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Merge branch 'develop' into moran-query-ordering-fix

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This commit is contained in:
Andy Eschbacher 2016-09-23 13:25:36 -04:00
commit 07e4062237
114 changed files with 18496 additions and 82 deletions
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.brackets.json Normal file
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{
"sbruchmann.staticpreview.basepath": "/home/carto/Projects/crankshaft/"
}

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NEWS.md
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0.4.2 (2016-09-22)
------------------
* Bugfix for cdb_areasofinterestglobal: import correct modules
0.4.1 (2016-09-21)
------------------
* Let the user set the resolution in CDB_Contour function
* Add Nearest Neighbors method to CDB_SpatialInterpolation
* Improve error reporting for moran and markov functions
0.4.0 (2016-08-30)
------------------
* Add CDB_Contour
* Add CDB_PIA
* Add CDB_Densify
* Add CDB_TINmap
0.3.1 (2016-08-18) 0.3.1 (2016-08-18)
------------------ ------------------
* Fix Voronoi projection issue * Fix Voronoi projection issue

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@ -15,11 +15,12 @@ shall be performed by the designated *Release Manager*.
1. Generate an upgrade path from the previous to the next release by copying the generated release file. E.g: 1. Generate an upgrade path from the previous to the next release by copying the generated release file. E.g:
```shell ```shell
cp release/cranckshaft--X.Y.Z.sql release/cranckshaft--A.B.C--X.Y.Z.sql cp release/crankshaft--X.Y.Z.sql release/crankshaft--A.B.C--X.Y.Z.sql
``` ```
NOTE: you can rely on this thanks to the compatibility checks. NOTE: you can rely on this thanks to the compatibility checks.
TODO: automate this step [#94](https://github.com/CartoDB/crankshaft/issues/94) TODO: automate this step [#94](https://github.com/CartoDB/crankshaft/issues/94)
2. Update the [NEWS.md](https://github.com/CartoDB/crankshaft/blob/master/NEWS.md) file
1. Commit and push the generated files. 1. Commit and push the generated files.
1. Tag the release: 1. Tag the release:
@ -29,7 +30,6 @@ shall be performed by the designated *Release Manager*.
``` ```
1. Deploy and test in staging 1. Deploy and test in staging
1. Deploy and test in production 1. Deploy and test in production
2. Update the [NEWS.md](https://github.com/CartoDB/crankshaft/blob/master/NEWS.md) file
1. Merge back into develop 1. Merge back into develop

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@ -37,7 +37,7 @@ SELECT
aoi.quads, aoi.quads,
aoi.significance, aoi.significance,
c.num_cyclists_per_total_population c.num_cyclists_per_total_population
FROM CDB_GetAreasOfInterestLocal('SELECT * FROM commute_data' FROM CDB_AreasOfInterestLocal('SELECT * FROM commute_data'
'num_cyclists_per_total_population') As aoi 'num_cyclists_per_total_population') As aoi
JOIN commute_data As c JOIN commute_data As c
ON c.cartodb_id = aoi.rowid; ON c.cartodb_id = aoi.rowid;
@ -113,7 +113,7 @@ SELECT
aoi.quads, aoi.quads,
aoi.significance, aoi.significance,
c.cyclists_per_total_population c.cyclists_per_total_population
FROM CDB_GetAreasOfInterestLocalRate('SELECT * FROM commute_data' FROM CDB_AreasOfInterestLocalRate('SELECT * FROM commute_data'
'num_cyclists', 'num_cyclists',
'total_population') As aoi 'total_population') As aoi
JOIN commute_data As c JOIN commute_data As c

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Function to interpolate a numeric attribute of a point in a scatter dataset of points, using one of three methos: Function to interpolate a numeric attribute of a point in a scatter dataset of points, using one of three methos:
* [Nearest neighbor](https://en.wikipedia.org/wiki/Nearest-neighbor_interpolation) * [Nearest neighbor(s)](https://en.wikipedia.org/wiki/Nearest-neighbor_interpolation)
* [Barycentric](https://en.wikipedia.org/wiki/Barycentric_coordinate_system) * [Barycentric](https://en.wikipedia.org/wiki/Barycentric_coordinate_system)
* [IDW](https://en.wikipedia.org/wiki/Inverse_distance_weighting) * [IDW](https://en.wikipedia.org/wiki/Inverse_distance_weighting)
@ -15,7 +15,7 @@ Function to interpolate a numeric attribute of a point in a scatter dataset of p
| query | text | query that returns at least `the_geom` and a numeric value as `attrib` | | query | text | query that returns at least `the_geom` and a numeric value as `attrib` |
| point | geometry | The target point to calc the value | | point | geometry | The target point to calc the value |
| method | integer | 0:nearest neighbor, 1: barycentric, 2: IDW| | method | integer | 0:nearest neighbor, 1: barycentric, 2: IDW|
| p1 | integer | IDW: limit the number of neighbors, 0->no limit| | p1 | integer | limit the number of neighbors, IDW: 0->no limit, NN: 0-> closest one|
| p2 | integer | IDW: order of distance decay, 0-> order 1| | p2 | integer | IDW: order of distance decay, 0-> order 1|
### CDB_SpatialInterpolation (geom geometry[], values numeric[], point geometry, method integer DEFAULT 1, p1 integer DEFAULT 0, ps integer DEFAULT 0) ### CDB_SpatialInterpolation (geom geometry[], values numeric[], point geometry, method integer DEFAULT 1, p1 integer DEFAULT 0, ps integer DEFAULT 0)
@ -28,7 +28,7 @@ Function to interpolate a numeric attribute of a point in a scatter dataset of p
| values | numeric[] | Array of points' values for the param under study| | values | numeric[] | Array of points' values for the param under study|
| point | geometry | The target point to calc the value | | point | geometry | The target point to calc the value |
| method | integer | 0:nearest neighbor, 1: barycentric, 2: IDW| | method | integer | 0:nearest neighbor, 1: barycentric, 2: IDW|
| p1 | integer | IDW: limit the number of neighbors, 0->no limit| | p1 | integer | limit the number of neighbors, IDW: 0->no limit, NN: 0-> closest one|
| p2 | integer | IDW: order of distance decay, 0-> order 1| | p2 | integer | IDW: order of distance decay, 0-> order 1|
### Returns ### Returns
@ -37,6 +37,9 @@ Function to interpolate a numeric attribute of a point in a scatter dataset of p
|-------------|------|-------------| |-------------|------|-------------|
| value | numeric | Interpolated value at the given point, `-888.888` if the given point is out of the boundaries of the source points set | | value | numeric | Interpolated value at the given point, `-888.888` if the given point is out of the boundaries of the source points set |
Default values:
* -888.888: when using Barycentric, the target point is out of the realm of the input points
* -777.777: asking for a method not available
#### Example Usage #### Example Usage

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## Pole of inaccessibility (PIA)
Function to find the [PIA](https://en.wikipedia.org/wiki/Pole_of_inaccessibility) from a given polygon and tolerance, following the quadtree approach by [Vladimir Agafonkin](https://github.com/mourner) described [here](https://github.com/mapbox/polylabel)
### CDB_PIA (polygon geometry, tolerance numeric DEFAULT 1.0)
#### Arguments
| Name | Type | Description |
|------|------|-------------|
| polygon | geometry | Target polygon |
| tolerance | numeric | Threshold to decide to take a cell into account |
### Returns
| Column Name | Type | Description |
|-------------|------|-------------|
| point | geometry| Pole of inaccessibility |
#### Example Usage
```sql
with a as(
select st_geomfromtext('POLYGON((-432540.453078056 4949775.20452642,-432329.947920966 4951361.232584,-431245.028163694 4952223.31516671,-429131.071033529 4951768.00415574,-424622.07505895 4952843.13503987,-423688.327170174 4953499.20752423,-424086.294349759 4954968.38274191,-423068.388925945 4954378.63345336,-423387.653225542 4953355.67417084,-420594.869840519 4953781.00230592,-416026.095299382 4951484.06849063,-412483.018546414 4951024.5410983,-410490.399661215 4954502.24032205,-408186.197521284 4956398.91417441,-407627.262358013 4959300.94633864,-406948.770061627 4959874.85407739,-404949.583326472 4959047.74518163,-402570.908447199 4953743.46829807,-400971.358683991 4952193.11680804,-403533.488084088 4949649.89857885,-406335.177028373 4950193.19571096,-407790.456731515 4952391.46015616,-412060.672398345 4950381.2389307,-410716.93482498 4949156.7509561,-408464.162289794 4943912.8940387,-409350.599394983 4942819.84896006,-408087.791091424 4942451.6711778,-407274.045613725 4940572.4807777,-404446.196589102 4939976.71501489,-402422.964843936 4940450.3670813,-401010.654464241 4939054.8061663,-397647.247369412 4940679.80737878,-395658.413346901 4940528.84765185,-395536.852462953 4938829.79565997,-394268.923462818 4938003.7277717,-393388.720249116 4934757.80596815,-392393.301362444 4934326.71675815,-392573.527618037 4932323.40974412,-393464.640141837 4931903.10653605,-393085.597275686 4931094.7353605,-398426.261165985 4929156.87541607,-398261.174361137 4926238.00816416,-394045.059966834 4925765.18668498,-392982.960705174 4926391.81893628,-393090.272694301 4927176.84692181,-391648.240010564 4924626.06386961,-391889.914625075 4923086.14787613,-394345.177314013 4923235.086036,-395550.878718795 4917812.79243978,-399009.463978251 4912927.7157945,-398948.794855767 4911941.91010796,-398092.636652078 4911806.57392519,-401991.601817112 4911722.9204501,-406225.972607907 4914505.47286319,-411104.994569885 4912569.26941163,-412925.513522316 4913030.3608866,-414630.148884835 4914436.69169949,-414207.691417276 4919205.78028405,-418306.141109809 4917994.9580478,-424184.700779621 4918938.12432889,-426816.961458921 4923664.37379373,-420956.324227126 4923381.98014807,-420186.661267781 4924286.48693378,-420943.411166194 4926812.76394433,-419779.45457046 4928527.43466337,-419768.767899344 4930681.94459216,-421911.668097113 4930432.40620397,-423482.386112205 4933451.28047252,-427272.814773717 4934151.56473242,-427144.908678797 4939731.77191996,-428982.125554848 4940522.84445172,-428986.133056516 4942437.17281266,-431237.792396792 4947309.68284815,-432476.889648814 4947791.74800037,-432540.453078056 4949775.20452642))', 3857) as g
),
b as (
select ST_Transform(g, 4326) as g from a
)
SELECT st_astext(CDB_PIA(g)) from b;
```

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## Densify function
Iterative densification of a set of scattered points using Delaunay triangulation. The new points are located at the centroids of the grid cells and have as assigned value the barycentric average value of the cell's vertex.
### CDB_Densify(geomin geometry[], colin numeric[], iterations integer)
#### Arguments
| Name | Type | Description |
|------|------|-------------|
| geomin | geometry[] | Array of points geometries |
| colin | numeric[] | Array of points' values |
| iterations | integer | Number of iterations |
### Returns
Returns a table object
| Name | Type | Description |
|------|------|-------------|
| geomout | geometry | Geometries of new dataset of points|
| colout | numeric | Values of points|
#### Example Usage
```sql
with data as (
select
ARRAY[7.0,8.0,1.0,2.0,3.0,5.0,6.0,4.0] as colin,
ARRAY[ST_GeomFromText('POINT(2.1744 41.4036)'),ST_GeomFromText('POINT(2.1228 41.3809)'),ST_GeomFromText('POINT(2.1511 41.3742)'),ST_GeomFromText('POINT(2.1528 41.4136)'),ST_GeomFromText('POINT(2.165 41.3917)'),ST_GeomFromText('POINT(2.1498 41.3713)'),ST_GeomFromText('POINT(2.1533 41.3683)'),ST_GeomFromText('POINT(2.131386 41.413998)')] as geomin
)
select CDB_Densify(geomin, colin, 2) from data;
```

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## TINMAP function
Generates a fake contour map, in the form of a TIN map, from a set of scattered points.Depends on **CDB_Densify**.
Its iterative nature lets the user smooth the final result as much as desired, but with a exponential time cost increase.
### CDB_TINmap(geomin geometry[], colin numeric[], iterations integer)
#### Arguments
| Name | Type | Description |
|------|------|-------------|
| geomin | geometry[] | Array of points geometries |
| colin | numeric[] | Array of points' values |
| iterations | integer | Number of iterations |
### Returns
Returns a table object
| Name | Type | Description |
|------|------|-------------|
| geomout | geometry | Geometries of new dataset of polygons|
| colout | numeric | Values of each cell|
#### Example Usage
```sql
with data as (
select
ARRAY[7.0,8.0,1.0,2.0,3.0,5.0,6.0,4.0] as colin,
ARRAY[ST_GeomFromText('POINT(2.1744 41.4036)'),ST_GeomFromText('POINT(2.1228 41.3809)'),ST_GeomFromText('POINT(2.1511 41.3742)'),ST_GeomFromText('POINT(2.1528 41.4136)'),ST_GeomFromText('POINT(2.165 41.3917)'),ST_GeomFromText('POINT(2.1498 41.3713)'),ST_GeomFromText('POINT(2.1533 41.3683)'),ST_GeomFromText('POINT(2.131386 41.413998)')] as geomin
)
select CDB_TINmap(geomin, colin, 2) from data;
```

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## Contour maps
Function to generate a contour map from an scatter dataset of points, using one of these three methods:
* [Nearest neighbor](https://en.wikipedia.org/wiki/Nearest-neighbor_interpolation)
* [Barycentric](https://en.wikipedia.org/wiki/Barycentric_coordinate_system)
* [IDW](https://en.wikipedia.org/wiki/Inverse_distance_weighting)
### CDB_Contour (geom geometry[], values numeric[], resolution integer, buffer numeric, method, classmethod integer, steps integer)
#### Arguments
| Name | Type | Description |
|------|------|-------------|
| geom | geometry[] | Array of points's geometries |
| values | numeric[] | Array of points' values for the param under study|
| buffer | numeric | Value between 0 and 1 for spatial buffer of the set of points
| method | integer | 0:nearest neighbor, 1: barycentric, 2: IDW|
| classmethod | integer | 0:equals, 1: heads&tails, 2:jenks, 3:quantiles |
| steps | integer | Number of steps in the classification|
| max_time | integer | if <= 0: max processing time in seconds (smart resolution) , if >0: resolution in meters
### Returns
Returns a table object
| Name | Type | Description |
|------|------|-------------|
| the_geom | geometry | Geometries of the classified contour map|
| avg_value | numeric | Avg value of the area|
| min_value | numeric | Min value of the area|
| max_value | numeric | Max value of the areal|
| bin | integer | Index of the class of the area|
#### Example Usage
```sql
WITH a AS (
SELECT
ARRAY[800, 700, 600, 500, 400, 300, 200, 100]::numeric[] AS vals,
ARRAY[ST_GeomFromText('POINT(2.1744 41.403)',4326),ST_GeomFromText('POINT(2.1228 41.380)',4326),ST_GeomFromText('POINT(2.1511 41.374)',4326),ST_GeomFromText('POINT(2.1528 41.413)',4326),ST_GeomFromText('POINT(2.165 41.391)',4326),ST_GeomFromText('POINT(2.1498 41.371)',4326),ST_GeomFromText('POINT(2.1533 41.368)',4326),ST_GeomFromText('POINT(2.131386 41.41399)',4326)] AS g
),
b as(
SELECT
foo.*
FROM
a,
cdb_crankshaft.CDB_contour(a.g, a.vals, 0.0, 1, 3, 5, 60) foo
)
SELECT bin, avg_value from b order by bin;
```

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comment = 'CartoDB Spatial Analysis extension' comment = 'CartoDB Spatial Analysis extension'
default_version = '0.3.1' default_version = '0.4.2'
requires = 'plpythonu, postgis' requires = 'plpythonu, postgis'
superuser = true superuser = true
schema = cdb_crankshaft schema = cdb_crankshaft

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"""Import all modules"""
import crankshaft.random_seeds
import crankshaft.clustering
import crankshaft.space_time_dynamics
import crankshaft.segmentation

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"""Import all functions from for clustering"""
from moran import *
from kmeans import *

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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)

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"""
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
from collections import OrderedDict
# 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 = OrderedDict([("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 = OrderedDict([("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 = OrderedDict([("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
qvals = OrderedDict([("id_col", id_col),
("numerator", numerator),
("denominator", denominator),
("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)
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 quadrants for each geometry
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 = OrderedDict([("id_col", id_col),
("attr1", attr1),
("attr2", attr2),
("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(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]

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"""Import all functions for pysal_utils"""
from crankshaft.pysal_utils.pysal_utils import *

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"""
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 dict-like: 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}
print 'len of neighbors: %d' % len(neighbors)
built_weight = ps.W(neighbors)
built_weight.transform = 'r'
return built_weight
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.)
"""
attr_string = ""
template = "i.\"%(col)s\"::numeric As attr%(alias_num)s, "
if 'time_cols' in params:
## if markov analysis
attrs = params['time_cols']
for idx, val in enumerate(attrs):
attr_string += template % {"col": val, "alias_num": idx + 1}
else:
## if moran's analysis
attrs = [k for k in params
if k not in ('id_col', 'geom_col', 'subquery', 'num_ngbrs', 'subquery')]
for idx, val in enumerate(sorted(attrs)):
attr_string += template % {"col": params[val], "alias_num": idx + 1}
return attr_string
def query_attr_where(params):
"""
Construct where conditions when building neighbors query
Create portion of WHERE clauses for weeding out NULL-valued geometries
Input: dict of params:
{'subquery': ...,
'numerator': 'data1',
'denominator': 'data2',
'': ...}
Output: 'idx_replace."data1" IS NOT NULL AND idx_replace."data2" IS NOT NULL'
Input:
{'subquery': ...,
'time_cols': ['time1', 'time2', 'time3'],
'etc': ...}
Output: 'idx_replace."time1" IS NOT NULL AND idx_replace."time2" IS NOT
NULL AND idx_replace."time3" IS NOT NULL'
"""
attr_string = []
template = "idx_replace.\"%s\" IS NOT NULL"
if 'time_cols' in params:
## markov where clauses
attrs = params['time_cols']
# add values to template
for attr in attrs:
attr_string.append(template % attr)
else:
## moran where clauses
# get keys
attrs = sorted([k for k in params
if k not in ('id_col', 'geom_col', 'subquery', 'num_ngbrs', 'subquery')])
# add values to template
for attr in attrs:
attr_string.append(template % params[attr])
if len(attrs) == 2:
attr_string.append("idx_replace.\"%s\" <> 0" % params[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)]

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"""Random seed generator used for non-deterministic functions in crankshaft"""
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)

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from segmentation import *

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"""
Segmentation creation and prediction
"""
import sklearn
import numpy as np
import plpy
from sklearn.ensemble import GradientBoostingRegressor
from sklearn import metrics
from sklearn.cross_validation import train_test_split
# Lower level functions
#----------------------
def replace_nan_with_mean(array):
"""
Input:
@param array: an array of floats which may have null-valued entries
Output:
array with nans filled in with the mean of the dataset
"""
# returns an array of rows and column indices
indices = np.where(np.isnan(array))
# iterate through entries which have nan values
for row, col in zip(*indices):
array[row, col] = np.mean(array[~np.isnan(array[:, col]), col])
return array
def get_data(variable, feature_columns, query):
"""
Fetch data from the database, clean, and package into
numpy arrays
Input:
@param variable: name of the target variable
@param feature_columns: list of column names
@param query: subquery that data is pulled from for the packaging
Output:
prepared data, packaged into NumPy arrays
"""
columns = ','.join(['array_agg("{col}") As "{col}"'.format(col=col) for col in feature_columns])
try:
data = plpy.execute('''SELECT array_agg("{variable}") As target, {columns} FROM ({query}) As a'''.format(
variable=variable,
columns=columns,
query=query))
except Exception, e:
plpy.error('Failed to access data to build segmentation model: %s' % e)
# extract target data from plpy object
target = np.array(data[0]['target'])
# put n feature data arrays into an n x m array of arrays
features = np.column_stack([np.array(data[0][col], dtype=float) for col in feature_columns])
return replace_nan_with_mean(target), replace_nan_with_mean(features)
# High level interface
# --------------------
def create_and_predict_segment_agg(target, features, target_features, target_ids, model_parameters):
"""
Version of create_and_predict_segment that works on arrays that come stright form the SQL calling
the function.
Input:
@param target: The 1D array of lenth NSamples containing the target variable we want the model to predict
@param features: Thw 2D array of size NSamples * NFeatures that form the imput to the model
@param target_ids: A 1D array of target_ids that will be used to associate the results of the prediction with the rows which they come from
@param model_parameters: A dictionary containing parameters for the model.
"""
clean_target = replace_nan_with_mean(target)
clean_features = replace_nan_with_mean(features)
target_features = replace_nan_with_mean(target_features)
model, accuracy = train_model(clean_target, clean_features, model_parameters, 0.2)
prediction = model.predict(target_features)
accuracy_array = [accuracy]*prediction.shape[0]
return zip(target_ids, prediction, np.full(prediction.shape, accuracy_array))
def create_and_predict_segment(query, variable, target_query, model_params):
"""
generate a segment with machine learning
Stuart Lynn
"""
## fetch column names
try:
columns = plpy.execute('SELECT * FROM ({query}) As a LIMIT 1 '.format(query=query))[0].keys()
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
## extract column names to be used in building the segmentation model
feature_columns = set(columns) - set([variable, 'cartodb_id', 'the_geom', 'the_geom_webmercator'])
## get data from database
target, features = get_data(variable, feature_columns, query)
model, accuracy = train_model(target, features, model_params, 0.2)
cartodb_ids, result = predict_segment(model, feature_columns, target_query)
accuracy_array = [accuracy]*result.shape[0]
return zip(cartodb_ids, result, accuracy_array)
def train_model(target, features, model_params, test_split):
"""
Train the Gradient Boosting model on the provided data and calculate the accuracy of the model
Input:
@param target: 1D Array of the variable that the model is to be trianed to predict
@param features: 2D Array NSamples * NFeatures to use in trining the model
@param model_params: A dictionary of model parameters, the full specification can be found on the
scikit learn page for [GradientBoostingRegressor](http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.GradientBoostingRegressor.html)
@parma test_split: The fraction of the data to be withheld for testing the model / calculating the accuray
"""
features_train, features_test, target_train, target_test = train_test_split(features, target, test_size=test_split)
model = GradientBoostingRegressor(**model_params)
model.fit(features_train, target_train)
accuracy = calculate_model_accuracy(model, features, target)
return model, accuracy
def calculate_model_accuracy(model, features, target):
"""
Calculate the mean squared error of the model prediction
Input:
@param model: model trained from input features
@param features: features to make a prediction from
@param target: target to compare prediction to
Output:
mean squared error of the model prection compared to the target
"""
prediction = model.predict(features)
return metrics.mean_squared_error(prediction, target)
def predict_segment(model, features, target_query):
"""
Use the provided model to predict the values for the new feature set
Input:
@param model: The pretrained model
@features: A list of features to use in the model prediction (list of column names)
@target_query: The query to run to obtain the data to predict on and the cartdb_ids associated with it.
