ViSUS Convert

Introduction

ViSUS convert is the tool that allows to convert data from different file formats (i.e. mainly image formats and raw) to IDX.

The supported formats are the ones supported by FreeImage.

In the following examples we will use the variable $CONVERT as the visus convert executable. You can set this variable using your OS commands like:

export CONVERT=/path/to/visus_executable

or

setenv CONVERT /path/to/visus_executable

The variable $RESOURCES is used instead to indicate a folder that contains the data to convert.

Some useful definitions:

a box defines the extent of the domain where the samples are placed for each dimension
the dims are the number of samples for each dimension
the dtype (i.e. datatype) is defined as a combination of the number type and the number of components (e.g. an RGB vector uint8 with 3 components will be uint8[3], for single component a simple uint8 can be used)

Examples

Simple conversion

For very simple conversions, all you need is:

$CONVERT import $RESOURCES/cat_gray.tga create temp/cat_gray.idx

Get information

To *get information* about any file (including non-idx), use info

$CONVERT info $RESOURCES/cat_gray.tga
$CONVERT info $RESOURCES/cat_rgb.tga
$CONVERT info temp/cat_gray.idx
$CONVERT info temp/cat_rgb.idx

Create the IDX dataset

To explicitly create the idx volume

You can define a set of fields:

fields="scalar uint8 compressed + vector uint8[3] compressed"

and use the following to create the dataset

$CONVERT create temp/test_formats.idx --box "0 511 0 511" --fields "$fields"

Convert a stack of images

Very often microscopy images or MRI are simply bit stack of 2D images. Here is how you can easily convert them in a single IDX dataset using visusconver:

# path to your brand new IDX file
IDXFILE="G:/visus_dataset/2kbit1/visus.idx"

# box is specified as [x1 x2] [y1 y2] [z1 z2], min-max included (in this case the dataset has size 2048^3)
BOX="0 2047 0 2047 0 2047"

# change your data DTYPE (in this case a single Uint8)
DTYPE="uint8[1]"

$CONVERT --create "$IDXFILE" --box "$BOX" --fields "DATA $DTYPE $COMPRESSION"

# example of conversion of png slices to IDX
for sliceid in $(seq -f "%04g" 0 2047)
do
  $CONVERT \
     --import "G:/visus_dataset/2kbit1/png/$sliceid.png" \
     --export "$IDXFILE" --box "0 2047 0 2047 $sliceid $sliceid" 
done

Tiled dataset

Multiple images can be combined (as tiles) to compose a panorama or volume (e.g. stack of images from an MRI scan).

This can be easily performed specifying the destination box of each image, as following:

$CONVERT import $RESOURCES/cat_gray.tga export temp/test_formats.idx --field scalar --box "  0 255     0 255" 
$CONVERT import $RESOURCES/cat_gray.tga export temp/test_formats.idx --field scalar --box "256 511     0 255"
$CONVERT import $RESOURCES/cat_gray.tga export temp/test_formats.idx --field scalar --box "  0 255   256 511"
$CONVERT import $RESOURCES/cat_gray.tga export temp/test_formats.idx --field scalar --box "256 511   256 511"

Conversion from IDX to image

Conversion from IDX to image formats can be performed as well using the same technique, as following:

$CONVERT import temp/test_formats.idx --field scalar --box "  0 255     0 255"  export temp/test_formats_scalar.tga 
$CONVERT import temp/test_formats.idx --field scalar --box "256 511     0 255"  export temp/test_formats_scalar.jpg  
$CONVERT import temp/test_formats.idx --field scalar --box "  0 255   256 511"  export temp/test_formats_scalar.tif  
$CONVERT import temp/test_formats.idx --field scalar --box "256 511   256 511"  export temp/test_formats_scalar.bmp 
$CONVERT import temp/test_formats.idx --field scalar --box "128 383   128 383"  export temp/test_formats_scalar.png

Compression

You can compress your dataset (already created) using zip or lz4, as following

$CONVERT --compress-dataset your_dataset.idx lz4

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