def init(cfg):
save_path = cfg.save_path + cfg.save_dir_prefix + str(
cfg.experiment_idx).zfill(3)
mkdir(save_path)
trial_id = (len([dir for dir in os.listdir(save_path) if 'trial' in dir]) +
1) if cfg.trial_id is None else cfg.trial_id
trial_save_path = save_path + '/trial_' + str(trial_id)
if not os.path.isdir(trial_save_path):
mkdir(trial_save_path)
copytree(os.getcwd(),
trial_save_path + '/source_code',
ignore=ignore_patterns('*.git', '*.txt', '*.tif', '*.pkl',
'*.off', '*.so', '*.json', '*.jsonl',
'*.log', '*.patch', '*.yaml', 'wandb',
'run-*'))
seed = trial_id
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
torch.backends.cudnn.enabled = True # speeds up the computation
return trial_save_path, trial_id
def test(unet, all_data, sampler, save_path):
# result parent dir
save_path = save_path + '/IoUs'
mkdir(save_path)
all_results = {}
for tag, d in all_data.items():
logger.info(tag + ' set evaluation...')
results = dict()
loss = compute_loss(d.x, d.seed, d.y, results, sampler, unet.config.num_classes, unet, d.seed_ids)
all_results[tag] = {'loss':loss, 'predictions':results}
save_line(list_to_string(loss), save_path + '/' + tag + '_IoU.txt')
return all_results
def evaluate(self, epoch, writer=None, backup_writer=None):
# self.net = self.net.eval()
performences = {}
predictions = {}
for split in [DataModes.TESTING]:
dataloader = DataLoader(self.data[split],
batch_size=1,
shuffle=False)
performences[split], predictions[split] = self.evaluate_set(
dataloader)
write_to_wandb(writer, epoch, split, performences,
self.config.num_classes)
if self.support.update_checkpoint(best_so_far=self.current_best,
new_value=performences):
mkdir(self.save_path)
mkdir(self.save_path + '/mesh')
mkdir(self.save_path + '/voxels')
self.save_model(epoch)
self.save_results(predictions[DataModes.TESTING], epoch,
performences[DataModes.TESTING], self.save_path,
'/testing_')
self.current_best = performences
def write_to_disk_em(synapse_list, unet, save_at, mode, results_for_log):
gap = np.ones((388, 20))
cmap = plt.get_cmap('jet')
jc_sum_all = np.zeros(unet.config.num_classes)
jc_count_all = 0
save_at = save_at + '/' + mode
for syn in synapse_list:
syn_path = save_at + '/' + syn
mkdir(syn_path)
mkdir(syn_path + '/y_hat')
mkdir(syn_path + '/y_hat_overlayed')
jc_sum, count = synapse_list[syn].IoU()
jc_sum_all += jc_sum
jc_count_all += count
save_line(list_to_string(jc_sum/count), syn_path + '/jaccard_average_synapse.txt')
for slice in synapse_list[syn].slices:
y_hat = 255 * slice.y_hat / unet.config.num_classes
io.imsave(syn_path + '/y_hat/y_hat_' + str(slice.slice_id) + '.png', np.uint8(y_hat))
io.imsave(syn_path + '/y_hat_overlayed/y_hat_overlayed_' + str(slice.slice_id) + '.png', slice.overlayed)
save_line(list_to_string(slice.jaccard_indx), syn_path + '/jaccard_slice.txt')
save_line(str(slice.slice_id) + ' : ' + list_to_string(slice.center), syn_path + '/centers.txt')
jc_avg = jc_sum_all/jc_count_all
for i in range(unet.config.num_classes):
results_for_log[mode + '_jaccard_index_' + str(i)] = jc_avg[i]
save_line(list_to_string(jc_avg), save_at + '/jaccard_average_all.txt')
def save_predictions(iter, all_results, unet, save_path):
results_for_log = dict()
# result parent dir
if unet.config.more_options.synapse_layer_mode=='synapse_dtf':
save_path = save_path + '/doc_manual_label_synapses_dtf'
elif unet.config.more_options.synapse_layer_mode=='center_dot_dtf':
save_path = save_path + '/doc_manual_label_center_dot_dtf'
mkdir(save_path)
# result dir for the niter
save_path = save_path + '/itr_' + str(iter)
mkdir(save_path)
for tag, results in all_results.items():
mkdir(save_path + '/' + tag)
if unet.config.more_options.dataset_name == 'EM':
write_to_disk_em(results['predictions'], unet, save_path, tag, results_for_log)
else:
write_to_disk(results['predictions'], unet, save_path, tag, results_for_log)
return results_for_log
def write_to_disk_em_old(synapse_list, unet, save_at, mode, results_for_log):
gap = np.ones((388, 20))
cmap = plt.get_cmap('jet')
jc_sum_all = np.zeros(unet.config.num_classes)
jc_count_all = 0
save_at = save_at + '/' + mode
for syn in synapse_list:
syn_path = save_at + '/' + syn
mkdir(syn_path)
mkdir(syn_path + '/x')
mkdir(syn_path + '/y')
mkdir(syn_path + '/y_hat_heat_map')
mkdir(syn_path + '/y_hat')
mkdir(syn_path + '/y_hat_overlayed')
jc_sum, count = synapse_list[syn].IoU()
jc_sum_all += jc_sum
jc_count_all += count
save_line(list_to_string(jc_sum/count), syn_path + '/jaccard_average_synapse.txt')
for slice in synapse_list[syn].slices:
x = slice.x
io.imsave(syn_path + '/x/x_0' + str(slice.slice_id) + '.png', np.uint8(255 * x[0]))
io.imsave(syn_path + '/x/x_1' + str(slice.slice_id) + '.png', np.uint8(255 * x[1]))
y = 255 * slice.y / unet.config.num_classes
io.imsave(syn_path + '/y/y_' + str(slice.slice_id) + '.png', np.uint8(y))
y_hat = 255 * slice.y_hat / unet.config.num_classes
io.imsave(syn_path + '/y_hat/y_hat_' + str(slice.slice_id) + '.png', np.uint8(y_hat))
heat_maps = slice.y_hat_heat_map
color_heat_maps = [np.delete(cmap(map), 3, 2) for map in heat_maps]
#color_heat_maps = np.concatenate( (color_heat_maps[0], gap3, color_heat_maps[1], gap3, color_heat_maps[2]), axis=1)
color_heat_maps = np.concatenate( [np.concatenate((map, np.ones((map.shape[0], 20, 3))), axis=1) for map in color_heat_maps ], axis=1)
color_heat_maps = np.uint8(255 * color_heat_maps)
io.imsave(syn_path + '/y_hat_heat_map/y_hat_heat_map_' + str(slice.slice_id) + '.png', color_heat_maps)
io.imsave(syn_path + '/y_hat_overlayed/y_hat_overlayed_' + str(slice.slice_id) + '.png', slice.overlayed)
save_line(list_to_string(slice.jaccard_indx), syn_path + '/jaccard_slice.txt')
save_line(str(slice.slice_id) + ' : ' + list_to_string(slice.center), syn_path + '/centers.txt')
jc_avg = jc_sum_all/jc_count_all
for i in range(unet.config.num_classes):
results_for_log[mode + '_jaccard_index_' + str(i)] = jc_avg[i]
save_line(list_to_string(jc_avg), save_at + '/jaccard_average_all.txt')