"""
batch_size = 1000
joined_features = ','.join(['"{0}"::numeric'.format(a) for a in features])
try:
cursor = plpy.cursor('SELECT Array[{joined_features}] As features FROM ({target_query}) As a'.format(
joined_features=joined_features,
target_query=target_query))
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
results = []
while True:
rows = cursor.fetch(batch_size)
if not rows:
break
batch = np.row_stack([np.array(row['features'], dtype=float) for row in rows])
#Need to fix this. Should be global mean. This will cause weird effects
batch = replace_nan_with_mean(batch)
prediction = model.predict(batch)
results.append(prediction)
try:
cartodb_ids = plpy.execute('''SELECT array_agg(cartodb_id ORDER BY cartodb_id) As cartodb_ids FROM ({0}) As a'''.format(target_query))[0]['cartodb_ids']
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
return cartodb_ids, np.concatenate(results)

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"""Import all functions from clustering libraries."""
from markov import *

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"""
Spatial dynamics measurements using Spatial Markov
"""
import numpy as np
import pysal as ps
import plpy
import crankshaft.pysal_utils as pu
def spatial_markov_trend(subquery, time_cols, num_classes=7,
w_type='knn', num_ngbrs=5, permutations=0,
geom_col='the_geom', id_col='cartodb_id'):
"""
Predict the trends of a unit based on:
1. history of its transitions to different classes (e.g., 1st quantile -> 2nd quantile)
2. average class of its neighbors
Inputs:
@param subquery string: e.g., SELECT the_geom, cartodb_id,
interesting_time_column FROM table_name
@param time_cols list of strings: list of strings of column names
@param num_classes (optional): number of classes to break distribution
of values into. Currently uses quantile bins.
@param w_type string (optional): weight type ('knn' or 'queen')
@param num_ngbrs int (optional): number of neighbors (if knn type)
@param permutations int (optional): number of permutations for test
stats
@param geom_col string (optional): name of column which contains the
geometries
@param id_col string (optional): name of column which has the ids of
the table
Outputs:
@param trend_up float: probablity that a geom will move to a higher
class
@param trend_down float: probablity that a geom will move to a lower
class
@param trend float: (trend_up - trend_down) / trend_static
@param volatility float: a measure of the volatility based on
probability stddev(prob array)
"""
if len(time_cols) < 2:
plpy.error('More than one time column needs to be passed')
qvals = {"id_col": id_col,
"time_cols": time_cols,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs}
try:
query_result = plpy.execute(
pu.construct_neighbor_query(w_type, qvals)
)
if len(query_result) == 0:
return zip([None], [None], [None], [None], [None])
except plpy.SPIError, err:
plpy.debug('Query failed with exception %s: %s' % (err, pu.construct_neighbor_query(w_type, qvals)))
plpy.error('Query failed, check the input parameters')
return zip([None], [None], [None], [None], [None])
## build weight
weights = pu.get_weight(query_result, w_type)
weights.transform = 'r'
## prep time data
t_data = get_time_data(query_result, time_cols)
plpy.debug('shape of t_data %d, %d' % t_data.shape)
plpy.debug('number of weight objects: %d, %d' % (weights.sparse).shape)
plpy.debug('first num elements: %f' % t_data[0, 0])
sp_markov_result = ps.Spatial_Markov(t_data,
weights,
k=num_classes,
fixed=False,
permutations=permutations)
## get lag classes
lag_classes = ps.Quantiles(
ps.lag_spatial(weights, t_data[:, -1]),
k=num_classes).yb
## look up probablity distribution for each unit according to class and lag class
prob_dist = get_prob_dist(sp_markov_result.P,
lag_classes,
sp_markov_result.classes[:, -1])
## find the ups and down and overall distribution of each cell
trend_up, trend_down, trend, volatility = get_prob_stats(prob_dist,
sp_markov_result.classes[:, -1])
## output the results
return zip(trend, trend_up, trend_down, volatility, weights.id_order)
def get_time_data(markov_data, time_cols):
"""
Extract the time columns and bin appropriately
"""
num_attrs = len(time_cols)
return np.array([[x['attr' + str(i)] for x in markov_data]
for i in range(1, num_attrs+1)], dtype=float).transpose()
## not currently used
def rebin_data(time_data, num_time_per_bin):
"""
Convert an n x l matrix into an (n/m) x l matrix where the values are
reduced (averaged) for the intervening states:
1 2 3 4 1.5 3.5
5 6 7 8 -> 5.5 7.5
9 8 7 6 8.5 6.5
5 4 3 2 4.5 2.5
if m = 2, the 4 x 4 matrix is transformed to a 2 x 4 matrix.
This process effectively resamples the data at a longer time span n
units longer than the input data.
For cases when there is a remainder (remainder(5/3) = 2), the remaining
two columns are binned together as the last time period, while the
first three are binned together for the first period.
Input:
@param time_data n x l ndarray: measurements of an attribute at
different time intervals
@param num_time_per_bin int: number of columns to average into a new
column
Output:
ceil(n / m) x l ndarray of resampled time series
"""
if time_data.shape[1] % num_time_per_bin == 0:
## if fit is perfect, then use it
n_max = time_data.shape[1] / num_time_per_bin
else:
## fit remainders into an additional column
n_max = time_data.shape[1] / num_time_per_bin + 1
return np.array([time_data[:, num_time_per_bin * i:num_time_per_bin * (i+1)].mean(axis=1)
for i in range(n_max)]).T
def get_prob_dist(transition_matrix, lag_indices, unit_indices):
"""
Given an array of transition matrices, look up the probability
associated with the arrangements passed
Input:
@param transition_matrix ndarray[k,k,k]:
@param lag_indices ndarray:
@param unit_indices ndarray:
Output:
Array of probability distributions
"""
return np.array([transition_matrix[(lag_indices[i], unit_indices[i])]
for i in range(len(lag_indices))])
def get_prob_stats(prob_dist, unit_indices):
"""
get the statistics of the probability distributions
Outputs:
@param trend_up ndarray(float): sum of probabilities for upward
movement (relative to the unit index of that prob)
@param trend_down ndarray(float): sum of probabilities for downward
movement (relative to the unit index of that prob)
@param trend ndarray(float): difference of upward and downward
movements
"""
num_elements = len(unit_indices)
trend_up = np.empty(num_elements, dtype=float)
trend_down = np.empty(num_elements, dtype=float)
trend = np.empty(num_elements, dtype=float)
for i in range(num_elements):
trend_up[i] = prob_dist[i, (unit_indices[i]+1):].sum()
trend_down[i] = prob_dist[i, :unit_indices[i]].sum()
if prob_dist[i, unit_indices[i]] > 0.0:
trend[i] = (trend_up[i] - trend_down[i]) / prob_dist[i, unit_indices[i]]
else:
trend[i] = None
## calculate volatility of distribution
volatility = prob_dist.std(axis=1)
return trend_up, trend_down, trend, volatility

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"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.0',
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.
# IMPORTANT NOTE: please don't change this line. Instead issue a ticket to systems for evaluation.
install_requires=['joblib==0.8.3', 'numpy==1.6.1', 'scipy==0.14.0', 'pysal==1.11.2', 'scikit-learn==0.14.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

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"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.0',
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.
# IMPORTANT NOTE: please don't change this line. Instead issue a ticket to systems for evaluation.
install_requires=['joblib==0.8.3', 'numpy==1.6.1', 'scipy==0.14.0', 'pysal==1.11.2', 'scikit-learn==0.14.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

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[[0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 0], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 1], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 2], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 3], [0.0, 0.065217391304347824, 0.065217391304347824, 0.33605067580764519, 4], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 5], [0.1875, 0.23999999999999999, 0.12, 0.23731835158706122, 6], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 7], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 8], [0.19047619047619049, 0.16, 0.0, 0.32594478059941379, 9], [-0.23529411764705882, 0.0, 0.19047619047619047, 0.31356338348865387, 10], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 11], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 12], [0.027777777777777783, 0.11111111111111112, 0.088888888888888892, 0.30339641183779581, 13], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 14], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 15], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 16], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 17], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 18], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 19], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 20], [0.078947368421052641, 0.073170731707317083, 0.0, 0.36451788667842738, 21], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 22], [-0.16666666666666663, 0.18181818181818182, 0.27272727272727271, 0.20246415864836445, 23], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 24], [0.1875, 0.23999999999999999, 0.12, 0.23731835158706122, 25], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 26], [-0.043478260869565216, 0.0, 0.041666666666666664, 0.37950991789118999, 27], [0.22222222222222221, 0.18181818181818182, 0.0, 0.31701083225750354, 28], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 29], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 30], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 31], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 32], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 33], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 34], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 35], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 36], [0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 37], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 38], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 39], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 40], [0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 41], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 42], [0.0, 0.0, 0.0, 0.40000000000000002, 43], [0.0, 0.065217391304347824, 0.065217391304347824, 0.33605067580764519, 44], [0.078947368421052641, 0.073170731707317083, 0.0, 0.36451788667842738, 45], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 46], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 47]]

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[[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"]]

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[
{"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}
]

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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)

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import re
class MockCursor:
def __init__(self, data):
self.cursor_pos = 0
self.data = data
def fetch(self, batch_size):
batch = self.data[self.cursor_pos : self.cursor_pos + batch_size]
self.cursor_pos += batch_size
return batch
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 debug(self, msg):
self.notices.append(msg)
def info(self, msg):
self.infos.append(msg)
def cursor(self, query):
data = self.execute(query)
return MockCursor(data)
def execute(self, query): # TODO: additional arguments
for result in self.results:
if result[0].match(query):
return result[1]
return []

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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)

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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.params_markov = {"id_col": "cartodb_id",
"time_cols": ["_2013_dec", "_2014_jan", "_2014_feb"],
"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)

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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}
self.params_array = {"id_col": "cartodb_id",
"time_cols": ["_2013_dec", "_2014_jan", "_2014_feb"],
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
def test_query_attr_select(self):
"""Test query_attr_select"""
ans = "i.\"andy\"::numeric As attr1, " \
"i.\"jay_z\"::numeric As attr2, "
ans_array = "i.\"_2013_dec\"::numeric As attr1, " \
"i.\"_2014_jan\"::numeric As attr2, " \
"i.\"_2014_feb\"::numeric As attr3, "
self.assertEqual(pu.query_attr_select(self.params), ans)
self.assertEqual(pu.query_attr_select(self.params_array), ans_array)
def test_query_attr_where(self):
"""Test pu.query_attr_where"""
ans = "idx_replace.\"andy\" IS NOT NULL AND " \
"idx_replace.\"jay_z\" IS NOT NULL AND " \
"idx_replace.\"jay_z\" <> 0"
ans_array = "idx_replace.\"_2013_dec\" IS NOT NULL AND " \
"idx_replace.\"_2014_jan\" IS NOT NULL AND " \
"idx_replace.\"_2014_feb\" IS NOT NULL"
self.assertEqual(pu.query_attr_where(self.params), ans)
self.assertEqual(pu.query_attr_where(self.params_array), ans_array)
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;"
ans_array = "SELECT i.\"cartodb_id\" As id, " \
"i.\"_2013_dec\"::numeric As attr1, " \
"i.\"_2014_jan\"::numeric As attr2, " \
"i.\"_2014_feb\"::numeric As attr3, " \
"(SELECT ARRAY(SELECT j.\"cartodb_id\" " \
"FROM (SELECT * FROM a_list) As j " \
"WHERE i.\"cartodb_id\" <> j.\"cartodb_id\" AND " \
"j.\"_2013_dec\" IS NOT NULL AND " \
"j.\"_2014_jan\" IS NOT NULL AND " \
"j.\"_2014_feb\" IS NOT NULL " \
"ORDER BY j.\"the_geom\" <-> i.\"the_geom\" ASC " \
"LIMIT 321)) As neighbors " \
"FROM (SELECT * FROM a_list) As i " \
"WHERE i.\"_2013_dec\" IS NOT NULL AND " \
"i.\"_2014_jan\" IS NOT NULL AND " \
"i.\"_2014_feb\" IS NOT NULL "\
"ORDER BY i.\"cartodb_id\" ASC;"
self.assertEqual(pu.knn(self.params), ans)
self.assertEqual(pu.knn(self.params_array), ans_array)
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)

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import unittest
import numpy as np
from helper import plpy, fixture_file
import crankshaft.segmentation as segmentation
import json
class SegmentationTest(unittest.TestCase):
"""Testing class for Moran's I functions"""
def setUp(self):
plpy._reset()
def generate_random_data(self,n_samples,random_state, row_type=False):
x1 = random_state.uniform(size=n_samples)
x2 = random_state.uniform(size=n_samples)
x3 = random_state.randint(0, 4, size=n_samples)
y = x1+x2*x2+x3
cartodb_id = range(len(x1))
if row_type:
return [ {'features': vals} for vals in zip(x1,x2,x3)], y
else:
return [dict( zip(['x1','x2','x3','target', 'cartodb_id'],[x1,x2,x3,y,cartodb_id]))]
def test_replace_nan_with_mean(self):
test_array = np.array([1.2, np.nan, 3.2, np.nan, np.nan])
def test_create_and_predict_segment(self):
n_samples = 1000
random_state_train = np.random.RandomState(13)
random_state_test = np.random.RandomState(134)
training_data = self.generate_random_data(n_samples, random_state_train)
test_data, test_y = self.generate_random_data(n_samples, random_state_test, row_type=True)
ids = [{'cartodb_ids': range(len(test_data))}]
rows = [{'x1': 0,'x2':0,'x3':0,'y':0,'cartodb_id':0}]
plpy._define_result('select \* from \(select \* from training\) a limit 1',rows)
plpy._define_result('.*from \(select \* from training\) as a' ,training_data)
plpy._define_result('select array_agg\(cartodb\_id order by cartodb\_id\) as cartodb_ids from \(.*\) a',ids)
plpy._define_result('.*select \* from test.*' ,test_data)
model_parameters = {'n_estimators': 1200,
'max_depth': 3,
'subsample' : 0.5,
'learning_rate': 0.01,
'min_samples_leaf': 1}
result = segmentation.create_and_predict_segment(
'select * from training',
'target',
'select * from test',
model_parameters)
prediction = [r[1] for r in result]
accuracy =np.sqrt(np.mean( np.square( np.array(prediction) - np.array(test_y))))
self.assertEqual(len(result),len(test_data))
self.assertTrue( result[0][2] < 0.01)
self.assertTrue( accuracy < 0.5*np.mean(test_y) )

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import unittest
import numpy as np
import unittest
# from mock_plpy import MockPlPy
# plpy = MockPlPy()
#
# import sys
# sys.modules['plpy'] = plpy
from helper import plpy, fixture_file
import crankshaft.space_time_dynamics as std
from crankshaft import random_seeds
import json
class SpaceTimeTests(unittest.TestCase):
"""Testing class for Markov Functions."""
def setUp(self):
plpy._reset()
self.params = {"id_col": "cartodb_id",
"time_cols": ['dec_2013', 'jan_2014', 'feb_2014'],
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
self.neighbors_data = json.loads(open(fixture_file('neighbors_markov.json')).read())
self.markov_data = json.loads(open(fixture_file('markov.json')).read())
self.time_data = np.array([i * np.ones(10, dtype=float) for i in range(10)]).T
self.transition_matrix = np.array([
[[ 0.96341463, 0.0304878 , 0.00609756, 0. , 0. ],
[ 0.06040268, 0.83221477, 0.10738255, 0. , 0. ],
[ 0. , 0.14 , 0.74 , 0.12 , 0. ],
[ 0. , 0.03571429, 0.32142857, 0.57142857, 0.07142857],
[ 0. , 0. , 0. , 0.16666667, 0.83333333]],
[[ 0.79831933, 0.16806723, 0.03361345, 0. , 0. ],
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0.00537634, 0.06989247, 0.8655914 , 0.05913978, 0. ],
[ 0. , 0. , 0.06372549, 0.90196078, 0.03431373],
[ 0. , 0. , 0. , 0.19444444, 0.80555556]],
[[ 0.84693878, 0.15306122, 0. , 0. , 0. ],
[ 0.08133971, 0.78947368, 0.1291866 , 0. , 0. ],
[ 0.00518135, 0.0984456 , 0.79274611, 0.0984456 , 0.00518135],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0. , 0. , 0. , 0.10204082, 0.89795918]],
[[ 0.8852459 , 0.09836066, 0. , 0.01639344, 0. ],
[ 0.03875969, 0.81395349, 0.13953488, 0. , 0.00775194],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0.02339181, 0.12865497, 0.75438596, 0.09356725],
[ 0. , 0. , 0. , 0.09661836, 0.90338164]],
[[ 0.33333333, 0.66666667, 0. , 0. , 0. ],
[ 0.0483871 , 0.77419355, 0.16129032, 0.01612903, 0. ],
[ 0.01149425, 0.16091954, 0.74712644, 0.08045977, 0. ],
[ 0. , 0.01036269, 0.06217617, 0.89637306, 0.03108808],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]]]
)
def test_spatial_markov(self):
"""Test Spatial Markov."""
