superdsm.atoms

class superdsm.atoms.AtomAdjacencyGraph(atoms, clusters, fg_mask, seeds, status=None)

Bases: object

Graph representation of the adjacencies of atomic image regions.

This corresponds to the adjacency graph \(\mathcal G\) as defined in Coarse-to-fine region analysis.

Parameters:

atoms – Integer-valued image representing the universe of atomic image regions. Each atomic image region has a unique label, which is the integer value.
clusters – Integer-valued image representing the regions of possibly clustered obejcts. Each region has a unique label, which is the integer value.
fg_mask – Binary image corresponding to a rough representation of the image foreground. This means that an image point \(x \in \Omega\) is True if \(Y_\omega|_{\omega=\{x\}} > 0\) and False otherwise.
seeds – The seed points which were used to determine the atomic image regions, represented by a list of tuples of coordinates. The The SuperDSM pipeline only uses these for rendering the adjacency graph (see the get_edge_lines() method).
status – A repype.status.Status object or None if no output should be produced.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

property atom_labels

The set of labels of all atomic image regions.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

property cluster_labels

The set of labels of all regions of possibly clustered objects.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

get_atom_degree(atom_label)

Returns the number of adjacent atomic image regions.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

get_atoms_in_cluster(cluster_label)

Returns the set of labels of all atomic image regions, which are part of a region of possibly clustered objects.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

get_cluster_label(atom_label)

Returns the label of the region of possibly clustered objects, which an atomic image region is a part of.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

get_edge_lines(accept='all', reduce=True)

Returns a list of lines corresponding to the edges of the graph.

Parameters:

accept – Must be either all or a callable. If all is used, all edges of the graph are included. Otherwise, an edge (i,j) is included only if accept(i) and accept(j) evaluate to True, where i and j are the labels of two adjacent atomic image regions.
reduce – If True, then an edge (i,j) is included only if i > j. Otherwise, both edges (i,j) and (j,i) are included.

Each line is a tuple of two seed points, and each seed point is a tuple of coordinates.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

get_seed(atom_label)

Returns the seed point which was used to determine an atomic image region.

Returns:: Tuple of the coordinates of the seed point.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined

property max_degree

The maximum degree of the graph.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/checkouts/develop/superdsm/atoms.py", line 80, in __init__
    repype.status.update(status, 'Processed atom %d / %d' % (l0, atoms.max()), intermediate=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/superdsm/envs/develop/lib/python3.11/site-packages/repype/status.py", line 651, in update
    status.intermediate(dict(**kwargs) if kwargs else plain_text)
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'intermediate'
Traceback (most recent call last):
  File "<input>", line 1, in <module>
NameError: name 'adj' is not defined