The pyminc version of hello world.
Keeping with other tutorials on how to program with the MINC toolkit, here's a simple example for how to open a volume, add one to every voxel, then write it out again. This being python, the code is nice and short!
#!/usr/bin/env python
from pyminc.volumes.factory import *
from numpy import *
import sys
if __name__ == "__main__":
# get the input file
infile = volumeFromFile(sys.argv[1])
# get the output file using the same dimension info as the input file
outfile = volumeLikeFile(sys.argv[1], sys.argv[2])
# add one to the data
outfile.data = infile.data + 1
# write out and close the volumes
outfile.writeFile()
outfile.closeVolume()
infile.closeVolume()
Here's what the code does. The first bits are the imports of different modules - the one non-standard module is pyminc.volumes.factory. Most all creation of pyminc volume instances is done through a set of factory methods. They are:
| Function | Description |
|---|---|
| volumeFromFile | opens minc volume from an existing file - useful for reading existing data. |
| volumeLikeFile | creates a new minc volume from an existing file - useful for writing data. |
| volumeFromInstance | creates a new minc volume from an existing instance (python object) |
| volumeFromDescription | creates a new minc volume by specifying the dimensions, sizes, starts, etc. |
The next line of the code assigns the output files data to be the input files data plus 1. Every pyminc volume has a data attribute, which is a numpy array. Note that the data is not actually read until the data attribute is accessed. The last bits then write the output file to disk and closes both volumes.