def test_nopoints():
with pytest.raises(TypeError):
shapely_to_ogr_type('Point')
with pytest.raises(TypeError):
shapely_to_ogr_type('MultiPoint')
zonal_stats(geoms, raster, global_src_extent=True)
def zonal_stats(vectors,
raster,
layer_num=0,
band_num=1,
func=None,
nodata_value=None,
categorical=False,
stats=None,
copy_properties=False,
all_touched=False,
transform=None):
if not stats:
if not categorical:
stats = ['count', 'min', 'max', 'mean', 'std']
if func:
stats.append('func')
# must have transform arg
if not transform:
raise Exception("Must provide the 'transform' kwarg")
rgt = transform
rsize = (raster.shape[1], raster.shape[0])
rbounds = raster_extent_as_bounds(rgt, rsize)
features_iter, strategy, spatial_ref = get_features(vectors, layer_num)
global_src_offset = (0, 0, raster.shape[0], raster.shape[1])
global_src_array = raster
mem_drv = ogr.GetDriverByName('Memory')
driver = gdal.GetDriverByName('MEM')
results = []
entity_images = []
for i, feat in enumerate(features_iter):
if feat['type'] == "Feature":
geom = shape(feat['geometry'])
else: # it's just a geometry
geom = shape(feat)
# Point and MultiPoint don't play well with GDALRasterize
# convert them into box polygons the size of a raster cell
buff = rgt[1] / 2.0
if geom.type == "MultiPoint":
geom = MultiPolygon(
[box(*(pt.buffer(buff).bounds)) for pt in geom.geoms])
elif geom.type == 'Point':
geom = box(*(geom.buffer(buff).bounds))
ogr_geom_type = shapely_to_ogr_type(geom.type)
# "Clip" the geometry bounds to the overall raster bounding box
# This should avoid any rasterIO errors for partially overlapping polys
geom_bounds = list(geom.bounds)
if geom_bounds[0] < rbounds[0]:
geom_bounds[0] = rbounds[0]
if geom_bounds[1] < rbounds[1]:
geom_bounds[1] = rbounds[1]
if geom_bounds[2] > rbounds[2]:
geom_bounds[2] = rbounds[2]
if geom_bounds[3] > rbounds[3]:
geom_bounds[3] = rbounds[3]
# calculate new geotransform of the feature subset
src_offset = bbox_to_pixel_offsets(rgt, geom_bounds)
new_gt = ((rgt[0] + (src_offset[0] * rgt[1])), rgt[1], 0.0,
(rgt[3] + (src_offset[1] * rgt[5])), 0.0, rgt[5])
if src_offset[2] <= 0 or src_offset[3] <= 0:
# we're off the raster completely, no overlap at all
# so there's no need to even bother trying to calculate
feature_stats = dict([(s, None) for s in stats])
img = {'__fid__': i, 'img': None}
else:
# derive array from global source extent array
# useful *only* when disk IO or raster format inefficiencies
# are your limiting factor
# advantage: reads raster data in one pass before loop
# disadvantage: large vector extents combined with big rasters
# need lotsa memory
xa = src_offset[0] - global_src_offset[0]
ya = src_offset[1] - global_src_offset[1]
xb = xa + src_offset[2]
yb = ya + src_offset[3]
src_array = global_src_array[ya:yb, xa:xb]
# Create a temporary vector layer in memory
mem_ds = mem_drv.CreateDataSource('out')
mem_layer = mem_ds.CreateLayer('out', spatial_ref, ogr_geom_type)
ogr_feature = ogr.Feature(feature_def=mem_layer.GetLayerDefn())
ogr_geom = ogr.CreateGeometryFromWkt(geom.wkt)
ogr_feature.SetGeometryDirectly(ogr_geom)
mem_layer.CreateFeature(ogr_feature)
# Rasterize it
rvds = driver.Create('rvds', src_offset[2], src_offset[3], 1,
gdal.GDT_Byte)
rvds.SetGeoTransform(new_gt)
if all_touched:
gdal.RasterizeLayer(rvds, [1],
mem_layer,
None,
None,
burn_values=[1],
options=['ALL_TOUCHED=True'])
