Training section now works

pg/crankshaft--0.0.1.sql

@@ -137,6 +137,33 @@ BEGIN
 END;
 $$
 LANGUAGE plpgsql VOLATILE;
+CREATE OR REPLACE FUNCTION
+  cdb_create_segment (
+      segment_name TEXT,
+      table_name TEXT,
+  	  column_name TEXT,
+      geoid_column TEXT DEFAULT 'geoid',
+      census_table TEXT DEFAULT 'block_groups'
+  )
+RETURNS NUMERIC
+AS $$
+  from crankshaft import segmentation
+  # TODO: use named parameters or a dictionary
+  return segmentation.create_segment(segment_name,table_name,column_name,geoid_column,census_table,'random_forest')
+$$ LANGUAGE plpythonu;
+
+CREATE OR REPLACE FUNCTION
+  cdb_predict_segment (
+      segment_name TEXT,
+      geoid_column TEXT DEFAULT 'geoid',
+      census_table TEXT DEFAULT 'block_groups'
+  )
+RETURNS TABLE(geoid TEXT, prediction NUMERIC)
+AS $$
+  from crankshaft.segmentation import create_segemnt
+  # TODO: use named parameters or a dictionary
+  return create_segment('table')
+$$ LANGUAGE plpythonu;
 -- Make sure by default there are no permissions for publicuser
 -- NOTE: this happens at extension creation time, as part of an implicit transaction.
 -- REVOKE ALL PRIVILEGES ON SCHEMA cdb_crankshaft FROM PUBLIC, publicuser CASCADE;

pg/sql/0.0.1/05_segmentation.sql

@@ -8,9 +8,9 @@ CREATE OR REPLACE FUNCTION
   )
 RETURNS NUMERIC
 AS $$
-  from crankshaft.segmentation import create_segemnt
+  from crankshaft import segmentation
   # TODO: use named parameters or a dictionary
-  return create_segment('table')
+  return segmentation.create_segment(segment_name,table_name,column_name,geoid_column,census_table,'random_forest')
 $$ LANGUAGE plpythonu;
 
 CREATE OR REPLACE FUNCTION

python/crankshaft/crankshaft/segmentation/segmentation.py

@@ -13,57 +13,71 @@ from sklearn.cross_validation import train_test_split
 
 # High level interface ---------------------------------------
 
-def cdb_create_segment(segment_name,table_name,column_name,geoid_column,census_table,method):
+def create_segment(segment_name,table_name,column_name,geoid_column,census_table,method):
     """
     generate a segment with machine learning
     Stuart Lynn
     """
-    data     = pd.DataFrame(join_with_census(table_name, column_name,geoid_column, census_table,))
+    data     = pd.DataFrame(join_with_census(table_name, column_name,geoid_column, census_table))
-    features = data[data.columns.difference([column_name, 'geoid'])]
+    features = data[data.columns.difference([column_name, 'geoid','the_geom'])]
     target, mean, std = normalize(data[column_name])
     model, accuracy = train_model(target,features, test_split=0.2)
-    save_model(segment_name, model, accuracy, table_name, column_name, census_table, geoid_column, method)
+    # save_model(segment_name, model, accuracy, table_name, column_name, census_table, geoid_column, method)
+    # predict_segment
     return accuracy
 
 def normalize(target):
     mean = np.mean(target)
-    std  = no.std(target)
+    std  = np.std(target)
+    plpy.notice('mean '+str(mean)+" std : "+str(std))
     return (target - mean)/std, mean, std
 
 def denormalize(target, mean ,std):
     return target*std + mean
 
 def train_model(target,features,test_split):
+    plpy.notice('training the model')
+    plpy.notice('dataframe shape '+ str(np.shape(features)))
+    plpy.notice('dataframe columns '+ str(features.dtypes))
+    features = features.dropna(axis =1, how='all').fillna(0)
+    target = target.fillna(0)
     features_train, features_test, target_train, target_test = train_test_split(features, target, test_size=test_split)
+    plpy.notice('training the model test train split')
     model = ExtraTreesRegressor(n_estimators = 40, max_features=len(features.columns))
+    plpy.notice('training the model created tree')
+    plpy.notice('features '+str(np.shape(features_train))+" "+str(np.shape(features_test)) )
+
     model.fit(features_train, target_train)
+    plpy.notice('training the model fitting model')
     accuracy = calculate_model_accuracy(model,features,target)
     return model, accuracy
 
