def test_nocrs_wgs84_geojson(self):
vector_io = VectorFileIO(
uri=os.path.join(testfile_path, 'iraq_hospitals.geojson'))
raw_json = json.loads(vector_io.read(format=geo.formats.JSON))
self.assertFalse(hasattr(raw_json, 'crs'))
epsg = vector_io.get_epsg()
self.assertEquals(epsg, 4326)
def __init__(self, **kwargs):
"""
Create an instance of LeastCostProcess class.
:param kwargs:
"""
super(LeastCostProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result', uri=self.get_outpath())
self.validate()
def test_validationInputsMax(self):
"""
Test the GaiaProcess.validate() function - fail on > max input types
"""
vector_io1 = VectorFileIO(uri='/fake/path')
vector_io2 = VectorFileIO(uri='/fake/path')
with self.assertRaises(geo.GaiaException) as ge:
geo.LengthProcess(inputs=[vector_io1, vector_io2])
self.assertIn('Incorrect # of inputs; expected 1', str(ge.exception))
def test_mercator_geojson(self):
vector_io = VectorFileIO(
uri=os.path.join(testfile_path, 'iraq_hospitals_3857.json'))
self.assertEquals(vector_io.get_epsg(), 3857)
jsonwm = json.loads(vector_io.read(format=geo.formats.JSON))
self.assertEquals(jsonwm['crs']['properties']['name'], 'EPSG:3857')
self.assertEquals(jsonwm['features'][0]['geometry']['coordinates'],
[4940150.544527022, 3941210.867854486])
json84 = json.loads(vector_io.read(format=geo.formats.JSON, epsg=4326))
self.assertEquals(json84['crs']['properties']['name'], 'EPSG:4326')
self.assertEquals(json84['features'][0]['geometry']['coordinates'],
[44.378127400000004, 33.34517919999999])
def test_within(self):
"""
Test WithinProcess for vector inputs
"""
vector1_io = VectorFileIO(
uri=os.path.join(testfile_path, 'iraq_hospitals.geojson'))
vector2_io = VectorFileIO(
uri=os.path.join(testfile_path, 'baghdad_districts.geojson'))
process = geo.WithinProcess(inputs=[vector1_io, vector2_io])
try:
process.compute()
self.assertEquals(len(process.output.data), 19)
finally:
if process:
process.purge()
def test_within_reproject(self):
"""
Test WithinProcess for vector inputs, where output should be in
same projection as first input (in this case, 3857).
"""
vector1_io = VectorFileIO(
uri=os.path.join(testfile_path, 'iraq_hospitals_3857.json'))
vector2_io = VectorFileIO(
uri=os.path.join(testfile_path, 'baghdad_districts.geojson'))
process = geo.WithinProcess(inputs=[vector1_io, vector2_io])
try:
process.compute()
self.assertEquals(process.output.data.crs, {'init': u'epsg:3857'})
self.assertEquals(len(process.output.data), 19)
finally:
if process:
process.purge()
def test_validationInputsMin(self):
"""
Test the GaiaProcess.validate() function - fail on < minimum input types
"""
vector_io = VectorFileIO(uri='/fake/path1')
with self.assertRaises(geo.GaiaException) as ge:
geo.IntersectsProcess(inputs=[vector_io])
self.assertIn('Not enough inputs for process', str(ge.exception))
def test_validationInputsPass(self):
"""
Test the GaiaProcess.validate() function - pass on valid input
"""
raster_io = RasterFileIO(uri='/fake/path')
vector_io = VectorFileIO(uri='/fake/path')
try:
geo.ZonalStatsProcess(inputs=[raster_io, vector_io])
except geo.GaiaException:
self.fail("ZonalProcess should have passed validation but did not")
def test_validationInputsOrder(self):
"""
Test the GaiaProcess.validate() function - fail on incorrect order
"""
raster_iO = RasterFileIO(uri='/fake/path1')
vector_io = VectorFileIO(uri='/fake/path2')
with self.assertRaises(geo.GaiaException) as ge:
geo.ZonalStatsProcess(inputs=[vector_io, raster_iO])
self.assertIn('Input #1 is of incorrect type.', str(ge.exception))
def test_distance(self):
"""
Test DistanceProcess for vector inputs
"""
vector1_io = VectorFileIO(
uri=os.path.join(testfile_path, 'baghdad_districts.geojson'))
vector2_io = VectorFileIO(
uri=os.path.join(testfile_path, 'iraq_hospitals.geojson'))
process = geo.DistanceProcess(inputs=[vector1_io, vector2_io])
try:
process.compute()
with open(
os.path.join(testfile_path,
'distance_process_results.json')) as exp:
expected_json = json.load(exp)
actual_json = json.loads(
process.output.read(format=geo.formats.JSON))
self.assertEquals(len(expected_json['features']),
len(actual_json['features']))
finally:
if process:
process.purge()
class ZonalStatsProcess(GaiaProcess):
"""
Calculates statistical values from a raster dataset for each polygon
in a vector dataset.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Raster image',
'type': types.RASTER,
'max': 1
},
{'description': 'Zones',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(ZonalStatsProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def compute(self):
"""
Run the process
"""
self.output.create_output_dir(self.output.uri)
features = gdal_zonalstats(
self.inputs[1].read(format=formats.JSON,
epsg=self.inputs[0].get_epsg()),
self.inputs[0].read())
