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−
== CongealingCLI ==
+
= Congealing Commandline Wrapper =
 +
 
 +
CongealingCLI is a wrapper to access the Congealing Un-biased Groupwise Registration tool. It is now possible to generate a configuration file for Congealing by using a GUI or command line arguments. In fact, by not specifying any arguments and just running the wrapper, a default configuration file for congeal is generated.
 +
 
 +
==Module Type & Category==
 +
 
 +
Type: CLI
 +
 
 +
Category: Registration
 +
 
 +
==Authors, Collaborators & Contact==
 +
 
 +
Author: Daniel Haehn and Kilian Pohl, University of Pennsylvania
 +
 
 +
Collaborators: J. De Bonet, L. Zöllei and W.M. Wells III
 +
 
 +
Acknowledgment: The research was funded by an ARRA supplement to NIH NCRR (P41 RR13218).
 +
 
 +
== Graphical User Interface in 3D Slicer ==
 +
{|
 +
|[[Image:CongealingCLIdefault.png|thumb|300px|The '''simple GUI''' mask, directly usable to create a default configuration file or to launch Congeal after specifying the path.]]
 +
|[[Image:CongealingCLItop.png|thumb|300px|The '''advanced GUI''' after the first couple of panels were expanded.]]
 +
|[[Image:CongealingCLIbottom.png|thumb|300px|The '''advanced GUI''' after the last couple of panels were expanded.]]
 +
|}
 +
 
 +
 
 +
===Module Description===
 +
 
 +
{| style="color:green" border="1"
 +
 
 +
|Program title || CongealingCLI
 +
 
 +
 
 +
|-
 +
|Program version || 0.1.1
 +
 
 +
|-
 +
|Program documentation-url || https://www.slicer.org/wiki/Modules:AtlasCreator |-
 +
|}
 +
 
 +
* <span style="color:blue">'''''Input parameters''''' </span> The input parameters for Congealing.
 +
** <span style="color:green">'''congeal_inputfiles'''</span> [<span style="color:orange">----congeal_inputfiles</span>] : number of input files to use. Use '0' for all files when used in conjuctions with congeal_inputfiles.list
 +
** <span style="color:green">'''congeal_inputfile_format'''</span> [<span style="color:orange">----congeal_inputfile_format</span>] : format of input files. Currently only 'nifti' is supported
 +
** <span style="color:green">'''congeal_inputfiles_list'''</span> [<span style="color:orange">----congeal_inputfiles_list</span>] : a path to a file containing a list of input data files. The list file should contain one filename per line. Only congeal_inputfiles files will be used as input unless congeal_inputfiles is set to '0' in which case all the files in the list will be used     
 +
     
