def is_near(input_path, radius, distance_path, out_path):
"""Make binary raster of which pixels are within a radius of a '1' pixel.
Args:
input_path (str): path to a binary raster where '1' pixels are what
we're measuring distance to, in this case roads/connected areas
radius (float): distance in pixels which is considered "near".
pixels this distance or less from a '1' pixel are marked '1' in
the output. Distances are measured centerpoint to centerpoint.
distance_path (str): path to write out the raster of distances
out_path (str): path to write out the final thresholded raster.
Pixels marked '1' are near to a '1' pixel in the input, pixels
marked '0' are not.
Returns:
None
"""
# Calculate the distance from each pixel to the nearest '1' pixel
pygeoprocessing.distance_transform_edt(
(input_path, 1),
distance_path)
def lte_threshold_op(array, threshold):
"""Binary array of elements less than or equal to the threshold."""
# no need to mask nodata because distance_transform_edt doesn't
# output any nodata pixels
return array <= threshold
# Threshold that to a binary array so '1' means it's within the radius
pygeoprocessing.raster_calculator(
[(distance_path, 1), (radius, 'raw')],
lte_threshold_op,
out_path,
gdal.GDT_Byte,
UINT8_NODATA)
def _map_distance_from_forest_edge(lulc_uri, biophysical_table_uri,
edge_distance_uri):
"""Generates a raster of forest edge distances where each pixel is the
distance to the edge of the forest in meters.
Parameters:
lulc_uri (string): path to the landcover raster that contains integer
landcover codes
biophysical_table_uri (string): a path to a csv table that indexes
landcover codes to forest type, contains at least the fields
'lucode' (landcover integer code) and 'is_forest' (0 or 1 depending
on landcover code type)
edge_distance_uri (string): path to output raster where each pixel
contains the euclidian pixel distance to nearest forest edges on
all non-nodata values of lulc_uri
Returns:
None"""
# Build a list of forest lucodes
biophysical_table = pygeoprocessing.get_lookup_from_table(
biophysical_table_uri, 'lucode')
forest_codes = [
lucode for (lucode, ludata) in biophysical_table.iteritems()
if int(ludata['is_forest']) == 1
]
# Make a raster where 1 is non-forest landcover types and 0 is forest
forest_mask_nodata = 255
lulc_nodata = pygeoprocessing.get_nodata_from_uri(lulc_uri)
def mask_non_forest_op(lulc_array):
"""converts forest lulc codes to 1"""
non_forest_mask = ~numpy.in1d(lulc_array.flatten(),
forest_codes).reshape(lulc_array.shape)
nodata_mask = lulc_array == lulc_nodata
return numpy.where(nodata_mask, forest_mask_nodata, non_forest_mask)
non_forest_mask_uri = pygeoprocessing.temporary_filename()
out_pixel_size = pygeoprocessing.get_cell_size_from_uri(lulc_uri)
pygeoprocessing.vectorize_datasets([lulc_uri],
mask_non_forest_op,
non_forest_mask_uri,
gdal.GDT_Byte,
forest_mask_nodata,
out_pixel_size,
"intersection",
vectorize_op=False)
# Do the distance transform on non-forest pixels
pygeoprocessing.distance_transform_edt(non_forest_mask_uri,
edge_distance_uri)
# good practice to delete temporary files when we're done with them
os.remove(non_forest_mask_uri)
def _map_distance_from_tropical_forest_edge(base_lulc_raster_path,
biophysical_table_path,
edge_distance_path,
target_non_forest_mask_path):
"""Generates a raster of forest edge distances where each pixel is the
distance to the edge of the forest in meters.
