parse warp grids in python

warp_grid_parse.py

from lxml import etree

json_file = "/Users/burta2/data/fakery/MotionAndCTF2D/average/20170629_00021_frameImage_motion.json"

# <GridMovementX Width="1" Height="1" Depth="3" MarginX="0" MarginY="0" MarginZ="0">
# 		<Node X="0" Y="0" Z="0" Value="-5.1639977" />
# 		<Node X="0" Y="0" Z="1" Value="0.7089546" />
# 		<Node X="0" Y="0" Z="2" Value="4.455043" />
# 	</GridMovementX>
# 	<GridMovementY Width="1" Height="1" Depth="3" MarginX="0" MarginY="0" MarginZ="0">
# 		<Node X="0" Y="0" Z="0" Value="5.4425087" />
# 		<Node X="0" Y="0" Z="1" Value="-0.63774544" />
# 		<Node X="0" Y="0" Z="2" Value="-4.8047633" />
# 	</GridMovementY>
# 	<GridLocalMovementX Width="1" Height="1" Depth="1" MarginX="0" MarginY="0" MarginZ="0">
# 		<Node X="0" Y="0" Z="0" Value="0.008896833" />
# 	</GridLocalMovementX>

tree = etree.parse(xml_file)
root = tree.getroot()

# get motion grid
gy = root.find('./GridMovementY')
gx = root.find('./GridMovementX')
ny = gy.findall('./Node')
nx = gx.findall('./Node')

d, h, w = gx.attrib['Depth'], gx.attrib['Height'], gx.attrib['Width']
d, h, w = int(d), int(h), int(w)

motion_grid = np.zeros(shape=(d, h, w, 2))  # (d, h, w, yx)

for node_y, node_x in zip(ny, nx):
    z, y, x = node_y.attrib['Z'], node_y.attrib['Y'], node_y.attrib['X']
    z, y, x = int(z), int(y), int(x)
    y_value, x_value = node_y.attrib['Value'], node_x.attrib['Value']
    y_value, x_value = float(y_value), float(x_value)
    motion_grid[z, y, x] = (y_value, x_value)

print(motion_grid)