def transfer_map(in_map, H, x, y, w, h, zoom, out_map):
"""
Transfer the heights computed on the rectified grid to the original
Pleiades image grid.
Args:
in_map: path to the input map, usually a height map or a mask, sampled
on the rectified grid
H: path to txt file containing a numpy 3x3 array representing the
rectifying homography
x, y, w, h: four integers defining the rectangular ROI in the original
image. (x, y) is the top-left corner, and (w, h) are the dimensions
of the rectangle.
zoom: zoom factor (usually 1, 2 or 4) used to produce the input height
map
out_map: path to the output map
"""
# write the inverse of the resampling transform matrix. In brief it is:
# homography * translation * zoom
# This matrix transports the coordinates of the original cropped and
# zoomed grid (the one desired for out_height) to the rectified cropped and
# zoomed grid (the one we have for height)
Z = np.diag([zoom, zoom, 1])
A = common.matrix_translation(x, y)
HH = np.dot(np.loadtxt(H), np.dot(A, Z))
# apply the homography
# write the 9 coefficients of the homography to a string, then call synflow
# to produce the flow, then backflow to apply it
# zero:256x256 is the iio way to create a 256x256 image filled with zeros
hij = ' '.join(['%r' % num for num in HH.flatten()])
common.run('synflow hom "%s" zero:%dx%d /dev/null - | BILINEAR=1 backflow - %s %s' % (
hij, w/zoom, h/zoom, in_map, out_map))
def transfer_map(in_map, H, x, y, w, h, zoom, out_map):
"""
Transfer the heights computed on the rectified grid to the original
Pleiades image grid.
Args:
in_map: path to the input map, usually a height map or a mask, sampled
on the rectified grid
H: path to txt file containing a numpy 3x3 array representing the
rectifying homography
x, y, w, h: four integers defining the rectangular ROI in the original
image. (x, y) is the top-left corner, and (w, h) are the dimensions
of the rectangle.
zoom: zoom factor (usually 1, 2 or 4) used to produce the input height
map
out_map: path to the output map
"""
# write the inverse of the resampling transform matrix. In brief it is:
# homography * translation * zoom
# This matrix transports the coordinates of the original cropped and
# zoomed grid (the one desired for out_height) to the rectified cropped and
# zoomed grid (the one we have for height)
Z = np.diag([zoom, zoom, 1])
A = common.matrix_translation(x, y)
HH = np.dot(np.loadtxt(H), np.dot(A, Z))
# apply the homography
# write the 9 coefficients of the homography to a string, then call synflow
# to produce the flow, then backflow to apply it
# zero:256x256 is the iio way to create a 256x256 image filled with zeros
hij = ' '.join(['%r' % num for num in HH.flatten()])
common.run('synflow hom "%s" zero:%dx%d /dev/null - | BILINEAR=1 backflow - %s %s' % (
hij, w/zoom, h/zoom, in_map, out_map))
def cloud_water_image_domain(x,
y,
w,
h,
rpc,
roi_gml=None,
cld_gml=None,
wat_msk=None):
"""
Compute a mask for pixels masked by clouds, water, or out of image domain.
Args:
x, y, w, h: coordinates of the ROI
roi_gml (optional): path to a gml file containing a mask
defining the area contained in the full image
cld_gml (optional): path to a gml file containing a mask
defining the areas covered by clouds
Returns:
2D array containing the output binary mask. 0 indicate masked pixels, 1
visible pixels.
"""
# coefficients of the transformation associated to the crop
H = common.matrix_translation(-x, -y)
hij = ' '.join([str(el) for el in H.flatten()])
mask = np.ones((h, w), dtype=np.bool)
if roi_gml is not None: # image domain mask (polygons)
tmp = common.tmpfile('.png')
subprocess.check_call('cldmask %d %d -h "%s" %s %s' %
(w, h, hij, roi_gml, tmp),
shell=True)
f = gdal.Open(tmp)
mask = np.logical_and(mask, f.ReadAsArray())
f = None # this is the gdal way of closing files
if not mask.any():
return mask
if cld_gml is not None: # cloud mask (polygons)
tmp = common.tmpfile('.png')
subprocess.check_call('cldmask %d %d -h "%s" %s %s' %
(w, h, hij, cld_gml, tmp),
shell=True)
f = gdal.Open(tmp)
mask = np.logical_and(mask, ~f.ReadAsArray().astype(bool))
f = None # this is the gdal way of closing files
if not mask.any():
return mask
if wat_msk is not None: # water mask (raster)
f = gdal.Open(wat_msk)
mask = np.logical_and(mask, f.ReadAsArray(x, y, w, h))
f = None # this is the gdal way of closing files
return mask
def heights_to_ply(tile):
"""
Generate a ply cloud.
Args:
tile: a dictionary that provides all you need to process a tile
"""
# merge the n-1 height maps of the tile (n = nb of images)
heights_fusion(tile)
# compute a ply from the merged height map
out_dir = tile['dir']
x, y, w, h = tile['coordinates']
z = cfg['subsampling_factor']
plyfile = os.path.join(out_dir, 'cloud.ply')
plyextrema = os.path.join(out_dir, 'plyextrema.txt')
height_map = os.path.join(out_dir, 'height_map.tif')
if cfg['skip_existing'] and os.path.isfile(plyfile):
print('ply file already exists for tile {} {}'.format(x, y))
return
# H is the homography transforming the coordinates system of the original
# full size image into the coordinates system of the crop
H = np.dot(np.diag([1 / z, 1 / z, 1]), common.matrix_translation(-x, -y))
colors = os.path.join(out_dir, 'ref.png')
if cfg['images'][0]['clr']:
common.image_crop_gdal(cfg['images'][0]['clr'], x, y, w, h, colors)
else:
common.image_qauto(
common.image_crop_gdal(cfg['images'][0]['img'], x, y, w, h),
colors)
common.image_safe_zoom_fft(colors, z, colors)
triangulation.height_map_to_point_cloud(plyfile,
height_map,
cfg['images'][0]['rpc'],
H,
colors,
utm_zone=cfg['utm_zone'],
llbbx=tuple(cfg['ll_bbx']))
# compute the point cloud extrema (xmin, xmax, xmin, ymax)
common.run("plyextrema %s %s" % (plyfile, plyextrema))
if cfg['clean_intermediate']:
common.remove(height_map)
common.remove(colors)
common.remove(
os.path.join(out_dir, 'cloud_water_image_domain_mask.png'))
def register_horizontally_translation(matches, H1, H2, flag='center'):
"""
Adjust rectifying homographies with a translation to modify the disparity range.
