Modules:AtlasCreator:CongealingCLI

CongealingCLI

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.

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>] [--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.

   --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 /var/tmp/tmp.0.YQNbrV

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 /var/tmp/tmp.0.YQNbrV

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.