data = [ { 'id': d['id'],
'attr1': d['y1995'],
'attr2': d['y1996'],
'attr3': d['y1997'],
'attr4': d['y1998'],
'attr5': d['y1999'],
'attr6': d['y2000'],
'attr7': d['y2001'],
'attr8': d['y2002'],
'attr9': d['y2003'],
'attr10': d['y2004'],
'attr11': d['y2005'],
'attr12': d['y2006'],
'attr13': d['y2007'],
'attr14': d['y2008'],
'attr15': d['y2009'],
'neighbors': d['neighbors'] } for d in self.neighbors_data]
print(str(data[0]))
plpy._define_result('select', data)
random_seeds.set_random_seeds(1234)
result = std.spatial_markov_trend('subquery', ['y1995', 'y1996', 'y1997', 'y1998', 'y1999', 'y2000', 'y2001', 'y2002', 'y2003', 'y2004', 'y2005', 'y2006', 'y2007', 'y2008', 'y2009'], 5, 'knn', 5, 0, 'the_geom', 'cartodb_id')
self.assertTrue(result != None)
result = [(row[0], row[1], row[2], row[3], row[4]) for row in result]
print result[0]
expected = self.markov_data
for ([res_trend, res_up, res_down, res_vol, res_id],
[exp_trend, exp_up, exp_down, exp_vol, exp_id]
) in zip(result, expected):
self.assertAlmostEqual(res_trend, exp_trend)
def test_get_time_data(self):
"""Test get_time_data"""
data = [ { 'attr1': d['y1995'],
'attr2': d['y1996'],
'attr3': d['y1997'],
'attr4': d['y1998'],
'attr5': d['y1999'],
'attr6': d['y2000'],
'attr7': d['y2001'],
'attr8': d['y2002'],
'attr9': d['y2003'],
'attr10': d['y2004'],
'attr11': d['y2005'],
'attr12': d['y2006'],
'attr13': d['y2007'],
'attr14': d['y2008'],
'attr15': d['y2009'] } for d in self.neighbors_data]
result = std.get_time_data(data, ['y1995', 'y1996', 'y1997', 'y1998', 'y1999', 'y2000', 'y2001', 'y2002', 'y2003', 'y2004', 'y2005', 'y2006', 'y2007', 'y2008', 'y2009'])
## expected was prepared from PySAL example:
### f = ps.open(ps.examples.get_path("usjoin.csv"))
### pci = np.array([f.by_col[str(y)] for y in range(1995, 2010)]).transpose()
### rpci = pci / (pci.mean(axis = 0))
expected = np.array([[ 0.87654416, 0.863147, 0.85637567, 0.84811668, 0.8446154, 0.83271652
, 0.83786314, 0.85012593, 0.85509656, 0.86416612, 0.87119375, 0.86302631
, 0.86148267, 0.86252252, 0.86746356],
[ 0.9188951, 0.91757931, 0.92333258, 0.92517289, 0.92552388, 0.90746978
, 0.89830489, 0.89431991, 0.88924794, 0.89815176, 0.91832091, 0.91706054
, 0.90139505, 0.87897455, 0.86216858],
[ 0.82591007, 0.82548596, 0.81989793, 0.81503235, 0.81731522, 0.78964559
, 0.80584442, 0.8084998, 0.82258551, 0.82668196, 0.82373724, 0.81814804
, 0.83675961, 0.83574199, 0.84647177],
[ 1.09088176, 1.08537689, 1.08456418, 1.08415404, 1.09898841, 1.14506948
, 1.12151133, 1.11160697, 1.10888621, 1.11399806, 1.12168029, 1.13164797
, 1.12958508, 1.11371818, 1.09936775],
[ 1.10731446, 1.11373944, 1.13283638, 1.14472559, 1.15910025, 1.16898201
, 1.17212488, 1.14752303, 1.11843284, 1.11024964, 1.11943471, 1.11736468
, 1.10863242, 1.09642516, 1.07762337],
[ 1.42269757, 1.42118434, 1.44273502, 1.43577571, 1.44400684, 1.44184737
, 1.44782832, 1.41978227, 1.39092208, 1.4059372, 1.40788646, 1.44052766
, 1.45241216, 1.43306098, 1.4174431 ],
[ 1.13073885, 1.13110513, 1.11074708, 1.13364636, 1.13088149, 1.10888138
, 1.11856629, 1.13062931, 1.11944984, 1.12446239, 1.11671008, 1.10880034
, 1.08401709, 1.06959206, 1.07875225],
[ 1.04706124, 1.04516831, 1.04253372, 1.03239987, 1.02072545, 0.99854316
, 0.9880258, 0.99669587, 0.99327676, 1.01400905, 1.03176742, 1.040511
, 1.01749645, 0.9936394, 0.98279746],
[ 0.98996986, 1.00143564, 0.99491, 1.00188408, 1.00455845, 0.99127006
, 0.97925917, 0.9683482, 0.95335147, 0.93694787, 0.94308213, 0.92232874
, 0.91284091, 0.89689833, 0.88928858],
[ 0.87418391, 0.86416601, 0.84425695, 0.8404494, 0.83903044, 0.8578708
, 0.86036185, 0.86107306, 0.8500772, 0.86981998, 0.86837929, 0.87204141
, 0.86633032, 0.84946077, 0.83287146],
[ 1.14196118, 1.14660262, 1.14892712, 1.14909594, 1.14436624, 1.14450183
, 1.12349752, 1.12596664, 1.12213996, 1.1119989, 1.10257792, 1.10491258
, 1.11059842, 1.10509795, 1.10020097],
[ 0.97282463, 0.96700147, 0.96252588, 0.9653878, 0.96057687, 0.95831051
, 0.94480909, 0.94804195, 0.95430286, 0.94103989, 0.92122519, 0.91010201
, 0.89280392, 0.89298243, 0.89165385],
[ 0.94325468, 0.96436902, 0.96455242, 0.95243009, 0.94117647, 0.9480927
, 0.93539182, 0.95388718, 0.94597005, 0.96918424, 0.94781281, 0.93466815
, 0.94281559, 0.96520315, 0.96715441],
[ 0.97478408, 0.98169225, 0.98712809, 0.98474769, 0.98559897, 0.98687073
, 0.99237486, 0.98209969, 0.9877653, 0.97399471, 0.96910087, 0.98416665
, 0.98423613, 0.99823861, 0.99545704],
[ 0.85570269, 0.85575915, 0.85986132, 0.85693406, 0.8538012, 0.86191535
, 0.84981451, 0.85472102, 0.84564835, 0.83998883, 0.83478547, 0.82803648
, 0.8198736, 0.82265395, 0.8399404 ],
[ 0.87022047, 0.85996258, 0.85961813, 0.85689572, 0.83947136, 0.82785597
, 0.86008789, 0.86776298, 0.86720209, 0.8676334, 0.89179317, 0.94202108
, 0.9422231, 0.93902708, 0.94479184],
[ 0.90134907, 0.90407738, 0.90403991, 0.90201769, 0.90399238, 0.90906632
, 0.92693339, 0.93695966, 0.94242697, 0.94338265, 0.91981796, 0.91108804
, 0.90543476, 0.91737138, 0.94793657],
[ 1.1977611, 1.18222564, 1.18439158, 1.18267865, 1.19286723, 1.20172869
, 1.21328691, 1.22624778, 1.22397075, 1.23857042, 1.24419893, 1.23929384
, 1.23418676, 1.23626739, 1.26754398],
[ 1.24919678, 1.25754773, 1.26991161, 1.28020651, 1.30625667, 1.34790023
, 1.34399863, 1.32575181, 1.30795492, 1.30544841, 1.30303302, 1.32107766
, 1.32936244, 1.33001241, 1.33288462],
[ 1.06768004, 1.03799276, 1.03637303, 1.02768449, 1.03296093, 1.05059016
, 1.03405057, 1.02747623, 1.03162734, 0.9961416, 0.97356208, 0.94241549
, 0.92754547, 0.92549227, 0.92138102],
[ 1.09475614, 1.11526796, 1.11654299, 1.13103948, 1.13143264, 1.13889622
, 1.12442212, 1.13367018, 1.13982256, 1.14029944, 1.11979401, 1.10905389
, 1.10577769, 1.11166825, 1.09985155],
[ 0.76530058, 0.76612841, 0.76542451, 0.76722683, 0.76014284, 0.74480073
, 0.76098396, 0.76156903, 0.76651952, 0.76533288, 0.78205934, 0.76842416
, 0.77487118, 0.77768683, 0.78801192],
[ 0.98391336, 0.98075816, 0.98295341, 0.97386015, 0.96913803, 0.97370819
, 0.96419154, 0.97209861, 0.97441313, 0.96356162, 0.94745352, 0.93965462
, 0.93069645, 0.94020973, 0.94358232],
[ 0.83561828, 0.82298088, 0.81738502, 0.81748588, 0.80904801, 0.80071489
, 0.83358256, 0.83451613, 0.85175032, 0.85954307, 0.86790024, 0.87170334
, 0.87863799, 0.87497981, 0.87888675],
[ 0.98845573, 1.02092428, 0.99665283, 0.99141823, 0.99386619, 0.98733195
, 0.99644997, 0.99669587, 1.02559097, 1.01116651, 0.99988024, 0.97906749
, 0.99323123, 1.00204939, 0.99602148],
[ 1.14930913, 1.15241949, 1.14300962, 1.14265542, 1.13984683, 1.08312397
, 1.05192626, 1.04230892, 1.05577278, 1.08569751, 1.12443486, 1.08891079
, 1.08603695, 1.05997314, 1.02160943],
[ 1.11368269, 1.1057147, 1.11893431, 1.13778669, 1.1432272, 1.18257029
, 1.16226243, 1.16009196, 1.14467789, 1.14820235, 1.12386598, 1.12680236
, 1.12357937, 1.1159258, 1.12570828],
[ 1.30379431, 1.30752186, 1.31206366, 1.31532267, 1.30625667, 1.31210239
, 1.29989156, 1.29203193, 1.27183516, 1.26830786, 1.2617743, 1.28656675
, 1.29734097, 1.29390205, 1.29345446],
[ 0.83953719, 0.82701448, 0.82006005, 0.81188876, 0.80294864, 0.78772975
, 0.82848011, 0.8259679, 0.82435705, 0.83108634, 0.84373784, 0.83891093
, 0.84349247, 0.85637272, 0.86539395],
[ 1.23450087, 1.2426022, 1.23537935, 1.23581293, 1.24522626, 1.2256767
, 1.21126648, 1.19377804, 1.18355337, 1.19674434, 1.21536573, 1.23653297
, 1.27962009, 1.27968392, 1.25907738],
[ 0.9769662, 0.97400719, 0.98035944, 0.97581531, 0.95543282, 0.96480308
, 0.94686376, 0.93679073, 0.92540049, 0.92988835, 0.93442917, 0.92100464
, 0.91475304, 0.90249622, 0.9021363 ],
[ 0.84986886, 0.8986851, 0.84295997, 0.87280534, 0.85659368, 0.88937573
, 0.894401, 0.90448993, 0.95495898, 0.92698333, 0.94745352, 0.92562488
, 0.96635366, 1.02520312, 1.0394296 ],
[ 1.01922808, 1.00258203, 1.00974428, 1.00303417, 0.99765073, 1.00759019
, 0.99192968, 0.99747298, 0.99550759, 0.97583768, 0.9610168, 0.94779638
, 0.93759089, 0.93353431, 0.94121705],
[ 0.86367411, 0.85558932, 0.85544346, 0.85103025, 0.84336613, 0.83434854
, 0.85813595, 0.84667961, 0.84374558, 0.85951183, 0.87194227, 0.89455097
, 0.88283929, 0.90349491, 0.90600675],
[ 1.00947534, 1.00411055, 1.00698819, 0.99513687, 0.99291086, 1.00581626
, 0.98850522, 0.99291168, 0.98983209, 0.97511924, 0.96134615, 0.96382634
, 0.95011401, 0.9434686, 0.94637765],
[ 1.05712571, 1.05459419, 1.05753012, 1.04880786, 1.05103857, 1.04800023
, 1.03024941, 1.04200483, 1.0402554, 1.03296979, 1.02191682, 1.02476275
, 1.02347523, 1.02517684, 1.04359571],
[ 1.07084189, 1.06669497, 1.07937623, 1.07387988, 1.0794043, 1.0531801
, 1.07452771, 1.09383478, 1.1052447, 1.10322136, 1.09167939, 1.08772756
, 1.08859544, 1.09177338, 1.1096083 ],
[ 0.86719222, 0.86628896, 0.86675156, 0.86425632, 0.86511809, 0.86287327
, 0.85169796, 0.85411285, 0.84886336, 0.84517414, 0.84843858, 0.84488343
, 0.83374329, 0.82812044, 0.82878599],
[ 0.88389211, 0.92288667, 0.90282398, 0.91229186, 0.92023286, 0.92652175
, 0.94278865, 0.93682452, 0.98655146, 0.992237, 0.9798497, 0.93869677
, 0.96947771, 1.00362626, 0.98102351],
[ 0.97082064, 0.95320233, 0.94534081, 0.94215593, 0.93967, 0.93092109
, 0.92662519, 0.93412152, 0.93501274, 0.92879506, 0.92110542, 0.91035556
, 0.90430364, 0.89994694, 0.90073864],
[ 0.95861858, 0.95774543, 0.98254811, 0.98919472, 0.98684824, 0.98882205
, 0.97662234, 0.95601578, 0.94905385, 0.94934888, 0.97152609, 0.97163004
, 0.9700702, 0.97158948, 0.95884908],
[ 0.83980439, 0.84726737, 0.85747, 0.85467221, 0.8556751, 0.84818516
, 0.85265681, 0.84502402, 0.82645665, 0.81743586, 0.83550406, 0.83338919
, 0.83511679, 0.82136617, 0.80921874],
[ 0.95118156, 0.9466212, 0.94688098, 0.9508583, 0.9512441, 0.95440787
, 0.96364363, 0.96804412, 0.97136214, 0.97583768, 0.95571724, 0.96895368
, 0.97001634, 0.97082733, 0.98782366],
[ 1.08910044, 1.08248968, 1.08492895, 1.08656923, 1.09454249, 1.10558188
, 1.1214086, 1.12292577, 1.13021031, 1.13342735, 1.14686068, 1.14502975
, 1.14474747, 1.14084037, 1.16142926],
[ 1.06336033, 1.07365823, 1.08691496, 1.09764846, 1.11669863, 1.11856702
, 1.09764283, 1.08815849, 1.08044313, 1.09278827, 1.07003204, 1.08398066
, 1.09831768, 1.09298232, 1.09176125],
[ 0.79772065, 0.78829196, 0.78581151, 0.77615922, 0.77035744, 0.77751194
, 0.79902974, 0.81437881, 0.80788828, 0.79603865, 0.78966436, 0.79949807
, 0.80172182, 0.82168155, 0.85587911],
[ 1.0052447, 1.00007696, 1.00475899, 1.00613942, 1.00639561, 1.00162979
, 0.99860739, 1.00814981, 1.00574316, 0.99030032, 0.97682565, 0.97292596
, 0.96519561, 0.96173403, 0.95890284],
[ 0.95808419, 0.9382568, 0.9654441, 0.95561201, 0.96987289, 0.96608031
, 0.99727185, 1.00781194, 1.03484236, 1.05333619, 1.0983263, 1.1704974
, 1.17025154, 1.18730553, 1.14242645]])
self.assertTrue(np.allclose(result, expected))
self.assertTrue(type(result) == type(expected))
self.assertTrue(result.shape == expected.shape)
def test_rebin_data(self):
"""Test rebin_data"""
## sample in double the time (even case since 10 % 2 = 0):
## (0+1)/2, (2+3)/2, (4+5)/2, (6+7)/2, (8+9)/2
## = 0.5, 2.5, 4.5, 6.5, 8.5
ans_even = np.array([(i + 0.5) * np.ones(10, dtype=float)
for i in range(0, 10, 2)]).T
self.assertTrue(np.array_equal(std.rebin_data(self.time_data, 2), ans_even))
## sample in triple the time (uneven since 10 % 3 = 1):
## (0+1+2)/3, (3+4+5)/3, (6+7+8)/3, (9)/1
## = 1, 4, 7, 9
ans_odd = np.array([i * np.ones(10, dtype=float)
for i in (1, 4, 7, 9)]).T
self.assertTrue(np.array_equal(std.rebin_data(self.time_data, 3), ans_odd))
def test_get_prob_dist(self):
"""Test get_prob_dist"""
lag_indices = np.array([1, 2, 3, 4])
unit_indices = np.array([1, 3, 2, 4])
answer = np.array([
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]
])
result = std.get_prob_dist(self.transition_matrix, lag_indices, unit_indices)
self.assertTrue(np.array_equal(result, answer))
def test_get_prob_stats(self):
"""Test get_prob_stats"""
probs = np.array([
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]
])
unit_indices = np.array([1, 3, 2, 4])
answer_up = np.array([0.04245283, 0.03529412, 0.12376238, 0.])
answer_down = np.array([0.0754717, 0.09411765, 0.0990099, 0.02352941])
answer_trend = np.array([-0.03301887 / 0.88207547, -0.05882353 / 0.87058824, 0.02475248 / 0.77722772, -0.02352941 / 0.97647059])
answer_volatility = np.array([ 0.34221495, 0.33705421, 0.29226542, 0.38834223])
result = std.get_prob_stats(probs, unit_indices)
result_up = result[0]
result_down = result[1]
result_trend = result[2]
result_volatility = result[3]
self.assertTrue(np.allclose(result_up, answer_up))
self.assertTrue(np.allclose(result_down, answer_down))
self.assertTrue(np.allclose(result_trend, answer_trend))
self.assertTrue(np.allclose(result_volatility, answer_volatility))

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"""Import all modules"""
import crankshaft.random_seeds
import crankshaft.clustering
import crankshaft.space_time_dynamics
import crankshaft.segmentation

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"""Import all functions from for clustering"""
from moran import *
from kmeans import *

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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)

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"""
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
from collections import OrderedDict
# 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 = OrderedDict([("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)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(2)
except plpy.SPIError, e:
plpy.error('Analysis failed: %s' % e)
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 = OrderedDict([("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, e:
plpy.error('Analysis failed: %s' % e)
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 = OrderedDict([("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)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(2)
except plpy.SPIError, e:
plpy.error('Analysis failed: %s' % e)
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
qvals = OrderedDict([("id_col", id_col),
("numerator", numerator),
("denominator", denominator),
("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, e:
plpy.error('Analysis failed: %s' % e)
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 quadrants for each geometry
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)
"""
qvals = OrderedDict([("id_col", id_col),
("attr1", attr1),
("attr2", attr2),
("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(4)
except plpy.SPIError:
plpy.error("Error: areas of interest query failed, " \
"check input parameters")
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)
# find clustering of significance
lisa_sig = quad_position(lisa.q)
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]

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"""Import all functions for pysal_utils"""
from crankshaft.pysal_utils.pysal_utils import *

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"""
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 dict-like: 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}
print 'len of neighbors: %d' % len(neighbors)
built_weight = ps.W(neighbors)
built_weight.transform = 'r'
return built_weight
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.)
"""
attr_string = ""
template = "i.\"%(col)s\"::numeric As attr%(alias_num)s, "
if 'time_cols' in params:
## if markov analysis
attrs = params['time_cols']
for idx, val in enumerate(attrs):
attr_string += template % {"col": val, "alias_num": idx + 1}
else:
## if moran's analysis
attrs = [k for k in params
if k not in ('id_col', 'geom_col', 'subquery', 'num_ngbrs', 'subquery')]
for idx, val in enumerate(sorted(attrs)):
attr_string += template % {"col": params[val], "alias_num": idx + 1}
return attr_string
def query_attr_where(params):
"""
Construct where conditions when building neighbors query
Create portion of WHERE clauses for weeding out NULL-valued geometries
Input: dict of params:
{'subquery': ...,
'numerator': 'data1',
'denominator': 'data2',
'': ...}
Output: 'idx_replace."data1" IS NOT NULL AND idx_replace."data2" IS NOT NULL'
Input:
{'subquery': ...,
'time_cols': ['time1', 'time2', 'time3'],
'etc': ...}
Output: 'idx_replace."time1" IS NOT NULL AND idx_replace."time2" IS NOT
NULL AND idx_replace."time3" IS NOT NULL'
"""
attr_string = []
template = "idx_replace.\"%s\" IS NOT NULL"
if 'time_cols' in params:
## markov where clauses
attrs = params['time_cols']
# add values to template
for attr in attrs:
attr_string.append(template % attr)
else:
## moran where clauses
# get keys
attrs = sorted([k for k in params
if k not in ('id_col', 'geom_col', 'subquery', 'num_ngbrs', 'subquery')])
# add values to template
for attr in attrs:
attr_string.append(template % params[attr])
if len(attrs) == 2:
attr_string.append("idx_replace.\"%s\" <> 0" % params[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)]

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"""Random seed generator used for non-deterministic functions in crankshaft"""
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)

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from segmentation import *

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"""
Segmentation creation and prediction
"""
import sklearn
import numpy as np
import plpy
from sklearn.ensemble import GradientBoostingRegressor
from sklearn import metrics
from sklearn.cross_validation import train_test_split
# Lower level functions
#----------------------
def replace_nan_with_mean(array):
"""
Input:
@param array: an array of floats which may have null-valued entries
Output:
array with nans filled in with the mean of the dataset
"""
# returns an array of rows and column indices
indices = np.where(np.isnan(array))
# iterate through entries which have nan values
for row, col in zip(*indices):
array[row, col] = np.mean(array[~np.isnan(array[:, col]), col])
return array
def get_data(variable, feature_columns, query):
"""
Fetch data from the database, clean, and package into
numpy arrays
Input:
@param variable: name of the target variable
@param feature_columns: list of column names
@param query: subquery that data is pulled from for the packaging
Output:
prepared data, packaged into NumPy arrays
"""
columns = ','.join(['array_agg("{col}") As "{col}"'.format(col=col) for col in feature_columns])
try:
data = plpy.execute('''SELECT array_agg("{variable}") As target, {columns} FROM ({query}) As a'''.format(
variable=variable,
columns=columns,
query=query))
except Exception, e:
plpy.error('Failed to access data to build segmentation model: %s' % e)
# extract target data from plpy object
target = np.array(data[0]['target'])
# put n feature data arrays into an n x m array of arrays
features = np.column_stack([np.array(data[0][col], dtype=float) for col in feature_columns])
return replace_nan_with_mean(target), replace_nan_with_mean(features)
# High level interface
# --------------------
def create_and_predict_segment_agg(target, features, target_features, target_ids, model_parameters):
"""
Version of create_and_predict_segment that works on arrays that come stright form the SQL calling
the function.
Input:
@param target: The 1D array of lenth NSamples containing the target variable we want the model to predict
@param features: Thw 2D array of size NSamples * NFeatures that form the imput to the model
@param target_ids: A 1D array of target_ids that will be used to associate the results of the prediction with the rows which they come from
@param model_parameters: A dictionary containing parameters for the model.
"""
clean_target = replace_nan_with_mean(target)
clean_features = replace_nan_with_mean(features)
target_features = replace_nan_with_mean(target_features)
model, accuracy = train_model(clean_target, clean_features, model_parameters, 0.2)
prediction = model.predict(target_features)
accuracy_array = [accuracy]*prediction.shape[0]
return zip(target_ids, prediction, np.full(prediction.shape, accuracy_array))
def create_and_predict_segment(query, variable, target_query, model_params):
"""
generate a segment with machine learning
Stuart Lynn
"""
## fetch column names
try:
columns = plpy.execute('SELECT * FROM ({query}) As a LIMIT 1 '.format(query=query))[0].keys()
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
## extract column names to be used in building the segmentation model
feature_columns = set(columns) - set([variable, 'cartodb_id', 'the_geom', 'the_geom_webmercator'])
## get data from database
target, features = get_data(variable, feature_columns, query)
model, accuracy = train_model(target, features, model_params, 0.2)
cartodb_ids, result = predict_segment(model, feature_columns, target_query)
accuracy_array = [accuracy]*result.shape[0]
return zip(cartodb_ids, result, accuracy_array)
def train_model(target, features, model_params, test_split):
"""
Train the Gradient Boosting model on the provided data and calculate the accuracy of the model
Input:
@param target: 1D Array of the variable that the model is to be trianed to predict
@param features: 2D Array NSamples * NFeatures to use in trining the model
@param model_params: A dictionary of model parameters, the full specification can be found on the
scikit learn page for [GradientBoostingRegressor](http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.GradientBoostingRegressor.html)
@parma test_split: The fraction of the data to be withheld for testing the model / calculating the accuray
"""
features_train, features_test, target_train, target_test = train_test_split(features, target, test_size=test_split)
model = GradientBoostingRegressor(**model_params)
model.fit(features_train, target_train)
accuracy = calculate_model_accuracy(model, features, target)
return model, accuracy
def calculate_model_accuracy(model, features, target):
"""
Calculate the mean squared error of the model prediction
Input:
@param model: model trained from input features
@param features: features to make a prediction from
@param target: target to compare prediction to
Output:
mean squared error of the model prection compared to the target
"""
prediction = model.predict(features)
return metrics.mean_squared_error(prediction, target)
def predict_segment(model, features, target_query):
"""
Use the provided model to predict the values for the new feature set
Input:
@param model: The pretrained model
@features: A list of features to use in the model prediction (list of column names)
@target_query: The query to run to obtain the data to predict on and the cartdb_ids associated with it.
