cartodb4/crankshaft
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Release 0.0.3

Browse Source
This commit is contained in:
Raul Ochoa 2016-06-16 14:16:32 +02:00
parent d08a2b6d2d
commit 8b5e910234
22 changed files with 1907 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
NEWS.md
View File

@ -1,3 +1,8 @@
0.0.3 (2016-06-16)
------------------
* Adds new functions: kmeans, weighted centroids.
* Replaces moran functions with new areas of interest naming.
0.0.2 (2016-03-16)
------------------
* New versioning approach using per-version Python virtual environments

413
release/crankshaft--0.0.2--0.0.3.sql Normal file
View File

@ -0,0 +1,413 @@
--DO NOT MODIFY THIS FILE, IT IS GENERATED AUTOMATICALLY FROM SOURCES
-- Complain if script is sourced in psql, rather than via CREATE EXTENSION
\echo Use "CREATE EXTENSION crankshaft" to load this file. \quit
-- [MANUALLY] DROP FUNCTIONS REMOVED SINCE 0.0.2 version
DROP FUNCTION IF EXISTS cdb_moran_local(TEXT, TEXT, float, INT, INT, TEXT, TEXT, TEXT);
DROP FUNCTION IF EXISTS cdb_moran_local_rate(TEXT, TEXT, TEXT, FLOAT, INT, INT, TEXT, TEXT, TEXT);
DROP FUNCTION IF EXISTS _cdb_crankshaft_virtualenvs_path();
DROP FUNCTION IF EXISTS _cdb_crankshaft_activate_py();
-- [END MANUALLY] DROP FUNCTIONS REMOVED SINCE 0.0.2 version
-- Version number of the extension release
CREATE OR REPLACE FUNCTION cdb_crankshaft_version()
RETURNS text AS $$
SELECT '0.0.3'::text;
$$ language 'sql' STABLE STRICT;
-- Internal identifier of the installed extension instence
-- e.g. 'dev' for current development version
CREATE OR REPLACE FUNCTION _cdb_crankshaft_internal_version()
RETURNS text AS $$
SELECT installed_version FROM pg_available_extensions where name='crankshaft' and pg_available_extensions IS NOT NULL;
$$ language 'sql' STABLE STRICT;
-- Internal function.
-- Set the seeds of the RNGs (Random Number Generators)
-- used internally.
CREATE OR REPLACE FUNCTION
_cdb_random_seeds (seed_value INTEGER) RETURNS VOID
AS $$
from crankshaft import random_seeds
random_seeds.set_random_seeds(seed_value)
$$ LANGUAGE plpythonu;
-- Moran's I Global Measure (public-facing)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestGlobal(
subquery TEXT,
column_name TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, significance NUMERIC)
AS $$
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local (internal function)
CREATE OR REPLACE FUNCTION
_CDB_AreasOfInterestLocal(
subquery TEXT,
column_name TEXT,
w_type TEXT,
num_ngbrs INT,
permutations INT,
geom_col TEXT,
id_col TEXT)
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran_local(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestLocal(
subquery TEXT,
column_name TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col);
$$ LANGUAGE SQL;
-- Moran's I only for HH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialHotspots(
subquery TEXT,
column_name TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HH', 'HL');
$$ LANGUAGE SQL;
-- Moran's I only for LL and LH (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialColdspots(
subquery TEXT,
attr TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, attr, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('LL', 'LH');
$$ LANGUAGE SQL;
-- Moran's I only for LH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialOutliers(
subquery TEXT,
attr TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, attr, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HL', 'LH');
$$ LANGUAGE SQL;
-- Moran's I Global Rate (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestGlobalRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran FLOAT, significance FLOAT)
AS $$
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran_rate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local Rate (internal function)
CREATE OR REPLACE FUNCTION
_CDB_AreasOfInterestLocalRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT,
num_ngbrs INT,
permutations INT,
geom_col TEXT,
id_col TEXT)
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
from crankshaft.clustering import moran_local_rate
# TODO: use named parameters or a dictionary
return moran_local_rate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local Rate (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestLocalRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col);
$$ LANGUAGE SQL;
-- Moran's I Local Rate only for HH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialHotspotsRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HH', 'HL');
$$ LANGUAGE SQL;
-- Moran's I Local Rate only for LL and LH (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialColdspotsRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('LL', 'LH');
$$ LANGUAGE SQL;
-- Moran's I Local Rate only for LH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialOutliersRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HL', 'LH');
$$ LANGUAGE SQL;
CREATE OR REPLACE FUNCTION CDB_KMeans(query text, no_clusters integer,no_init integer default 20)
RETURNS table (cartodb_id integer, cluster_no integer) as $$
from crankshaft.clustering import kmeans
return kmeans(query,no_clusters,no_init)
$$ language plpythonu;
CREATE OR REPLACE FUNCTION CDB_WeightedMeanS(state Numeric[],the_geom GEOMETRY(Point, 4326), weight NUMERIC)
RETURNS Numeric[] AS
$$
DECLARE
newX NUMERIC;
newY NUMERIC;
newW NUMERIC;
BEGIN
IF weight IS NULL OR the_geom IS NULL THEN
newX = state[1];
newY = state[2];
newW = state[3];
ELSE
newX = state[1] + ST_X(the_geom)*weight;
newY = state[2] + ST_Y(the_geom)*weight;
newW = state[3] + weight;
END IF;
RETURN Array[newX,newY,newW];
END
$$ LANGUAGE plpgsql;
CREATE OR REPLACE FUNCTION CDB_WeightedMeanF(state Numeric[])
RETURNS GEOMETRY AS
$$
BEGIN
IF state[3] = 0 THEN
RETURN ST_SetSRID(ST_MakePoint(state[1],state[2]), 4326);
ELSE
RETURN ST_SETSRID(ST_MakePoint(state[1]/state[3], state[2]/state[3]),4326);
END IF;
END
$$ LANGUAGE plpgsql;
CREATE AGGREGATE CDB_WeightedMean(geometry(Point, 4326), NUMERIC)(
SFUNC = CDB_WeightedMeanS,
FINALFUNC = CDB_WeightedMeanF,
STYPE = Numeric[],
INITCOND = "{0.0,0.0,0.0}"
);
-- Function by Stuart Lynn for a simple interpolation of a value
-- from a polygon table over an arbitrary polygon
-- (weighted by the area proportion overlapped)
-- Aereal weighting is a very simple form of aereal interpolation.
--
-- Parameters:
-- * geom a Polygon geometry which defines the area where a value will be
-- estimated as the area-weighted sum of a given table/column
-- * target_table_name table name of the table that provides the values
-- * target_column column name of the column that provides the values
-- * schema_name optional parameter to defina the schema the target table
-- belongs to, which is necessary if its not in the search_path.
-- Note that target_table_name should never include the schema in it.
-- Return value:
-- Aereal-weighted interpolation of the column values over the geometry
CREATE OR REPLACE
FUNCTION cdb_overlap_sum(geom geometry, target_table_name text, target_column text, schema_name text DEFAULT NULL)
RETURNS numeric AS
$$
DECLARE
result numeric;
qualified_name text;
BEGIN
IF schema_name IS NULL THEN
qualified_name := Format('%I', target_table_name);
ELSE
qualified_name := Format('%I.%s', schema_name, target_table_name);
END IF;
EXECUTE Format('
SELECT sum(%I*ST_Area(St_Intersection($1, a.the_geom))/ST_Area(a.the_geom))
FROM %s AS a
WHERE $1 && a.the_geom
', target_column, qualified_name)
USING geom
INTO result;
RETURN result;
END;
$$ LANGUAGE plpgsql;
--
-- Creates N points randomly distributed arround the polygon
--
-- @param g - the geometry to be turned in to points
--
-- @param no_points - the number of points to generate
--
-- @params max_iter_per_point - the function generates points in the polygon's bounding box
-- and discards points which don't lie in the polygon. max_iter_per_point specifies how many
-- misses per point the funciton accepts before giving up.
--
-- Returns: Multipoint with the requested points
CREATE OR REPLACE FUNCTION cdb_dot_density(geom geometry , no_points Integer, max_iter_per_point Integer DEFAULT 1000)
RETURNS GEOMETRY AS $$
DECLARE
extent GEOMETRY;
test_point Geometry;
width NUMERIC;
height NUMERIC;
x0 NUMERIC;
y0 NUMERIC;
xp NUMERIC;
yp NUMERIC;
no_left INTEGER;
remaining_iterations INTEGER;
points GEOMETRY[];
bbox_line GEOMETRY;
intersection_line GEOMETRY;
BEGIN
extent := ST_Envelope(geom);
width := ST_XMax(extent) - ST_XMIN(extent);
height := ST_YMax(extent) - ST_YMIN(extent);
x0 := ST_XMin(extent);
y0 := ST_YMin(extent);
no_left := no_points;
LOOP
if(no_left=0) THEN
EXIT;
END IF;
yp = y0 + height*random();
bbox_line = ST_MakeLine(
ST_SetSRID(ST_MakePoint(yp, x0),4326),
ST_SetSRID(ST_MakePoint(yp, x0+width),4326)
);
intersection_line = ST_Intersection(bbox_line,geom);
test_point = ST_LineInterpolatePoint(st_makeline(st_linemerge(intersection_line)),random());
points := points || test_point;
no_left = no_left - 1 ;
END LOOP;
RETURN ST_Collect(points);
END;
$$
LANGUAGE plpgsql VOLATILE;
-- 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;
-- Grant permissions on the schema to publicuser (but just the schema)
GRANT USAGE ON SCHEMA cdb_crankshaft TO publicuser;
-- Revoke execute permissions on all functions in the schema by default
-- REVOKE EXECUTE ON ALL FUNCTIONS IN SCHEMA cdb_crankshaft FROM PUBLIC, publicuser;

