• XSliceSmooth: First, an initial pass of smoothing is performed across the slices.
• DMG: Then, gradient domain fusion is performed for each (2D) slice in order to generate new slices that have inter-slice coherence while preserving the intra-slice detail.

• Flat: In this representation, all tiles for all (input and output) slices are contained in the same directory:
  

  	<in_dir>/<in_tile_name>.<tile_extension>
  	<tmp_dir>/<tmp_tile_name>.<tile_extension>
  	<out_dir>/<out_tile_name>.<tile_extension>
  

  For this represenation, the --slices parameter (see below) gives the number of different slices.
• Sliced: In this representation, the tiles for each slice are stored in separate directories:
  

  	<in_dir>/<in_slice_dir>/<in_tile_name>.<tile_extension>
  	<tmp_dir>/<out_slice_dir>/<out_tile_name>.<tile_extension>
  	<out_dir>/<out_slice_dir>/<out_tile_name>.<tile_extension>
  

  For this represenation, the --slices parameter (see below) gives the name of the file containg the list of slice directories. Each slice directory is assumed to be stored on a separate line and the total number of (non-empty) lines defines the number of slices.
  For technical reasons, the

  <out_slice_dir>

  string is obtained by replacing all instances of the file separator character ("/" on Linux, "\" on Windows) in

  <in_slice_dir>

  with the character "_". (i.e. Collapsing a multi-level directory structure down to one directory.)

• SCRIPTS
  Executing the scripts is done in two steps.
  • parameters.pl: This script must be edited to indicate the location of the executables and the data. Specifically, the user must modify/set the following variables and functions:
    • $X_SLICE_SMOOTH: The location of the executable performing the cross-slice smoothing,
    • $GRADIENT_DOMAIN_SERVER: The location of the distributed multigrid server executable,
    • $GRADIENT_DOMAIN_CLIENT: The location of the distributed multigrid client executable,
    • input_name: This function takes in indices of the tile (column, row, depth) and returns the name of the correponding input tile.
      This corresponds to the

      <in_tile_name>

      string described in the DATA LAYOUT section above.
    • output_name: This function takes in the indices of the tile (column, row, depth) and returns the name of the corresponding output tile.
      This corresponds to the

      <out_tile_name>

      string described in the DATA LAYOUT section above.

  • gdf.pl: This script uses the information in parameters.pl to invoke the cross-slice smoothing and gradient domain fusion code.
    This script takes the following parameters (the first five are required, the remainder are optional):

    --params <parameters.pl file>

    This required string specifies the location of the parameters file described above.

    --slices <slice directory count/slice directory list>

    This required parameter can be used either to specify the number of z-slices in the 3D dataset (the integer D) or the file enumberating the directories containing the slice tiles (the strings

    <in_slice_dir>

    ).
    For more details, see the DATA LAYOUT section above.

    --columns <columns per slice>

    This required integer values specifies the number columns in the tile-grid representing each slice (C).

    --rows <rows per slice>

    This required integer values specifies the number rows in the tile-grid representing each slice (R).

    --ext <extension>

    This required string specifies the file extension used to represent the tile images in the input/output.
    This corresponds to the

    <tile_extension>

    string described in the DATA LAYOUT section above.
    The code currently supports JPEG, PNG, and TIFF formats.

    [--inDir <input directory>]

    This optional string specifies the (base) directory from which the input tiles are to be read.
    The default value for this parameter is ".".
    This corresponds to the

    <in_dir>

    string described in the DATA LAYOUT section above.

    [--tempDir <temporary directory>]

    This optional string specifies the (base) directory to/from which the temporary tiles are to be written/read.
    The default value for this parameter is ".".
    This corresponds to the

    <tmp_dir>

    string described in the DATA LAYOUT section above.

    [--outDir <output directory>]

    This optional string specifies the (base) directory to which the output tiles are to be written.
    The default value for this parameter is ".".
    This corresponds to the

    <out_dir>

    string described in the DATA LAYOUT section above.

    [--xySigma <xy sigma>]

    This optional floating point value specifies the standard deviation (in pixels) of the Gaussian filter used for smoothing within each slice.
    The default value for this parameter is 1.

    [--zSigma <z sigma>]

    This optional floating point value specifies the standard deviation (in pixels) of the Gaussian filter used for smoothing across each slice.
    The default value for this parameter is 3.

    [--blockSize <tile block size>]

    This optional integer value specifies the width/height (in pixels) of the output tiles.
    The default value for this parameter is 2048.

    [--iWeight <tile block size>]

    This optional floating point value specifies the interpolation weight used for the gradient domain fusion. (Larger values mean less cross-slice smoothing.)
    The default value for this parameter is 0.001.

    [--port <dmg connection port>]

    This optional integer value specifies the port over which the distributed multigrid client/server communicate.
    On Windows, the default value for this parameter is 3672. On Linux it is 45674.

    [--threads <parallelization threads>]

    This optional integer value specifies the number of threads to be used for parallelization.
    The default value for this parameter is 4.

    [--color]

    This optional parameter indicates that the input tiles contain color values.
    By default, the input is assumed to be gray-scale.

    [--progress]

    This optional parameter indicates that the progress of the gradient domain fusion should be output to STDOUT.

• EXECUTABLES
  Though the executables are invoked by the Perl script and do not need to be called directly by the user, their parameters are provided for completeness:
  • XSliceSmooth

    --in <input image file>

    This required string is the name of the file containing the list of the tiles in the input 3D volume. The first three lines contain the width/height/depth of the tile grid, followed by a list of the tile names.

    [--out <output image file>]

    This optional string is the name of the file containing the list of the tiles in the output 3D volume. The first three lines contain the width/height/depth of the tile grid, followed by a list of the tile names.

    [--header <output file header>]

    This optional string specifies the header to prepended to the output tile names.

    [--ext] <output file extension>]

    This optional string specifies the file extension to be used for the output tiles.
    The default value for this parameter is "tiff".

    [--scratchHeader] <scratch header extension>

    This optional string specifies the header to prepended to the temporary tile names.

    [--xySigma <xy sigma>]

    This optional floating point value specifies the standard deviation (in pixels) of the Gaussian filter used for smoothing within each slice.
    The default value for this parameter is 0.

    [--zSigma <z sigma>]

    This optional floating point value specifies the standard deviation (in pixels) of the Gaussian filter used for smoothing across each slice.
    The default value for this parameter is 0.

    [--threads <parallelization threads>]

    This optional integer value specifies the number of threads to be used for parallelization.
    The default value for this parameter is 1.

    [--channels <color channels>]

    This optional integer value specifies the number of channels used for representing a pixel's color.
    The default value for this parameter is 1.

    [--verbose]

    This optional parameter indicates that the state of the cross-slice smoother should be output to STDOUT.

    [--progress]

    This optional parameter indicates that the more detailed progress of the gradient domain fusion should be output to STDOUT.

  • DMG
    Parameters for the distributed gradient domain executables can be found here.

	$X_SLICE_SMOOTH = ...;
	$GRADIENT_DOMAIN_SERVER = ...;
	$GRADIENT_DOMAIN_CLIENT = ...;
	sub input_name
	{
		my( $i , $j , $k ) = @_;
		return "in" . ".x" . ($i+1) . ".y" . ($j+1) . ".z" . ($k+1);
	}
	sub output_name
	{
		my( $i , $j , $k ) = @_;
		return "out" . ".x" . ($i+1) . ".y" . ($j+1) . ".z" . ($k+1);
	}	

	% perl gdf.pl --params parameters.pl --columns 32 --rows 16 --slices 100 --ext jpg --blockSize 1024