Merge pull request #15 from jagterberg/hh-dev

adding lcc

jhu_primitives/__init__.py

@@ -12,6 +12,7 @@
 from .lse import LaplacianSpectralEmbedding
 from .dimselect import DimensionSelection
 from .gclust import GaussianClustering
+from .lcc import LargestConnectedComponent
 from .nonpar import NonParametricClustering
 from .numclust import NumberOfClusters
 from .oocase import OutOfCoreAdjacencySpectralEmbedding

jhu_primitives/lcc/__init__.py

@@ -0,0 +1 @@
+from .lcc import LargestConnectedComponent

jhu_primitives/lcc/lcc.py

@@ -0,0 +1,170 @@
+from rpy2 import robjects
+from typing import Sequence, TypeVar, Union, Dict
+import os
+from d3m.primitive_interfaces.transformer import TransformerPrimitiveBase
+import numpy
+from d3m import container
+from d3m import utils
+from d3m.metadata import hyperparams, base as metadata_module, params
+from d3m.primitive_interfaces import base
+from d3m.primitive_interfaces.base import CallResult
+import igraph
+import networkx
+
+
+Inputs = container.ndarray
+Outputs = container.ndarray
+
+class Params(params.Params):
+    pass
+
+class Hyperparams(hyperparams.Hyperparams):
+    #dim = hyperparams.Hyperparameter[None](default=None)
+    dim = None
+
+def file_path_conversion(abs_file_path, uri="file"):
+    local_drive, file_path = abs_file_path.split(':')[0], abs_file_path.split(':')[1]
+    path_sep = file_path[0]
+    file_path = file_path[1:]  # Remove initial separator
+    if len(file_path) == 0:
+        print("Invalid file path: len(file_path) == 0")
+        return
+
+    s = ""
+    if path_sep == "/":
+        s = file_path
+    elif path_sep == "\\":
+        splits = file_path.split("\\")
+        data_folder = splits[-1]
+        for i in splits:
+            if i != "":
+                s += "/" + i
+    else:
+        print("Unsupported path separator!")
+        return
+
+    if uri == "file":
+        return "file://localhost" + s
+    else:
+        return local_drive + ":" + s
+
+class LargestConnectedComponent(TransformerPrimitiveBase[Inputs, Outputs, Hyperparams]):
+    # This should contain only metadata which cannot be automatically determined from the code.
+    metadata = metadata_module.PrimitiveMetadata({
+        # Simply an UUID generated once and fixed forever. Generated using "uuid.uuid4()".
+        'id': '32fec24f-6861-4a4c-88f3-d4ec2bc1b486',
+        'version': "0.1.0",
+        'name': "jhu.lcc",
+        # The same path the primitive is registered with entry points in setup.py.
+        'python_path': 'd3m.primitives.jhu_primitives.LargestConnectedComponent',
+        # Keywords do not have a controlled vocabulary. Authors can put here whatever they find suitable.
+        'keywords': ['spectral clustering'],
+        'source': {
+            'name': "JHU",
+            'uris': [
+                # Unstructured URIs. Link to file and link to repo in this case.
+                'https://github.com/neurodata/primitives-interfaces/jhu_primitives/lcc/lcc.py',
+#                'https://github.com/youngser/primitives-interfaces/blob/jp-devM1/jhu_primitives/ase/ase.py',
+                'https://github.com/neurodata/primitives-interfaces.git',
+            ],
+        },
+        # A list of dependencies in order. These can be Python packages, system packages, or Docker images.
+        # Of course Python packages can also have their own dependencies, but sometimes it is necessary to
+        # install a Python package first to be even able to run setup.py of another package. Or you have
+        # a dependency which is not on PyPi.
+        'installation': [
+            {
+            'type': 'UBUNTU',
+            'package': 'r-base',
+            'version': '3.4.2'
+            },
+            {
+            'type': 'UBUNTU',
+            'package': 'libxml2-dev',
+            'version': '2.9.4'
+            },
+            {
+            'type': 'UBUNTU',
+            'package': 'libpcre3-dev',
+            'version': '2.9.4'
+            },
+#            {
+#            'type': 'UBUNTU',
+#            'package': 'r-base-dev',
+#            'version': '3.4.2'
+#            },
+#            {
+#            'type': 'UBUNTU',
+#            'package': 'r-recommended',
+#            'version': '3.4.2'
+#            },
+            {
+            'type': 'PIP',
+            'package_uri': 'git+https://github.com/neurodata/primitives-interfaces.git@{git_commit}#egg=jhu_primitives'.format(
+                git_commit=utils.current_git_commit(os.path.dirname(__file__)),),
+            },
+            {
+            'type': 'PIP',
+            'package': 'python_igraph',
+            'version': '0.7.1'
+            },
+            {
+            'type': 'PIP',
+            'package': 'networkx',
+            'version': '2.1'
+            }
+            ],
+        # URIs at which one can obtain code for the primitive, if available.
+        # 'location_uris': [
+        #     'https://gitlab.com/datadrivendiscovery/tests-data/raw/{git_commit}/primitives/test_primitives/monomial.py'.format(
+        #         git_commit=utils.current_git_commit(os.path.dirname(__file__)),
+        #     ),
+        # ],
+        # Choose these from a controlled vocabulary in the schema. If anything is missing which would
+        # best describe the primitive, make a merge request.
+        'algorithm_types': [
+            "GAUSSIAN_PROCESS"
+        ],
+        'primitive_family': "GRAPH_CLUSTERING"
+    })
+
+    def __init__(self, *, hyperparams: Hyperparams, random_seed: int = 0, docker_containers: Dict[str, base.DockerContainer] = None) -> None:
+        super().__init__(hyperparams=hyperparams, random_seed=random_seed, docker_containers=docker_containers)
+
+    def produce(self, *, inputs: Inputs, timeout: float = None, iterations: int = None) -> CallResult[Outputs]:
+        """
+        Input: g: an n x n matrix, n x 2 edge list, a networkx Graph, or igraph Graph 
+        Output: The largest connected component of g
+
+        """
+
+        g = inputs
+
+        if type(g) == list:
+            g = igraph.Graph(g)
+
+        if type(g) == numpy.ndarray:
+            if g.shape[0] == g.shape[1]: # n x n matrix
+                g = networkx.Graph(g) # convert to networkx graph to be able to extract edge list 
+            elif g.shape[1] == 2: # n x 2 matrix
+                g = igraph.Graph(list(g))
+            else:
+                print("Neither n x n nor n x 2. Please submit a square matrix or edge list.")
+                return
+
+        if type(g) == networkx.classes.graph.Graph: # networkx graph
+            g = igraph.Graph(list(g.edges)) # convert to igraph graph, find the clusters
+
+        if type(g) == igraph.Graph: # igraph graph
+            components = g.clusters()
+            components_len = [len(components[i]) for i in range(len(components))] # find lengths of components (faster way?)
+            largest_component = components[numpy.argmax(components_len)]
+        else:
+            print("Unsupported graph type")
+            return
+
+        result = numpy.array(largest_component)
+
+        outputs = container.ndarray(result)
+
+        return base.CallResult(outputs)