 +
* <span style="color:blue">'''''Optimization parameters''''' </span> Options to configure the optimization.
 +
** <span style="color:green">'''congeal_optimize_algorithm'''</span> [<span style="color:orange">----congeal_optimize_algorithm</span>] : determines the optimization algorithm used
 +
* <span style="color:blue">'''''RandomWalk parameters''''' </span> Options to configure RandomWalk.
 +
** <span style="color:green">'''congeal_optimize__randomwalk__kernel'''</span> [<span style="color:orange">----congeal_optimize_randomwalk_kernel</span>] : size of support to use for computing initial stepsize. This factor is multiplied by *.initialsteps to establish a maximum step radius for each dimensions
 +
** <span style="color:green">'''congeal_optimize__randomwalk__steps'''</span> [<span style="color:orange">----congeal_optimize__randomwalk__steps</span>] : maximum number of steps to take along any beam
 +
** <span style="color:green">'''congeal_optimize__randomwalk__directions'''</span> [<span style="color:orange">----congeal_optimize__randomwalk__directions</span>] : number of beams to try during each iteration
 +
* <span style="color:blue">'''''Error function parameters''''' </span> Options to configure the error function
 +
** <span style="color:green">'''congeal_optimize_error'''</span> [<span style="color:orange">----congeal_optimize_error</span>] : selects the error metric to be used. parzen -- entropy estimate based on Parzen density estimator. variance -- variance of voxel stack.
 +
** <span style="color:green">'''congeal_error__parzen__sigma'''</span> [<span style="color:orange">----congeal_error__parzen__sigma</span>] : sigma of Gaussian used as kernel in Parzen density estimator. Measured in voxel intensity
 +
** <span style="color:green">'''congeal_error__parzen__apriori'''</span> [<span style="color:orange">----congeal_error__parzen__apriori</span>] : constant factor added to each Parzen estimate
 +
* <span style="color:blue">'''''Output display options''''' </span> Options to configure the output display
 +
** <span style="color:green">'''congeal_output_prefix'''</span> [<span style="color:orange">----congeal_output_prefix</span>] : string prepended to the filenames of the outputfiles. This value can include an absolute or relative path, as well as a file prefix
 +
** <span style="color:green">'''congeal_output_colors_mid'''</span> [<span style="color:orange">----congeal_output_colors_mid</span>] : color equalization intercept. This value determines which data value will be mapped to mid gray
 +
** <span style="color:green">'''congeal_output_colors_range'''</span> [<span style="color:orange">----congeal_output_colors_range</span>] : color equalization slope. This value determines the relationship between changes in data value and changes in output image gray value
 +
** <span style="color:green">'''congeal_output_sourcegrid'''</span> [<span style="color:orange">----congeal_output_sourcegrid</span>] : determines how many of the transformed source values are shown in the *-inputs* images
 +
** <span style="color:green">'''congeal_optimize_progresspoints'''</span> [<span style="color:orange">----congeal_optimize_progresspoints</span>] : determines how many output file sets will be generated during each schedule
 +
** <span style="color:green">'''congeal_output_average_width'''</span> [<span style="color:orange">----congeal_output_average_width</span>] : determines the width of the congealing average visualization
 +
** <span style="color:green">'''congeal_output_average_height'''</span> [<span style="color:orange">----congeal_output_average_height</span>] : determines the height of the congealing average visualization
 +
* <span style="color:blue">'''''Initial step sizes for kernels''''' </span> Option to configure the initial kernels
 +
** <span style="color:green">'''congeal_initialsteps_translate'''</span> [<span style="color:orange">----congeal_initialsteps_translate</span>] : relative scaling of translation parameters when computing kernels and step sizes. Scale: translation as fraction of image size
 +
** <span style="color:green">'''congeal_initialsteps_rotate'''</span> [<span style="color:orange">----congeal_initialsteps_rotate</span>] : relative scaling of rotation parameters when computing kernels and step sizes. Scale: rotation in degrees
 +
** <span style="color:green">'''congeal_initialsteps_scale'''</span> [<span style="color:orange">----congeal_initialsteps_scale</span>] : relative scaling of scaling parameters when computing kernels and step sizes. Scale: Scale as fraction of image size
 +
** <span style="color:green">'''congeal_initialsteps_warp'''</span> [<span style="color:orange">----congeal_initialsteps_warp</span>] : relative scaling of warp control point displacement when computing kernels and step sizes. Scale: Warp as fraction of control point's region
 +
* <span style="color:blue">'''''Schedule options''''' </span> Options to configure the schedules
 +
** <span style="color:green">'''congeal_schedule__n__cache'''</span> [<span style="color:orange">----congeal_schedule__n__cache</span>] : determines whether or not the schedules results can be retrieved from the previous run. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__downsample'''</span> [<span style="color:orange">----congeal_schedule__n__downsample</span>] : determines how many times the input data should be downsampled (by factor of 2 in each dimension) prior to congealing. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_affine'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_affine</span>] : determines if affine parameters should be optimized or left fixed. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__warpfield__0__size'''</span> [<span style="color:orange">----congeal_schedule__n__warpfield__0__size</span>] : determines number of support points in each dimension of of B-Spline mesh for field 0. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__warpfield__1__size'''</span> [<span style="color:orange">----congeal_schedule__n__warpfield__1__size</span>] : determines number of support points in each dimension of of B-Spline mesh for field 1. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__warpfield__2__size'''</span> [<span style="color:orange">----congeal_schedule__n__warpfield__2__size</span>] : determines number of support points in each dimension of of B-Spline mesh for field 2. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__warpfield__3__size'''</span> [<span style="color:orange">----congeal_schedule__n__warpfield__3__size</span>] : determines number of support points in each dimension of of B-Spline mesh for field 3. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_warp__0__'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_warp__0__</span>] : determines if the B-spline parameters for B-spline field 0 should be optimized or left fixed. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_warp__1__'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_warp__1__</span>] : determines if the B-spline parameters for B-spline field 1 should be optimized or left fixed. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_warp__2__'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_warp__2__</span>] : determines if the B-spline parameters for B-spline field 2 should be optimized or left fixed. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_warp__3__'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_warp__3__</span>] : determines if the B-spline parameters for B-spline field 3 should be optimized or left fixed. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_iterations'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_iterations</span>] : number of optimzation iterations to be taken in the schedules. Separated by comma for each schedule run.
 +
** <span style="color:green">'''congeal_schedule__n__optimize_samples'''</span> [<span style="color:orange">----congeal_schedule__n__optimize_samples</span>] : number of samples to be compared in each transformed input volume. Separated by comma for each schedule run.
 +
* <span style="color:blue">'''''Experimental''''' </span> Experimental options
 +
** <span style="color:green">'''congeal_optimize_bestpoints'''</span> [<span style="color:orange">----congeal_optimize_bestpoints</span>] :
 +
** <span style="color:green">'''test'''</span> [<span style="color:orange">----test</span>] : Currently unused. "Must be congeal."
 +
* <span style="color:blue">'''''Write and Execution options''''' </span> Options to configure the execution
 +
** <span style="color:green">'''Output path for configuration'''</span> [<span style="color:orange">----outputPath</span>] : The output path for the congeal configuration file. The file will only be written, if this is set.
 +
** <span style="color:green">'''Congeal executable'''</span> [<span style="color:orange">----launch</span>] : The path to the congeal executable. Congeal will only be executed, if this is set.
 +
 
  
−
CongealingCLI is a wrapper to access the Congealing Un-biased Groupwise Registration tool. It is now possible to generate a configuration file for Congealing by using a GUI or command line arguments.
 
  
−
=== Graphical User Interface in 3D Slicer ===
 
  
 