209
release/crankshaft--0.0.3--0.0.2.sql Normal file
View File

@ -0,0 +1,209 @@
--DO NOT MODIFY THIS FILE, IT IS GENERATED AUTOMATICALLY FROM SOURCES
-- Complain if script is sourced in psql, rather than via CREATE EXTENSION
\echo Use "CREATE EXTENSION crankshaft" to load this file. \quit
-- [MANUALLY] DROP FUNCTIONS INTRODUCED IN 0.0.3 version
DROP FUNCTION IF EXISTS CDB_AreasOfInterestGlobal(TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS _CDB_AreasOfInterestLocal(TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_AreasOfInterestLocal(TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_GetSpatialHotspots(TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_GetSpatialColdspots(TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_GetSpatialOutliers(TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_AreasOfInterestGlobalRate(TEXT,TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_AreasOfInterestLocalRate(TEXT,TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS _CDB_AreasOfInterestLocalRate(TEXT,TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_GetSpatialHotspotsRate(TEXT,TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_GetSpatialColdspotsRate(TEXT,TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_GetSpatialOutliersRate(TEXT,TEXT,TEXT,TEXT,INT,INT,TEXT,TEXT);
DROP FUNCTION IF EXISTS CDB_KMeans(text,integer,integer);
DROP AGGREGATE IF EXISTS CDB_WeightedMean(geometry(Point, 4326), NUMERIC);
DROP FUNCTION IF EXISTS CDB_WeightedMeanS(Numeric[], GEOMETRY(Point, 4326), NUMERIC);
DROP FUNCTION IF EXISTS CDB_WeightedMeanF(Numeric[]);
-- [END MANUALLY] DROP FUNCTIONS INTRODUCED IN 0.0.3 version
-- Version number of the extension release
CREATE OR REPLACE FUNCTION cdb_crankshaft_version()
RETURNS text AS $$
SELECT '0.0.2'::text;
$$ language 'sql' STABLE STRICT;
-- Internal identifier of the installed extension instence
-- e.g. 'dev' for current development version
CREATE OR REPLACE FUNCTION _cdb_crankshaft_internal_version()
RETURNS text AS $$
SELECT installed_version FROM pg_available_extensions where name='crankshaft' and pg_available_extensions IS NOT NULL;
$$ language 'sql' STABLE STRICT;
CREATE OR REPLACE FUNCTION _cdb_crankshaft_virtualenvs_path()
RETURNS text
AS $$
BEGIN
-- RETURN '/opt/virtualenvs/crankshaft';
RETURN '/home/ubuntu/crankshaft/envs';
END;
$$ language plpgsql IMMUTABLE STRICT;
-- Use the crankshaft python module
CREATE OR REPLACE FUNCTION _cdb_crankshaft_activate_py()
RETURNS VOID
AS $$
import os
# plpy.notice('%',str(os.environ))
# activate virtualenv
crankshaft_version = plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_internal_version()')[0]['_cdb_crankshaft_internal_version']
base_path = plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_virtualenvs_path()')[0]['_cdb_crankshaft_virtualenvs_path']
default_venv_path = os.path.join(base_path, crankshaft_version)
venv_path = os.environ.get('CRANKSHAFT_VENV', default_venv_path)
activate_path = venv_path + '/bin/activate_this.py'
exec(open(activate_path).read(), dict(__file__=activate_path))
$$ LANGUAGE plpythonu;
-- Internal function.
-- Set the seeds of the RNGs (Random Number Generators)
-- used internally.
CREATE OR REPLACE FUNCTION
_cdb_random_seeds (seed_value INTEGER) RETURNS VOID
AS $$
plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_activate_py()')
from crankshaft import random_seeds
random_seeds.set_random_seeds(seed_value)
$$ LANGUAGE plpythonu;
-- Moran's I
CREATE OR REPLACE FUNCTION
cdb_moran_local (
t TEXT,
attr TEXT,
significance float DEFAULT 0.05,
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_column TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id',
w_type TEXT DEFAULT 'knn')
RETURNS TABLE (moran FLOAT, quads TEXT, significance FLOAT, ids INT)
AS $$
plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_activate_py()')
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran_local(t, attr, significance, num_ngbrs, permutations, geom_column, id_col, w_type)
$$ LANGUAGE plpythonu;
-- Moran's I Local Rate
CREATE OR REPLACE FUNCTION
cdb_moran_local_rate(t TEXT,
numerator TEXT,
denominator TEXT,
significance FLOAT DEFAULT 0.05,
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_column TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id',
w_type TEXT DEFAULT 'knn')
RETURNS TABLE(moran FLOAT, quads TEXT, significance FLOAT, ids INT, y numeric)
AS $$
plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_activate_py()')
from crankshaft.clustering import moran_local_rate
# TODO: use named parameters or a dictionary
return moran_local_rate(t, numerator, denominator, significance, num_ngbrs, permutations, geom_column, id_col, w_type)
$$ LANGUAGE plpythonu;
-- Function by Stuart Lynn for a simple interpolation of a value
-- from a polygon table over an arbitrary polygon
-- (weighted by the area proportion overlapped)
-- Aereal weighting is a very simple form of aereal interpolation.
--
-- Parameters:
-- * geom a Polygon geometry which defines the area where a value will be
-- estimated as the area-weighted sum of a given table/column
-- * target_table_name table name of the table that provides the values
-- * target_column column name of the column that provides the values
-- * schema_name optional parameter to defina the schema the target table
-- belongs to, which is necessary if its not in the search_path.
-- Note that target_table_name should never include the schema in it.
-- Return value:
-- Aereal-weighted interpolation of the column values over the geometry
CREATE OR REPLACE
FUNCTION cdb_overlap_sum(geom geometry, target_table_name text, target_column text, schema_name text DEFAULT NULL)
RETURNS numeric AS
$$
DECLARE
result numeric;
qualified_name text;
BEGIN
IF schema_name IS NULL THEN
qualified_name := Format('%I', target_table_name);
ELSE
qualified_name := Format('%I.%s', schema_name, target_table_name);
END IF;
EXECUTE Format('
SELECT sum(%I*ST_Area(St_Intersection($1, a.the_geom))/ST_Area(a.the_geom))
FROM %s AS a
WHERE $1 && a.the_geom
', target_column, qualified_name)
USING geom
INTO result;
RETURN result;
END;
$$ LANGUAGE plpgsql;
--
-- Creates N points randomly distributed arround the polygon
--
-- @param g - the geometry to be turned in to points
--
-- @param no_points - the number of points to generate
--
-- @params max_iter_per_point - the function generates points in the polygon's bounding box
-- and discards points which don't lie in the polygon. max_iter_per_point specifies how many
-- misses per point the funciton accepts before giving up.
--
-- Returns: Multipoint with the requested points
CREATE OR REPLACE FUNCTION cdb_dot_density(geom geometry , no_points Integer, max_iter_per_point Integer DEFAULT 1000)
RETURNS GEOMETRY AS $$
DECLARE
extent GEOMETRY;
test_point Geometry;
width NUMERIC;
height NUMERIC;
x0 NUMERIC;
y0 NUMERIC;
xp NUMERIC;
yp NUMERIC;
no_left INTEGER;
remaining_iterations INTEGER;
points GEOMETRY[];
bbox_line GEOMETRY;
intersection_line GEOMETRY;
BEGIN
extent := ST_Envelope(geom);
width := ST_XMax(extent) - ST_XMIN(extent);
height := ST_YMax(extent) - ST_YMIN(extent);
x0 := ST_XMin(extent);
y0 := ST_YMin(extent);
no_left := no_points;
LOOP
if(no_left=0) THEN
EXIT;
END IF;
yp = y0 + height*random();
bbox_line = ST_MakeLine(
ST_SetSRID(ST_MakePoint(yp, x0),4326),
ST_SetSRID(ST_MakePoint(yp, x0+width),4326)
);
intersection_line = ST_Intersection(bbox_line,geom);
test_point = ST_LineInterpolatePoint(st_makeline(st_linemerge(intersection_line)),random());
points := points || test_point;
no_left = no_left - 1 ;
END LOOP;
RETURN ST_Collect(points);
END;
$$
LANGUAGE plpgsql VOLATILE;
-- 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;
-- Grant permissions on the schema to publicuser (but just the schema)
GRANT USAGE ON SCHEMA cdb_crankshaft TO publicuser;
-- Revoke execute permissions on all functions in the schema by default
-- REVOKE EXECUTE ON ALL FUNCTIONS IN SCHEMA cdb_crankshaft FROM PUBLIC, publicuser;