Args:
matches: list of pairs of 2D points, stored as a Nx4 numpy array
H1, H2: two homographies, stored as numpy 3x3 matrices
flag: option needed to control how to modify the disparity range:
'center': move the barycenter of disparities of matches to zero
'positive': make all the disparities positive
'negative': make all the disparities negative. Required for
Hirshmuller stereo (java)
Returns:
H2: corrected homography H2
The matches are provided in the original images coordinate system. By
transforming these coordinates with the provided homographies, we obtain
matches whose disparity is only along the x-axis. The second homography H2
is corrected with a horizontal translation to obtain the desired property
on the disparity range.
"""
# transform the matches according to the homographies
p1 = common.points_apply_homography(H1, matches[:, :2])
x1 = p1[:, 0]
y1 = p1[:, 1]
p2 = common.points_apply_homography(H2, matches[:, 2:])
x2 = p2[:, 0]
y2 = p2[:, 1]
# for debug, print the vertical disparities. Should be zero.
if cfg['debug']:
print("Residual vertical disparities: max, min, mean. Should be zero")
print(np.max(y2 - y1), np.min(y2 - y1), np.mean(y2 - y1))
# compute the disparity offset according to selected option
t = 0
if (flag == 'center'):
t = np.mean(x2 - x1)
if (flag == 'positive'):
t = np.min(x2 - x1)
if (flag == 'negative'):
t = np.max(x2 - x1)
# correct H2 with a translation
return np.dot(common.matrix_translation(-t, 0), H2)
def register_horizontally_translation(matches, H1, H2, flag='center'):
"""
Adjust rectifying homographies with a translation to modify the disparity range.
Args:
matches: list of pairs of 2D points, stored as a Nx4 numpy array
H1, H2: two homographies, stored as numpy 3x3 matrices
flag: option needed to control how to modify the disparity range:
'center': move the barycenter of disparities of matches to zero
'positive': make all the disparities positive
'negative': make all the disparities negative. Required for
Hirshmuller stereo (java)
Returns:
H2: corrected homography H2
The matches are provided in the original images coordinate system. By
transforming these coordinates with the provided homographies, we obtain
matches whose disparity is only along the x-axis. The second homography H2
is corrected with a horizontal translation to obtain the desired property
on the disparity range.
"""
# transform the matches according to the homographies
p1 = common.points_apply_homography(H1, matches[:, :2])
x1 = p1[:, 0]
y1 = p1[:, 1]
p2 = common.points_apply_homography(H2, matches[:, 2:])
x2 = p2[:, 0]
y2 = p2[:, 1]
# for debug, print the vertical disparities. Should be zero.
if cfg['debug']:
print("Residual vertical disparities: max, min, mean. Should be zero")
print(np.max(y2 - y1), np.min(y2 - y1), np.mean(y2 - y1))
# compute the disparity offset according to selected option
t = 0
if (flag == 'center'):
t = np.mean(x2 - x1)
if (flag == 'positive'):
t = np.min(x2 - x1)
if (flag == 'negative'):
t = np.max(x2 - x1)
# correct H2 with a translation
return np.dot(common.matrix_translation(-t, 0), H2)
def heights_to_ply(tile):
"""
Generate a ply cloud.
Args:
tile: a dictionary that provides all you need to process a tile
"""
# merge the n-1 height maps of the tile (n = nb of images)
heights_fusion(tile)
# compute a ply from the merged height map
out_dir = tile['dir']
x, y, w, h = tile['coordinates']
z = cfg['subsampling_factor']
plyfile = os.path.join(out_dir, 'cloud.ply')
plyextrema = os.path.join(out_dir, 'plyextrema.txt')
height_map = os.path.join(out_dir, 'height_map.tif')
if cfg['skip_existing'] and os.path.isfile(plyfile):
print('ply file already exists for tile {} {}'.format(x, y))
return
# H is the homography transforming the coordinates system of the original
# full size image into the coordinates system of the crop
H = np.dot(np.diag([1 / z, 1 / z, 1]), common.matrix_translation(-x, -y))
colors = os.path.join(out_dir, 'ref.png')
if cfg['images'][0]['clr']:
common.image_crop_gdal(cfg['images'][0]['clr'], x, y, w, h, colors)
else:
common.image_qauto(common.image_crop_gdal(cfg['images'][0]['img'], x, y,
w, h), colors)
common.image_safe_zoom_fft(colors, z, colors)
triangulation.height_map_to_point_cloud(plyfile, height_map,
cfg['images'][0]['rpc'], H, colors,
utm_zone=cfg['utm_zone'],
llbbx=tuple(cfg['ll_bbx']))
# compute the point cloud extrema (xmin, xmax, xmin, ymax)
common.run("plyextrema %s %s" % (plyfile, plyextrema))
if cfg['clean_intermediate']:
common.remove(height_map)
common.remove(colors)
common.remove(os.path.join(out_dir,
'cloud_water_image_domain_mask.png'))
def rectification_homographies(matches, x, y, w, h, hmargin=0, vmargin=0):
"""
Computes rectifying homographies from point matches for a given ROI.