=== Command Line Interface ===
 
=== Command Line Interface ===
 +
 +
The option '''--help''' prints the possible command line arguments:
 +
 +
<pre>
 +
$ ./CongealingCLI --help
 +
 +
USAGE:
 +
 +
  ./CongealingCLI  [--returnparameterfile <std::string>]
 +
                    [--processinformationaddress <std::string>] [--xml]
 +
                    [--echo] [--launch <std::string>] [--outputPath
 +
                    <std::string>] [--test <std::string>]
 +
                    [--congeal_optimize_bestpoints <int>]
 +
                    [--congeal_schedule__n__optimize_samples
 +
                    <std::vector<int>>]
 +
                    [--congeal_schedule__n__optimize_iterations
 +
                    <std::vector<int>>]
 +
                    [--congeal_schedule__n__optimize_warp__3__
 +
                    <std::vector<std::string>>]
 +
                    [--congeal_schedule__n__optimize_warp__2__
 +
                    <std::vector<std::string>>]
 +
                    [--congeal_schedule__n__optimize_warp__1__
 +
                    <std::vector<std::string>>]
 +
                    [--congeal_schedule__n__optimize_warp__0__
 +
                    <std::vector<std::string>>]
 +
                    [--congeal_schedule__n__warpfield__3__size
 +
                    <std::vector<int>>]
 +
                    [--congeal_schedule__n__warpfield__2__size
 +
                    <std::vector<int>>]
 +
                    [--congeal_schedule__n__warpfield__1__size
 +
                    <std::vector<int>>]
 +
                    [--congeal_schedule__n__warpfield__0__size
 +
                    <std::vector<int>>]
 +
                    [--congeal_schedule__n__optimize_affine
 +
                    <std::vector<std::string>>]
 +
                    [--congeal_schedule__n__downsample <std::vector<int>>]
 +
                    [--congeal_schedule__n__cache
 +
                    <std::vector<std::string>>]
 +
                    [--congeal_initialsteps_warp <float>]
 +
                    [--congeal_initialsteps_scale <float>]
 +
                    [--congeal_initialsteps_rotate <float>]
 +
                    [--congeal_initialsteps_translate <float>]
 +
                    [--congeal_output_average_height <int>]
 +
                    [--congeal_output_average_width <int>]
 +
                    [--congeal_optimize_progresspoints <int>]
 +
                    [--congeal_output_sourcegrid <int>]
 +
                    [--congeal_output_colors_range <int>]
 +
                    [--congeal_output_colors_mid <int>]
 +
                    [--congeal_output_prefix <std::string>]
 +
                    [--congeal_error__parzen__apriori <float>]
 +
                    [--congeal_error__parzen__sigma <float>]
 +
                    [--congeal_optimize_error <parzen|variance>]
 +
                    [--congeal_optimize__randomwalk__directions <int>]
 +
                    [--congeal_optimize__randomwalk__steps <int>]
 +
                    [--congeal_optimize_randomwalk_kernel <float>]
 +
                    [--congeal_optimize_algorithm <lbfgs|bruteforce
 +
                    |randomwalk|gradientdescent>]
 +
                    [--congeal_inputfiles_list <std::string>]
 +
                    [--congeal_inputfile_format <nifti>]
 +
                    [--congeal_inputfiles <int>] [--] [--version] [-h]
 +
 +
 +
Where:
 +
 +
  --returnparameterfile <std::string>
 +
    Filename in which to write simple return parameters (int, float,
 +
    int-vector, etc.) as opposed to bulk return parameters (image,
 +
    geometry, transform, measurement, table).
 +
 +
  --processinformationaddress <std::string>
 +
    Address of a structure to store process information (progress, abort,
 +
    etc.). (default: 0)
 +
 +
  --xml
 +
    Produce xml description of command line arguments (default: 0)
 +
 +
  --echo
 +
    Echo the command line arguments (default: 0)
 +
 +
  --launch <std::string>
 +
    The path to the congeal executable. Congeal will only be executed, if
 +
    this is set.
 +
 +
  --outputPath <std::string>
 +
    The output path for the congeal configuration file. The file will only
 +
    be written, if this is set. (default: /tmp/congeal.config)
 +
 +
  --test <std::string>
 +
    Currently unused. 'Must be congeal.' (default: congeal)
 +
 +
  --congeal_optimize_bestpoints <int>
 +
      (default: 1000)
 +
 +
  --congeal_schedule__n__optimize_samples <std::vector<int>>
 +
    number of samples to be compared in each transformed input volume.
 +
    Separated by comma for each schedule run. (default: 50000,50000,500000
 +
    ,500000,500000)
 +
 +
  --congeal_schedule__n__optimize_iterations <std::vector<int>>
 +
    number of optimzation iterations to be taken in the schedules.
 +
    Separated by comma for each schedule run. (default: 30,30,30,30,30)
 +
 +
  --congeal_schedule__n__optimize_warp__3__ <std::vector<std::string>>
 +
    determines if the B-spline parameters for B-spline field 3 should be
 +
    optimized or left fixed. Separated by comma for each schedule run.
 +
    (default: false,false,false,false,true)
 +
 +
  --congeal_schedule__n__optimize_warp__2__ <std::vector<std::string>>
 +
    determines if the B-spline parameters for B-spline field 2 should be
 +
    optimized or left fixed. Separated by comma for each schedule run.
 +
    (default: false,false,false,true,false)
 +
 +
  --congeal_schedule__n__optimize_warp__1__ <std::vector<std::string>>
 +
    determines if the B-spline parameters for B-spline field 1 should be
 +
    optimized or left fixed. Separated by comma for each schedule run.
 +
    (default: false,false,true,false,false)
 +
 +
  --congeal_schedule__n__optimize_warp__0__ <std::vector<std::string>>
 +
    determines if the B-spline parameters for B-spline field 0 should be
 +
    optimized or left fixed. Separated by comma for each schedule run.
 +
    (default: false,true,false,false,false)
 +
 +
  --congeal_schedule__n__warpfield__3__size <std::vector<int>>
 +
    determines number of support points in each dimension of of B-Spline
 +
    mesh for field 3. Separated by comma for each schedule run. (default:
 +
    1,1,1,1,32)
 +
 +
  --congeal_schedule__n__warpfield__2__size <std::vector<int>>
 +
    determines number of support points in each dimension of of B-Spline
 +
    mesh for field 2. Separated by comma for each schedule run. (default:
 +
    1,1,1,16,16)
 +
 +
  --congeal_schedule__n__warpfield__1__size <std::vector<int>>
 +
    determines number of support points in each dimension of of B-Spline
 +
    mesh for field 1. Separated by comma for each schedule run. (default:
 +
    1,1,8,8,8)
 +
 +
  --congeal_schedule__n__warpfield__0__size <std::vector<int>>
 +
    determines number of support points in each dimension of of B-Spline
 +
    mesh for field 0. Separated by comma for each schedule run. (default:
 +
    1,4,4,4,4)
 +
 +
  --congeal_schedule__n__optimize_affine <std::vector<std::string>>
 +
    determines if affine parameters should be optimized or left fixed.
 +
    Separated by comma for each schedule run. (default: true,false,false
 +
    ,false,false)
 +
 +
  --congeal_schedule__n__downsample <std::vector<int>>
 +
    determines how many times the input data should be downsampled (by
 +
    factor of 2 in each dimension) prior to congealing. Separated by comma
 +
    for each schedule run. (default: 0,0,0,0,0)
 +
 +
  --congeal_schedule__n__cache <std::vector<std::string>>
 +
    determines whether or not the schedules results can be retrieved from
 +
    the previous run. Separated by comma for each schedule run. (default:
 +
    true,true,true,true,true)
 +
 +
  --congeal_initialsteps_warp <float>
 +
    relative scaling of warp control point displacement when computing
 +
    kernels and step sizes. Scale: Warp as fraction of control point's
 +
    region (default: 0.15)
 +
 +
  --congeal_initialsteps_scale <float>
 +
    relative scaling of scaling parameters when computing kernels and step
 +
    sizes. Scale: Scale as fraction of image size (default: 0.2)
 +
 +
  --congeal_initialsteps_rotate <float>
 +
    relative scaling of rotation parameters when computing kernels and
 +
    step sizes. Scale: rotation in degrees (default: 30)
 +
 +
  --congeal_initialsteps_translate <float>
 +
    relative scaling of translation parameters when computing kernels and
 +
    step sizes. Scale: translation as fraction of image size (default:
 +
    0.2)
 +
 +
  --congeal_output_average_height <int>
 +
    determines the height of the congealing average visualization
 +
    (default: 512)
 +
 +
  --congeal_output_average_width <int>
 +
    determines the width of the congealing average visualization (default:
 +
    512)
 +
 +
  --congeal_optimize_progresspoints <int>
 +
    determines how many output file sets will be generated during each
 +
    schedule (default: 4)
 +
 +
  --congeal_output_sourcegrid <int>
 +
    determines how many of the transformed source values are shown in the
 +
    *-inputs* images (default: 9)
 +
 +
  --congeal_output_colors_range <int>
 +
    color equalization slope. This value determines the relationship
 +
    between changes in data value and changes in output image gray value
 +
    (default: 256)
 +
 +
  --congeal_output_colors_mid <int>
 +
    color equalization intercept. This value determines which data value
 +
    will be mapped to mid gray (default: 128)
 +
 +
  --congeal_output_prefix <std::string>
 +
    string prepended to the filenames of the outputfiles. This value can
 +
    include an absolute or relative path, as well as a file prefix
 +
    (default: ../output/congeal/)
 +
 +
  --congeal_error__parzen__apriori <float>
 +
    constant factor added to each Parzen estimate (default: 1e-06)
 +
 +
  --congeal_error__parzen__sigma <float>
 +
    sigma of Gaussian used as kernel in Parzen density estimator. Measured
 +
    in voxel intensity (default: 30)
 +
 +
  --congeal_optimize_error <parzen|variance>
 +
    selects the error metric to be used. parzen -- entropy estimate based
 +
    on Parzen density estimator. variance -- variance of voxel stack.
 +
    (default: parzen)
 +
 +
  --congeal_optimize__randomwalk__directions <int>
 +
    number of beams to try during each iteration (default: 20)
 +
 +
  --congeal_optimize__randomwalk__steps <int>
 +
    maximum number of steps to take along any beam (default: 10)
 +
 +
  --congeal_optimize_randomwalk_kernel <float>
 +
    size of support to use for computing initial stepsize. This factor is
 +
    multiplied by *.initialsteps to establish a maximum step radius for
 +
    each dimensions (default: 0.1)
 +
 +
  --congeal_optimize_algorithm <lbfgs|bruteforce|randomwalk
 +
      |gradientdescent>
 +
    determines the optimization algorithm used (default: randomwalk)
 +
 +
  --congeal_inputfiles_list <std::string>
 +
    a path to a file containing a list of input data files. The list file
 +
    should contain one filename per line. Only congeal_inputfiles files
 +
    will be used as input unless congeal_inputfiles is set to '0' in which
 +
    case all the files in the list will be used (default:
 +
    ../input/sample/allfiles)
 +
 +
  --congeal_inputfile_format <nifti>
 +
    format of input files. Currently only 'nifti' is supported (default:
 +
    nifti)
 +
 +
  --congeal_inputfiles <int>
 +
    number of input files to use. Use '0' for all files when used in
 +
    conjuctions with congeal_inputfiles.list (default: 30)
 +
 +
  --,  --ignore_rest
 +
    Ignores the rest of the labeled arguments following this flag.
 +
 +
  --version
 +
    Displays version information and exits.
 +
 +
  -h,  --help
 +
    Displays usage information and exits.
 +
 +
 +
  Description: Generates a configuration file for the Congealing
 +
  Registration tool.
 +
 +
  Author(s): Daniel Haehn and Kilian Pohl, University of
 +
  Pennsylvania
 +
 +
  Acknowledgements: The research was funded by an ARRA supplement to NIH
 +
  NCRR (P41 RR13218).
 +
 +
</pre>
  
