipped.
- Microns per pixel (MPP) is taken from microns per pixel of the reader if not provided. If microns per pixel is set to None, microns per pixel will not be written to the file.
- The SVS MPP metadata is the mean of microns_per_pixel from init or the reader.
- Apparent magnification (AppMag) can be specified as a float to the optional "app_mag" kwarg.
- If only an MPP resolution is given, the AppMag will be approximated from the MPP (by AppMag = 10 / MPP) and rounded to the nearest common AppMag (10, 20,40, 50, 60, 80, 100, 125, 150, 200, 250, 312.5, 375, 500, 600, 750, 1000, 1250). If neither MPP or AppMag are given, no resolution will be written to the file.

Codecov Report

:exclamation: No coverage uploaded for pull request base (dev@efa93ca). Click here to learn what that means. The diff coverage is 92.30%.

:exclamation: Current head 2a584dd differs from pull request most recent head 0f46cf7. Consider uploading reports for the commit 0f46cf7 to get more accurate results

@@          Coverage Diff           @@
##             dev      #58   +/-   ##
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  Coverage       ?   89.82%           
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  Files          ?       12           
  Lines          ?     1347           
  Branches       ?        0           
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  Hits           ?     1210           
  Misses         ?      137           
  Partials       ?        0

Impacted Files	Coverage Δ
wsic/writers.py	`86.01% <92.30%> (ø)`

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John-P / wsic

:bug: Fix MPP/AppMag Writing in SVSWriter #58

Codecov Report