The affine fundamental matrix F is estimated with the gold-standard
algorithm, then two rectifying similarities (rotation, zoom, translation)
are computed directly from F.
Args:
matches: numpy array of shape (n, 4) containing a list of 2D point
correspondences between the two images.
x, y, w, h: four integers defining the rectangular ROI in the first
image. (x, y) is the top-left corner, and (w, h) are the dimensions
of the rectangle.
{h,v}margin: translations added to the rectifying similarities to extend the
horizontal and vertical footprint of the rectified images
Returns:
S1, S2, F: three numpy arrays of shape (3, 3) representing the
two rectifying similarities to be applied to the two images and the
corresponding affine fundamental matrix.
"""
# estimate the affine fundamental matrix with the Gold standard algorithm
F = estimation.affine_fundamental_matrix(matches)
# compute rectifying similarities
S1, S2 = estimation.rectifying_similarities_from_affine_fundamental_matrix(
F, cfg['debug'])
if cfg['debug']:
y1 = common.points_apply_homography(S1, matches[:, :2])[:, 1]
y2 = common.points_apply_homography(S2, matches[:, 2:])[:, 1]
err = np.abs(y1 - y2)
print("max, min, mean rectification error on point matches: ", end=' ')
print(np.max(err), np.min(err), np.mean(err))
# pull back top-left corner of the ROI to the origin (plus margin)
pts = common.points_apply_homography(
S1, [[x, y], [x + w, y], [x + w, y + h], [x, y + h]])
x0, y0 = common.bounding_box2D(pts)[:2]
T = common.matrix_translation(-x0 + hmargin, -y0 + vmargin)
return np.dot(T, S1), np.dot(T, S2), F
def rectification_homographies(matches, x, y, w, h, hmargin=0, vmargin=0):
"""
Computes rectifying homographies from point matches for a given ROI.
The affine fundamental matrix F is estimated with the gold-standard
algorithm, then two rectifying similarities (rotation, zoom, translation)
are computed directly from F.
Args:
matches: numpy array of shape (n, 4) containing a list of 2D point
correspondences between the two images.
x, y, w, h: four integers defining the rectangular ROI in the first
image. (x, y) is the top-left corner, and (w, h) are the dimensions
of the rectangle.
{h,v}margin: translations added to the rectifying similarities to extend the
horizontal and vertical footprint of the rectified images
Returns:
S1, S2, F: three numpy arrays of shape (3, 3) representing the
two rectifying similarities to be applied to the two images and the
corresponding affine fundamental matrix.
"""
# estimate the affine fundamental matrix with the Gold standard algorithm
F = estimation.affine_fundamental_matrix(matches)
# compute rectifying similarities
S1, S2 = estimation.rectifying_similarities_from_affine_fundamental_matrix(F, cfg['debug'])
if cfg['debug']:
y1 = common.points_apply_homography(S1, matches[:, :2])[:, 1]
y2 = common.points_apply_homography(S2, matches[:, 2:])[:, 1]
err = np.abs(y1 - y2)
print("max, min, mean rectification error on point matches: ", end=' ')
print(np.max(err), np.min(err), np.mean(err))
# pull back top-left corner of the ROI to the origin (plus margin)
pts = common.points_apply_homography(S1, [[x, y], [x+w, y], [x+w, y+h], [x, y+h]])
x0, y0 = common.bounding_box2D(pts)[:2]
T = common.matrix_translation(-x0 + hmargin, -y0 + vmargin)
return np.dot(T, S1), np.dot(T, S2), F
def rectify_pair(im1,
im2,
rpc1,
rpc2,
x,
y,
w,
h,
out1,
out2,
A=None,
sift_matches=None,
method='rpc',
hmargin=0,
vmargin=0):
"""
Rectify a ROI in a pair of images.
Args:
im1, im2: paths to two image files
rpc1, rpc2: paths to the two xml files containing RPC data
x, y, w, h: four integers defining the rectangular ROI in the first
image. (x, y) is the top-left corner, and (w, h) are the dimensions
of the rectangle.
out1, out2: paths to the output rectified crops
A (optional): 3x3 numpy array containing the pointing error correction
for im2. This matrix is usually estimated with the pointing_accuracy
module.
sift_matches (optional): Nx4 numpy array containing a list of sift
matches, in the full image coordinates frame
method (default: 'rpc'): option to decide wether to use rpc of sift
matches for the fundamental matrix estimation.
{h,v}margin (optional): horizontal and vertical margins added on the
sides of the rectified images
Returns:
H1, H2: Two 3x3 matrices representing the rectifying homographies that
have been applied to the two original (large) images.