self.output.data = GeoDataFrame.from_features(features)
self.output.write()
def test_union(self):
"""
Test UnionProcess for vector inputs
"""
vector1_io = VectorFileIO(uri=os.path.join(
testfile_path, 'baghdad_districts.geojson'),
filters=[('NNAME', 'contains', '^A')])
vector2_io = VectorFileIO(uri=os.path.join(
testfile_path, 'baghdad_districts.geojson'),
filters=[('NNAME', 'contains', '^B')])
process = geo.UnionProcess(inputs=[vector1_io, vector2_io])
try:
process.compute()
with open(os.path.join(testfile_path,
'union_process_results.json')) as exp:
expected_json = json.load(exp)
actual_json = json.loads(
process.output.read(format=geo.formats.JSON))
self.assertEquals(len(expected_json['features']),
len(actual_json['features']))
finally:
if process:
process.purge()
def test_length(self):
"""
Test LengthProcess for vector inputs
"""
vector_roads = VectorFileIO(uri=os.path.join(testfile_path,
'iraq_roads.geojson'),
filters=[('type', '=', 'motorway'),
('bridge', '=', 1)])
process = geo.LengthProcess(inputs=[vector_roads])
try:
process.compute()
with open(
os.path.join(testfile_path,
'length_process_results.json')) as exp:
expected_json = json.load(exp)
actual_json = json.loads(
process.output.read(format=geo.formats.JSON))
self.assertEquals(len(expected_json['features']),
len(actual_json['features']))
finally:
if process:
process.purge()
def test_subset_raster(self):
"""
Test SubsetProcess for vector & raster inputs
"""
zipfile = ZipFile(os.path.join(testfile_path, '2states.zip'), 'r')
zipfile.extract('2states.geojson', testfile_path)
vector_io = VectorFileIO(
uri=os.path.join(testfile_path, '2states.geojson'))
raster_io = RasterFileIO(
uri=os.path.join(testfile_path, 'globalairtemp.tif'))
process = geo.SubsetProcess(inputs=[raster_io, vector_io])
try:
process.compute()
self.assertEquals(type(process.output.data).__name__, 'Dataset')
self.assertTrue(os.path.exists(process.output.uri))
self.assertIsNotNone(process.id)
self.assertIn(process.id, process.output.uri)
finally:
testfile = os.path.join(testfile_path, '2states.geojson')
if os.path.exists(testfile):
os.remove(testfile)
if process:
process.purge()
class LengthProcess(GaiaProcess):
"""
Calculate the length of each feature in a dataset.
If the dataset projection is not in metric units, it will
be temporarily reprojected to EPSG:3857 to calculate the area.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Line/Polygon dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(LengthProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate lengths using pandas
:return: Result as a GeoDataFrame
"""
featureio = self.inputs[0]
original_projection = featureio.get_epsg()
epsg = original_projection
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(original_projection))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
epsg = 3857
else:
original_projection = None
feature_df = GeoDataFrame.copy(featureio.read(epsg=epsg))
feature_df['length'] = feature_df.geometry.length
if original_projection:
feature_df[feature_df.geometry.name] = feature_df.geometry.to_crs(
epsg=original_projection)
feature_df.crs = fiona.crs.from_epsg(original_projection)
return feature_df
def calc_postgis(self):
"""
Calculate lengths using PostGIS
:return: Result as a GeoDataFrame
"""
featureio = self.inputs[0]
geom0, epsg = featureio.geom_column, featureio.epsg
srs = osr.SpatialReference()
srs.ImportFromEPSG(epsg)
geom_query = geom0
geometry_type = featureio.geometry_type
length_func = 'ST_Perimeter' if 'POLYGON' in geometry_type.upper() \
else 'ST_Length'
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
geom_query = 'ST_Transform({}, {})'.format(
geom_query, 3857)
geom_query = ', {}({}) as length'.format(length_func, geom_query)
query, params = featureio.get_query()
query = query.replace('FROM', '{} FROM'.format(geom_query))
logger.debug(query)
return df_from_postgis(featureio.engine, query, params, geom0, epsg)
def compute(self):
"""
Run the length process
"""
if self.inputs[0].__class__.__name__ == 'PostgisIO':
data = self.calc_postgis()
else:
data = self.calc_pandas()
self.output.data = data
self.output.write()
def __init__(self, inputs=None, buffer_size=None, **kwargs):
self.buffer_size = buffer_size
super(BufferProcess, self).__init__(inputs, **kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def __init__(self, distance=None, **kwargs):
super(NearProcess, self).__init__(**kwargs)
self.distance = distance
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
class NearProcess(GaiaProcess):
"""
Takes two inputs, the second assumed to contain a single feature,
the first a vector dataset. Requires a distance argument, and the unit of
measure should be meters. If inputs are not in a
metric projection they will be reprojected to EPSG:3857.
