run.py

# Provided under BSD license
# Copyright (c) 2017, Jeremy Wohlwend
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
#  - Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
#  - Redistributions in binary form must reproduce the above copyright notice,
#    this list of conditions and the following disclaimer in the documentation
#    and/or other materials provided with the distribution.
#  - Neither the name of SimExm nor the names of its contributors may be used
#    to endorse or promote products derived from this software without specific
#    prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL JEREMY WOHLWEND BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
# EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

"""
run.py

Main script to run the simulation.
"""

import argparse
from configobj import ConfigObj, flatten_errors
from validate import Validator
from src.load import load_gt
from src.labeling import label
from src.optics import resolve
from src.output import save, save_gt
from tifffile import imshow
import numpy as np
import matplotlib
import matplotlib.pyplot as plt

def run(config, show_output = False):
    """
    Runs the simulation using the given config.
    For more information on the available parameters, see configspecs.ini and the readme

    Args:
        config: dictionary
            the configuration dict outputed by the configobj library
        show_output: boolean
            if True, shows the output in a new window
    """
    gt_params = config['groundtruth']
    volume_dim = gt_params['bounds']
    voxel_dim = gt_params['voxel_dim']
    #Remove voxel dim so that we can pass gt_params to the load_gt function
    del gt_params['voxel_dim']

    print "Loading data..."
    gt_dataset = load_gt(**gt_params)

    print "Labeling..."
    labeling_params = config['labeling']
    labeled_volumes, labeled_cells = label(gt_dataset, volume_dim, voxel_dim, labeling_params)

    print "Imaging..."
    expansion_params = config['expansion']
    optics_params = config['optics']
    volumes = resolve(labeled_volumes, volume_dim, voxel_dim, expansion_params, optics_params)
    print "Saving..."
    #Save to desired output
    output_params = config['output']
    save(volumes, **output_params)
    save_gt(gt_dataset, labeled_cells, volume_dim, volumes[0].shape, voxel_dim,\
            expansion_params, optics_params, **output_params)
    print "Done!"
    if show_output:
        imshow(np.moveaxis(np.array(volumes), 0, 3))
        plt.show()

if __name__ == "__main__":
    #Read config file
    parser = argparse.ArgumentParser(description='Run a SimExm simulation.')
    parser.add_argument('config', type=str, help='an input config file')
    parser.add_argument('-v', action='store_true', help='show output')
    args = parser.parse_args()
    config_file = args.config
    config = ConfigObj(config_file, list_values = True,  configspec='configspecs.ini')
    #Validate input configuration
    validator = Validator()
    results = config.validate(validator)

    if results != True:
        for (section_list, key, _) in flatten_errors(config, results):
            if key is not None:
                print 'The "%s" key in the section "%s" failed validation' % (key, ', '.join(section_list))
            else:
                print 'The following section was missing:%s ' % ', '.join(section_list)
    #Run simulation
    run(config, args.v)