def on_menu_reset(self, event):
yes = utils.make_yesno_dlg(_(u'Are you sure you want to reset?'),
_(u'Are you sure?'))
if yes:
configs.load(self, app.get_real_path('default.cfg'))
self.picker.view.path.SetValue(u'')
self.picker.clear_all()
def run_command(command, override_path=None, force=False):
# Nondestructive commands that don't require cache.
if command == Command.configs:
config_list = configs.load(override_path=override_path)
configs.print_configs(config_list)
# Destructive commands that require cache but not configs.
elif command == Command.purge:
file_cache = FileCache(configs.set_up_cache_dir())
file_cache.purge()
# Commands that require cache and configs.
else:
config_list = configs.load(override_path=override_path)
file_cache = FileCache(configs.set_up_cache_dir())
if command == Command.publish:
for config in config_list:
file_cache.publish(config, version_for(config), force=force)
elif command == Command.install:
for config in config_list:
file_cache.install(config, version_for(config), force=force)
else:
raise AssertionError("unknown command: " + command)
def get_environment():
conf = configs.load(ENV_FILE, defaults={'generals': {
'TASKS_PER_SECOND': '1'
}})
return conf['generals'].dict_props
def configure():
# Load config
with open("config.yaml") as config_f:
config = Struct(**yaml.load(config_f))
config = configs.load(config)
# Set up experiment
config.experiment_dir = os.path.join("experiments/%s" % config.name)
if not os.path.exists(config.experiment_dir):
os.mkdir(config.experiment_dir)
files = glob.glob(os.path.join(config.experiment_dir, "*"))
for f in files:
os.remove(f)
# Set up logging
log_name = os.path.join(config.experiment_dir, "run.log")
logging.basicConfig(
filename=log_name, level=logging.DEBUG,
format='%(asctime)s %(levelname)-8s %(message)s')
def handler(type, value, tb):
logging.exception("Uncaught exception: %s", str(value))
logging.exception("\n".join(traceback.format_exception(type, value, tb)))
sys.excepthook = handler
logging.info("BEGIN")
logging.info(str(config))
return config
def load_sources_from_config_file(path):
c = configs.load(path)
srcs = dict()
for s in c['sources']:
props = c[s].dict_props
props['id'] = s
srcs[s] = props
return srcs
def load_configs(self, configurations=None):
if not configurations:
configurations = configs.load()
if not "token" in configurations:
raise Exception("'token' not found on loaded configurations.")
if not "req_updates_timeout_sec" in configurations:
raise Exception(
"'req_updates_timeout_sec' not found on loaded configurations."
)
self.token = configurations["token"]
self.req_updates_timeout_sec = configurations[
"req_updates_timeout_sec"]
self.url = "https://api.telegram.org/bot{}/".format(
configurations["token"])
def __init__(self):
"""Initialization interface."""
self.config = configs.Config()
with open('languages.dat', 'rb') as lang_file:
lang_dict = pickle.load(lang_file)
self.config.set_languages(lang_dict['languages'])
self.phrases = configs.load(
lang_dict[self.config.general_language])
super().__init__(None, wx.ID_ANY, self.phrases.titles.caption)
self.command = Commands(self)
self.menu = Menu(self)
self.panel = wx.Panel(self, wx.ID_ANY)
sizer_panel = wx.BoxSizer(wx.HORIZONTAL)
sizer_panel.Add(self.panel, 1, wx.EXPAND | wx.ALL)
self.SetSizer(sizer_panel)
self.CreateStatusBar()
self.__create_widgets()
self.__create_bindings()
self.set_values()
def train(config=None, gpu_queue=None):
try:
gpu_idx = maybe_get_a_gpu() if gpu_queue is None else gpu_queue.get()
os.environ["CUDA_VISIBLE_DEVICES"] = gpu_idx
except Exception as e:
print(str(e))
day, hour = timestamp(separate=True)
out_dir = os.path.join("models", config["model_name"],
config.get("model_type", ""), day, hour)
os.makedirs(out_dir, exist_ok=True)
configs.deep_update(config, {"out_dir": out_dir})
configs.add(config, to=".running")
model = MODELS[config["model_name"]](config)
try:
train_seq = model.get_sequence(config)
eval_seq = model.get_sequence(config, istraining=False)
configs.deep_update(config, {
"train_seq": train_seq,
"eval_seq": eval_seq
})
checkpoints = out_dir + '/inter_model_{epoch:02d}-{val_loss:.4f}.h5'
if "RNN" in config["model_name"]:
configs.deep_update(config,
{"reset_batches": train_seq.reset_batches})
configs.deep_update(config, {"filepath": checkpoints})
if 'Trackifier' in config['model_name']:
configs.deep_update(config, {"filepath": checkpoints})
callbacks = parse_callbacks(config["callbacks"])
optimizer = getattr(keras_optimizers,
config["optimizer"])(**config["opt_params"])
model.compile(optimizer)
if isinstance(config['train_path'], list):
for i, subject in enumerate(config['train_path']):
samples_config = os.path.join(os.path.dirname(subject),
'config.yml')
samples_config = configs.load(samples_config)
config['input_sampels_config_{0}'.format(i)] = samples_config
else:
samples_config = os.path.join(
os.path.dirname(config['train_path']), 'config.yml')
samples_config = configs.load(samples_config)
config['input_sampels_config'] = samples_config
repo = git.Repo(".")