403
release/crankshaft--0.0.3.sql Normal file
View File

@ -0,0 +1,403 @@
--DO NOT MODIFY THIS FILE, IT IS GENERATED AUTOMATICALLY FROM SOURCES
-- Complain if script is sourced in psql, rather than via CREATE EXTENSION
\echo Use "CREATE EXTENSION crankshaft" to load this file. \quit
-- Version number of the extension release
CREATE OR REPLACE FUNCTION cdb_crankshaft_version()
RETURNS text AS $$
SELECT '0.0.3'::text;
$$ language 'sql' STABLE STRICT;
-- Internal identifier of the installed extension instence
-- e.g. 'dev' for current development version
CREATE OR REPLACE FUNCTION _cdb_crankshaft_internal_version()
RETURNS text AS $$
SELECT installed_version FROM pg_available_extensions where name='crankshaft' and pg_available_extensions IS NOT NULL;
$$ language 'sql' STABLE STRICT;
-- Internal function.
-- Set the seeds of the RNGs (Random Number Generators)
-- used internally.
CREATE OR REPLACE FUNCTION
_cdb_random_seeds (seed_value INTEGER) RETURNS VOID
AS $$
from crankshaft import random_seeds
random_seeds.set_random_seeds(seed_value)
$$ LANGUAGE plpythonu;
-- Moran's I Global Measure (public-facing)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestGlobal(
subquery TEXT,
column_name TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, significance NUMERIC)
AS $$
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local (internal function)
CREATE OR REPLACE FUNCTION
_CDB_AreasOfInterestLocal(
subquery TEXT,
column_name TEXT,
w_type TEXT,
num_ngbrs INT,
permutations INT,
geom_col TEXT,
id_col TEXT)
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran_local(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestLocal(
subquery TEXT,
column_name TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col);
$$ LANGUAGE SQL;
-- Moran's I only for HH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialHotspots(
subquery TEXT,
column_name TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HH', 'HL');
$$ LANGUAGE SQL;
-- Moran's I only for LL and LH (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialColdspots(
subquery TEXT,
attr TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, attr, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('LL', 'LH');
$$ LANGUAGE SQL;
-- Moran's I only for LH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialOutliers(
subquery TEXT,
attr TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocal(subquery, attr, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HL', 'LH');
$$ LANGUAGE SQL;
-- Moran's I Global Rate (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestGlobalRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran FLOAT, significance FLOAT)
AS $$
from crankshaft.clustering import moran_local
# TODO: use named parameters or a dictionary
return moran_rate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local Rate (internal function)
CREATE OR REPLACE FUNCTION
_CDB_AreasOfInterestLocalRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT,
num_ngbrs INT,
permutations INT,
geom_col TEXT,
id_col TEXT)
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
from crankshaft.clustering import moran_local_rate
# TODO: use named parameters or a dictionary
return moran_local_rate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu;
-- Moran's I Local Rate (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_AreasOfInterestLocalRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col);
$$ LANGUAGE SQL;
-- Moran's I Local Rate only for HH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialHotspotsRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HH', 'HL');
$$ LANGUAGE SQL;
-- Moran's I Local Rate only for LL and LH (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialColdspotsRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('LL', 'LH');
$$ LANGUAGE SQL;
-- Moran's I Local Rate only for LH and HL (public-facing function)
CREATE OR REPLACE FUNCTION
CDB_GetSpatialOutliersRate(
subquery TEXT,
numerator TEXT,
denominator TEXT,
w_type TEXT DEFAULT 'knn',
num_ngbrs INT DEFAULT 5,
permutations INT DEFAULT 99,
geom_col TEXT DEFAULT 'the_geom',
id_col TEXT DEFAULT 'cartodb_id')
RETURNS
TABLE(moran NUMERIC, quads TEXT, significance NUMERIC, rowid INT, vals NUMERIC)
AS $$
SELECT moran, quads, significance, rowid, vals
FROM cdb_crankshaft._CDB_AreasOfInterestLocalRate(subquery, numerator, denominator, w_type, num_ngbrs, permutations, geom_col, id_col)
WHERE quads IN ('HL', 'LH');
$$ LANGUAGE SQL;
CREATE OR REPLACE FUNCTION CDB_KMeans(query text, no_clusters integer,no_init integer default 20)
RETURNS table (cartodb_id integer, cluster_no integer) as $$
from crankshaft.clustering import kmeans
return kmeans(query,no_clusters,no_init)
$$ language plpythonu;
CREATE OR REPLACE FUNCTION CDB_WeightedMeanS(state Numeric[],the_geom GEOMETRY(Point, 4326), weight NUMERIC)
RETURNS Numeric[] AS
$$
DECLARE
newX NUMERIC;
newY NUMERIC;
newW NUMERIC;
BEGIN
IF weight IS NULL OR the_geom IS NULL THEN
newX = state[1];
newY = state[2];
newW = state[3];
ELSE
newX = state[1] + ST_X(the_geom)*weight;
