def _combine_envelopes(geometries, use_bb=True, use_distance=False):
"""Inner support function for combine_envelopes."""
import ambry.geo as dg
reductions = 0
new_geometries = []
accum = None
reduced = set()
for i1 in range(len(geometries)):
if i1 in reduced:
continue
g1 = geometries[i1]
for i2 in range(i1 + 1, len(geometries)):
if i2 in reduced:
continue
g2 = geometries[i2]
intersects = False
if (g1.Intersects(g2) or g1.Contains(g2) or g2.Contains(g1)
or g1.Touches(g2)):
intersects = True
# If the final output is to onvert the reduced geometries to bounding boxes, it
# can have BBs that intersect that were not reduced, because the underlying geometries
# didn't intersect
if use_bb and not intersects:
bb1 = dg.create_bb(g1.GetEnvelope(), g1.GetSpatialReference())
bb2 = dg.create_bb(g2.GetEnvelope(), g2.GetSpatialReference())
if bb1.Intersects(bb2):
intersects = True
if use_distance and not intersects:
if use_bb:
if bb1.Distance(bb2) < use_distance:
intersects = True
else:
if g1.Distance(g2) < use_distance:
intersects = True
if intersects:
reductions += 1
reduced.add(i2)
if not accum:
accum = g1.Union(g2)
else:
accum = accum.Union(g2)
if accum is not None:
new_geometries.append(accum.Clone())
accum = None
else:
new_geometries.append(g1.Clone())
return reductions, new_geometries
def _combine_envelopes(geometries, use_bb = True, use_distance=False):
"""Inner support function for combine_envelopes"""
import ambry.geo as dg
reductions = 0
new_geometries = []
accum = None
reduced = set()
for i1 in range(len(geometries)):
if i1 in reduced:
continue
g1 = geometries[i1]
for i2 in range(i1+1, len(geometries)):
if i2 in reduced:
continue
g2 = geometries[i2]
intersects = False
if (g1.Intersects(g2) or g1.Contains(g2) or g2.Contains(g1) or g1.Touches(g2)):
intersects = True
# If the final output is to onvert the reduced geometries to bounding boxes, it
# can have BBs that intersect that were not reduced, because the underlying geometries
# didn't intersect
if use_bb and not intersects:
bb1 = dg.create_bb(g1.GetEnvelope(), g1.GetSpatialReference())
bb2 = dg.create_bb(g2.GetEnvelope(), g2.GetSpatialReference())
if bb1.Intersects(bb2):
intersects = True
if use_distance and not intersects:
if use_bb:
if bb1.Distance(bb2) < use_distance:
intersects = True
else:
if g1.Distance(g2) < use_distance:
intersects = True
if intersects:
reductions += 1
reduced.add(i2)
if not accum:
accum = g1.Union(g2)
else:
accum = accum.Union(g2)
if accum is not None:
new_geometries.append(accum.Clone())
accum = None
else:
new_geometries.append(g1.Clone())
return reductions, new_geometries
def bound_clusters_in_raster(a,
aa,
shape_file_dir,
contour_interval,
contour_value,
use_bb=True,
use_distance=False):
"""Create a shapefile that contains contours and bounding boxes for
clusters of contours.
:param a: A numpy array that contains the data inwhich to find clusters
:type a: Numpy array
:param aa: The analysis object that sets the coordinate system for the area that contains the array
:type aa: ambry.geo.AnalysisArea
:param shape_file_dir: The path to a directory where generated files will be stored.
:type shape_file_dir: string
:param contour_interval: The difference between successive contour intervals.
:type contour_interval: float
:param contour_value:
:type contour_value: float
:param use_bb: If True, compute nearness and intersection using the contours bounding boxes, not the geometry
:type use_bb: bool
:param use_distance: If not False, consider contours that are closer than this value to be overlapping.
:type : number
:rtype: Returns a list of dictionaries, one for each of the combined bounding boxes
This method will store, in the `shape_file_dir` directory:
* a GeoTIFF representation of the array `a`
* An ERSI shapefile layer named `countours`, holding all of the countours.
* A layer named `contour_bounds` with the bounding boxes for all of the contours with value `contour_value`
* A layer named `combined_bounds` with bounding boxes of intersecting and nearby boxes rom `contour_bounds`
The routine will iteratively combine contours that overlap.
