From 3ce013afc21df5d05d663dd17a6640cec9af4aed Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 24 Apr 2018 12:31:44 +0000 Subject: Fix Python tangential complex version git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3392 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f0d9e008229a6cd7868f4afd11eaf3c566e81adf --- .../tangential_complex_plain_homology_from_off_file_example.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'src/cython/example/tangential_complex_plain_homology_from_off_file_example.py') diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py index 6145e7f2..08ae5d07 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -33,10 +33,11 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from ' 'points read in a OFF file.', epilog='Example: ' 'example/tangential_complex_plain_homology_from_off_file_example.py ' - '-f ../data/points/tore3D_300.off' + '-f ../data/points/tore3D_300.off -i 3' '- Constructs a tangential complex with the ' 'points from the given OFF file') parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-i", "--intrisic_dim", type=int, required=True) parser.add_argument("-b", "--band_boot", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') @@ -48,7 +49,7 @@ with open(args.file, 'r') as f: print("#####################################################################") print("TangentialComplex creation from points read in a OFF file") - tc = gudhi.TangentialComplex(off_file=args.file) + tc = gudhi.TangentialComplex(intrisic_dim = args.intrisic_dim, off_file=args.file) st = tc.create_simplex_tree() message = "Number of simplices=" + repr(st.num_simplices()) -- cgit v1.2.3 From 7ac3c086c6c794ac8c493a2c3abbd59624e81c06 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 27 Apr 2018 13:00:38 +0000 Subject: Code and doc review with IFPEN : plot_*: c'est quoi ce paramètre alpha ? MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit band_boot: Renommer en 'band', sans référence au bootstrap. Ne pas l'utiliser dans la majorité des exemples / tutos. max_plots: mettre une valeur par défaut, pour éviter qu'on se retrouve trop facilement coincé à attendre 1h qu'il affiche des points. Éventuellement afficher un message indiquant que certains points n'ont pas été affichés et comment changer ça. barcode: trier les barres par date de naissance (le faire tout le temps ou avoir une option et le faire par défaut). git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3404 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cfa775e425fbf12da1758d601ccbd80a2c7d3bc9 --- src/cython/cython/persistence_graphical_tools.py | 41 +++++++++++++--------- .../doc/persistence_graphical_tools_user.rst | 4 +-- src/cython/doc/pyplots/diagram_persistence.py | 2 +- ...ex_diagram_persistence_from_off_file_example.py | 4 +-- ...ex_diagram_persistence_from_off_file_example.py | 4 +-- ...ex_diagram_persistence_from_off_file_example.py | 4 +-- .../example/gudhi_graphical_tools_example.py | 2 +- ...istence_from_correlation_matrix_file_example.py | 4 +-- ...ersistence_from_distance_matrix_file_example.py | 4 +-- ...ex_diagram_persistence_from_off_file_example.py | 4 +-- ...complex_plain_homology_from_off_file_example.py | 4 +-- 11 files changed, 42 insertions(+), 35 deletions(-) (limited to 'src/cython/example/tangential_complex_plain_homology_from_off_file_example.py') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index fb837e29..f7dadb53 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -28,13 +28,13 @@ __author__ = "Vincent Rouvreau, Bertrand Michel" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" -def __min_birth_max_death(persistence, band_boot=0.): +def __min_birth_max_death(persistence, band=0.): """This function returns (min_birth, max_death) from the persistence. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param band_boot: bootstrap band - :type band_boot: float. + :param band: band + :type band: float. :returns: (float, float) -- (min_birth, max_death). """ # Look for minimum birth date and maximum death date for plot optimisation @@ -48,8 +48,8 @@ def __min_birth_max_death(persistence, band_boot=0.): max_death = float(interval[1][0]) if float(interval[1][0]) < min_birth: min_birth = float(interval[1][0]) - if band_boot > 0.: - max_death += band_boot + if band > 0.: + max_death += band return (min_birth, max_death) """ @@ -77,16 +77,17 @@ def show_palette_values(alpha=0.6): plt.title('Dimension palette values') return plt -def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0): +def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=1000): """This function plots the persistence bar code. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). :param persistence_file: A persistence file style name (reset persistence if both are set). :type persistence_file: string - :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6). + :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6). :type alpha: float. - :param max_barcodes: number of maximal barcodes to be displayed + :param max_barcodes: number of maximal barcodes to be displayed. + Set it to 0 to see all, Default value is 1000. (persistence will be sorted by life time if max_barcodes is set) :type max_barcodes: int. :returns: plot -- An horizontal bar plot of persistence. @@ -107,6 +108,8 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max # Sort by life time, then takes only the max_plots elements persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes] + persistence = sorted(persistence, key=lambda birth: birth[1][0]) + (min_birth, max_death) = __min_birth_max_death(persistence) ind = 0 delta = ((max_death - min_birth) / 10.0) @@ -120,12 +123,14 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max # Finite death case plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8, left = interval[1][0], alpha=alpha, - color = palette[interval[0]]) + color = palette[interval[0]], + linewidth=0) else: # Infinite death case for diagram to be nicer plt.barh(ind, (infinity - interval[1][0]), height=0.8, left = interval[1][0], alpha=alpha, - color = palette[interval[0]]) + color = palette[interval[0]], + linewidth=0) ind = ind + 1 plt.title('Persistence barcode') @@ -133,18 +138,20 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max plt.axis([axis_start, infinity, 0, ind]) return plt -def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0): +def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band=0., max_plots=1000): """This function plots the persistence diagram with an optional confidence band. :param persistence: The persistence to plot. :type persistence: list of tuples(dimension, tuple(birth, death)). :param persistence_file: A persistence file style name (reset persistence if both are set). :type persistence_file: string - :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6). + :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6). :type alpha: float. - :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.) - :type band_boot: float. + :param band: band (not displayed if :math:`\leq` 0. - default is 0.) + :type band: float. :param max_plots: number of maximal plots to be displayed + Set it to 0 to see all, Default value is 1000. + (persistence will be sorted by life time if max_plots is set) :type max_plots: int. :returns: plot -- A diagram plot of persistence. """ @@ -164,7 +171,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban # Sort by life time, then takes only the max_plots elements persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] - (min_birth, max_death) = __min_birth_max_death(persistence, band_boot) + (min_birth, max_death) = __min_birth_max_death(persistence, band) ind = 0 delta = ((max_death - min_birth) / 10.0) # Replace infinity values with max_death + delta for diagram to be more @@ -179,8 +186,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha) plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha) # bootstrap band - if band_boot > 0.: - plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red') + if band > 0.: + plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red') # Draw points in loop for interval in reversed(persistence): diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index a5523d23..290b13c3 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -62,7 +62,7 @@ This function can display the persistence result as a diagram: rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + plt = gudhi.plot_persistence_diagram(diag) plt.show() .. plot:: @@ -73,5 +73,5 @@ This function can display the persistence result as a diagram: rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + plt = gudhi.plot_persistence_diagram(diag) plt.show() diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py index ac20bf47..5abf52b9 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -5,5 +5,5 @@ point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \ rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() -plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) +plt = gudhi.plot_persistence_diagram(diag) plt.show() diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py index b4487be4..10d4867a 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from ' 'points from the given OFF file.') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -64,7 +64,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index e3f362dc..28a8599c 100755 --- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) parser.add_argument("-d", "--limit_dimension", type=int, required=True) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -71,7 +71,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index c236d992..b19d7d8c 100755 --- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-a", "--max_alpha_square", type=float, required=True) parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) parser.add_argument("-d", "--limit_dimension", type=int, required=True) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -71,7 +71,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py index ed87806b..97983262 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -50,5 +50,5 @@ pplot.show() print("#####################################################################") print("Show diagram persistence example with a confidence band") -pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2) +pplot = gudhi.plot_persistence_diagram(persistence, band=0.2) pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index aa82ef71..0af4397a 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -40,7 +40,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -80,5 +80,5 @@ print(simplex_tree.betti_numbers()) invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))] if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band) pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index c8aac240..266c09ca 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -63,5 +63,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 544b68c9..fede920c 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -66,7 +66,7 @@ with open(args.file, 'r') as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py index 08ae5d07..1f562b5c 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from ' 'points from the given OFF file') parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-i", "--intrisic_dim", type=int, required=True) -parser.add_argument("-b", "--band_boot", type=float, default=0.) +parser.add_argument("-b", "--band", type=float, default=0.) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -61,7 +61,7 @@ with open(args.file, 'r') as f: print(st.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(diag, band=args.band) pplot.show() else: print(args.file, "is not a valid OFF file") -- cgit v1.2.3