newY = state[2] + ST_Y(the_geom)*weight;
newW = state[3] + weight;
END IF;
RETURN Array[newX,newY,newW];
END
$$ LANGUAGE plpgsql;
CREATE OR REPLACE FUNCTION CDB_WeightedMeanF(state Numeric[])
RETURNS GEOMETRY AS
$$
BEGIN
IF state[3] = 0 THEN
RETURN ST_SetSRID(ST_MakePoint(state[1],state[2]), 4326);
ELSE
RETURN ST_SETSRID(ST_MakePoint(state[1]/state[3], state[2]/state[3]),4326);
END IF;
END
$$ LANGUAGE plpgsql;
CREATE AGGREGATE CDB_WeightedMean(geometry(Point, 4326), NUMERIC)(
SFUNC = CDB_WeightedMeanS,
FINALFUNC = CDB_WeightedMeanF,
STYPE = Numeric[],
INITCOND = "{0.0,0.0,0.0}"
);
-- Function by Stuart Lynn for a simple interpolation of a value
-- from a polygon table over an arbitrary polygon
-- (weighted by the area proportion overlapped)
-- Aereal weighting is a very simple form of aereal interpolation.
--
-- Parameters:
-- * geom a Polygon geometry which defines the area where a value will be
-- estimated as the area-weighted sum of a given table/column
-- * target_table_name table name of the table that provides the values
-- * target_column column name of the column that provides the values
-- * schema_name optional parameter to defina the schema the target table
-- belongs to, which is necessary if its not in the search_path.
-- Note that target_table_name should never include the schema in it.
-- Return value:
-- Aereal-weighted interpolation of the column values over the geometry
CREATE OR REPLACE
FUNCTION cdb_overlap_sum(geom geometry, target_table_name text, target_column text, schema_name text DEFAULT NULL)
RETURNS numeric AS
$$
DECLARE
result numeric;
qualified_name text;
BEGIN
IF schema_name IS NULL THEN
qualified_name := Format('%I', target_table_name);
ELSE
qualified_name := Format('%I.%s', schema_name, target_table_name);
END IF;
EXECUTE Format('
SELECT sum(%I*ST_Area(St_Intersection($1, a.the_geom))/ST_Area(a.the_geom))
FROM %s AS a
WHERE $1 && a.the_geom
', target_column, qualified_name)
USING geom
INTO result;
RETURN result;
END;
$$ LANGUAGE plpgsql;
--
-- Creates N points randomly distributed arround the polygon
--
-- @param g - the geometry to be turned in to points
--
-- @param no_points - the number of points to generate
--
-- @params max_iter_per_point - the function generates points in the polygon's bounding box
-- and discards points which don't lie in the polygon. max_iter_per_point specifies how many
-- misses per point the funciton accepts before giving up.
--
-- Returns: Multipoint with the requested points
CREATE OR REPLACE FUNCTION cdb_dot_density(geom geometry , no_points Integer, max_iter_per_point Integer DEFAULT 1000)
RETURNS GEOMETRY AS $$
DECLARE
extent GEOMETRY;
test_point Geometry;
width NUMERIC;
height NUMERIC;
x0 NUMERIC;
y0 NUMERIC;
xp NUMERIC;
yp NUMERIC;
no_left INTEGER;
remaining_iterations INTEGER;
points GEOMETRY[];
bbox_line GEOMETRY;
intersection_line GEOMETRY;
BEGIN
extent := ST_Envelope(geom);
width := ST_XMax(extent) - ST_XMIN(extent);
height := ST_YMax(extent) - ST_YMIN(extent);
x0 := ST_XMin(extent);
y0 := ST_YMin(extent);
no_left := no_points;
LOOP
if(no_left=0) THEN
EXIT;
END IF;
yp = y0 + height*random();
bbox_line = ST_MakeLine(
ST_SetSRID(ST_MakePoint(yp, x0),4326),
ST_SetSRID(ST_MakePoint(yp, x0+width),4326)
);
intersection_line = ST_Intersection(bbox_line,geom);
test_point = ST_LineInterpolatePoint(st_makeline(st_linemerge(intersection_line)),random());
points := points || test_point;
no_left = no_left - 1 ;
END LOOP;
RETURN ST_Collect(points);
END;
$$
LANGUAGE plpgsql VOLATILE;
-- 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;
-- Grant permissions on the schema to publicuser (but just the schema)
GRANT USAGE ON SCHEMA cdb_crankshaft TO publicuser;
-- Revoke execute permissions on all functions in the schema by default
-- REVOKE EXECUTE ON ALL FUNCTIONS IN SCHEMA cdb_crankshaft FROM PUBLIC, publicuser;

2
release/crankshaft.control
View File

@ -1,5 +1,5 @@
comment = 'CartoDB Spatial Analysis extension'
default_version = '0.0.2'
default_version = '0.0.3'
requires = 'plpythonu, postgis, cartodb'
superuser = true
schema = cdb_crankshaft

2
release/python/0.0.3/crankshaft/crankshaft/__init__.py Normal file
View File

@ -0,0 +1,2 @@
import random_seeds
import clustering

2
release/python/0.0.3/crankshaft/crankshaft/clustering/__init__.py Normal file
View File

@ -0,0 +1,2 @@
from moran import *
from kmeans import *

18
release/python/0.0.3/crankshaft/crankshaft/clustering/kmeans.py Normal file
View File

@ -0,0 +1,18 @@
from sklearn.cluster import KMeans
import plpy
def kmeans(query, no_clusters, no_init=20):
data = plpy.execute('''select array_agg(cartodb_id order by cartodb_id) as ids,
array_agg(ST_X(the_geom) order by cartodb_id) xs,
array_agg(ST_Y(the_geom) order by cartodb_id) ys from ({query}) a
where the_geom is not null
'''.format(query=query))
xs = data[0]['xs']
ys = data[0]['ys']
ids = data[0]['ids']
km = KMeans(n_clusters= no_clusters, n_init=no_init)
labels = km.fit_predict(zip(xs,ys))
return zip(ids,labels)

260
release/python/0.0.3/crankshaft/crankshaft/clustering/moran.py Normal file
View File

