def geotransform2resolution(geotransform, isotropic=False, rtol=1.0e-6, atol=1.0e-8):
"""Convert geotransform to resolution
Args:
* geotransform: GDAL geotransform (6-tuple).
(top left x, w-e pixel resolution, rotation,
top left y, rotation, n-s pixel resolution).
See e.g. http://www.gdal.org/gdal_tutorial.html
* isotropic: If True, verify that dx == dy and return dx
If False (default) return 2-tuple (dx, dy)
* rtol, atol: Used to control how close dx and dy must be
to quality for isotropic. These are passed on to
numpy.allclose for comparison.
Returns:
* resolution: grid spacing (resx, resy) in (positive) decimal
degrees ordered as longitude first, then latitude.
or resx (if isotropic is True)
"""
resx = geotransform[1] # w-e pixel resolution
resy = -geotransform[5] # n-s pixel resolution (always negative)
if isotropic:
msg = (
"Resolution requested with "
"isotropic=True, but "
"resolutions in the horizontal and vertical "
"are different: resx = %.12f, resy = %.12f. " % (resx, resy)
)
verify(numpy.allclose(resx, resy, rtol=rtol, atol=atol), msg)
return resx
else:
return resx, resy
def convert_polygons_to_centroids(V):
"""Convert polygon vector data to point vector data
:param V: Vector layer with polygon data
:type V: Vector
:returns: Vector layer with point data and the same attributes as V
:rtype: Vector
"""
msg = 'Input data %s must be polygon vector data' % V
verify(V.is_polygon_data, msg)
geometry = V.get_geometry()
N = len(V)
# Calculate points for each polygon
centroids = []
for i in range(N):
c = calculate_polygon_centroid(geometry[i])
centroids.append(c)
# Create new point vector layer with same attributes and return
V = Vector(data=V.get_data(),
projection=V.get_projection(),
geometry=centroids,
name='%s_centroid_data' % V.get_name(),
keywords=V.get_keywords())
return V
def rings_equal(x, y, rtol=1.0e-6, atol=1.0e-8):
"""Compares to linear rings as numpy arrays
Args
* x, y: Nx2 numpy arrays
Returns:
* True if x == y or x' == y (up to the specified tolerance)
where x' is x reversed in the first dimension. This corresponds to
linear rings being seen as equal irrespective of whether they are
organised in clock wise or counter clock wise order
"""
x = ensure_numeric(x, numpy.float)
y = ensure_numeric(y, numpy.float)
msg = 'Arrays must a 2d arrays of vertices. I got %s and %s' % (x, y)
verify(len(x.shape) == 2 and len(y.shape) == 2, msg)
msg = 'Arrays must have two columns. I got %s and %s' % (x, y)
verify(x.shape[1] == 2 and y.shape[1] == 2, msg)
if (numpy.allclose(x, y, rtol=rtol, atol=atol)
or numpy.allclose(x, y[::-1], rtol=rtol, atol=atol)):
return True
else:
return False
def bboxstring2list(bbox_string):
"""Convert bounding box string to list
Args:
* bbox_string: String of bounding box coordinates of the form 'W,S,E,N'
Returns:
* bbox: List of floating point numbers with format [W, S, E, N]
"""
msg = ('Bounding box must be a string with coordinates following the '
'format 105.592,-7.809,110.159,-5.647\n'
'Instead I got %s of type %s.' % (str(bbox_string),
type(bbox_string)))
verify(isinstance(bbox_string, basestring), msg)
fields = bbox_string.split(',')
msg = ('Bounding box string must have 4 coordinates in the form '
'"W,S,E,N". I got bbox == "%s"' % bbox_string)
try:
verify(len(fields) == 4, msg)
except VerificationError:
raise BoundingBoxError(msg)
for x in fields:
try:
float(x)
except ValueError, e:
msg = ('Bounding box %s contained non-numeric entry %s, '
'original error was "%s".' % (bbox_string, x, e))
raise BoundingBoxError(msg)
def rings_equal(x, y, rtol=1.0e-6, atol=1.0e-8):
"""Compares to linear rings as numpy arrays
Args
* x, y: Nx2 numpy arrays
Returns:
* True if x == y or x' == y (up to the specified tolerance)
where x' is x reversed in the first dimension. This corresponds to
linear rings being seen as equal irrespective of whether they are
organised in clock wise or counter clock wise order
"""
x = ensure_numeric(x, numpy.float)
y = ensure_numeric(y, numpy.float)
msg = 'Arrays must a 2d arrays of vertices. I got %s and %s' % (x, y)
verify(len(x.shape) == 2 and len(y.shape) == 2, msg)
msg = 'Arrays must have two columns. I got %s and %s' % (x, y)
verify(x.shape[1] == 2 and y.shape[1] == 2, msg)
if (numpy.allclose(x, y, rtol=rtol, atol=atol) or
numpy.allclose(x, y[::-1], rtol=rtol, atol=atol)):
return True
else:
return False
def bboxlist2string(bbox, decimals=6):
"""Convert bounding box list to comma separated string
Args:
* bbox: List of coordinates of the form [W, S, E, N]
Returns:
* bbox_string: Format 'W,S,E,N' - each will have 6 decimal points
"""
msg = 'Got string %s, but expected bounding box as a list' % str(bbox)
verify(not isinstance(bbox, basestring), msg)
try:
bbox = list(bbox)
except:
msg = 'Could not coerce bbox %s into a list' % str(bbox)
raise BoundingBoxError(msg)
msg = ('Bounding box must have 4 coordinates [W, S, E, N]. '
'I got %s' % str(bbox))
try:
verify(len(bbox) == 4, msg)
except VerificationError:
raise BoundingBoxError(msg)
for x in bbox:
try:
float(x)
except ValueError, e:
msg = ('Bounding box %s contained non-numeric entry %s, '
'original error was "%s".' % (bbox, x, e))
raise BoundingBoxError(msg)
def bboxstring2list(bbox_string):
"""Convert bounding box string to list
Args:
* bbox_string: String of bounding box coordinates of the form 'W,S,E,N'
Returns:
* bbox: List of floating point numbers with format [W, S, E, N]
"""
msg = ('Bounding box must be a string with coordinates following the '
'format 105.592,-7.809,110.159,-5.647\n'
'Instead I got %s of type %s.' % (str(bbox_string),
type(bbox_string)))
verify(isinstance(bbox_string, basestring), msg)
fields = bbox_string.split(',')
msg = ('Bounding box string must have 4 coordinates in the form '
'"W,S,E,N". I got bbox == "%s"' % bbox_string)
try:
verify(len(fields) == 4, msg)
except VerificationError:
raise BoundingBoxError(msg)
for x in fields:
try:
float(x)
except ValueError, e:
msg = ('Bounding box %s contained non-numeric entry %s, '
'original error was "%s".' % (bbox_string, x, e))
raise BoundingBoxError(msg)
def bboxlist2string(bbox, decimals=6):
"""Convert bounding box list to comma separated string
Args:
* bbox: List of coordinates of the form [W, S, E, N]
Returns:
* bbox_string: Format 'W,S,E,N' - each will have 6 decimal points
"""
msg = 'Got string %s, but expected bounding box as a list' % str(bbox)
verify(not isinstance(bbox, basestring), msg)
try:
bbox = list(bbox)
except:
msg = 'Could not coerce bbox %s into a list' % str(bbox)
raise BoundingBoxError(msg)
msg = ('Bounding box must have 4 coordinates [W, S, E, N]. '
'I got %s' % str(bbox))
try:
verify(len(bbox) == 4, msg)
except VerificationError:
raise BoundingBoxError(msg)
for x in bbox:
try:
float(x)
except ValueError, e:
msg = ('Bounding box %s contained non-numeric entry %s, '
'original error was "%s".' % (bbox, x, e))
raise BoundingBoxError(msg)
def grid_to_points(A, x, y):
"""Convert grid data to point data
:param A: Array of pixel values
:type A: numpy.ndarray
:param x: Longitudes corresponding to columns in A (west->east)
:type x: numpy.ndarray
:param y: Latitudes corresponding to rows in A (south->north)
:type y: numpy.ndarray
Returns:
* P: Nx2 array of point coordinates
* V: N array of point values
"""
msg = ('Longitudes must be increasing (west to east). I got %s' % str(x))
verify(x[0] < x[1], msg)
msg = ('Latitudes must be increasing (south to north). I got %s' % str(y))
verify(y[0] < y[1], msg)
# Create Nx2 array of x, y points corresponding to each
# element in A.
points = axes_to_points(x, y)
# Create flat 1D row-major view of A cast as
# one column vector of length MxN where M, N = A.shape
# values = A.reshape((-1, 1))
values = A.reshape(-1)
# Return Nx3 array with rows: x, y, value
return points, values
def convert_polygons_to_centroids(V):
"""Convert polygon vector data to point vector data
Args:
* V: Vector layer with polygon data
Returns:
* Vector layer with point data and the same attributes as V
"""
msg = 'Input data %s must be polygon vector data' % V
verify(V.is_polygon_data, msg)
geometry = V.get_geometry()
N = len(V)
# Calculate points for each polygon
centroids = []
for i in range(N):
c = calculate_polygon_centroid(geometry[i])
centroids.append(c)
# Create new point vector layer with same attributes and return
V = Vector(data=V.get_data(),
projection=V.get_projection(),
geometry=centroids,
name='%s_centroid_data' % V.get_name(),
keywords=V.get_keywords())
return V
def _keywords_to_string(keywords, sublayer=None):
"""Create a string from a keywords dict.
