def difference_dems(dem1, dem2, out_dem=None, in_mem=False):
logger.debug('Difference DEMs:\nDEM1: {}\nDEM2:{}'.format(dem1, dem2))
clipped = clip_minbb([dem1, dem2], in_mem=True)
dem1_clipped = Raster(clipped[0])
dem2_clipped = Raster(clipped[1])
diff = dem1_clipped.MaskedArray - dem2_clipped.MaskedArray
if out_dem:
logger.debug('Writing difference to: {}'.format(out_dem))
dem1_clipped.WriteArray(diff, out_path=out_dem)
return out_dem
def dem_rmse(dem1_path,
dem2_path,
max_diff=None,
outfile=None,
out_diff=None,
plot=False,
show_plot=False,
save_plot=None,
bins=10,
log_scale=True):
# Load DEMs as arrays
logger.info('Loading DEMs...')
dem1 = Raster(dem1_path)
dem2 = Raster(dem2_path)
if dem1.geotransform != dem2.geotransform:
logger.warning('''DEM geotransforms do not match.
Clipping to minimum bounding box in memory....''')
dem1 = None
dem2 = None
clipped = clip_minbb(rasters=[dem1_path, dem2_path],
in_mem=True,
out_format='vrt')
logger.debug('Clipping complete. Reloading DEMs...')
dem1 = Raster(clipped[0])
arr1 = dem1.MaskedArray
dem1 = None
logger.debug('DEM1 loaded and array extracted...')
dem2 = Raster(clipped[1])
arr2 = dem2.MaskedArray
dem2 = None
logger.debug('DEM2 loaded and array extracted...')
else:
arr1 = dem1.MaskedArray
dem1 = None
arr2 = dem2.MaskedArray
dem2 = None
# Compute RMSE
logger.info('Computing RMSE...')
diffs = arr1 - arr2
# Remove any differences bigger than max_diff
if max_diff:
logger.debug(
'Checking for large differences, max_diff: {}'.format(max_diff))
size_uncleaned = diffs.size
diffs = diffs[abs(diffs) < max_diff]
size_cleaned = diffs.size
if size_uncleaned != size_cleaned:
logger.debug(
'Removed differences over max_diff ({}) from RMSE calculation...'
.format(max_diff))
logger.debug('Size before: {:,}'.format(size_uncleaned))
logger.debug('Size after: {:,}'.format(size_cleaned))
logger.debug('Pixels removed: {:.2f}% of overlap area'.format(
((size_uncleaned - size_cleaned) / size_uncleaned) * 100))
sq_diff = diffs**2
mean_sq = sq_diff.sum() / sq_diff.count()
logger.debug('Mean square error: {}'.format(mean_sq))
rmse = np.sqrt(mean_sq)
# Report differences
diffs_valid_count = diffs.count()
min_diff = diffs.min()
max_diff = diffs.max()
logger.debug('Minimum difference: {:.2f}'.format(min_diff))
logger.debug('Maximum difference: {:.2f}'.format(max_diff))
logger.debug('Pixels considered: {:,}'.format(diffs_valid_count))
logger.info('RMSE: {:.2f}'.format(rmse))
# Write text file of results
if outfile:
with open(outfile, 'w') as of:
of.write("DEM1: {}\n".format(dem1_path))
of.write("DEM2: {}\n".format(dem2_path))
of.write('RMSE: {:.2f}\n'.format(rmse))
of.write('Pixels considered: {:,}\n'.format(diffs_valid_count))
of.write('Minimum difference: {:.2f}\n'.format(min_diff))
of.write('Maximum difference: {:.2f}\n'.format(max_diff))
# Write raster file of results
if out_diff:
logger.info('Out diff not supported, skipping writing.')
# dem1.WriteArray(diffs, out_diff)
# Plot results
# TODO: Add legend
# TODO: Incorporate min/max differences based on max_diff argument
if plot:
plt.style.use('ggplot')
fig, ax = plt.subplots(1, 1)
ax.hist(diffs.compressed().flatten(),
log=log_scale,
bins=bins,
edgecolor='white',
alpha=0.875)
ax.annotate('RMSE: {:.3f}'.format(rmse),
xy=(76, 0.75),
xycoords='axes fraction')
plt.legend(loc="upper left")
plt.tight_layout()
if save_plot:
plt.savefig(save_plot)
if show_plot:
plt.show()
return rmse
def stack_rasters(rasters, minbb=True, rescale=False):
"""
Stack single band rasters into a multiband raster.
Parameters
----------
rasters : list
List of rasters to stack. Reference raster for NoData value, projection, etc.
is the first raster provided.
rescale : bool
True to rescale rasters to 0 to 1.
Returns
-------
np.array : path.abspath : path to write multiband raster to.