@ -0,0 +1,260 @@
"""
Moran's I geostatistics (global clustering & outliers presence)
"""
# TODO: Fill in local neighbors which have null/NoneType values with the
# average of the their neighborhood
import pysal as ps
import plpy
# crankshaft module
import crankshaft.pysal_utils as pu
# High level interface ---------------------------------------
def moran(subquery, attr_name,
w_type, num_ngbrs, permutations, geom_col, id_col):
"""
Moran's I (global)
Implementation building neighbors with a PostGIS database and Moran's I
core clusters with PySAL.
Andy Eschbacher
"""
qvals = {"id_col": id_col,
"attr1": attr_name,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs}
query = pu.construct_neighbor_query(w_type, qvals)
plpy.notice('** Query: %s' % query)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(2)
plpy.notice('** Query returned with %d rows' % len(result))
except plpy.SPIError:
plpy.error('Error: areas of interest query failed, check input parameters')
plpy.notice('** Query failed: "%s"' % query)
plpy.notice('** Error: %s' % plpy.SPIError)
return pu.empty_zipped_array(2)
## collect attributes
attr_vals = pu.get_attributes(result)
## calculate weights
weight = pu.get_weight(result, w_type, num_ngbrs)
## calculate moran global
moran_global = ps.esda.moran.Moran(attr_vals, weight,
permutations=permutations)
return zip([moran_global.I], [moran_global.EI])
def moran_local(subquery, attr,
w_type, num_ngbrs, permutations, geom_col, id_col):
"""
Moran's I implementation for PL/Python
Andy Eschbacher
"""
# geometries with attributes that are null are ignored
# resulting in a collection of not as near neighbors
qvals = {"id_col": id_col,
"attr1": attr,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs}
query = pu.construct_neighbor_query(w_type, qvals)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(5)
except plpy.SPIError:
plpy.error('Error: areas of interest query failed, check input parameters')
plpy.notice('** Query failed: "%s"' % query)
return pu.empty_zipped_array(5)
attr_vals = pu.get_attributes(result)
weight = pu.get_weight(result, w_type, num_ngbrs)
# calculate LISA values
lisa = ps.esda.moran.Moran_Local(attr_vals, weight,
permutations=permutations)
# find quadrants for each geometry
quads = quad_position(lisa.q)
return zip(lisa.Is, quads, lisa.p_sim, weight.id_order, lisa.y)
def moran_rate(subquery, numerator, denominator,
w_type, num_ngbrs, permutations, geom_col, id_col):
"""
Moran's I Rate (global)
Andy Eschbacher
"""
qvals = {"id_col": id_col,
"attr1": numerator,
"attr2": denominator,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs}
query = pu.construct_neighbor_query(w_type, qvals)
plpy.notice('** Query: %s' % query)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(2)
plpy.notice('** Query returned with %d rows' % len(result))
except plpy.SPIError:
plpy.error('Error: areas of interest query failed, check input parameters')
plpy.notice('** Query failed: "%s"' % query)
plpy.notice('** Error: %s' % plpy.SPIError)
return pu.empty_zipped_array(2)
## collect attributes
numer = pu.get_attributes(result, 1)
denom = pu.get_attributes(result, 2)
weight = pu.get_weight(result, w_type, num_ngbrs)
## calculate moran global rate
lisa_rate = ps.esda.moran.Moran_Rate(numer, denom, weight,
permutations=permutations)
return zip([lisa_rate.I], [lisa_rate.EI])
def moran_local_rate(subquery, numerator, denominator,
w_type, num_ngbrs, permutations, geom_col, id_col):
"""
Moran's I Local Rate
Andy Eschbacher
"""
# geometries with values that are null are ignored
# resulting in a collection of not as near neighbors
query = pu.construct_neighbor_query(w_type,
{"id_col": id_col,
"numerator": numerator,
"denominator": denominator,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs})
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(5)
except plpy.SPIError:
plpy.error('Error: areas of interest query failed, check input parameters')
plpy.notice('** Query failed: "%s"' % query)
plpy.notice('** Error: %s' % plpy.SPIError)
return pu.empty_zipped_array(5)
## collect attributes
numer = pu.get_attributes(result, 1)
denom = pu.get_attributes(result, 2)
weight = pu.get_weight(result, w_type, num_ngbrs)
# calculate LISA values
lisa = ps.esda.moran.Moran_Local_Rate(numer, denom, weight,
permutations=permutations)
# find units of significance
quads = quad_position(lisa.q)
return zip(lisa.Is, quads, lisa.p_sim, weight.id_order, lisa.y)
def moran_local_bv(subquery, attr1, attr2,
permutations, geom_col, id_col, w_type, num_ngbrs):
"""
Moran's I (local) Bivariate (untested)
"""
plpy.notice('** Constructing query')
qvals = {"num_ngbrs": num_ngbrs,
"attr1": attr1,
"attr2": attr2,
"subquery": subquery,
"geom_col": geom_col,
"id_col": id_col}
query = pu.construct_neighbor_query(w_type, qvals)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(4)
except plpy.SPIError:
plpy.error("Error: areas of interest query failed, " \
"check input parameters")
plpy.notice('** Query failed: "%s"' % query)
return pu.empty_zipped_array(4)
## collect attributes
attr1_vals = pu.get_attributes(result, 1)
attr2_vals = pu.get_attributes(result, 2)
# create weights
weight = pu.get_weight(result, w_type, num_ngbrs)
# calculate LISA values
lisa = ps.esda.moran.Moran_Local_BV(attr1_vals, attr2_vals, weight,
permutations=permutations)
plpy.notice("len of Is: %d" % len(lisa.Is))
# find clustering of significance
lisa_sig = quad_position(lisa.q)
plpy.notice('** Finished calculations')
return zip(lisa.Is, lisa_sig, lisa.p_sim, weight.id_order)
# Low level functions ----------------------------------------
def map_quads(coord):
"""
Map a quadrant number to Moran's I designation
HH=1, LH=2, LL=3, HL=4
Input:
@param coord (int): quadrant of a specific measurement
Output:
classification (one of 'HH', 'LH', 'LL', or 'HL')
"""
if coord == 1:
return 'HH'
elif coord == 2:
return 'LH'
elif coord == 3:
return 'LL'
elif coord == 4:
return 'HL'
else:
return None
def quad_position(quads):
"""
Produce Moran's I classification based of n
Input:
@param quads ndarray: an array of quads classified by
1-4 (PySAL default)
Output:
@param list: an array of quads classied by 'HH', 'LL', etc.
"""
return [map_quads(q) for q in quads]

1
release/python/0.0.3/crankshaft/crankshaft/pysal_utils/__init__.py Normal file
View File

@ -0,0 +1 @@
from pysal_utils import *

152
release/python/0.0.3/crankshaft/crankshaft/pysal_utils/pysal_utils.py Normal file
View File

