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BioinformaticDataCompression
QcmpCompressionLibrary
Commits
40825276
Commit
40825276
authored
4 years ago
by
Vojtech Moravec
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Update the README.
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# DataCompressor usage
# DataCompressor usage
**
This branch support loading of 16-bit input files via SCIFIO readers. RAW files will be loaded as before,
DataCompressor allows compression of image files using scalar and vector quantization.
anything else will be loaded by SCIFIO.
**
The application can load RAW image files and all formats supported by the
[
SCIFIO
](
https://imagej.net/SCIFIO
)
library.
Help output:
Help output:
```
```
...
@@ -13,8 +15,8 @@ usage: azgracompress.DataCompressor [options] input
...
@@ -13,8 +15,8 @@ usage: azgracompress.DataCompressor [options] input
-d,--decompress Decompress 16 bit raw image
-d,--decompress Decompress 16 bit raw image
-h,--help Print help
-h,--help Print help
-i,--inspect Inspect the compressed file
-i,--inspect Inspect the compressed file
-mp,--middle-plane Use middle plane for codebook creation
-o,--output <arg> Custom output file
-o,--output <arg> Custom output file
-mp,--middle-plane Use middle plane for codebook training.
-sq,--scalar-quantization Use scalar quantization.
-sq,--scalar-quantization Use scalar quantization.
-tcb,--train-codebook Train codebook and save learned
-tcb,--train-codebook Train codebook and save learned
codebook to cache file.
codebook to cache file.
...
@@ -25,12 +27,13 @@ usage: azgracompress.DataCompressor [options] input
...
@@ -25,12 +27,13 @@ usage: azgracompress.DataCompressor [options] input
```
```
### Quantization types (QT):
### Quantization types (QT):
-
This program supports two
(
*three*
)
different quantization types:
-
This program supports two different quantization types:
-
Scalar quantization, selected by
`-sq`
or
`--scalar-quantization`
-
Scalar quantization, selected by
`-sq`
or
`--scalar-quantization`
-
Vector quantization, selected by
`-vq`
or
`--vector-quantization`
-
Vector quantization, selected by
`-vq`
or
`--vector-quantization`
-
Vector quantization requires you to input the vector dimension after the flag
-
Vector quantization requires you to input the vector dimension after the flag
-
For One-Dimensional row vectors you can the length as
`9`
or
`9x1`
-
For one-dimensional row vectors you can the length as
`9`
or
`9x1`
-
For Two-Dimensional matrix vectors the dimensions is set by
`DxD`
format, eg.
`3x3`
,
`5x3`
-
For two-dimensional matrix vectors the dimensions is set by
`DxD`
format, eg.
`3x3`
,
`5x3`
-
For three-dimensional voxel vectors the dimensions is set by
`DxDxD`
format, eg.
`3x3x3`
,
`5x3x2`
## Main program methods
## Main program methods
...
@@ -51,7 +54,8 @@ usage: azgracompress.DataCompressor [options] input
...
@@ -51,7 +54,8 @@ usage: azgracompress.DataCompressor [options] input
### Inspect
### Inspect
-
Use with
`-i`
or
`--inspect`
-
Use with
`-i`
or
`--inspect`
-
Inspect the compressed file. Read compressed file header are write the information from that header.
-
Inspect the compressed image file or cached codebook.
-
Read compressed file header are write the information from that header.
### Train codebook
### Train codebook
-
Use with
`-tcb`
or
`--train-codebook`
-
Use with
`-tcb`
or
`--train-codebook`
...
@@ -67,12 +71,13 @@ usage: azgracompress.DataCompressor [options] input
...
@@ -67,12 +71,13 @@ usage: azgracompress.DataCompressor [options] input
### Input file
### Input file
-
Input file is required for all methods.
-
Input file is required for all methods.
-
decompress and inspect require only the input file path, while other also require its dimensions
-
Decompress and inspect require only the input file path, while other also require its dimensions
-
Input file dimensions are inputed in format of DxDxD [D] [D-D]
-
If the input file is RAW data file, then image dimensions must be provided as follows:
-
DxDxD is image dimension. Eg. 1920x1080x1, 1041x996x946 (946 planes of 1041x996 images)
-
Input file dimensions are inputed in format of DxDxD [D] [D-D]
-
[D] is optional plane index. Only this plane will be compressed.
-
DxDxD is image dimension. Eg. 1920x1080x1, 1041x996x946 (946 planes of 1041x996 images)
-
[D-D] is optional plane range. Only plane in this range will be compressed.
-
[D] is optional plane index. Only this plane will be compressed.
-
D stands for integer values.
-
[D-D] is optional plane range. Only plane in this range will be compressed.
-
D stands for integer values.
-
Planes selected by the index or plane range are used for:
-
Planes selected by the index or plane range are used for:
-
Compression
-
Compression
-
Training of codebook
-
Training of codebook
...
@@ -83,4 +88,3 @@ usage: azgracompress.DataCompressor [options] input
...
@@ -83,4 +88,3 @@ usage: azgracompress.DataCompressor [options] input
-
`-v`
,
`--verbose`
- Make program output verbose.
-
`-v`
,
`--verbose`
- Make program output verbose.
-
`-o`
,
`--output`
- Set the ouput of compression, decompression, codebook training, benchmark.
-
`-o`
,
`--output`
- Set the ouput of compression, decompression, codebook training, benchmark.
-
`-wc`
,
`--worker-count`
- Set the number of worker threads.
-
`-wc`
,
`--worker-count`
- Set the number of worker threads.
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