disp_min, disp_max: horizontal disparity range
"""
# read RPC data
rpc1 = rpc_model.RPCModel(rpc1)
rpc2 = rpc_model.RPCModel(rpc2)
# compute real or virtual matches
if method == 'rpc':
# find virtual matches from RPC camera models
matches = rpc_utils.matches_from_rpc(rpc1, rpc2, x, y, w, h,
cfg['n_gcp_per_axis'])
# correct second image coordinates with the pointing correction matrix
if A is not None:
matches[:, 2:] = common.points_apply_homography(
np.linalg.inv(A), matches[:, 2:])
else:
matches = sift_matches
# compute rectifying homographies
H1, H2, F = rectification_homographies(matches, x, y, w, h, hmargin,
vmargin)
if cfg['register_with_shear']:
# compose H2 with a horizontal shear to reduce the disparity range
a = np.mean(rpc_utils.altitude_range(rpc1, x, y, w, h))
lon, lat, alt = rpc_utils.ground_control_points(
rpc1, x, y, w, h, a, a, 4)
x1, y1 = rpc1.inverse_estimate(lon, lat, alt)[:2]
x2, y2 = rpc2.inverse_estimate(lon, lat, alt)[:2]
m = np.vstack([x1, y1, x2, y2]).T
m = np.vstack({tuple(row)
for row in m}) # remove duplicates due to no alt range
H2 = register_horizontally_shear(m, H1, H2)
# compose H2 with a horizontal translation to center disp range around 0
if sift_matches is not None:
sift_matches = filter_matches_epipolar_constraint(
F, sift_matches, cfg['epipolar_thresh'])
if len(sift_matches) < 10:
print('WARNING: no registration with less than 10 matches')
else:
H2 = register_horizontally_translation(sift_matches, H1, H2)
# compute disparity range
if cfg['debug']:
out_dir = os.path.dirname(out1)
np.savetxt(os.path.join(out_dir, 'sift_matches_disp.txt'),
sift_matches,
fmt='%9.3f')
visualisation.plot_matches(
im1, im2, rpc1, rpc2, sift_matches, x, y, w, h,
os.path.join(out_dir, 'sift_matches_disp.png'))
disp_m, disp_M = disparity_range(rpc1, rpc2, x, y, w, h, H1, H2,
sift_matches, A)
# compute rectifying homographies for non-epipolar mode (rectify the secondary tile only)
if block_matching.rectify_secondary_tile_only(cfg['matching_algorithm']):
H1_inv = np.linalg.inv(H1)
H1 = np.eye(
3
) # H1 is replaced by 2-D array with ones on the diagonal and zeros elsewhere
H2 = np.dot(H1_inv, H2)
T = common.matrix_translation(-x + hmargin, -y + vmargin)
H1 = np.dot(T, H1)
H2 = np.dot(T, H2)
# compute output images size
roi = [[x, y], [x + w, y], [x + w, y + h], [x, y + h]]
pts1 = common.points_apply_homography(H1, roi)
x0, y0, w0, h0 = common.bounding_box2D(pts1)
# check that the first homography maps the ROI in the positive quadrant
np.testing.assert_allclose(np.round([x0, y0]), [hmargin, vmargin],
atol=.01)
# apply homographies and do the crops
common.image_apply_homography(out1, im1, H1, w0 + 2 * hmargin,
h0 + 2 * vmargin)
common.image_apply_homography(out2, im2, H2, w0 + 2 * hmargin,
h0 + 2 * vmargin)
if block_matching.rectify_secondary_tile_only(cfg['matching_algorithm']):
pts_in = [[0, 0], [disp_m, 0], [disp_M, 0]]
pts_out = common.points_apply_homography(H1_inv, pts_in)
disp_m = pts_out[1, :] - pts_out[0, :]
disp_M = pts_out[2, :] - pts_out[0, :]
return H1, H2, disp_m, disp_M
def multidisparities_to_ply(tile):
"""
Compute a point cloud from the disparity maps of N-pairs of image tiles.
Args:
tile: dictionary containing the information needed to process a tile.
# There is no guarantee that this function works with z!=1
"""
out_dir = os.path.join(tile['dir'])
ply_file = os.path.join(out_dir, 'cloud.ply')
plyextrema = os.path.join(out_dir, 'plyextrema.txt')
x, y, w, h = tile['coordinates']
rpc_ref = cfg['images'][0]['rpc']
disp_list = list()
rpc_list = list()
if cfg['skip_existing'] and os.path.isfile(ply_file):
print('triangulation done on tile {} {}'.format(x, y))
return
mask_orig = os.path.join(out_dir, 'cloud_water_image_domain_mask.png')
print('triangulating tile {} {}...'.format(x, y))
n = len(cfg['images']) - 1
for i in range(n):
pair = 'pair_%d' % (i+1)
H_ref = os.path.join(out_dir, pair, 'H_ref.txt')
H_sec = os.path.join(out_dir, pair, 'H_sec.txt')
disp = os.path.join(out_dir, pair, 'rectified_disp.tif')
mask_rect = os.path.join(out_dir, pair, 'rectified_mask.png')
disp2D = os.path.join(out_dir, pair, 'disp2D.tif')
rpc_sec = cfg['images'][i+1]['rpc']
if os.path.exists(disp):
# homography for warp
T = common.matrix_translation(x, y)
hom_ref = np.loadtxt(H_ref)
hom_ref_shift = np.dot(hom_ref, T)
# homography for 1D to 2D conversion
hom_sec = np.loadtxt(H_sec)
if cfg["use_global_pointing_for_geometric_triangulation"] is True:
pointing = os.path.join(cfg['out_dir'], 'global_pointing_%s.txt' % pair)
hom_pointing = np.loadtxt(pointing)
hom_sec = np.dot(hom_sec,np.linalg.inv(hom_pointing))
hom_sec_shift_inv = np.linalg.inv(hom_sec)
h1 = " ".join(str(x) for x in hom_ref_shift.flatten())
h2 = " ".join(str(x) for x in hom_sec_shift_inv.flatten())
# relative disparity map to absolute disparity map
tmp_abs = common.tmpfile('.tif')
os.environ["PLAMBDA_GETPIXEL"] = "0"
common.run('plambda %s %s "y 0 = nan x[0] :i + x[1] :j + 1 3 njoin if" -o %s' % (disp, mask_rect, tmp_abs))
# 1d to 2d conversion
tmp_1d_to_2d = common.tmpfile('.tif')
common.run('plambda %s "%s 9 njoin x mprod" -o %s' % (tmp_abs, h2, tmp_1d_to_2d))
# warp
tmp_warp = common.tmpfile('.tif')
common.run('homwarp -o 2 "%s" %d %d %s %s' % (h1, w, h, tmp_1d_to_2d, tmp_warp))
# set masked value to NaN
exp = 'y 0 = nan x if'
common.run('plambda %s %s "%s" -o %s' % (tmp_warp, mask_orig, exp, disp2D))
# disp2D contains positions in the secondary image
# added input data for triangulation module
disp_list.append(disp2D)
rpc_list.append(rpc_sec)
if cfg['clean_intermediate']:
common.remove(H_ref)
common.remove(H_sec)
common.remove(disp)
common.remove(mask_rect)
common.remove(mask_orig)
colors = os.path.join(out_dir, 'ref.png')
if cfg['images'][0]['clr']:
common.image_crop_gdal(cfg['images'][0]['clr'], x, y, w, h, colors)
else:
common.image_qauto(common.image_crop_gdal(cfg['images'][0]['img'], x, y,
w, h), colors)
# compute the point cloud
triangulation.multidisp_map_to_point_cloud(ply_file, disp_list, rpc_ref, rpc_list,
colors,
utm_zone=cfg['utm_zone'],
llbbx=tuple(cfg['ll_bbx']),
xybbx=(x, x+w, y, y+h))
# compute the point cloud extrema (xmin, xmax, xmin, ymax)
common.run("plyextrema %s %s" % (ply_file, plyextrema))
if cfg['clean_intermediate']:
common.remove(colors)
def local_translation_rectified(r1, r2, x, y, w, h, m):
"""
Estimates the optimal translation to minimise the relative pointing error
on a given tile.
