21 Oct 2019

Load a Numpy array into PerGeos/Amira-Avizo using the Python API

This script simply reads and loads numpy arrays in a user specified directory into PerGeos/Amira-Avizo as an image.

6-28-2019 2-38-06 PM

Numpy arrays are commonly used by Python users and this script allows for a quick plug-and-play solution to read these arrays into memory from disk into PerGeos/Amira-Avizo. This will give researchers an easy platform to visualize the arrays using powerful existing visualization tools. There are currently no size restrictions and only limited by numpy itself. Restricted to 2D/3D arrays only as a Numpy array is converted to internal PerGeos/Amira-Avizo native data structures. Also, note that the arrays are loaded in double format and users can use the Convert Image tool to convert to other formats.

Inputs include specifying a directory that contains one or more numpy array.

Load one or more Numpy arrays into Avizo-Amira

Steps :

  • Drag and drop the numpy_import2.pyscro into Avizo/Amira 2019.3
  • Provide a directory under 'Input Directory' that contains one or more numpy array/s (User can use the browse button). Note that one sample numpy array (test20.npy) is provided in the xtra. You may point to a directory containing this file to test loading of numpy file.
  • Use 'Load One Numpy File' or 'Load Numpy Files' for single or all numpy arrays under the folder.