@ -0,0 +1,152 @@
"""
Utilities module for generic PySAL functionality, mainly centered on translating queries into numpy arrays or PySAL weights objects
"""
import numpy as np
import pysal as ps
def construct_neighbor_query(w_type, query_vals):
"""Return query (a string) used for finding neighbors
@param w_type text: type of neighbors to calculate ('knn' or 'queen')
@param query_vals dict: values used to construct the query
"""
if w_type.lower() == 'knn':
return knn(query_vals)
else:
return queen(query_vals)
## Build weight object
def get_weight(query_res, w_type='knn', num_ngbrs=5):
"""
Construct PySAL weight from return value of query
@param query_res: query results with attributes and neighbors
"""
if w_type.lower() == 'knn':
row_normed_weights = [1.0 / float(num_ngbrs)] * num_ngbrs
weights = {x['id']: row_normed_weights for x in query_res}
else:
weights = {x['id']: [1.0 / len(x['neighbors'])] * len(x['neighbors'])
if len(x['neighbors']) > 0
else [] for x in query_res}
neighbors = {x['id']: x['neighbors'] for x in query_res}
return ps.W(neighbors, weights)
def query_attr_select(params):
"""
Create portion of SELECT statement for attributes inolved in query.
@param params: dict of information used in query (column names,
table name, etc.)
"""
attrs = [k for k in params
if k not in ('id_col', 'geom_col', 'subquery', 'num_ngbrs')]
template = "i.\"{%(col)s}\"::numeric As attr%(alias_num)s, "
attr_string = ""
for idx, val in enumerate(sorted(attrs)):
attr_string += template % {"col": val, "alias_num": idx + 1}
return attr_string
def query_attr_where(params):
"""
Create portion of WHERE clauses for weeding out NULL-valued geometries
"""
attrs = sorted([k for k in params
if k not in ('id_col', 'geom_col', 'subquery', 'num_ngbrs')])
attr_string = []
for attr in attrs:
attr_string.append("idx_replace.\"{%s}\" IS NOT NULL" % attr)
if len(attrs) == 2:
attr_string.append("idx_replace.\"{%s}\" <> 0" % attrs[1])
out = " AND ".join(attr_string)
return out
def knn(params):
"""SQL query for k-nearest neighbors.
@param vars: dict of values to fill template
"""
attr_select = query_attr_select(params)
attr_where = query_attr_where(params)
replacements = {"attr_select": attr_select,
"attr_where_i": attr_where.replace("idx_replace", "i"),
"attr_where_j": attr_where.replace("idx_replace", "j")}
query = "SELECT " \
"i.\"{id_col}\" As id, " \
"%(attr_select)s" \
"(SELECT ARRAY(SELECT j.\"{id_col}\" " \
"FROM ({subquery}) As j " \
"WHERE " \
"i.\"{id_col}\" <> j.\"{id_col}\" AND " \
"%(attr_where_j)s " \
"ORDER BY " \
"j.\"{geom_col}\" <-> i.\"{geom_col}\" ASC " \
"LIMIT {num_ngbrs})" \
") As neighbors " \
"FROM ({subquery}) As i " \
"WHERE " \
"%(attr_where_i)s " \
"ORDER BY i.\"{id_col}\" ASC;" % replacements
return query.format(**params)
## SQL query for finding queens neighbors (all contiguous polygons)
def queen(params):
"""SQL query for queen neighbors.
@param params dict: information to fill query
"""
attr_select = query_attr_select(params)
attr_where = query_attr_where(params)
replacements = {"attr_select": attr_select,
"attr_where_i": attr_where.replace("idx_replace", "i"),
"attr_where_j": attr_where.replace("idx_replace", "j")}
query = "SELECT " \
"i.\"{id_col}\" As id, " \
"%(attr_select)s" \
"(SELECT ARRAY(SELECT j.\"{id_col}\" " \
"FROM ({subquery}) As j " \
"WHERE i.\"{id_col}\" <> j.\"{id_col}\" AND " \
"ST_Touches(i.\"{geom_col}\", j.\"{geom_col}\") AND " \
"%(attr_where_j)s)" \
") As neighbors " \
"FROM ({subquery}) As i " \
"WHERE " \
"%(attr_where_i)s " \
"ORDER BY i.\"{id_col}\" ASC;" % replacements
return query.format(**params)
## to add more weight methods open a ticket or pull request
def get_attributes(query_res, attr_num=1):
"""
@param query_res: query results with attributes and neighbors
@param attr_num: attribute number (1, 2, ...)
"""
return np.array([x['attr' + str(attr_num)] for x in query_res], dtype=np.float)
def empty_zipped_array(num_nones):
"""
prepare return values for cases of empty weights objects (no neighbors)
Input:
@param num_nones int: number of columns (e.g., 4)
Output:
[(None, None, None, None)]
"""
return [tuple([None] * num_nones)]

10
release/python/0.0.3/crankshaft/crankshaft/random_seeds.py Normal file
View File

@ -0,0 +1,10 @@
import random
import numpy
def set_random_seeds(value):
"""
Set the seeds of the RNGs (Random Number Generators)
used internally.
"""
random.seed(value)
numpy.random.seed(value)

48
release/python/0.0.3/crankshaft/setup.py Normal file
View File

@ -0,0 +1,48 @@
"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.3',
description='CartoDB Spatial Analysis Python Library',
url='https://github.com/CartoDB/crankshaft',
author='Data Services Team - CartoDB',
author_email='dataservices@cartodb.com',
license='MIT',
classifiers=[
'Development Status :: 3 - Alpha',
'Intended Audience :: Mapping comunity',
'Topic :: Maps :: Mapping Tools',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 2.7',
],
keywords='maps mapping tools spatial analysis geostatistics',
packages=find_packages(exclude=['contrib', 'docs', 'tests']),
extras_require={
'dev': ['unittest'],
'test': ['unittest', 'nose', 'mock'],
},
# The choice of component versions is dictated by what's
# provisioned in the production servers.
install_requires=['pysal==1.9.1', 'scikit-learn==0.17.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

1
release/python/0.0.3/crankshaft/test/fixtures/kmeans.json vendored Normal file
View File

@ -0,0 +1 @@
[{"xs": [9.917239463463458, 9.042767302696836, 10.798929825304187, 8.763751051762995, 11.383882954810852, 11.018206993460897, 8.939526075734316, 9.636159342565252, 10.136336896960058, 11.480610059427342, 12.115011910725082, 9.173267848893428, 10.239300931201738, 8.00012512174072, 8.979962292282131, 9.318376124429575, 10.82259513754284, 10.391747171927115, 10.04904588886165, 9.96007160443463, -0.78825626804569, -0.3511819898577426, -1.2796410003764271, -0.3977049391203402, 2.4792311265774667, 1.3670311632092624, 1.2963504112955613, 2.0404844103073025, -1.6439708506073223, 0.39122885445645805, 1.026031821452462, -0.04044477160482201, -0.7442346929085072, -0.34687120826243034, -0.23420359971379054, -0.5919629143336708, -0.202903054395391, -0.1893399644841902, 1.9331834251176807, -0.12321054392851609], "ys": [8.735627063679981, 9.857615954045011, 10.81439096759407, 10.586727233537191, 9.232919976568622, 11.54281262696508, 8.392787912674466, 9.355119689665944, 9.22380703532752, 10.542142541823122, 10.111980619367035, 10.760836265570738, 8.819773453269804, 10.25325722424816, 9.802077905695608, 8.955420161552611, 9.833801181904477, 10.491684241001613, 12.076108669877556, 11.74289693140474, -0.5685725015474191, -0.5715728344759778, -0.20180907868635137, 0.38431336480089595, -0.3402202083684184, -2.4652736827783586, 0.08295159401756182, 0.8503818775816505, 0.6488691600321166, 0.5794762568230527, -0.6770063922144103, -0.6557616416449478, -1.2834289177624947, 0.1096318195532717, -0.38986922166834853, -1.6224497706950238, 0.09429787743230483, 0.4005097316394031, -0.508002811195673, -1.2473463371366507], "ids": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]}]

52
release/python/0.0.3/crankshaft/test/fixtures/moran.json vendored Normal file
View File

@ -0,0 +1,52 @@
[[0.9319096128346788, "HH"],
[-1.135787401862846, "HL"],
[0.11732030672508517, "LL"],
[0.6152779669180425, "LL"],
[-0.14657336660125297, "LH"],
[0.6967858120189607, "LL"],
[0.07949310115714454, "HH"],
[0.4703198759258987, "HH"],
[0.4421125200498064, "HH"],
[0.5724288737143592, "LL"],
[0.8970743435692062, "LL"],
[0.18327334401918674, "LL"],
[-0.01466729201304962, "HL"],
[0.3481559372544409, "LL"],
[0.06547094736902978, "LL"],
[0.15482141569329988, "HH"],
[0.4373841193538136, "HH"],
[0.15971286468915544, "LL"],
[1.0543588860308968, "HH"],
[1.7372866900020818, "HH"],
[1.091998586053999, "LL"],
[0.1171572584252222, "HH"],
[0.08438455015300014, "LL"],
[0.06547094736902978, "LL"],
[0.15482141569329985, "HH"],
[1.1627044812890683, "HH"],
[0.06547094736902978, "LL"],
[0.795275137550483, "HH"],
[0.18562939195219, "LL"],
[0.3010757406693439, "LL"],
[2.8205795942839376, "HH"],
[0.11259190602909264, "LL"],
[-0.07116352791516614, "HL"],
[-0.09945240794119009, "LH"],
[0.18562939195219, "LL"],
[0.1832733440191868, "LL"],
[-0.39054253768447705, "HL"],
[-0.1672071289487642, "HL"],
[0.3337669247916343, "HH"],
[0.2584386102554792, "HH"],
[-0.19733845476322634, "HL"],
[-0.9379282899805409, "LH"],
[-0.028770969951095866, "LH"],
[0.051367269430983485, "LL"],
[-0.2172548045913472, "LH"],
[0.05136726943098351, "LL"],
[0.04191046803899837, "LL"],
[0.7482357030403517, "HH"],
[-0.014585767863118111, "LH"],
[0.5410013139159929, "HH"],
[1.0223932668429925, "LL"],
[1.4179402898927476, "LL"]]