"""
batch_size = 1000
joined_features = ','.join(['"{0}"::numeric'.format(a) for a in features])
try:
cursor = plpy.cursor('SELECT Array[{joined_features}] As features FROM ({target_query}) As a'.format(
joined_features=joined_features,
target_query=target_query))
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
results = []
while True:
rows = cursor.fetch(batch_size)
if not rows:
break
batch = np.row_stack([np.array(row['features'], dtype=float) for row in rows])
#Need to fix this. Should be global mean. This will cause weird effects
batch = replace_nan_with_mean(batch)
prediction = model.predict(batch)
results.append(prediction)
try:
cartodb_ids = plpy.execute('''SELECT array_agg(cartodb_id ORDER BY cartodb_id) As cartodb_ids FROM ({0}) As a'''.format(target_query))[0]['cartodb_ids']
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
return cartodb_ids, np.concatenate(results)

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"""Import all functions from clustering libraries."""
from markov import *

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"""
Spatial dynamics measurements using Spatial Markov
"""
import numpy as np
import pysal as ps
import plpy
import crankshaft.pysal_utils as pu
def spatial_markov_trend(subquery, time_cols, num_classes=7,
w_type='knn', num_ngbrs=5, permutations=0,
geom_col='the_geom', id_col='cartodb_id'):
"""
Predict the trends of a unit based on:
1. history of its transitions to different classes (e.g., 1st quantile -> 2nd quantile)
2. average class of its neighbors
Inputs:
@param subquery string: e.g., SELECT the_geom, cartodb_id,
interesting_time_column FROM table_name
@param time_cols list of strings: list of strings of column names
@param num_classes (optional): number of classes to break distribution
of values into. Currently uses quantile bins.
@param w_type string (optional): weight type ('knn' or 'queen')
@param num_ngbrs int (optional): number of neighbors (if knn type)
@param permutations int (optional): number of permutations for test
stats
@param geom_col string (optional): name of column which contains the
geometries
@param id_col string (optional): name of column which has the ids of
the table
Outputs:
@param trend_up float: probablity that a geom will move to a higher
class
@param trend_down float: probablity that a geom will move to a lower
class
@param trend float: (trend_up - trend_down) / trend_static
@param volatility float: a measure of the volatility based on
probability stddev(prob array)
"""
if len(time_cols) < 2:
plpy.error('More than one time column needs to be passed')
qvals = {"id_col": id_col,
"time_cols": time_cols,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs}
try:
query_result = plpy.execute(
pu.construct_neighbor_query(w_type, qvals)
)
if len(query_result) == 0:
return zip([None], [None], [None], [None], [None])
except plpy.SPIError, e:
plpy.debug('Query failed with exception %s: %s' % (err, pu.construct_neighbor_query(w_type, qvals)))
plpy.error('Analysis failed: %s' % e)
return zip([None], [None], [None], [None], [None])
## build weight
weights = pu.get_weight(query_result, w_type)
weights.transform = 'r'
## prep time data
t_data = get_time_data(query_result, time_cols)
plpy.debug('shape of t_data %d, %d' % t_data.shape)
plpy.debug('number of weight objects: %d, %d' % (weights.sparse).shape)
plpy.debug('first num elements: %f' % t_data[0, 0])
sp_markov_result = ps.Spatial_Markov(t_data,
weights,
k=num_classes,
fixed=False,
permutations=permutations)
## get lag classes
lag_classes = ps.Quantiles(
ps.lag_spatial(weights, t_data[:, -1]),
k=num_classes).yb
## look up probablity distribution for each unit according to class and lag class
prob_dist = get_prob_dist(sp_markov_result.P,
lag_classes,
sp_markov_result.classes[:, -1])
## find the ups and down and overall distribution of each cell
trend_up, trend_down, trend, volatility = get_prob_stats(prob_dist,
sp_markov_result.classes[:, -1])
## output the results
return zip(trend, trend_up, trend_down, volatility, weights.id_order)
def get_time_data(markov_data, time_cols):
"""
Extract the time columns and bin appropriately
"""
num_attrs = len(time_cols)
return np.array([[x['attr' + str(i)] for x in markov_data]
for i in range(1, num_attrs+1)], dtype=float).transpose()
## not currently used
def rebin_data(time_data, num_time_per_bin):
"""
Convert an n x l matrix into an (n/m) x l matrix where the values are
reduced (averaged) for the intervening states:
1 2 3 4 1.5 3.5
5 6 7 8 -> 5.5 7.5
9 8 7 6 8.5 6.5
5 4 3 2 4.5 2.5
if m = 2, the 4 x 4 matrix is transformed to a 2 x 4 matrix.
This process effectively resamples the data at a longer time span n
units longer than the input data.
For cases when there is a remainder (remainder(5/3) = 2), the remaining
two columns are binned together as the last time period, while the
first three are binned together for the first period.
Input:
@param time_data n x l ndarray: measurements of an attribute at
different time intervals
@param num_time_per_bin int: number of columns to average into a new
column
Output:
ceil(n / m) x l ndarray of resampled time series
"""
if time_data.shape[1] % num_time_per_bin == 0:
## if fit is perfect, then use it
n_max = time_data.shape[1] / num_time_per_bin
else:
## fit remainders into an additional column
n_max = time_data.shape[1] / num_time_per_bin + 1
return np.array([time_data[:, num_time_per_bin * i:num_time_per_bin * (i+1)].mean(axis=1)
for i in range(n_max)]).T
def get_prob_dist(transition_matrix, lag_indices, unit_indices):
"""
Given an array of transition matrices, look up the probability
associated with the arrangements passed
Input:
@param transition_matrix ndarray[k,k,k]:
@param lag_indices ndarray:
@param unit_indices ndarray:
Output:
Array of probability distributions
"""
return np.array([transition_matrix[(lag_indices[i], unit_indices[i])]
for i in range(len(lag_indices))])
def get_prob_stats(prob_dist, unit_indices):
"""
get the statistics of the probability distributions
Outputs:
@param trend_up ndarray(float): sum of probabilities for upward
movement (relative to the unit index of that prob)
@param trend_down ndarray(float): sum of probabilities for downward
movement (relative to the unit index of that prob)
@param trend ndarray(float): difference of upward and downward
movements
"""
num_elements = len(unit_indices)
trend_up = np.empty(num_elements, dtype=float)
trend_down = np.empty(num_elements, dtype=float)
trend = np.empty(num_elements, dtype=float)
for i in range(num_elements):
trend_up[i] = prob_dist[i, (unit_indices[i]+1):].sum()
trend_down[i] = prob_dist[i, :unit_indices[i]].sum()
if prob_dist[i, unit_indices[i]] > 0.0:
trend[i] = (trend_up[i] - trend_down[i]) / prob_dist[i, unit_indices[i]]
else:
trend[i] = None
## calculate volatility of distribution
volatility = prob_dist.std(axis=1)
return trend_up, trend_down, trend, volatility

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"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.0',
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.
# IMPORTANT NOTE: please don't change this line. Instead issue a ticket to systems for evaluation.
install_requires=['joblib==0.8.3', 'numpy==1.6.1', 'scipy==0.14.0', 'pysal==1.11.2', 'scikit-learn==0.14.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

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"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.0',
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.
# IMPORTANT NOTE: please don't change this line. Instead issue a ticket to systems for evaluation.
install_requires=['joblib==0.8.3', 'numpy==1.6.1', 'scipy==0.14.0', 'pysal==1.11.2', 'scikit-learn==0.14.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

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[[0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 0], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 1], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 2], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 3], [0.0, 0.065217391304347824, 0.065217391304347824, 0.33605067580764519, 4], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 5], [0.1875, 0.23999999999999999, 0.12, 0.23731835158706122, 6], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 7], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 8], [0.19047619047619049, 0.16, 0.0, 0.32594478059941379, 9], [-0.23529411764705882, 0.0, 0.19047619047619047, 0.31356338348865387, 10], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 11], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 12], [0.027777777777777783, 0.11111111111111112, 0.088888888888888892, 0.30339641183779581, 13], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 14], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 15], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 16], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 17], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 18], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 19], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 20], [0.078947368421052641, 0.073170731707317083, 0.0, 0.36451788667842738, 21], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 22], [-0.16666666666666663, 0.18181818181818182, 0.27272727272727271, 0.20246415864836445, 23], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 24], [0.1875, 0.23999999999999999, 0.12, 0.23731835158706122, 25], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 26], [-0.043478260869565216, 0.0, 0.041666666666666664, 0.37950991789118999, 27], [0.22222222222222221, 0.18181818181818182, 0.0, 0.31701083225750354, 28], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 29], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 30], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 31], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 32], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 33], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 34], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 35], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 36], [0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 37], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 38], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 39], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 40], [0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 41], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 42], [0.0, 0.0, 0.0, 0.40000000000000002, 43], [0.0, 0.065217391304347824, 0.065217391304347824, 0.33605067580764519, 44], [0.078947368421052641, 0.073170731707317083, 0.0, 0.36451788667842738, 45], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 46], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 47]]

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[[0.9319096128346788, "HH"],
[-1.135787401862846, "HL"],
[0.11732030672508517, "LL"],
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[1.0223932668429925, "LL"],
[1.4179402898927476, "LL"]]

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[
{"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},
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{"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}
]

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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)

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import re
class MockCursor:
def __init__(self, data):
self.cursor_pos = 0
self.data = data
def fetch(self, batch_size):
batch = self.data[self.cursor_pos : self.cursor_pos + batch_size]
self.cursor_pos += batch_size
return batch
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 debug(self, msg):
self.notices.append(msg)
def info(self, msg):
self.infos.append(msg)
def cursor(self, query):
data = self.execute(query)
return MockCursor(data)
def execute(self, query): # TODO: additional arguments
for result in self.results:
if result[0].match(query):
return result[1]
return []

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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)

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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.params_markov = {"id_col": "cartodb_id",
"time_cols": ["_2013_dec", "_2014_jan", "_2014_feb"],
"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)

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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}
self.params_array = {"id_col": "cartodb_id",
"time_cols": ["_2013_dec", "_2014_jan", "_2014_feb"],
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
def test_query_attr_select(self):
"""Test query_attr_select"""
ans = "i.\"andy\"::numeric As attr1, " \
"i.\"jay_z\"::numeric As attr2, "
ans_array = "i.\"_2013_dec\"::numeric As attr1, " \
"i.\"_2014_jan\"::numeric As attr2, " \
"i.\"_2014_feb\"::numeric As attr3, "
self.assertEqual(pu.query_attr_select(self.params), ans)
self.assertEqual(pu.query_attr_select(self.params_array), ans_array)
def test_query_attr_where(self):
"""Test pu.query_attr_where"""
ans = "idx_replace.\"andy\" IS NOT NULL AND " \
"idx_replace.\"jay_z\" IS NOT NULL AND " \
"idx_replace.\"jay_z\" <> 0"
ans_array = "idx_replace.\"_2013_dec\" IS NOT NULL AND " \
"idx_replace.\"_2014_jan\" IS NOT NULL AND " \
"idx_replace.\"_2014_feb\" IS NOT NULL"
self.assertEqual(pu.query_attr_where(self.params), ans)
self.assertEqual(pu.query_attr_where(self.params_array), ans_array)
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;"
ans_array = "SELECT i.\"cartodb_id\" As id, " \
"i.\"_2013_dec\"::numeric As attr1, " \
"i.\"_2014_jan\"::numeric As attr2, " \
"i.\"_2014_feb\"::numeric As attr3, " \
"(SELECT ARRAY(SELECT j.\"cartodb_id\" " \
"FROM (SELECT * FROM a_list) As j " \
"WHERE i.\"cartodb_id\" <> j.\"cartodb_id\" AND " \
"j.\"_2013_dec\" IS NOT NULL AND " \
"j.\"_2014_jan\" IS NOT NULL AND " \
"j.\"_2014_feb\" IS NOT NULL " \
"ORDER BY j.\"the_geom\" <-> i.\"the_geom\" ASC " \
"LIMIT 321)) As neighbors " \
"FROM (SELECT * FROM a_list) As i " \
"WHERE i.\"_2013_dec\" IS NOT NULL AND " \
"i.\"_2014_jan\" IS NOT NULL AND " \
"i.\"_2014_feb\" IS NOT NULL "\
"ORDER BY i.\"cartodb_id\" ASC;"
self.assertEqual(pu.knn(self.params), ans)
self.assertEqual(pu.knn(self.params_array), ans_array)
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)

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import unittest
import numpy as np
from helper import plpy, fixture_file
import crankshaft.segmentation as segmentation
import json
class SegmentationTest(unittest.TestCase):
"""Testing class for Moran's I functions"""
def setUp(self):
plpy._reset()
def generate_random_data(self,n_samples,random_state, row_type=False):
x1 = random_state.uniform(size=n_samples)
x2 = random_state.uniform(size=n_samples)
x3 = random_state.randint(0, 4, size=n_samples)
y = x1+x2*x2+x3
cartodb_id = range(len(x1))
if row_type:
return [ {'features': vals} for vals in zip(x1,x2,x3)], y
else:
return [dict( zip(['x1','x2','x3','target', 'cartodb_id'],[x1,x2,x3,y,cartodb_id]))]
def test_replace_nan_with_mean(self):
test_array = np.array([1.2, np.nan, 3.2, np.nan, np.nan])
def test_create_and_predict_segment(self):
n_samples = 1000
random_state_train = np.random.RandomState(13)
random_state_test = np.random.RandomState(134)
training_data = self.generate_random_data(n_samples, random_state_train)
test_data, test_y = self.generate_random_data(n_samples, random_state_test, row_type=True)
ids = [{'cartodb_ids': range(len(test_data))}]
rows = [{'x1': 0,'x2':0,'x3':0,'y':0,'cartodb_id':0}]
plpy._define_result('select \* from \(select \* from training\) a limit 1',rows)
plpy._define_result('.*from \(select \* from training\) as a' ,training_data)
plpy._define_result('select array_agg\(cartodb\_id order by cartodb\_id\) as cartodb_ids from \(.*\) a',ids)
plpy._define_result('.*select \* from test.*' ,test_data)
model_parameters = {'n_estimators': 1200,
'max_depth': 3,
'subsample' : 0.5,
'learning_rate': 0.01,
'min_samples_leaf': 1}
result = segmentation.create_and_predict_segment(
'select * from training',
'target',
'select * from test',
model_parameters)
prediction = [r[1] for r in result]
accuracy =np.sqrt(np.mean( np.square( np.array(prediction) - np.array(test_y))))
self.assertEqual(len(result),len(test_data))
self.assertTrue( result[0][2] < 0.01)
self.assertTrue( accuracy < 0.5*np.mean(test_y) )

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import unittest
import numpy as np
import unittest
# from mock_plpy import MockPlPy
# plpy = MockPlPy()
#
# import sys
# sys.modules['plpy'] = plpy
from helper import plpy, fixture_file
import crankshaft.space_time_dynamics as std
from crankshaft import random_seeds
import json
class SpaceTimeTests(unittest.TestCase):
"""Testing class for Markov Functions."""
def setUp(self):
plpy._reset()
self.params = {"id_col": "cartodb_id",
"time_cols": ['dec_2013', 'jan_2014', 'feb_2014'],
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
self.neighbors_data = json.loads(open(fixture_file('neighbors_markov.json')).read())
self.markov_data = json.loads(open(fixture_file('markov.json')).read())
self.time_data = np.array([i * np.ones(10, dtype=float) for i in range(10)]).T
self.transition_matrix = np.array([
[[ 0.96341463, 0.0304878 , 0.00609756, 0. , 0. ],
[ 0.06040268, 0.83221477, 0.10738255, 0. , 0. ],
[ 0. , 0.14 , 0.74 , 0.12 , 0. ],
[ 0. , 0.03571429, 0.32142857, 0.57142857, 0.07142857],
[ 0. , 0. , 0. , 0.16666667, 0.83333333]],
[[ 0.79831933, 0.16806723, 0.03361345, 0. , 0. ],
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0.00537634, 0.06989247, 0.8655914 , 0.05913978, 0. ],
[ 0. , 0. , 0.06372549, 0.90196078, 0.03431373],
[ 0. , 0. , 0. , 0.19444444, 0.80555556]],
[[ 0.84693878, 0.15306122, 0. , 0. , 0. ],
[ 0.08133971, 0.78947368, 0.1291866 , 0. , 0. ],
[ 0.00518135, 0.0984456 , 0.79274611, 0.0984456 , 0.00518135],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0. , 0. , 0. , 0.10204082, 0.89795918]],
[[ 0.8852459 , 0.09836066, 0. , 0.01639344, 0. ],
[ 0.03875969, 0.81395349, 0.13953488, 0. , 0.00775194],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0.02339181, 0.12865497, 0.75438596, 0.09356725],
[ 0. , 0. , 0. , 0.09661836, 0.90338164]],
[[ 0.33333333, 0.66666667, 0. , 0. , 0. ],
[ 0.0483871 , 0.77419355, 0.16129032, 0.01612903, 0. ],
[ 0.01149425, 0.16091954, 0.74712644, 0.08045977, 0. ],
[ 0. , 0.01036269, 0.06217617, 0.89637306, 0.03108808],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]]]
)
def test_spatial_markov(self):
"""Test Spatial Markov."""
