def processFrameUV(i, node, outputBase, ofs_U, ofs_V, ar, cw, imgfmt):
uvframe = hdf5lflib.compute_uvframe(node, ar, cw, ofs_U, ofs_V)
global gridsize_last
gridsize_last = uvframe.shape
if imgfmt == 'png':
scipy.misc.imsave(outputBase + '-' + str(i) + '.png', uvframe)
else:
f = open(outputBase + '-' + str(i) + '.raw', 'wb')
uvframe.tofile(f)
f.close()
def processFrame(i, node, ar, cw):
uvframe = hdf5lflib.compute_uvframe(node, ar, cw)
if PROGRESS_FIGURES:
plt.figure()
imgplot = plt.imshow(uvframe, cmap=plt.cm.gray)
plt.show()
# Smooth twice
uvframe = cv2.medianBlur(uvframe, 5)
uvframe = cv2.medianBlur(uvframe, 5)
if PROGRESS_FIGURES:
plt.figure()
imgplot = plt.imshow(uvframe, cmap=plt.cm.gray)
plt.show()
# Threshold
background_color = uvframe.mean()
foreground_i = uvframe > background_color
uvframe[foreground_i] = 255.
uvframe[numpy.invert(foreground_i)] = 0.
# Fill holes in "dead" regions of the worm
uvframe = scipy.ndimage.morphology.binary_fill_holes(uvframe)
if PROGRESS_FIGURES:
plt.figure()
imgplot = plt.imshow(uvframe, cmap=plt.cm.gray)
plt.show()
# Annotate with information regarding the nearest edge
(edgedists, edgedirs) = computeEdgeDistances(uvframe)
if PROGRESS_FIGURES:
fig, axes = plt.subplots(ncols = 2)
axes[0].imshow(uvframe, cmap=plt.cm.gray)
axes[1].imshow(edgedists)
plt.show()
# Determine the backbone
backbone = poseExtract(uvframe, edgedists, edgedirs)
# Convert to TSV and output
printTSV(backbone, edgedists)
if __name__ == '__main__':
filename = sys.argv[1]
frameNo = int(sys.argv[2])
bbfilename = sys.argv[3]
outputfile = None
if len(sys.argv) >= 5:
outputfile = sys.argv[4]
h5file = tables.open_file(filename, mode = "r")
node = h5file.get_node('/', '/images/' + str(frameNo))
ar = h5file.get_node('/', '/autorectification')
try:
cw = h5file.get_node('/', '/cropwindow')
except tables.NoSuchNodeError:
cw = None
uvframe = hdf5lflib.compute_uvframe(node, ar, cw)
(points, edgedists) = poselib.bbLoad(bbfilename)
(spline, bblength) = poselib.bbToSpline(points)
bbpoints = poselib.bbTraceSpline(spline, bblength, uvframe)
# Draw the backbone
#plt.figure()
#plt.plot(bbpoints[:,0,1], bbpoints[:,0,0], 'o') # (x, y) order
#plt.axis([0,100,100,0])
#plt.show()
restackframe = restackBySpline(bbpoints, uvframe, points, edgedists)
if outputfile:
scipy.misc.imsave(outputfile, restackframe)
