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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,29 @@ | ||
| #!/bin/bash -e | ||
| # | ||
| # Set up a new python2.7 virtualenv for the GWpy software stack | ||
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| # get name | ||
| target=$1 | ||
| [[ -z ${target} ]] && target=${HOME}/opt/gwpysoft | ||
| packagefile=$2 | ||
| rm -rf ~/opt/GravitySpy-py27 | ||
| virtualenv-2.7 ~/opt/GravitySpy-py27 | ||
| . ~/opt/GravitySpy-py27/bin/activate | ||
| python -m pip install --upgrade --quiet pip setuptools | ||
| pip install . | ||
| pip install cython | ||
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| # -- install dependencies for virtualenv itself | ||
| # get python2.7 version | ||
| if [[ -z ${PYTHON_VERSION} ]]; then | ||
| PYTHON_VERSION=`python2.7 -c ' | ||
| import sys; | ||
| print(".".join(map(str, sys.version_info[:2])))'` | ||
| fi | ||
| if [[ -z ${PYTHON_USER_BASE} ]]; then | ||
| PYTHON_USER_BASE=`python2.7 -c 'import site; print(site.USER_BASE)'` | ||
| PYTHON_USER_BASE=${HOME}/python | ||
| fi | ||
| if [[ -z ${PYTHON_USER_SITE} ]]; then | ||
| PYTHON_USER_SITE=`python2.7 -c 'import site; print(site.USER_SITE)'` | ||
| PYTHON_USER_SITE=${HOME}/python/lib/python2.7/site-packages | ||
| fi | ||
| # create local directories | ||
| mkdir -p ${PYTHON_USER_SITE} 1>/dev/null | ||
| export PATH=$PATH:/usr/local/cuda/bin/ | ||
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| echo ${PYTHON_USER_BASE} | ||
| echo ${PYTHON_USER_SITE} | ||
| git clone https://github.com/Theano/libgpuarray.git | ||
| cd libgpuarray | ||
| rm -rf build Build | ||
| mkdir Build | ||
| cd Build | ||
| cmake .. -DCMAKE_INSTALL_PREFIX=~/opt/GravitySpy-py27 -DCMAKE_BUILD_TYPE=Release | ||
| make | ||
| make install | ||
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| # install pip | ||
| which pip &>/dev/null || easy_install -U --prefix=${PYTHON_USER_BASE} pip | ||
| export PATH=${PATH}:${PYTHON_USER_BASE}/bin | ||
| cd .. | ||
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| # install virtualenv | ||
| pip install "virtualenv" --prefix=${PYTHON_USER_BASE} | ||
| echo "Virtualenv is now installed" | ||
| # Run the following export and add them in your ~/.bashrc file | ||
| export CPATH=$CPATH:~/opt/GravitySpy-py27/include | ||
| export LIBRARY_PATH=$LIBRARY_PATH:~/opt/GravitySpy-py27/lib | ||
| export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/opt/GravitySpy-py27/lib | ||
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| # -- create virtualenv | ||
| virtualenv $target --system-site-packages --clear | ||
| . $target/bin/activate | ||
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| # Upgrading pip | ||
| pip install pip --upgrade | ||
| pip install -r $packagefile | ||
| python setup.py build | ||
| python setup.py install --prefix=~/opt/GravitySpy-py27/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,37 +1,78 @@ | ||
| #!/usr/bin/env python | ||
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| import ConfigParser | ||
| import optparse | ||
| import argparse | ||
| import os | ||
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| from matplotlib import use | ||
| use('agg') | ||
| from matplotlib import (pyplot as plt, cm) | ||
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| import gravityspy.ML.make_pickle_for_linux as make_pickle | ||
| import gravityspy.ML.train_classifier as train_classifier | ||
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| # Definite Command line arguments here | ||
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| def parse_commandline(): | ||
| """Parse the options given on the command-line. | ||
| """ | ||
| parser = optparse.OptionParser() | ||
| parser.add_option("--path-to-golden", help="folder where labeled images live") | ||
| parser.add_option("--path-to-pickle", help="folder where pickled files will live") | ||
| parser.add_option("--path-to-trained-model", help="folder where the training model will live.") | ||
| parser.add_option("--batch-size", type=int, default=30,help="defines the batch size, 30 is a reasonable size") | ||
| parser.add_option("--nb-epoch", type=int, default=130,help="defines the number of iterations, 130 is reasonable. You can set it to 100 or below, if you have time concern for training.") | ||