Parameters:
base_lulc_raster_path (string): path to the landcover raster that
contains integer landcover codes
biophysical_table_path (string): path to a csv table that indexes
landcover codes to forest type, contains at least the fields
'lucode' (landcover integer code) and 'is_tropical_forest' (0 or 1
depending on landcover code type)
edge_distance_path (string): path to output raster where each pixel
contains the euclidean pixel distance to nearest forest edges on
all non-nodata values of base_lulc_raster_path
target_non_forest_mask_path (string): path to the output non forest
mask raster
Returns:
None
"""
# Build a list of forest lucodes
biophysical_table = utils.build_lookup_from_csv(biophysical_table_path,
'lucode',
to_lower=False)
forest_codes = [
lucode for (lucode, ludata) in biophysical_table.items()
if int(ludata['is_tropical_forest']) == 1
]
# Make a raster where 1 is non-forest landcover types and 0 is forest
forest_mask_nodata = 255
lulc_nodata = pygeoprocessing.get_raster_info(
base_lulc_raster_path)['nodata']
def mask_non_forest_op(lulc_array):
"""converts forest lulc codes to 1"""
non_forest_mask = ~numpy.in1d(lulc_array.flatten(),
forest_codes).reshape(lulc_array.shape)
nodata_mask = lulc_array == lulc_nodata
return numpy.where(nodata_mask, forest_mask_nodata, non_forest_mask)
pygeoprocessing.raster_calculator([(base_lulc_raster_path, 1)],
mask_non_forest_op,
target_non_forest_mask_path,
gdal.GDT_Byte, forest_mask_nodata)
# Do the distance transform on non-forest pixels
pygeoprocessing.distance_transform_edt((target_non_forest_mask_path, 1),
edge_distance_path)
def _convert_landscape(
base_lulc_uri, replacement_lucode, area_to_convert,
focal_landcover_codes, convertible_type_list, score_weight, n_steps,
smooth_distance_from_edge_uri, output_landscape_raster_uri,
stats_uri):
"""Expand replacement lucodes in relation to the focal lucodes.
If the sign on `score_weight` is positive, expansion occurs marches
away from the focal types, while if `score_weight` is negative conversion
marches toward the focal types.
Parameters:
base_lulc_uri (string): path to landcover raster that will be used as
the base landcover map to agriculture pixels
replacement_lucode (int): agriculture landcover code type found in the
raster at `base_lulc_uri`
area_to_convert (float): area (Ha) to convert to agriculture
focal_landcover_codes (list of int): landcover codes that are used to
calculate proximity
convertible_type_list (list of int): landcover codes that are allowable
to be converted to agriculture
score_weight (float): this value is used to multiply the distance from
the focal landcover types when prioritizing which pixels in
`convertable_type_list` are to be converted. If negative,
conversion occurs toward the focal types, if positive occurs away
from the focal types.
n_steps (int): number of steps to convert the landscape. On each step
the distance transform will be applied on the
current value of the `focal_landcover_codes` pixels in
`output_landscape_raster_uri`. On the first step the distance
is calculated from `base_lulc_uri`.
smooth_distance_from_edge_uri (string): an intermediate output showing
the pixel distance from the edge of the base landcover types
output_landscape_raster_uri (string): an output raster that will
contain the final fragmented forest layer.
stats_uri (string): a path to an output csv that records the number
type, and area of pixels converted in `output_landscape_raster_uri`
Returns:
None.