setup.py

@@ -39,6 +39,7 @@ def read_package_variable(key):
     packages=[
               PACKAGE_NAME,
               'jhu_primitives.ase',
+              'jhu_primitives.lcc',
               'jhu_primitives.lse',
               'jhu_primitives.dimselect',
               'jhu_primitives.gclust',
@@ -54,6 +55,7 @@ def read_package_variable(key):
         'd3m.primitives': [
             'jhu_primitives.AdjacencySpectralEmbedding=jhu_primitives.ase:AdjacencySpectralEmbedding',
             'jhu_primitives.LaplacianSpectralEmbedding=jhu_primitives.lse:LaplacianSpectralEmbedding',
+            'jhu_primitives.LargestConnectedComponent'
             'jhu_primitives.DimensionSelection=jhu_primitives.dimselect:DimensionSelection',
             'jhu_primitives.GaussianClustering=jhu_primitives.gclust:GaussianClustering',
             'jhu_primitives.NonParametricClustering=jhu_primitives.nonpar:NonParametricClustering',
@@ -67,7 +69,7 @@ def read_package_variable(key):
     },
     package_data = {'': ['*.r', '*.R']},
     include_package_data = True,
-    install_requires=['typing', 'numpy', 'scipy',
+    install_requires=['typing', 'numpy', 'scipy', 'networkx',
         'python-igraph', 'rpy2', 'sklearn', 'jinja2', 'd3m'],
     url='https://github.com/neurodata/primitives-interfaces',
 )
@@ -77,6 +79,7 @@ def read_package_variable(key):
               PACKAGE_NAME,
               'jhu_primitives.ase',
               'jhu_primitives.lse',
+              'jhu_primitives.lcc',
               'jhu_primitives.dimselect',
               'jhu_primitives.gclust',
               'jhu_primitives.nonpar',