| parser.add_option("--train-flag", type=int, default=0,help="a flag that shows all the golden set should be used for training the ML classifier, if 1, use training, validation and test set from golden set (ML experiments)") | ||
| parser.add_option("--number-of-classes", type=int, help="") | ||
| parser.add_option("--verbose", action="store_true", default=False,help="Run in Verbose Mode") | ||
| opts, args = parser.parse_args() | ||
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| return opts | ||
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| # example script | ||
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| #THEANO_FLAGS=mode=FAST_RUN,device=gpu,floatX=float32 trainmodel --path-to-golden /home/scoughlin/public_html/GravitySpy/TrainingSet2/H1L1/ --path-to-pickle ./pickleddata/ --path-to-trained-model ./model --number-of-classes 22 --batch-size 500 | ||
| opts = parse_commandline() | ||
| make_pickle.main(opts.path_to_golden,opts.path_to_pickle,0,opts.verbose) | ||
| train_classifier.main(opts.batch_size,opts.nb_epoch,opts.train_flag,opts.path_to_pickle,opts.path_to_trained_model,opts.number_of_classes,opts.verbose) | ||
| parser = argparse.ArgumentParser(description= | ||
| "An examples commandline of how to obtain a model is given below: " | ||
| "THEANO_FLAGS=mode=FAST_RUN,device=cuda,floatX=float32 trainmodel " | ||
| "--path-to-trainingset='somedir' --number-of-classes='somenum'") | ||
| parser.add_argument("--path-to-trainingset", | ||
| help="folder where labeled images live", required=True) | ||
| parser.add_argument("--number-of-classes", type=int, | ||
| help="How many classes do you have", required=True) | ||
| parser.add_argument("--path-to-pickle", | ||
| help="folder where the entire pickled training set " | ||
| "will live. This pickle file should be read in " | ||
| "by pandas", default='pickeleddata') | ||
| parser.add_argument("--path-to-trained-model", | ||
| help="folder where the final trained model will go.", | ||
| default='model') | ||
| parser.add_argument("--batch-size", type=int, default=30, | ||
| help="defines the batch size, 30 is a reasonable size") | ||
| parser.add_argument("--nb-epoch", type=int, default=20, | ||
| help="defines the number of iterations, " | ||
| "130 is reasonable. You can set it to 100 or below, " | ||
| "if you have time concern for training.") | ||
| parser.add_argument("--fraction-validation", type=float, default=0.125, | ||
| help="Perentage of trianing set to save for validation") | ||
| parser.add_argument("--fraction-testing", type=float, default=0, | ||
| help="Percentage of training set to save for testing") | ||
| parser.add_argument("--randomseed", type=int, default=1986, | ||
| help="Set random seed") | ||
| parser.add_argument("--verbose", action="store_true", default=False, | ||
| help="Run in Verbose Mode") | ||
| args = parser.parse_args() | ||
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| return args | ||
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| # Parse commandline | ||
| args = parse_commandline() | ||
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| # Pixelate and pickle the traiing set images | ||
| train_classifier.pickle_trainingset( | ||
| path_to_trainingset=args.path_to_trainingset, | ||
| save_address=args.path_to_pickle, | ||
| verbose=args.verbose | ||
| ) | ||
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| # Check if teting percentage is 0, set to None | ||
| if not args.fraction_testing: | ||
| fraction_testing = None | ||
| else: | ||
| fraction_testing = args.fraction_testing | ||
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| # Train model | ||
| train_classifier.make_model( | ||
| data=os.path.join(args.path_to_pickle, 'trainingset.pkl'), | ||
| model_folder=args.path_to_trained_model, | ||
| batch_size=args.batch_size, | ||
| nb_epoch=args.nb_epoch, | ||
| nb_classes=args.number_of_classes, | ||
| fraction_validation=args.fraction_validation, | ||
| fraction_testing=fraction_testing, | ||
| best_model_based_validset=0, | ||
| image_size=[140, 170], | ||
| random_seed=args.randomseed, | ||
| verbose=True | ||
| ) |
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