If `use_distance` is set to a number, and contours that are closer than this value will be joined.
If `use_bb` is set, the intersection and distance computations use the bounding boxes of the contours,
not the contours themselves.
"""
import ambry.geo as dg
from osgeo.gdalconst import GDT_Float32
import ambry.util as util
from osgeo import gdal
import ogr
import os
import numpy as np
if os.path.exists(shape_file_dir):
util.rm_rf(shape_file_dir)
os.makedirs(shape_file_dir)
rasterf = os.path.join(shape_file_dir, 'contour.tiff')
ogr_ds = ogr.GetDriverByName('ESRI Shapefile').CreateDataSource(
shape_file_dir)
# Setup the countour layer.
ogr_lyr = ogr_ds.CreateLayer('contours', aa.srs)
ogr_lyr.CreateField(ogr.FieldDefn('id', ogr.OFTInteger))
ogr_lyr.CreateField(ogr.FieldDefn('value', ogr.OFTReal))
# Create the contours from the GeoTIFF file.
ds = aa.get_geotiff(rasterf, data_type=GDT_Float32)
ds.GetRasterBand(1).SetNoDataValue(0)
ds.GetRasterBand(1).WriteArray(np.flipud(a))
gdal.ContourGenerate(
ds.GetRasterBand(1),
contour_interval, # contourInterval
0, # contourBase
[], # fixedLevelCount
0, # useNoData
0, # noDataValue
ogr_lyr, # destination layer
0, # idField
1 # elevation field
)
# Get buffered bounding boxes around each of the hotspots,
# and put them into a new layer.
bound_lyr = ogr_ds.CreateLayer('contour_bounds', aa.srs)
for i in range(ogr_lyr.GetFeatureCount()):
f1 = ogr_lyr.GetFeature(i)
if f1.GetFieldAsDouble('value') != contour_value:
continue
g1 = f1.GetGeometryRef()
bb = dg.create_bb(g1.GetEnvelope(), g1.GetSpatialReference())
f = ogr.Feature(bound_lyr.GetLayerDefn())
f.SetGeometry(bb)
bound_lyr.CreateFeature(f)
# Doing a full loop instead of a list comprehension b/c the way that comprehensions
# compose arrays results in segfaults, probably because a copied geometry
# object is being released before being used.
geos = []
for i in range(bound_lyr.GetFeatureCount()):
f = bound_lyr.GetFeature(i)
g = f.geometry()
geos.append(g.Clone())
# Combine hot spots that have intersecting bounding boxes, to get larger
# areas that cover all of the adjacent intersecting smaller areas.
geos = dg.combine_envelopes(geos, use_bb=use_bb, use_distance=use_distance)
# Write out the combined bounds areas.
lyr = ogr_ds.CreateLayer('combined_bounds', aa.srs)
lyr.CreateField(ogr.FieldDefn('id', ogr.OFTInteger))
lyr.CreateField(ogr.FieldDefn('area', ogr.OFTReal))
lyr.CreateField(ogr.FieldDefn('name', ogr.OFTString))
lyr.CreateField(ogr.FieldDefn('code', ogr.OFTString))
envelopes = []
id = 1
for env in geos:
f = ogr.Feature(lyr.GetLayerDefn())
bb = dg.create_bb(env.GetEnvelope(), env.GetSpatialReference())
f.SetGeometry(bb)
f.SetField(0, id)
f.SetField(1, bb.Area())
f.SetField(2, None)
f.SetField(3, None)
id += 1
lyr.CreateFeature(f)
envelopes.append({
'id': id,
'env': bb.GetEnvelope(),
'area': bb.Area()
})
return envelopes
def bound_clusters_in_raster( a, aa, shape_file_dir,
contour_interval,contour_value, use_bb=True, use_distance=False):
"""Create a shapefile that contains contours and bounding boxes for clusters
of contours.
:param a: A numpy array that contains the data inwhich to find clusters
:type a: Numpy array
:param aa: The analysis object that sets the coordinate system for the area that contains the array
:type aa: ambry.geo.AnalysisArea
:param shape_file_dir: The path to a directory where generated files will be stored.
:type shape_file_dir: string
:param contour_interval: The difference between successive contour intervals.
