example2_space.rst

Example 2: Geometry-related features

The code snippet below shows a simple scenario for geometry analysis of the reconstructed cytoskelton.

from cytoskeleton_analyser.inout import Paths      # simulation-specific paths
from cytoskeleton_analyser.position.drivers import process  # driver fuction
from sim_specs import cell, data_in, data_out, rinds

# Set general parameters of the input simulation. (a shortlist
# of config settings).
params = {
   'edge_len_fine': 0.008,    # (μm) length of filament edge.
   'iscoarse': True,          # use coarse-grained representation
   'coarsegraining': 25,      # coarse-graining factor
   'use_final': False,        # if True, limit to final snapshot only
   'cell': cell,              # cell object
   'slice_limits': {'bottom': 0., 'top': 0.8},  # z-pos. of slicing planes
}

# Specify features to process. If this is None,
# all features are included.
features = [
   'RadialMass',
]

# Decide if this is a new analysis, or we merely want to import one.
new = True

# This dict will become populated only if analysis
# is imported ('new' = False).
# Otherwise, the results are stored on a disc.
result = {}

if __name__ == '__main__':

   for ci in rinds:
      paths = Paths(data_in, data_out, params['cell'], ci)
      result[str(ci)] = process(new, paths, ci, params, True, features)