Args:
* keywords: A required dictionary containing the keywords to stringify.
* sublayer: str optional group marker for a sub layer.
Returns:
str: a String containing the rendered keywords list
Raises:
Any exceptions are propogated.
.. note: Only simple keyword dicts should be passed here, not multilayer
dicts.
For example you pass a dict like this::
{'datatype': 'osm',
'category': 'exposure',
'title': 'buildings_osm_4326',
'subcategory': 'building',
'purpose': 'dki'}
and the following string would be returned:
datatype: osm
category: exposure
title: buildings_osm_4326
subcategory: building
purpose: dki
If sublayer is provided e.g. _keywords_to_string(keywords, sublayer='foo'),
the following:
[foo]
datatype: osm
category: exposure
title: buildings_osm_4326
subcategory: building
purpose: dki
"""
# Write
result = get_unicode("")
if sublayer is not None:
result = "[%s]\n" % sublayer
for k, value in keywords.items():
# Create key
msg = "Key in keywords dictionary must be a string. " "I got %s with type %s" % (k, str(type(k))[1:-1])
verify(isinstance(k, basestring), msg)
key = k
msg = 'Key in keywords dictionary must not contain the ":" ' 'character. I got "%s"' % key
verify(":" not in key, msg)
# Store
result += "%s: %s\n" % (key, value)
return result
def interpolate_raster_vector(source,
target,
layer_name=None,
attribute_name=None,
mode='linear'):
"""Interpolate from raster layer to vector data
Args:
* source: Raster data set (grid)
* target: Vector data set (points or polygons)
* layer_name: Optional name of returned interpolated layer.
If None the name of V is used for the returned layer.
* attribute_name: Name for new attribute.
If None (default) the name of R is used
Returns:
I: Vector data set; points located as target with values
interpolated from source
Note: If target geometry is polygon, data will be interpolated to
its centroids and the output is a point data set.
"""
# Input checks
verify(source.is_raster)
verify(target.is_vector)
if target.is_point_data:
# Interpolate from raster to point data
R = interpolate_raster_vector_points(source,
target,
layer_name=layer_name,
attribute_name=attribute_name,
mode=mode)
# elif target.is_line_data:
# TBA - issue https://github.com/AIFDR/inasafe/issues/36
#
elif target.is_polygon_data:
# Use centroids, in case of polygons
P = convert_polygons_to_centroids(target)
R = interpolate_raster_vector_points(source,
P,
layer_name=layer_name,
attribute_name=attribute_name,
mode=mode)
# In case of polygon data, restore the polygon geometry
# Do this setting the geometry of the returned set to
# that of the original polygon
R = Vector(data=R.get_data(),
projection=R.get_projection(),
geometry=target.get_geometry(),
name=R.get_name())
else:
msg = ('Unknown datatype for raster2vector interpolation: '
'I got %s' % str(target))
raise InaSAFEError(msg)
# Return interpolated vector layer
return R
def bbox_intersection(*args):
"""Compute intersection between two or more bounding boxes
Args:
* args: two or more bounding boxes.
Each is assumed to be a list or a tuple with
four coordinates (W, S, E, N)
Returns:
* result: The minimal common bounding box
"""
msg = 'Function bbox_intersection must take at least 2 arguments.'
verify(len(args) > 1, msg)
result = [-180, -90, 180, 90]
for a in args:
if a is None:
continue
msg = ('Bounding box expected to be a list of the '
'form [W, S, E, N]. '
'Instead i got "%s"' % str(a))
try:
box = list(a)
except:
raise Exception(msg)
if not len(box) == 4:
raise BoundingBoxError(msg)
msg = ('Western boundary must be less than or equal to eastern. '
'I got %s' % box)
if not box[0] <= box[2]:
raise BoundingBoxError(msg)
msg = ('Southern boundary must be less than or equal to northern. '
'I got %s' % box)
if not box[1] <= box[3]:
raise BoundingBoxError(msg)
# Compute intersection
# West and South
for i in [0, 1]:
result[i] = max(result[i], box[i])
# East and North
for i in [2, 3]:
result[i] = min(result[i], box[i])
# Check validity and return
if result[0] <= result[2] and result[1] <= result[3]:
return result
else:
return None
def bbox_intersection(*args):
"""Compute intersection between two or more bounding boxes
Args:
* args: two or more bounding boxes.
Each is assumed to be a list or a tuple with
four coordinates (W, S, E, N)
Returns:
* result: The minimal common bounding box
"""
msg = 'Function bbox_intersection must take at least 2 arguments.'
verify(len(args) > 1, msg)
result = [-180, -90, 180, 90]
for a in args:
if a is None:
continue
msg = ('Bounding box expected to be a list of the '
'form [W, S, E, N]. '
'Instead i got "%s"' % str(a))
try:
box = list(a)
except:
raise Exception(msg)
if not len(box) == 4:
raise BoundingBoxError(msg)
msg = ('Western boundary must be less than or equal to eastern. '
'I got %s' % box)
if not box[0] <= box[2]:
raise BoundingBoxError(msg)
msg = ('Southern boundary must be less than or equal to northern. '
'I got %s' % box)
if not box[1] <= box[3]:
raise BoundingBoxError(msg)
# Compute intersection
# West and South
for i in [0, 1]:
result[i] = max(result[i], box[i])
# East and North
for i in [2, 3]:
result[i] = min(result[i], box[i])
# Check validity and return
if result[0] <= result[2] and result[1] <= result[3]:
return result
else:
return None
def interpolate_raster_vector(source,
target,
layer_name=None,
attribute_name=None,
mode='linear'):
"""Interpolate from raster layer to vector data
Args:
* source: Raster data set (grid)
* target: Vector data set (points or polygons)
* layer_name: Optional name of returned interpolated layer.
If None the name of V is used for the returned layer.
* attribute_name: Name for new attribute.
If None (default) the name of R is used
Returns:
I: Vector data set; points located as target with values
interpolated from source
Note: If target geometry is polygon, data will be interpolated to
its centroids and the output is a point data set.
"""
# Input checks
verify(source.is_raster)
verify(target.is_vector)
if target.is_point_data:
# Interpolate from raster to point data
R = interpolate_raster_vector_points(
source,
target,
layer_name=layer_name,
attribute_name=attribute_name,
mode=mode)
#elif target.is_line_data:
# TBA - issue https://github.com/AIFDR/inasafe/issues/36
#
elif target.is_polygon_data:
# Use centroids, in case of polygons
P = convert_polygons_to_centroids(target)
R = interpolate_raster_vector_points(
source, P, layer_name=layer_name, attribute_name=attribute_name)
# In case of polygon data, restore the polygon geometry
# Do this setting the geometry of the returned set to
# that of the original polygon
R = Vector(
data=R.get_data(),
projection=R.get_projection(),
geometry=target.get_geometry(),
name=R.get_name())
else:
msg = ('Unknown datatype for raster2vector interpolation: '
'I got %s' % str(target))
raise InaSAFEError(msg)
# Return interpolated vector layer
return R
def geotransform_to_axes(G, nx, ny):
"""Convert geotransform to coordinate axes
:param G: GDAL geotransform (6-tuple).
(top left x, w-e pixel resolution, rotation,
top left y, rotation, n-s pixel resolution).
:type G: tuple
:param nx: Number of cells in the w-e direction
:type nx: int
:param ny: Number of cells in the n-s direction
:type nx: int
:returns: Two vectors (longitudes and latitudes) representing the grid
defined by the geotransform.
The values are offset by half a pixel size to correspond to
pixel registration.
I.e. If the grid origin (top left corner) is (105, 10) and the
resolution is 1 degrees in each direction, then the vectors will
take the form
longitudes = [100.5, 101.5, ..., 109.5]
latitudes = [0.5, 1.5, ..., 9.5]
"""
lon_ul = float(G[0]) # Longitude of upper left corner
lat_ul = float(G[3]) # Latitude of upper left corner
dx = float(G[1]) # Longitudinal resolution
dy = -float(G[5]) # Latitudinal resolution (always(?) negative)
verify(dx > 0)
verify(dy > 0)
# Coordinates of lower left corner
lon_ll = lon_ul
lat_ll = lat_ul - ny * dy
# Coordinates of upper right corner
lon_ur = lon_ul + nx * dx
# Define pixel centers along each directions
# This is to achieve pixel registration rather
# than gridline registration
dx2 = dx / 2
dy2 = dy / 2
# Define longitudes and latitudes for each axes
x = numpy.linspace(lon_ll + dx2, lon_ur - dx2, nx)
y = numpy.linspace(lat_ll + dy2, lat_ul - dy2, ny)
# Return
return x, y
def dom2object(node):
"""Convert DOM representation to XML_object hierarchy.