"""
tmp_file_registry = {
'non_base_mask': pygeoprocessing.temporary_filename(),
'base_mask': pygeoprocessing.temporary_filename(),
'gaussian_kernel': pygeoprocessing.temporary_filename(),
'distance_from_base_mask_edge': pygeoprocessing.temporary_filename(),
'distance_from_non_base_mask_edge':
pygeoprocessing.temporary_filename(),
'convertible_distances': pygeoprocessing.temporary_filename(),
'smooth_distance_from_edge': pygeoprocessing.temporary_filename(),
'distance_from_edge': pygeoprocessing.temporary_filename(),
}
# a sigma of 1.0 gives nice visual results to smooth pixel level artifacts
# since a pixel is the 1.0 unit
_make_gaussian_kernel_uri(1.0, tmp_file_registry['gaussian_kernel'])
# create the output raster first as a copy of the base landcover so it can
# be looped on for each step
lulc_nodata = pygeoprocessing.get_nodata_from_uri(base_lulc_uri)
pixel_size_out = pygeoprocessing.get_cell_size_from_uri(base_lulc_uri)
mask_nodata = 2
pygeoprocessing.vectorize_datasets(
[base_lulc_uri], lambda x: x, output_landscape_raster_uri,
gdal.GDT_Int32, lulc_nodata, pixel_size_out, "intersection",
vectorize_op=False, datasets_are_pre_aligned=True)
# convert everything furthest from edge for each of n_steps
pixel_area_ha = (
pygeoprocessing.get_cell_size_from_uri(base_lulc_uri)**2 / 10000.0)
max_pixels_to_convert = int(math.ceil(area_to_convert / pixel_area_ha))
convertible_type_nodata = -1
pixels_left_to_convert = max_pixels_to_convert
pixels_to_convert = max_pixels_to_convert / n_steps
stats_cache = collections.defaultdict(int)
# pylint complains when these are defined inside the loop
invert_mask = None
distance_nodata = None
for step_index in xrange(n_steps):
LOGGER.info('step %d of %d', step_index+1, n_steps)
pixels_left_to_convert -= pixels_to_convert
# Often the last segement of the steps will overstep the number of
# pixels to convert, this check converts the exact amount
if pixels_left_to_convert < 0:
pixels_to_convert += pixels_left_to_convert
# create distance transforms for inside and outside the base lulc codes
LOGGER.info('create distance transform for current landcover')
for invert_mask, mask_id, distance_id in [
(False, 'non_base_mask', 'distance_from_non_base_mask_edge'),
(True, 'base_mask', 'distance_from_base_mask_edge')]:
def _mask_base_op(lulc_array):
"""Create a mask of valid non-base pixels only."""
base_mask = numpy.in1d(
lulc_array.flatten(), focal_landcover_codes).reshape(
lulc_array.shape)
if invert_mask:
base_mask = ~base_mask
return numpy.where(
lulc_array == lulc_nodata, mask_nodata, base_mask)
pygeoprocessing.vectorize_datasets(
[output_landscape_raster_uri], _mask_base_op,
tmp_file_registry[mask_id], gdal.GDT_Byte,
mask_nodata, pixel_size_out, "intersection",
vectorize_op=False, datasets_are_pre_aligned=True)
# create distance transform for the current mask
pygeoprocessing.distance_transform_edt(
tmp_file_registry[mask_id], tmp_file_registry[distance_id])
# combine inner and outer distance transforms into one
distance_nodata = pygeoprocessing.get_nodata_from_uri(
tmp_file_registry['distance_from_base_mask_edge'])
def _combine_masks(base_distance_array, non_base_distance_array):
"""create a mask of valid non-base pixels only."""
result = non_base_distance_array
valid_base_mask = base_distance_array > 0.0
result[valid_base_mask] = base_distance_array[valid_base_mask]
return result
pygeoprocessing.vectorize_datasets(
[tmp_file_registry['distance_from_base_mask_edge'],
tmp_file_registry['distance_from_non_base_mask_edge']],
_combine_masks, tmp_file_registry['distance_from_edge'],
gdal.GDT_Float32, distance_nodata, pixel_size_out, "intersection",
vectorize_op=False, datasets_are_pre_aligned=True)
# smooth the distance transform to avoid scanline artifacts
pygeoprocessing.convolve_2d_uri(
tmp_file_registry['distance_from_edge'],
tmp_file_registry['gaussian_kernel'],
smooth_distance_from_edge_uri)
# turn inside and outside masks into a single mask
def _mask_to_convertible_codes(distance_from_base_edge, lulc):
"""Mask out the distance transform to a set of lucodes."""