else:
gdal.RasterizeLayer(rvds, [1],
mem_layer,
None,
None,
burn_values=[1],
options=['ALL_TOUCHED=False'])
rv_array = rvds.ReadAsArray()
# Mask the source data array with our current feature
# we take the logical_not to flip 0<->1 to get the correct mask effect
# we also mask out nodata values explictly
masked = np.ma.MaskedArray(src_array,
mask=np.logical_or(
src_array == nodata_value,
np.logical_not(rv_array)))
feature_stats = {}
if 'min' in stats:
feature_stats['min'] = float(masked.min())
if 'max' in stats:
feature_stats['max'] = float(masked.max())
if 'mean' in stats:
feature_stats['mean'] = float(masked.mean())
if 'count' in stats:
feature_stats['count'] = int(masked.count())
if 'std' in stats:
feature_stats['std'] = float(masked.std())
# optional
if 'func' in stats:
feature_stats[func.__name__] = func(masked)
if 'sum' in stats:
feature_stats['sum'] = float(masked.sum())
if 'std' in stats:
feature_stats['std'] = float(masked.std())
if 'median' in stats:
feature_stats['median'] = float(np.median(masked.compressed()))
if 'range' in stats:
try:
rmin = feature_stats['min']
except KeyError:
rmin = float(masked.min())
try:
rmax = feature_stats['max']
except KeyError:
rmax = float(masked.max())
feature_stats['range'] = rmax - rmin
img = {'__fid__': i, 'img': masked}
# Use the enumerated id as __fid__
feature_stats['__fid__'] = i
if 'properties' in feat and copy_properties:
for key, val in list(feat['properties'].items()):
feature_stats[key] = val
results.append(feature_stats)
entity_images.append(img)
return results, entity_images
def test_nopoints():
with pytest.raises(TypeError):
shapely_to_ogr_type('Point')
with pytest.raises(TypeError):
shapely_to_ogr_type('MultiPoint')
def mask_from_geom( geom, rds, band_num=1, epsg=32760, nodata_value=None,
all_touched=False, full_extent=False ):
"""
Return a binary mask to mask off everything outside of geom.
Parameters
----------
geom : shapely.geometry
Cells inside this geometry will be `False`. Cells outside will be `True`
rds : RasterDS
The raster dataset to create a mask for.
full_extent : bool
If `True`, return a mask that's the full extent of `rds`. If `False`
(default), return a mask that's the extent of `geom`.
Returns
-------
numpy boolean array
An array with `True` outside `geom` and `False` inside.
"""
spatial_ref = osr.SpatialReference()
spatial_ref.ImportFromEPSG(epsg)
mem_drv = ogr.GetDriverByName('Memory')
driver = gdal.GetDriverByName('MEM')
rb = rds.gdal_ds.GetRasterBand(band_num)
rgt = rds.gdal_ds.GetGeoTransform()
rsize = (rds.gdal_ds.RasterXSize, rds.gdal_ds.RasterYSize)
if nodata_value is not None:
nodata_value = float(nodata_value)
rb.SetNoDataValue(nodata_value)
else:
nodata_value = rb.GetNoDataValue()
# Point and MultiPoint don't play well with GDALRasterize
# convert them into box polygons the size of a raster cell
# buff = rgt[1] / 2.0
# if geom.type == "MultiPoint":
# geom = MultiPolygon([box(*(pt.buffer(buff).bounds))
# for pt in geom.geoms])
# elif geom.type == 'Point':
# geom = box(*(geom.buffer(buff).bounds))
ogr_geom_type = shapely_to_ogr_type(geom.type)
if full_extent:
geom_bounds = list(rds.raster_extent.bounds)
else:
geom_bounds = list(geom.bounds)
# calculate new pixel coordinates of the feature subset
src_offset = bbox_to_pixel_offsets(rgt, geom_bounds, rsize)
new_gt = (
(rgt[0] + (src_offset[0] * rgt[1])),
