def test_sa_h5py_14():
"""
Test gridding tracks with dx, dy.
"""
tracks = {
"x": numpy.array([10, 20, 30]),
"y": numpy.array([10, 10, 10]),
"z": numpy.array([-0.2, 0.0, 0.2])
}
dx = 1
dy = 2
h5_name = storm_analysis.getPathOutputTest("test_sa_hdf5.hdf5")
# Tracks.
with saH5Py.SAH5Py(h5_name, is_existing=False, overwrite=True) as h5:
h5.setMovieInformation(40, 40, 1, "")
h5.addTracks(tracks)
with saH5Py.SAH5Grid(filename=h5_name, scale=1, z_bins=3) as h5g:
im_2d = h5g.gridTracks2D(dx=dx, dy=dy)
im_3d = h5g.gridTracks3D(-0.201, 0.201, dx=dx, dy=dy)
for i in range(tracks["x"].size):
assert (im_2d[int(tracks["x"][i] + dx),
int(tracks["y"][i] + dy)] == 1)
assert (im_3d[int(tracks["x"][i] + dx),
int(tracks["y"][i] + dy), i] == 1)
def alignAndMerge(file1,
file2,
results_file,
scale=2,
dx=0,
dy=0,
z_min=-0.5,
z_max=0.5):
"""
Note: This only aligns and merges the tracks not the localizations.
"""
z_bins = int((z_max - z_min) / 0.05)
with saH5Py.SAH5Py(results_file, is_existing=False) as h5_out:
# Process first file, this has no offset.
with saH5Py.SAH5Grid(filename=file1, scale=scale,
z_bins=z_bins) as h5g_in1:
[mx, my] = h5g_in1.getMovieInformation()[:2]
h5_out.setMovieInformation(mx, my, 0, "")
h5_out.setPixelSize(h5g_in1.getPixelSize())
h5_out.addMetadata(h5g_in1.getMetadata())
for tracks in h5g_in1.tracksIterator():
sys.stdout.write(".")
sys.stdout.flush()
h5_out.addTracks(tracks)
sys.stdout.write("\n")
im1_xy = h5g_in1.gridTracks2D()
im1_xyz = h5g_in1.gridTracks3D(z_min, z_max)
# Process second file.
with saH5Py.SAH5Grid(filename=file2, scale=scale,
z_bins=z_bins) as h5g_in2:
# Determine X/Y offset.
im2_xy = h5g_in2.gridTracks2D()
[corr, offx, offy, xy_success
] = imagecorrelation.xyOffset(im1_xy,
im2_xy,
scale,
center=[dx * scale, dy * scale])
if False:
tifffile.imsave("im1_xy.tif", im1_xy)
tifffile.imsave("im2_xy.tif", im2_xy)
assert xy_success, "Could not align images in X/Y."
offx = offx / float(scale)
offy = offy / float(scale)
# Determine Z offset.
im2_xyz = h5g_in2.gridTracks3D(z_min, z_max, dx=offx, dy=offy)
[corr, fit, offz,
z_success] = imagecorrelation.zOffset(im1_xyz, im2_xyz)
assert z_success, "Could not align images in Z."
offz = -offz * (z_max - z_min) / float(z_bins)
for tracks in h5g_in2.tracksIterator():
sys.stdout.write(".")
sys.stdout.flush()
tracks["x"] += offx
tracks["y"] += offy
tracks["z"] += offz
h5_out.addTracks(tracks)
sys.stdout.write("\n")
return [offx, offy, offz]