Screened Poisson Surface Reconstruction (Version 5.5)
This version is still in progress as it turns out to run slower and require more memory than Version 5.1

--in <input points>

This string is the name of the file from which the point set will be read.
If the file extension is .ply, the file should be in PLY format, giving the list of oriented vertices with the x-, y-, and z-coordinates of the positions encoded by the properties x, y, and z and the x-, y-, and z-coordinates of the normals encoded by the properties nx, ny, and nz .
If the file extension is .bnpts, the file should be a binary file, consisting of blocks of 6 32-bit floats: x-, y-, and z-coordinates of the point's position, followed by the x-, y-, and z-coordinates of the point's normal. (No information about the number of oriented point samples should be specified.)
Otherwise, the file should be an ascii file with groups of 6, white space delimited, numbers: x-, y-, and z-coordinates of the point's position, followed by the x-, y- and z-coordinates of the point's normal. (No information about the number of oriented point samples should be specified.)


[--out <output triangle mesh>]

This string is the name of the file to which the triangle mesh will be written. The file is written in PLY format.

[--depth <reconstruction depth>]

This integer is the maximum depth of the tree that will be used for surface reconstruction. Running at depth d corresponds to solving on a voxel grid whose resolution is no larger than 2^d x 2^d x 2^d. Note that since the reconstructor adapts the octree to the sampling density, the specified reconstruction depth is only an upper bound.
The default value for this parameter is 8.

[--minDepth <adaptive octree depth>]

This integer specifies the depth beyond depth the octree will be adapted. At coarser depths, the octree will be complete, containing all 2^d x 2^d x 2^d nodes.
The default value for this parameter is 5.

[--pointWeight <interpolation weight>]

This floating point value specifies the importants that interpolation of the point samples is given in the formulation of the screened Poisson equation.
The results of the original (unscreened) Poisson Reconstruction can be obtained by setting this value to 0.
The default value for this parameter is 4.

[--threads <number of processing threads>]

This integer specifies the number of threads across which the reconstruction algorithm should be parallelized.
The default value for this parameter is equal to the numer of (virtual) processors on the executing machine.

[--scale <scale factor>]

This floating point value specifies the ratio between the diameter of the cube used for reconstruction and the diameter of the samples' bounding cube.
The default value is 1.1.

[--solverDivide <solver subdivision depth>]

This integer argument specifies the depth at which a block Gauss-Seidel solver is used to solve the Laplacian equation. Using this parameter helps reduce the memory overhead at the cost of a small increase in reconstruction time. (In practice, we have found that for reconstructions of depth 9 or higher a subdivide depth of 7 or 8 can greatly reduce the memory usage.)
The default value is 8.

[--isoDivide <iso-surface extraction subdivision depth>]

This integer argument specifies the depth at which a block iso-surface extractor should be used to extract the iso-surface. Using this parameter helps reduce the memory overhead at the cost of a small increase in extraction time. (In practice, we have found that for reconstructions of depth 9 or higher a subdivide depth of 7 or 8 can greatly reduce the memory usage.)
The default value is 8.

[--samplesPerNode <minimum number of samples>]

This floating point value specifies the minimum number of sample points that should fall within an octree node as the octree construction is adapted to sampling density. For noise-free samples, small values in the range [1.0 - 5.0] can be used. For more noisy samples, larger values in the range [15.0 - 20.0] may be needed to provide a smoother, noise-reduced, reconstruction.
The default value is 1.0.

[--confidence]

Enabling this flag tells the reconstructor to use the size of the normals as confidence information. When the flag is not enabled, all normals are normalized to have unit-length prior to reconstruction.

[--polygonMesh]

Enabling this flag tells the reconstructor to output a polygon mesh (rather than triangulating the results of Marching Cubes).

[--density]

Enabling this flag tells the reconstructor to output the estimated depth values of the iso-surface vertices.

[--verbose]

Enabling this flag provides a more verbose description of the running times and memory usages of individual components of the surface reconstructor.