Returns the features in the first input within a specified distance
of the point in the second input.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Features',
'type': types.VECTOR,
'max': 1
},
{'description': 'Point',
'type': types.VECTOR,
'max': 1
}
]
#: Required arguments, data types as dict
required_args = [{
'name': 'distance',
'title': 'Distance',
'description': 'Distance to search for features, in meters',
'type': float
}]
#: Default output format
default_output = formats.JSON
def __init__(self, distance=None, **kwargs):
super(NearProcess, self).__init__(**kwargs)
self.distance = distance
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculates the features within the specified distance using pandas
:return: results as a GeoDataFrame
"""
features = self.inputs[0]
original_projection = self.inputs[0].get_epsg()
epsg = original_projection
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(original_projection))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
epsg = 3857
else:
original_projection = None
features_df = features.read(epsg=epsg)
features_gs = features_df.geometry
point_df = self.inputs[1].read(epsg=epsg)[:1]
point_gs = point_df.geometry
features_length = len(features_gs)
min_dist = np.empty(features_length)
for i, feature in enumerate(features_gs):
min_dist[i] = np.min([feature.distance(point_gs[0])])
nearby_df = GeoDataFrame.copy(features_df)
nearby_df['distance'] = min_dist
distance_max = self.distance
nearby_df = nearby_df[(nearby_df['distance'] <= distance_max)]\
.sort_values('distance')
if original_projection:
nearby_df[nearby_df.geometry.name] = \
nearby_df.geometry.to_crs(epsg=original_projection)
return nearby_df
def calc_postgis(self):
"""
Calculates the features within the specified distance using PostGIS
via DWithin plus K-Nearest Neighbor (KNN) query
:return: results as a GeoDataFrame
"""
featureio = self.inputs[0]
pointio = self.inputs[1]
feature_geom, epsg = featureio.geom_column, featureio.epsg
point_json = json.loads(pointio.read(
format=formats.JSON))['features'][0]
point_epsg = pointio.get_epsg()
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(epsg))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
epsg = 3857
io_query, params = featureio.get_query()
point_geom = 'ST_Transform(ST_SetSRID(ST_GeomFromGeoJSON(\'' \
'{geojson}\'),{point_epsg}), {epsg})'.\
format(geojson=json.dumps(point_json['geometry']),
point_epsg=point_epsg, epsg=epsg)
dist1 = """, (SELECT ST_Distance(
ST_Transform({table0}.{geom0},{epsg}),
ST_Transform(point, {epsg}))
FROM {point_geom} as point
ORDER BY {table0}.{geom0} <#> point LIMIT 1) as distance FROM
""".format(table0=featureio.table,
geom0=feature_geom,
point_geom=point_geom,
epsg=epsg)
dist2 = """
WHERE ST_DWithin({point_geom},
ST_Transform({table0}.{geom0},{epsg}), {distance})
""".format(table0=featureio.table,
geom0=feature_geom,
point_geom=point_geom,
epsg=epsg,
distance=self.distance)
dist3 = ' ORDER BY distance ASC'
query = re.sub('FROM', dist1, io_query).rstrip(';')
if 'WHERE' in query:
query = re.sub('WHERE', dist2 + ' AND ', query)
else:
query += dist2
query += dist3
logger.debug(query)
return df_from_postgis(featureio.engine,
query, params, feature_geom, epsg)
def compute(self):
"""
Run the process
"""
if self.inputs[0].__class__.__name__ == 'PostgisIO':
data = self.calc_postgis()
else:
data = self.calc_pandas()
self.output.data = data
self.output.write()
class DistanceProcess(GaiaProcess):
"""
Calculates the minimum distance from each feature of the first dataset
to the nearest feature of the second dataset.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'From dataset',
'type': types.VECTOR,
'max': 1
},
{'description': 'To dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(DistanceProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate the minimum distance between features using pandas
GeoDataFrames.