 
=== Examples ===
 
=== Examples ===
Line 13: Line 366:
 
<pre>
 
<pre>
 
$ ./CongealingCLI  
 
$ ./CongealingCLI  
−
Configuration file written to /var/tmp/tmp.0.YQNbrV
+
Configuration file written to /tmp/congealing.config
 
</pre>
 
</pre>
  
Line 32: Line 385:
 
  --congeal_schedule__n__optimize_warp__3__ false,false,false,false,true --congeal_schedule__n__optimize_iterations 30,30,30,30,30  
 
  --congeal_schedule__n__optimize_warp__3__ false,false,false,false,true --congeal_schedule__n__optimize_iterations 30,30,30,30,30  
 
  --congeal_schedule__n__optimize_samples 50000,50000,500000,500000,500000 --congeal_optimize_bestpoints 1000 --test congeal
 
  --congeal_schedule__n__optimize_samples 50000,50000,500000,500000,500000 --congeal_optimize_bestpoints 1000 --test congeal
−
Configuration file written to /var/tmp/tmp.0.YQNbrV
+
Configuration file written to /tmp/congealing.config
 
</pre>
 
</pre>
  
−
and the output is the same for both (thanks to the default values):
+
and the output is the same for both (thanks to the default values, they also equal a press on the Apply button in the GUI without any changes to the input fields):
  
 
<pre>
 
<pre>
Line 155: Line 508:
  
 
</pre>
 
</pre>
 +
 +
==== Using '''--launch''' ====
 +
 +
When adding a '''--launch PATH_TO_CONGEAL_EXEC''', the congeal executable gets launched rather than printing the path to the generated configuration file.
 +
 +
For example
 +
 +
<pre>
 +
$ ./CongealingCLI --launch congeal
 +
</pre>
 +
 +
starts the congeal executable with the configuration file shown above.

