Diff of /test_fpred_scan.py [000000] .. [70b6b3]

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a b/test_fpred_scan.py
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import sys
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import lasagne as nn
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import numpy as np
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import theano
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import pathfinder
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import utils
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from configuration import config, set_configuration
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from utils_plots import plot_slice_3d_3
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import theano.tensor as T
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import utils_lung
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import blobs_detection
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import logger
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from collections import defaultdict
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theano.config.warn_float64 = 'raise'
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if len(sys.argv) < 2:
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    sys.exit("Usage: test_luna_scan.py <configuration_name>")
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config_name = sys.argv[1]
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set_configuration('configs_fpred_scan', config_name)
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# predictions path
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predictions_dir = utils.get_dir_path('model-predictions', pathfinder.METADATA_PATH)
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outputs_path = predictions_dir + '/%s' % config_name
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utils.auto_make_dir(outputs_path)
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# logs
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logs_dir = utils.get_dir_path('logs', pathfinder.METADATA_PATH)
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sys.stdout = logger.Logger(logs_dir + '/%s.log' % config_name)
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sys.stderr = sys.stdout
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# builds model and sets its parameters
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model = config().build_model()
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x_shared = nn.utils.shared_empty(dim=len(model.l_in.shape))
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givens_valid = {}
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givens_valid[model.l_in.input_var] = x_shared
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get_predictions_patch = theano.function([],
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                                        nn.layers.get_output(model.l_out, deterministic=True),
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                                        givens=givens_valid,
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                                        on_unused_input='ignore')
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data_iterator = config().data_iterator
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print
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print 'Data'
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print 'n samples: %d' % data_iterator.nsamples
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nblob2prob, nblob2label = {}, {}
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pid2candidates = defaultdict(list)
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for n, (x, candidate_zyxd, id) in enumerate(data_iterator.generate()):
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    pid = id[0]
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    x_shared.set_value(x)
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    predictions = get_predictions_patch()
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    label = candidate_zyxd[-1]
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    p1 = predictions[0][1]
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    nblob2prob[n] = p1
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    nblob2label[n] = label
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    candidate_zyxdp = np.append(candidate_zyxd, [[p1]])
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    pid2candidates[pid].append(candidate_zyxdp)
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for k in pid2candidates.iterkeys():
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    candidates = np.asarray(pid2candidates[k])
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    candidates_wo_dupes = utils_lung.filter_close_neighbors(candidates)
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    a = np.asarray(sorted(candidates_wo_dupes, key=lambda x: x[-1], reverse=True))
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    utils.save_pkl(a, outputs_path + '/%s.pkl' % k)