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Add notes on --downsample-type #235

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Jan 18, 2024
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Add notes on --downsample-type #235

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Add notes on --downsample-type
melissalinkert Jan 15, 2024
19829f1
Add single space to fix indenting
melissalinkert Jan 17, 2024
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18 changes: 18 additions & 0 deletions README.md
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Expand Up @@ -24,6 +24,13 @@ The native libraries are not packaged with any relevant jars. See also note in
* Ubuntu 18.04+: `apt-get install libblosc1`
* conda: Installing `bioformats2raw` via conda (see below) will include `blosc` as a dependency.

If using features that rely on OpenCV (see the [Downsampling type](#downsampling-type) section below), minimum supported versions are:

* Ubuntu 18.04
* RHEL 8
* Windows 10
- expect to see warnings as described in https://github.com/opencv/opencv/issues/20113; these can be ignored
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This renders at the same level as the previous bullet point. Maybe turn into parentheses?

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19829f1 should fix the bullet points, I just missed a single space. Can put the note about warnings on the same line in parentheses if you think that's clearer though?


__NOTE:__ If you are setting `jna.library.path` via the `JAVA_OPTS` environment variable, make sure the path is to the folder __containing__ the library not path to the library itself.

Installation
Expand Down Expand Up @@ -309,6 +316,17 @@ This is particularly helpful if you do not have write permissions in the input d
As of version 0.5.0, `.*.bfmemo` files are deleted at the end of conversion by default. We do not recommend keeping these files for normal
conversions, but if they are needed for troubleshooting then the `--keep-memo-files` option can be used.

Downsampling type
=================

By default, pyramid resolutions are generated using a [very simple downsampling algorithm](https://github.com/ome/ome-common-java/blob/master/src/main/java/loci/common/image/SimpleImageScaler.java).
For some input data types, this may not be ideal. The `--downsample-type` option can be used to specify an alternative algorithm.
Supported values are `SIMPLE` (default), `GAUSSIAN`, `AREA`, `LINEAR`, `CUBIC`, and `LANCZOS`, as declared in the [Downsampling enum](https://github.com/glencoesoftware/bioformats2raw/blob/master/src/main/java/com/glencoesoftware/bioformats2raw/Downsampling.java).
No additional downsampling algorithms are directly implemented in bioformats2raw; OpenCV is used to for any value of `--downsample-type` other than the default.

If the minimum system requirements (see above) are not met, or the input data type is int8 or int32 (see https://github.com/glencoesoftware/bioformats2raw/pull/199),
then any value of `--downsample-type` other than the default is expected to throw an exception.

Additional readers
==================

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