data = [ { 'id': d['id'],
'attr1': d['y1995'],
'attr2': d['y1996'],
'attr3': d['y1997'],
'attr4': d['y1998'],
'attr5': d['y1999'],
'attr6': d['y2000'],
'attr7': d['y2001'],
'attr8': d['y2002'],
'attr9': d['y2003'],
'attr10': d['y2004'],
'attr11': d['y2005'],
'attr12': d['y2006'],
'attr13': d['y2007'],
'attr14': d['y2008'],
'attr15': d['y2009'],
'neighbors': d['neighbors'] } for d in self.neighbors_data]
print(str(data[0]))
plpy._define_result('select', data)
random_seeds.set_random_seeds(1234)
result = std.spatial_markov_trend('subquery', ['y1995', 'y1996', 'y1997', 'y1998', 'y1999', 'y2000', 'y2001', 'y2002', 'y2003', 'y2004', 'y2005', 'y2006', 'y2007', 'y2008', 'y2009'], 5, 'knn', 5, 0, 'the_geom', 'cartodb_id')
self.assertTrue(result != None)
result = [(row[0], row[1], row[2], row[3], row[4]) for row in result]
print result[0]
expected = self.markov_data
for ([res_trend, res_up, res_down, res_vol, res_id],
[exp_trend, exp_up, exp_down, exp_vol, exp_id]
) in zip(result, expected):
self.assertAlmostEqual(res_trend, exp_trend)
def test_get_time_data(self):
"""Test get_time_data"""
data = [ { 'attr1': d['y1995'],
'attr2': d['y1996'],
'attr3': d['y1997'],
'attr4': d['y1998'],
'attr5': d['y1999'],
'attr6': d['y2000'],
'attr7': d['y2001'],
'attr8': d['y2002'],
'attr9': d['y2003'],
'attr10': d['y2004'],
'attr11': d['y2005'],
'attr12': d['y2006'],
'attr13': d['y2007'],
'attr14': d['y2008'],
'attr15': d['y2009'] } for d in self.neighbors_data]
result = std.get_time_data(data, ['y1995', 'y1996', 'y1997', 'y1998', 'y1999', 'y2000', 'y2001', 'y2002', 'y2003', 'y2004', 'y2005', 'y2006', 'y2007', 'y2008', 'y2009'])
## expected was prepared from PySAL example:
### f = ps.open(ps.examples.get_path("usjoin.csv"))
### pci = np.array([f.by_col[str(y)] for y in range(1995, 2010)]).transpose()
### rpci = pci / (pci.mean(axis = 0))
expected = np.array([[ 0.87654416, 0.863147, 0.85637567, 0.84811668, 0.8446154, 0.83271652
, 0.83786314, 0.85012593, 0.85509656, 0.86416612, 0.87119375, 0.86302631
, 0.86148267, 0.86252252, 0.86746356],
[ 0.9188951, 0.91757931, 0.92333258, 0.92517289, 0.92552388, 0.90746978
, 0.89830489, 0.89431991, 0.88924794, 0.89815176, 0.91832091, 0.91706054
, 0.90139505, 0.87897455, 0.86216858],
[ 0.82591007, 0.82548596, 0.81989793, 0.81503235, 0.81731522, 0.78964559
, 0.80584442, 0.8084998, 0.82258551, 0.82668196, 0.82373724, 0.81814804
, 0.83675961, 0.83574199, 0.84647177],
[ 1.09088176, 1.08537689, 1.08456418, 1.08415404, 1.09898841, 1.14506948
, 1.12151133, 1.11160697, 1.10888621, 1.11399806, 1.12168029, 1.13164797
, 1.12958508, 1.11371818, 1.09936775],
[ 1.10731446, 1.11373944, 1.13283638, 1.14472559, 1.15910025, 1.16898201
, 1.17212488, 1.14752303, 1.11843284, 1.11024964, 1.11943471, 1.11736468
, 1.10863242, 1.09642516, 1.07762337],
[ 1.42269757, 1.42118434, 1.44273502, 1.43577571, 1.44400684, 1.44184737
, 1.44782832, 1.41978227, 1.39092208, 1.4059372, 1.40788646, 1.44052766
, 1.45241216, 1.43306098, 1.4174431 ],
[ 1.13073885, 1.13110513, 1.11074708, 1.13364636, 1.13088149, 1.10888138
, 1.11856629, 1.13062931, 1.11944984, 1.12446239, 1.11671008, 1.10880034
, 1.08401709, 1.06959206, 1.07875225],
[ 1.04706124, 1.04516831, 1.04253372, 1.03239987, 1.02072545, 0.99854316
, 0.9880258, 0.99669587, 0.99327676, 1.01400905, 1.03176742, 1.040511
, 1.01749645, 0.9936394, 0.98279746],
[ 0.98996986, 1.00143564, 0.99491, 1.00188408, 1.00455845, 0.99127006
, 0.97925917, 0.9683482, 0.95335147, 0.93694787, 0.94308213, 0.92232874
, 0.91284091, 0.89689833, 0.88928858],
[ 0.87418391, 0.86416601, 0.84425695, 0.8404494, 0.83903044, 0.8578708
, 0.86036185, 0.86107306, 0.8500772, 0.86981998, 0.86837929, 0.87204141
, 0.86633032, 0.84946077, 0.83287146],
[ 1.14196118, 1.14660262, 1.14892712, 1.14909594, 1.14436624, 1.14450183
, 1.12349752, 1.12596664, 1.12213996, 1.1119989, 1.10257792, 1.10491258
, 1.11059842, 1.10509795, 1.10020097],
[ 0.97282463, 0.96700147, 0.96252588, 0.9653878, 0.96057687, 0.95831051
, 0.94480909, 0.94804195, 0.95430286, 0.94103989, 0.92122519, 0.91010201
, 0.89280392, 0.89298243, 0.89165385],
[ 0.94325468, 0.96436902, 0.96455242, 0.95243009, 0.94117647, 0.9480927
, 0.93539182, 0.95388718, 0.94597005, 0.96918424, 0.94781281, 0.93466815
, 0.94281559, 0.96520315, 0.96715441],
[ 0.97478408, 0.98169225, 0.98712809, 0.98474769, 0.98559897, 0.98687073
, 0.99237486, 0.98209969, 0.9877653, 0.97399471, 0.96910087, 0.98416665
, 0.98423613, 0.99823861, 0.99545704],
[ 0.85570269, 0.85575915, 0.85986132, 0.85693406, 0.8538012, 0.86191535
, 0.84981451, 0.85472102, 0.84564835, 0.83998883, 0.83478547, 0.82803648
, 0.8198736, 0.82265395, 0.8399404 ],
[ 0.87022047, 0.85996258, 0.85961813, 0.85689572, 0.83947136, 0.82785597
, 0.86008789, 0.86776298, 0.86720209, 0.8676334, 0.89179317, 0.94202108
, 0.9422231, 0.93902708, 0.94479184],
[ 0.90134907, 0.90407738, 0.90403991, 0.90201769, 0.90399238, 0.90906632
, 0.92693339, 0.93695966, 0.94242697, 0.94338265, 0.91981796, 0.91108804
, 0.90543476, 0.91737138, 0.94793657],
[ 1.1977611, 1.18222564, 1.18439158, 1.18267865, 1.19286723, 1.20172869
, 1.21328691, 1.22624778, 1.22397075, 1.23857042, 1.24419893, 1.23929384
, 1.23418676, 1.23626739, 1.26754398],
[ 1.24919678, 1.25754773, 1.26991161, 1.28020651, 1.30625667, 1.34790023
, 1.34399863, 1.32575181, 1.30795492, 1.30544841, 1.30303302, 1.32107766
, 1.32936244, 1.33001241, 1.33288462],
[ 1.06768004, 1.03799276, 1.03637303, 1.02768449, 1.03296093, 1.05059016
, 1.03405057, 1.02747623, 1.03162734, 0.9961416, 0.97356208, 0.94241549
, 0.92754547, 0.92549227, 0.92138102],
[ 1.09475614, 1.11526796, 1.11654299, 1.13103948, 1.13143264, 1.13889622
, 1.12442212, 1.13367018, 1.13982256, 1.14029944, 1.11979401, 1.10905389
, 1.10577769, 1.11166825, 1.09985155],
[ 0.76530058, 0.76612841, 0.76542451, 0.76722683, 0.76014284, 0.74480073
, 0.76098396, 0.76156903, 0.76651952, 0.76533288, 0.78205934, 0.76842416
, 0.77487118, 0.77768683, 0.78801192],
[ 0.98391336, 0.98075816, 0.98295341, 0.97386015, 0.96913803, 0.97370819
, 0.96419154, 0.97209861, 0.97441313, 0.96356162, 0.94745352, 0.93965462
, 0.93069645, 0.94020973, 0.94358232],
[ 0.83561828, 0.82298088, 0.81738502, 0.81748588, 0.80904801, 0.80071489
, 0.83358256, 0.83451613, 0.85175032, 0.85954307, 0.86790024, 0.87170334
, 0.87863799, 0.87497981, 0.87888675],
[ 0.98845573, 1.02092428, 0.99665283, 0.99141823, 0.99386619, 0.98733195
, 0.99644997, 0.99669587, 1.02559097, 1.01116651, 0.99988024, 0.97906749
, 0.99323123, 1.00204939, 0.99602148],
[ 1.14930913, 1.15241949, 1.14300962, 1.14265542, 1.13984683, 1.08312397
, 1.05192626, 1.04230892, 1.05577278, 1.08569751, 1.12443486, 1.08891079
, 1.08603695, 1.05997314, 1.02160943],
[ 1.11368269, 1.1057147, 1.11893431, 1.13778669, 1.1432272, 1.18257029
, 1.16226243, 1.16009196, 1.14467789, 1.14820235, 1.12386598, 1.12680236
, 1.12357937, 1.1159258, 1.12570828],
[ 1.30379431, 1.30752186, 1.31206366, 1.31532267, 1.30625667, 1.31210239
, 1.29989156, 1.29203193, 1.27183516, 1.26830786, 1.2617743, 1.28656675
, 1.29734097, 1.29390205, 1.29345446],
[ 0.83953719, 0.82701448, 0.82006005, 0.81188876, 0.80294864, 0.78772975
, 0.82848011, 0.8259679, 0.82435705, 0.83108634, 0.84373784, 0.83891093
, 0.84349247, 0.85637272, 0.86539395],
[ 1.23450087, 1.2426022, 1.23537935, 1.23581293, 1.24522626, 1.2256767
, 1.21126648, 1.19377804, 1.18355337, 1.19674434, 1.21536573, 1.23653297
, 1.27962009, 1.27968392, 1.25907738],
[ 0.9769662, 0.97400719, 0.98035944, 0.97581531, 0.95543282, 0.96480308
, 0.94686376, 0.93679073, 0.92540049, 0.92988835, 0.93442917, 0.92100464
, 0.91475304, 0.90249622, 0.9021363 ],
[ 0.84986886, 0.8986851, 0.84295997, 0.87280534, 0.85659368, 0.88937573
, 0.894401, 0.90448993, 0.95495898, 0.92698333, 0.94745352, 0.92562488
, 0.96635366, 1.02520312, 1.0394296 ],
[ 1.01922808, 1.00258203, 1.00974428, 1.00303417, 0.99765073, 1.00759019
, 0.99192968, 0.99747298, 0.99550759, 0.97583768, 0.9610168, 0.94779638
, 0.93759089, 0.93353431, 0.94121705],
[ 0.86367411, 0.85558932, 0.85544346, 0.85103025, 0.84336613, 0.83434854
, 0.85813595, 0.84667961, 0.84374558, 0.85951183, 0.87194227, 0.89455097
, 0.88283929, 0.90349491, 0.90600675],
[ 1.00947534, 1.00411055, 1.00698819, 0.99513687, 0.99291086, 1.00581626
, 0.98850522, 0.99291168, 0.98983209, 0.97511924, 0.96134615, 0.96382634
, 0.95011401, 0.9434686, 0.94637765],
[ 1.05712571, 1.05459419, 1.05753012, 1.04880786, 1.05103857, 1.04800023
, 1.03024941, 1.04200483, 1.0402554, 1.03296979, 1.02191682, 1.02476275
, 1.02347523, 1.02517684, 1.04359571],
[ 1.07084189, 1.06669497, 1.07937623, 1.07387988, 1.0794043, 1.0531801
, 1.07452771, 1.09383478, 1.1052447, 1.10322136, 1.09167939, 1.08772756
, 1.08859544, 1.09177338, 1.1096083 ],
[ 0.86719222, 0.86628896, 0.86675156, 0.86425632, 0.86511809, 0.86287327
, 0.85169796, 0.85411285, 0.84886336, 0.84517414, 0.84843858, 0.84488343
, 0.83374329, 0.82812044, 0.82878599],
[ 0.88389211, 0.92288667, 0.90282398, 0.91229186, 0.92023286, 0.92652175
, 0.94278865, 0.93682452, 0.98655146, 0.992237, 0.9798497, 0.93869677
, 0.96947771, 1.00362626, 0.98102351],
[ 0.97082064, 0.95320233, 0.94534081, 0.94215593, 0.93967, 0.93092109
, 0.92662519, 0.93412152, 0.93501274, 0.92879506, 0.92110542, 0.91035556
, 0.90430364, 0.89994694, 0.90073864],
[ 0.95861858, 0.95774543, 0.98254811, 0.98919472, 0.98684824, 0.98882205
, 0.97662234, 0.95601578, 0.94905385, 0.94934888, 0.97152609, 0.97163004
, 0.9700702, 0.97158948, 0.95884908],
[ 0.83980439, 0.84726737, 0.85747, 0.85467221, 0.8556751, 0.84818516
, 0.85265681, 0.84502402, 0.82645665, 0.81743586, 0.83550406, 0.83338919
, 0.83511679, 0.82136617, 0.80921874],
[ 0.95118156, 0.9466212, 0.94688098, 0.9508583, 0.9512441, 0.95440787
, 0.96364363, 0.96804412, 0.97136214, 0.97583768, 0.95571724, 0.96895368
, 0.97001634, 0.97082733, 0.98782366],
[ 1.08910044, 1.08248968, 1.08492895, 1.08656923, 1.09454249, 1.10558188
, 1.1214086, 1.12292577, 1.13021031, 1.13342735, 1.14686068, 1.14502975
, 1.14474747, 1.14084037, 1.16142926],
[ 1.06336033, 1.07365823, 1.08691496, 1.09764846, 1.11669863, 1.11856702
, 1.09764283, 1.08815849, 1.08044313, 1.09278827, 1.07003204, 1.08398066
, 1.09831768, 1.09298232, 1.09176125],
[ 0.79772065, 0.78829196, 0.78581151, 0.77615922, 0.77035744, 0.77751194
, 0.79902974, 0.81437881, 0.80788828, 0.79603865, 0.78966436, 0.79949807
, 0.80172182, 0.82168155, 0.85587911],
[ 1.0052447, 1.00007696, 1.00475899, 1.00613942, 1.00639561, 1.00162979
, 0.99860739, 1.00814981, 1.00574316, 0.99030032, 0.97682565, 0.97292596
, 0.96519561, 0.96173403, 0.95890284],
[ 0.95808419, 0.9382568, 0.9654441, 0.95561201, 0.96987289, 0.96608031
, 0.99727185, 1.00781194, 1.03484236, 1.05333619, 1.0983263, 1.1704974
, 1.17025154, 1.18730553, 1.14242645]])
self.assertTrue(np.allclose(result, expected))
self.assertTrue(type(result) == type(expected))
self.assertTrue(result.shape == expected.shape)
def test_rebin_data(self):
"""Test rebin_data"""
## sample in double the time (even case since 10 % 2 = 0):
## (0+1)/2, (2+3)/2, (4+5)/2, (6+7)/2, (8+9)/2
## = 0.5, 2.5, 4.5, 6.5, 8.5
ans_even = np.array([(i + 0.5) * np.ones(10, dtype=float)
for i in range(0, 10, 2)]).T
self.assertTrue(np.array_equal(std.rebin_data(self.time_data, 2), ans_even))
## sample in triple the time (uneven since 10 % 3 = 1):
## (0+1+2)/3, (3+4+5)/3, (6+7+8)/3, (9)/1
## = 1, 4, 7, 9
ans_odd = np.array([i * np.ones(10, dtype=float)
for i in (1, 4, 7, 9)]).T
self.assertTrue(np.array_equal(std.rebin_data(self.time_data, 3), ans_odd))
def test_get_prob_dist(self):
"""Test get_prob_dist"""
lag_indices = np.array([1, 2, 3, 4])
unit_indices = np.array([1, 3, 2, 4])
answer = np.array([
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]
])
result = std.get_prob_dist(self.transition_matrix, lag_indices, unit_indices)
self.assertTrue(np.array_equal(result, answer))
def test_get_prob_stats(self):
"""Test get_prob_stats"""
probs = np.array([
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]
])
unit_indices = np.array([1, 3, 2, 4])
answer_up = np.array([0.04245283, 0.03529412, 0.12376238, 0.])
answer_down = np.array([0.0754717, 0.09411765, 0.0990099, 0.02352941])
answer_trend = np.array([-0.03301887 / 0.88207547, -0.05882353 / 0.87058824, 0.02475248 / 0.77722772, -0.02352941 / 0.97647059])
answer_volatility = np.array([ 0.34221495, 0.33705421, 0.29226542, 0.38834223])
result = std.get_prob_stats(probs, unit_indices)
result_up = result[0]
result_down = result[1]
result_trend = result[2]
result_volatility = result[3]
self.assertTrue(np.allclose(result_up, answer_up))
self.assertTrue(np.allclose(result_down, answer_down))
self.assertTrue(np.allclose(result_trend, answer_trend))
self.assertTrue(np.allclose(result_volatility, answer_volatility))

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"""Import all modules"""
import crankshaft.random_seeds
import crankshaft.clustering
import crankshaft.space_time_dynamics
import crankshaft.segmentation

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"""Import all functions from for clustering"""
from moran import *
from kmeans import *

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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)

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"""
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
from collections import OrderedDict
# 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 = OrderedDict([("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)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(2)
except plpy.SPIError, e:
plpy.error('Analysis failed: %s' % e)
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 = OrderedDict([("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, e:
plpy.error('Analysis failed: %s' % e)
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 = OrderedDict([("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)
try:
result = plpy.execute(query)
# if there are no neighbors, exit
if len(result) == 0:
return pu.empty_zipped_array(2)
except plpy.SPIError, e:
plpy.error('Analysis failed: %s' % e)
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
qvals = OrderedDict([("id_col", id_col),
("numerator", numerator),
("denominator", denominator),
("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, e:
plpy.error('Analysis failed: %s' % e)
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 quadrants for each geometry
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)
"""
qvals = OrderedDict([("id_col", id_col),
("attr1", attr1),
("attr2", attr2),
("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(4)
except plpy.SPIError:
plpy.error("Error: areas of interest query failed, "
"check input parameters")
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)
# find clustering of significance
lisa_sig = quad_position(lisa.q)
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]

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"""Import all functions for pysal_utils"""
from crankshaft.pysal_utils.pysal_utils import *

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"""
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 dict-like: 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}
print 'len of neighbors: %d' % len(neighbors)
built_weight = ps.W(neighbors)
built_weight.transform = 'r'
return built_weight
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.)
"""
attr_string = ""
template = "i.\"%(col)s\"::numeric As attr%(alias_num)s, "
if 'time_cols' in params:
# if markov analysis
attrs = params['time_cols']
for idx, val in enumerate(attrs):
attr_string += template % {"col": val, "alias_num": idx + 1}
else:
# if moran's analysis
attrs = [k for k in params
if k not in ('id_col', 'geom_col', 'subquery',
'num_ngbrs', 'subquery')]
for idx, val in enumerate(sorted(attrs)):
attr_string += template % {"col": params[val],
"alias_num": idx + 1}
return attr_string
def query_attr_where(params):
"""
Construct where conditions when building neighbors query
Create portion of WHERE clauses for weeding out NULL-valued geometries
Input: dict of params:
{'subquery': ...,
'numerator': 'data1',
'denominator': 'data2',
'': ...}
Output: 'idx_replace."data1" IS NOT NULL AND idx_replace."data2"
IS NOT NULL'
Input:
{'subquery': ...,
'time_cols': ['time1', 'time2', 'time3'],
'etc': ...}
Output: 'idx_replace."time1" IS NOT NULL AND idx_replace."time2" IS NOT
NULL AND idx_replace."time3" IS NOT NULL'
"""
attr_string = []
template = "idx_replace.\"%s\" IS NOT NULL"
if 'time_cols' in params:
# markov where clauses
attrs = params['time_cols']
# add values to template
for attr in attrs:
attr_string.append(template % attr)
else:
# moran where clauses
# get keys
attrs = sorted([k for k in params
if k not in ('id_col', 'geom_col', 'subquery',
'num_ngbrs', 'subquery')])
# add values to template
for attr in attrs:
attr_string.append(template % params[attr])
if len(attrs) == 2:
attr_string.append("idx_replace.\"%s\" <> 0" % params[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)]

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"""Random seed generator used for non-deterministic functions in crankshaft"""
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)

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from segmentation import *

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"""
Segmentation creation and prediction
"""
import sklearn
import numpy as np
import plpy
from sklearn.ensemble import GradientBoostingRegressor
from sklearn import metrics
from sklearn.cross_validation import train_test_split
# Lower level functions
#----------------------
def replace_nan_with_mean(array):
"""
Input:
@param array: an array of floats which may have null-valued entries
Output:
array with nans filled in with the mean of the dataset
"""
# returns an array of rows and column indices
indices = np.where(np.isnan(array))
# iterate through entries which have nan values
for row, col in zip(*indices):
array[row, col] = np.mean(array[~np.isnan(array[:, col]), col])
return array
def get_data(variable, feature_columns, query):
"""
Fetch data from the database, clean, and package into
numpy arrays
Input:
@param variable: name of the target variable
@param feature_columns: list of column names
@param query: subquery that data is pulled from for the packaging
Output:
prepared data, packaged into NumPy arrays
"""
columns = ','.join(['array_agg("{col}") As "{col}"'.format(col=col) for col in feature_columns])
try:
data = plpy.execute('''SELECT array_agg("{variable}") As target, {columns} FROM ({query}) As a'''.format(
variable=variable,
columns=columns,
query=query))
except Exception, e:
plpy.error('Failed to access data to build segmentation model: %s' % e)
# extract target data from plpy object
target = np.array(data[0]['target'])
# put n feature data arrays into an n x m array of arrays
features = np.column_stack([np.array(data[0][col], dtype=float) for col in feature_columns])
return replace_nan_with_mean(target), replace_nan_with_mean(features)
# High level interface
# --------------------
def create_and_predict_segment_agg(target, features, target_features, target_ids, model_parameters):
"""
Version of create_and_predict_segment that works on arrays that come stright form the SQL calling
the function.
Input:
@param target: The 1D array of lenth NSamples containing the target variable we want the model to predict
@param features: Thw 2D array of size NSamples * NFeatures that form the imput to the model
@param target_ids: A 1D array of target_ids that will be used to associate the results of the prediction with the rows which they come from
@param model_parameters: A dictionary containing parameters for the model.
"""
clean_target = replace_nan_with_mean(target)
clean_features = replace_nan_with_mean(features)
target_features = replace_nan_with_mean(target_features)
model, accuracy = train_model(clean_target, clean_features, model_parameters, 0.2)
prediction = model.predict(target_features)
accuracy_array = [accuracy]*prediction.shape[0]
return zip(target_ids, prediction, np.full(prediction.shape, accuracy_array))
def create_and_predict_segment(query, variable, target_query, model_params):
"""
generate a segment with machine learning
Stuart Lynn
"""
## fetch column names
try:
columns = plpy.execute('SELECT * FROM ({query}) As a LIMIT 1 '.format(query=query))[0].keys()
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
## extract column names to be used in building the segmentation model
feature_columns = set(columns) - set([variable, 'cartodb_id', 'the_geom', 'the_geom_webmercator'])
## get data from database
target, features = get_data(variable, feature_columns, query)
model, accuracy = train_model(target, features, model_params, 0.2)
cartodb_ids, result = predict_segment(model, feature_columns, target_query)
accuracy_array = [accuracy]*result.shape[0]
return zip(cartodb_ids, result, accuracy_array)
def train_model(target, features, model_params, test_split):
"""
Train the Gradient Boosting model on the provided data and calculate the accuracy of the model
Input:
@param target: 1D Array of the variable that the model is to be trianed to predict
@param features: 2D Array NSamples * NFeatures to use in trining the model
@param model_params: A dictionary of model parameters, the full specification can be found on the
scikit learn page for [GradientBoostingRegressor](http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.GradientBoostingRegressor.html)
@parma test_split: The fraction of the data to be withheld for testing the model / calculating the accuray
"""
features_train, features_test, target_train, target_test = train_test_split(features, target, test_size=test_split)
model = GradientBoostingRegressor(**model_params)
model.fit(features_train, target_train)
accuracy = calculate_model_accuracy(model, features, target)
return model, accuracy
def calculate_model_accuracy(model, features, target):
"""
Calculate the mean squared error of the model prediction
Input:
@param model: model trained from input features
@param features: features to make a prediction from
@param target: target to compare prediction to
Output:
mean squared error of the model prection compared to the target
"""
prediction = model.predict(features)
return metrics.mean_squared_error(prediction, target)
def predict_segment(model, features, target_query):
"""
Use the provided model to predict the values for the new feature set
Input:
@param model: The pretrained model
@features: A list of features to use in the model prediction (list of column names)
@target_query: The query to run to obtain the data to predict on and the cartdb_ids associated with it.
"""
batch_size = 1000
joined_features = ','.join(['"{0}"::numeric'.format(a) for a in features])
try:
cursor = plpy.cursor('SELECT Array[{joined_features}] As features FROM ({target_query}) As a'.format(
joined_features=joined_features,
target_query=target_query))
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
results = []
while True:
rows = cursor.fetch(batch_size)
if not rows:
break
batch = np.row_stack([np.array(row['features'], dtype=float) for row in rows])
#Need to fix this. Should be global mean. This will cause weird effects
batch = replace_nan_with_mean(batch)
prediction = model.predict(batch)
results.append(prediction)
try:
cartodb_ids = plpy.execute('''SELECT array_agg(cartodb_id ORDER BY cartodb_id) As cartodb_ids FROM ({0}) As a'''.format(target_query))[0]['cartodb_ids']
except Exception, e:
plpy.error('Failed to build segmentation model: %s' % e)
return cartodb_ids, np.concatenate(results)

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"""Import all functions from clustering libraries."""
from markov import *

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"""
Spatial dynamics measurements using Spatial Markov
"""
import numpy as np
import pysal as ps
import plpy
import crankshaft.pysal_utils as pu
def spatial_markov_trend(subquery, time_cols, num_classes=7,
w_type='knn', num_ngbrs=5, permutations=0,
geom_col='the_geom', id_col='cartodb_id'):
"""
Predict the trends of a unit based on:
1. history of its transitions to different classes (e.g., 1st quantile -> 2nd quantile)
2. average class of its neighbors
Inputs:
@param subquery string: e.g., SELECT the_geom, cartodb_id,
interesting_time_column FROM table_name
@param time_cols list of strings: list of strings of column names
@param num_classes (optional): number of classes to break distribution
of values into. Currently uses quantile bins.