:return: Minimum distance results as a GeoDataFrame
"""
first = self.inputs[0]
original_projection = first.get_epsg()
epsg = original_projection
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(original_projection))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
epsg = 3857
else:
original_projection = None
first_df = first.read(epsg=epsg)
first_gs = first_df.geometry
first_length = len(first_gs)
second_df = self.inputs[1].read(epsg=epsg)
second_gs = second_df.geometry
min_dist = np.empty(first_length)
for i, first_features in enumerate(first_gs):
min_dist[i] = np.min([first_features.distance(second_features)
for second_features in second_gs])
distance_df = GeoDataFrame.copy(first_df)
distance_df['distance'] = min_dist
distance_df.sort_values('distance', inplace=True)
if original_projection:
distance_df[distance_df.geometry.name] = \
distance_df.geometry.to_crs(epsg=original_projection)
return distance_df
def calc_postgis(self):
"""
Calculate the minimum distance between features using PostGIS
K-Nearest Neighbor (KNN) query
:return: Minimum distance results as a GeoDataFrame
"""
diff_queries = []
diff_params = []
first = self.inputs[0]
geom0, epsg = first.geom_column, first.epsg
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(epsg))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
epsg = 3857
geom1 = self.inputs[1].geom_column
for pg_io in self.inputs:
io_query, params = pg_io.get_query()
diff_queries.append(io_query.rstrip(';'))
diff_params.insert(0, params)
diff_params = [item for x in diff_params for item in x]
dist1 = """, (SELECT ST_Distance(
ST_Transform({table0}.{geom0},{epsg}),
ST_Transform(query2.{geom1},{epsg}))
as distance
""".format(table0=self.inputs[0].table,
geom0=geom0,
geom1=geom1,
epsg=epsg)
dist2 = """
ORDER BY {table0}.{geom0} <#> query2.{geom1} LIMIT 1) FROM
""".format(table0=self.inputs[0].table,
geom0=geom0,
geom1=geom1,
epsg=epsg)
dist3 = ' ORDER BY distance ASC'
query = re.sub('FROM', dist1 + ' FROM (' + diff_queries[1] +
') as query2 ' + dist2, diff_queries[0]) + dist3
return df_from_postgis(first.engine, query, diff_params, geom0, epsg)
def compute(self):
"""
Run the distance process
"""
input_classes = list(self.get_input_classes())
use_postgis = (len(input_classes) == 1 and
input_classes[0] == 'PostgisIO')
data = self.calc_postgis() if use_postgis else self.calc_pandas()
self.output.data = data
self.output.write()
def __init__(self, combined=False, **kwargs):
super(CentroidProcess, self).__init__(**kwargs)
self.combined = combined
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
class CentroidProcess(GaiaProcess):
"""
Calculates the centroid point of a vector dataset.
"""
#: List of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Line/Polygon dataset',
'type': types.VECTOR,
'max': 1
}
]
optional_args = [{
'name': 'combined',
'title': 'Combined',
'description': 'Get centroid of features combined (default False)',
'type': bool,
}]
#: Default output format
default_output = formats.JSON
def __init__(self, combined=False, **kwargs):
super(CentroidProcess, self).__init__(**kwargs)
self.combined = combined
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate the centroid using pandas GeoDataFrames
:return: centroid as a GeoDataFrame
"""
df_in = self.inputs[0].read()
df = GeoDataFrame(df_in.copy(), geometry=df_in.geometry.name)
if self.combined:
gs = GeoSeries(df.geometry.unary_union.centroid,
name=df_in.geometry.name)
return GeoDataFrame(gs)
else:
df[df.geometry.name] = df.geometry.centroid
return df
def calc_postgis(self):
"""
Calculate the centroid using PostGIS
:return: centroid as a GeoDataFrame
"""
pg_io = self.inputs[0]
io_query, params = pg_io.get_query()
geom0, epsg = pg_io.geom_column, pg_io.epsg
if self.combined:
query = 'SELECT ST_Centroid(ST_Union({geom})) as {geom}' \
' from ({query}) as foo'.format(geom=geom0,
query=io_query.rstrip(';'))
else:
query = re.sub('"{}"'.format(geom0),
'ST_Centroid("{geom}") as {geom}'.format(
geom=geom0), io_query, 1)
return df_from_postgis(pg_io.engine, query, params, geom0, epsg)
def compute(self):
"""
Run the centroid process
"""
use_postgis = self.inputs[0].__class__.__name__ == 'PostgisIO'
data = self.calc_postgis() if use_postgis else self.calc_pandas()
self.output.data = data
self.output.write()
logger.debug(self.output)
class BufferProcess(GaiaProcess):
"""
Generates a buffer polygon around the geometries of the input data.
