Starting A Project

In order to begin using TomoSuite, one must create a project for their .h5 data. Sometimes it is necessary to create multiple projects for a single task, but this is only when one is to use a sacraficial sample for network training. All use cases of a second project are detailed in the documentation of TomoSuite

Importing TomoSuite

import sys
sys.path.append('/path/to/tomosuite/github/clone/tomosuite/')
import tomosuite

from tomosuite.base.start_project import start_project
from tomosuite.base.extract_projections import extract

The Project

# The directory path where the raw experimental file lives
datadir = '/local/data/experimental/'

# The file name of the data the User would like to import
fname = 'Experiment_01.h5'

# The folder path where the User would like to store project data to
basedir = '/local/data/project_01/'


start_project(basedir=basedir)


extract(datadir=datadir,
            fname=fname,
            basedir=basedir,
            chunk_size4downsample=10) # Set chunk_size4downsample to 1 if you have a lot of RAM