@param w_type string (optional): weight type ('knn' or 'queen')
@param num_ngbrs int (optional): number of neighbors (if knn type)
@param permutations int (optional): number of permutations for test
stats
@param geom_col string (optional): name of column which contains the
geometries
@param id_col string (optional): name of column which has the ids of
the table
Outputs:
@param trend_up float: probablity that a geom will move to a higher
class
@param trend_down float: probablity that a geom will move to a lower
class
@param trend float: (trend_up - trend_down) / trend_static
@param volatility float: a measure of the volatility based on
probability stddev(prob array)
"""
if len(time_cols) < 2:
plpy.error('More than one time column needs to be passed')
qvals = {"id_col": id_col,
"time_cols": time_cols,
"geom_col": geom_col,
"subquery": subquery,
"num_ngbrs": num_ngbrs}
try:
query_result = plpy.execute(
pu.construct_neighbor_query(w_type, qvals)
)
if len(query_result) == 0:
return zip([None], [None], [None], [None], [None])
except plpy.SPIError, e:
plpy.debug('Query failed with exception %s: %s' % (err, pu.construct_neighbor_query(w_type, qvals)))
plpy.error('Analysis failed: %s' % e)
return zip([None], [None], [None], [None], [None])
## build weight
weights = pu.get_weight(query_result, w_type)
weights.transform = 'r'
## prep time data
t_data = get_time_data(query_result, time_cols)
plpy.debug('shape of t_data %d, %d' % t_data.shape)
plpy.debug('number of weight objects: %d, %d' % (weights.sparse).shape)
plpy.debug('first num elements: %f' % t_data[0, 0])
sp_markov_result = ps.Spatial_Markov(t_data,
weights,
k=num_classes,
fixed=False,
permutations=permutations)
## get lag classes
lag_classes = ps.Quantiles(
ps.lag_spatial(weights, t_data[:, -1]),
k=num_classes).yb
## look up probablity distribution for each unit according to class and lag class
prob_dist = get_prob_dist(sp_markov_result.P,
lag_classes,
sp_markov_result.classes[:, -1])
## find the ups and down and overall distribution of each cell
trend_up, trend_down, trend, volatility = get_prob_stats(prob_dist,
sp_markov_result.classes[:, -1])
## output the results
return zip(trend, trend_up, trend_down, volatility, weights.id_order)
def get_time_data(markov_data, time_cols):
"""
Extract the time columns and bin appropriately
"""
num_attrs = len(time_cols)
return np.array([[x['attr' + str(i)] for x in markov_data]
for i in range(1, num_attrs+1)], dtype=float).transpose()
## not currently used
def rebin_data(time_data, num_time_per_bin):
"""
Convert an n x l matrix into an (n/m) x l matrix where the values are
reduced (averaged) for the intervening states:
1 2 3 4 1.5 3.5
5 6 7 8 -> 5.5 7.5
9 8 7 6 8.5 6.5
5 4 3 2 4.5 2.5
if m = 2, the 4 x 4 matrix is transformed to a 2 x 4 matrix.
This process effectively resamples the data at a longer time span n
units longer than the input data.
For cases when there is a remainder (remainder(5/3) = 2), the remaining
two columns are binned together as the last time period, while the
first three are binned together for the first period.
Input:
@param time_data n x l ndarray: measurements of an attribute at
different time intervals
@param num_time_per_bin int: number of columns to average into a new
column
Output:
ceil(n / m) x l ndarray of resampled time series
"""
if time_data.shape[1] % num_time_per_bin == 0:
## if fit is perfect, then use it
n_max = time_data.shape[1] / num_time_per_bin
else:
## fit remainders into an additional column
n_max = time_data.shape[1] / num_time_per_bin + 1
return np.array([time_data[:, num_time_per_bin * i:num_time_per_bin * (i+1)].mean(axis=1)
for i in range(n_max)]).T
def get_prob_dist(transition_matrix, lag_indices, unit_indices):
"""
Given an array of transition matrices, look up the probability
associated with the arrangements passed
Input:
@param transition_matrix ndarray[k,k,k]:
@param lag_indices ndarray:
@param unit_indices ndarray:
Output:
Array of probability distributions
"""
return np.array([transition_matrix[(lag_indices[i], unit_indices[i])]
for i in range(len(lag_indices))])
def get_prob_stats(prob_dist, unit_indices):
"""
get the statistics of the probability distributions
Outputs:
@param trend_up ndarray(float): sum of probabilities for upward
movement (relative to the unit index of that prob)
@param trend_down ndarray(float): sum of probabilities for downward
movement (relative to the unit index of that prob)
@param trend ndarray(float): difference of upward and downward
movements
"""
num_elements = len(unit_indices)
trend_up = np.empty(num_elements, dtype=float)
trend_down = np.empty(num_elements, dtype=float)
trend = np.empty(num_elements, dtype=float)
for i in range(num_elements):
trend_up[i] = prob_dist[i, (unit_indices[i]+1):].sum()
trend_down[i] = prob_dist[i, :unit_indices[i]].sum()
if prob_dist[i, unit_indices[i]] > 0.0:
trend[i] = (trend_up[i] - trend_down[i]) / prob_dist[i, unit_indices[i]]
else:
trend[i] = None
## calculate volatility of distribution
volatility = prob_dist.std(axis=1)
return trend_up, trend_down, trend, volatility

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"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.0',
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.
# IMPORTANT NOTE: please don't change this line. Instead issue a ticket to systems for evaluation.
install_requires=['joblib==0.8.3', 'numpy==1.6.1', 'scipy==0.14.0', 'pysal==1.11.2', 'scikit-learn==0.14.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

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"""
CartoDB Spatial Analysis Python Library
See:
https://github.com/CartoDB/crankshaft
"""
from setuptools import setup, find_packages
setup(
name='crankshaft',
version='0.0.0',
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.
# IMPORTANT NOTE: please don't change this line. Instead issue a ticket to systems for evaluation.
install_requires=['joblib==0.8.3', 'numpy==1.6.1', 'scipy==0.14.0', 'pysal==1.11.2', 'scikit-learn==0.14.1'],
requires=['pysal', 'numpy', 'sklearn'],
test_suite='test'
)

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[[0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 0], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 1], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 2], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 3], [0.0, 0.065217391304347824, 0.065217391304347824, 0.33605067580764519, 4], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 5], [0.1875, 0.23999999999999999, 0.12, 0.23731835158706122, 6], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 7], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 8], [0.19047619047619049, 0.16, 0.0, 0.32594478059941379, 9], [-0.23529411764705882, 0.0, 0.19047619047619047, 0.31356338348865387, 10], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 11], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 12], [0.027777777777777783, 0.11111111111111112, 0.088888888888888892, 0.30339641183779581, 13], [0.03125, 0.030303030303030304, 0.0, 0.3850273981640871, 14], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 15], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 16], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 17], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 18], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 19], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 20], [0.078947368421052641, 0.073170731707317083, 0.0, 0.36451788667842738, 21], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 22], [-0.16666666666666663, 0.18181818181818182, 0.27272727272727271, 0.20246415864836445, 23], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 24], [0.1875, 0.23999999999999999, 0.12, 0.23731835158706122, 25], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 26], [-0.043478260869565216, 0.0, 0.041666666666666664, 0.37950991789118999, 27], [0.22222222222222221, 0.18181818181818182, 0.0, 0.31701083225750354, 28], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 29], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 30], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 31], [0.030303030303030304, 0.078947368421052627, 0.052631578947368418, 0.33560628561957595, 32], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 33], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 34], [0.0, 0.10000000000000001, 0.10000000000000001, 0.30331501776206204, 35], [-0.054054054054054057, 0.0, 0.05128205128205128, 0.37488547451276033, 36], [0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 37], [-0.22222222222222224, 0.13333333333333333, 0.26666666666666666, 0.22310934040908681, 38], [-0.0625, 0.095238095238095233, 0.14285714285714285, 0.28634850244519822, 39], [0.034482758620689655, 0.0625, 0.03125, 0.35388469167230169, 40], [0.11111111111111112, 0.10000000000000001, 0.0, 0.35213633723318016, 41], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 42], [0.0, 0.0, 0.0, 0.40000000000000002, 43], [0.0, 0.065217391304347824, 0.065217391304347824, 0.33605067580764519, 44], [0.078947368421052641, 0.073170731707317083, 0.0, 0.36451788667842738, 45], [0.052631578947368425, 0.090909090909090912, 0.045454545454545456, 0.33352611505171165, 46], [-0.20512820512820512, 0.0, 0.1702127659574468, 0.32172013908826891, 47]]

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[[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"]]

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[
{"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}
]

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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)

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import re
class MockCursor:
def __init__(self, data):
self.cursor_pos = 0
self.data = data
def fetch(self, batch_size):
batch = self.data[self.cursor_pos : self.cursor_pos + batch_size]
self.cursor_pos += batch_size
return batch
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 debug(self, msg):
self.notices.append(msg)
def info(self, msg):
self.infos.append(msg)
def cursor(self, query):
data = self.execute(query)
return MockCursor(data)
def execute(self, query): # TODO: additional arguments
for result in self.results:
if result[0].match(query):
return result[1]
return []

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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)

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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.params_markov = {"id_col": "cartodb_id",
"time_cols": ["_2013_dec", "_2014_jan",
"_2014_feb"],
"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]
zipped_values = zip(result, self.moran_data)
for ([res_val, res_quad], [exp_val, exp_quad]) in zipped_values:
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')
result = [(row[0], row[1]) for row in result]
zipped_values = zip(result, self.moran_data)
for ([res_val, res_quad], [exp_val, exp_quad]) in zipped_values:
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')
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)

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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}
self.params_array = {"id_col": "cartodb_id",
"time_cols": ["_2013_dec", "_2014_jan", "_2014_feb"],
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
def test_query_attr_select(self):
"""Test query_attr_select"""
ans = "i.\"andy\"::numeric As attr1, " \
"i.\"jay_z\"::numeric As attr2, "
ans_array = "i.\"_2013_dec\"::numeric As attr1, " \
"i.\"_2014_jan\"::numeric As attr2, " \
"i.\"_2014_feb\"::numeric As attr3, "
self.assertEqual(pu.query_attr_select(self.params), ans)
self.assertEqual(pu.query_attr_select(self.params_array), ans_array)
def test_query_attr_where(self):
"""Test pu.query_attr_where"""
ans = "idx_replace.\"andy\" IS NOT NULL AND " \
"idx_replace.\"jay_z\" IS NOT NULL AND " \
"idx_replace.\"jay_z\" <> 0"
ans_array = "idx_replace.\"_2013_dec\" IS NOT NULL AND " \
"idx_replace.\"_2014_jan\" IS NOT NULL AND " \
"idx_replace.\"_2014_feb\" IS NOT NULL"
self.assertEqual(pu.query_attr_where(self.params), ans)
self.assertEqual(pu.query_attr_where(self.params_array), ans_array)
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;"
ans_array = "SELECT i.\"cartodb_id\" As id, " \
"i.\"_2013_dec\"::numeric As attr1, " \
"i.\"_2014_jan\"::numeric As attr2, " \
"i.\"_2014_feb\"::numeric As attr3, " \
"(SELECT ARRAY(SELECT j.\"cartodb_id\" " \
"FROM (SELECT * FROM a_list) As j " \
"WHERE i.\"cartodb_id\" <> j.\"cartodb_id\" AND " \
"j.\"_2013_dec\" IS NOT NULL AND " \
"j.\"_2014_jan\" IS NOT NULL AND " \
"j.\"_2014_feb\" IS NOT NULL " \
"ORDER BY j.\"the_geom\" <-> i.\"the_geom\" ASC " \
"LIMIT 321)) As neighbors " \
"FROM (SELECT * FROM a_list) As i " \
"WHERE i.\"_2013_dec\" IS NOT NULL AND " \
"i.\"_2014_jan\" IS NOT NULL AND " \
"i.\"_2014_feb\" IS NOT NULL "\
"ORDER BY i.\"cartodb_id\" ASC;"
self.assertEqual(pu.knn(self.params), ans)
self.assertEqual(pu.knn(self.params_array), ans_array)
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)

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import unittest
import numpy as np
from helper import plpy, fixture_file
import crankshaft.segmentation as segmentation
import json
class SegmentationTest(unittest.TestCase):
"""Testing class for Moran's I functions"""
def setUp(self):
plpy._reset()
def generate_random_data(self,n_samples,random_state, row_type=False):
x1 = random_state.uniform(size=n_samples)
x2 = random_state.uniform(size=n_samples)
x3 = random_state.randint(0, 4, size=n_samples)
y = x1+x2*x2+x3
cartodb_id = range(len(x1))
if row_type:
return [ {'features': vals} for vals in zip(x1,x2,x3)], y
else:
return [dict( zip(['x1','x2','x3','target', 'cartodb_id'],[x1,x2,x3,y,cartodb_id]))]
def test_replace_nan_with_mean(self):
test_array = np.array([1.2, np.nan, 3.2, np.nan, np.nan])
def test_create_and_predict_segment(self):
n_samples = 1000
random_state_train = np.random.RandomState(13)
random_state_test = np.random.RandomState(134)
training_data = self.generate_random_data(n_samples, random_state_train)
test_data, test_y = self.generate_random_data(n_samples, random_state_test, row_type=True)
ids = [{'cartodb_ids': range(len(test_data))}]
rows = [{'x1': 0,'x2':0,'x3':0,'y':0,'cartodb_id':0}]
plpy._define_result('select \* from \(select \* from training\) a limit 1',rows)
plpy._define_result('.*from \(select \* from training\) as a' ,training_data)
plpy._define_result('select array_agg\(cartodb\_id order by cartodb\_id\) as cartodb_ids from \(.*\) a',ids)
plpy._define_result('.*select \* from test.*' ,test_data)
model_parameters = {'n_estimators': 1200,
'max_depth': 3,
'subsample' : 0.5,
'learning_rate': 0.01,
'min_samples_leaf': 1}
result = segmentation.create_and_predict_segment(
'select * from training',
'target',
'select * from test',
model_parameters)
prediction = [r[1] for r in result]
accuracy =np.sqrt(np.mean( np.square( np.array(prediction) - np.array(test_y))))
self.assertEqual(len(result),len(test_data))
self.assertTrue( result[0][2] < 0.01)
self.assertTrue( accuracy < 0.5*np.mean(test_y) )

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import unittest
import numpy as np
import unittest
# from mock_plpy import MockPlPy
# plpy = MockPlPy()
#
# import sys
# sys.modules['plpy'] = plpy
from helper import plpy, fixture_file
import crankshaft.space_time_dynamics as std
from crankshaft import random_seeds
import json
class SpaceTimeTests(unittest.TestCase):
"""Testing class for Markov Functions."""
def setUp(self):
plpy._reset()
self.params = {"id_col": "cartodb_id",
"time_cols": ['dec_2013', 'jan_2014', 'feb_2014'],
"subquery": "SELECT * FROM a_list",
"geom_col": "the_geom",
"num_ngbrs": 321}
self.neighbors_data = json.loads(open(fixture_file('neighbors_markov.json')).read())
self.markov_data = json.loads(open(fixture_file('markov.json')).read())
self.time_data = np.array([i * np.ones(10, dtype=float) for i in range(10)]).T
self.transition_matrix = np.array([
[[ 0.96341463, 0.0304878 , 0.00609756, 0. , 0. ],
[ 0.06040268, 0.83221477, 0.10738255, 0. , 0. ],
[ 0. , 0.14 , 0.74 , 0.12 , 0. ],
[ 0. , 0.03571429, 0.32142857, 0.57142857, 0.07142857],
[ 0. , 0. , 0. , 0.16666667, 0.83333333]],
[[ 0.79831933, 0.16806723, 0.03361345, 0. , 0. ],
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0.00537634, 0.06989247, 0.8655914 , 0.05913978, 0. ],
[ 0. , 0. , 0.06372549, 0.90196078, 0.03431373],
[ 0. , 0. , 0. , 0.19444444, 0.80555556]],
[[ 0.84693878, 0.15306122, 0. , 0. , 0. ],
[ 0.08133971, 0.78947368, 0.1291866 , 0. , 0. ],
[ 0.00518135, 0.0984456 , 0.79274611, 0.0984456 , 0.00518135],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0. , 0. , 0. , 0.10204082, 0.89795918]],
[[ 0.8852459 , 0.09836066, 0. , 0.01639344, 0. ],
[ 0.03875969, 0.81395349, 0.13953488, 0. , 0.00775194],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0.02339181, 0.12865497, 0.75438596, 0.09356725],
[ 0. , 0. , 0. , 0.09661836, 0.90338164]],
[[ 0.33333333, 0.66666667, 0. , 0. , 0. ],
[ 0.0483871 , 0.77419355, 0.16129032, 0.01612903, 0. ],
[ 0.01149425, 0.16091954, 0.74712644, 0.08045977, 0. ],
[ 0. , 0.01036269, 0.06217617, 0.89637306, 0.03108808],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]]]
)
def test_spatial_markov(self):
"""Test Spatial Markov."""
