# Data compression project

### TODO LIST
- [x] Tweak Z-Order reordering
  - Values, which are stored in more than one byte, must stay together.
  - Pixels, which contains more `channels`, can be separeted in final z order. (Try both separeted and not-separated)
    - Right now, when we `reorder` bytes we move *whole* pixel (*all channels*), but when pixel's channels will be separated we will move just one channel.
- [x] Feed binary data to existing compressors and produce results (tables, graphs)
- Try both data in their order and in `Z-order`
- Compressors to try:
  - [x] gzip (zLib, huffman deflate combination)
  - [x] bzip2
  - [x] LZMA (7-zip)
  - [x] Add *level* CLI option to specify compression level for above algorithms
  - [x] Add CSV writer, which will write test results to file and test function taking folder with test files to parse.
- **DEADLINE 04.03.2019**
- [ ] Write about Z-Curve order, plot Z-Curve comparsion with normal order.
- [ ] Plot/into tables, BPP (Bits Per Pixel), Compression throughput (MB/s).
- [ ] Benchmark B^3D cuda library
- [ ] Look at *Image difference*
  - Negative values can be mapped to odd/even numbers. But the difference must be saved in more than one byte.
  - Save difference in different type than byte (`short`, `uint`, `ulong`)


## CZI parser TODO list
This is list of things, which have to be done first:
- [x] Parse `SubBlockDirectory` (there will be collection of `DirectoryEntryDV`'s)
  - [x] Exact copy of `DirectoryEntryDV` will be located in the referenced `SubBlock`
  - [x] Parse dimensions entries
- [x] Parse IEEE 4 / 8 byte float.
  - Parsing is done via `memcpy` call. Other alternative is using `union`, but double parsing wass't working with it. Later we can take a look on this and maybe improve the conversion and get rid of the copy.
- [x] Parse `SubBlock`
    - [ ] ~~Parse image data to proper pixel type~~. Do we really want to do that? We really care only about **bytes**. Parsing image data into some `PixelType` Matrix may be good, only if we want to do some operation on the image. This is moved to *later* section then.
- [x] Parse / extract image data from `SubBlock`
  - We are aware of position and size of the data in CZI file. With that two informations we can extract the data easily.
- [x] Parse image values into matrices. `Matrix<Gray8>` etc.
- **This is outside the scope of this project. Main goal is to try and compare different compressions on image data. Right now we are able to obtain image data and more, so it is enaugh for now.**
  - ~~Parse important informations from XML metadata (e.g. BitsPerPixel and compare with value from parsed binary data)~~
  - ~~Support multi-file situations~~
    - ~~Obtain multi-file CZI files. Currently we don't have any multi-files, so we can't really parse them. Secondary files should have different GUID than master file, also filepart should be different from 0. Files we have right now have (0) in their name, but theirs filepart is 0 and GUID of master file isn't set correctly.~~
    - ~~One master file and more *secondary files* files (our current `CziFile` class kinda support that situations, so keep going that way)~~

## Compression of images
- I tested [FLIF](https://flif.info/) compression on ~200 MB file. Compression ratio was good but the speed on the other hand was really bad. Decompression wasn't better, it was slow too.
  - Even lossy compression was slow. This compression is probably only good for small images.

## Space filling (*Peano*) curves
- [Wikipedia](https://en.wikipedia.org/wiki/Space-filling_curve)
- Find out what is this about
- Look specifinally at [Z-order curve](https://en.wikipedia.org/wiki/Z-order_curve) and [Hilbert curve](https://en.wikipedia.org/wiki/Hilbert_curve)
- 


## Image difference
- Find difference between included images.
- Plot those differences and find out if certain images aren't same, just positioned little bit differently 
- *Pattern matching* - Find if there are some patterns in image sets.