Args:
r1, r2: two instances of the rpc_model.RPCModel class
x, y, w, h: region of interest in the reference image (r1)
m: Nx4 numpy array containing a list of matches, one per line. Each
match is given by (p1, p2, q1, q2) where (p1, p2) is a point of the
reference view and (q1, q2) is the corresponding point in the
secondary view.
Returns:
3x3 numpy array containing the homogeneous representation of the
optimal planar translation, to be applied to the secondary image in
order to correct the pointing error.
"""
# estimate the affine fundamental matrix between the two views
n = cfg['n_gcp_per_axis']
rpc_matches = rpc_utils.matches_from_rpc(r1, r2, x, y, w, h, n)
F = estimation.affine_fundamental_matrix(rpc_matches)
# Apply rectification on image 1
S1p1 = common.points_apply_homography(S1, m[:,0:2])
S1p1 = np.column_stack((S1p1,np.ones((N,1))))
print("Points 1 rectied")
print(S1p1[:10])
# Apply rectification on image 2
S2p2 = common.points_apply_homography(S1, m[:,2:4])
S2p2 = np.column_stack((S2p2, np.ones((N,1))))
print("Points 2 rectied")
print(S2p2[:10])
# Compute F in the rectified space
rect_matches = np.column_stack((S1p1[:,0:2], S2p2[:, 0:2]))
F_rect2 = estimation.affine_fundamental_matrix(rect_matches)
# Compute epipolar lines
FS1p1 = np.dot(F_rect2, S1p1.T).T
print(FS1p1[:10])
# Normalize epipolar lines
c1 = -FS1p1[:, 1]
FS1p1_norm = FS1p1/c1[:, np.newaxis]
print(FS1p1_norm[:10])
b_ = np.abs(S2p2[:, 1] - S1p1[:, 1])
t_med = np.median(b_)
print(t_med)
t_med2 = np.sort(b_)[int(N/2)]
print("t_med2", t_med2)
# Compute epipolar lines witout recitifcation
p1 = np.column_stack((m[:,0:2],np.ones((N,1))))
Fp1 = np.dot(F, p1.T).T
# Compute normal vector to epipolar liness
ab = np.array([Fp1[0][0], Fp1[0][1]])
ab = ab/np.linalg.norm(ab)
tx = t_med*ab[0]
ty = t_med*ab[1]
print(tx, ty)
# Get translation in not rectified image
T = common.matrix_translation(0, -t_med)
T = np.linalg.inv(S2).dot(T).dot(S2)
# T = np.dot(S2_inv, T)
print(T)
# the correction to be applied to the second view is the opposite
A = np.array([[1, 0, -out_x],
[0, 1, -out_y],
[0, 0, 1]])
return A, F
def rectify_pair(im1, im2, rpc1, rpc2, x, y, w, h, out1, out2, A=None,
sift_matches=None, method='rpc', hmargin=0, vmargin=0):
"""
Rectify a ROI in a pair of images.
Args:
im1, im2: paths to two image files
rpc1, rpc2: paths to the two xml files containing RPC data
x, y, w, h: four integers defining the rectangular ROI in the first
image. (x, y) is the top-left corner, and (w, h) are the dimensions
of the rectangle.
out1, out2: paths to the output rectified crops
A (optional): 3x3 numpy array containing the pointing error correction
for im2. This matrix is usually estimated with the pointing_accuracy
module.
sift_matches (optional): Nx4 numpy array containing a list of sift
matches, in the full image coordinates frame
method (default: 'rpc'): option to decide wether to use rpc of sift
matches for the fundamental matrix estimation.
{h,v}margin (optional): horizontal and vertical margins added on the
sides of the rectified images
This function uses the parameter subsampling_factor from the
config module. If the factor z > 1 then the output images will
be subsampled by a factor z. The output matrices H1, H2, and the
ranges are also updated accordingly:
Hi = Z * Hi with Z = diag(1/z, 1/z, 1) and
disp_min = disp_min / z (resp _max)
Returns:
H1, H2: Two 3x3 matrices representing the rectifying homographies that
have been applied to the two original (large) images.