convertible_mask = numpy.in1d(
lulc.flatten(), convertible_type_list).reshape(lulc.shape)
return numpy.where(
convertible_mask, distance_from_base_edge,
convertible_type_nodata)
pygeoprocessing.vectorize_datasets(
[smooth_distance_from_edge_uri, output_landscape_raster_uri],
_mask_to_convertible_codes,
tmp_file_registry['convertible_distances'], gdal.GDT_Float32,
convertible_type_nodata, pixel_size_out, "intersection",
vectorize_op=False, datasets_are_pre_aligned=True)
LOGGER.info(
'convert %d pixels to lucode %d', pixels_to_convert,
replacement_lucode)
_convert_by_score(
tmp_file_registry['convertible_distances'], pixels_to_convert,
output_landscape_raster_uri, replacement_lucode, stats_cache,
score_weight)
_log_stats(stats_cache, pixel_area_ha, stats_uri)
for filename in tmp_file_registry.values():
os.remove(filename)
def _map_distance_from_tropical_forest_edge(base_lulc_raster_path,
biophysical_table_path,
edge_distance_path,
target_non_forest_mask_path):
"""Generates a raster of forest edge distances.
Generates a raster of forest edge distances where each pixel is the
distance to the edge of the forest in meters.
Args:
base_lulc_raster_path (string): path to the landcover raster that
contains integer landcover codes
biophysical_table_path (string): path to a csv table that indexes
landcover codes to forest type, contains at least the fields
'lucode' (landcover integer code) and 'is_tropical_forest' (0 or 1
depending on landcover code type)
edge_distance_path (string): path to output raster where each pixel
contains the euclidean pixel distance to nearest forest edges on
all non-nodata values of base_lulc_raster_path
target_non_forest_mask_path (string): path to the output non forest
mask raster
Returns:
None
"""
# Build a list of forest lucodes
biophysical_table = utils.build_lookup_from_csv(biophysical_table_path,
'lucode',
to_lower=False)
forest_codes = [
lucode for (lucode, ludata) in biophysical_table.items()
if int(ludata['is_tropical_forest']) == 1
]
# Make a raster where 1 is non-forest landcover types and 0 is forest
lulc_nodata = pygeoprocessing.get_raster_info(
base_lulc_raster_path)['nodata']
forest_mask_nodata = 255
def mask_non_forest_op(lulc_array):
"""Convert forest lulc codes to 0.
Args:
lulc_array (numpy.ndarray): array representing a LULC raster where
each forest LULC code is in `forest_codes`.
Returns:
numpy.ndarray with the same shape as lulc_array. All pixels are
0 (forest), 1 (non-forest), or 255 (nodata).
"""
non_forest_mask = ~numpy.isin(lulc_array, forest_codes)
nodata_mask = lulc_array == lulc_nodata
# where LULC has nodata, set value to nodata value (255)
# where LULC has data, set to 0 if LULC is a forest type, 1 if it's not
return numpy.where(nodata_mask, forest_mask_nodata, non_forest_mask)
pygeoprocessing.raster_calculator([(base_lulc_raster_path, 1)],
mask_non_forest_op,
target_non_forest_mask_path,
gdal.GDT_Byte, forest_mask_nodata)
