diff --git a/README.md b/README.md index f1ec12c..de1e01c 100644 --- a/README.md +++ b/README.md @@ -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 + __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 @@ -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 ==================