Latest revision as of 13:19, 27 November 2019

Home < Modules:AtlasCreator:CongealingCLI

Congealing Commandline Wrapper

CongealingCLI is a wrapper to access the Congealing Un-biased Groupwise Registration tool. It is now possible to generate a configuration file for Congealing by using a GUI or command line arguments. In fact, by not specifying any arguments and just running the wrapper, a default configuration file for congeal is generated.

Module Type & Category

Type: CLI

Category: Registration

Authors, Collaborators & Contact

Author: Daniel Haehn and Kilian Pohl, University of Pennsylvania

Collaborators: J. De Bonet, L. Zöllei and W.M. Wells III

Acknowledgment: The research was funded by an ARRA supplement to NIH NCRR (P41 RR13218).

Graphical User Interface in 3D Slicer

The simple GUI mask, directly usable to create a default configuration file or to launch Congeal after specifying the path.
The advanced GUI after the first couple of panels were expanded.
The advanced GUI after the last couple of panels were expanded.


Module Description

Program title CongealingCLI


Program version 0.1.1
Program documentation-url -
  • Input parameters The input parameters for Congealing.
    • congeal_inputfiles [----congeal_inputfiles] : number of input files to use. Use '0' for all files when used in conjuctions with congeal_inputfiles.list
    • congeal_inputfile_format [----congeal_inputfile_format] : format of input files. Currently only 'nifti' is supported
    • congeal_inputfiles_list [----congeal_inputfiles_list] : a path to a file containing a list of input data files. The list file should contain one filename per line. Only congeal_inputfiles files will be used as input unless congeal_inputfiles is set to '0' in which case all the files in the list will be used
  • Optimization parameters Options to configure the optimization.
    • congeal_optimize_algorithm [----congeal_optimize_algorithm] : determines the optimization algorithm used
  • RandomWalk parameters Options to configure RandomWalk.
    • congeal_optimize__randomwalk__kernel [----congeal_optimize_randomwalk_kernel] : size of support to use for computing initial stepsize. This factor is multiplied by *.initialsteps to establish a maximum step radius for each dimensions
    • congeal_optimize__randomwalk__steps [----congeal_optimize__randomwalk__steps] : maximum number of steps to take along any beam
    • congeal_optimize__randomwalk__directions [----congeal_optimize__randomwalk__directions] : number of beams to try during each iteration
  • Error function parameters Options to configure the error function
    • congeal_optimize_error [----congeal_optimize_error] : selects the error metric to be used. parzen -- entropy estimate based on Parzen density estimator. variance -- variance of voxel stack.
    • congeal_error__parzen__sigma [----congeal_error__parzen__sigma] : sigma of Gaussian used as kernel in Parzen density estimator. Measured in voxel intensity
    • congeal_error__parzen__apriori [----congeal_error__parzen__apriori] : constant factor added to each Parzen estimate
  • Output display options Options to configure the output display
    • congeal_output_prefix [----congeal_output_prefix] : string prepended to the filenames of the outputfiles. This value can include an absolute or relative path, as well as a file prefix
    • congeal_output_colors_mid [----congeal_output_colors_mid] : color equalization intercept. This value determines which data value will be mapped to mid gray
    • congeal_output_colors_range [----congeal_output_colors_range] : color equalization slope. This value determines the relationship between changes in data value and changes in output image gray value
    • congeal_output_sourcegrid [----congeal_output_sourcegrid] : determines how many of the transformed source values are shown in the *-inputs* images
    • congeal_optimize_progresspoints [----congeal_optimize_progresspoints] : determines how many output file sets will be generated during each schedule
    • congeal_output_average_width [----congeal_output_average_width] : determines the width of the congealing average visualization
    • congeal_output_average_height [----congeal_output_average_height] : determines the height of the congealing average visualization
  • Initial step sizes for kernels Option to configure the initial kernels
    • congeal_initialsteps_translate [----congeal_initialsteps_translate] : relative scaling of translation parameters when computing kernels and step sizes. Scale: translation as fraction of image size
    • congeal_initialsteps_rotate [----congeal_initialsteps_rotate] : relative scaling of rotation parameters when computing kernels and step sizes. Scale: rotation in degrees
    • congeal_initialsteps_scale [----congeal_initialsteps_scale] : relative scaling of scaling parameters when computing kernels and step sizes. Scale: Scale as fraction of image size
    • congeal_initialsteps_warp [----congeal_initialsteps_warp] : relative scaling of warp control point displacement when computing kernels and step sizes. Scale: Warp as fraction of control point's region
  • Schedule options Options to configure the schedules
    • congeal_schedule__n__cache [----congeal_schedule__n__cache] : determines whether or not the schedules results can be retrieved from the previous run. Separated by comma for each schedule run.
    • congeal_schedule__n__downsample [----congeal_schedule__n__downsample] : determines how many times the input data should be downsampled (by factor of 2 in each dimension) prior to congealing. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_affine [----congeal_schedule__n__optimize_affine] : determines if affine parameters should be optimized or left fixed. Separated by comma for each schedule run.
    • congeal_schedule__n__warpfield__0__size [----congeal_schedule__n__warpfield__0__size] : determines number of support points in each dimension of of B-Spline mesh for field 0. Separated by comma for each schedule run.
    • congeal_schedule__n__warpfield__1__size [----congeal_schedule__n__warpfield__1__size] : determines number of support points in each dimension of of B-Spline mesh for field 1. Separated by comma for each schedule run.
    • congeal_schedule__n__warpfield__2__size [----congeal_schedule__n__warpfield__2__size] : determines number of support points in each dimension of of B-Spline mesh for field 2. Separated by comma for each schedule run.
    • congeal_schedule__n__warpfield__3__size [----congeal_schedule__n__warpfield__3__size] : determines number of support points in each dimension of of B-Spline mesh for field 3. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_warp__0__ [----congeal_schedule__n__optimize_warp__0__] : determines if the B-spline parameters for B-spline field 0 should be optimized or left fixed. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_warp__1__ [----congeal_schedule__n__optimize_warp__1__] : determines if the B-spline parameters for B-spline field 1 should be optimized or left fixed. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_warp__2__ [----congeal_schedule__n__optimize_warp__2__] : determines if the B-spline parameters for B-spline field 2 should be optimized or left fixed. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_warp__3__ [----congeal_schedule__n__optimize_warp__3__] : determines if the B-spline parameters for B-spline field 3 should be optimized or left fixed. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_iterations [----congeal_schedule__n__optimize_iterations] : number of optimzation iterations to be taken in the schedules. Separated by comma for each schedule run.
    • congeal_schedule__n__optimize_samples [----congeal_schedule__n__optimize_samples] : number of samples to be compared in each transformed input volume. Separated by comma for each schedule run.
  • Experimental Experimental options
    • congeal_optimize_bestpoints [----congeal_optimize_bestpoints] :
    • test [----test] : Currently unused. "Must be congeal."
  • Write and Execution options Options to configure the execution
    • Output path for configuration [----outputPath] : The output path for the congeal configuration file. The file will only be written, if this is set.
    • Congeal executable [----launch] : The path to the congeal executable. Congeal will only be executed, if this is set.