The size of the buffer is determined by the 'buffer_size' args key
and the unit of measure should be meters. If inputs are not in a
metric projection they will be reprojected to EPSG:3857.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Feature dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Required arguments, data types as dict
required_args = [
{
'name': 'buffer_size',
'title': 'Buffer Size',
'description': 'Size of the buffer in meters',
'type': float
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, inputs=None, buffer_size=None, **kwargs):
self.buffer_size = buffer_size
super(BufferProcess, self).__init__(inputs, **kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate the buffer using pandas GeoDataFrames
:return: Buffer as a pandas GeoDataFrame
"""
featureio = self.inputs[0]
original_projection = featureio.get_epsg()
epsg = original_projection
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(original_projection))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
epsg = 3857
else:
original_projection = None
feature_df = featureio.read(epsg=epsg)
buffer = GeoSeries(feature_df.buffer(self.buffer_size).unary_union)
buffer_df = GeoDataFrame(geometry=buffer)
buffer_df.crs = feature_df.crs
if original_projection:
buffer_df[buffer_df.geometry.name] = buffer_df.to_crs(
epsg=original_projection)
buffer_df.crs = fiona.crs.from_epsg(original_projection)
return buffer_df
def calc_postgis(self):
"""
Calculate the buffer using PostGIS
:return: Buffer as a pandas GeoDataFrame
"""
pg_io = self.inputs[0]
original_projection = pg_io.epsg
io_query, params = pg_io.get_query()
srs = osr.SpatialReference()
srs.ImportFromEPSG(int(original_projection))
if not srs.GetAttrValue('UNIT').lower().startswith('met'):
geom_query = 'ST_Transform({}, {})'.format(
pg_io.geom_column, 3857)
else:
original_projection = None
buffer_query = 'ST_Union(ST_Buffer({}, %s))'.format(geom_query)
if original_projection:
buffer_query = 'ST_Transform({}, {})'.format(buffer_query,
original_projection)
query = 'SELECT {buffer} as {geocol} ' \
'FROM ({query}) as foo'.format(buffer=buffer_query,
geocol=pg_io.geom_column,
query=io_query.rstrip(';'))
params.insert(0, self.buffer_size)
logger.debug(query)
return df_from_postgis(pg_io.engine, query, params,
pg_io.geom_column, pg_io.epsg)
def compute(self):
"""
Run the buffer process.
"""
if self.inputs[0].__class__.__name__ == 'PostgisIO':
data = self.calc_postgis()
else:
data = self.calc_pandas()
self.output.data = data
self.output.write()
class UnionProcess(GaiaProcess):
"""
Combines two vector datasets into one.
They datasets should have the same columns.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'First dataset',
'type': types.VECTOR,
'max': 1
},
{'description': 'Second dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(UnionProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate the union using pandas GeoDataFrames
:return: union result as a GeoDataFrame
"""
first, second = self.inputs[0], self.inputs[1]
first_df = first.read()
second_df = second.read(epsg=first.get_epsg())
if ''.join(first_df.columns) != ''.join(second_df.columns):
raise GaiaException('Inputs must have the same columns')
uniondf = GeoDataFrame(pd.concat([first_df, second_df]))
return uniondf
def calc_postgis(self):
"""
Calculate the union using PostGIS
:return: union result as a GeoDataFrame
"""
union_queries = []
union_params = []
first = self.inputs[0]
second = self.inputs[1]
geom0, epsg = first.geom_column, first.epsg
geom1, epsg1 = second.geom_column, second.epsg
if ''.join(first.columns) != ''.join(second.columns):
raise GaiaException('Inputs must have the same columns')
for pg_io in self.inputs:
io_query, params = pg_io.get_query()
union_queries.append(io_query.rstrip(';'))
union_params.extend(params)
if epsg1 != epsg:
geom1_query = 'ST_Transform({},{})'.format(geom1, epsg)
union_queries[1] = union_queries[1].replace(
'"{}"'.format(geom1), geom1_query)
query = '({query0}) UNION ({query1})'\
.format(query0=union_queries[0], query1=union_queries[1])
return df_from_postgis(first.engine,
query, union_params, geom0, epsg)
def compute(self):
"""
Run the union process.