"""
value = []
textnode_encountered = None
for n in node.childNodes:
if n.nodeType == 3:
# Child is a text element - omit the dom tag #text and
# go straight to the text value.
# Note - only the last text value will be recorded
msg = 'Text element has child nodes - this shouldn\'t happen'
verify(len(n.childNodes) == 0, msg)
x = n.nodeValue.strip()
if len(x) == 0:
# Skip empty text children
continue
textnode_encountered = value = x
else:
# XML element
if textnode_encountered is not None:
msg = 'A text node was followed by a non-text tag. This is not allowed.\n'
msg += 'Offending text node: "%s" ' %str(textnode_encountered)
msg += 'was followed by node named: "<%s>"' %str(n.nodeName)
raise Exception, msg
value.append(dom2object(n))
# Deal with empty elements
if len(value) == 0: value = ''
if node.nodeType == 9:
# Root node (document)
tag = None
else:
# Normal XML node
tag = node.nodeName
X = XML_element(tag=tag,
value=value)
return X
def tag_polygons_by_grid(polygons, grid, threshold=0, tag='affected'):
"""Tag polygons by raster values
Args:
* polygons: Polygon layer
* grid: Raster layer
* threshold: Threshold for grid value to tag polygon
* tag: Name of new tag
Returns:
Polygon layer: Same as input polygon but with extra attribute tag
set according to grid values
"""
verify(polygons.is_polygon_data)
verify(grid.is_raster)
polygon_attributes = polygons.get_data()
polygon_geometry = polygons.get_geometry(as_geometry_objects=True)
# Separate grid points by polygon
res, _ = clip_grid_by_polygons(
grid.get_data(),
grid.get_geotransform(),
polygon_geometry)
# Create new polygon layer with tag set according to grid values
# and threshold
new_attributes = []
for i, (_, values) in enumerate(res):
# For each polygon check if any grid value in it exceeds the threshold
affected = False
for val in values:
# Check each grid value in this polygon
if val > threshold:
affected = True
# Existing attributes for this polygon
attr = polygon_attributes[i].copy()
# Create tagged polygon feature
if affected:
attr[tag] = True
else:
attr[tag] = False
new_attributes.append(attr)
R = Vector(data=new_attributes,
projection=polygons.get_projection(),
geometry=polygon_geometry,
name='%s_tagged_by_%s' % (polygons.name, grid.name))
return R
def copy_keywords(
self,
source_layer,
destination_file,
extra_keywords=None):
"""Helper to copy the keywords file from a source to a target dataset.
e.g.::
copyKeywords('foo.shp', 'bar.shp')
Will result in the foo.keywords file being copied to bar.keyword.
Optional argument extraKeywords is a dictionary with additional
keywords that will be added to the destination file e.g::
copyKeywords('foo.shp', 'bar.shp', {'resolution': 0.01})
:param source_layer: A QGIS QgsMapLayer instance.
:type source_layer: QgsMapLayer
:param destination_file: The output filename that should be used
to store the keywords in. It can be a .shp or a .keywords for
example since the suffix will always be replaced with .keywords.
:type destination_file: str
:param extra_keywords: A dict containing all the extra keywords
to be written for the layer. The written keywords will consist of
any original keywords from the source layer's keywords file and
and the extra keywords (which will replace the source layers
keywords if the key is identical).
:type extra_keywords: dict
"""
keywords = self.read_keywords(source_layer)
if extra_keywords is None:
extra_keywords = {}
message = self.tr(
'Expected extraKeywords to be a dictionary. Got '
'%s' % str(type(extra_keywords))[1:-1])
verify(isinstance(extra_keywords, dict), message)
# compute the output keywords file name
destination_base = os.path.splitext(destination_file)[0]
new_destination = destination_base + '.keywords'
# write the extra keywords into the source dict
try:
for key in extra_keywords:
keywords[key] = extra_keywords[key]
write_keywords_to_file(new_destination, keywords)
except Exception, e:
message = self.tr(
'Failed to copy keywords file from : \n%s\nto\n%s: %s' % (
source_layer.source(), new_destination, str(e)))
raise Exception(message)
def dom2object(node):
"""Convert DOM representation to XML_object hierarchy.
"""
value = []
textnode_encountered = None
for n in node.childNodes:
if n.nodeType == 3:
# Child is a text element - omit the dom tag #text and
# go straight to the text value.
# Note - only the last text value will be recorded
msg = 'Text element has child nodes - this shouldn\'t happen'
verify(len(n.childNodes) == 0, msg)
x = n.nodeValue.strip()
if len(x) == 0:
# Skip empty text children
continue
textnode_encountered = value = x
else:
# XML element
if textnode_encountered is not None:
msg = 'A text node was followed by a non-text tag. This is not allowed.\n'
msg += 'Offending text node: "%s" ' %str(textnode_encountered)
msg += 'was followed by node named: "<%s>"' %str(n.nodeName)
raise Exception, msg
value.append(dom2object(n))
# Deal with empty elements
if len(value) == 0: value = ''
if node.nodeType == 9:
# Root node (document)
tag = None
else:
# Normal XML node
tag = node.nodeName
X = XML_element(tag=tag,
value=value)
return X
def tag_polygons_by_grid(polygons, grid, threshold=0, tag='affected'):
"""Tag polygons by raster values
Args:
* polygons: Polygon layer
* grid: Raster layer
* threshold: Threshold for grid value to tag polygon
* tag: Name of new tag
Returns:
Polygon layer: Same as input polygon but with extra attribute tag
set according to grid values
"""
verify(polygons.is_polygon_data)
verify(grid.is_raster)
polygon_attributes = polygons.get_data()
polygon_geometry = polygons.get_geometry(as_geometry_objects=True)
# Separate grid points by polygon
res = clip_grid_by_polygons(grid.get_data(),
grid.get_geotransform(),
polygon_geometry)
# Create new polygon layer with tag set according to grid values
# and threshold
new_attributes = []
for i, (_, values) in enumerate(res):
# For each polygon check if any grid value in it exceeds the threshold
affected = False
for val in values:
# Check each grid value in this polygon
if val > threshold:
affected = True
# Existing attributes for this polygon
attr = polygon_attributes[i].copy()
# Create tagged polygon feature
if affected:
attr[tag] = True
else:
attr[tag] = False
new_attributes.append(attr)
R = Vector(data=new_attributes,
projection=polygons.get_projection(),
geometry=polygon_geometry,
name='%s_tagged_by_%s' % (polygons.name, grid.name))
return R
def sigab2bnpb(E, target_attribute='VCLASS'):
"""Map SIGAB point data to BNPB vulnerability classes
Input
E: Vector object representing the OSM data
target_attribute: Optional name of the attribute containing
the mapped vulnerability class. Default
value is 'VCLASS'
Output:
Vector object like E, but with one new attribute (e.g. 'VCLASS')
representing the vulnerability class used in the guidelines
"""
# Input check
required = ['Struktur_B', 'Lantai', 'Atap', 'Dinding', 'Tingkat']
actual = E.get_attribute_names()
msg = ('Input data to sigab2bnpb must have attributes %s. '
'It has %s' % (str(required), str(actual)))
for attribute in required:
verify(attribute in actual, msg)
# Start mapping
N = len(E)
attributes = E.get_data()
for i in range(N):
levels = E.get_data('Tingkat', i).lower()
structure = E.get_data('Struktur_B', i).lower()
roof_type = E.get_data('Atap', i).lower()
wall_type = E.get_data('Dinding', i).lower()
floor_type = E.get_data('Lantai', i).lower()
if levels == 'none' or structure == 'none':
vulnerability_class = 'URM'
elif structure.startswith('beton') or structure.startswith('kayu'):
vulnerability_class = 'RM'
else:
if int(levels) >= 2:
vulnerability_class = 'RM'
else:
vulnerability_class = 'URM'
# Store new attribute value
attributes[i][target_attribute] = vulnerability_class
# Create new vector instance and return
V = Vector(data=attributes,
projection=E.get_projection(),
geometry=E.get_geometry(),
name=E.get_name() + ' mapped to BNPB vulnerability classes',
keywords=E.get_keywords())
return V
def axes_to_points(x, y):
"""Generate all combinations of grid point coordinates from x and y axes
:param x: x coordinates (array)
:type x: numpy.ndarray
:param y: y coordinates (array)
:type y: numpy.ndarray
:returns:
* P: Nx2 array consisting of coordinates for all
grid points defined by x and y axes. The x coordinate
will vary the fastest to match the way 2D numpy
arrays are laid out by default ('C' order). That way,
the x and y coordinates will match a corresponding
2D array A when flattened (A.flat[:] or A.reshape(-1))
Note:
Example
x = [1, 2, 3]
y = [10, 20]
P = [[1, 10],
[2, 10],
[3, 10],
[1, 20],
[2, 20],
[3, 20]]
"""
# Reverse y coordinates to have them start at bottom of array
y = numpy.flipud(y)
# Repeat x coordinates for each y (fastest varying)
# noinspection PyTypeChecker
X = numpy.kron(numpy.ones(len(y)), x)
# Repeat y coordinates for each x (slowest varying)
Y = numpy.kron(y, numpy.ones(len(x)))
# Check
N = len(X)
verify(len(Y) == N)
# Create Nx2 array of x and y coordinates
X = numpy.reshape(X, (N, 1))
Y = numpy.reshape(Y, (N, 1))
P = numpy.concatenate((X, Y), axis=1)
# Return
return P
def sigab2bnpb(E, target_attribute='VCLASS'):
"""Map SIGAB point data to BNPB vulnerability classes
Input E:
Vector object representing the OSM data
target_attribute: Optional name of the attribute containing
the mapped vulnerability class. Default value is 'VCLASS'
Output:
Vector object like E, but with one new attribute (e.g. 'VCLASS')
representing the vulnerability class used in the guidelines
"""
# Input check
required = ['Struktur_B', 'Lantai', 'Atap', 'Dinding', 'Tingkat']
actual = E.get_attribute_names()
msg = ('Input data to sigab2bnpb must have attributes %s. '
'It has %s' % (str(required), str(actual)))
for attribute in required:
verify(attribute in actual, msg)
# Start mapping
N = len(E)
attributes = E.get_data()
for i in range(N):
levels = E.get_data('Tingkat', i).lower()
structure = E.get_data('Struktur_B', i).lower()
# roof_type = E.get_data('Atap', i).lower()
# wall_type = E.get_data('Dinding', i).lower()
# floor_type = E.get_data('Lantai', i).lower()
if levels == 'none' or structure == 'none':
vulnerability_class = 'URM'
elif structure.startswith('beton') or structure.startswith('kayu'):
vulnerability_class = 'RM'
else:
if int(levels) >= 2:
vulnerability_class = 'RM'
else:
vulnerability_class = 'URM'
# Store new attribute value
attributes[i][target_attribute] = vulnerability_class
# Create new vector instance and return
V = Vector(data=attributes,
projection=E.get_projection(),
geometry=E.get_geometry(),
name=E.get_name() + ' mapped to BNPB vulnerability classes',
keywords=E.get_keywords())
return V
def calculate_polygon_area(polygon, signed=False):
"""Calculate the signed area of non-self-intersecting polygon
:param polygon: Numeric array of points (longitude, latitude). It is
assumed to be closed, i.e. first and last points are identical
:type polygon: numpy.ndarray
:param signed: Optional flag deciding whether returned area retains its
sign:
If points are ordered counter clockwise, the signed area
will be positive.