commit = repo.head.commit
config['commit'] = str(commit)
configs.save(config)
print("\nStart training...")
no_exception = True
model.keras.fit_generator(
train_seq,
callbacks=callbacks,
validation_data=eval_seq,
epochs=config["epochs"],
shuffle=config["shuffle"],
max_queue_size=2000,
verbose=1,
workers=5,
use_multiprocessing=True,
)
except KeyboardInterrupt:
model.stop_training = True
except Exception as e:
shutil.rmtree(out_dir)
no_exception = False
raise e
finally:
configs.remove(config, _from=".running")
if no_exception:
configs.add(config, to=".archive")
model_path = os.path.join(out_dir, "final_model.h5")
print("\nSaving {}".format(model_path))
model.keras.save(model_path)
if gpu_queue is not None:
gpu_queue.put(gpu_idx)
return model.keras
def load_config(self, event):
configs.load(self)
def on_menu_reset(self, event):
yes = utils.make_yesno_dlg(_(u'Are you sure you want to reset?'), _(u'Are you sure?'))
if yes:
configs.load(self, app.get_real_path('default.cfg'))
self.picker.view.path.SetValue(u'')
self.picker.clear_all()
def load_config(self, event):
configs.load(self)
def run_rf_inference(config=None, gpu_queue=None):
""""""
try:
gpu_idx = maybe_get_a_gpu() if gpu_queue is None else gpu_queue.get()
os.environ["CUDA_VISIBLE_DEVICES"] = gpu_idx
except Exception as e:
print(str(e))
print(
"Loading DWI...") ####################################################
dwi_img = nib.load(config['dwi_path'])
dwi_img = nib.funcs.as_closest_canonical(dwi_img)
dwi_aff = dwi_img.affine
dwi_affi = np.linalg.inv(dwi_aff)
dwi = dwi_img.get_data()
def xyz2ijk(coords, snap=False):
ijk = (coords.T).copy()
dwi_affi.dot(ijk, out=ijk)
if snap:
return np.round(ijk, out=ijk).astype(int, copy=False).T
else:
return ijk.T
with open(os.path.join(config['model_dir'], 'model'), 'rb') as f:
model = pickle.load(f)
train_config_file = os.path.join(config['model_dir'], 'config.yml')
bvec_path = configs.load(train_config_file, 'bvecs')
_, bvecs = read_bvals_bvecs(None, bvec_path)
terminator = Terminator(config['term_path'], config['thresh'])
prior = Prior(config['prior_path'])
print(
"Initializing Fibers...") ############################################
seed_file = nib.streamlines.load(config['seed_path'])
xyz = seed_file.tractogram.streamlines.data
n_seeds = 2 * len(xyz)
xyz = np.vstack([xyz, xyz]) # Duplicate seeds for both directions
xyz = np.hstack([xyz, np.ones([n_seeds, 1])]) # add affine dimension
xyz = xyz.reshape(-1, 1, 4) # (fiber, segment, coord)
fiber_idx = np.hstack([
np.arange(n_seeds // 2, dtype="int32"),
np.arange(n_seeds // 2, dtype="int32")
])
fibers = [[] for _ in range(n_seeds // 2)]
print(
"Start Iteration...") ################################################
input_shape = model.n_features_
block_size = int(np.cbrt(input_shape / dwi.shape[-1]))
d = np.zeros([n_seeds, dwi.shape[-1] * block_size**3])
dnorm = np.zeros([n_seeds, 1])
vout = np.zeros([n_seeds, 3])
for i in range(config['max_steps']):
t0 = time()
# Get coords of latest segement for each fiber
ijk = xyz2ijk(xyz[:, -1, :], snap=True)
n_ongoing = len(ijk)
for ii, idx in enumerate(ijk):
d[ii] = dwi[idx[0] - (block_size // 2):idx[0] + (block_size // 2) +
1, idx[1] - (block_size // 2):idx[1] +
(block_size // 2) + 1,
idx[2] - (block_size // 2):idx[2] + (block_size // 2) +
1, :].flatten() # returns copy
dnorm[ii] = np.linalg.norm(d[ii])
d[ii] /= dnorm[ii]
if i == 0:
inputs = np.hstack(
[prior(xyz[:, 0, :]), d[:n_ongoing], dnorm[:n_ongoing]])
else:
inputs = np.hstack(
[vout[:n_ongoing], d[:n_ongoing], dnorm[:n_ongoing]])
chunk = 2**15 # 32768
n_chunks = np.ceil(n_ongoing / chunk).astype(int)
for c in range(n_chunks):
outputs = model.predict(inputs[c * chunk:(c + 1) * chunk])
v = bvecs[outputs, ...]
