ch2_result_center = np.mean(centers, axis=0)
ch2_result_radius = np.max(
np.sqrt((centers - ch2_result_center)**2))
sid = ch2['slice_id']
slice2roi[pid][sid] = {
'roi_center': tuple(ch2_result_center),
'roi_radii': (ch2_result_radius, ch2_result_radius)
}
filename = data_path.split('/')[-1] + '_slice2roi_joni.pkl'
with open(filename, 'w') as f:
pickle.dump(slice2roi, f)
print 'saved to ', filename
return slice2roi
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
required = parser.add_argument_group('required arguments')
#required.add_argument('-c', '--config',
# help='configuration to run',
# required=True)
args = parser.parse_args()
data_paths = [PKL_TRAIN_DATA_PATH, PKL_TEST_DATA_PATH]
log_path = LOGS_PATH + "generate_roi.log"
with print_to_file(log_path):
for d in data_paths:
get_slice2roi(d, plot=True)
print "log saved to '%s'" % log_path
centers = np.array(ch2_centers)
ch2_result_center = np.mean(centers, axis=0)
ch2_result_radius = np.max(np.sqrt((centers - ch2_result_center) ** 2))
sid = ch2["slice_id"]
slice2roi[pid][sid] = {
"roi_center": tuple(ch2_result_center),
"roi_radii": (ch2_result_radius, ch2_result_radius),
}
filename = data_path.split("/")[-1] + "_slice2roi_joni.pkl"
with open(filename, "w") as f:
pickle.dump(slice2roi, f)
print "saved to ", filename
return slice2roi
if __name__ == "__main__":
parser = argparse.ArgumentParser(description=__doc__)
required = parser.add_argument_group("required arguments")
# required.add_argument('-c', '--config',
# help='configuration to run',
# required=True)
args = parser.parse_args()
data_paths = [PKL_TRAIN_DATA_PATH, PKL_TEST_DATA_PATH]
log_path = LOGS_PATH + "generate_roi.log"
with print_to_file(log_path):
for d in data_paths:
get_slice2roi(d, plot=True)
print "log saved to '%s'" % log_path
)
train_data["intermediates"] = iter_train(0)
pickle.dump(train_data, open(metadata_path + "-dump", "wb"))
return
if __name__ == "__main__":
parser = argparse.ArgumentParser(description=__doc__)
required = parser.add_argument_group('required arguments')
required.add_argument('-c', '--config',
help='configuration to run',
required=True)
args = parser.parse_args()
set_configuration(args.config)
expid = utils.generate_expid(args.config)
log_file = LOGS_PATH + "%s.log" % expid
with print_to_file(log_file):
print "Running configuration:", config().__name__
print "Current git version:", utils.get_git_revision_hash()
train_model(expid)
print "log saved to '%s'" % log_file
predict_model(expid)
print "log saved to '%s'" % log_file