If points are ordered clockwise, it will be negative
Default is False which means that the area is always
positive.
:type signed: bool
:returns: area: Area of polygon (subject to the value of argument signed)
:rtype: numpy.ndarray
Note:
Sources
http://paulbourke.net/geometry/polyarea/
http://en.wikipedia.org/wiki/Centroid
"""
# Make sure it is numeric
P = numpy.array(polygon)
msg = ('Polygon is assumed to consist of coordinate pairs. '
'I got second dimension %i instead of 2' % P.shape[1])
verify(P.shape[1] == 2, msg)
x = P[:, 0]
y = P[:, 1]
# Calculate 0.5 sum_{i=0}^{N-1} (x_i y_{i+1} - x_{i+1} y_i)
a = x[:-1] * y[1:]
b = y[:-1] * x[1:]
A = numpy.sum(a - b) / 2.
if signed:
return A
else:
return abs(A)
def write_to_file(self, filename):
"""Save raster data to file
Args:
* filename: filename with extension .tif
Gdal documentation at: http://www.gdal.org/classGDALRasterBand.html
"""
# Check file format
basename, extension = os.path.splitext(filename)
msg = ('Invalid file type for file %s. Only extension '
'tif allowed.' % filename)
verify(extension in ['.tif'], msg)
file_format = DRIVER_MAP[extension]
# Get raster data
A = self.get_data()
# Get Dimensions. Note numpy and Gdal swap order
N, M = A.shape
# Create empty file.
# FIXME (Ole): It appears that this is created as single
# precision even though Float64 is specified
# - see issue #17
driver = gdal.GetDriverByName(file_format)
fid = driver.Create(get_string(filename), M, N, 1, gdal.GDT_Float64)
if fid is None:
msg = ('Gdal could not create filename %s using '
'format %s' % (filename, file_format))
raise WriteLayerError(msg)
self.filename = filename
# Write metadata
fid.SetProjection(str(self.projection))
fid.SetGeoTransform(self.geotransform)
# Write data
fid.GetRasterBand(1).WriteArray(A)
fid.GetRasterBand(1).SetNoDataValue(self.get_nodata_value())
# noinspection PyUnusedLocal
fid = None # Close
# Write keywords if any
write_iso19115_metadata(filename, self.keywords)
def calculate_polygon_area(polygon, signed=False):
"""Calculate the signed area of non-self-intersecting polygon
:param polygon: Numeric array of points (longitude, latitude). It is
assumed to be closed, i.e. first and last points are identical
:type polygon: numpy.ndarray
:param signed: Optional flag deciding whether returned area retains its
sign:
If points are ordered counter clockwise, the signed area
will be positive.
If points are ordered clockwise, it will be negative
Default is False which means that the area is always
positive.
:type signed: bool
:returns: area: Area of polygon (subject to the value of argument signed)
:rtype: numpy.ndarray
Note:
Sources
http://paulbourke.net/geometry/polyarea/
http://en.wikipedia.org/wiki/Centroid
"""
# Make sure it is numeric
P = numpy.array(polygon)
msg = ('Polygon is assumed to consist of coordinate pairs. '
'I got second dimension %i instead of 2' % P.shape[1])
verify(P.shape[1] == 2, msg)
x = P[:, 0]
y = P[:, 1]
# Calculate 0.5 sum_{i=0}^{N-1} (x_i y_{i+1} - x_{i+1} y_i)
a = x[:-1] * y[1:]
b = y[:-1] * x[1:]
A = numpy.sum(a - b) / 2.
if signed:
return A
else:
return abs(A)
def raster_geometry_to_geotransform(longitudes, latitudes):
"""Convert vectors of longitudes and latitudes to geotransform
Note:
This is the inverse operation of Raster.get_geometry().
:param longitudes: Vectors of geographic coordinates
:type longitudes:
:param latitudes: Vectors of geographic coordinates
:type latitudes:
:returns: geotransform: 6-tuple (top left x, w-e pixel resolution,
rotation, top left y, rotation, n-s pixel resolution)
"""
nx = len(longitudes)
ny = len(latitudes)
msg = ('You must specify more than 1 longitude to make geotransform: '
'I got %s' % str(longitudes))
verify(nx > 1, msg)
msg = ('You must specify more than 1 latitude to make geotransform: '
'I got %s' % str(latitudes))
verify(ny > 1, msg)
dx = float(longitudes[1] - longitudes[0]) # Longitudinal resolution
dy = float(latitudes[0] - latitudes[1]) # Latitudinal resolution (neg)
# Define pixel centers along each directions
# This is to achieve pixel registration rather
# than gridline registration
dx2 = dx / 2
dy2 = dy / 2
geotransform = (
longitudes[0] - dx2, # Longitude of upper left corner
dx, # w-e pixel resolution
0, # rotation
latitudes[-1] - dy2, # Latitude of upper left corner
0, # rotation
dy) # n-s pixel resolution
return geotransform
def raster_geometry_to_geotransform(longitudes, latitudes):
"""Convert vectors of longitudes and latitudes to geotransform
Note:
This is the inverse operation of Raster.get_geometry().
:param longitudes: Vectors of geographic coordinates
:type longitudes:
:param latitudes: Vectors of geographic coordinates
:type latitudes:
:returns: geotransform: 6-tuple (top left x, w-e pixel resolution,
rotation, top left y, rotation, n-s pixel resolution)
"""
nx = len(longitudes)
ny = len(latitudes)
msg = ('You must specify more than 1 longitude to make geotransform: '
'I got %s' % str(longitudes))
verify(nx > 1, msg)
msg = ('You must specify more than 1 latitude to make geotransform: '
'I got %s' % str(latitudes))
verify(ny > 1, msg)
dx = float(longitudes[1] - longitudes[0]) # Longitudinal resolution
dy = float(latitudes[0] - latitudes[1]) # Latitudinal resolution (neg)
# Define pixel centers along each directions
# This is to achieve pixel registration rather
# than gridline registration
dx2 = dx / 2
dy2 = dy / 2
geotransform = (longitudes[0] - dx2, # Longitude of upper left corner
dx, # w-e pixel resolution
0, # rotation
latitudes[-1] - dy2, # Latitude of upper left corner
0, # rotation
dy) # n-s pixel resolution
return geotransform
def write_to_file(self, filename):
"""Save raster data to file
Args:
* filename: filename with extension .tif
"""
# Check file format
basename, extension = os.path.splitext(filename)
msg = ('Invalid file type for file %s. Only extension '
'tif allowed.' % filename)
verify(extension in ['.tif', '.asc'], msg)
file_format = DRIVER_MAP[extension]
# Get raster data
A = self.get_data()
# Get Dimensions. Note numpy and Gdal swap order
N, M = A.shape
# Create empty file.
# FIXME (Ole): It appears that this is created as single
# precision even though Float64 is specified
# - see issue #17
driver = gdal.GetDriverByName(file_format)
fid = driver.Create(filename, M, N, 1, gdal.GDT_Float64)
if fid is None:
msg = ('Gdal could not create filename %s using '
'format %s' % (filename, file_format))
raise WriteLayerError(msg)
self.filename = filename
# Write metada
fid.SetProjection(str(self.projection))
fid.SetGeoTransform(self.geotransform)
# Write data
fid.GetRasterBand(1).WriteArray(A)
# Write keywords if any
write_keywords(self.keywords, basename + '.keywords')
def check_geotransform(geotransform):
"""Check that geotransform is valid
:param geotransform: GDAL geotransform (6-tuple).
(top left x, w-e pixel resolution, rotation,
top left y, rotation, n-s pixel resolution).
See e.g. http://www.gdal.org/gdal_tutorial.html
:type geotransform: tuple
.. note::
This assumes that the spatial reference uses geographic coordinates,
so will not work for projected coordinate systems.