rgt[1],
0.0,
(rgt[3] + (src_offset[1] * rgt[5])),
0.0,
rgt[5]
)
if src_offset[2] <= 0 or src_offset[3] <= 0:
# we're off the raster completely, no overlap at all
# so there's no need to even bother trying to calculate
return None
else:
# use feature's source extent and read directly from source
# fastest option when you have fast disks and well-indexed raster
# advantage: each feature uses the smallest raster chunk
# disadvantage: lots of disk reads on the source raster
#src_array = rb.ReadAsArray(*src_offset)
# Create a temporary vector layer in memory
mem_ds = mem_drv.CreateDataSource('out')
mem_layer = mem_ds.CreateLayer('out', spatial_ref, ogr_geom_type)
ogr_feature = ogr.Feature(feature_def=mem_layer.GetLayerDefn())
ogr_geom = ogr.CreateGeometryFromWkt(geom.wkt)
ogr_feature.SetGeometryDirectly(ogr_geom)
mem_layer.CreateFeature(ogr_feature)
# Rasterize it
rvds = driver.Create('rvds', src_offset[2], src_offset[3], 1, gdal.GDT_Byte)
rvds.SetGeoTransform(new_gt)
if all_touched:
gdal.RasterizeLayer(rvds, [1], mem_layer, None, None, burn_values=[1], options = ['ALL_TOUCHED=True'])
else:
gdal.RasterizeLayer(rvds, [1], mem_layer, None, None, burn_values=[1], options = ['ALL_TOUCHED=False'])
rv_array = rvds.ReadAsArray()
# Mask the source data array with our current feature
# we take the logical_not to flip 0<->1 to get the correct mask effect
# we also mask out nodata values explictly
# masked = np.ma.MaskedArray(
# src_array,
# mask=np.logical_or(
# src_array == nodata_value,
# np.logical_not(rv_array)
# )
# )
# return masked
# return np.logical_or( src_array == nodata_value, np.logical_not( rv_array ) )
return ~rv_array.astype('bool')
def zonal_stats(vectors, raster, layer_num=0, band_num=1, func=None,
nodata_value=None, categorical=False, stats=None,
copy_properties=False, all_touched=False, transform=None):
if not stats:
if not categorical:
stats = ['count', 'min', 'max', 'mean', 'std']
if func:
stats.append('func')
# must have transform arg
if not transform:
raise Exception("Must provide the 'transform' kwarg")
rgt = transform
rsize = (raster.shape[1], raster.shape[0])
rbounds = raster_extent_as_bounds(rgt, rsize)
features_iter, strategy, spatial_ref = get_features(vectors, layer_num)
global_src_offset = (0, 0, raster.shape[0], raster.shape[1])
global_src_array = raster
mem_drv = ogr.GetDriverByName('Memory')
driver = gdal.GetDriverByName('MEM')
results = []
entity_images = []
for i, feat in enumerate(features_iter):
if feat['type'] == "Feature":
geom = shape(feat['geometry'])
else: # it's just a geometry
geom = shape(feat)
# Point and MultiPoint don't play well with GDALRasterize
# convert them into box polygons the size of a raster cell
buff = rgt[1] / 2.0
if geom.type == "MultiPoint":
geom = MultiPolygon([box(*(pt.buffer(buff).bounds))
for pt in geom.geoms])
elif geom.type == 'Point':
geom = box(*(geom.buffer(buff).bounds))
ogr_geom_type = shapely_to_ogr_type(geom.type)
# "Clip" the geometry bounds to the overall raster bounding box
# This should avoid any rasterIO errors for partially overlapping polys
geom_bounds = list(geom.bounds)
if geom_bounds[0] < rbounds[0]:
geom_bounds[0] = rbounds[0]
if geom_bounds[1] < rbounds[1]:
geom_bounds[1] = rbounds[1]
if geom_bounds[2] > rbounds[2]:
geom_bounds[2] = rbounds[2]
if geom_bounds[3] > rbounds[3]:
geom_bounds[3] = rbounds[3]
