Module: Convert To Large Data Format ()

Description:

This module allows the conversion of large image data to LDA file format (default) or to Large Disk Data.

Conversion to LDA format can be applied to original data of the following formats: , Raw Data, Stacked Slices (stacks of SGI, TIFF, GIF, JPEG, BMP, PNG, JPEG2000, PGX, PNM, and RAS raster files), SEG-Y and Bio-Formats (The license is required).

To create a Convert To Large Data Format module, use the File menu's Convert To Large Data Format submenu. Select the input files with the Inputs port, specify the output with the Output port. Press the Apply button to start the conversion process.

Depending on the input format, you may be asked to supply parameters as described in TIFF format or Raw Data during the conversion process. If the input file is a SEG-Y file, the SEG-Y Wizard will be displayed.

After a successful conversion, a new data object appears in the Project View.

Ports:

Inputs

The list of input files.
Note: For the moment, only one file must be added using Bio-Formats.

Output

One output file.
Note: Using Bio-Formats, the convert generates one file per 3D volume, e.g. a time series with 10 time steps would generate 10 individual files.

Tile Size

The size of the tiles which are build by LDM.

Compression

To activate gzip compression or not.

Sampling Type

To specify the algorithm used to build low resolution tiles:

• Sharp: to use decimation algorithm.
• Average: to use weighted average algorithm.

Commands:

convertToDiskData
To convert large image data to LDA file format (default) or to Large Disk Data. Allowed options:

• format: format type should be one of the following expressions: "" "BMP" "DICOM" "JPEG" "JPEG 2000" "PNG" "PNM" "Raw Data" "SGI-RGB" "TIFF".
• lda: output directory for LDA data set.
• dims: output dimension. Should be: -dims xdims ydims zdims [for raw data only].
• ptype: primitive type. Should be one of the following expressions: "byte" "short" "int" "float" "double" "ushort" "uint" [for raw data only].
• ndatavar: numbers of components per voxel [for raw data only].
• header: size of the header file for RAW data (in bytes) [for raw data only].
• endianess: word format. Should be "little" or "big" for respectively little endian and big endian [for raw data only].
• bbox: bounding box. Should be -bbox xmin xmax ymin ymax zmin zmax.
• tilesize: size of the tiles which are build by LDM.
• compressor: data compression. To activate compression type: -compressor gzip. if the value is different from 'gzip' there is no compression.
• channel: channel to use for conversion. 0:maximum ; 1:weighted average - luminance ; 2:channel 1 ; 3:channel 2 ; 4:channel 3 ; 5:alpha channel ; 10:colorfield.
• s: specifies the algorithm used to build low resolution tiles. 0 to use decimation algorithm (one voxel out of two). n to use weighted average algorithm voxels of tile of resolution N+1 are built from the average of the 6 neighbors from resolution N and the current voxel value weighted by n.
• m: maximum size of memory to use in MB. Dynamically computed if the parameter is not specified.
• doNotCompute: do not compute. Internal use only.
• files: input files to be converted.

convertBioFormatsToDiskData
To convert large image data using Bio-Formats to LDA file format (The license is required). Allowed options:

• lda: output directory for LDA data set.
• tilesize: size of the tiles which are build by LDM.
• compressor: data compression. To activate compression type: -compressor gzip. if the value is different from 'gzip' there is no compression.
• s: specifies the algorithm used to build low resolution tiles. 0 to use decimation algorithm (one voxel out of two). n to use weighted average algorithm voxels of tile of resolution N+1 are built from the average of the 6 neighbors from resolution N and the current voxel value weighted by n.
• file: input file to be converted.

forceAmira311Format {0|1}
Provided for compatibility with Amira 3.1 and earlier. Lets you select the output data format.
0 = LDA file format,
1 = Large Disk Data = Amira 3.1 format.
Notes:

• The Amira 3.1 format does not support SEG-Y file conversion.

forceBioFormatsReader {0|1}
Force to use HxConvertToDiskData with Bio-Formats (The license is required).
0 = Do not force to use Bio-Formats,
1 = Force to use Bio-Formats.