:type contour_interval: float
:param contour_value:
:type contour_value: float
:param use_bb: If True, compute nearness and intersection using the contours bounding boxes, not the geometry
:type use_bb: bool
:param use_distance: If not False, consider contours that are closer than this value to be overlapping.
:type : number
:rtype: Returns a list of dictionaries, one for each of the combined bounding boxes
This method will store, in the `shape_file_dir` directory:
* a GeoTIFF representation of the array `a`
* An ERSI shapefile layer named `countours`, holding all of the countours.
* A layer named `contour_bounds` with the bounding boxes for all of the contours with value `contour_value`
* A layer named `combined_bounds` with bounding boxes of intersecting and nearby boxes rom `contour_bounds`
The routine will iteratively combine contours that overlap.
If `use_distance` is set to a number, and contours that are closer than this value will be joined.
If `use_bb` is set, the intersection and distance computations use the bounding boxes of the contours,
not the contours themselves.
"""
import ambry.geo as dg
from osgeo.gdalconst import GDT_Float32
import ambry.util as util
from osgeo import gdal
import ogr, os
import numpy as np
if os.path.exists(shape_file_dir):
util.rm_rf(shape_file_dir)
os.makedirs(shape_file_dir)
rasterf = os.path.join(shape_file_dir,'contour.tiff')
ogr_ds = ogr.GetDriverByName('ESRI Shapefile').CreateDataSource(shape_file_dir)
# Setup the countour layer.
ogr_lyr = ogr_ds.CreateLayer('contours', aa.srs)
ogr_lyr.CreateField(ogr.FieldDefn('id', ogr.OFTInteger))
ogr_lyr.CreateField(ogr.FieldDefn('value', ogr.OFTReal))
# Create the contours from the GeoTIFF file.
ds = aa.get_geotiff(rasterf, data_type=GDT_Float32)
ds.GetRasterBand(1).SetNoDataValue(0)
ds.GetRasterBand(1).WriteArray(np.flipud(a))
gdal.ContourGenerate(ds.GetRasterBand(1),
contour_interval, # contourInterval
0, # contourBase
[], # fixedLevelCount
0, # useNoData
0, # noDataValue
ogr_lyr, #destination layer
0, #idField
1 # elevation field
)
# Get buffered bounding boxes around each of the hotspots,
# and put them into a new layer.
bound_lyr = ogr_ds.CreateLayer('contour_bounds', aa.srs)
for i in range(ogr_lyr.GetFeatureCount()):
f1 = ogr_lyr.GetFeature(i)
if f1.GetFieldAsDouble('value') != contour_value:
continue
g1 = f1.GetGeometryRef()
bb = dg.create_bb(g1.GetEnvelope(), g1.GetSpatialReference())
f = ogr.Feature(bound_lyr.GetLayerDefn())
f.SetGeometry(bb)
bound_lyr.CreateFeature(f)
# Doing a full loop instead of a list comprehension b/c the way that comprehensions
# compose arrays results in segfaults, probably because a copied geometry
# object is being released before being used.
geos = []
for i in range(bound_lyr.GetFeatureCount()):
f = bound_lyr.GetFeature(i)
g = f.geometry()
geos.append(g.Clone())
# Combine hot spots that have intersecting bounding boxes, to get larger
# areas that cover all of the adjacent intersecting smaller areas.
geos = dg.combine_envelopes(geos, use_bb=use_bb, use_distance = use_distance)
# Write out the combined bounds areas.
lyr = ogr_ds.CreateLayer('combined_bounds', aa.srs)
lyr.CreateField(ogr.FieldDefn('id', ogr.OFTInteger))
lyr.CreateField(ogr.FieldDefn('area', ogr.OFTReal))
lyr.CreateField(ogr.FieldDefn('name', ogr.OFTString))
lyr.CreateField(ogr.FieldDefn('code', ogr.OFTString))
envelopes = []
id = 1
for env in geos:
f = ogr.Feature(lyr.GetLayerDefn())
bb = dg.create_bb(env.GetEnvelope(), env.GetSpatialReference())
f.SetGeometry(bb)
f.SetField(0, id)
f.SetField(1, bb.Area())
f.SetField(2, None)
f.SetField(3, None)
id += 1
lyr.CreateFeature(f)
envelopes.append({'id':id, 'env':bb.GetEnvelope(), 'area':bb.Area()})
return envelopes
