diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/README.rst | 10 | ||||
| -rw-r--r-- | python/_phat.cpp | 10 | ||||
| -rw-r--r-- | python/phat.py | 52 | ||||
| -rw-r--r-- | python/src/simple_example.py | 6 |
4 files changed, 38 insertions, 40 deletions
diff --git a/python/README.rst b/python/README.rst index 0c6c391..7de641d 100644 --- a/python/README.rst +++ b/python/README.rst @@ -70,7 +70,7 @@ Other configurations are untested. Please note that this package DOES NOT work with the Python 2.7.10 that ships with the operating system in Mac OS X. These words of wisdom from `python.org`_ are worth heeding: - The version of Python that ships with OS X is great for learning but it’s not good for development. + The version of Python that ships with OS X is great for learning but it is not good for development. The version shipped with OS X may be out of date from the official current Python release, which is considered the stable production version. @@ -99,8 +99,10 @@ Now the code:: import phat - # define a boundary matrix with the chosen internal representation - boundary_matrix = phat.boundary_matrix(representation = phat.representations.vector_vector) + boundary_matrix = phat.boundary_matrix() + + # or define a boundary matrix with the chosen internal representation + # boundary_matrix = phat.boundary_matrix(representation = phat.representations.bit_tree_pivot_column) # set the respective columns -- (dimension, boundary) pairs boundary_matrix.columns = [ (0, []), @@ -138,5 +140,5 @@ References: .. [3] C.Chen, M.Kerber: Persistent Homology Computation With a Twist. 27th European Workshop on Computational Geometry, 2011. .. [4] U.Bauer, M.Kerber, J.Reininghaus: Clear and Compress: Computing Persistent Homology in Chunks. arXiv:1303.0477_ .. _arXiv:1303.0477: http://arxiv.org/pdf/1303.0477.pdf -.. _`Persistent Homology Algorithm Toolkit`: https://bitbucket.org/phat/phat-code +.. _`Persistent Homology Algorithm Toolbox`: https://bitbucket.org/phat/phat-code .. _`python.org`:http://docs.python-guide.org/en/latest/starting/install/osx/ diff --git a/python/_phat.cpp b/python/_phat.cpp index df7449d..f0a1516 100644 --- a/python/_phat.cpp +++ b/python/_phat.cpp @@ -12,15 +12,7 @@ #include "phat/persistence_pairs.h" #include "phat/compute_persistence_pairs.h" #include "phat/boundary_matrix.h" -#include "phat/representations/abstract_pivot_column.h" -#include <phat/representations/vector_vector.h> -#include <phat/representations/vector_heap.h> -#include <phat/representations/vector_set.h> -#include <phat/representations/vector_list.h> -#include <phat/representations/sparse_pivot_column.h> -#include <phat/representations/heap_pivot_column.h> -#include <phat/representations/full_pivot_column.h> -#include <phat/representations/bit_tree_pivot_column.h> +#include "phat/representations/default_representations.h" #include <phat/algorithms/twist_reduction.h> #include <phat/algorithms/standard_reduction.h> #include <phat/algorithms/row_reduction.h> diff --git a/python/phat.py b/python/phat.py index 70f5b39..c5ad686 100644 --- a/python/phat.py +++ b/python/phat.py @@ -70,7 +70,7 @@ import enum from _phat import persistence_pairs -#The public API for the module +# The public API for the module __all__ = ['boundary_matrix', 'persistence_pairs', @@ -102,6 +102,7 @@ class reductions(enum.Enum): class column(object): """A view on one column of data in a boundary matrix""" + def __init__(self, matrix, index): """INTERNAL. Columns are created automatically by boundary matrices. There is no need to construct them directly""" @@ -120,7 +121,7 @@ class column(object): @dimension.setter def dimension(self, value): - return self._matrix._matrix.set_dim(self._index, value) + self._matrix._matrix.set_dim(self._index, value) @property def boundary(self): @@ -129,16 +130,17 @@ class column(object): @boundary.setter def boundary(self, values): - return self._matrix._matrix.set_col(self._index, values) + self._matrix._matrix.set_col(self._index, values) def __str__(self): return "(%d, %s)" % (self.dimension, self.boundary) + class boundary_matrix(object): """Boundary matrices that store the shape information of a cell complex. """ - def __init__(self, representation = representations.bit_tree_pivot_column, source = None, columns = None): + def __init__(self, representation=representations.bit_tree_pivot_column, source=None, columns=None): """ The boundary matrix will use the specified implementation for storing its column data. If the `source` parameter is specified, it will be assumed to @@ -178,8 +180,8 @@ class boundary_matrix(object): @columns.setter def columns(self, columns): for col in columns: - if not (isinstance(col, column) or isinstance(col, tuple)): - raise TypeError("All columns must be column objects, or (dimension, values) tuples") + if not (isinstance(col, column) or isinstance(col, tuple)): + raise TypeError("All columns must be column objects, or (dimension, values) tuples") if