"""
input_classes = list(self.get_input_classes())
use_postgis = (len(input_classes) == 1 and
input_classes[0] == 'PostgisIO')
data = self.calc_postgis() if use_postgis else self.calc_pandas()
self.output.data = data
self.output.write()
logger.debug(self.output)
class WithinProcess(GaiaProcess):
"""
Similar to SubsetProcess but for vectors: calculates the features within
a vector dataset that are within (or whose centroids are within) the
polygons of a second vector dataset.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Feature dataset',
'type': types.VECTOR,
'max': 1
},
{'description': 'Within dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(WithinProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate the within process using pandas GeoDataFrames
:return: within result as a GeoDataFrame
"""
first, second = self.inputs[0], self.inputs[1]
first_df = first.read()
second_df = second.read(epsg=first.get_epsg())
first_within = first_df[first_df.geometry.within(
second_df.geometry.unary_union)]
return first_within
def calc_postgis(self):
"""
Calculate the within process using PostGIS
:return: within result as a GeoDataFrame
"""
first = self.inputs[0]
within_queries = []
within_params = []
geom0 = first.geom_column
epsg = first.epsg
geom1 = self.inputs[1].geom_column
for pg_io in self.inputs:
io_query, params = pg_io.get_query()
within_queries.append(io_query.rstrip(';'))
within_params.extend(params)
joinstr = ' AND ' if 'WHERE' in within_queries[0].upper() else ' WHERE '
query = '{query0} {join} ST_Within(ST_Transform({geom0},{epsg}), ' \
'(SELECT ST_Union(ST_TRANSFORM({geom1},{epsg})) ' \
'from ({query1}) as q2))'\
.format(query0=within_queries[0], join=joinstr, geom0=geom0,
geom1=geom1, epsg=epsg, query1=within_queries[1])
return df_from_postgis(first.engine, query, params, geom0, epsg)
def compute(self):
"""
Run the Within process
"""
if len(self.inputs) != 2:
raise GaiaException('WithinProcess requires 2 inputs')
input_classes = list(self.get_input_classes())
use_postgis = (len(input_classes) == 1 and
input_classes[0] == 'PostgisIO')
data = self.calc_postgis() if use_postgis else self.calc_pandas()
self.output.data = data
self.output.write()
class EqualsProcess(GaiaProcess):
"""
Calculates the features within the first vector dataset that are the same as
the features of the second vector dataset.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'First dataset',
'type': types.VECTOR,
'max': 1
},
{'description': 'Second dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(EqualsProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate which features are equal using pandas
:return: result as a GeoDataFrame
"""
first, second = self.inputs[0], self.inputs[1]
first_df = first.read()
second_df = second.read(epsg=first.get_epsg())
first_gs = first_df.geometry
first_length = len(first_gs)
second_gs = second_df.geometry
matches = np.empty(first_length)
for i, first_features in enumerate(first_gs):
matched = [first_features.equals(second_features)
for second_features in second_gs]
matches[i] = True if (True in matched) else False
output_df = GeoDataFrame.copy(first_df)
output_df['equals'] = matches
output_df = output_df[
(output_df['equals'] == 1)].drop('equals', 1)
return output_df
def calc_postgis(self):
"""
Calculate which features are equal using PostGIS
:return: result as a GeoDataFrame
"""
equals_queries = []
equals_params = []
first = self.inputs[0]
geom0, epsg = first.geom_column, first.epsg
geom1 = self.inputs[1].geom_column
for pg_io in self.inputs:
io_query, params = pg_io.get_query()
equals_queries.append(io_query.rstrip(';'))
equals_params.extend(params)
joinstr = ' AND ' if 'WHERE' in equals_queries[0].upper() else ' WHERE '
query = '{query0} {join} {geom0} IN (SELECT {geom1} ' \
'FROM ({query1}) as second)'.format(query0=equals_queries[0],
query1=equals_queries[1],
join=joinstr,
geom0=geom0,
geom1=geom1)
logger.debug(query)
return df_from_postgis(first.engine, query, equals_params, geom0, epsg)
def compute(self):
"""
Run the process
"""
input_classes = list(self.get_input_classes())
use_postgis = (len(input_classes) == 1 and
input_classes[0] == 'PostgisIO')
data = self.calc_postgis() if use_postgis else self.calc_pandas()
self.output.data = data
self.output.write()
logger.debug(self.output)
class LeastCostProcess(GaiaProcess):
"""
Process to calculate the least cost path between
two points over a raster grid.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [{
'description': 'Raster dataset',
'type': types.RASTER,
'max': 1
}, {
'description': 'Start/end point dataset(s)',
'type': types.VECTOR,
'max': 2
}]
default_output = formats.JSON
def __init__(self, **kwargs):
"""
Create an instance of LeastCostProcess class.