"""
# TODO: Add default clipping to reference window
if minbb:
logger.info('Clipping to overlap area...')
rasters = clip_minbb(rasters, in_mem=True, out_format='vrt')
# Determine a raster to use for reference
ref = Raster(rasters[0])
# Check for SRS match between reference and other rasters
srs_matches = [same_srs(rasters[0], r) for r in rasters[1:]]
if not all(srs_matches):
logger.warning("""Spatial references do not match, match status between
reference and rest:\n{}""".format(
'\n'.join(srs_matches)))
# Initialize the stacked array with just the reference array
if ref.depth > 1:
stacked = ref.GetBandAsArray(1, mask=True)
if rescale:
stacked = (stacked - stacked.min()) / (stacked.max() -
stacked.min())
for i in range(ref.depth - 1):
band = ref.GetBandAsArray(i + 2, mask=True)
if rescale:
band = (band - band.min()) / (band.max() - band.min())
stacked = np.ma.dstack([stacked, band])
for i, rast in enumerate(rasters[1:]):
ma = Raster(rast).MaskedArray
if np.ma.isMaskedArray(ma):
if rescale:
# Rescale to between 0 and 1
ma = (ma - ma.min()) / (ma.max() - ma.min())
# Replace mask/nodata value in array with reference values
# ma_mask = ma.mask
# ma = np.ma.masked_where(ma_mask, ma)
# ma.set_fill_value(ref.nodata_val)
# ma = ma.filled(ma.fill_value)
stacked = np.ma.dstack([stacked, ma])
ma = None
# Revert to original NoData value (stacking changes)
# stacked.set_fill_value(ref.nodata_val)
ref = None
return stacked
def rmse_compare(dem1_path, dem2_path, dem2pca_path, max_diff=None, outfile=None, plot=False,
save_plot=None, show_plot=False, bins=20, log_scale=True):
# Load DEMs as arrays
logger.info('Loading DEMs...')
dem1 = Raster(dem1_path)
dem2 = Raster(dem2_path)
dem2pca = Raster(dem2pca_path)
if dem1.geotransform != dem2.geotransform or dem1.geotransform != dem2pca.geotransform:
logger.warning('DEM geotransforms do not match.')
# Check for pixel size match
if (((dem1.geotransform[1] != dem2.geotransform[1]) or (dem1.geotransform[1] != dem2pca.geotransform[1]) or
(dem1.geotransform[5] != dem2.geotransform[5]) or (dem2.geotransform[5] != dem2pca.geotransform[5]))):
logger.info('DEM pixel sizes do not match, translating to match.')
p1 = dem1.src_path
p2 = dem2.src_path
dem1 = None
dem2 = None
# max = match_pixel_size([p1, p2], r'/vsimem/matching_px.tif', resampleAlg='cubic', in_mem=True)
dem1 = Raster(p1)
dem2 = Raster(p2)
logger.info('DEM1 sz: {} {}'.format(dem1.x_sz, dem1.y_sz))
logger.info('DEM2 sz: {} {}'.format(dem2.x_sz, dem2.y_sz))
# Check for size match
if ((dem1.x_sz != dem2.x_sz) or (dem1.x_sz != dem2pca.x_sz) or
(dem1.y_sz != dem2.y_sz) or (dem1.y_sz != dem2pca.y_sz)):
logger.info('DEM sizes do not match. Clipping to minimum bounding box in memory....')
dem1 = None
dem2 = None
clipped = clip_minbb(rasters=[dem1_path, dem2_path, dem2pca_path],
in_mem=True,
out_format='vrt')
logger.debug('Clipping complete. Reloading DEMs...')
dem1 = Raster(clipped[0])
logger.debug('DEM1 loaded and array extracted...')
dem2 = Raster(clipped[1])
logger.debug('DEM2 loaded and array extracted...')
dem2pca = Raster(clipped[2])
logger.debug('DEM1 sz: {} {}'.format(dem1.x_sz, dem1.y_sz))
logger.debug('DEM2 sz: {} {}'.format(dem2.x_sz, dem2.y_sz))
arr1 = dem1.MaskedArray
dem1 = None
arr2 = dem2.MaskedArray
dem2 = None
arr2pca = dem2pca.MaskedArray
else:
arr1 = dem1.MaskedArray
dem1 = None
arr2 = dem2.MaskedArray
dem2 = None
arr2pca = dem2pca.MaskedArray
dem2pca = None
#### PRE-ALIGNMENT ####
# Compute RMSE
logger.info('Computing RMSE pre-alignment...')
