imodmodel

Read IMOD model files as pandas dataframes in Python.

Usage

As pandas DataFrame

import imodmodel

df = imodmodel.read('my_model_file.mod')

In [3]: df.head()
Out[3]: 
   object_id  contour_id          x          y     z
0          0           0  64.333336  64.666664  80.0
1          0           0  47.000000  77.333336  80.0
2          0           0  51.333332  45.666668  80.0
3          0           0  87.333336  49.666668  80.0
4          0           0  76.000000  82.000000  80.0

As ImodModel object

from imodmodel import ImodModel
model = ImodModel.from_file("my_model_file.mod")

In [3]: model.objects[0].contours[0].points
Out[3]: 
array([[  6.875,  62.875, 124.   ], ...])

In [4]: model.objects[0].meshes[0].vertices
Out[4]: 
array([[ 6.87500000e+00,  6.28750000e+01,  1.24000000e+02], ...])

In [5]: model.objects[0].meshes[0].indices
Out[5]: 
array([[156,  18, 152], ...])

In [6]: model.objects[0].meshes[0].face_values
Out[6]: 
array([0., 0., 35.22094345, ...])

That's it!

Installation

imodmodel can be installed from the Python Package Index (PyPI)

pip install imodmodel

We recommend installing into a clean virtual environment.