54
release/python/0.0.3/crankshaft/test/fixtures/neighbors.json vendored Normal file
View File

@ -0,0 +1,54 @@
[
{"neighbors": [48, 26, 20, 9, 31], "id": 1, "value": 0.5},
{"neighbors": [30, 16, 46, 3, 4], "id": 2, "value": 0.7},
{"neighbors": [46, 30, 2, 12, 16], "id": 3, "value": 0.2},
{"neighbors": [18, 30, 23, 2, 52], "id": 4, "value": 0.1},
{"neighbors": [47, 40, 45, 37, 28], "id": 5, "value": 0.3},
{"neighbors": [10, 21, 41, 14, 37], "id": 6, "value": 0.05},
{"neighbors": [8, 17, 43, 25, 12], "id": 7, "value": 0.4},
{"neighbors": [17, 25, 43, 22, 7], "id": 8, "value": 0.7},
{"neighbors": [39, 34, 1, 26, 48], "id": 9, "value": 0.5},
{"neighbors": [6, 37, 5, 45, 49], "id": 10, "value": 0.04},
{"neighbors": [51, 41, 29, 21, 14], "id": 11, "value": 0.08},
{"neighbors": [44, 46, 43, 50, 3], "id": 12, "value": 0.2},
{"neighbors": [45, 23, 14, 28, 18], "id": 13, "value": 0.4},
{"neighbors": [41, 29, 13, 23, 6], "id": 14, "value": 0.2},
{"neighbors": [36, 27, 32, 33, 24], "id": 15, "value": 0.3},
{"neighbors": [19, 2, 46, 44, 28], "id": 16, "value": 0.4},
{"neighbors": [8, 25, 43, 7, 22], "id": 17, "value": 0.6},
{"neighbors": [23, 4, 29, 14, 13], "id": 18, "value": 0.3},
{"neighbors": [42, 16, 28, 26, 40], "id": 19, "value": 0.7},
{"neighbors": [1, 48, 31, 26, 42], "id": 20, "value": 0.8},
{"neighbors": [41, 6, 11, 14, 10], "id": 21, "value": 0.1},
{"neighbors": [25, 50, 43, 31, 44], "id": 22, "value": 0.4},
{"neighbors": [18, 13, 14, 4, 2], "id": 23, "value": 0.1},
{"neighbors": [33, 49, 34, 47, 27], "id": 24, "value": 0.3},
{"neighbors": [43, 8, 22, 17, 50], "id": 25, "value": 0.4},
{"neighbors": [1, 42, 20, 31, 48], "id": 26, "value": 0.6},
{"neighbors": [32, 15, 36, 33, 24], "id": 27, "value": 0.3},
{"neighbors": [40, 45, 19, 5, 13], "id": 28, "value": 0.8},
{"neighbors": [11, 51, 41, 14, 18], "id": 29, "value": 0.3},
{"neighbors": [2, 3, 4, 46, 18], "id": 30, "value": 0.1},
{"neighbors": [20, 26, 1, 50, 48], "id": 31, "value": 0.9},
{"neighbors": [27, 36, 15, 49, 24], "id": 32, "value": 0.3},
{"neighbors": [24, 27, 49, 34, 32], "id": 33, "value": 0.4},
{"neighbors": [47, 9, 39, 40, 24], "id": 34, "value": 0.3},
{"neighbors": [38, 51, 11, 21, 41], "id": 35, "value": 0.3},
{"neighbors": [15, 32, 27, 49, 33], "id": 36, "value": 0.2},
{"neighbors": [49, 10, 5, 47, 24], "id": 37, "value": 0.5},
{"neighbors": [35, 21, 51, 11, 41], "id": 38, "value": 0.4},
{"neighbors": [9, 34, 48, 1, 47], "id": 39, "value": 0.6},
{"neighbors": [28, 47, 5, 9, 34], "id": 40, "value": 0.5},
{"neighbors": [11, 14, 29, 21, 6], "id": 41, "value": 0.4},
{"neighbors": [26, 19, 1, 9, 31], "id": 42, "value": 0.2},
{"neighbors": [25, 12, 8, 22, 44], "id": 43, "value": 0.3},
{"neighbors": [12, 50, 46, 16, 43], "id": 44, "value": 0.2},
{"neighbors": [28, 13, 5, 40, 19], "id": 45, "value": 0.3},
{"neighbors": [3, 12, 44, 2, 16], "id": 46, "value": 0.2},
{"neighbors": [34, 40, 5, 49, 24], "id": 47, "value": 0.3},
{"neighbors": [1, 20, 26, 9, 39], "id": 48, "value": 0.5},
{"neighbors": [24, 37, 47, 5, 33], "id": 49, "value": 0.2},
{"neighbors": [44, 22, 31, 42, 26], "id": 50, "value": 0.6},
{"neighbors": [11, 29, 41, 14, 21], "id": 51, "value": 0.01},
{"neighbors": [4, 18, 29, 51, 23], "id": 52, "value": 0.01}
]

13
release/python/0.0.3/crankshaft/test/helper.py Normal file
View File

@ -0,0 +1,13 @@
import unittest
from mock_plpy import MockPlPy
plpy = MockPlPy()
import sys
sys.modules['plpy'] = plpy
import os
def fixture_file(name):
dir = os.path.dirname(os.path.realpath(__file__))
return os.path.join(dir, 'fixtures', name)

34
release/python/0.0.3/crankshaft/test/mock_plpy.py Normal file
View File

@ -0,0 +1,34 @@
import re
class MockPlPy:
def __init__(self):
self._reset()
def _reset(self):
self.infos = []
self.notices = []
self.debugs = []
self.logs = []
self.warnings = []
self.errors = []
self.fatals = []
self.executes = []
self.results = []
self.prepares = []
self.results = []
def _define_result(self, query, result):
pattern = re.compile(query, re.IGNORECASE | re.MULTILINE)
self.results.append([pattern, result])
def notice(self, msg):
self.notices.append(msg)
def info(self, msg):
self.infos.append(msg)
def execute(self, query): # TODO: additional arguments
for result in self.results:
if result[0].match(query):
return result[1]
return []

38
release/python/0.0.3/crankshaft/test/test_cluster_kmeans.py Normal file
View File

@ -0,0 +1,38 @@
import unittest
import numpy as np
# from mock_plpy import MockPlPy
# plpy = MockPlPy()
#
# import sys
# sys.modules['plpy'] = plpy
from helper import plpy, fixture_file
import numpy as np
import crankshaft.clustering as cc
import crankshaft.pysal_utils as pu
from crankshaft import random_seeds
import json
class KMeansTest(unittest.TestCase):
"""Testing class for Moran's I functions"""
def setUp(self):
plpy._reset()
self.cluster_data = json.loads(open(fixture_file('kmeans.json')).read())
self.params = {"subquery": "select * from table",
"no_clusters": "10"
}
def test_kmeans(self):
data = self.cluster_data
plpy._define_result('select' ,data)
clusters = cc.kmeans('subquery', 2)
labels = [a[1] for a in clusters]
c1 = [a for a in clusters if a[1]==0]
c2 = [a for a in clusters if a[1]==1]
self.assertEqual(len(np.unique(labels)),2)
self.assertEqual(len(c1),20)
self.assertEqual(len(c2),20)