diffs = arr1 - arr2
# Remove any differences bigger than max_diff
if max_diff:
logger.debug('Checking for large differences, max_diff: '
'{}'.format(max_diff))
size_uncleaned = diffs.size
diffs = diffs[abs(diffs) < max_diff]
size_cleaned = diffs.size
if size_uncleaned != size_cleaned:
logger.debug('Removed differences over max_diff ({}) from RMSE '
'calculation...'.format(max_diff))
logger.debug('Size before: {:,}'.format(size_uncleaned))
logger.debug('Size after: {:,}'.format(size_cleaned))
logger.debug('Pixels removed: {:.2f}% of overlap area'.format(
((size_uncleaned-size_cleaned)/size_uncleaned)*100))
sq_diff = diffs**2
mean_sq = sq_diff.sum() / sq_diff.count()
rmse = np.sqrt(mean_sq)
# Report differences
diffs_valid_count = diffs.count()
min_diff = diffs.min()
max_diff = diffs.max()
logger.debug('Minimum difference: {:.2f}'.format(min_diff))
logger.debug('Maximum difference: {:.2f}'.format(max_diff))
logger.debug('Pixels considered: {:,}'.format(diffs_valid_count))
logger.info('RMSE: {:.2f}'.format(rmse))
# Write text file of results
if outfile:
with open(outfile, 'w') as of:
of.write("DEM1: {}\n".format(dem1_path))
of.write("DEM2: {}\n".format(dem2_path))
of.write('Pixels considered: {:,}\n'.format(diffs_valid_count))
of.write('Minimum difference: {:.2f}\n'.format(min_diff))
of.write('Maximum difference: {:.2f}\n\n'.format(max_diff))
of.write('RMSE: {:.2f}\n'.format(rmse))
#### POST ALIGNMENT ####
# Compute RMSE
logger.info('Computing RMSE post-alignment...')
diffs_pca = arr1 - arr2pca
# Remove any differences bigger than max_diff
if max_diff:
size_uncleaned = diffs.size
diffs_pca = diffs_pca[abs(diffs_pca) < max_diff]
size_cleaned = diffs.size
if size_uncleaned != size_cleaned:
logger.debug('Removed differences over max_diff ({}) from RMSE '
'calculation...'.format(max_diff))
logger.debug('Size before: {:,}'.format(size_uncleaned))
logger.debug('Size after: {:,}'.format(size_cleaned))
logger.debug('Pixels removed: {:.2f}% of overlap area'.format(
((size_uncleaned-size_cleaned)/size_uncleaned)*100))
# Remove any differences bigger than max_diff
if max_diff:
logger.debug('Checking for large differences, max_diff: '
'{}'.format(max_diff))
size_uncleaned = diffs.size
diffs = diffs[abs(diffs) < max_diff]
size_cleaned = diffs.size
if size_uncleaned != size_cleaned:
logger.debug('Removed differences over max_diff ({}) from RMSE '
'calculation...'.format(max_diff))
logger.debug('Size before: {:,}'.format(size_uncleaned))
logger.debug('Size after: {:,}'.format(size_cleaned))
logger.debug('Pixels removed: {:.2f}% of overlap area'.format(
((size_uncleaned-size_cleaned)/size_uncleaned)*100))
sq_diff_pca = diffs_pca**2
mean_sq_pca = sq_diff_pca.sum() / sq_diff_pca.count()
rmse_pca = np.sqrt(mean_sq_pca)
# Report differences
diffs_pca_valid_count = diffs_pca.count()
min_diff_pca = diffs_pca.min()
max_diff_pca = diffs_pca.max()
logger.debug('Minimum difference: {:.2f}'.format(min_diff_pca))
logger.debug('Maximum difference: {:.2f}'.format(max_diff_pca))
logger.debug('Pixels considered: {:,}'.format(diffs_pca_valid_count))
logger.info('RMSE: {:.2f}'.format(rmse_pca))
# Add to text file of results
if outfile:
with open(outfile, 'a') as of:
of.write("DEM1: {}\n".format(dem1_path))
of.write("DEM2pca: {}\n".format(dem2pca_path))
of.write('Pixels considered pca: {:,}\n'.format(diffs_pca_valid_count))
of.write('Minimum difference pca: {:.2f}\n'.format(min_diff_pca))
of.write('Maximum difference pca: {:.2f}\n\n'.format(max_diff_pca))
of.write('RMSEpca: {:.2f}\n'.format(rmse_pca))
# Plot results
# TODO: Add legend and RMSE annotations
# TODO: Incorporate min/max differences based on max_diff argument
if plot:
plt.style.use('ggplot')
fig, ax = plt.subplots(2, 1)
# Plot unaligned differences with line at 0
ax[0].hist(diffs.compressed().flatten(), log=log_scale, bins=bins,
edgecolor='white', alpha=0.75,
range=[min([diffs.min(), diffs_pca.min()]),
max([diffs.min(), diffs_pca.max()])
])
ax[0].axvline(x=0, linewidth=2, color='black')
# Plot aligned differences with line at 0
ax[1].hist(diffs_pca.compressed().flatten(), log=log_scale, bins=bins,
edgecolor='white', color='b', alpha=0.75,
range=[min([diffs.min(), diffs_pca.min()]),
max([diffs.min(), diffs_pca.max()])])
ax[1].axvline(x=0, linewidth=2, color='black')
# Annotation and titles
ax[0].set_title('Pre-Alignment')
ax[0].annotate('RMSE: {:.2f}'.format(rmse), xy=(0.05, 0.95),
xycoords='axes fraction')
ax[1].set_title('Post-Alignment')
ax[1].annotate('RMSE: {:.2f}'.format(rmse_pca), xy=(0.05, 0.95),
xycoords='axes fraction')
plt.legend()
plt.tight_layout()
if save_plot:
plt.savefig(save_plot)
if show_plot:
plt.show()