# Do the distance transform on non-forest pixels
# This is the distance from each pixel to the nearest pixel with value 1.
# - for forest pixels, this is the distance to the forest edge
# - for non-forest pixels, this is 0
# - for nodata pixels, distance is calculated but is meaningless
pygeoprocessing.distance_transform_edt((target_non_forest_mask_path, 1),
edge_distance_path)
# mask out the meaningless distance pixels so they don't affect the output
lulc_raster = gdal.OpenEx(base_lulc_raster_path)
lulc_band = lulc_raster.GetRasterBand(1)
edge_distance_raster = gdal.OpenEx(edge_distance_path, gdal.GA_Update)
edge_distance_band = edge_distance_raster.GetRasterBand(1)
for offset_dict in pygeoprocessing.iterblocks((base_lulc_raster_path, 1),
offset_only=True):
# where LULC has nodata, overwrite edge distance with nodata value
lulc_block = lulc_band.ReadAsArray(**offset_dict)
distance_block = edge_distance_band.ReadAsArray(**offset_dict)
masked_distance_block = numpy.where(lulc_block == lulc_nodata,
NODATA_VALUE, distance_block)
edge_distance_band.WriteArray(masked_distance_block,
xoff=offset_dict['xoff'],
yoff=offset_dict['yoff'])
def _convert_landscape(
base_lulc_path, replacement_lucode, area_to_convert,
focal_landcover_codes, convertible_type_list, score_weight, n_steps,
smooth_distance_from_edge_path, output_landscape_raster_path,
stats_path, workspace_dir):
"""Expand replacement lucodes in relation to the focal lucodes.
If the sign on `score_weight` is positive, expansion occurs marches
away from the focal types, while if `score_weight` is negative conversion
marches toward the focal types.
Parameters:
base_lulc_path (string): path to landcover raster that will be used as
the base landcover map to agriculture pixels
replacement_lucode (int): agriculture landcover code type found in the
raster at `base_lulc_path`
area_to_convert (float): area (Ha) to convert to agriculture
focal_landcover_codes (list of int): landcover codes that are used to
calculate proximity
convertible_type_list (list of int): landcover codes that are allowable
to be converted to agriculture
score_weight (float): this value is used to multiply the distance from
the focal landcover types when prioritizing which pixels in
`convertable_type_list` are to be converted. If negative,
conversion occurs toward the focal types, if positive occurs away
from the focal types.
n_steps (int): number of steps to convert the landscape. On each step
the distance transform will be applied on the
current value of the `focal_landcover_codes` pixels in
`output_landscape_raster_path`. On the first step the distance
is calculated from `base_lulc_path`.
smooth_distance_from_edge_path (string): an intermediate output showing
the pixel distance from the edge of the base landcover types
output_landscape_raster_path (string): an output raster that will
contain the final fragmented forest layer.
stats_path (string): a path to an output csv that records the number
type, and area of pixels converted in `output_landscape_raster_path`
workspace_dir (string): workspace directory that will be used to
hold temporary files. On a successful run of this function,
the temporary directory will be removed.
Returns:
None.
"""
temp_dir = tempfile.mkdtemp(prefix='temp_dir', dir=workspace_dir)
tmp_file_registry = {
'non_base_mask': os.path.join(temp_dir, 'non_base_mask.tif'),
'base_mask': os.path.join(temp_dir, 'base_mask.tif'),
'gaussian_kernel': os.path.join(temp_dir, 'gaussian_kernel.tif'),
'distance_from_base_mask_edge': os.path.join(
temp_dir, 'distance_from_base_mask_edge.tif'),
'distance_from_non_base_mask_edge': os.path.join(
temp_dir, 'distance_from_non_base_mask_edge.tif'),
'convertible_distances': os.path.join(
temp_dir, 'convertible_distances.tif'),
'distance_from_edge': os.path.join(
temp_dir, 'distance_from_edge.tif'),
}
# a sigma of 1.0 gives nice visual results to smooth pixel level artifacts
# since a pixel is the 1.0 unit
_make_gaussian_kernel_path(1.0, tmp_file_registry['gaussian_kernel'])
# create the output raster first as a copy of the base landcover so it can
# be looped on for each step
lulc_raster_info = pygeoprocessing.get_raster_info(base_lulc_path)
lulc_nodata = lulc_raster_info['nodata'][0]
mask_nodata = 2
pygeoprocessing.raster_calculator(
[(base_lulc_path, 1)], lambda x: x, output_landscape_raster_path,
gdal.GDT_Int32, lulc_nodata)
# convert everything furthest from edge for each of n_steps
pixel_area_ha = (
abs(lulc_raster_info['pixel_size'][0]) *
abs(lulc_raster_info['pixel_size'][1])) / 10000.0
max_pixels_to_convert = int(math.ceil(area_to_convert / pixel_area_ha))
convertible_type_nodata = -1
pixels_left_to_convert = max_pixels_to_convert
pixels_to_convert = max_pixels_to_convert / n_steps
stats_cache = collections.defaultdict(int)
# pylint complains when these are defined inside the loop
invert_mask = None
distance_nodata = None
for step_index in range(n_steps):
LOGGER.info('step %d of %d', step_index+1, n_steps)
pixels_left_to_convert -= pixels_to_convert
# Often the last segement of the steps will overstep the number of
# pixels to convert, this check converts the exact amount
if pixels_left_to_convert < 0:
pixels_to_convert += pixels_left_to_convert
# create distance transforms for inside and outside the base lulc codes
LOGGER.info('create distance transform for current landcover')
for invert_mask, mask_id, distance_id in [
(False, 'non_base_mask', 'distance_from_non_base_mask_edge'),
(True, 'base_mask', 'distance_from_base_mask_edge')]:
def _mask_base_op(lulc_array):
"""Create a mask of valid non-base pixels only."""