:param kwargs:
"""
super(LeastCostProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result', uri=self.get_outpath())
self.validate()
def array2shp(self, array, outSHPfn, rasterfn, pixelValue):
"""
Convert a grid array representation of the path into a shapefile
:param array: least cost path as numeric grid array
:param outSHPfn: output shapefile
:param rasterfn: raster file used to calculate path
:param pixelValue: cell value of path in grid array
"""
raster = get_dataset(rasterfn.uri)
geotransform = raster.GetGeoTransform()
pixelWidth = geotransform[1]
maxDistance = ceil(sqrt(2 * pixelWidth * pixelWidth))
count = 0
roadList = np.where(array == pixelValue)
pointDict = {}
for indexY in roadList[0]:
indexX = roadList[1][count]
Xcoord, Ycoord = self.pixel_offset2coord(rasterfn, indexX, indexY)
pointDict[count] = (Xcoord, Ycoord)
count += 1
multiline = ogr.Geometry(ogr.wkbMultiLineString)
for i in itertools.combinations(pointDict.values(), 2):
point1 = ogr.Geometry(ogr.wkbPoint)
point1.AddPoint(i[0][0], i[0][1])
point2 = ogr.Geometry(ogr.wkbPoint)
point2.AddPoint(i[1][0], i[1][1])
distance = point1.Distance(point2)
# calculate the distance between two points
if distance < maxDistance:
line = ogr.Geometry(ogr.wkbLineString)
line.AddPoint(i[0][0], i[0][1])
line.AddPoint(i[1][0], i[1][1])
multiline.AddGeometry(line)
shpDriver = ogr.GetDriverByName("GeoJSON")
if os.path.exists(outSHPfn):
shpDriver.DeleteDataSource(outSHPfn)
else:
self.output.create_output_dir(outSHPfn)
outDataSource = shpDriver.CreateDataSource(outSHPfn)
outLayer = outDataSource.CreateLayer(outSHPfn,
geom_type=ogr.wkbMultiLineString)
featureDefn = outLayer.GetLayerDefn()
outFeature = ogr.Feature(featureDefn)
outFeature.SetGeometry(multiline)
outLayer.CreateFeature(outFeature)
def raster_to_array(self, rasterfn):
"""
Convert a raster grid into an array
:param raster: input raster
:return: array
"""
raster = get_dataset(rasterfn.uri)
band = raster.GetRasterBand(1)
array = band.ReadAsArray()
return array
def coord2pixeloffset(self, rasterfn, x, y):
"""
Convert lat/long coordinates to pixel coordinates
:param rasterfn: raster file
:param x: longitude
:param y: latitude
:return:
"""
raster = get_dataset(rasterfn.uri)
geotransform = raster.GetGeoTransform()
originX = geotransform[0]
originY = geotransform[3]
pixelWidth = geotransform[1]
pixelHeight = geotransform[5]
xOffset = int((x - originX) / pixelWidth)
yOffset = int((y - originY) / pixelHeight)
return xOffset, yOffset
def pixel_offset2coord(self, rasterfn, xOffset, yOffset):
"""
Convert pixel coordinates to lat/long coordinates
:param rasterfn: raster dataset
:param xOffset: longitude offset
:param yOffset: latitude offset
:return: coordinates
"""
raster = get_dataset(rasterfn.uri)
geotransform = raster.GetGeoTransform()
originX = geotransform[0]
originY = geotransform[3]
pixelWidth = geotransform[1]
pixelHeight = geotransform[5]
coordX = originX + pixelWidth * xOffset
coordY = originY + pixelHeight * yOffset
return coordX, coordY
def create_path(self, raster, costSurfaceArray, start, end):
"""
Calculate the least cost path
:param raster: Raster file
:param costSurfaceArray: raster file as numeric array
:param start: start point
:param end: end point
:return: least cost path as grid array
"""
# coordinates to array index
startCoordX = start.x
startCoordY = start.y
startIndexX, startIndexY = self.coord2pixeloffset(
raster, startCoordX, startCoordY)
stopCoordX = end.x
stopCoordY = end.y
stopIndexX, stopIndexY = self.coord2pixeloffset(
raster, stopCoordX, stopCoordY)
# create path
indices, weight = route_through_array(costSurfaceArray,
(startIndexY, startIndexX),
(stopIndexY, stopIndexX),
geometric=True,
fully_connected=True)
indices = np.array(indices).T
path = np.zeros_like(costSurfaceArray)
path[indices[0], indices[1]] = 1
return path
def calculate_path(self, raster, start, end):
"""
Convert the input raster into an array and calculate the least
cost path as an array
:param raster: raster file
:param start: start point
:param end: end point
"""
costSurfaceArray = self.raster_to_array(raster)
pathArray = self.create_path(raster, costSurfaceArray, start, end)
self.array2shp(pathArray, self.output.uri, raster, 1)
def compute(self):
"""
Perform the process calculations
"""
if len(self.inputs) == 3:
start_point = self.inputs[1].read().iloc[0].geometry.centroid
end_point = self.inputs[2].read().iloc[0].geometry.centroid
else:
start_point = self.inputs[1].read().iloc[0].geometry.centroid
end_point = self.inputs[1].read().iloc[1].geometry.centroid
self.calculate_path(self.inputs[0], start_point, end_point)
class CrossesProcess(GaiaProcess):
"""
Calculates the features within the first vector dataset that cross
the combined features of the second vector dataset.