# calculate new geotransform of the feature subset
src_offset = bbox_to_pixel_offsets(rgt, geom_bounds)
new_gt = (
(rgt[0] + (src_offset[0] * rgt[1])),
rgt[1],
0.0,
(rgt[3] + (src_offset[1] * rgt[5])),
0.0,
rgt[5]
)
if src_offset[2] <= 0 or src_offset[3] <= 0:
# we're off the raster completely, no overlap at all
# so there's no need to even bother trying to calculate
feature_stats = dict([(s, None) for s in stats])
img = {'__fid__': i, 'img': None}
else:
# derive array from global source extent array
# useful *only* when disk IO or raster format inefficiencies
# are your limiting factor
# advantage: reads raster data in one pass before loop
# disadvantage: large vector extents combined with big rasters
# need lotsa memory
xa = src_offset[0] - global_src_offset[0]
ya = src_offset[1] - global_src_offset[1]
xb = xa + src_offset[2]
yb = ya + src_offset[3]
src_array = global_src_array[ya:yb, xa:xb]
# Create a temporary vector layer in memory
mem_ds = mem_drv.CreateDataSource('out')
mem_layer = mem_ds.CreateLayer('out', spatial_ref, ogr_geom_type)
ogr_feature = ogr.Feature(feature_def=mem_layer.GetLayerDefn())
ogr_geom = ogr.CreateGeometryFromWkt(geom.wkt)
ogr_feature.SetGeometryDirectly(ogr_geom)
mem_layer.CreateFeature(ogr_feature)
# Rasterize it
rvds = driver.Create(
'rvds', src_offset[2], src_offset[3], 1, gdal.GDT_Byte)
rvds.SetGeoTransform(new_gt)
if all_touched:
gdal.RasterizeLayer(
rvds, [1], mem_layer, None, None,
burn_values=[1], options=['ALL_TOUCHED=True'])
else:
gdal.RasterizeLayer(
rvds, [1], mem_layer, None, None,
burn_values=[1], options=['ALL_TOUCHED=False'])
rv_array = rvds.ReadAsArray()
# Mask the source data array with our current feature
# we take the logical_not to flip 0<->1 to get the correct mask effect
# we also mask out nodata values explictly
masked = np.ma.MaskedArray(
src_array,
mask=np.logical_or(
src_array == nodata_value,
np.logical_not(rv_array)
)
)
feature_stats = {}
if 'min' in stats:
feature_stats['min'] = float(masked.min())
if 'max' in stats:
feature_stats['max'] = float(masked.max())
if 'mean' in stats:
feature_stats['mean'] = float(masked.mean())
if 'count' in stats:
feature_stats['count'] = int(masked.count())
if 'std' in stats:
feature_stats['std'] = float(masked.std())
# optional
if 'func' in stats:
feature_stats[func.__name__] = func(masked)
if 'sum' in stats:
feature_stats['sum'] = float(masked.sum())
if 'std' in stats:
feature_stats['std'] = float(masked.std())
if 'median' in stats:
feature_stats['median'] = float(np.median(masked.compressed()))
if 'range' in stats:
try:
rmin = feature_stats['min']
except KeyError:
rmin = float(masked.min())
try:
rmax = feature_stats['max']
except KeyError:
rmax = float(masked.max())
feature_stats['range'] = rmax - rmin
img = {'__fid__': i, 'img': masked}
# Use the enumerated id as __fid__
feature_stats['__fid__'] = i
if 'properties' in feat and copy_properties:
for key, val in list(feat['properties'].items()):
feature_stats[key] = val
results.append(feature_stats)
entity_images.append(img)
return results, entity_images
def test_nopoints():
with pytest.raises(TypeError):
shapely_to_ogr_type('Point')
with pytest.raises(TypeError):
shapely_to_ogr_type('MultiPoint')
def mask_from_geom(geom,
rds,
band_num=1,
epsg=32760,
nodata_value=None,
all_touched=False,
full_extent=False):
"""
Return a binary mask to mask off everything outside of geom.