Command Line Interface

The option --help prints the possible command line arguments: 

$ ./CongealingCLI --help

USAGE: 

   ./CongealingCLI  [--returnparameterfile <std::string>]
                    [--processinformationaddress <std::string>] [--xml]
                    [--echo] [--launch <std::string>] [--outputPath
                    <std::string>] [--test <std::string>] 
                    [--congeal_optimize_bestpoints <int>]
                    [--congeal_schedule__n__optimize_samples
                    <std::vector<int>>]
                    [--congeal_schedule__n__optimize_iterations
                    <std::vector<int>>]
                    [--congeal_schedule__n__optimize_warp__3__
                    <std::vector<std::string>>]
                    [--congeal_schedule__n__optimize_warp__2__
                    <std::vector<std::string>>]
                    [--congeal_schedule__n__optimize_warp__1__
                    <std::vector<std::string>>]
                    [--congeal_schedule__n__optimize_warp__0__
                    <std::vector<std::string>>]
                    [--congeal_schedule__n__warpfield__3__size
                    <std::vector<int>>]
                    [--congeal_schedule__n__warpfield__2__size
                    <std::vector<int>>]
                    [--congeal_schedule__n__warpfield__1__size
                    <std::vector<int>>]
                    [--congeal_schedule__n__warpfield__0__size
                    <std::vector<int>>]
                    [--congeal_schedule__n__optimize_affine
                    <std::vector<std::string>>]
                    [--congeal_schedule__n__downsample <std::vector<int>>]
                    [--congeal_schedule__n__cache
                    <std::vector<std::string>>]
                    [--congeal_initialsteps_warp <float>]
                    [--congeal_initialsteps_scale <float>]
                    [--congeal_initialsteps_rotate <float>]
                    [--congeal_initialsteps_translate <float>]
                    [--congeal_output_average_height <int>]
                    [--congeal_output_average_width <int>]
                    [--congeal_optimize_progresspoints <int>]
                    [--congeal_output_sourcegrid <int>]
                    [--congeal_output_colors_range <int>]
                    [--congeal_output_colors_mid <int>]
                    [--congeal_output_prefix <std::string>]
                    [--congeal_error__parzen__apriori <float>]
                    [--congeal_error__parzen__sigma <float>]
                    [--congeal_optimize_error <parzen|variance>]
                    [--congeal_optimize__randomwalk__directions <int>]
                    [--congeal_optimize__randomwalk__steps <int>]
                    [--congeal_optimize_randomwalk_kernel <float>]
                    [--congeal_optimize_algorithm <lbfgs|bruteforce
                    |randomwalk|gradientdescent>]
                    [--congeal_inputfiles_list <std::string>]
                    [--congeal_inputfile_format <nifti>]
                    [--congeal_inputfiles <int>] [--] [--version] [-h]


Where: 

   --returnparameterfile <std::string>
     Filename in which to write simple return parameters (int, float,
     int-vector, etc.) as opposed to bulk return parameters (image,
     geometry, transform, measurement, table).

   --processinformationaddress <std::string>
     Address of a structure to store process information (progress, abort,
     etc.). (default: 0)

   --xml
     Produce xml description of command line arguments (default: 0)

   --echo
     Echo the command line arguments (default: 0)

   --launch <std::string>
     The path to the congeal executable. Congeal will only be executed, if
     this is set.

   --outputPath <std::string>
     The output path for the congeal configuration file. The file will only
     be written, if this is set. (default: /tmp/congeal.config)

   --test <std::string>
     Currently unused. 'Must be congeal.' (default: congeal)

   --congeal_optimize_bestpoints <int>
      (default: 1000)

   --congeal_schedule__n__optimize_samples <std::vector<int>>
     number of samples to be compared in each transformed input volume.
     Separated by comma for each schedule run. (default: 50000,50000,500000
     ,500000,500000)

   --congeal_schedule__n__optimize_iterations <std::vector<int>>
     number of optimzation iterations to be taken in the schedules.
     Separated by comma for each schedule run. (default: 30,30,30,30,30)

   --congeal_schedule__n__optimize_warp__3__ <std::vector<std::string>>
     determines if the B-spline parameters for B-spline field 3 should be
     optimized or left fixed. Separated by comma for each schedule run.
     (default: false,false,false,false,true)

   --congeal_schedule__n__optimize_warp__2__ <std::vector<std::string>>
     determines if the B-spline parameters for B-spline field 2 should be
     optimized or left fixed. Separated by comma for each schedule run.
     (default: false,false,false,true,false)

   --congeal_schedule__n__optimize_warp__1__ <std::vector<std::string>>
     determines if the B-spline parameters for B-spline field 1 should be
     optimized or left fixed. Separated by comma for each schedule run.
     (default: false,false,true,false,false)

   --congeal_schedule__n__optimize_warp__0__ <std::vector<std::string>>
     determines if the B-spline parameters for B-spline field 0 should be
     optimized or left fixed. Separated by comma for each schedule run.
     (default: false,true,false,false,false)