"""
msg = ('Supplied geotransform must be a tuple with '
'6 numbers. I got %s' % str(geotransform))
verify(len(geotransform) == 6, msg)
for x in geotransform:
try:
float(x)
except TypeError:
raise InaSAFEError(msg)
# Check longitude
msg = ('Element in 0 (first) geotransform must be a valid '
'longitude. I got %s' % geotransform[0])
verify(-180 <= geotransform[0] <= 180, msg)
# Check latitude
msg = ('Element 3 (fourth) in geotransform must be a valid '
'latitude. I got %s' % geotransform[3])
verify(-90 <= geotransform[3] <= 90, msg)
# Check cell size
msg = ('Element 1 (second) in geotransform must be a positive '
'number. I got %s' % geotransform[1])
verify(geotransform[1] > 0, msg)
msg = ('Element 5 (sixth) in geotransform must be a negative '
'number. I got %s' % geotransform[1])
verify(geotransform[5] < 0, msg)
def check_geotransform(geotransform):
"""Check that geotransform is valid
Args
* geotransform: GDAL geotransform (6-tuple).
(top left x, w-e pixel resolution, rotation,
top left y, rotation, n-s pixel resolution).
See e.g. http://www.gdal.org/gdal_tutorial.html
Note
This assumes that the spatial reference uses geographic coordinaties,
so will not work for projected coordinate systems.
"""
msg = ('Supplied geotransform must be a tuple with '
'6 numbers. I got %s' % str(geotransform))
verify(len(geotransform) == 6, msg)
for x in geotransform:
try:
float(x)
except TypeError:
raise InaSAFEError(msg)
# Check longitude
msg = ('Element in 0 (first) geotransform must be a valid '
'longitude. I got %s' % geotransform[0])
verify(-180 <= geotransform[0] <= 180, msg)
# Check latitude
msg = ('Element 3 (fourth) in geotransform must be a valid '
'latitude. I got %s' % geotransform[3])
verify(-90 <= geotransform[3] <= 90, msg)
# Check cell size
msg = ('Element 1 (second) in geotransform must be a positive '
'number. I got %s' % geotransform[1])
verify(geotransform[1] > 0, msg)
msg = ('Element 5 (sixth) in geotransform must be a negative '
'number. I got %s' % geotransform[1])
verify(geotransform[5] < 0, msg)
def write_to_file(self, filename):
"""Save raster data to file
Args:
* filename: filename with extension .tif
"""
# Check file format
basename, extension = os.path.splitext(filename)
msg = ('Invalid file type for file %s. Only extension '
'tif allowed.' % filename)
verify(extension in ['.tif', '.asc'], msg)
file_format = DRIVER_MAP[extension]
# Get raster data
A = self.get_data()
# Get Dimensions. Note numpy and Gdal swap order
N, M = A.shape
# Create empty file.
# FIXME (Ole): It appears that this is created as single
# precision even though Float64 is specified
# - see issue #17
driver = gdal.GetDriverByName(file_format)
fid = driver.Create(filename, M, N, 1, gdal.GDT_Float64)
if fid is None:
msg = ('Gdal could not create filename %s using '
'format %s' % (filename, file_format))
raise WriteLayerError(msg)
# Write metada
fid.SetProjection(str(self.projection))
fid.SetGeoTransform(self.geotransform)
# Write data
fid.GetRasterBand(1).WriteArray(A)
# Write keywords if any
write_keywords(self.keywords, basename + '.keywords')
def interpolate_polygon_vector(source,
target,
layer_name=None,
attribute_name=None):
"""Interpolate from polygon vector layer to vector data
Args:
* source: Vector data set (polygon)
* target: Vector data set (points or polygons) - TBA also lines
* layer_name: Optional name of returned interpolated layer.
If None the name of target is used for the returned layer.
* attribute_name: Name for new attribute.
If None (default) the name of source is used
Output
I: Vector data set; points located as target with values interpolated
from source
Note:
If target geometry is polygon, data will be interpolated to
its centroids and the output is a point data set.
"""
# Input checks
verify(source.is_vector)
verify(target.is_vector)
verify(source.is_polygon_data)
if target.is_point_data:
R = interpolate_polygon_points(source,
target,
layer_name=layer_name,
attribute_name=attribute_name)
elif target.is_line_data:
R = interpolate_polygon_lines(source,
target,
layer_name=layer_name,
attribute_name=attribute_name)
elif target.is_polygon_data:
# Use polygon centroids
X = convert_polygons_to_centroids(target)
P = interpolate_polygon_points(source,
X,
layer_name=layer_name,
attribute_name=attribute_name)
# In case of polygon data, restore the polygon geometry
# Do this setting the geometry of the returned set to
# that of the original polygon
R = Vector(data=P.get_data(),
projection=P.get_projection(),
geometry=X.get_geometry(),
name=P.get_name())
else:
msg = ('Unknown datatype for polygon2vector interpolation: '
'I got %s' % str(target))
raise InaSAFEError(msg)
# Return interpolated vector layer
return R
def check_inputs(hazard, exposure, layer_name, attribute_name):
"""Check inputs and establish default values
Args:
* hazard: Hazard layer instance (any type)
* exposure: Exposure layer instance (any type)
* layer_name: Name of returned layer or None
* attribute_name: Name of interpolated attribute or None
Returns:
* layer_name
* attribute_name
Raises:
VerificationError
"""
msg = "Projections must be the same: I got %s and %s" % (hazard.projection, exposure.projection)
verify(hazard.projection == exposure.projection, msg)
msg = "Parameter attribute_name must be either a string or None. " "I got %s" % (str(type(exposure)))[1:-1]
verify(attribute_name is None or isinstance(attribute_name, basestring), msg)
msg = "Parameter layer_name must be either a string or None. " "I got %s" % (str(type(exposure)))[1:-1]
verify(layer_name is None or isinstance(layer_name, basestring), msg)
# Establish default names
if layer_name is None:
layer_name = exposure.get_name()
if hazard.is_raster and attribute_name is None:
layer_name = hazard.get_name()
return layer_name, attribute_name
def get_topN(self, attribute, N=10):
"""Get top N features
Args:
* attribute: The name of attribute where values are sought
* N: How many
Returns:
* layer: New vector layer with selected features
"""
# Input checks
msg = "Specfied attribute must be a string. " "I got %s" % (type(attribute))
verify(isinstance(attribute, basestring), msg)
msg = "Specified attribute was empty"
verify(attribute != "", msg)
msg = "N must be a positive number. I got %i" % N
verify(N > 0, msg)
# Create list of values for specified attribute
values = self.get_data(attribute)
# Sort and select using Schwarzian transform
A = zip(values, self.data, self.geometry)
A.sort()
# Pick top N and unpack
data, geometry = zip(*A[-N:])[1:]
# Create new Vector instance and return
return Vector(data=data, projection=self.get_projection(), geometry=geometry, keywords=self.get_keywords())
def get_bins(self, N=10, quantiles=False):
"""Get N values between the min and the max occurred in this dataset.
Return sorted list of length N+1 where the first element is min and
the last is max. Intermediate values depend on the keyword quantiles:
If quantiles is True, they represent boundaries between quantiles.
If quantiles is False, they represent equidistant interval boundaries.
"""
rmin, rmax = self.get_extrema()
levels = []
if quantiles is False:
# Linear intervals
d = (rmax - rmin) / N
for i in range(N):
levels.append(rmin + i * d)
else:
# Quantiles
# FIXME (Ole): Not 100% sure about this algorithm,
# but it is close enough
A = self.get_data().flat[:]
mask = numpy.logical_not(numpy.isnan(A)) # Omit NaN's
A = A.compress(mask)
A.sort()
verify(len(A) == A.shape[0])
d = float(len(A) + 0.5) / N
for i in range(N):
levels.append(A[int(i * d)])
levels.append(rmax)
return levels
def get_bins(self, N=10, quantiles=False):
"""Get N values between the min and the max occurred in this dataset.
Return sorted list of length N+1 where the first element is min and
the last is max. Intermediate values depend on the keyword quantiles:
If quantiles is True, they represent boundaries between quantiles.
If quantiles is False, they represent equidistant interval boundaries.
"""
rmin, rmax = self.get_extrema()
levels = []
if quantiles is False:
# Linear intervals
d = (rmax - rmin) / N
for i in range(N):
levels.append(rmin + i * d)
else:
# Quantiles
# FIXME (Ole): Not 100% sure about this algorithm,
# but it is close enough
A = self.get_data().flat[:]
mask = numpy.logical_not(numpy.isnan(A)) # Omit NaN's
A = A.compress(mask)
A.sort()
verify(len(A) == A.shape[0])
d = float(len(A) + 0.5) / N
for i in range(N):
levels.append(A[int(i * d)])
levels.append(rmax)
return levels
def convert_line_to_points(V, delta):
"""Convert line vector data to point vector data
:param V: Vector layer with line data
:type V: Vector
:param delta: Incremental step to find the points
:type delta: float
:returns: Vector layer with point data and the same attributes as V
:rtype: Vector
"""
msg = 'Input data %s must be line vector data' % V
verify(V.is_line_data, msg)
geometry = V.get_geometry()
data = V.get_data()
N = len(V)
# Calculate centroids for each polygon
points = []
new_data = []
for i in range(N):
c = points_along_line(geometry[i], delta)
# We need to create a data entry for each point.
# FIXME (Ole): What on earth is this?
# pylint: disable=W0621
new_data.extend([data[i] for _ in c])
# pylint: enable=W0621
points.extend(c)
# Create new point vector layer with same attributes and return
V = Vector(data=new_data,
projection=V.get_projection(),
geometry=points,
name='%s_point_data' % V.get_name(),
keywords=V.get_keywords())
return V
def convert_line_to_points(V, delta):
"""Convert line vector data to point vector data
:param V: Vector layer with line data
:type V: Vector
:param delta: Incremental step to find the points
:type delta: float
:returns: Vector layer with point data and the same attributes as V
:rtype: Vector
"""
msg = 'Input data %s must be line vector data' % V
verify(V.is_line_data, msg)
geometry = V.get_geometry()
data = V.get_data()
N = len(V)
# Calculate centroids for each polygon
points = []
new_data = []
for i in range(N):
c = points_along_line(geometry[i], delta)
# We need to create a data entry for each point.
# FIXME (Ole): What on earth is this?
# pylint: disable=W0621
new_data.extend([data[i] for _ in c])
# pylint: enable=W0621
points.extend(c)
# Create new point vector layer with same attributes and return
V = Vector(data=new_data,
projection=V.get_projection(),
geometry=points,
name='%s_point_data' % V.get_name(),
keywords=V.get_keywords())
return V
def data(self):
"""Property for the data of this layer.