vout[c * chunk:(c + 1) * chunk] = v
rout = xyz[:, -1, :3] + config['step_size'] * vout
rout = np.hstack([rout, np.ones((n_ongoing, 1))]).reshape(-1, 1, 4)
xyz = np.concatenate([xyz, rout], axis=1)
terminal_indices = terminator(xyz[:, -1, :])
for idx in terminal_indices:
gidx = fiber_idx[idx]
# Other end not yet added
if not fibers[gidx]:
fibers[gidx].append(np.copy(xyz[idx, :, :3]))
# Other end already added
else:
this_end = xyz[idx, :, :3]
other_end = fibers[gidx][0]
merged_fiber = np.vstack(
[np.flip(this_end[1:], axis=0),
other_end]) # stitch ends together
fibers[gidx] = [merged_fiber]
xyz = np.delete(xyz, terminal_indices, axis=0)
vout = np.delete(vout, terminal_indices, axis=0)
fiber_idx = np.delete(fiber_idx, terminal_indices)
print(
"Iter {:4d}/{}, finished {:5d}/{:5d} ({:3.0f}%) of all seeds with"
" {:6.0f} steps/sec".format(
(i + 1), config['max_steps'], n_seeds - n_ongoing, n_seeds,
100 * (1 - n_ongoing / n_seeds), n_ongoing / (time() - t0)),
end="\r")
if n_ongoing == 0:
break
gc.collect()
# Include unfinished fibers:
fibers = [
fibers[gidx] for gidx in range(len(fibers)) if gidx not in fiber_idx
]
# Save Result
fibers = [f[0] for f in fibers]
tractogram = Tractogram(streamlines=ArraySequence(fibers),
affine_to_rasmm=np.eye(4))
timestamp = datetime.datetime.now().strftime("%Y-%m-%d-%H:%M:%S")
out_dir = os.path.join(os.path.dirname(config["dwi_path"]),
"predicted_fibers", timestamp)
configs.deep_update(config, {"out_dir": out_dir})
os.makedirs(out_dir, exist_ok=True)
fiber_path = os.path.join(out_dir, timestamp + ".trk")
print("\nSaving {}".format(fiber_path))
TrkFile(tractogram, seed_file.header).save(fiber_path)
config_path = os.path.join(out_dir, "config.yml")
print("Saving {}".format(config_path))
with open(config_path, "w") as file:
yaml.dump(config, file, default_flow_style=False)
if config["score"]:
score_on_tm(fiber_path)
return tractogram
def getConfig(self):
try:
self.config = configs.load(self.configFile())
return self.config
except Exception:
self.getLogger().exception('Error: ')
os.makedirs(out_dir, exist_ok=True)
config_path = os.path.join(out_dir, "config" + ".yml")
print("Saving {}".format(config_path))
with open(config_path, "w") as file:
yaml.dump(configs, file, default_flow_style=False)
model_path = os.path.join(out_dir, 'model')
print("Saving {}".format(model_path))
with open(model_path, 'wb') as f:
pickle.dump(clf, f)
return clf, inputs, outputs, output_classes
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Train the entrack model")
parser.add_argument("config_path", type=str, nargs="?",
help="Path to model config.")
parser.add_argument("--max_n_samples", type=int,
help="Maximum number of samples to be used for both "
"training and evaluation")
args = parser.parse_args()
configs = load(args.config_path)
if args.max_n_samples is not None:
configs['max_n_samples'] = args.max_n_samples
train_model(configs)