disp_min, disp_max: horizontal disparity range
"""
# read RPC data
rpc1 = rpc_model.RPCModel(rpc1)
rpc2 = rpc_model.RPCModel(rpc2)
# compute real or virtual matches
if method == 'rpc':
# find virtual matches from RPC camera models
matches = rpc_utils.matches_from_rpc(rpc1, rpc2, x, y, w, h,
cfg['n_gcp_per_axis'])
# correct second image coordinates with the pointing correction matrix
if A is not None:
matches[:, 2:] = common.points_apply_homography(np.linalg.inv(A),
matches[:, 2:])
else:
matches = sift_matches
# compute rectifying homographies
H1, H2, F = rectification_homographies(matches, x, y, w, h, hmargin, vmargin)
if cfg['register_with_shear']:
# compose H2 with a horizontal shear to reduce the disparity range
a = np.mean(rpc_utils.altitude_range(rpc1, x, y, w, h))
lon, lat, alt = rpc_utils.ground_control_points(rpc1, x, y, w, h, a, a, 4)
x1, y1 = rpc1.inverse_estimate(lon, lat, alt)[:2]
x2, y2 = rpc2.inverse_estimate(lon, lat, alt)[:2]
m = np.vstack([x1, y1, x2, y2]).T
m = np.vstack({tuple(row) for row in m}) # remove duplicates due to no alt range
H2 = register_horizontally_shear(m, H1, H2)
# compose H2 with a horizontal translation to center disp range around 0
if sift_matches is not None:
sift_matches = filter_matches_epipolar_constraint(F, sift_matches,
cfg['epipolar_thresh'])
if len(sift_matches) < 10:
print('WARNING: no registration with less than 10 matches')
else:
H2 = register_horizontally_translation(sift_matches, H1, H2)
# compute disparity range
if cfg['debug']:
out_dir = os.path.dirname(out1)
np.savetxt(os.path.join(out_dir, 'sift_matches_disp.txt'),
sift_matches, fmt='%9.3f')
visualisation.plot_matches(im1, im2, rpc1, rpc2, sift_matches, x, y, w, h,
os.path.join(out_dir, 'sift_matches_disp.png'))
disp_m, disp_M = disparity_range(rpc1, rpc2, x, y, w, h, H1, H2,
sift_matches, A)
# impose a minimal disparity range (TODO this is valid only with the
# 'center' flag for register_horizontally_translation)
disp_m = min(-3, disp_m)
disp_M = max(3, disp_M)
# compute rectifying homographies for non-epipolar mode (rectify the secondary tile only)
if block_matching.rectify_secondary_tile_only(cfg['matching_algorithm']):
H1_inv = np.linalg.inv(H1)
H1 = np.eye(3) # H1 is replaced by 2-D array with ones on the diagonal and zeros elsewhere
H2 = np.dot(H1_inv,H2)
T = common.matrix_translation(-x + hmargin, -y + vmargin)
H1 = np.dot(T, H1)
H2 = np.dot(T, H2)
# if subsampling_factor'] the homographies are altered to reflect the zoom
z = cfg['subsampling_factor']
if z != 1:
Z = np.diag((1/z, 1/z, 1))
H1 = np.dot(Z, H1)
H2 = np.dot(Z, H2)
disp_m = np.floor(disp_m / z)
disp_M = np.ceil(disp_M / z)
hmargin = int(np.floor(hmargin / z))
vmargin = int(np.floor(vmargin / z))
# compute output images size
roi = [[x, y], [x+w, y], [x+w, y+h], [x, y+h]]
pts1 = common.points_apply_homography(H1, roi)
x0, y0, w0, h0 = common.bounding_box2D(pts1)
# check that the first homography maps the ROI in the positive quadrant
np.testing.assert_allclose(np.round([x0, y0]), [hmargin, vmargin], atol=.01)
# apply homographies and do the crops
common.image_apply_homography(out1, im1, H1, w0 + 2*hmargin, h0 + 2*vmargin)
common.image_apply_homography(out2, im2, H2, w0 + 2*hmargin, h0 + 2*vmargin)
if cfg['disp_min'] is not None: disp_m = cfg['disp_min']
if cfg['disp_max'] is not None: disp_M = cfg['disp_max']
if block_matching.rectify_secondary_tile_only(cfg['matching_algorithm']):
pts_in = [[0, 0], [disp_m, 0], [disp_M, 0]]
pts_out = common.points_apply_homography(H1_inv,
pts_in)
disp_m = pts_out[1,:] - pts_out[0,:]
disp_M = pts_out[2,:] - pts_out[0,:]
return H1, H2, disp_m, disp_M
def cloud_water_image_domain(x,
y,
w,
h,
rpc,
roi_gml=None,
cld_gml=None,
wat_msk=None,
use_srtm_for_water=False):
"""
Compute a mask for pixels masked by clouds, water, or out of image domain.
Args:
x, y, w, h: coordinates of the ROI
rpc: path to the xml file containing the rpc coefficients of the image
RPC model is used with SRTM data to derive the water mask
roi_gml (optional): path to a gml file containing a mask
defining the area contained in the full image
cld_gml (optional): path to a gml file containing a mask
defining the areas covered by clouds
wat_msk (optional): path to an image file containing a water mask
Returns:
2D array containing the output binary mask. 0 indicate masked pixels, 1
visible pixels.
