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Accompanying paper: M. Kerber, D. Morozov, A. Nigmetov. Geometry Helps To Compare Persistence Diagrams (ALENEX 2016, http://www.geometrie.tugraz.at/nigmetov/geom_dist.pdf)
Bug reports can be sent to "nigmetov EMAIL SIGN tugraz DOT at".
# Dependencies
Your compiler must support C++11.
# Usage:
1. To use a standalone command-line utility bottleneck_dist:
bottleneck_dist file1 file2 [relative_error].
If relative error is not supplied, the exact distance is computed and printed.
If two diagrams are equal, then the exact distance 0.0 is printed (the order
of points in file1 and file2 need not be the same).
Otherwise the output is an approximation of the exact distance. Precisely:
if d_exact is the true distance and d_approx is the output, then
| d_exact - d_approx | / d_exact < relative_error.
file1 and file2 must contain persistence diagrams in plain text format
(one point per line, empty lines are ignored, comments can be made with #):
# this is how your input can look like
x_1 y_1 # two real numbers per line
...
# empty lines or comments are ignored
x_n y_n
2. To use from your code:
#include "bottleneck.h"
// the functions hera::bottleneckDistExact, hera::bottleneckDistApprox
// return the exact and approximate bottleneck distance.
// function hera::readDiagramPointSet reads diagram from a plain-text file.
std::vector<std::pair<double, double>> diagram1, diagram2;
// any container class that supports range-for loops will do.
// A pair represents a single point,
// first component = x-coordinate,
// second component = y-coordinate.
// ...
// load your diagrams into diagram1, diagram2 (off-diagonal points).
// If you data is in plain text format, you can use readDiagramPointSet function:
if (!hera::readDiagramPointSet("diagram1.txt", diagram1)) {
// something went wrong: function returns true if it successfully read the file
}
// OK: diagram1.txt was read.
// ...
// to get exact distance:
double btDist = hera::bottleneckDistExact(diagram1, diagram2);
// to get 1% approximation
double btDistApprox = hera::bottleneckDistApprox(diagram1, diagram2, 0.01);
// ..............................................................................
// if diagrams will be used many times, you may want to avoid copying them
// to hera::bt::DiagramPointSet (which is done internally in each call to
bottleneckDistExact/bottleneckDistApprox) and do it yourself once.
// Constructor takes two iterators:
hera::bt::DiagramPointSet ds1(diagram1.begin(), diagram1.end());
hera::bt::DiagramPointSet ds2(diagram2.begin(), diagram2.end());
btDist = hera::bt::bottleneckDistExact(ds1, ds2);
btDistApprox = hera::bt::bottleneckDistApprox(ds1, ds2, 0.01);
Necessary projections (diagonal points) will be added in the bottleneckDistApprox
function.
See also code in example/bottleneck_dist.cpp.
# Remarks:
1) If bottleneckDistApprox is called with epsilon = 0.0, it will never return.
2) Empty diagrams are not considered as error.
# License
See licence.txt
# Building
CMakeLists.txt in the root directory can be used to build
the command-line utility (in example/ directory).
The library itself is header-only and does not require separate compilation.
On Linux/Mac:
mkdir build
cd build
cmake ..
make
On Windows:
use cmake-gui to create the solution in build directory and build it with VS.
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