Merge branch 'clustering' into dev

workflows/cforange/db/package_data.json

@@ -895,6 +895,184 @@
       "description": ""
     }
   },
+  {
+    "pk": 103,
+    "model": "workflows.abstractwidget",
+    "fields": {
+      "category": 19,
+      "treeview_image": "",
+      "name": "Hierarchical clustering",
+      "is_streaming": false,
+      "uid": "12b0d57d-1cbc-4e9d-8087-2dcd8ced2a27",
+      "interaction_view": "cforange_hierarchical_clustering",
+      "image": "",
+      "package": "cforange",
+      "static_image": "",
+      "post_interact_action": "cforange_hierarchical_clustering_finished",
+      "user": null,
+      "visualization_view": "",
+      "action": "cforange_hierarchical_clustering",
+      "wsdl_method": "",
+      "wsdl": "",
+      "interactive": true,
+      "has_progress_bar": false,
+      "order": 1,
+      "description": ""
+    }
+  },
+  {
+    "pk": 210,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 103,
+      "name": "Distance Matrix",
+      "short_name": "dm",
+      "uid": "bc238f40-be7b-48c4-a526-f17d461a1e10",
+      "default": "",
+      "required": false,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "dm",
+      "parameter": false,
+      "order": 1,
+      "description": ""
+    }
+  },
+  {
+    "pk": 211,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 103,
+      "name": "Linkage",
+      "short_name": "lin",
+      "uid": "9804f098-f6b6-4858-9d83-df2a45e6174a",
+      "default": "0",
+      "required": false,
+      "multi": false,
+      "parameter_type": "select",
+      "variable": "linkage",
+      "parameter": true,
+      "order": 2,
+      "description": ""
+    }
+  },
+  {
+    "pk": 64,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "e5a0e0cd-aefe-4d2f-b2dd-26c54aecda41",
+      "abstract_input": 211,
+      "value": "1",
+      "name": "Average linkage"
+    }
+  },
+  {
+    "pk": 66,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "e7ab085c-59a2-469b-b4e0-aeef40685a1f",
+      "abstract_input": 211,
+      "value": "3",
+      "name": "Complete linkage"
+    }
+  },
+  {
+    "pk": 63,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "e751309c-0f24-409e-b21e-94692c3fa5cf",
+      "abstract_input": 211,
+      "value": "0",
+      "name": "Single linkage"
+    }
+  },
+  {
+    "pk": 65,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "16d7b4ca-b14d-4a93-bda3-ca3478efd316",
+      "abstract_input": 211,
+      "value": "2",
+      "name": "Ward's linkage"
+    }
+  },
+  {
+    "pk": 212,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 103,
+      "name": "Visualization type",
+      "short_name": "viz",
+      "uid": "f0c1c618-f7c4-4b9c-8780-d03e1ab29834",
+      "default": "circle",
+      "required": false,
+      "multi": false,
+      "parameter_type": "select",
+      "variable": "visualization",
+      "parameter": true,
+      "order": 3,
+      "description": ""
+    }
+  },
+  {
+    "pk": 67,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "ea7c03eb-b596-4b7f-82ea-840ca44daaad",
+      "abstract_input": 212,
+      "value": "circle",
+      "name": "Circle"
+    }
+  },
+  {
+    "pk": 68,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "4bd2311e-3051-451e-8c47-5bb526a885e6",
+      "abstract_input": 212,
+      "value": "tree",
+      "name": "Tree"
+    }
+  },
+  {
+    "pk": 114,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 103,
+      "name": "Centroids",
+      "short_name": "ctr",
+      "variable": "centroids",
+      "uid": "da9b8816-0ed4-4159-8a7e-ff915d5eb2d2",
+      "order": 1,
+      "description": ""
+    }
+  },
+  {
+    "pk": 115,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 103,
+      "name": "Selected examples",
+      "short_name": "sel",
+      "variable": "selected_examples",
+      "uid": "2055c99d-b2cd-4270-94e7-688eb86ae00b",
+      "order": 2,
+      "description": ""
+    }
+  },
+  {
+    "pk": 116,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 103,
+      "name": "Unselected examples",
+      "short_name": "uns",
+      "variable": "unselected_examples",
+      "uid": "d23df6ab-e4ec-4c09-8d4b-9457f666efca",
+      "order": 3,
+      "description": ""
+    }
+  },
   {
     "pk": 12,
     "model": "workflows.category",

workflows/cforange/interaction_views.py

 from django.shortcuts import render
+import json
 
 def cforange_filter_integers(request,input_dict,output_dict,widget):
-    return render(request, 'interactions/cforange_filter_integers.html',{'widget':widget,'intList':input_dict['intList']})
\ No newline at end of file
+    return render(request, 'interactions/cforange_filter_integers.html',{'widget':widget,'intList':input_dict['intList']})
+
+def cforange_hierarchical_clustering(request,input_dict,output_dict,widget):
+    import orange
+    from library import Clustering
+    matrix = input_dict['dm']
+    linkage = int(input_dict['linkage'])
+    root = Clustering.hierarchical_clustering(linkage, matrix)
+    dm_examples = True
+    try:
+        attributes = [x.name for x in matrix.items.domain]
+    except:
+        attributes = ['attribute']
+        dm_examples = False
+    def build_hierarchy(node, root=False):
+        if dm_examples:
+            values_dict = dict([(x,matrix.items[node.first][x].value) for x in attributes]) if not node.branches else {}
+        else:
+            values_dict = dict([(x,matrix.items[node.first].name) for x in attributes]) if not node.branches else {}
+        for attribute in values_dict.keys():
+            if type(values_dict[attribute]) == float:
+                values_dict[attribute]="%.3f" % values_dict[attribute]
+        return {
+            'name' : 'root' if root else '',
+            'id' : node.first if not node.branches else -1,
+            'height' : node.height if node.branches else 0,
+            'children' : [build_hierarchy(node.left), build_hierarchy(node.right)] if node.branches else [],
+            'values' : values_dict,
+            'leaf' : True if not node.branches else False
+        }
+    hierarchy = json.dumps(build_hierarchy(root, root=True))
+    return render(request, 'interactions/cforange_hierarchical_clustering.html', {'widget' : widget, 'hierarchy' : hierarchy, 'attributes':attributes,'vizualization':input_dict['visualization']})