83
release/python/0.0.3/crankshaft/test/test_clustering_moran.py Normal file
View File

@ -0,0 +1,83 @@
import unittest
import numpy as np
# from mock_plpy import MockPlPy
# plpy = MockPlPy()
#
# import sys
# sys.modules['plpy'] = plpy
from helper import plpy, fixture_file
import crankshaft.clustering as cc
import crankshaft.pysal_utils as pu
from crankshaft import random_seeds
import json
class MoranTest(unittest.TestCase):
"""Testing class for Moran's I functions"""
def setUp(self):
plpy._reset()
self.params = {"id_col": "cartodb_id",
"attr1": "andy",
"attr2": "jay_z",
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
self.neighbors_data = json.loads(open(fixture_file('neighbors.json')).read())
self.moran_data = json.loads(open(fixture_file('moran.json')).read())
def test_map_quads(self):
"""Test map_quads"""
self.assertEqual(cc.map_quads(1), 'HH')
self.assertEqual(cc.map_quads(2), 'LH')
self.assertEqual(cc.map_quads(3), 'LL')
self.assertEqual(cc.map_quads(4), 'HL')
self.assertEqual(cc.map_quads(33), None)
self.assertEqual(cc.map_quads('andy'), None)
def test_quad_position(self):
"""Test lisa_sig_vals"""
quads = np.array([1, 2, 3, 4], np.int)
ans = np.array(['HH', 'LH', 'LL', 'HL'])
test_ans = cc.quad_position(quads)
self.assertTrue((test_ans == ans).all())
def test_moran_local(self):
"""Test Moran's I local"""
data = [ { 'id': d['id'], 'attr1': d['value'], 'neighbors': d['neighbors'] } for d in self.neighbors_data]
plpy._define_result('select', data)
random_seeds.set_random_seeds(1234)
result = cc.moran_local('subquery', 'value', 'knn', 5, 99, 'the_geom', 'cartodb_id')
result = [(row[0], row[1]) for row in result]
expected = self.moran_data
for ([res_val, res_quad], [exp_val, exp_quad]) in zip(result, expected):
self.assertAlmostEqual(res_val, exp_val)
self.assertEqual(res_quad, exp_quad)
def test_moran_local_rate(self):
"""Test Moran's I rate"""
data = [ { 'id': d['id'], 'attr1': d['value'], 'attr2': 1, 'neighbors': d['neighbors'] } for d in self.neighbors_data]
plpy._define_result('select', data)
random_seeds.set_random_seeds(1234)
result = cc.moran_local_rate('subquery', 'numerator', 'denominator', 'knn', 5, 99, 'the_geom', 'cartodb_id')
print 'result == None? ', result == None
result = [(row[0], row[1]) for row in result]
expected = self.moran_data
for ([res_val, res_quad], [exp_val, exp_quad]) in zip(result, expected):
self.assertAlmostEqual(res_val, exp_val)
def test_moran(self):
"""Test Moran's I global"""
data = [{ 'id': d['id'], 'attr1': d['value'], 'neighbors': d['neighbors'] } for d in self.neighbors_data]
plpy._define_result('select', data)
random_seeds.set_random_seeds(1235)
result = cc.moran('table', 'value', 'knn', 5, 99, 'the_geom', 'cartodb_id')
print 'result == None?', result == None
result_moran = result[0][0]
expected_moran = np.array([row[0] for row in self.moran_data]).mean()
self.assertAlmostEqual(expected_moran, result_moran, delta=10e-2)

107
release/python/0.0.3/crankshaft/test/test_pysal_utils.py Normal file
View File

@ -0,0 +1,107 @@
import unittest
import crankshaft.pysal_utils as pu
from crankshaft import random_seeds
class PysalUtilsTest(unittest.TestCase):
"""Testing class for utility functions related to PySAL integrations"""
def setUp(self):
self.params = {"id_col": "cartodb_id",
"attr1": "andy",
"attr2": "jay_z",
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
def test_query_attr_select(self):
"""Test query_attr_select"""
ans = "i.\"{attr1}\"::numeric As attr1, " \
"i.\"{attr2}\"::numeric As attr2, "
self.assertEqual(pu.query_attr_select(self.params), ans)
def test_query_attr_where(self):
"""Test pu.query_attr_where"""
ans = "idx_replace.\"{attr1}\" IS NOT NULL AND " \
"idx_replace.\"{attr2}\" IS NOT NULL AND " \
"idx_replace.\"{attr2}\" <> 0"
self.assertEqual(pu.query_attr_where(self.params), ans)
def test_knn(self):
"""Test knn neighbors constructor"""
ans = "SELECT i.\"cartodb_id\" As id, " \
"i.\"andy\"::numeric As attr1, " \
"i.\"jay_z\"::numeric As attr2, " \
"(SELECT ARRAY(SELECT j.\"cartodb_id\" " \
"FROM (SELECT * FROM a_list) As j " \
"WHERE " \
"i.\"cartodb_id\" <> j.\"cartodb_id\" AND " \
"j.\"andy\" IS NOT NULL AND " \
"j.\"jay_z\" IS NOT NULL AND " \
"j.\"jay_z\" <> 0 " \
"ORDER BY " \
"j.\"the_geom\" <-> i.\"the_geom\" ASC " \
"LIMIT 321)) As neighbors " \
"FROM (SELECT * FROM a_list) As i " \
"WHERE i.\"andy\" IS NOT NULL AND " \
"i.\"jay_z\" IS NOT NULL AND " \
"i.\"jay_z\" <> 0 " \
"ORDER BY i.\"cartodb_id\" ASC;"
self.assertEqual(pu.knn(self.params), ans)
def test_queen(self):
"""Test queen neighbors constructor"""
ans = "SELECT i.\"cartodb_id\" As id, " \
"i.\"andy\"::numeric As attr1, " \
"i.\"jay_z\"::numeric As attr2, " \
"(SELECT ARRAY(SELECT j.\"cartodb_id\" " \
"FROM (SELECT * FROM a_list) As j " \
"WHERE " \
"i.\"cartodb_id\" <> j.\"cartodb_id\" AND " \
"ST_Touches(i.\"the_geom\", " \
"j.\"the_geom\") AND " \
"j.\"andy\" IS NOT NULL AND " \
"j.\"jay_z\" IS NOT NULL AND " \
"j.\"jay_z\" <> 0)" \
") As neighbors " \
"FROM (SELECT * FROM a_list) As i " \
"WHERE i.\"andy\" IS NOT NULL AND " \
"i.\"jay_z\" IS NOT NULL AND " \
"i.\"jay_z\" <> 0 " \
"ORDER BY i.\"cartodb_id\" ASC;"
self.assertEqual(pu.queen(self.params), ans)
def test_construct_neighbor_query(self):
"""Test construct_neighbor_query"""
# Compare to raw knn query
self.assertEqual(pu.construct_neighbor_query('knn', self.params),
pu.knn(self.params))
def test_get_attributes(self):
"""Test get_attributes"""
## need to add tests
self.assertEqual(True, True)
def test_get_weight(self):
"""Test get_weight"""
self.assertEqual(True, True)
def test_empty_zipped_array(self):
"""Test empty_zipped_array"""
ans2 = [(None, None)]
ans4 = [(None, None, None, None)]
self.assertEqual(pu.empty_zipped_array(2), ans2)
self.assertEqual(pu.empty_zipped_array(4), ans4)

2
src/pg/crankshaft.control
View File

@ -1,5 +1,5 @@
comment = 'CartoDB Spatial Analysis extension'
default_version = '0.0.2'
default_version = '0.0.3'
requires = 'plpythonu, postgis, cartodb'
superuser = true
schema = cdb_crankshaft