"""
# coefficients of the transformation associated to the crop and zoom
z = cfg['subsampling_factor']
H = np.dot(np.diag((1 / z, 1 / z, 1)), common.matrix_translation(-x, -y))
hij = ' '.join([str(x) for x in H.flatten()])
w, h = int(w / z), int(h / z)
mask = np.ones((h, w), dtype=np.bool)
if roi_gml is not None: # image domain mask (polygons)
tmp = common.tmpfile('.png')
subprocess.check_call('cldmask %d %d -h "%s" %s %s' %
(w, h, hij, roi_gml, tmp),
shell=True)
f = gdal.Open(tmp)
mask = np.logical_and(mask, f.ReadAsArray())
f = None # this is the gdal way of closing files
if not mask.any():
return mask
if cld_gml is not None: # cloud mask (polygons)
tmp = common.tmpfile('.png')
subprocess.check_call('cldmask %d %d -h "%s" %s %s' %
(w, h, hij, cld_gml, tmp),
shell=True)
f = gdal.Open(tmp)
mask = np.logical_and(mask, ~f.ReadAsArray().astype(bool))
f = None # this is the gdal way of closing files
if not mask.any():
return mask
if wat_msk is not None: # water mask (raster)
f = gdal.Open(wat_msk)
mask = np.logical_and(mask, f.ReadAsArray(x, y, w, h))
f = None # this is the gdal way of closing files
elif use_srtm_for_water: # water mask (srtm)
tmp = common.tmpfile('.png')
env = os.environ.copy()
env['SRTM4_CACHE'] = cfg['srtm_dir']
subprocess.check_call('watermask %d %d -h "%s" %s %s' %
(w, h, hij, rpc, tmp),
shell=True,
env=env)
f = gdal.Open(tmp)
mask = np.logical_and(mask, f.ReadAsArray())
f = None # this is the gdal way of closing files
return mask
def cloud_water_image_domain(x, y, w, h, rpc, roi_gml=None, cld_gml=None,
wat_msk=None, use_srtm_for_water=False):
"""
Compute a mask for pixels masked by clouds, water, or out of image domain.
Args:
x, y, w, h: coordinates of the ROI
rpc: path to the xml file containing the rpc coefficients of the image
RPC model is used with SRTM data to derive the water mask
roi_gml (optional): path to a gml file containing a mask
defining the area contained in the full image
cld_gml (optional): path to a gml file containing a mask
defining the areas covered by clouds
wat_msk (optional): path to an image file containing a water mask
Returns:
2D array containing the output binary mask. 0 indicate masked pixels, 1
visible pixels.
"""
# coefficients of the transformation associated to the crop and zoom
z = cfg['subsampling_factor']
H = np.dot(np.diag((1/z, 1/z, 1)), common.matrix_translation(-x, -y))
hij = ' '.join([str(el) for el in H.flatten()])
w, h = int(w/z), int(h/z)
mask = np.ones((h, w), dtype=np.bool)
if roi_gml is not None: # image domain mask (polygons)
tmp = common.tmpfile('.png')
subprocess.check_call('cldmask %d %d -h "%s" %s %s' % (w, h, hij,
roi_gml, tmp),
shell=True)
f = gdal.Open(tmp)
mask = np.logical_and(mask, f.ReadAsArray())
f = None # this is the gdal way of closing files
if not mask.any():
return mask
if cld_gml is not None: # cloud mask (polygons)
tmp = common.tmpfile('.png')
subprocess.check_call('cldmask %d %d -h "%s" %s %s' % (w, h, hij,
cld_gml, tmp),
shell=True)
f = gdal.Open(tmp)
mask = np.logical_and(mask, ~f.ReadAsArray().astype(bool))
f = None # this is the gdal way of closing files
if not mask.any():
return mask
if wat_msk is not None: # water mask (raster)
f = gdal.Open(wat_msk)
mask = np.logical_and(mask, f.ReadAsArray(x, y, w, h))
f = None # this is the gdal way of closing files
elif use_srtm_for_water: # water mask (srtm)
tmp = common.tmpfile('.png')
env = os.environ.copy()
env['SRTM4_CACHE'] = cfg['srtm_dir']
subprocess.check_call('watermask %d %d -h "%s" %s %s' % (w, h, hij, rpc,
tmp),
shell=True, env=env)
f = gdal.Open(tmp)
mask = np.logical_and(mask, f.ReadAsArray())
f = None # this is the gdal way of closing files
return mask
def multidisparities_to_ply(tile):
"""
Compute a point cloud from the disparity maps of N-pairs of image tiles.
Args:
tile: dictionary containing the information needed to process a tile.
# There is no guarantee that this function works with z!=1
"""
out_dir = os.path.join(tile['dir'])
ply_file = os.path.join(out_dir, 'cloud.ply')
plyextrema = os.path.join(out_dir, 'plyextrema.txt')
x, y, w, h = tile['coordinates']
rpc_ref = cfg['images'][0]['rpc']
disp_list = list()
rpc_list = list()
if cfg['skip_existing'] and os.path.isfile(ply_file):
print('triangulation done on tile {} {}'.format(x, y))
return
mask_orig = os.path.join(out_dir, 'cloud_water_image_domain_mask.png')
print('triangulating tile {} {}...'.format(x, y))
n = len(cfg['images']) - 1
for i in range(n):
pair = 'pair_%d' % (i + 1)
H_ref = os.path.join(out_dir, pair, 'H_ref.txt')
H_sec = os.path.join(out_dir, pair, 'H_sec.txt')
disp = os.path.join(out_dir, pair, 'rectified_disp.tif')
mask_rect = os.path.join(out_dir, pair, 'rectified_mask.png')
disp2D = os.path.join(out_dir, pair, 'disp2D.tif')
rpc_sec = cfg['images'][i + 1]['rpc']
if os.path.exists(disp):
# homography for warp
T = common.matrix_translation(x, y)
hom_ref = np.loadtxt(H_ref)
