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scifio-tutorials's Introduction

This project contains example code for working with SCIFIO.

GETTING STARTED

These tutorials are heavily commented to explain the SCIFIO API. Simply running a given tutorial may not be meaningful; it is highly recommended to open the source files and follow the code step by step.

You can import these projects into your favorite IDE:

  • Eclipse: File > Import > Existing Maven Projects
  • NetBeans: File > Open Project
  • IDEA: File > Open Project... (select pom.xml)

Or build and run from the command line:

mvn
mvn exec:java -Dexec.mainClass=io.scif.tutorials.T1aIntroToSCIFIO

TUTORIAL ORDER

SCIFIO provides multiple paths to read and write images. Convenience methods are present to make the IO process as simple as possible. The individual components of SCIFIO allow more precise control.

The tutorials are named in a suggested order for execution:

  • Tutorials 1a-d focus on basic image IO using convenience methods
  • Tutorials 2a-b cover individual component use
  • Tutorials 3a-b explain the discovery mechanism and defining your own SCIFIO Formats and components.

LICENSING

To the extent possible under law, the SCIFIO developers have waived all copyright and related or neighboring rights to this tutorial code.

See the CC0 1.0 Universal license for details.

scifio-tutorials's People

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scifio-tutorials's Issues

Better explain planar/non-planar axes

I think this concept is very confusing, as the phrase "planar axis" conveys an idea of "contributing to plane count" to many people. At the least it a there should be a good tutorial explaining this distinction and why it is this way (abstraction that was necessary to handle interleaved/non-interleaved/non-planar Channel scenarios)

Exception in T1cReadingTilesGood

I'm trying to use T1cReadingTilesGood with a real image, using SCIFIO 0.27.1. I changed the hugeImage variable to the pathname of a tiled TIFF image. When I run it, I get an exception:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 2
at io.scif.util.FormatTools.checkTileSize(FormatTools.java:671)
at io.scif.util.FormatTools.checkPlaneForWriting(FormatTools.java:647)
at io.scif.util.FormatTools.checkPlaneForReading(FormatTools.java:632)
at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:610)
at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:537)
at io.scif.AbstractReader.openPlane(AbstractReader.java:150)
at io.scif.AbstractReader.openPlane(AbstractReader.java:52)
at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
at T1cReadingTilesGood.main(T1cReadingTilesGood.java:96)

This is on the first iteration of the inner for loop. The arguments passed to openPlane() are 0, 0, { 0,0 }, { 128, 128 }.

The same ArrayIndexOutOfBoundsException happens with every type of image I try, though the stack trace differs.

Add a tutorial on how to use the TIFF classes

From a thread on forum.image.sc:

But build and write of a standard Tiff file should be possible, as there are lots of TIFF classes in the io.scif.media.imageio.plugins.tiff. library? And GeoTiff is just Tiff Standard Version 6 plus some additional, geo-specific tags.

Hence, question without Geo would be: But which classes are needed (Writer, TIFFSaver, โ€ฆ?) to construct and write a Tiff file? How to build the dataset and tag entities and save them as a Tiff file?

Create "Advanced" tutorials

Would be nice to create some tutorials to highlight the features of SCIFIO that stand out, e.g. compared to Bio-Formats.

Some ideas for this series of tutorials:

  • Modifying reader behavior via filters
  • Configuration through high-level API via SCIFIOConfig
  • Opening a large dataset and manipulating the planes, using caching

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