These tools are, for the most part, developed specifically to convert the Kalypso slice-based data.
The One-Click All-In-One Converter is wrapper for the other four mentioned tools provided to easily convert the Kalypso slice-based data into a compressed format that the VIDI-VSR can read. It converts 508 8192x8192 slices into chunks and then into compressed blocks, then generates a small downsampled version to use for navigation. Simply point it to the first slice, put in a destination directory, and click OK (and probably go out to dinner or something). It'll be done in a few (7-8 on this machine) hours.
Just pick your first slice, a destination, and click go.
The only options provided are the ones for the compressor and skipping a step (should you have completed the previous steps and say your computer shut off). The steps go in the following order:
Note: The Nav Cube step is really two steps, and will also tally a histogram for the entire data set.
This is the chunker. It will take the slices and make chunks out of it that the compressor can handle. It will also generate the inital header file. The default options are those used in the all-in-one converter.
Just pick your first slice, and click Start.
This is the compressor. It works by taking smaller chunks from chunks created by the chunker, and using a 5/3 wavelet transform to allow for a JPEG2000-like compression scheme. Just point it to your header file that was generated by the chunker (it will be in a directory called chunks in your slices directory) and choose a destination.
Point it at a header file, pick an output folder, and go!
As you can see, the compressor has many options to tinker with. These options are the same as in the All-In-One.
This field determines whether the data in the chunk will be quantized to 16 bits, 12 bits, or 8 bits. If the Max in the data set is less than the 8 bit threshold multiplied by the RMS of the data set, it will be quantized to 8 bits. If it's larger than that, but less than the 12 bit threshold multiplier, then it will be quantized to 12 bits. Everything else will be quantized to 16 bits.
Each block keeps its own relative noise level, and that's determined by these fields. The threshold will be stored as (Multiplier)*RMS of the block.
This determinds how lossy the compression for each type of block is. 0 would be lossless compression, and the higher the number the smaller the compressed blocks will be (but the more likely there will be artifacts.
There are two downsamplers that the VIDI-VLSVR needs to build its navigation cube. Along the way, it also samples the data set to make the histogram.
Enter the slice dimensions and number of slices, choose which directions you'd like to downsample, pick how many times you want to downsample each slice (each time reducing the selected dimensions by half), and click go. When it's done, it will have saved all the downsampled slices as a single volume called 'navorig' in the destination folder. It's also necessary to point this program to the header file generated by the chunker, as that will contain the minimum and maximum of the entire data set so that each slice can be correctly scaled between [0,1].
Point it at the first slice you want to downsample, a header file, pick an output folder, and go!
This is used to change downsample the original nav cube from 512x512x508 to 256x256x254 in the One-Click coverter.
This program can downsample a volume of just about any (reasonable) size and will save it as a block of 16-bit unsigned shorts.
