Python interface to PHAT

1 files changed, 88 insertions, 0 deletions

diff --git a/python/phat.py b/python/phat.py
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+import _phat
+import enum
+
+from _phat import persistence_pairs
+
+__all__ = ['boundary_matrix',
+           'persistence_pairs',
+           'compute_persistence_pairs',
+           'compute_persistence_pairs_dualized']
+
+
+"""Bindings for the Persistent Homology Algorithm Toolbox
+
+
+Please see https://bitbucket.org/phat-code/phat for more information.
+"""
+
+
+class representations(enum.Enum):
+    """Available representations for internal storage of columns in
+    a `boundary_matrix`
+    """
+    bit_tree_pivot_column = 1
+    sparse_pivot_column = 2
+    full_pivot_column = 3
+    vector_vector = 4
+    vector_heap = 5
+    vector_set = 6
+    vector_list = 7
+
+class reductions(enum.Enum):
+    "Available reduction algorithms"
+    twist_reduction = 1
+    chunk_reduction = 2
+    standard_reduction = 3
+    row_reduction = 4
+    spectral_sequence_reduction = 5
+
+def __short_name(name):
+    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.__class__.__name__
+    source_rep_short_name = class_name[len('boundary_matrix_'):]
+    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)
+
+def boundary_matrix(representation = representations.bit_tree_pivot_column, source = None):
+    """Returns an instance of a `boundary_matrix` class.
+    The boundary matrix will use the specified implementation for storing its column data.
+    If the `source` parameter is specified, it will be assumed to be another boundary matrix,
+    whose data should be copied into the new matrix.
+    """
+    if source:
+        return convert(source, representation)
+    else:
+        class_name = representation.name
+        short_name = __short_name(class_name)
+        function = getattr(_phat, "boundary_matrix_" + short_name)
+        return function()
+
+def compute_persistence_pairs(matrix,
+                              reduction = reductions.twist_reduction):
+    """Computes persistence pairs (birth, death) for the given boundary matrix."""
+    class_name = matrix.__class__.__name__
+    representation_short_name = class_name[len('boundary_matrix_'):]
+    algo_name = reduction.name
+    algo_short_name = __short_name(algo_name)
+    function = getattr(_phat, "compute_persistence_pairs_" + representation_short_name + "_" + algo_short_name)
+    return function(matrix)
+
+def compute_persistence_pairs_dualized(matrix,
+                                       reduction = reductions.twist_reduction):
+    """Computes persistence pairs (birth, death) from the dualized form of the given boundary matrix."""
+    class_name = matrix.__class__.__name__
+    representation_short_name = class_name[len('boundary_matrix_'):]
+    algo_name = reduction.name
+    algo_short_name = __short_name(algo_name)
+    function = getattr(_phat, "compute_persistence_pairs_dualized_" + representation_short_name + "_" + algo_short_name)
+    return function(matrix)
+
+
+
+
+
+