Print help message on -h/--help or when invalid options are passed

[hanslovsky]

It is unclear how to open a cremi data set in BigCAT from the command line without looking at the source code. In case of failure or -h/--help no help message is printed to assist with what command line arguments/parameters to use.

For example:

$ java -jar $PWD/target/bigcat-0.0.4-SNAPSHOT-jar-with-dependencies.jar -i ~/Downloads/sample_B_padded_20160501.hdf
creating default input trigger config
Opening raw from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Opening canvas from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Exception in thread "main" java.lang.IllegalArgumentException: dimensions[ 0 ] <= 0
        at net.imglib2.img.cell.CellImgFactory.verifyDimensions(CellImgFactory.java:116)
        at net.imglib2.img.cell.CellImgFactory.createInstance(CellImgFactory.java:205)
        at net.imglib2.img.cell.CellImgFactory.createLongInstance(CellImgFactory.java:177)
        at net.imglib2.img.cell.CellImgFactory.createLongInstance(CellImgFactory.java:62)
        at net.imglib2.type.numeric.integer.LongType.createSuitableNativeImg(LongType.java:81)
        at net.imglib2.img.cell.CellImgFactory.create(CellImgFactory.java:147)
        at bdv.bigcat.BigCat.initCanvas(BigCat.java:204)
        at bdv.bigcat.BigCat.init(BigCat.java:148)
        at bdv.bigcat.BigCat.main(BigCat.java:121)

does not help me in figuring out what parameters to use.

I guessed that I need to add use -l volumes/labels/neuron_ids:

$ java -Xmx16g -jar $PWD/target/bigcat-0.0.4-SNAPSHOT-jar-with-dependencies.jar -i ~/Downloads/sample_B_padded_20160501.hdf -l volumes/labels/neuron_ids
Opening raw from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Opening canvas from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Opening labels from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Exception in thread "main" java.lang.IllegalArgumentException: invalid range properties
        at javax.swing.DefaultBoundedRangeModel.<init>(DefaultBoundedRangeModel.java:102)
        at javax.swing.JSlider.<init>(JSlider.java:274)
        at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:302)
        at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:94)
        at bdv.BigDataViewer.<init>(BigDataViewer.java:339)
        at bdv.bigcat.ui.Util.createViewer(Util.java:225)
        at bdv.bigcat.BigCat.setupBdv(BigCat.java:309)
        at bdv.bigcat.BigCat.main(BigCat.java:122)

Some progress was made, the error looks different now, but still not there, maybe '-r volumes/raw

java -Xmx16g -jar $PWD/target/bigcat-0.0.4-SNAPSHOT-jar-with-dependencies.jar -i ~/Downloads/sample_B_padded_20160501.hdf -l volumes/labels/neuron_ids -r volumes/raw
creating default input trigger config
Opening raw from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Opening canvas from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
Opening labels from /home/hanslovskyp/Downloads/sample_B_padded_20160501.hdf
AnnotationsHdf5Store: detected file format 0.2

This works now but a sanity check of the inputs and/or a --help/-h message would have sped up the process significantly.

[axtimwalde]

You are right, but BigCAT is phasing out for Paintera anyways---right?

[hanslovsky]

It is but as long as there are no annotations in paintera (and it is unclear to me when they will be there), BigCAT will always be useful. Whenever I try to help people, I have to figure it out again. At least, the readme should have a working exapmle with all the required parameters.