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Installation of Connectome File Format Library

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How to use the Connectome File Format LibraryΒΆ

Note

Example connectome files are provided in the GitHub repository cffdata.

Import the library. Subsequently, we assume that this has been done:

from cfflib import *

Load the dataset from the file system:

a=load_from_meta_cml('example_dataset_01/meta.cml')

You can print all the loaded connectome objects:

print a.get_all()

If you have a zipped file with ending .cff, you can load it as well with:

a=load_from_cff('datasets/ds1/connectomefile.cff')

You can get the first network and load it like this:

mynetwork = a.get_by_name('Network Lausanne83')[0]
mynetwork.load()

The loaded network object accessible through the data attribute (a NetworkX object):

print mynetwork.data

You see that it is a NetworkX graph. You can modify it as you like.

After modification, you can store it, which stores it in the corresponding file that this CNetwork was referenced to (relative path):

print mynetwork.src
mynetwork.save()

Show other attributes:

print mynetwork.name
print mynetwork.dtype
print mynetwork.description

To show the metadata attributes as dictionary:

print mynetwork.get_metadata_as_dict()

You can save the currently loaded connectome file:

save_to_cff('myconnectome.cff', a)

The same you can do for other connectome objects, if the corresponding Python libraries are installed correctly:

# CVolume
obj = a.get_by_name('Example Volume')
obj.load()
print obj.data

# CSurface
obj = a.get_by_name('Example Surface')
obj.load()
print obj.data

# CTrack
obj = a.get_by_name('Tractography')
obj.load()
# You do not want to display all fibers, just show the header
print obj.data[1]

# CTimeseries
obj = a.get_by_name('Generated timeseries data')
obj.load()
print obj.data

# CData
obj = a.get_by_name('Arbitrary data file')
obj.load()
print obj.data

# CScript
obj = a.get_by_name('Analysis Script MMXXXIV')
obj.load()
print obj.data

# CImagestack
obj = a.get_by_name('FIB Rat Striatum')
obj.load()
print obj.data