The setter does a lazy read so that the data matrix is only
initialised if is is actually wanted.
:returns: A matrix containing the layer data or None if the layer
has no band.
:rtype: numpy.array
"""
if self._data is None:
if self.band is None:
return None
# Read from raster file
data = self.band.ReadAsArray()
# Convert to double precision (issue #75)
data = numpy.array(data, dtype=numpy.float64)
# Self check
M, N = data.shape
msg = (
'Dimensions of raster array do not match those of '
'raster file %s' % self.filename)
verify(M == self.rows, msg)
verify(N == self.columns, msg)
nodata = self.band.GetNoDataValue()
if nodata is None:
nodata = -9999
if nodata is not numpy.nan:
NaN = numpy.ones((M, N), numpy.float64) * numpy.nan
data = numpy.where(data == nodata, NaN, data)
self._data = data
return self._data
def bbox_intersection(*args):
"""Compute intersection between two or more bounding boxes
Args:
* args: two or more bounding boxes.
Each is assumed to be a list or a tuple with
four coordinates (W, S, E, N)
Returns:
* result: The minimal common bounding box
"""
msg = "Function bbox_intersection must take at least 2 arguments."
verify(len(args) > 1, msg)
result = [-180, -90, 180, 90]
for a in args:
msg = "Bounding box expected to be a list of the " "form [W, S, E, N]. " 'Instead i got "%s"' % str(a)
try:
box = list(a)
except:
raise Exception(msg)
verify(len(box) == 4, msg)
msg = "Western boundary must be less than eastern. I got %s" % box
verify(box[0] < box[2], msg)
msg = "Southern boundary must be less than northern. I got %s" % box
verify(box[1] < box[3], msg)
# Compute intersection
# West and South
for i in [0, 1]:
result[i] = max(result[i], box[i])
# East and North
for i in [2, 3]:
result[i] = min(result[i], box[i])
# Check validity and return
if result[0] < result[2] and result[1] < result[3]:
return result
else:
return None
def geotransform2resolution(geotransform,
isotropic=False,
rtol=1.0e-6,
atol=1.0e-8):
"""Convert geotransform to resolution
Args:
* geotransform: GDAL geotransform (6-tuple).
(top left x, w-e pixel resolution, rotation,
top left y, rotation, n-s pixel resolution).
See e.g. http://www.gdal.org/gdal_tutorial.html
* isotropic: If True, verify that dx == dy and return dx
If False (default) return 2-tuple (dx, dy)
* rtol, atol: Used to control how close dx and dy must be
to quality for isotropic. These are passed on to
numpy.allclose for comparison.
Returns:
* resolution: grid spacing (resx, resy) in (positive) decimal
degrees ordered as longitude first, then latitude.
or resx (if isotropic is True)
"""
resx = geotransform[1] # w-e pixel resolution
resy = -geotransform[5] # n-s pixel resolution (always negative)
if isotropic:
msg = ('Resolution requested with '
'isotropic=True, but '
'resolutions in the horizontal and vertical '
'are different: resx = %.12f, resy = %.12f. ' % (resx, resy))
verify(numpy.allclose(resx, resy, rtol=rtol, atol=atol), msg)
return resx
else:
return resx, resy
def rings_equal(x, y, rtol=1.0e-6, atol=1.0e-8):
"""Compares to linear rings as numpy arrays
:param x: A 2d array of the first ring
:type x: numpy.ndarray
:param y: A 2d array of the second ring
:type y: numpy.ndarray
:param rtol: The relative tolerance parameter
:type rtol: float
:param atol: The relative tolerance parameter
:type rtol: float
Returns:
* True if x == y or x' == y (up to the specified tolerance)
where x' is x reversed in the first dimension. This corresponds to
linear rings being seen as equal irrespective of whether they are
organised in clock wise or counter clock wise order
"""
x = ensure_numeric(x, numpy.float)
y = ensure_numeric(y, numpy.float)
msg = "Arrays must a 2d arrays of vertices. I got %s and %s" % (x, y)
verify(len(x.shape) == 2 and len(y.shape) == 2, msg)
msg = "Arrays must have two columns. I got %s and %s" % (x, y)
verify(x.shape[1] == 2 and y.shape[1] == 2, msg)
if numpy.allclose(x, y, rtol=rtol, atol=atol) or numpy.allclose(x, y[::-1], rtol=rtol, atol=atol):
return True
else:
return False
def interpolate_polygon_raster(source,
target,
layer_name=None,
attribute_name=None):
"""Interpolate from polygon layer to raster data
Args
* source: Polygon data set
* target: Raster data set
* layer_name: Optional name of returned interpolated layer.
If None the name of source is used for the returned layer.
* attribute_name: Name for new attribute.
If None (default) the name of layer target is used
Output
I: Vector data set; points located as target with
values interpolated from source
Note:
Each point in the resulting dataset will have an attribute
'polygon_id' which refers to the polygon it belongs to.
"""
# Input checks
verify(target.is_raster)
verify(source.is_vector)
verify(source.is_polygon_data)
# Run underlying clipping algorithm
polygon_geometry = source.get_geometry(as_geometry_objects=True)
polygon_attributes = source.get_data()
res = clip_grid_by_polygons(
target.get_data(scaling=False), target.get_geotransform(),
polygon_geometry)
# Create one new point layer with interpolated attributes
new_geometry = []
new_attributes = []
for i, (geometry, values) in enumerate(res):
# For each polygon assign attributes to points that fall inside it
for j, geom in enumerate(geometry):
attr = polygon_attributes[i].copy() # Attributes for this polygon
attr[attribute_name] = values[j] # Attribute value from grid cell
attr['polygon_id'] = i # Store id for associated polygon
new_attributes.append(attr)
new_geometry.append(geom)
R = Vector(
data=new_attributes,
projection=source.get_projection(),
geometry=new_geometry,
name=layer_name)
return R
def interpolate_polygon_vector(source, target,
layer_name=None, attribute_name=None):
"""Interpolate from polygon vector layer to vector data
Args:
* source: Vector data set (polygon)
* target: Vector data set (points or polygons) - TBA also lines
* layer_name: Optional name of returned interpolated layer.
If None the name of target is used for the returned layer.
* attribute_name: Name for new attribute.
If None (default) the name of source is used
Output
I: Vector data set; points located as target with values interpolated
from source
Note:
If target geometry is polygon, data will be interpolated to
its centroids and the output is a point data set.
"""
# Input checks
verify(source.is_vector)
verify(target.is_vector)
verify(source.is_polygon_data)
if target.is_point_data:
R = interpolate_polygon_points(source, target,
layer_name=layer_name,
attribute_name=attribute_name)
elif target.is_line_data:
R = interpolate_polygon_lines(source, target,
layer_name=layer_name,
attribute_name=attribute_name)
elif target.is_polygon_data:
# Use polygon centroids
X = convert_polygons_to_centroids(target)
P = interpolate_polygon_points(source, X,
layer_name=layer_name,
attribute_name=attribute_name)
# In case of polygon data, restore the polygon geometry
# Do this setting the geometry of the returned set to
# that of the original polygon
R = Vector(data=P.get_data(),
projection=P.get_projection(),
geometry=X.get_geometry(),
name=P.get_name())
else:
msg = ('Unknown datatype for polygon2vector interpolation: '
'I got %s' % str(target))
raise InaSAFEError(msg)
# Return interpolated vector layer
return R
def interpolate_polygon_raster(source,
target,
layer_name=None,
attribute_name=None):
"""Interpolate from polygon layer to raster data
Args
* source: Polygon data set
* target: Raster data set
* layer_name: Optional name of returned interpolated layer.
If None the name of source is used for the returned layer.
* attribute_name: Name for new attribute.
If None (default) the name of layer target is used
Output
I: Vector data set; points located as target with
values interpolated from source
Note:
Each point in the resulting dataset will have an attribute
'polygon_id' which refers to the polygon it belongs to.
