Homec4science
Diffusion bonepro (master) Browse

bonepro/pipeline/pipeline_fast.py
eb8aedd61366master

Last Change
Raw File

pipeline_fast.py
View Options

"""
This script runs FAST pipeline, converted from Denis's Bash script.
Author: Jarunan Panyasantisuk, ETH Scientific IT Services
Date: 30 November 2018
"""
import os
import argparse
import yaml
import time
import shutil
from bonepy import io_utils
from bonepy.aim2fe import aim2fe
parser = argparse.ArgumentParser()
# model parameters
parser.add_argument(
"--configfile",
type=str,
default="config.yaml",
help="A configuration file containing parameter values",
)
def main(args):
# timing
start_full = time.time()
time_record = {}
# read config
config = io_utils.read_config_file(args.configfile)
print(yaml.dump(config, default_flow_style=False))
# Sets the paths to the data
workdir = config["workdir"]
aimdir = config["aimdir"]
feadir = config["feadir"]
umat = config["umat"]
sumdir = config["sumdir"]
if not os.path.isdir(sumdir):
os.mkdir(sumdir)
grayscale_filenames = config["grayscale_filenames"]
folder_id = config["folder_id"]
current_version = config["current_version"]
abaqus = config["abaqus"]
nprocs = config["nprocs"]
for sample in grayscale_filenames:
# timing
start_sample = time.time()
# set path
folder = folder_id[sample]
sampledir = os.path.join(feadir, folder)
inputfilename = "{}_V_{}.inp".format(sample, current_version)
inputfile = os.path.join(aimdir, folder, inputfilename)
# preprocessing
aim2fe(config, sample)
# solving
os.chdir(sampledir)
shutil.copy(inputfile, sampledir)
command = "{} interactive cpus={:d} job={} inp={} user={} ask_delete=OFF".format(
abaqus, nprocs, sample, inputfile, umat
)
os.system(command)
# postprocessing
output_filename = "{}.dat".format(sample)
io_utils.datfilereader(output_filename)
resultdir = os.path.join(feadir, "Results_{}".format(current_version))
resultfile = "{}.txt".format(sample)
shutil.copy(
os.path.join(sampledir, resultfile), os.path.join(resultdir, resultfile)
)
# timing
end_sample = time.time()
time_record[sample] = end_sample - start_sample
end_full = time.time()
time_record["full"] = end_full - start_full
print(yaml.dump(time_record, default_flow_style=False))
if __name__ == "__main__":
args = parser.parse_args()
main(args)
c4science · Help