   --congeal_schedule__n__warpfield__3__size <std::vector<int>>
     determines number of support points in each dimension of of B-Spline
     mesh for field 3. Separated by comma for each schedule run. (default:
     1,1,1,1,32)

   --congeal_schedule__n__warpfield__2__size <std::vector<int>>
     determines number of support points in each dimension of of B-Spline
     mesh for field 2. Separated by comma for each schedule run. (default:
     1,1,1,16,16)

   --congeal_schedule__n__warpfield__1__size <std::vector<int>>
     determines number of support points in each dimension of of B-Spline
     mesh for field 1. Separated by comma for each schedule run. (default:
     1,1,8,8,8)

   --congeal_schedule__n__warpfield__0__size <std::vector<int>>
     determines number of support points in each dimension of of B-Spline
     mesh for field 0. Separated by comma for each schedule run. (default:
     1,4,4,4,4)

   --congeal_schedule__n__optimize_affine <std::vector<std::string>>
     determines if affine parameters should be optimized or left fixed.
     Separated by comma for each schedule run. (default: true,false,false
     ,false,false)

   --congeal_schedule__n__downsample <std::vector<int>>
     determines how many times the input data should be downsampled (by
     factor of 2 in each dimension) prior to congealing. Separated by comma
     for each schedule run. (default: 0,0,0,0,0)

   --congeal_schedule__n__cache <std::vector<std::string>>
     determines whether or not the schedules results can be retrieved from
     the previous run. Separated by comma for each schedule run. (default:
     true,true,true,true,true)

   --congeal_initialsteps_warp <float>
     relative scaling of warp control point displacement when computing
     kernels and step sizes. Scale: Warp as fraction of control point's
     region (default: 0.15)

   --congeal_initialsteps_scale <float>
     relative scaling of scaling parameters when computing kernels and step
     sizes. Scale: Scale as fraction of image size (default: 0.2)

   --congeal_initialsteps_rotate <float>
     relative scaling of rotation parameters when computing kernels and
     step sizes. Scale: rotation in degrees (default: 30)

   --congeal_initialsteps_translate <float>
     relative scaling of translation parameters when computing kernels and
     step sizes. Scale: translation as fraction of image size (default:
     0.2)

   --congeal_output_average_height <int>
     determines the height of the congealing average visualization
     (default: 512)

   --congeal_output_average_width <int>
     determines the width of the congealing average visualization (default:
     512)

   --congeal_optimize_progresspoints <int>
     determines how many output file sets will be generated during each
     schedule (default: 4)

   --congeal_output_sourcegrid <int>
     determines how many of the transformed source values are shown in the
     *-inputs* images (default: 9)

   --congeal_output_colors_range <int>
     color equalization slope. This value determines the relationship
     between changes in data value and changes in output image gray value
     (default: 256)

   --congeal_output_colors_mid <int>
     color equalization intercept. This value determines which data value
     will be mapped to mid gray (default: 128)

   --congeal_output_prefix <std::string>
     string prepended to the filenames of the outputfiles. This value can
     include an absolute or relative path, as well as a file prefix
     (default: ../output/congeal/)

   --congeal_error__parzen__apriori <float>
     constant factor added to each Parzen estimate (default: 1e-06)

   --congeal_error__parzen__sigma <float>
     sigma of Gaussian used as kernel in Parzen density estimator. Measured
     in voxel intensity (default: 30)

   --congeal_optimize_error <parzen|variance>
     selects the error metric to be used. parzen -- entropy estimate based
     on Parzen density estimator. variance -- variance of voxel stack.
     (default: parzen)

   --congeal_optimize__randomwalk__directions <int>
     number of beams to try during each iteration (default: 20)

   --congeal_optimize__randomwalk__steps <int>
     maximum number of steps to take along any beam (default: 10)

   --congeal_optimize_randomwalk_kernel <float>
     size of support to use for computing initial stepsize. This factor is
     multiplied by *.initialsteps to establish a maximum step radius for
     each dimensions (default: 0.1)

   --congeal_optimize_algorithm <lbfgs|bruteforce|randomwalk
      |gradientdescent>
     determines the optimization algorithm used (default: randomwalk)

   --congeal_inputfiles_list <std::string>
     a path to a file containing a list of input data files. The list file
     should contain one filename per line. Only congeal_inputfiles files
     will be used as input unless congeal_inputfiles is set to '0' in which
     case all the files in the list will be used (default:
     ../input/sample/allfiles)

   --congeal_inputfile_format <nifti>
     format of input files. Currently only 'nifti' is supported (default:
     nifti)

   --congeal_inputfiles <int>
     number of input files to use. Use '0' for all files when used in
     conjuctions with congeal_inputfiles.list (default: 30)

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.


   Description: Generates a configuration file for the Congealing
   Registration tool.

   Author(s): Daniel Haehn and Kilian Pohl, University of
   Pennsylvania

   Acknowledgements: The research was funded by an ARRA supplement to NIH
   NCRR (P41 RR13218).

Examples

The following commands are possible: 

$ ./CongealingCLI 
Configuration file written to /tmp/congealing.config

or 

$ ./CongealingCLI --congeal_inputfiles 30 --congeal_inputfile_format nifti --congeal_inputfiles_list ../input/sample/allfiles 
--congeal_optimize_algorithm randomwalk --congeal_optimize_randomwalk_kernel 0.1 --congeal_optimize__randomwalk__steps 10 
--congeal_optimize__randomwalk__directions 20 --congeal_optimize_error parzen --congeal_error__parzen__sigma 30 
--congeal_error__parzen__apriori 1e-06 --congeal_output_prefix ../output/congeal/ --congeal_output_colors_mid 128 
--congeal_output_colors_range 256 --congeal_output_sourcegrid 9 --congeal_optimize_progresspoints 4 --congeal_output_average_width 512 
--congeal_output_average_height 512 --congeal_initialsteps_translate 0.2 --congeal_initialsteps_rotate 30 --congeal_initialsteps_scale 0.2 
--congeal_initialsteps_warp 0.15 --congeal_schedule__n__cache true,true,true,true,true --congeal_schedule__n__downsample 0,0,0,0,0 
--congeal_schedule__n__optimize_affine true,false,false,false,false --congeal_schedule__n__warpfield__0__size 1,4,4,4,4 
--congeal_schedule__n__warpfield__1__size 1,1,8,8,8 --congeal_schedule__n__warpfield__2__size 1,1,1,16,16 
--congeal_schedule__n__warpfield__3__size 1,1,1,1,32 --congeal_schedule__n__optimize_warp__0__ false,true,false,false,false 
 --congeal_schedule__n__optimize_warp__1__ false,false,true,false,false --congeal_schedule__n__optimize_warp__2__ false,false,false,true,false 
 --congeal_schedule__n__optimize_warp__3__ false,false,false,false,true --congeal_schedule__n__optimize_iterations 30,30,30,30,30 
 --congeal_schedule__n__optimize_samples 50000,50000,500000,500000,500000 --congeal_optimize_bestpoints 1000 --test congeal
Configuration file written to /tmp/congealing.config