len(columns) != len(self.dimensions): self._matrix.set_dims([0] * len(columns)) for i, col in enumerate(columns): @@ -189,7 +191,7 @@ class boundary_matrix(object): else: dimension, values = col self._matrix.set_dim(i, dimension) - self._matrix.set_col(i, values) + self._matrix.set_col(i, sorted(values)) @property def dimensions(self): @@ -198,7 +200,7 @@ class boundary_matrix(object): @dimensions.setter def dimensions(self, dimensions): - return self._matrix.set_dims(dimensions) + self._matrix.set_dims(dimensions) def __matrix_for_representation(self, representation): short_name = _short_name(representation.name) @@ -207,27 +209,27 @@ class boundary_matrix(object): def __eq__(self, other): return self._matrix == other._matrix - #Note Python 2.7 needs BOTH __eq__ and __ne__ otherwise you get things that - #are both equal and not equal + # Note Python 2.7 needs BOTH __eq__ and __ne__ otherwise you get things that + # are both equal and not equal def __ne__(self, other): return self._matrix != other._matrix def __len__(self): return self._matrix.get_num_entries() - #Pickle support + # Pickle support def __getstate__(self): (dimensions, columns) = self._matrix.get_vector_vector() return (self._representation, dimensions, columns) - #Pickle support + # Pickle support def __setstate__(self, state): presentation, dimensions, columns = state self._representation = representation self._matrix = self.__matrix_for_representation(representation) self._matrix.set_vector_vector(dimensions, columns) - def load(self, file_name, mode = 'b'): + def load(self, file_name, mode='b'): """Load this boundary matrix from a file Parameters @@ -252,7 +254,7 @@ class boundary_matrix(object): else: raise ValueError("Only 'b' - binary and 't' - text modes are supported") - def save(self, file_name, mode = 'b'): + def save(self, file_name, mode='b'): """Save this boundary matrix to a file Parameters @@ -278,37 +280,40 @@ class boundary_matrix(object): raise ValueError("Only 'b' - binary and 't' - text modes are supported") def compute_persistence_pairs(self, - reduction = reductions.twist_reduction): + reduction=reductions.twist_reduction): """Computes persistence pairs (birth, death) for the given boundary matrix.""" representation_short_name = _short_name(self._representation.name) algo_name = reduction.name algo_short_name = _short_name(algo_name) - #Look up an implementation that matches the requested characteristics - #in the _phat module + # Look up an implementation that matches the requested characteristics + # in the _phat module function = getattr(_phat, "compute_persistence_pairs_" + representation_short_name + "_" + algo_short_name) return function(self._matrix) - def compute_persistence_pairs_dualized(self, - reduction = reductions.twist_reduction): + def compute_persistence_pairs_dualized(self, + reduction=reductions.twist_reduction): """Computes persistence pairs (birth, death) from the dualized form of the given boundary matrix.""" representation_short_name = _short_name(self._representation.name) algo_name = reduction.name algo_short_name = _short_name(algo_name) - #Look up an implementation that matches the requested characteristics - #in the _phat module - function = getattr(_phat, "compute_persistence_pairs_dualized_" + representation_short_name + "_" + algo_short_name) + # Look up an implementation that matches the requested characteristics + # in the _phat module + function = getattr(_phat, + "compute_persistence_pairs_dualized_" + representation_short_name + "_" + algo_short_name) return function(self._matrix) def convert(self, representation): """Copy this matrix to another with a different representation""" return boundary_matrix(representation, self) + def _short_name(name): """An internal API that takes leading characters from words For instance, 'bit_tree_pivot_column' becomes 'btpc' """ return "".join([n[0] for n in name.split("_")]) + def _convert(source, to_representation): """Internal - function to convert from one `boundary_matrix` implementation to another""" class_name = source._representation.name @@ -316,6 +321,3 @@ def _convert(source, to_representation): to_rep_short_name = _short_name(to_representation.name) function = getattr(_phat, "convert_%s_to_%s" % (source_rep_short_name, to_rep_short_name)) return function(source._matrix) - - - diff --git a/python/src/simple_example.py b/python/src/simple_example.py index 955e213..7aa6214 100644 --- a/python/src/simple_example.py +++ b/python/src/simple_example.py @@ -21,8 +21,10 @@ if __name__ == "__main__": import phat - # define a boundary matrix with the chosen internal representation - boundary_matrix = phat.boundary_matrix(representation = phat.representations.vector_vector) + boundary_matrix = phat.boundary_matrix() + + # or define a boundary matrix with the chosen internal representation + # boundary_matrix = phat.boundary_matrix(representation = phat.representations.bit_tree_pivot_column) # set the respective columns -- (dimension, boundary) pairs boundary_matrix.columns = [ (0, []), |