diff options
author | pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-08-22 19:38:57 +0000 |
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committer | pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-08-22 19:38:57 +0000 |
commit | d7797ccdc896a06977155b16df327eb6c379907a (patch) | |
tree | ca7a9f273a7d2709894d3754e2b36f9c9f639216 /src | |
parent | c415445c6a30cfdc7abc63dba23e4eb5e7ff98da (diff) |
First almost working version.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2619 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 6f677549e1889ffe29125d2550b2a4a57099b3f5
Diffstat (limited to 'src')
4 files changed, 121 insertions, 65 deletions
diff --git a/src/cython/cython/persistence_representations_intervals.pyx b/src/cython/cython/persistence_representations_intervals.pyx index 29027801..887010e5 100644 --- a/src/cython/cython/persistence_representations_intervals.pyx +++ b/src/cython/cython/persistence_representations_intervals.pyx @@ -91,11 +91,14 @@ cdef class PersistenceIntervals: # The real cython constructor - def __cinit__(self, vector_of_intervals=None, dimension = None, file_with_intervals=''): + def __cinit__(self, vector_of_intervals=None, dimension = None, file_with_intervals=''): if (vector_of_intervals is None) and (file_with_intervals is not ''): - self.thisptr = new Persistence_intervals_interface(file_with_intervals, dimension) - elif (file_with_intervals is not '') and (vector_of_intervals is not None): - if os.path.isfile(file_with_intervals): + if ( dimension is not None ): + self.thisptr = new Persistence_intervals_interface(file_with_intervals, dimension) + else: + self.thisptr = new Persistence_intervals_interface(file_with_intervals) + elif (file_with_intervals is '') and (vector_of_intervals is not None): + if os.path.isfile(file_with_intervals): self.thisptr = new Persistence_intervals_interface(str.encode(file_with_intervals)) else: print("file " + file_with_intervals + " not found.") diff --git a/src/cython/example/persistence_representations_diagrams_example.py b/src/cython/example/persistence_representations_diagrams_example.py index 62dc84d7..bcf17f5a 100755 --- a/src/cython/example/persistence_representations_diagrams_example.py +++ b/src/cython/example/persistence_representations_diagrams_example.py @@ -33,15 +33,6 @@ print("#####################################################################") print("Persistence representations diagrams example") - - - - - - - - - parser = argparse.ArgumentParser(description='Statistics od persistence diagrams from file ', epilog='Example: ' 'example/persistence_representations_diagrams_example.py ' @@ -53,55 +44,27 @@ args = parser.parse_args() print "Here are the parameters of the program: ",args.file," , " ,args.dimension - -p = gudhi.PersistenceIntervals(args.file,args.dimension); +p = gudhi.PersistenceDiagrams(None,args.dimension,args.file); min_max_ = p.get_x_range(); -print( "Birth-death range : ", min_max_) -""" -std::vector<double> dominant_ten_intervals_length = p.length_of_dominant_intervals(10); -std::cout << "Length of ten dominant intervals : " << std::endl; -for (size_t i = 0; i != dominant_ten_intervals_length.size(); ++i) { -std::cout << dominant_ten_intervals_length[i] << std::endl; -} - -std::vector<std::pair<double, double> > ten_dominant_intervals = p.dominant_intervals(10); -std::cout << "Here are the dominant intervals : " << std::endl; -for (size_t i = 0; i != ten_dominant_intervals.size(); ++i) { -std::cout << "( " << ten_dominant_intervals[i].first << "," << ten_dominant_intervals[i].second << std::endl; -} - -std::vector<size_t> histogram = p.histogram_of_lengths(10); -std::cout << "Here is the histogram of barcode's length : " << std::endl; -for (size_t i = 0; i != histogram.size(); ++i) { -std::cout << histogram[i] << " "; -} -std::cout << std::endl; - -std::vector<size_t> cumulative_histogram = p.cumulative_histogram_of_lengths(10); -std::cout << "Cumulative histogram : " << std::endl; -for (size_t i = 0; i != cumulative_histogram.size(); ++i) { -std::cout << cumulative_histogram[i] << " "; -} -std::cout << std::endl; - -std::vector<double> char_funct_diag = p.characteristic_function_of_diagram(min_max_.first, min_max_.second); -std::cout << "Characteristic function of diagram : " << std::endl; -for (size_t i = 0; i != char_funct_diag.size(); ++i) { -std::cout << char_funct_diag[i] << " "; -} -std::cout << std::endl; - -std::vector<double> cumul_char_funct_diag = - p.cumulative_characteristic_function_of_diagram(min_max_.first, min_max_.second); -std::cout << "Cumulative characteristic function of diagram : " << std::endl; -for (size_t i = 0; i != cumul_char_funct_diag.size(); ++i) { -std::cout << cumul_char_funct_diag[i] << " "; -} -std::cout << std::endl; - -std::cout << "Persistence Betti numbers \n"; -std::vector<std::pair<double, size_t> > pbns = p.compute_persistent_betti_numbers(); -for (size_t i = 0; i != pbns.size(); ++i) { -std::cout << pbns[i].first << " " << pbns[i].second << std::endl; -} -""" +print "Birth-death range : ", min_max_ + +dominant_ten_intervals_length = p.length_of_dominant_intervals(10) +print "Length of ten dominant intervals : ", dominant_ten_intervals_length + +ten_dominant_intervals = p.dominant_intervals(10); +print "Here are the dominant intervals : " , ten_dominant_intervals + +histogram = p.histogram_of_lengths(10); +print "Here is the histogram of barcode's length : ", histogram + +cumulative_histogram = p.cumulative_histogram_of_lengths(10) +print "Cumulative histogram : " ,cumulative_histogram + +char_funct_diag = p.characteristic_function_of_diagram(min_max_[0], min_max_[1],None) +print "Characteristic function of diagram : ",char_funct_diag + +cumul_char_funct_diag = p.cumulative_characteristic_function_of_diagram(min_max_[0], min_max_[1],None) +print "Cumulative characteristic function of diagram : ",cumul_char_funct_diag + +pbns = p.compute_persistent_betti_numbers() +print "Persistence Betti numbers ", pbns diff --git a/src/cython/include/persistence_representations_intervals.h b/src/cython/include/persistence_representations_intervals.h index eb440f1a..a4ad0e0f 100644 --- a/src/cython/include/persistence_representations_intervals.h +++ b/src/cython/include/persistence_representations_intervals.h @@ -43,6 +43,7 @@ class Persistence_intervals_interface : public Persistence_intervals public: Persistence_intervals_interface(const char* filename, unsigned dimension = std::numeric_limits<unsigned>::max()) : Persistence_intervals(filename, dimension) { + std::cout << "CONTSTRUCTOR \n"; } Persistence_intervals_interface(const std::vector<std::pair<double, double> >& intervals) @@ -51,7 +52,9 @@ class Persistence_intervals_interface : public Persistence_intervals std::pair<double, double> get_x_range_interface() const { - return this->get_x_range(); + std::pair<double, double> range = this->get_x_range(); + std::cout << std::endl << std::endl << range.first << " " << range.second << std::endl << std::endl <<std::endl; + return range; } std::pair<double, double> get_y_range_interface() const diff --git a/src/cython/test/test_persistence_representations_diagrams.py b/src/cython/test/test_persistence_representations_diagrams.py new file mode 100755 index 00000000..5be95a68 --- /dev/null +++ b/src/cython/test/test_persistence_representations_diagrams.py @@ -0,0 +1,87 @@ +import gudhi + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Pawel Dlotko + + Copyright (C) 2017 Swansea University + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. +""" + +__author__ = "Pawel Dlotko" +__copyright__ = "Copyright (C) 2017 Swansea University" +__license__ = "GPL v3" + +epsilon = 0.0000005; + +def test_check_min_max_function(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + min_max_ = p.get_x_range() + assert fabs(min_max_[0] - 0.0290362) <= epsilon + assert fabs(min_max_[1] - 0.994537) <= epsilon + +def test_check_length_of_dominant_intervals(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + dominant_ten_intervals_length = p.length_of_dominant_intervals(10) + dominant_intervals_length_ = [0.862625,0.800893,0.762061,0.756501,0.729367,0.718177,0.708395,0.702844,0.700468,0.622177] + assert dominant_ten_intervals_length == dominant_intervals_length_ + + +def check_dominant_intervals(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram"); + ten_dominant_intervals = p.dominant_intervals(10); + templ = [ (0.114718, 0.977343) , (0.133638, 0.93453) , (0.104599, 0.866659) , (0.149798, 0.906299), (0.247352, 0.976719) , (0.192675, 0.910852) , (0.191836, 0.900231) , (0.284998, 0.987842) , (0.294069, 0.994537), (0.267421, 0.889597)] + assert fabs(ten_dominant_intervals - templ) <= epsilon + + +def check_histogram_of_lengths(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + histogram = p.histogram_of_lengths(10); + template_histogram = [10,5,3,4,4,3,6,1,7,1,1] + assert fabs(histogram - template_histogram) <= epsilon + + +def check_cumulative_histograms_of_lengths(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + cumulative_histogram = p.cumulative_histogram_of_lengths(10) + template_cumulative_histogram = [10,15,18,22,26,29,35,36,43,44,45] + assert fabs(cumulative_histogram - template_cumulative_histogram) <= epsilon + + +def check_characteristic_function_of_diagram(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + min_max_ = p.get_x_range(); + char_funct_diag = p.characteristic_function_of_diagram(min_max_[0], min_max_[1]); + template_char_funct_diag = [0.370665,0.84058,1.24649,1.3664,1.34032,1.31904,1.14076,0.991259,0.800714,0.0676303] + assert fabs(char_funct_diag - template_char_funct_diag) <= 0.0001 + + +def check_cumulative_characteristic_function_of_diagram(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + min_max_ = p.get_x_range() + cumul_char_funct_diag = p.cumulative_characteristic_function_of_diagram(min_max_.first, min_max_.second,None); + template_char_funct_diag_cumul = [0.370665,1.21125,2.45774,3.82414,5.16446,6.4835,7.62426,8.61552,9.41623,9.48386] + assert fabs(cumul_char_funct_diag - template_char_funct_diag_cumul) <= 0.0001 + + +def check_compute_persistent_betti_numbers(): + p = gudhi.PersistenceDiagrams(None,None,"data/file_with_diagram") + pbns = [(0.0290362, 1),(0.0307676, 2),(0.0366312, 3),(0.0544614, 4),(0.0920033, 5),(0.104599, 6),(0.114718, 7),(0.117379, 8),(0.123493, 9),(0.133638, 10)(0.137798, 9),(0.149798, 10),(0.155421, 11),(0.158443, 12)(0.176956, 13),(0.183234, 12),(0.191069, 13),(0.191333, 14),(0.191836, 15),(0.192675, 16),(0.208564, 17),(0.218425, 18),(0.219902, 17),(0.23233, 16),(0.234558, 17),(0.237166, 16),(0.247352, 17),(0.267421, 18),(0.268093, 19),(0.278734, 18),(0.284722, 19),(0.284998, 20),(0.294069, 21),(0.306293, 22),(0.322361, 21),(0.323152, 22),(0.371021, 23),(0.372395, 24),(0.387744, 25),(0.435537, 26),(0.462911, 25),(0.483569, 26),(0.489209, 25),(0.517115, 24),(0.522197, 23),(0.532665, 22),(0.545262, 23),(0.587227, 22),(0.593036, 23),(0.602647, 24),(0.605044, 25),(0.621962, 24),(0.629449, 23),(0.636719, 22),(0.64957, 21),(0.650781, 22),(0.654951, 23),(0.683489, 24),(0.687172, 23),(0.69703, 22),(0.701174, 21),(0.717623, 22),(0.722023, 21),(0.722298, 20),(0.725347, 19),(0.73071, 18),(0.758355, 17),(0.770913, 18),(0.790833, 17),(0.821211, 16),(0.849305, 17),(0.853669, 16),(0.866659, 15),(0.872896, 16),(0.889597, 15),(0.900231, 14),(0.903847, 13),(0.906299, 12),(0.910852, 11),(0.93453, 10),(0.944757, 9),(0.947812, 8),(0.959154, 7),(0.975654, 6),(0.976719, 5),(0.977343, 4),(0.980129, 3),(0.987842, 2),(0.990127, 1),(0.994537, 0)] + pbns_new = p.compute_persistent_betti_numbers(); + assert fabs(pbns - pbns_new) <= epsilon + + |