hom_ref_shift = np.dot(hom_ref, T)
# homography for 1D to 2D conversion
hom_sec = np.loadtxt(H_sec)
if cfg["use_global_pointing_for_geometric_triangulation"] is True:
pointing = os.path.join(cfg['out_dir'],
'global_pointing_%s.txt' % pair)
hom_pointing = np.loadtxt(pointing)
hom_sec = np.dot(hom_sec, np.linalg.inv(hom_pointing))
hom_sec_shift_inv = np.linalg.inv(hom_sec)
h1 = " ".join(str(x) for x in hom_ref_shift.flatten())
h2 = " ".join(str(x) for x in hom_sec_shift_inv.flatten())
# relative disparity map to absolute disparity map
tmp_abs = common.tmpfile('.tif')
os.environ["PLAMBDA_GETPIXEL"] = "0"
common.run(
'plambda %s %s "y 0 = nan x[0] :i + x[1] :j + 1 3 njoin if" -o %s'
% (disp, mask_rect, tmp_abs))
# 1d to 2d conversion
tmp_1d_to_2d = common.tmpfile('.tif')
common.run('plambda %s "%s 9 njoin x mprod" -o %s' %
(tmp_abs, h2, tmp_1d_to_2d))
# warp
tmp_warp = common.tmpfile('.tif')
common.run('homwarp -o 2 "%s" %d %d %s %s' %
(h1, w, h, tmp_1d_to_2d, tmp_warp))
# set masked value to NaN
exp = 'y 0 = nan x if'
common.run('plambda %s %s "%s" -o %s' %
(tmp_warp, mask_orig, exp, disp2D))
# disp2D contains positions in the secondary image
# added input data for triangulation module
disp_list.append(disp2D)
rpc_list.append(rpc_sec)
if cfg['clean_intermediate']:
common.remove(H_ref)
common.remove(H_sec)
common.remove(disp)
common.remove(mask_rect)
common.remove(mask_orig)
colors = os.path.join(out_dir, 'ref.png')
if cfg['images'][0]['clr']:
common.image_crop_gdal(cfg['images'][0]['clr'], x, y, w, h, colors)
else:
common.image_qauto(
common.image_crop_gdal(cfg['images'][0]['img'], x, y, w, h),
colors)
# compute the point cloud
triangulation.multidisp_map_to_point_cloud(ply_file,
disp_list,
rpc_ref,
rpc_list,
colors,
utm_zone=cfg['utm_zone'],
llbbx=tuple(cfg['ll_bbx']),
xybbx=(x, x + w, y, y + h))
# compute the point cloud extrema (xmin, xmax, xmin, ymax)
common.run("plyextrema %s %s" % (ply_file, plyextrema))
if cfg['clean_intermediate']:
common.remove(colors)
def local_translation_rotation(r1, r2, x, y, w, h, m):
"""
Estimates the optimal translation to minimise the relative pointing error
on a given tile.
Args:
r1, r2: two instances of the rpc_model.RPCModel class
x, y, w, h: region of interest in the reference image (r1)
m: Nx4 numpy array containing a list of matches, one per line. Each
match is given by (p1, p2, q1, q2) where (p1, p2) is a point of the
reference view and (q1, q2) is the corresponding point in the
secondary view.
Returns:
3x3 numpy array containing the homogeneous representation of the
optimal planar translation, to be applied to the secondary image in
order to correct the pointing error.
"""
# estimate the affine fundamental matrix between the two views
n = cfg['n_gcp_per_axis']
rpc_matches = rpc_utils.matches_from_rpc(r1, r2, x, y, w, h, n)
F = estimation.affine_fundamental_matrix(rpc_matches)
# Compute rectification homographies
# S1, S2 = estimation.rectifying_similarities_from_affine_fundamental_matrix(F, cfg['debug'])
hmargin = cfg['horizontal_margin']
vmargin = cfg['vertical_margin']
S1, S2, F_rect = rectification.rectification_homographies(rpc_matches, x, y, w, h, hmargin, vmargin)
N = len(m)
# Apply rectification on image 1
S1p1 = common.points_apply_homography(S1, m[:,0:2])
S1p1 = np.column_stack((S1p1,np.ones((N,1))))
print("Points 1 rectied")
print(S1p1[:10])
# Apply rectification on image 2
S2p2 = common.points_apply_homography(S1, m[:,2:4])
S2p2 = np.column_stack((S2p2, np.ones((N,1))))
print("Points 2 rectied")
print(S2p2[:10])
# Compute F in the rectified space
rect_matches = np.column_stack((S1p1[:,0:2], S2p2[:, 0:2]))
F_rect2 = estimation.affine_fundamental_matrix(rect_matches)
# Compute epipolar lines
FS1p1 = np.dot(F_rect2, S1p1.T).T
print(FS1p1[:10])
# Normalize epipolar lines
c1 = -FS1p1[:, 1]
FS1p1_norm = FS1p1/c1[:, np.newaxis]
print(FS1p1_norm[:10])
# Variable of optimization problem
A_ = np.ones((N,1))
# A_ = np.column_stack((S2p2[:,0].reshape(N, 1),np.ones((N,1))))
# b_ = S2p2[:, 1] - FS1p1_norm[:, 2]
b_ = S2p2[:, 1] - S1p1[:, 1]
t_med = np.median(b_)
print(t_med)
t_med2 = np.sort(b_)[int(N/2)]
print("t_med2", t_med2)
# min ||Ax + b||^2 => x = - (A^T A )^-1 A^T b
# X_ = - np.dot(np.linalg.inv(np.dot(A_.T, A_)), np.dot(A_.T, b_))
# [theta, t] = X_
# print(t, theta)
# t = X_[0]
# Compute epipolar lines witout recitifcation
p1 = np.column_stack((m[:,0:2],np.ones((N,1))))
Fp1 = np.dot(F, p1.T).T
# Compute normal vector to epipolar liness
ab = np.array([Fp1[0][0], Fp1[0][1]])
ab = ab/np.linalg.norm(ab)
tx = t_med*ab[0]
ty = t_med*ab[1]
print(tx, ty)
# Get translation in not rectified image
T = common.matrix_translation(0, -t_med)
T = np.linalg.inv(S2).dot(T).dot(S2)
# T = np.dot(S2_inv, T)
print(T)
theta = 0
cos_theta = np.cos(theta)
sin_theta = np.sin(theta)
A = np.array([[cos_theta, -sin_theta, tx],
[sin_theta, cos_theta, ty],
[0, 0, 1]])
return A, F