workflows/cforange/library.py

@@ -169,7 +169,6 @@ def cforange_confusion_matrix(input_dict):
         cm = orngStat.confusionMatrices(results,classIndex=classIndex)
     if len(cm)==1:
         cm = cm[0]
-    print cm
     output_dict = {}
     output_dict['cm']=cm
     return output_dict
@@ -380,4 +379,62 @@ def cforange_attribute_distance(input_dict):
                     matrix[a1, a2] = (1.0 - statc.spearmanr(f1, filleds[a2])[0]) / 2.0
     output_dict = {}
     output_dict['dm']=matrix        
-    return output_dict
\ No newline at end of file
+    return output_dict
+
+def cforange_hierarchical_clustering(input_dict):
+    return {'centroids' : None, 'selected_examples' : None, 'unselected_examples' : None}
+
+class Clustering:
+    @staticmethod
+    def hierarchical_clustering(linkage, distance_matrix):
+        import orange
+        linkages = [("Single linkage", orange.HierarchicalClustering.Single),
+                    ("Average linkage", orange.HierarchicalClustering.Average),
+                    ("Ward's linkage", orange.HierarchicalClustering.Ward),
+                    ("Complete linkage", orange.HierarchicalClustering.Complete)]
+        return orange.HierarchicalClustering(distance_matrix, linkage=linkages[linkage][1])
+
+def cforange_hierarchical_clustering_finished(postdata, input_dict, output_dict):
+    import json
+    import orange
+    matrix = input_dict['dm']
+    linkage = int(input_dict['linkage'])
+    widget_pk = postdata['widget_id'][0]
+    try:
+        selected_nodes = json.loads(postdata.get('selected_nodes')[0])
+    except:
+        raise Exception('Please select a threshold for determining clusters.')
+    if isinstance(matrix.items, orange.ExampleTable):
+        root = Clustering.hierarchical_clustering(linkage, matrix)
+        cluster_ids = set([cluster for _,_,cluster in selected_nodes])
+        selected_clusters = set([cluster for _,selected,cluster in selected_nodes if selected])
+        clustVar = orange.EnumVariable(str('Cluster'), values=["Cluster %d" % i for i in cluster_ids] + ["Other"])
+        origDomain = matrix.items.domain
+        domain = orange.Domain(origDomain.attributes, origDomain.classVar)
+        domain.addmeta(orange.newmetaid(), clustVar)
+        domain.addmetas(origDomain.getmetas())
+        # Build table with selected clusters
+        selected_table, unselected_table = orange.ExampleTable(domain), orange.ExampleTable(domain)
+        for id, selected, cluster in selected_nodes:
+            new_ex = orange.Example(domain, matrix.items[id])
+            if selected:
+                new_ex[clustVar] = clustVar("Cluster %d" % cluster)
+                selected_table.append(new_ex)
+            else:
+                new_ex[clustVar] = clustVar("Other")
+                unselected_table.append(new_ex)
+        # Build table of centroids
+        centroids = orange.ExampleTable(selected_table.domain)
+        if len(selected_table) > 0:
+            for cluster in sorted(selected_clusters):
+                clusterEx = orange.ExampleTable([ex for ex in selected_table if ex[clustVar] == "Cluster %d" % cluster])
+                # Attribute statistics
+                contstat = orange.DomainBasicAttrStat(clusterEx)
+                discstat = orange.DomainDistributions(clusterEx, 0, 0, 1)
+                ex = [cs.avg if cs else (ds.modus() if ds else "?") for cs, ds in zip(contstat, discstat)]
+                example = orange.Example(centroids.domain, ex)
+                example[clustVar] = clustVar("Cluster %d" % cluster)
+                centroids.append(example)
+    else: # Attribute distance
+        centroids, selected_table, unselected_table = None, None, None
+    return {'centroids' : centroids, 'selected_examples' : selected_table, 'unselected_examples' : unselected_table}

workflows/templates/index.html

@@ -37,6 +37,9 @@
 <script type="text/javascript" src="{{ STATIC_URL }}js/new-script.js"></script>
 <script src="{{STATIC_URL}}js/highcharts-2.2.5-tooltip-id.js"></script>
 <script src="{{STATIC_URL}}js/highcharts-exporting.js"></script>
+<script src="{{STATIC_URL}}js/d3/d3.v3.min.js"></script>
+<!-- <script src="{{STATIC_URL}}js/d3/d3.js"></script>
+<script src="{{STATIC_URL}}js/d3/d3.layout.js"></script> -->
 <script type="text/javascript">
 {% load url from future %}