and the output is the same for both (thanks to the default values, they also equal a press on the Apply button in the GUI without any changes to the input fields): 

$ cat /var/tmp/tmp.0.YQNbrV
# experimental
congeal.optimize.bestpoints 1000
test congeal

# input
congeal.inputfiles 30
congeal.inputfile.format nifti
congeal.inputfiles.list ../input/sample/allfiles

# optimization
congeal.optimize.algorithm randomwalk

# randomwalk
congeal.optimize[randomwalk].kernel 0.1
congeal.optimize[randomwalk].steps 10
congeal.optimize[randomwalk].directions 20

# error function
congeal.optimize.error parzen

# parzen error function
congeal.error[parzen].sigma 30
congeal.error[parzen].apriori 1e-06

# output
congeal.output.prefix ../output/congeal/
congeal.output.colors.mid 128
congeal.output.colors.range 256
congeal.output.sourcegrid 9
congeal.optimize.progresspoints 4
congeal.output.average.width 512
congeal.output.average.height 512

# initial steps
congeal.initialsteps.translate 0.2
congeal.initialsteps.rotate 30
congeal.initialsteps.scale 0.2
congeal.initialsteps.warp 0.15

# schedules

n -1
congeal.schedule[{++n}].cache true
congeal.schedule[{$n}].downsample 0
congeal.schedule[{$n}].optimize.affine true
congeal.schedule[{$n}].warpfield[0].size 1
congeal.schedule[{$n}].warpfield[1].size 1
congeal.schedule[{$n}].warpfield[2].size 1
congeal.schedule[{$n}].warpfield[3].size 1
congeal.schedule[{$n}].optimize.warp[0] false
congeal.schedule[{$n}].optimize.warp[1] false
congeal.schedule[{$n}].optimize.warp[2] false
congeal.schedule[{$n}].optimize.warp[3] false
congeal.schedule[{$n}].optimize.iterations 30
congeal.schedule[{$n}].optimize.samples 50000

congeal.schedule[{++n}].cache true
congeal.schedule[{$n}].downsample 0
congeal.schedule[{$n}].optimize.affine false
congeal.schedule[{$n}].warpfield[0].size 4
congeal.schedule[{$n}].warpfield[1].size 1
congeal.schedule[{$n}].warpfield[2].size 1
congeal.schedule[{$n}].warpfield[3].size 1
congeal.schedule[{$n}].optimize.warp[0] true
congeal.schedule[{$n}].optimize.warp[1] false
congeal.schedule[{$n}].optimize.warp[2] false
congeal.schedule[{$n}].optimize.warp[3] false
congeal.schedule[{$n}].optimize.iterations 30
congeal.schedule[{$n}].optimize.samples 50000

congeal.schedule[{++n}].cache true
congeal.schedule[{$n}].downsample 0
congeal.schedule[{$n}].optimize.affine false
congeal.schedule[{$n}].warpfield[0].size 4
congeal.schedule[{$n}].warpfield[1].size 8
congeal.schedule[{$n}].warpfield[2].size 1
congeal.schedule[{$n}].warpfield[3].size 1
congeal.schedule[{$n}].optimize.warp[0] false
congeal.schedule[{$n}].optimize.warp[1] true
congeal.schedule[{$n}].optimize.warp[2] false
congeal.schedule[{$n}].optimize.warp[3] false
congeal.schedule[{$n}].optimize.iterations 30
congeal.schedule[{$n}].optimize.samples 500000

congeal.schedule[{++n}].cache true
congeal.schedule[{$n}].downsample 0
congeal.schedule[{$n}].optimize.affine false
congeal.schedule[{$n}].warpfield[0].size 4
congeal.schedule[{$n}].warpfield[1].size 8
congeal.schedule[{$n}].warpfield[2].size 16
congeal.schedule[{$n}].warpfield[3].size 1
congeal.schedule[{$n}].optimize.warp[0] false
congeal.schedule[{$n}].optimize.warp[1] false
congeal.schedule[{$n}].optimize.warp[2] true
congeal.schedule[{$n}].optimize.warp[3] false
congeal.schedule[{$n}].optimize.iterations 30
congeal.schedule[{$n}].optimize.samples 500000

congeal.schedule[{++n}].cache true
congeal.schedule[{$n}].downsample 0
congeal.schedule[{$n}].optimize.affine false
congeal.schedule[{$n}].warpfield[0].size 4
congeal.schedule[{$n}].warpfield[1].size 8
congeal.schedule[{$n}].warpfield[2].size 16
congeal.schedule[{$n}].warpfield[3].size 32
congeal.schedule[{$n}].optimize.warp[0] false
congeal.schedule[{$n}].optimize.warp[1] false
congeal.schedule[{$n}].optimize.warp[2] false
congeal.schedule[{$n}].optimize.warp[3] true
congeal.schedule[{$n}].optimize.iterations 30
congeal.schedule[{$n}].optimize.samples 500000


congeal.schedules {++n}

Using --launch

When adding a --launch PATH_TO_CONGEAL_EXEC, the congeal executable gets launched rather than printing the path to the generated configuration file.

For example 

$ ./CongealingCLI --launch congeal

starts the congeal executable with the configuration file shown above.

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