A simple example trying to walk through dereferencing of a Matlab structure array in Python

deference_hdf5

#ViewWormMovement

import matplotlib.pyplot as plt
import h5py

file_path = u'F:/worm_data/segworm_data/features/798 JU258 on food R_2010_11_25__16_34_17___1___9_features.mat'

h = h5py.File(file_path, 'r')

#dv - Distance Value
dv = h["worm"]["locomotion"]["motion"]["backward"]["frames"]["distance"].value

#NOTE, frames has an attribute:
#'MATLAB_class':  'struct'
#
#In Matlab, the object should really be an array of objects
#where the # of references of any given property are really
#indicative of the # of objects
#
#i.e. if distance has 28 values, then frames should be of length 28
#
# The value held by the reference can be any length, however
# for many of our structure arrays (I think all) the values
# are scalar, so we can translate this all into an array of values or a list
#

#dv -> holds an array of references
#pass references to file to dereference
#
#   h[dv[#,0]]
#
#Once we dereference to a dataset, we need to grab its value
#
#   .value
#
#This value is an array, for which we grab the first value
#i.e. ASSUMES a scalar
#
#   [0,0]
value = [h[dv[x,0]].value[0,0] for x in range(0,dv.size)]


plt.plot(value)
plt.show()

#NOTE: Should check len(value) == dv.size