data = [ { 'id': d['id'],
'attr1': d['y1995'],
'attr2': d['y1996'],
'attr3': d['y1997'],
'attr4': d['y1998'],
'attr5': d['y1999'],
'attr6': d['y2000'],
'attr7': d['y2001'],
'attr8': d['y2002'],
'attr9': d['y2003'],
'attr10': d['y2004'],
'attr11': d['y2005'],
'attr12': d['y2006'],
'attr13': d['y2007'],
'attr14': d['y2008'],
'attr15': d['y2009'],
'neighbors': d['neighbors'] } for d in self.neighbors_data]
print(str(data[0]))
plpy._define_result('select', data)
random_seeds.set_random_seeds(1234)
result = std.spatial_markov_trend('subquery', ['y1995', 'y1996', 'y1997', 'y1998', 'y1999', 'y2000', 'y2001', 'y2002', 'y2003', 'y2004', 'y2005', 'y2006', 'y2007', 'y2008', 'y2009'], 5, 'knn', 5, 0, 'the_geom', 'cartodb_id')
self.assertTrue(result != None)
result = [(row[0], row[1], row[2], row[3], row[4]) for row in result]
print result[0]
expected = self.markov_data
for ([res_trend, res_up, res_down, res_vol, res_id],
[exp_trend, exp_up, exp_down, exp_vol, exp_id]
) in zip(result, expected):
self.assertAlmostEqual(res_trend, exp_trend)
def test_get_time_data(self):
"""Test get_time_data"""
data = [ { 'attr1': d['y1995'],
'attr2': d['y1996'],
'attr3': d['y1997'],
'attr4': d['y1998'],
'attr5': d['y1999'],
'attr6': d['y2000'],
'attr7': d['y2001'],
'attr8': d['y2002'],
'attr9': d['y2003'],
'attr10': d['y2004'],
'attr11': d['y2005'],
'attr12': d['y2006'],
'attr13': d['y2007'],
'attr14': d['y2008'],
'attr15': d['y2009'] } for d in self.neighbors_data]
result = std.get_time_data(data, ['y1995', 'y1996', 'y1997', 'y1998', 'y1999', 'y2000', 'y2001', 'y2002', 'y2003', 'y2004', 'y2005', 'y2006', 'y2007', 'y2008', 'y2009'])
## expected was prepared from PySAL example:
### f = ps.open(ps.examples.get_path("usjoin.csv"))
### pci = np.array([f.by_col[str(y)] for y in range(1995, 2010)]).transpose()
### rpci = pci / (pci.mean(axis = 0))
expected = np.array([[ 0.87654416, 0.863147, 0.85637567, 0.84811668, 0.8446154, 0.83271652
, 0.83786314, 0.85012593, 0.85509656, 0.86416612, 0.87119375, 0.86302631
, 0.86148267, 0.86252252, 0.86746356],
[ 0.9188951, 0.91757931, 0.92333258, 0.92517289, 0.92552388, 0.90746978
, 0.89830489, 0.89431991, 0.88924794, 0.89815176, 0.91832091, 0.91706054
, 0.90139505, 0.87897455, 0.86216858],
[ 0.82591007, 0.82548596, 0.81989793, 0.81503235, 0.81731522, 0.78964559
, 0.80584442, 0.8084998, 0.82258551, 0.82668196, 0.82373724, 0.81814804
, 0.83675961, 0.83574199, 0.84647177],
[ 1.09088176, 1.08537689, 1.08456418, 1.08415404, 1.09898841, 1.14506948
, 1.12151133, 1.11160697, 1.10888621, 1.11399806, 1.12168029, 1.13164797
, 1.12958508, 1.11371818, 1.09936775],
[ 1.10731446, 1.11373944, 1.13283638, 1.14472559, 1.15910025, 1.16898201
, 1.17212488, 1.14752303, 1.11843284, 1.11024964, 1.11943471, 1.11736468
, 1.10863242, 1.09642516, 1.07762337],
[ 1.42269757, 1.42118434, 1.44273502, 1.43577571, 1.44400684, 1.44184737
, 1.44782832, 1.41978227, 1.39092208, 1.4059372, 1.40788646, 1.44052766
, 1.45241216, 1.43306098, 1.4174431 ],
[ 1.13073885, 1.13110513, 1.11074708, 1.13364636, 1.13088149, 1.10888138
, 1.11856629, 1.13062931, 1.11944984, 1.12446239, 1.11671008, 1.10880034
, 1.08401709, 1.06959206, 1.07875225],
[ 1.04706124, 1.04516831, 1.04253372, 1.03239987, 1.02072545, 0.99854316
, 0.9880258, 0.99669587, 0.99327676, 1.01400905, 1.03176742, 1.040511
, 1.01749645, 0.9936394, 0.98279746],
[ 0.98996986, 1.00143564, 0.99491, 1.00188408, 1.00455845, 0.99127006
, 0.97925917, 0.9683482, 0.95335147, 0.93694787, 0.94308213, 0.92232874
, 0.91284091, 0.89689833, 0.88928858],
[ 0.87418391, 0.86416601, 0.84425695, 0.8404494, 0.83903044, 0.8578708
, 0.86036185, 0.86107306, 0.8500772, 0.86981998, 0.86837929, 0.87204141
, 0.86633032, 0.84946077, 0.83287146],
[ 1.14196118, 1.14660262, 1.14892712, 1.14909594, 1.14436624, 1.14450183
, 1.12349752, 1.12596664, 1.12213996, 1.1119989, 1.10257792, 1.10491258
, 1.11059842, 1.10509795, 1.10020097],
[ 0.97282463, 0.96700147, 0.96252588, 0.9653878, 0.96057687, 0.95831051
, 0.94480909, 0.94804195, 0.95430286, 0.94103989, 0.92122519, 0.91010201
, 0.89280392, 0.89298243, 0.89165385],
[ 0.94325468, 0.96436902, 0.96455242, 0.95243009, 0.94117647, 0.9480927
, 0.93539182, 0.95388718, 0.94597005, 0.96918424, 0.94781281, 0.93466815
, 0.94281559, 0.96520315, 0.96715441],
[ 0.97478408, 0.98169225, 0.98712809, 0.98474769, 0.98559897, 0.98687073
, 0.99237486, 0.98209969, 0.9877653, 0.97399471, 0.96910087, 0.98416665
, 0.98423613, 0.99823861, 0.99545704],
[ 0.85570269, 0.85575915, 0.85986132, 0.85693406, 0.8538012, 0.86191535
, 0.84981451, 0.85472102, 0.84564835, 0.83998883, 0.83478547, 0.82803648
, 0.8198736, 0.82265395, 0.8399404 ],
[ 0.87022047, 0.85996258, 0.85961813, 0.85689572, 0.83947136, 0.82785597
, 0.86008789, 0.86776298, 0.86720209, 0.8676334, 0.89179317, 0.94202108
, 0.9422231, 0.93902708, 0.94479184],
[ 0.90134907, 0.90407738, 0.90403991, 0.90201769, 0.90399238, 0.90906632
, 0.92693339, 0.93695966, 0.94242697, 0.94338265, 0.91981796, 0.91108804
, 0.90543476, 0.91737138, 0.94793657],
[ 1.1977611, 1.18222564, 1.18439158, 1.18267865, 1.19286723, 1.20172869
, 1.21328691, 1.22624778, 1.22397075, 1.23857042, 1.24419893, 1.23929384
, 1.23418676, 1.23626739, 1.26754398],
[ 1.24919678, 1.25754773, 1.26991161, 1.28020651, 1.30625667, 1.34790023
, 1.34399863, 1.32575181, 1.30795492, 1.30544841, 1.30303302, 1.32107766
, 1.32936244, 1.33001241, 1.33288462],
[ 1.06768004, 1.03799276, 1.03637303, 1.02768449, 1.03296093, 1.05059016
, 1.03405057, 1.02747623, 1.03162734, 0.9961416, 0.97356208, 0.94241549
, 0.92754547, 0.92549227, 0.92138102],
[ 1.09475614, 1.11526796, 1.11654299, 1.13103948, 1.13143264, 1.13889622
, 1.12442212, 1.13367018, 1.13982256, 1.14029944, 1.11979401, 1.10905389
, 1.10577769, 1.11166825, 1.09985155],
[ 0.76530058, 0.76612841, 0.76542451, 0.76722683, 0.76014284, 0.74480073
, 0.76098396, 0.76156903, 0.76651952, 0.76533288, 0.78205934, 0.76842416
, 0.77487118, 0.77768683, 0.78801192],
[ 0.98391336, 0.98075816, 0.98295341, 0.97386015, 0.96913803, 0.97370819
, 0.96419154, 0.97209861, 0.97441313, 0.96356162, 0.94745352, 0.93965462
, 0.93069645, 0.94020973, 0.94358232],
[ 0.83561828, 0.82298088, 0.81738502, 0.81748588, 0.80904801, 0.80071489
, 0.83358256, 0.83451613, 0.85175032, 0.85954307, 0.86790024, 0.87170334
, 0.87863799, 0.87497981, 0.87888675],
[ 0.98845573, 1.02092428, 0.99665283, 0.99141823, 0.99386619, 0.98733195
, 0.99644997, 0.99669587, 1.02559097, 1.01116651, 0.99988024, 0.97906749
, 0.99323123, 1.00204939, 0.99602148],
[ 1.14930913, 1.15241949, 1.14300962, 1.14265542, 1.13984683, 1.08312397
, 1.05192626, 1.04230892, 1.05577278, 1.08569751, 1.12443486, 1.08891079
, 1.08603695, 1.05997314, 1.02160943],
[ 1.11368269, 1.1057147, 1.11893431, 1.13778669, 1.1432272, 1.18257029
, 1.16226243, 1.16009196, 1.14467789, 1.14820235, 1.12386598, 1.12680236
, 1.12357937, 1.1159258, 1.12570828],
[ 1.30379431, 1.30752186, 1.31206366, 1.31532267, 1.30625667, 1.31210239
, 1.29989156, 1.29203193, 1.27183516, 1.26830786, 1.2617743, 1.28656675
, 1.29734097, 1.29390205, 1.29345446],
[ 0.83953719, 0.82701448, 0.82006005, 0.81188876, 0.80294864, 0.78772975
, 0.82848011, 0.8259679, 0.82435705, 0.83108634, 0.84373784, 0.83891093
, 0.84349247, 0.85637272, 0.86539395],
[ 1.23450087, 1.2426022, 1.23537935, 1.23581293, 1.24522626, 1.2256767
, 1.21126648, 1.19377804, 1.18355337, 1.19674434, 1.21536573, 1.23653297
, 1.27962009, 1.27968392, 1.25907738],
[ 0.9769662, 0.97400719, 0.98035944, 0.97581531, 0.95543282, 0.96480308
, 0.94686376, 0.93679073, 0.92540049, 0.92988835, 0.93442917, 0.92100464
, 0.91475304, 0.90249622, 0.9021363 ],
[ 0.84986886, 0.8986851, 0.84295997, 0.87280534, 0.85659368, 0.88937573
, 0.894401, 0.90448993, 0.95495898, 0.92698333, 0.94745352, 0.92562488
, 0.96635366, 1.02520312, 1.0394296 ],
[ 1.01922808, 1.00258203, 1.00974428, 1.00303417, 0.99765073, 1.00759019
, 0.99192968, 0.99747298, 0.99550759, 0.97583768, 0.9610168, 0.94779638
, 0.93759089, 0.93353431, 0.94121705],
[ 0.86367411, 0.85558932, 0.85544346, 0.85103025, 0.84336613, 0.83434854
, 0.85813595, 0.84667961, 0.84374558, 0.85951183, 0.87194227, 0.89455097
, 0.88283929, 0.90349491, 0.90600675],
[ 1.00947534, 1.00411055, 1.00698819, 0.99513687, 0.99291086, 1.00581626
, 0.98850522, 0.99291168, 0.98983209, 0.97511924, 0.96134615, 0.96382634
, 0.95011401, 0.9434686, 0.94637765],
[ 1.05712571, 1.05459419, 1.05753012, 1.04880786, 1.05103857, 1.04800023
, 1.03024941, 1.04200483, 1.0402554, 1.03296979, 1.02191682, 1.02476275
, 1.02347523, 1.02517684, 1.04359571],
[ 1.07084189, 1.06669497, 1.07937623, 1.07387988, 1.0794043, 1.0531801
, 1.07452771, 1.09383478, 1.1052447, 1.10322136, 1.09167939, 1.08772756
, 1.08859544, 1.09177338, 1.1096083 ],
[ 0.86719222, 0.86628896, 0.86675156, 0.86425632, 0.86511809, 0.86287327
, 0.85169796, 0.85411285, 0.84886336, 0.84517414, 0.84843858, 0.84488343
, 0.83374329, 0.82812044, 0.82878599],
[ 0.88389211, 0.92288667, 0.90282398, 0.91229186, 0.92023286, 0.92652175
, 0.94278865, 0.93682452, 0.98655146, 0.992237, 0.9798497, 0.93869677
, 0.96947771, 1.00362626, 0.98102351],
[ 0.97082064, 0.95320233, 0.94534081, 0.94215593, 0.93967, 0.93092109
, 0.92662519, 0.93412152, 0.93501274, 0.92879506, 0.92110542, 0.91035556
, 0.90430364, 0.89994694, 0.90073864],
[ 0.95861858, 0.95774543, 0.98254811, 0.98919472, 0.98684824, 0.98882205
, 0.97662234, 0.95601578, 0.94905385, 0.94934888, 0.97152609, 0.97163004
, 0.9700702, 0.97158948, 0.95884908],
[ 0.83980439, 0.84726737, 0.85747, 0.85467221, 0.8556751, 0.84818516
, 0.85265681, 0.84502402, 0.82645665, 0.81743586, 0.83550406, 0.83338919
, 0.83511679, 0.82136617, 0.80921874],
[ 0.95118156, 0.9466212, 0.94688098, 0.9508583, 0.9512441, 0.95440787
, 0.96364363, 0.96804412, 0.97136214, 0.97583768, 0.95571724, 0.96895368
, 0.97001634, 0.97082733, 0.98782366],
[ 1.08910044, 1.08248968, 1.08492895, 1.08656923, 1.09454249, 1.10558188
, 1.1214086, 1.12292577, 1.13021031, 1.13342735, 1.14686068, 1.14502975
, 1.14474747, 1.14084037, 1.16142926],
[ 1.06336033, 1.07365823, 1.08691496, 1.09764846, 1.11669863, 1.11856702
, 1.09764283, 1.08815849, 1.08044313, 1.09278827, 1.07003204, 1.08398066
, 1.09831768, 1.09298232, 1.09176125],
[ 0.79772065, 0.78829196, 0.78581151, 0.77615922, 0.77035744, 0.77751194
, 0.79902974, 0.81437881, 0.80788828, 0.79603865, 0.78966436, 0.79949807
, 0.80172182, 0.82168155, 0.85587911],
[ 1.0052447, 1.00007696, 1.00475899, 1.00613942, 1.00639561, 1.00162979
, 0.99860739, 1.00814981, 1.00574316, 0.99030032, 0.97682565, 0.97292596
, 0.96519561, 0.96173403, 0.95890284],
[ 0.95808419, 0.9382568, 0.9654441, 0.95561201, 0.96987289, 0.96608031
, 0.99727185, 1.00781194, 1.03484236, 1.05333619, 1.0983263, 1.1704974
, 1.17025154, 1.18730553, 1.14242645]])
self.assertTrue(np.allclose(result, expected))
self.assertTrue(type(result) == type(expected))
self.assertTrue(result.shape == expected.shape)
def test_rebin_data(self):
"""Test rebin_data"""
## sample in double the time (even case since 10 % 2 = 0):
## (0+1)/2, (2+3)/2, (4+5)/2, (6+7)/2, (8+9)/2
## = 0.5, 2.5, 4.5, 6.5, 8.5
ans_even = np.array([(i + 0.5) * np.ones(10, dtype=float)
for i in range(0, 10, 2)]).T
self.assertTrue(np.array_equal(std.rebin_data(self.time_data, 2), ans_even))
## sample in triple the time (uneven since 10 % 3 = 1):
## (0+1+2)/3, (3+4+5)/3, (6+7+8)/3, (9)/1
## = 1, 4, 7, 9
ans_odd = np.array([i * np.ones(10, dtype=float)
for i in (1, 4, 7, 9)]).T
self.assertTrue(np.array_equal(std.rebin_data(self.time_data, 3), ans_odd))
def test_get_prob_dist(self):
"""Test get_prob_dist"""
lag_indices = np.array([1, 2, 3, 4])
unit_indices = np.array([1, 3, 2, 4])
answer = np.array([
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]
])
result = std.get_prob_dist(self.transition_matrix, lag_indices, unit_indices)
self.assertTrue(np.array_equal(result, answer))
def test_get_prob_stats(self):
"""Test get_prob_stats"""
probs = np.array([
[ 0.0754717 , 0.88207547, 0.04245283, 0. , 0. ],
[ 0. , 0. , 0.09411765, 0.87058824, 0.03529412],
[ 0.0049505 , 0.09405941, 0.77722772, 0.11881188, 0.0049505 ],
[ 0. , 0. , 0. , 0.02352941, 0.97647059]
])
unit_indices = np.array([1, 3, 2, 4])
answer_up = np.array([0.04245283, 0.03529412, 0.12376238, 0.])
answer_down = np.array([0.0754717, 0.09411765, 0.0990099, 0.02352941])
answer_trend = np.array([-0.03301887 / 0.88207547, -0.05882353 / 0.87058824, 0.02475248 / 0.77722772, -0.02352941 / 0.97647059])
answer_volatility = np.array([ 0.34221495, 0.33705421, 0.29226542, 0.38834223])
result = std.get_prob_stats(probs, unit_indices)
result_up = result[0]
result_down = result[1]
result_trend = result[2]
result_volatility = result[3]
self.assertTrue(np.allclose(result_up, answer_up))
self.assertTrue(np.allclose(result_down, answer_down))
self.assertTrue(np.allclose(result_trend, answer_trend))
self.assertTrue(np.allclose(result_volatility, answer_volatility))

2
src/pg/crankshaft.control
View File

@ -1,5 +1,5 @@
comment = 'CartoDB Spatial Analysis extension' comment = 'CartoDB Spatial Analysis extension'
default_version = '0.3.1' default_version = '0.4.2'
requires = 'plpythonu, postgis' requires = 'plpythonu, postgis'
superuser = true superuser = true
schema = cdb_crankshaft schema = cdb_crankshaft

24
src/pg/sql/08_interpolation.sql
View File

@ -1,6 +1,8 @@
-- 0: nearest neighbor -- 0: nearest neighbor(s)
-- 1: barymetric -- 1: barymetric
-- 2: IDW -- 2: IDW
-- 3: krigin ---> TO DO
CREATE OR REPLACE FUNCTION CDB_SpatialInterpolation( CREATE OR REPLACE FUNCTION CDB_SpatialInterpolation(
IN query text, IN query text,
@ -50,12 +52,19 @@ DECLARE
vc numeric; vc numeric;
output numeric; output numeric;
BEGIN BEGIN
output := -999.999; -- output := -999.999;
-- nearest
-- nearest neighbors
-- p1: limit the number of neighbors, 0-> closest one
IF method = 0 THEN IF method = 0 THEN
WITH a as (SELECT unnest(geomin) as g, unnest(colin) as v) IF p1 = 0 THEN
SELECT a.v INTO output FROM a ORDER BY point<->a.g LIMIT 1; p1 := 1;
END IF;
WITH a as (SELECT unnest(geomin) as g, unnest(colin) as v),
b as (SELECT a.v as v FROM a ORDER BY point<->a.g LIMIT p1::integer)
SELECT avg(b.v) INTO output FROM b;
RETURN output; RETURN output;
-- barymetric -- barymetric
@ -121,6 +130,11 @@ BEGIN
SELECT sum(b.f)/sum(b.k) INTO output FROM b; SELECT sum(b.f)/sum(b.k) INTO output FROM b;
RETURN output; RETURN output;
-- krigin
ELSIF method = 3 THEN
-- TO DO
END IF; END IF;
RETURN -777.777; RETURN -777.777;

2
src/pg/sql/10_moran.sql
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@ -10,7 +10,7 @@ CREATE OR REPLACE FUNCTION
id_col TEXT DEFAULT 'cartodb_id') id_col TEXT DEFAULT 'cartodb_id')
RETURNS TABLE (moran NUMERIC, significance NUMERIC) RETURNS TABLE (moran NUMERIC, significance NUMERIC)
AS $$ AS $$
from crankshaft.clustering import moran_local from crankshaft.clustering import moran
# TODO: use named parameters or a dictionary # TODO: use named parameters or a dictionary
return moran(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col) return moran(subquery, column_name, w_type, num_ngbrs, permutations, geom_col, id_col)
$$ LANGUAGE plpythonu; $$ LANGUAGE plpythonu;

123
src/pg/sql/13_PIA.sql Normal file
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@ -0,0 +1,123 @@
-- Based on:
-- https://github.com/mapbox/polylabel/blob/master/index.js
-- https://sites.google.com/site/polesofinaccessibility/
-- Requires: https://github.com/CartoDB/cartodb-postgresql
-- Based on:
-- https://github.com/mapbox/polylabel/blob/master/index.js
-- https://sites.google.com/site/polesofinaccessibility/
-- Requires: https://github.com/CartoDB/cartodb-postgresql
CREATE OR REPLACE FUNCTION CDB_PIA(
IN polygon geometry,
IN tolerance numeric DEFAULT 1.0
)
RETURNS geometry AS $$
DECLARE
env geometry[];
cells geometry[];
cell geometry;
best_c geometry;
best_d numeric;
test_d numeric;
test_mx numeric;
test_h numeric;
test_cells geometry[];
width numeric;
height numeric;
h numeric;
i integer;
n integer;
sqr numeric;
p geometry;
BEGIN
sqr := |/2;
polygon := ST_Transform(polygon, 3857);
-- grid #0 cell size
height := ST_YMax(polygon) - ST_YMin(polygon);
width := ST_XMax(polygon) - ST_XMin(polygon);
h := 0.5*LEAST(height, width);
-- grid #0
with c1 as(
SELECT cdb_crankshaft.CDB_RectangleGrid(polygon, h, h) as c
)
SELECT array_agg(c) INTO cells FROM c1;
-- 1st guess: centroid
best_d := cdb_crankshaft._Signed_Dist(polygon, ST_Centroid(Polygon));
-- looping the loop
n := array_length(cells,1);
i := 1;
LOOP
EXIT WHEN i > n;
cell := cells[i];
i := i+1;
-- cell side size, it's square
test_h := ST_XMax(cell) - ST_XMin(cell) ;
-- check distance
test_d := cdb_crankshaft._Signed_Dist(polygon, ST_Centroid(cell));
IF test_d > best_d THEN
best_d := test_d;
best_c := cells[i];
END IF;
-- longest distance within the cell
test_mx := test_d + (test_h/2 * sqr);
-- if the cell has no chance to contains the desired point, continue
CONTINUE WHEN test_mx - best_d <= tolerance;
-- resample the cell
with c1 as(
SELECT cdb_crankshaft.CDB_RectangleGrid(cell, test_h/2, test_h/2) as c
)
SELECT array_agg(c) INTO test_cells FROM c1;
-- concat the new cells to the former array
cells := cells || test_cells;
-- prepare next iteration
n := array_length(cells,1);
END LOOP;
RETURN ST_transform(ST_Centroid(best_c), 4326);
END;
$$ language plpgsql IMMUTABLE;
-- signed distance point to polygon with holes
-- negative is the point is out the polygon
CREATE OR REPLACE FUNCTION _Signed_Dist(
IN polygon geometry,
IN point geometry
)
RETURNS numeric AS $$
DECLARE
i integer;
within integer;
holes integer;
dist numeric;
BEGIN
dist := 1e999;
SELECT LEAST(dist, ST_distance(point, ST_ExteriorRing(polygon))::numeric) INTO dist;
SELECT CASE WHEN ST_Within(point,polygon) THEN 1 ELSE -1 END INTO within;
SELECT ST_NumInteriorRings(polygon) INTO holes;
IF holes > 0 THEN
FOR i IN 1..holes
LOOP
SELECT LEAST(dist, ST_distance(point, ST_InteriorRingN(polygon, i))::numeric) INTO dist;
END LOOP;
END IF;
dist := dist * within::numeric;
RETURN dist;
END;
$$ language plpgsql IMMUTABLE;

67
src/pg/sql/14_densify.sql Normal file
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@ -0,0 +1,67 @@
--
-- Iterative densification of a set of points using Delaunay triangulation
-- the new points have as assigned value the average value of the 3 vertex (centroid)
--
-- @param geomin - array of geometries (points)
--
-- @param colin - array of numeric values in that points
--
-- @param iterations - integer, number of iterations
--
--
-- Returns: TABLE(geomout geometry, colout numeric)
--
--
CREATE OR REPLACE FUNCTION CDB_Densify(
IN geomin geometry[],
IN colin numeric[],
IN iterations integer
)
RETURNS TABLE(geomout geometry, colout numeric) AS $$
DECLARE
geotemp geometry[];
coltemp numeric[];
i integer;
gs geometry[];
g geometry;
vertex geometry[];
va numeric;
vb numeric;
vc numeric;
center geometry;
centerval numeric;
tmp integer;
BEGIN
geotemp := geomin;
coltemp := colin;
FOR i IN 1..iterations
LOOP
-- generate TIN
WITH a as (SELECT unnest(geotemp) AS e),
b as (SELECT ST_DelaunayTriangles(ST_Collect(a.e),0.001, 0) AS t FROM a),
c as (SELECT (ST_Dump(t)).geom AS v FROM b)
SELECT array_agg(v) INTO gs FROM c;
-- loop cells
FOREACH g IN ARRAY gs
LOOP
-- append centroid
SELECT ST_Centroid(g) INTO center;
geotemp := array_append(geotemp, center);
-- retrieve the value of each vertex
WITH a AS (SELECT (ST_DumpPoints(g)).geom AS v)
SELECT array_agg(v) INTO vertex FROM a;
WITH a AS(SELECT unnest(geotemp) as geo, unnest(coltemp) as c)
SELECT c INTO va FROM a WHERE ST_Equals(geo, vertex[1]);
WITH a AS(SELECT unnest(geotemp) as geo, unnest(coltemp) as c)
SELECT c INTO vb FROM a WHERE ST_Equals(geo, vertex[2]);
WITH a AS(SELECT unnest(geotemp) as geo, unnest(coltemp) as c)
SELECT c INTO vc FROM a WHERE ST_Equals(geo, vertex[3]);
-- calc the value at the center
centerval := (va + vb + vc) / 3;
-- append the value
coltemp := array_append(coltemp, centerval);
END LOOP;
END LOOP;
RETURN QUERY SELECT unnest(geotemp ) as geomout, unnest(coltemp ) as colout;
END;
$$ language plpgsql IMMUTABLE;

43
src/pg/sql/15_tinmap.sql Normal file
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@ -0,0 +1,43 @@
CREATE OR REPLACE FUNCTION CDB_TINmap(
IN geomin geometry[],
IN colin numeric[],
IN iterations integer
)
RETURNS TABLE(geomout geometry, colout numeric) AS $$
DECLARE
p geometry[];
vals numeric[];
gs geometry[];
g geometry;
vertex geometry[];
centerval numeric;
va numeric;
vb numeric;
vc numeric;
coltemp numeric[];
BEGIN
SELECT array_agg(dens.geomout), array_agg(dens.colout) INTO p, vals FROM cdb_crankshaft.CDB_Densify(geomin, colin, iterations) dens;
WITH a as (SELECT unnest(p) AS e),
b as (SELECT ST_DelaunayTriangles(ST_Collect(a.e),0.001, 0) AS t FROM a),
c as (SELECT (ST_Dump(t)).geom AS v FROM b)
SELECT array_agg(v) INTO gs FROM c;
FOREACH g IN ARRAY gs
LOOP
-- retrieve the vertex of each triangle
WITH a AS (SELECT (ST_DumpPoints(g)).geom AS v)
SELECT array_agg(v) INTO vertex FROM a;
-- retrieve the value of each vertex
WITH a AS(SELECT unnest(p) as geo, unnest(vals) as c)
SELECT c INTO va FROM a WHERE ST_Equals(geo, vertex[1]);
WITH a AS(SELECT unnest(p) as geo, unnest(vals) as c)
SELECT c INTO vb FROM a WHERE ST_Equals(geo, vertex[2]);
WITH a AS(SELECT unnest(p) as geo, unnest(vals) as c)
SELECT c INTO vc FROM a WHERE ST_Equals(geo, vertex[3]);
-- calc the value at the center
centerval := (va + vb + vc) / 3;
-- append the value
coltemp := array_append(coltemp, centerval);
END LOOP;
RETURN QUERY SELECT unnest(gs) as geomout, unnest(coltemp ) as colout;
END;
$$ language plpgsql IMMUTABLE;

208
src/pg/sql/19_contour.sql Normal file
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@ -0,0 +1,208 @@
CREATE OR REPLACE FUNCTION CDB_Contour(
IN geomin geometry[],
IN colin numeric[],
IN buffer numeric,
IN intmethod integer,
IN classmethod integer,
IN steps integer,
IN max_time integer DEFAULT 60000
)
RETURNS TABLE(
the_geom geometry,
bin integer,
min_value numeric,
max_value numeric,
avg_value numeric
) AS $$
DECLARE
cell_count integer;
tin geometry[];
resolution integer;
BEGIN
-- nasty trick to override issue #121
IF max_time = 0 THEN
max_time = -90;
END IF;
resolution := max_time;
max_time := -1 * resolution;
-- calc the optimal number of cells for the current dataset
SELECT
CASE intmethod
WHEN 0 THEN round(3.7745903782 * max_time - 9.4399210051 * array_length(geomin,1) - 1350.8778213073)
WHEN 1 THEN round(2.2855592156 * max_time - 87.285217133 * array_length(geomin,1) + 17255.7085601797)
WHEN 2 THEN round(0.9799471999 * max_time - 127.0334085369 * array_length(geomin,1) + 22707.9579721218)
ELSE 10000
END INTO cell_count;
-- we don't have iterative barycentric interpolation in CDB_interpolation,
-- and it's a costy function, so let's make a custom one here till
-- we update the code
-- tin := ARRAY[]::geometry[];
IF intmethod=1 THEN
WITH
a as (SELECT unnest(geomin) AS e),
b as (SELECT ST_DelaunayTriangles(ST_Collect(a.e),0.001, 0) AS t FROM a),
c as (SELECT (ST_Dump(t)).geom as v FROM b)
SELECT array_agg(v) INTO tin FROM c;
END IF;
-- Delaunay stuff performed just ONCE!!