"""
# Input checks
verify(target.is_raster)
verify(source.is_vector)
verify(source.is_polygon_data)
# Run underlying clipping algorithm
polygon_geometry = source.get_geometry(as_geometry_objects=True)
polygon_attributes = source.get_data()
res = clip_grid_by_polygons(target.get_data(scaling=False),
target.get_geotransform(), polygon_geometry)
# Create one new point layer with interpolated attributes
new_geometry = []
new_attributes = []
for i, (geometry, values) in enumerate(res):
# For each polygon assign attributes to points that fall inside it
for j, geom in enumerate(geometry):
attr = polygon_attributes[i].copy() # Attributes for this polygon
attr[attribute_name] = values[j] # Attribute value from grid cell
attr['polygon_id'] = i # Store id for associated polygon
new_attributes.append(attr)
new_geometry.append(geom)
R = Vector(data=new_attributes,
projection=source.get_projection(),
geometry=new_geometry,
name=layer_name)
return R
def check_inputs(hazard, exposure, layer_name, attribute_name):
"""Check inputs and establish default values
Args:
* hazard: Hazard layer instance (any type)
* exposure: Exposure layer instance (any type)
* layer_name: Name of returned layer or None
* attribute_name: Name of interpolated attribute or None
Returns:
* layer_name
* attribute_name
Raises:
VerificationError
"""
msg = ('Projections must be the same: I got %s and %s'
% (hazard.projection, exposure.projection))
verify(hazard.projection == exposure.projection, msg)
msg = ('Parameter attribute_name must be either a string or None. '
'I got %s' % (str(type(exposure)))[1:-1])
verify(attribute_name is None
or isinstance(attribute_name, basestring), msg)
msg = ('Parameter layer_name must be either a string or None. '
'I got %s' % (str(type(exposure)))[1:-1])
verify(layer_name is None
or isinstance(layer_name, basestring), msg)
# Establish default names
if layer_name is None:
layer_name = exposure.get_name()
if hazard.is_raster and attribute_name is None:
layer_name = hazard.get_name()
if (exposure.is_raster and hazard.is_vector and hazard.is_polygon_data
and attribute_name is None):
attribute_name = exposure.get_name()
if (hazard.is_raster and exposure.is_vector and exposure.is_point_data
and attribute_name is None):
attribute_name = hazard.get_name()
# Launder for shape files
# FIXME (Ole): Remove when (if) we get rid of the shp format
if attribute_name is not None:
attribute_name = str(attribute_name[:10])
return layer_name, attribute_name
def check_inputs(hazard, exposure, layer_name, attribute_name):
"""Check inputs and establish default values
Args:
* hazard: Hazard layer instance (any type)
* exposure: Exposure layer instance (any type)
* layer_name: Name of returned layer or None
* attribute_name: Name of interpolated attribute or None
Returns:
* layer_name
* attribute_name
Raises:
VerificationError
"""
msg = ('Projections must be the same: I got %s and %s'
% (hazard.projection, exposure.projection))
verify(hazard.projection == exposure.projection, msg)
msg = ('Parameter attribute_name must be either a string or None. '
'I got %s' % (str(type(exposure)))[1:-1])
verify(attribute_name is None
or isinstance(attribute_name, basestring), msg)
msg = ('Parameter layer_name must be either a string or None. '
'I got %s' % (str(type(exposure)))[1:-1])
verify(layer_name is None
or isinstance(layer_name, basestring), msg)
# Establish default names
if layer_name is None:
layer_name = exposure.get_name()
if hazard.is_raster and attribute_name is None:
layer_name = hazard.get_name()
if (exposure.is_raster and hazard.is_vector and hazard.is_polygon_data
and attribute_name is None):
attribute_name = exposure.get_name()
if (hazard.is_raster and exposure.is_vector and exposure.is_point_data
and attribute_name is None):
attribute_name = hazard.get_name()
# Launder for shape files
# FIXME (Ole): Remove when (if) we get rid of the shp format
if attribute_name is not None:
attribute_name = str(attribute_name[:10])
return layer_name, attribute_name
def get_data(self, attribute=None, index=None, copy=False):
"""Get vector attributes
Note:
Data is returned as a list where each entry is a dictionary of
attributes for one feature. Entries in get_geometry() and
get_data() are related as 1-to-1
If optional argument attribute is specified and a valid name,
then the list of values for that attribute is returned.
If optional argument index is specified on the that value will
be returned. Any value of index is ignored if attribute is None.
If optional argument copy is True and all attributes are requested,
a copy will be returned. Otherwise a pointer to the data is
returned.
"""
if hasattr(self, "data"):
if attribute is None:
if copy:
return copy_module.deepcopy(self.data)
else:
return self.data
else:
msg = (
"Specified attribute %s does not exist in "
"vector layer %s. Valid names are %s"
"" % (attribute, self, self.data[0].keys())
)
verify(attribute in self.data[0], msg)
if index is None:
# Return all values for specified attribute
return [x[attribute] for x in self.data]
else:
# Return value for specified attribute and index
msg = "Specified index must be either None or " "an integer. I got %s" % index
verify(isinstance(index, int), msg)
msg = (
"Specified index must lie within the bounds "
"of vector layer %s which is [%i, %i]"
"" % (self, 0, len(self) - 1)
)
verify(0 <= index < len(self), msg)
return self.data[index][attribute]
else:
msg = "Vector data instance does not have any attributes"
raise GetDataError(msg)
def get_data(self, attribute=None, index=None, copy=False):
"""Get vector attributes
Note:
Data is returned as a list where each entry is a dictionary of
attributes for one feature. Entries in get_geometry() and
get_data() are related as 1-to-1
If optional argument attribute is specified and a valid name,
then the list of values for that attribute is returned.
If optional argument index is specified on the that value will
be returned. Any value of index is ignored if attribute is None.
If optional argument copy is True and all attributes are requested,
a copy will be returned. Otherwise a pointer to the data is
returned.
"""
if hasattr(self, 'data'):
if attribute is None:
if copy:
return copy_module.deepcopy(self.data)
else:
return self.data
else:
msg = ('Specified attribute %s does not exist in '
'vector layer %s. Valid names are %s'
'' % (attribute, self, self.data[0].keys()))
verify(attribute in self.data[0], msg)
if index is None:
# Return all values for specified attribute
return [x[attribute] for x in self.data]
else:
# Return value for specified attribute and index
msg = ('Specified index must be either None or '
'an integer. I got %s' % index)
verify(type(index) == type(0), msg)
msg = ('Specified index must lie within the bounds '
'of vector layer %s which is [%i, %i]'
'' % (self, 0, len(self) - 1))
verify(0 <= index < len(self), msg)
return self.data[index][attribute]
else:
msg = 'Vector data instance does not have any attributes'
raise GetDataError(msg)
def __init__(self,
name=None,
projection=None,
keywords=None,
style_info=None,
sublayer=None):
"""Common constructor for all types of layers
See docstrings for class Raster and class Vector for details.
"""
# Name
msg = ('Specified name must be a string or None. '
'I got %s with type %s' % (name, str(type(name))[1:-1]))
verify(isinstance(name, basestring) or name is None, msg)
self.name = name
# Projection
self.projection = Projection(projection)
# Keywords
if keywords is None:
self.keywords = {}
else:
msg = ('Specified keywords must be either None or a '
'dictionary. I got %s' % keywords)
verify(isinstance(keywords, dict), msg)
self.keywords = keywords
# Style info
if style_info is None:
self.style_info = {}
else:
msg = ('Specified style_info must be either None or a '
'dictionary. I got %s' % style_info)
verify(isinstance(style_info, dict), msg)
self.style_info = style_info
# Defaults
self.sublayer = sublayer
self.filename = None
self.data = None
def __init__(self, name=None, projection=None,
keywords=None, style_info=None,
sublayer=None):
"""Common constructor for all types of layers
See docstrings for class Raster and class Vector for details.
"""
# Name
msg = ('Specified name must be a string or None. '
'I got %s with type %s' % (name, str(type(name))[1:-1]))
verify(isinstance(name, basestring) or name is None, msg)
self.name = name
# Projection
self.projection = Projection(projection)
# Keywords
if keywords is None:
self.keywords = {}
else:
msg = ('Specified keywords must be either None or a '
'dictionary. I got %s' % keywords)
verify(isinstance(keywords, dict), msg)
self.keywords = keywords
# Style info
if style_info is None:
self.style_info = {}
else:
msg = ('Specified style_info must be either None or a '
'dictionary. I got %s' % style_info)
verify(isinstance(style_info, dict), msg)
self.style_info = style_info
# Defaults
self.sublayer = sublayer
self.filename = None
self.data = None
def get_topN(self, attribute, N=10):
"""Get top N features
:param attribute: The name of attribute where values are sought
:type attribute: str
:param N: How many
:type N: int
:returns: New vector layer with selected features
"""
# Input checks
msg = ('Specfied attribute must be a string. '
'I got %s' % (type(attribute)))
verify(isinstance(attribute, basestring), msg)
msg = 'Specified attribute was empty'
verify(attribute != '', msg)
msg = 'N must be a positive number. I got %i' % N
verify(N > 0, msg)
# Create list of values for specified attribute
values = self.get_data(attribute)
# Sort and select using Schwarzian transform
A = zip(values, self.data, self.geometry)
A.sort()
# Pick top N and unpack
data, geometry = zip(*A[-N:])[1:]
# Create new Vector instance and return
return Vector(data=data,
projection=self.get_projection(),
geometry=geometry,
keywords=self.get_keywords())
def check_inputs(hazard, exposure, layer_name, attribute_name):
"""Check inputs and establish default values
Args:
* hazard: Hazard layer instance (any type)
* exposure: Exposure layer instance (any type)
* layer_name: Name of returned layer or None
* attribute_name: Name of interpolated attribute or None
Returns:
* layer_name
* attribute_name
Raises:
VerificationError
"""
msg = ('Projections must be the same: I got %s and %s' %
(hazard.projection, exposure.projection))
verify(hazard.projection == exposure.projection, msg)
msg = ('Parameter attribute_name must be either a string or None. '
'I got %s' % (str(type(exposure)))[1:-1])
verify(attribute_name is None or isinstance(attribute_name, basestring),
msg)
msg = ('Parameter layer_name must be either a string or None. '
'I got %s' % (str(type(exposure)))[1:-1])
verify(layer_name is None or isinstance(layer_name, basestring), msg)
# Establish default names
if layer_name is None:
layer_name = exposure.get_name()
if hazard.is_raster and attribute_name is None:
layer_name = hazard.get_name()
return layer_name, attribute_name
def write_to_file(self, filename, sublayer=None):
"""Save vector data to file
Args:
* filename: filename with extension .shp or .gml
* sublayer: Optional string for writing a sublayer. Ignored
unless we are writing to an sqlite file.