--in <input triangle mesh>

This string is the name of the file from which the triangle mesh will be read. The file is read in PLY format and it is assumed that the vertices have a value field which stores the signal's value. (When run with --density flag, the reconstructor will output this field with the mesh vertices.)

--trim <trimming value>

This floating point values specifies the value for mesh trimming. The subset of the mesh with signal value less than the trim value is discarded.

[--out <output triangle mesh>]

This string is the name of the file to which the triangle mesh will be written. The file is written in PLY format.

[--smooth <smoothing iterations>]

This integer values the number of umbrella smoothing operations to perform on the signal before trimming.
The default value is 5.

[--aRatio <island area ratio>]

This floating point value specifies the area ratio that defines a disconnected component as an "island". Connected components whose area, relative to the total area of the mesh, are smaller than this value will be merged into the output surface to close small holes, and will be discarded from the output surface to remove small disconnected components.
The default value 0.001.

[--polygonMesh]

Enabling this flag tells the trimmer to output a polygon mesh (rather than triangulating the trimming results).

1. Bunny: A set of 362,271 oriented point samples (represented in PLY format) was obtained by merging the data from the original Stanford Bunny range scans. The orientation of the sample points was estimated using the connectivity information within individual range scans.
   The original Poisson Reconstruction algorithm can be invoked by calling:

   % PoissonRecon --in bunny.points.ply --out bunny.unscreened.ply --depth 10 --pointWeight 0

   using the --pointWeight 0 argument to disable the screening.
   By default, screening is enabled so the call:

   % PoissonRecon --in bunny.points.ply --out bunny.screened.ply --depth 10

   produces a reconstruction that more faithfully fits the input point positions.
   A reconstruction of the bunny that does not close up the holes can be obtained by first calling:

   % PoissonRecon --in bunny.points.ply --out bunny.screened.ply --depth 10 --density

   to obtain a surface storing depth estimates with each vertex, and then calling:

   % SurfaceTrimmer --in bunny.screened.ply --out bunny.screened.trimmed.ply --trim 7 --aRatio 0

   to remove all subsets of the surface where the sampling density corresponds to a depth smaller than 7.
   To fill in small holes in the reconstruction, the default value of the area ratio can be used instead:

   % SurfaceTrimmer --in bunny.screened.ply --out bunny.screened.trimmed.ply --trim 7

2. Horse: A set of 100,000 oriented point samples (represented in ASCII format) was obtained by sampling a virtual horse model with a sampling density proportional to curvature, giving a set of non-uniformly distributed points.
   The surface of the model can be reconstructed by calling the surface reconstructor as follows:

   % PoissonRecon --in horse.npts --out horse.ply --depth 10

% ply2mesh.pl bunny.ply > bunny.m

1. The implementation of the --samplesPerNode parameter has been modified so that a value of "1" more closely corresponds to a distribution with one sample per leaf node.
2. The code has been modified to support compilation under MSVC 2010 and the associated solution and project files are now provided. (Due to a bug in the Visual Studios compiler, this required modifying the implementation of some of the bit-shifting operators.)

1. The code supports screened reconstruction, with interpolation weight specified through the --pointWeight parameter.
2. The code has been implemented to support parallel processing, with the number of threads used for parallelization specified by the --threads parameter.
3. The input point set can now also be in PLY format, and the file-type is determined by the extension, so that the --binary flag is now obsolete.
4. At depths coarser than the one specified by the value --minDepth the octree is no longer adaptive but rather complete, simplifying the prolongation operator.

1. The algorithmic complexity of the solver was reduced from log-linear to linear.

1. Smart pointers were added to ensure that memory accesses were in bounds.

1. The --density flag was added to the reconstructor to output the estimated depth of the iso-vertices.
2. The SurfaceTrimmer executable was added to support trimming off the subset of the reconstructed surface that are far away from the input samples, thereby allowing for the generation of non-water-tight surface.

1. Minor bug-fix to address incorrect neighborhood estimation in the octree finalization.

1. Modified to support depths greater than 14. (Should work up to 18 or 19 now.)
2. Improved speed and memory performance by removing the construction of integral and value tables.