def main():
try:
stackdir = sys.argv[1]
except IndexError:
print "Usage: %s stack_dir [output_dir] [sdx] [sdy] [sdz]" % os.path.basename(sys.argv[0])
sys.exit(1)
ifiles = stackhandle.get_stack_files(stackdir)
try:
output_dir = sys.argv[2]
except IndexError:
output_dir = 'output/'
print "Using default output directory output/"
print "Called with", stackdir, output_dir
try:
sdx, sdy, sdz = int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5])
except IndexError:
print "Using default values for standard deviation"
sdx, sdy, sdz = 8, 8, 6
sds = 5
print "Using standard deviations: %d, %d, %d" % (sdx, sdy, sdz)
ma = load_png_stack(ifiles)
flush_message("Applying 3D gaussian filter...")
bl = nd.gaussian_filter(ma, [sdx, sdy, sdz])
print "done"
flush_message("Finding projection surface...")
ps = proj.max_indices_z(bl)
print "done"
sps = nd.gaussian_filter(ps, sds)
_, _, zmax = ma.shape
vis_factor = 255 / zmax
sfilename = os.path.join(output_dir, "surface-g3d-%d-%d-%d-%d.png" % (sdx, sdy, sdz, sds))
scipy.misc.imsave(sfilename, sps * vis_factor)
flush_message("Generating projection from surface...")
res = proj.projection_from_surface_z(ma, sps, dm=3, dp=0)
print "done"
filename = os.path.join(output_dir, "proj-g3d-%d-%d-%d-%d.png" % (sdx, sdy, sdz, sds))
pmax = np.amax(res)
vis_scale = 255 / pmax
scipy.misc.imsave(filename, res * vis_scale)
flush_message("Post processing...")
pp = projpp.proj_filter(res * vis_scale, 3, 60, 15)
print "done"
filename = os.path.join(output_dir, 'proj-pp-%d-%d-%d-%d.png' % (sdx, sdy, sdz, sds))
scipy.misc.imsave(filename, pp)
def main(args):
javabridge.start_vm(class_path=bf.JARS)
try:
lifdir = sys.argv[1]
except IndexError:
print "Usage: %s lif_directory [sdx] [sdy] [sdz]" % os.path.basename(sys.argv[0])
sys.exit(1)
try:
sdx, sdy, sdz = int(sys.argv[2]), int(sys.argv[3]), int(sys.argv[4])
except IndexError:
print "Using default values for standard deviation"
sdx, sdy, sdz = 4, 4, 3
md = bf.get_omexml_metadata(lifdir)
mdo = bf.OMEXML(md)
rdr = bf.ImageReader(lifdir, perform_init=True)
names, sizes, resolutions = parse_xml_metadata(md)
print '%s contains:' % lifdir
for i in range(mdo.image_count):
print '%d, %s, %s' % (i,names[i],(sizes[i],))
for im_num in range(mdo.image_count):
im_size = ()
im_size = [sizes[im_num][1],sizes[im_num][2],sizes[im_num][0],3]
image3d = np.empty(im_size, np.uint8)
print 'projecting: %d, %s, %s' % (im_num,names[im_num],(sizes[im_num],))
z_size = sizes[im_num][0]
flush_message('Importing...')
for z in range(z_size):
image3d[:,:,z,:] = rdr.read(z=z, series=im_num, rescale=False)
print 'done'
#ma = greyScale(image3d)
ma = np.amax(image3d, 3)
#sdx, sdy, sdz = 4, 4, 3
sds = 4
output_dir = "./proj_%s_%s" % (lifdir, im_num)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
max_proj = np.amax(ma, axis=2)
mpfilename = os.path.join(output_dir, "max-proj.png")
scipy.misc.imsave(mpfilename, max_proj)
bl = nd.gaussian_filter(ma, [sdx, sdy, sdz])
#ps = find_projection_surface(bl)
ps = proj.max_indices_z(bl)
sps = nd.gaussian_filter(ps, sds)
vis_factor = 255 / z_size
sfilename = os.path.join(output_dir, "surface-g3d-%d-%d-%d-%d.png" % (sdx, sdy, sdz, sds))
scipy.misc.imsave(sfilename, sps * vis_factor)
res = proj.projection_from_surface(ma, sps, dm=3, dp=0)
filename = os.path.join(output_dir, "proj-g3d-%d-%d-%d-%d.png" % (sdx, sdy, sdz, sds))
pmax = np.amax(res)
vis_scale = 255 / pmax
scipy.misc.imsave(filename, res * vis_scale)
flush_message("Post processing...")
pp = projpp.proj_filter(res * vis_scale, 3, 60, 15)
print " done"
filename = os.path.join(output_dir, 'proj-pp-%d-%d-%d-%d.png' % (sdx, sdy, sdz, sds))
scipy.misc.imsave(filename, pp)
javabridge.kill_vm()
return 0