Note:
Shp limitation, if attribute names are longer than 10
characters they will be truncated. This is due to limitations in
the shp file driver and has to be done here since gdal v1.7 onwards
has changed its handling of this issue:
http://www.gdal.org/ogr/drv_shapefile.html
**For this reason we recommend writing to spatialite.**
"""
# Check file format
basename, extension = os.path.splitext(filename)
msg = ('Invalid file type for file %s. Only extensions '
'sqlite, shp or gml allowed.' % filename)
verify(extension in ['.sqlite', '.shp', '.gml'], msg)
driver = DRIVER_MAP[extension]
# FIXME (Ole): Tempory flagging of GML issue (ticket #18)
if extension == '.gml':
msg = ('OGR GML driver does not store geospatial reference.'
'This format is disabled for the time being. See '
'https://github.com/AIFDR/riab/issues/18')
raise WriteLayerError(msg)
# Derive layername from filename (excluding preceding dirs)
if sublayer is None or extension == '.shp':
layername = os.path.split(basename)[-1]
else:
layername = sublayer
# Get vector data
if self.is_polygon_data:
geometry = self.get_geometry(as_geometry_objects=True)
else:
geometry = self.get_geometry()
data = self.get_data()
N = len(geometry)
# Clear any previous file of this name (ogr does not overwrite)
try:
os.remove(filename)
except OSError:
pass
# Create new file with one layer
drv = ogr.GetDriverByName(driver)
if drv is None:
msg = 'OGR driver %s not available' % driver
raise WriteLayerError(msg)
ds = drv.CreateDataSource(filename)
if ds is None:
msg = 'Creation of output file %s failed' % filename
raise WriteLayerError(msg)
lyr = ds.CreateLayer(layername,
self.projection.spatial_reference,
self.geometry_type)
if lyr is None:
msg = 'Could not create layer %s' % layername
raise WriteLayerError(msg)
# Define attributes if any
store_attributes = False
fields = []
if data is not None:
if len(data) > 0:
try:
fields = data[0].keys()
except:
msg = ('Input parameter "attributes" was specified '
'but it does not contain list of dictionaries '
'with field information as expected. The first '
'element is %s' % data[0])
raise WriteLayerError(msg)
else:
# Establish OGR types for each element
ogrtypes = {}
for name in fields:
att = data[0][name]
py_type = type(att)
msg = ('Unknown type for storing vector '
'data: %s, %s' % (name, str(py_type)[1:-1]))
verify(py_type in TYPE_MAP, msg)
ogrtypes[name] = TYPE_MAP[py_type]
else:
#msg = ('Input parameter "data" was specified '
# 'but appears to be empty')
#raise InaSAFEError(msg)
pass
# Create attribute fields in layer
store_attributes = True
for name in fields:
fd = ogr.FieldDefn(name, ogrtypes[name])
# FIXME (Ole): Trying to address issue #16
# But it doesn't work and
# somehow changes the values of MMI in test
#width = max(128, len(name))
#print name, width
#fd.SetWidth(width)
# Silent handling of warnings like
# Warning 6: Normalized/laundered field name:
#'CONTENTS_LOSS_AUD' to 'CONTENTS_L'
gdal.PushErrorHandler('CPLQuietErrorHandler')
if lyr.CreateField(fd) != 0:
msg = 'Could not create field %s' % name
raise WriteLayerError(msg)
# Restore error handler
gdal.PopErrorHandler()
# Store geometry
geom = ogr.Geometry(self.geometry_type)
layer_def = lyr.GetLayerDefn()
for i in range(N):
# Create new feature instance
feature = ogr.Feature(layer_def)
# Store geometry and check
if self.is_point_data:
x = float(geometry[i][0])
y = float(geometry[i][1])
geom.SetPoint_2D(0, x, y)
elif self.is_line_data:
geom = array2line(geometry[i],
geometry_type=ogr.wkbLineString)
elif self.is_polygon_data:
# Create polygon geometry
geom = ogr.Geometry(ogr.wkbPolygon)
# Add outer ring
linear_ring = array2line(geometry[i].outer_ring,
geometry_type=ogr.wkbLinearRing)
geom.AddGeometry(linear_ring)
# Add inner rings if any
for A in geometry[i].inner_rings:
geom.AddGeometry(array2line(A,
geometry_type=ogr.wkbLinearRing))
else:
msg = 'Geometry type %s not implemented' % self.geometry_type
raise WriteLayerError(msg)
feature.SetGeometry(geom)
G = feature.GetGeometryRef()
if G is None:
msg = 'Could not create GeometryRef for file %s' % filename
raise WriteLayerError(msg)
# Store attributes
if store_attributes:
for j, name in enumerate(fields):
actual_field_name = layer_def.GetFieldDefn(j).GetNameRef()
val = data[i][name]
if type(val) == numpy.ndarray:
# A singleton of type <type 'numpy.ndarray'> works
# for gdal version 1.6 but fails for version 1.8
# in SetField with error: NotImplementedError:
# Wrong number of arguments for overloaded function
val = float(val)
elif val is None:
val = ''
# We do this because there is NaN problem on windows
# NaN value must be converted to _pseudo_in to solve the
# problem. But, when InaSAFE read the file, it'll be
# converted back to NaN value, so that NaN in InaSAFE is a
# numpy.nan
# please check https://github.com/AIFDR/inasafe/issues/269
# for more information
if val != val:
val = _pseudo_inf
feature.SetField(actual_field_name, val)
# Save this feature
if lyr.CreateFeature(feature) != 0:
msg = 'Failed to create feature %i in file %s' % (i, filename)
raise WriteLayerError(msg)
feature.Destroy()
# Write keywords if any
write_keywords(self.keywords, basename + '.keywords')
def osm2bnpb(E, target_attribute='VCLASS'):
"""
Map OSM attributes to BNPB vulnerability classes
This maps attributes collected in the OpenStreetMap exposure data
(data.kompetisiosm.org) to 2 vulnerability classes identified by
BNPB in Kajian Risiko Gempabumi VERS 1.0, 2011. They are
URM: Unreinforced Masonry and RM: Reinforced Masonry
Input E:
Vector object representing the OSM data
target_attribute: Optional name of the attribute containing
the mapped vulnerability class. Default value is 'VCLASS'
Output:
Vector object like E, but with one new attribute (e.g. 'VCLASS')
representing the vulnerability class used in the guidelines
"""
# Input check
required = ['building_l', 'building_s']
actual = E.get_attribute_names()
msg = ('Input data to osm2bnpb must have attributes %s. '
'It has %s' % (str(required), str(actual)))
for attribute in required:
verify(attribute in actual, msg)
# Start mapping
N = len(E)
attributes = E.get_data()
# FIXME (Ole): Pylint says variable count is unused. Why?
# pylint: disable=W0612
count = 0
# pylint: enable=W0612
for i in range(N):
levels = E.get_data('building_l', i)
structure = E.get_data('building_s', i)
if levels is None or structure is None:
vulnerability_class = 'URM'
count += 1
else:
# Map string variable levels to integer
if levels.endswith('+'):
levels = 100
try:
levels = int(levels)
except ValueError:
# E.g. 'ILP jalan'
vulnerability_class = 'URM'
count += 1
else:
# Start mapping depending on levels
if levels >= 4:
# High
vulnerability_class = 'RM'
elif 1 <= levels < 4:
# Low
if structure in ['reinforced_masonry', 'confined_masonry']:
vulnerability_class = 'RM'
elif 'kayu' in structure or 'wood' in structure:
vulnerability_class = 'RM'
else:
vulnerability_class = 'URM'
elif numpy.allclose(levels, 0):
# A few buildings exist with 0 levels.
# In general, we should be assigning here the most
# frequent building in the area which could be defined
# by admin boundaries.
vulnerability_class = 'URM'
else:
msg = 'Unknown number of levels: %s' % levels
raise Exception(msg)
# Store new attribute value
attributes[i][target_attribute] = vulnerability_class
# print 'Got %i without levels or structure (out of %i total)' % (count, N)
# Create new vector instance and return
V = Vector(data=attributes,
projection=E.get_projection(),
geometry=E.get_geometry(),
name=E.get_name() + ' mapped to BNPB vulnerability classes',
keywords=E.get_keywords())
return V