 def calculate_model_accuracy(model,features,target):
-    prediction = self.model.predict(features)
+    prediction = model.predict(features)
     return metrics.mean_squared_error(prediction,target)/np.std(target)
 
 def join_with_census(table_name, column_name, geoid_column, census_table):
-    coulmns        = plpy.execute('select {census_table}.* limit 1 ')
+    columns          = plpy.execute('select * from {census_table} limit 1 '.format(**locals()))
-    feature_names  = ",".join(columns.keys.difference(['the_geom','cartodb_id']))
+    combined_columns = [ a for a in columns[0].keys() if a not in ['the_geom','cartodb_id','geoid']]
+    feature_names    = ",".join([ " {census_table}.\"{a}\" as \"{a}\" ".format(**locals()) for a in combined_columns])
+    plpy.notice('joining with census data')
     join_data     = plpy.execute('''
-        WITH region_extent AS (
+
-            SELECT ST_Extent(the_geom) as table_extent FROM {table_name};
+        SELECT {feature_names}, {table_name}.{column_name}
-        )
+        FROM   {table_name}
-        SELECT {features_names}, {table_name}.{column_name}
-        FROM   {table_name} ,region_extent
         JOIN   {census_table}
-        ON  {table_name}.{geoid_column} = {census_table}.geoid
+        ON  {table_name}.{geoid_column}::numeric = {census_table}.geoid::numeric
-        WHERE {census_table}.the_geom && region_extent.table_extent
     '''.format(**locals()))
 
     if len(join_data) == 0:
         plpy.notice('Failed to join with census data')
 
-    return join_data
+    return  query_to_dictionary(join_data)
 
-def cdb_predict_segment(segment_name,geoid_column,census_table):
+def query_to_dictionary(result):
+    return [ dict(zip(r.keys(), r.values())) for r in result ]
+
+def predict_segment(model,features,geoid_column,census_table):
     """
     predict a segment with machine learning
     Stuart Lynn
@@ -89,30 +103,31 @@ def fetch_model(model_name):
     return data
 
 
-def create_model_table(model_name):
+def create_model_table():
     """
     create the model table if requred
     """
     plpy.execute('''
         CREATE table IF NOT EXISTS _cdb_models(
             name TEXT,
-            model BLOB,
+            model TEXT,
             features TEXT[],
             accuracy NUMERIC,
             table_name TEXT,
+            census_table_name TEXT,
+            method TEXT
     )''')
 
 def save_model(model_name,model,accuracy,table_name, column_name,census_table,geoid_column,method):
     """
     save a model to the model table for later use
     """
+    create_model_table()
 
     plpy.execute('''
-        DELETE FROM _cdb_models WHERE model_name = {model_name}
+        DELETE FROM _cdb_models WHERE name = '{model_name}'
     '''.format(**locals()))
-
+    model_pickle = pickle.dumps(model)
     plpy.execute("""
-        INSERT INTO _cdb_models ({model_name},{model_pickle},{accuracy})
+        INSERT INTO _cdb_models ('{model_name}','{model_pickle}',{accuracy}, '{table_name}', '{census_table}', '{method}')
-    """)
+    """.format(**locals()))
-
-def

python/crankshaft/setup.py

@@ -40,9 +40,8 @@ setup(
 
     # The choice of component versions is dictated by what's
     # provisioned in the production servers.
-    install_requires=['pysal==1.11.0','numpy==1.6.1','scipy==0.17.0'],
+    install_requires=['pysal==1.11.0','numpy==1.10.1','scipy==0.17.0','pandas','sklearn'],
 
-    requires=['pysal', 'numpy'],
 
     test_suite='test'
 )