base_mask = numpy.in1d(
lulc_array.flatten(), focal_landcover_codes).reshape(
lulc_array.shape)
if invert_mask:
base_mask = ~base_mask
return numpy.where(
lulc_array == lulc_nodata,
mask_nodata, base_mask)
pygeoprocessing.raster_calculator(
[(output_landscape_raster_path, 1)], _mask_base_op,
tmp_file_registry[mask_id], gdal.GDT_Byte,
mask_nodata)
# create distance transform for the current mask
pygeoprocessing.distance_transform_edt(
(tmp_file_registry[mask_id], 1),
tmp_file_registry[distance_id],
working_dir=temp_dir)
# combine inner and outer distance transforms into one
distance_nodata = pygeoprocessing.get_raster_info(
tmp_file_registry['distance_from_base_mask_edge'])['nodata'][0]
def _combine_masks(base_distance_array, non_base_distance_array):
"""Create a mask of valid non-base pixels only."""
result = non_base_distance_array
valid_base_mask = base_distance_array > 0.0
result[valid_base_mask] = base_distance_array[valid_base_mask]
return result
pygeoprocessing.raster_calculator(
[(tmp_file_registry['distance_from_base_mask_edge'], 1),
(tmp_file_registry['distance_from_non_base_mask_edge'], 1)],
_combine_masks, tmp_file_registry['distance_from_edge'],
gdal.GDT_Float32, distance_nodata)
# smooth the distance transform to avoid scanline artifacts
pygeoprocessing.convolve_2d(
(tmp_file_registry['distance_from_edge'], 1),
(tmp_file_registry['gaussian_kernel'], 1),
smooth_distance_from_edge_path)
# turn inside and outside masks into a single mask
def _mask_to_convertible_codes(distance_from_base_edge, lulc):
"""Mask out the distance transform to a set of lucodes."""
convertible_mask = numpy.in1d(
lulc.flatten(), convertible_type_list).reshape(lulc.shape)
return numpy.where(
convertible_mask, distance_from_base_edge,
convertible_type_nodata)
pygeoprocessing.raster_calculator(
[(smooth_distance_from_edge_path, 1),
(output_landscape_raster_path, 1)],
_mask_to_convertible_codes,
tmp_file_registry['convertible_distances'], gdal.GDT_Float32,
convertible_type_nodata)
LOGGER.info(
'convert %d pixels to lucode %d', pixels_to_convert,
replacement_lucode)
_convert_by_score(
tmp_file_registry['convertible_distances'], pixels_to_convert,
output_landscape_raster_path, replacement_lucode, stats_cache,
score_weight)
_log_stats(stats_cache, pixel_area_ha, stats_path)
try:
shutil.rmtree(temp_dir)
except OSError:
LOGGER.warn(
"Could not delete temporary working directory '%s'", temp_dir)