Parameters
----------
geom : shapely.geometry
Cells inside this geometry will be `False`. Cells outside will be `True`
rds : RasterDS
The raster dataset to create a mask for.
full_extent : bool
If `True`, return a mask that's the full extent of `rds`. If `False`
(default), return a mask that's the extent of `geom`.
Returns
-------
numpy boolean array
An array with `True` outside `geom` and `False` inside.
"""
spatial_ref = osr.SpatialReference()
spatial_ref.ImportFromEPSG(epsg)
mem_drv = ogr.GetDriverByName('Memory')
driver = gdal.GetDriverByName('MEM')
rb = rds.gdal_ds.GetRasterBand(band_num)
rgt = rds.gdal_ds.GetGeoTransform()
rsize = (rds.gdal_ds.RasterXSize, rds.gdal_ds.RasterYSize)
if nodata_value is not None:
nodata_value = float(nodata_value)
rb.SetNoDataValue(nodata_value)
else:
nodata_value = rb.GetNoDataValue()
# Point and MultiPoint don't play well with GDALRasterize
# convert them into box polygons the size of a raster cell
# buff = rgt[1] / 2.0
# if geom.type == "MultiPoint":
# geom = MultiPolygon([box(*(pt.buffer(buff).bounds))
# for pt in geom.geoms])
# elif geom.type == 'Point':
# geom = box(*(geom.buffer(buff).bounds))
ogr_geom_type = shapely_to_ogr_type(geom.type)
if full_extent:
geom_bounds = list(rds.raster_extent.bounds)
else:
geom_bounds = list(geom.bounds)
# calculate new pixel coordinates of the feature subset
src_offset = bbox_to_pixel_offsets(rgt, geom_bounds, rsize)
new_gt = ((rgt[0] + (src_offset[0] * rgt[1])), rgt[1], 0.0,
(rgt[3] + (src_offset[1] * rgt[5])), 0.0, rgt[5])
if src_offset[2] <= 0 or src_offset[3] <= 0:
# we're off the raster completely, no overlap at all
# so there's no need to even bother trying to calculate
return None
else:
# use feature's source extent and read directly from source
# fastest option when you have fast disks and well-indexed raster
# advantage: each feature uses the smallest raster chunk
# disadvantage: lots of disk reads on the source raster
#src_array = rb.ReadAsArray(*src_offset)
# Create a temporary vector layer in memory
mem_ds = mem_drv.CreateDataSource('out')
mem_layer = mem_ds.CreateLayer('out', spatial_ref, ogr_geom_type)
ogr_feature = ogr.Feature(feature_def=mem_layer.GetLayerDefn())
ogr_geom = ogr.CreateGeometryFromWkt(geom.wkt)
ogr_feature.SetGeometryDirectly(ogr_geom)
mem_layer.CreateFeature(ogr_feature)
# Rasterize it
rvds = driver.Create('rvds', src_offset[2], src_offset[3], 1,
gdal.GDT_Byte)
rvds.SetGeoTransform(new_gt)
if all_touched:
gdal.RasterizeLayer(rvds, [1],
mem_layer,
None,
None,
burn_values=[1],
options=['ALL_TOUCHED=True'])
else:
gdal.RasterizeLayer(rvds, [1],
mem_layer,
None,
None,
burn_values=[1],
options=['ALL_TOUCHED=False'])
rv_array = rvds.ReadAsArray()
# Mask the source data array with our current feature
# we take the logical_not to flip 0<->1 to get the correct mask effect
# we also mask out nodata values explictly
# masked = np.ma.MaskedArray(
# src_array,
# mask=np.logical_or(
# src_array == nodata_value,
# np.logical_not(rv_array)
# )
# )
# return masked
# return np.logical_or( src_array == nodata_value, np.logical_not( rv_array ) )
return ~rv_array.astype('bool')
