scifio / scifio-itk-bridge Goto Github PK

If ITK already has an ImageIO that covers the same format as SCIFIO, it is queried first. But the data isn't guaranteed properly formatted for the SCIFIO writer. It would be nice to ensure that SCIFIO Writers are only invoked if given a SCIFIO ImageIO.. and one way to do that would be to just always make SCIFIO ImageIO the top choice.

Tiles get scrambled at random when importing 2d images from czi. If czi has multiple channels, all the channels in the tile are scrambled. Following code used to import czi and write nrrd files for each channel.
https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp
Sample images sent to Mark Hiner.

Currently you have to recompile to change the pixel type, component type, etc...

these should be configuration options, as well as being RGB/Vector/etc...

Currently metadata key, value pairs are read during ReadImageInformation without any handshaking to signify the start of the read. This means that, say, starting the JVM with the agentlib flag - which prints a "listening on port xxxx" - destroys the metadata table, which kills the whole process.

So we just need a handshaking step that discards anything in the input stream before reading K,V pairs.

Currently the Vector image test makes a fixed 3x3 vector instead of a # of images x # components vector. This should be fixed (with number of vectors being a command line argument)

Unfortunately I don't think we can dynamically discover the dimensionality because it needs to be declared in the Test level and not the IO level. If it is possible though, it would be ideal to get the # of images in a dataset from the IO and then adjust the pixel type accordingly.

Currently the ITKBridge class still uses loci.formats IFormatReader to open images.

It should be converted to use the SCIFIO API.

Before this can happen we need a Bio-Formats Format and a sezpoz-safe loci-tools.jar.
Depends on:
scifio/scifio#5
scifio/scifio#6

The ITK Download script should also be updated to download both Bio-Formats and SCIFIO by default.