-- magic
RETURN QUERY
WITH
convexhull as (
SELECT
ST_ConvexHull(ST_Collect(geomin)) as g,
buffer * |/ st_area(ST_ConvexHull(ST_Collect(geomin)))/PI() as r
),
envelope as (
SELECT
st_expand(a.g, a.r) as e
FROM convexhull a
),
envelope3857 as(
SELECT
ST_Transform(e, 3857) as geom
FROM envelope
),
resolution as(
SELECT
CASE WHEN resolution <= 0 THEN
round(|/ (
ST_area(geom) / abs(cell_count)
))
ELSE
resolution
END AS cell
FROM envelope3857
),
grid as(
SELECT
ST_Transform(cdb_crankshaft.CDB_RectangleGrid(e.geom, r.cell, r.cell), 4326) as geom
FROM envelope3857 e, resolution r
),
interp as(
SELECT
geom,
CASE
WHEN intmethod=1 THEN cdb_crankshaft._interp_in_tin(geomin, colin, tin, ST_Centroid(geom))
ELSE cdb_crankshaft.CDB_SpatialInterpolation(geomin, colin, ST_Centroid(geom), intmethod)
END as val
FROM grid
),
classes as(
SELECT CASE
WHEN classmethod = 0 THEN
cdb_crankshaft.CDB_EqualIntervalBins(array_agg(val), steps)
WHEN classmethod = 1 THEN
cdb_crankshaft.CDB_HeadsTailsBins(array_agg(val), steps)
WHEN classmethod = 2 THEN
cdb_crankshaft.CDB_JenksBins(array_agg(val), steps)
ELSE
cdb_crankshaft.CDB_QuantileBins(array_agg(val), steps)
END as b
FROM interp
where val is not null
),
classified as(
SELECT
i.*,
width_bucket(i.val, c.b) as bucket
FROM interp i left join classes c
ON 1=1
),
classified2 as(
SELECT
geom,
val,
CASE
WHEN bucket = steps THEN bucket - 1
ELSE bucket
END as b
FROM classified
),
final as(
SELECT
st_union(geom) as the_geom,
b as bin,
min(val) as min_value,
max(val) as max_value,
avg(val) as avg_value
FROM classified2
GROUP BY bin
)
SELECT
*
FROM final
where final.bin is not null
;
END;
$$ language plpgsql;
-- =====================================================================
-- Interp in grid, so we can use barycentric with a precalculated tin (NNI)
-- =====================================================================
CREATE OR REPLACE FUNCTION _interp_in_tin(
IN geomin geometry[],
IN colin numeric[],
IN tin geometry[],
IN point geometry
)
RETURNS numeric AS
$$
DECLARE
g geometry;
vertex geometry[];
sg numeric;
sa numeric;
sb numeric;
sc numeric;
va numeric;
vb numeric;
vc numeric;
output numeric;
BEGIN
-- get the cell the point is within
WITH
a as (SELECT unnest(tin) as v),
b as (SELECT v FROM a WHERE ST_Within(point, v))
SELECT v INTO g FROM b;
-- if we're out of the data realm,
-- return null
IF g is null THEN
RETURN null;
END IF;
-- vertex of the selected cell
WITH a AS (
SELECT (ST_DumpPoints(g)).geom AS v
)
SELECT array_agg(v) INTO vertex FROM a;
-- retrieve the value of each vertex
WITH a AS(SELECT unnest(geomin) as geo, unnest(colin) as c)
SELECT c INTO va FROM a WHERE ST_Equals(geo, vertex[1]);
WITH a AS(SELECT unnest(geomin) as geo, unnest(colin) as c)
SELECT c INTO vb FROM a WHERE ST_Equals(geo, vertex[2]);
WITH a AS(SELECT unnest(geomin) as geo, unnest(colin) as c)
SELECT c INTO vc FROM a WHERE ST_Equals(geo, vertex[3]);
-- calc the areas
SELECT
ST_area(g),
ST_area(ST_MakePolygon(ST_MakeLine(ARRAY[point, vertex[2], vertex[3], point]))),
ST_area(ST_MakePolygon(ST_MakeLine(ARRAY[point, vertex[1], vertex[3], point]))),
ST_area(ST_MakePolygon(ST_MakeLine(ARRAY[point,vertex[1],vertex[2], point]))) INTO sg, sa, sb, sc;
output := (coalesce(sa,0) * coalesce(va,0) + coalesce(sb,0) * coalesce(vb,0) + coalesce(sc,0) * coalesce(vc,0)) / coalesce(sg,1);
RETURN output;
END;
$$
language plpgsql;

447
src/pg/sql/cdb_utils.sql Normal file
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@ -0,0 +1,447 @@
--
-- Fill given extent with a rectangular coverage
--
-- @param ext Extent to fill. Only rectangles with center point falling
-- inside the extent (or at the lower or leftmost edge) will
-- be emitted. The returned hexagons will have the same SRID
-- as this extent.
--
-- @param width With of each rectangle
--
-- @param height Height of each rectangle
--
-- @param origin Optional origin to allow for exact tiling.
-- If omitted the origin will be 0,0.
-- The parameter is checked for having the same SRID
-- as the extent.
--
--
CREATE OR REPLACE FUNCTION CDB_RectangleGrid(ext GEOMETRY, width FLOAT8, height FLOAT8, origin GEOMETRY DEFAULT NULL)
RETURNS SETOF GEOMETRY
AS $$
DECLARE
h GEOMETRY; -- rectangle cell
hstep FLOAT8; -- horizontal step
vstep FLOAT8; -- vertical step
hw FLOAT8; -- half width
hh FLOAT8; -- half height
vstart FLOAT8;
hstart FLOAT8;
hend FLOAT8;
vend FLOAT8;
xoff FLOAT8;
yoff FLOAT8;
xgrd FLOAT8;
ygrd FLOAT8;
x FLOAT8;
y FLOAT8;
srid INTEGER;
BEGIN
srid := ST_SRID(ext);
xoff := 0;
yoff := 0;
IF origin IS NOT NULL THEN
IF ST_SRID(origin) != srid THEN
RAISE EXCEPTION 'SRID mismatch between extent (%) and origin (%)', srid, ST_SRID(origin);
END IF;
xoff := ST_X(origin);
yoff := ST_Y(origin);
END IF;
--RAISE DEBUG 'X offset: %', xoff;
--RAISE DEBUG 'Y offset: %', yoff;
hw := width/2.0;
hh := height/2.0;
xgrd := hw;
ygrd := hh;
--RAISE DEBUG 'X grid size: %', xgrd;
--RAISE DEBUG 'Y grid size: %', ygrd;
hstep := width;
vstep := height;
-- Tweak horizontal start on hstep grid from origin
hstart := xoff + ceil((ST_XMin(ext)-xoff)/hstep)*hstep;
--RAISE DEBUG 'hstart: %', hstart;
-- Tweak vertical start on vstep grid from origin
vstart := yoff + ceil((ST_Ymin(ext)-yoff)/vstep)*vstep;
--RAISE DEBUG 'vstart: %', vstart;
hend := ST_XMax(ext);
vend := ST_YMax(ext);
--RAISE DEBUG 'hend: %', hend;
--RAISE DEBUG 'vend: %', vend;
x := hstart;
WHILE x < hend LOOP -- over X
y := vstart;
h := ST_MakeEnvelope(x-hw, y-hh, x+hw, y+hh, srid);
WHILE y < vend LOOP -- over Y
RETURN NEXT h;
h := ST_Translate(h, 0, vstep);
y := yoff + round(((y + vstep)-yoff)/ygrd)*ygrd; -- round to grid
END LOOP;
x := xoff + round(((x + hstep)-xoff)/xgrd)*xgrd; -- round to grid
END LOOP;
RETURN;
END
$$ LANGUAGE 'plpgsql' IMMUTABLE;
--
-- Calculate the equal interval bins for a given column
--
-- @param in_array A numeric array of numbers to determine the best
-- to determine the bin boundary
--
-- @param breaks The number of bins you want to find.
--
--
-- Returns: upper edges of bins
--
--
CREATE OR REPLACE FUNCTION CDB_EqualIntervalBins ( in_array NUMERIC[], breaks INT ) RETURNS NUMERIC[] as $$
DECLARE
diff numeric;
min_val numeric;
max_val numeric;
tmp_val numeric;
i INT := 1;
reply numeric[];
BEGIN
SELECT min(e), max(e) INTO min_val, max_val FROM ( SELECT unnest(in_array) e ) x WHERE e IS NOT NULL;
diff = (max_val - min_val) / breaks::numeric;
LOOP
IF i < breaks THEN
tmp_val = min_val + i::numeric * diff;
reply = array_append(reply, tmp_val);
i := i+1;
ELSE
reply = array_append(reply, max_val);
EXIT;
END IF;
END LOOP;
RETURN reply;
END;
$$ language plpgsql IMMUTABLE;
--
-- Determine the Heads/Tails classifications from a numeric array
--
-- @param in_array A numeric array of numbers to determine the best
-- bins based on the Heads/Tails method.
--
-- @param breaks The number of bins you want to find.
--
--
CREATE OR REPLACE FUNCTION CDB_HeadsTailsBins ( in_array NUMERIC[], breaks INT) RETURNS NUMERIC[] as $$
DECLARE
element_count INT4;
arr_mean numeric;
i INT := 2;
reply numeric[];
BEGIN
-- get the total size of our row
element_count := array_upper(in_array, 1) - array_lower(in_array, 1);
-- ensure the ordering of in_array
SELECT array_agg(e) INTO in_array FROM (SELECT unnest(in_array) e ORDER BY e) x;
-- stop if no rows
IF element_count IS NULL THEN
RETURN NULL;
END IF;
-- stop if our breaks are more than our input array size
IF element_count < breaks THEN
RETURN in_array;
END IF;
-- get our mean value
SELECT avg(v) INTO arr_mean FROM ( SELECT unnest(in_array) as v ) x;
reply = Array[arr_mean];
-- slice our bread
LOOP
IF i > breaks THEN EXIT; END IF;
SELECT avg(e) INTO arr_mean FROM ( SELECT unnest(in_array) e) x WHERE e > reply[i-1];
IF arr_mean IS NOT NULL THEN
reply = array_append(reply, arr_mean);
END IF;
i := i+1;
END LOOP;
RETURN reply;
END;
$$ language plpgsql IMMUTABLE;
--
-- Determine the Jenks classifications from a numeric array
--
-- @param in_array A numeric array of numbers to determine the best
-- bins based on the Jenks method.
--
-- @param breaks The number of bins you want to find.
--
-- @param iterations The number of different starting positions to test.
--
-- @param invert Optional wheter to return the top of each bin (default)
-- or the bottom. BOOLEAN, default=FALSE.
--
--
CREATE OR REPLACE FUNCTION CDB_JenksBins ( in_array NUMERIC[], breaks INT, iterations INT DEFAULT 5, invert BOOLEAN DEFAULT FALSE) RETURNS NUMERIC[] as $$
DECLARE
element_count INT4;
arr_mean NUMERIC;
bot INT;
top INT;
tops INT[];
classes INT[][];
i INT := 1; j INT := 1;
curr_result NUMERIC[];
best_result NUMERIC[];
seedtarget TEXT;
quant NUMERIC[];
shuffles INT;
BEGIN
-- get the total size of our row
element_count := array_length(in_array, 1); --array_upper(in_array, 1) - array_lower(in_array, 1);
-- ensure the ordering of in_array
SELECT array_agg(e) INTO in_array FROM (SELECT unnest(in_array) e ORDER BY e) x;
-- stop if no rows
IF element_count IS NULL THEN
RETURN NULL;
END IF;
-- stop if our breaks are more than our input array size
IF element_count < breaks THEN
RETURN in_array;
END IF;
shuffles := LEAST(GREATEST(floor(2500000.0/(element_count::float*iterations::float)), 1), 750)::int;
-- get our mean value
SELECT avg(v) INTO arr_mean FROM ( SELECT unnest(in_array) as v ) x;
-- assume best is actually Quantile
SELECT cdb_crankshaft.CDB_QuantileBins(in_array, breaks) INTO quant;
-- if data is very very large, just return quant and be done
IF element_count > 5000000 THEN
RETURN quant;
END IF;
-- change quant into bottom, top markers
LOOP
IF i = 1 THEN
bot = 1;
ELSE
-- use last top to find this bot
bot = top+1;
END IF;
IF i = breaks THEN
top = element_count;
ELSE
SELECT count(*) INTO top FROM ( SELECT unnest(in_array) as v) x WHERE v <= quant[i];
END IF;
IF i = 1 THEN
classes = ARRAY[ARRAY[bot,top]];
ELSE
classes = ARRAY_CAT(classes,ARRAY[bot,top]);
END IF;
IF i > breaks THEN EXIT; END IF;
i = i+1;
END LOOP;
best_result = cdb_crankshaft.CDB_JenksBinsIteration( in_array, breaks, classes, invert, element_count, arr_mean, shuffles);
--set the seed so we can ensure the same results
SELECT setseed(0.4567) INTO seedtarget;
--loop through random starting positions
LOOP
IF j > iterations-1 THEN EXIT; END IF;
i = 1;
tops = ARRAY[element_count];
LOOP
IF i = breaks THEN EXIT; END IF;
SELECT array_agg(distinct e) INTO tops FROM (SELECT unnest(array_cat(tops, ARRAY[floor(random()*element_count::float)::int])) as e ORDER BY e) x WHERE e != 1;
i = array_length(tops, 1);
END LOOP;
i = 1;
LOOP
IF i > breaks THEN EXIT; END IF;
IF i = 1 THEN
bot = 1;
ELSE
bot = top+1;
END IF;
top = tops[i];
IF i = 1 THEN
classes = ARRAY[ARRAY[bot,top]];
ELSE
classes = ARRAY_CAT(classes,ARRAY[bot,top]);
END IF;
i := i+1;
END LOOP;
curr_result = cdb_crankshaft.CDB_JenksBinsIteration( in_array, breaks, classes, invert, element_count, arr_mean, shuffles);
IF curr_result[1] > best_result[1] THEN
best_result = curr_result;
j = j-1; -- if we found a better result, add one more search
END IF;
j = j+1;
END LOOP;
RETURN (best_result)[2:array_upper(best_result, 1)];
END;
$$ language plpgsql IMMUTABLE;
--
-- Perform a single iteration of the Jenks classification
--
CREATE OR REPLACE FUNCTION CDB_JenksBinsIteration ( in_array NUMERIC[], breaks INT, classes INT[][], invert BOOLEAN, element_count INT4, arr_mean NUMERIC, max_search INT DEFAULT 50) RETURNS NUMERIC[] as $$
DECLARE
tmp_val numeric;
new_classes int[][];
tmp_class int[];
i INT := 1;
j INT := 1;
side INT := 2;
sdam numeric;
gvf numeric := 0.0;
new_gvf numeric;
arr_gvf numeric[];
class_avg numeric;
class_max_i INT;
class_min_i INT;
class_max numeric;
class_min numeric;
reply numeric[];
BEGIN
-- Calculate the sum of squared deviations from the array mean (SDAM).
SELECT sum((arr_mean - e)^2) INTO sdam FROM ( SELECT unnest(in_array) as e ) x;
--Identify the breaks for the lowest GVF
LOOP
i = 1;
LOOP
-- get our mean
SELECT avg(e) INTO class_avg FROM ( SELECT unnest(in_array[classes[i][1]:classes[i][2]]) as e) x;
-- find the deviation
SELECT sum((class_avg-e)^2) INTO tmp_val FROM ( SELECT unnest(in_array[classes[i][1]:classes[i][2]]) as e ) x;
IF i = 1 THEN
arr_gvf = ARRAY[tmp_val];
-- init our min/max map for later
class_max = arr_gvf[i];
class_min = arr_gvf[i];
class_min_i = 1;
class_max_i = 1;
ELSE
arr_gvf = array_append(arr_gvf, tmp_val);
END IF;
i := i+1;
IF i > breaks THEN EXIT; END IF;
END LOOP;
-- calculate our new GVF
SELECT sdam-sum(e) INTO new_gvf FROM ( SELECT unnest(arr_gvf) as e ) x;
-- if no improvement was made, exit
IF new_gvf < gvf THEN EXIT; END IF;
gvf = new_gvf;
IF j > max_search THEN EXIT; END IF;
j = j+1;
i = 1;
LOOP
--establish directionality (uppward through classes or downward)
IF arr_gvf[i] < class_min THEN
class_min = arr_gvf[i];
class_min_i = i;
END IF;
IF arr_gvf[i] > class_max THEN
class_max = arr_gvf[i];
class_max_i = i;
END IF;
i := i+1;
IF i > breaks THEN EXIT; END IF;
END LOOP;
IF class_max_i > class_min_i THEN
class_min_i = class_max_i - 1;
ELSE
class_min_i = class_max_i + 1;
END IF;
--Move from higher class to a lower gid order
IF class_max_i > class_min_i THEN
classes[class_max_i][1] = classes[class_max_i][1] + 1;
classes[class_min_i][2] = classes[class_min_i][2] + 1;
ELSE -- Move from lower class UP into a higher class by gid
classes[class_max_i][2] = classes[class_max_i][2] - 1;
classes[class_min_i][1] = classes[class_min_i][1] - 1;
END IF;
END LOOP;
i = 1;
LOOP
IF invert = TRUE THEN
side = 1; --default returns bottom side of breaks, invert returns top side
END IF;
reply = array_append(reply, in_array[classes[i][side]]);
i = i+1;
IF i > breaks THEN EXIT; END IF;
END LOOP;
RETURN array_prepend(gvf, reply);
END;
$$ language plpgsql IMMUTABLE;
--
-- Determine the Quantile classifications from a numeric array
--
-- @param in_array A numeric array of numbers to determine the best
-- bins based on the Quantile method.
--
-- @param breaks The number of bins you want to find.
--
--
CREATE OR REPLACE FUNCTION CDB_QuantileBins ( in_array NUMERIC[], breaks INT) RETURNS NUMERIC[] as $$
DECLARE
element_count INT4;
break_size numeric;
tmp_val numeric;
i INT := 1;
reply numeric[];
BEGIN
-- sort our values
SELECT array_agg(e) INTO in_array FROM (SELECT unnest(in_array) e ORDER BY e ASC) x;
-- get the total size of our data
element_count := array_length(in_array, 1);
break_size := element_count::numeric / breaks;
-- slice our bread
LOOP
IF i < breaks THEN
IF break_size * i % 1 > 0 THEN
SELECT e INTO tmp_val FROM ( SELECT unnest(in_array) e LIMIT 1 OFFSET ceil(break_size * i) - 1) x;
ELSE
SELECT avg(e) INTO tmp_val FROM ( SELECT unnest(in_array) e LIMIT 2 OFFSET ceil(break_size * i) - 1 ) x;
END IF;
ELSIF i = breaks THEN
-- select the last value
SELECT max(e) INTO tmp_val FROM ( SELECT unnest(in_array) e ) x;
ELSE
EXIT;
END IF;
reply = array_append(reply, tmp_val);
i := i+1;
END LOOP;
RETURN reply;
END;
$$ language plpgsql IMMUTABLE;

6
src/pg/test/expected/02_moran_test.out
View File

@ -5,6 +5,12 @@ SET client_min_messages TO WARNING;
\set ECHO none \set ECHO none
_cdb_random_seeds _cdb_random_seeds
(1 row)
moran|significance
0.3399|-0.0196
(1 row)
_cdb_random_seeds
(1 row) (1 row)
code|quads code|quads
01|HH 01|HH

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