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():
"""Generate a Gaussian blurred maximal intensity projection from a directory
containing a stack of image files"""
try:
stackdir = sys.argv[1]
stackdir2 = sys.argv[2]
except IndexError:
print "Usage: %s stack_dir1 stack_dir2 [output_dir] [sdx] [sdy] [sdz]" % os.path.basename(sys.argv[0])
sys.exit(1)
#imgpattern, istart, iend = stackhandle.get_stack_pattern(stackdir)
ifiles = stackhandle.get_stack_files(stackdir)
ifiles2 = stackhandle.get_stack_files(stackdir2)
try:
output_dir = sys.argv[3]
except IndexError:
output_dir = 'output/'
print "Using default output directory output/"
print "Called with", stackdir, output_dir
try:
sdx, sdy, sdz = int(sys.argv[4]), int(sys.argv[5]), int(sys.argv[6])
except IndexError:
print "Using default values for standard deviation"
sdx, sdy, sdz = 8, 8, 6
# Gaussian blur applied to surface after projection is taken
sds = 5
print "Using standard deviations: (%d, %d, %d), %d" % (sdx, sdy, sdz, sds)
# Load the two images from their stack representations
ma = load_png_stack(ifiles)
ma2 = load_png_stack(ifiles2)
# Apply the initial Gaussian blur in 3D to the first stack (which we will
# use to generate the surface)
bl = apply_gaussian_filter(ma, [sdx, sdy, sdz])
# Calculate the projection surface using numpy's function for finding the
# max of an array along a particular axis
ps = np.argmax(bl, 2)
# Apply the blur to the resultant surface and save the result
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))
save_numpy_as_png(sfilename, sps * vis_factor)
# Calculate the projection of the first image using the generated surface
# and save the result, scaling intensities after taking the projection
res1 = projection_from_surface(ma, sps)
filename = os.path.join(output_dir, "proj-1-g3d-%d-%d-%d-%d.png" % (sdx, sdy, sdz, sds))
pmax = np.amax(res1)
vis_scale = 255 / pmax
scipy.misc.imsave(filename, res1 * vis_scale)
res2 = projection_from_surface(ma2, sps)
filename = os.path.join(output_dir, "proj-2-g3d-%d-%d-%d-%d.png" % (sdx, sdy, sdz, sds))
pmax = np.amax(res2)
vis_scale = 255 / pmax
scipy.misc.imsave(filename, res1 * vis_scale)
flush_message("Post processing...")
pp = projpp.proj_filter(res1 * 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)