"""
#: Tuple of required inputs; name, type , max # of each; None = no max
required_inputs = [
{'description': 'Feature dataset',
'type': types.VECTOR,
'max': 1
},
{'description': 'Crosses dataset',
'type': types.VECTOR,
'max': 1
}
]
#: Default output format
default_output = formats.JSON
def __init__(self, **kwargs):
super(CrossesProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def calc_pandas(self):
"""
Calculate the process using pandas
:return: result as a GeoDataFrame
"""
first, second = self.inputs[0], self.inputs[1]
first_df = first.read()
second_df = second.read(epsg=first.get_epsg())
first_intersects = first_df[first_df.geometry.crosses(
second_df.geometry.unary_union)]
return first_intersects
def calc_postgis(self):
"""
Calculate the process using PostGIS
:return: result as a GeoDataFrame
"""
cross_queries = []
cross_params = []
first = self.inputs[0]
geom0, epsg = first.geom_column, first.epsg
geom1 = self.inputs[1].geom_column
for pg_io in self.inputs:
io_query, params = pg_io.get_query()
cross_queries.append(io_query.rstrip(';'))
cross_params.extend(params)
joinstr = ' AND ' if 'WHERE' in cross_queries[0].upper() else ' WHERE '
query = '{query0} {join} (SELECT ST_Crosses(ST_Transform(' \
'{table}.{geom0},{epsg}), ST_Union(ST_Transform(' \
'q2.{geom1},{epsg}))) from ({query1}) as q2)'\
.format(query0=cross_queries[0], join=joinstr, geom0=geom0,
geom1=geom1, epsg=epsg, query1=cross_queries[1],
table=first.table)
return df_from_postgis(first.engine, query, cross_params, geom0, epsg)
def compute(self):
"""
Run the crosses process
"""
input_classes = list(self.get_input_classes())
use_postgis = (len(input_classes) == 1 and
input_classes[0] == 'PostgisIO')
data = self.calc_postgis() if use_postgis else self.calc_pandas()
self.output.data = data
self.output.write()
logger.debug(self.output)
def __init__(self, **kwargs):
super(CrossesProcess, self).__init__(**kwargs)
if not self.output:
self.output = VectorFileIO(name='result',
uri=self.get_outpath())
def main(args):
parser = argparse.ArgumentParser(
description=
"Write a destination file with all features from source file "
"overlapping specified polygon")
parser.add_argument(
"source", help="Source vector file name that contain all features")
parser.add_argument(
"-p",
"--polygon",
nargs="+",
help="xmin ymin xmax ymax or vector file specifying the polygon")
parser.add_argument("destination",
help="Destination vector file with only features "
"overlapping the specified polygon")
args = parser.parse_args(args)
if (len(args.polygon) == 4):
xmin, ymin, xmax, ymax = [float(val) for val in args.polygon]
polygon = FeatureIO(features=[
{
"geometry": {
"type":
"Polygon",
"coordinates": [[[xmin, ymin], [xmax, ymin], [xmax, ymax],
[xmin, ymax]]]
},
"properties": {
"id": "Bounding box"
}
},
])
elif (len(args.polygon) == 1):
polygonImage = gdal.Open(args.polygon[0], gdal.GA_ReadOnly)
if (polygonImage):
gt = polygonImage.GetGeoTransform()
cols = polygonImage.RasterXSize
rows = polygonImage.RasterYSize
ext = GetExtent(gt, cols, rows)
src_srs = osr.SpatialReference()
src_srs.ImportFromWkt(polygonImage.GetProjection())
tgt_srs = src_srs.CloneGeogCS()
p = ReprojectCoords(ext, src_srs, tgt_srs)
polygon = FeatureIO(features=[
{
"geometry": {
"type":
"Polygon",
"coordinates": [[[p[0][0], p[0][1]], [
p[1][0], p[1][1]
], [p[2][0], p[2][1]], [p[3][0], p[3][1]]]]
},
"properties": {
"id": "Bounding box"
}
},
])
else:
polygon = VectorFileIO(uri=args.polygon[0])
else:
raise RuntimeError("Error: wrong number of parameters for polygon: {} "
"(can be 4 or 1)".format(len(args.polygon)))
source = VectorFileIO(uri=args.source)
destination = VectorFileIO(uri=args.destination)
intersectProcess = IntersectsProcess(inputs=[source, polygon],
output=destination)
intersectProcess.compute()