import torch import torch.nn.functional as F import random import numpy as np from src.utils.util import _bbox_mask from src.utils import scribble, boundary_selection from .trainer_basic import Trainer_basic class Trainer(Trainer_basic): def __init__(self, args, logger): super().__init__(args, logger) def forward(self, sam_model, image, label, iter_nums, train=False, return_each_iter=False): if return_each_iter: return_mask_total_iter = torch.zeros([iter_nums, 1, image.size(2), image.size(3), image.size(4)]) image_embedding, feature_list = self.sam.image_encoder(image) self.click_points = [] self.click_labels = [] return_loss = 0 prev_masks = torch.zeros_like(label, dtype=torch.float).to(label.device) for iter_num in range(iter_nums): loss = 0 prev_masks_sigmoid = torch.sigmoid(prev_masks) if iter_num > 0 else prev_masks points_input, labels_input, box_input = self.get_points(prev_masks_sigmoid, label, train_mode=train) mask, dice_pred = self.iteration_forward(sam_model, feature_list, image_embedding, prev_masks, points=[points_input, labels_input], boxes=box_input) # ======================================================== if self.args.multiple_outputs: dice_pred_best, max_label_index = torch.max(dice_pred, dim=1) mask_list = [mask[i, max_label_index[i], :].unsqueeze(0) for i in range(mask.size(0))] mask_best = torch.stack(mask_list, dim=0) else: mask_best = mask # ======================================================== if train: if self.args.multiple_outputs: for i in range(mask.size(1)): single_mask, single_dice = mask[:, i, :].unsqueeze(1), dice_pred[:, i] loss += self.calculate_loss(single_mask, prev_masks, single_dice, label, labels_input, iter_num) else: loss = self.calculate_loss(mask, prev_masks, dice_pred[:, 0], label, labels_input, iter_num) # ======================================================== if self.args.refine: if self.args.no_detach: mask_refine, error_map = self.sam.mask_decoder.refine(image, mask_best, [self.click_points, self.click_labels], mask_best) else: mask_refine, error_map = self.sam.mask_decoder.refine(image, mask_best, [self.click_points, self.click_labels], mask_best.detach()) print('dice before refine {} and after {}'.format( self.get_dice_score(torch.sigmoid(mask_best), label), self.get_dice_score(torch.sigmoid(mask_refine), label))) # ======================================================== loss += self.loss_segmentation(mask_refine, label) * 1 mask_best = mask_refine # ======================================================== else: if self.args.refine: if self.args.no_detach: mask_refine, error_map = self.sam.mask_decoder.refine(image, mask_best, [self.click_points, self.click_labels], mask_best) else: mask_refine, error_map = self.sam.mask_decoder.refine(image, mask_best, [self.click_points, self.click_labels], mask_best.detach()) if iter_num == iter_nums - 1 or iter_num == 0: self.logger.info('dice before refine {} and after {}, label 0: {}, label 1: {}'.format( self.get_dice_score(torch.sigmoid(mask_best), label), self.get_dice_score(torch.sigmoid(mask_refine), label), str(labels_input.numel() - torch.count_nonzero(labels_input)), str(torch.count_nonzero(labels_input)) ) ) mask_best = mask_refine loss = self.get_dice_score(torch.sigmoid(mask_best), label) return_loss += loss prev_masks = mask_best if return_each_iter: return_mask_total_iter[iter_num, :] = mask_best if return_each_iter: return return_loss / iter_nums, return_mask_total_iter else: return return_loss / iter_nums, prev_masks def get_points(self, prev_masks, label, train_mode=True): mode = 'train' if train_mode else 'validation' batch_points, batch_labels = self.get_next_point(prev_masks, label, mode=mode) points_co = torch.cat(batch_points, dim=0).to(self.args.device) # b x num_clicks x 3 points_la = torch.cat(batch_labels, dim=0).to(self.args.device) # b x num_clicks x 1 self.click_points.append(points_co) self.click_labels.append(points_la) points_input = points_co labels_input = points_la bbox_coords = _bbox_mask(label[:, 0, :], mode=mode, dynamic=self.args.dynamic_box).to(self.args.device) if self.args.use_box else None return points_input, labels_input, bbox_coords def get_next_point(self, prev_seg, label, mode='train'): # prev_seg --> probability batch_points = [] batch_labels = [] pred_masks = (prev_seg > 0.5) true_masks = (label > 0) fn_masks = torch.logical_and(true_masks, torch.logical_not(pred_masks)) fp_masks = torch.logical_and(torch.logical_not(true_masks), pred_masks) to_point_mask = torch.logical_or(fn_masks, fp_masks) # do_scribble = random.random() # sample_method = random.choice(['line', 'center', 'default']) sample_method = 'center' scribble_types = { 'line': 'LineScribble', 'center': 'CenterlineScribble', 'default': 'ContourScribble' } def create_scribble_mask(scribble_type, data): scribble_object = getattr(scribble, scribble_type)() scribble_mask = scribble_object.batch_scribble(data).permute(1, 2, 3, 0) return scribble_mask > 0 points_list = [len(torch.argwhere(to_point_mask[i])) for i in range(to_point_mask.size(0))] points_min = min(points_list) num_clicks = self.args.num_clicks if mode == 'train' else self.args.num_clicks_validation click_size = points_min if num_clicks > points_min else num_clicks dynamic_size = random.randint(1, click_size) if self.args.dynamic and mode == 'train' else click_size print(f"num_clicks {num_clicks} points_length: {points_min} dynamic_size: {dynamic_size}") for i in range(label.shape[0]): bp_list, bl_list = [], [] points = torch.argwhere(to_point_mask[i]) point_index = np.random.choice(len(points), size=dynamic_size, replace=False) points_select = points[point_index] # each row tensor([0, x, y, z]), size --> num_clicks x 4 for click_index in range(dynamic_size): point = points_select[click_index] if fn_masks[i, 0, point[1], point[2], point[3]]: is_positive = True else: is_positive = False bp = point[1:].clone().detach().reshape(1, 1, 3) bl = torch.tensor([int(is_positive), ]).reshape(1, 1) bp_list.append(bp) bl_list.append(bl) if self.args.use_scribble: fg, bg_orig = fn_masks[i].permute(3, 0, 1, 2).float(), fp_masks[i].permute(3, 0, 1, 2).float() # ====== with the purpose of efficiency only for first few epochs ====== bbx = _bbox_mask(label[i, 0, :].unsqueeze(0)) diff_ = 15 i_min, i_max = bbx[:, :, 0], bbx[:, :, 3] j_min, j_max = bbx[:, :, 1], bbx[:, :, 4] k_min, k_max = bbx[:, :, 2], bbx[:, :, 5] if max(0, i_min - diff_) < min(i_max + diff_, 126): i_min, i_max = max(0, i_min - diff_), min(i_max + diff_, 126) if max(0, j_min - diff_) < min(j_max + diff_, 126): j_min, j_max = max(0, j_min - diff_), min(j_max + diff_, 126) if max(0, k_min - diff_) < min(k_max + diff_, 126): k_min, k_max = max(0, k_min - diff_), min(k_max + diff_, 126) bg_mask = torch.zeros_like(bg_orig).permute(1, 2, 3, 0) bg_mask[:, i_min:i_max, j_min:j_max, k_min:k_max] = 1 bg = bg_orig * bg_mask.permute(3, 0, 1, 2) print('filter out voxels: {}'.format(torch.count_nonzero(bg_orig) - torch.count_nonzero(bg))) scribble_type = scribble_types.get(sample_method, scribble_types['default']) scribble_mask_fg = create_scribble_mask(scribble_type, fg) limit_num = 500 if torch.count_nonzero(scribble_mask_fg) >= limit_num + 50: a = torch.argwhere(scribble_mask_fg).size(0) - limit_num random_number = random.randint(0, a) fg_coors = torch.argwhere(scribble_mask_fg)[:, 1:].unsqueeze(0)[:, random_number: random_number + limit_num, :] # for computation only else: fg_coors = torch.argwhere(scribble_mask_fg)[:, 1:].unsqueeze(0) fg_coors_label = torch.ones(1, fg_coors.size(1)) bp_list.append(fg_coors) bl_list.append(fg_coors_label) scribble_mask_bg = create_scribble_mask(scribble_type, bg) if torch.count_nonzero(scribble_mask_bg) >= limit_num + 50: # dynamic_size is 50 a = torch.argwhere(scribble_mask_bg).size(0) - limit_num random_number = random.randint(0, a) bg_coors = torch.argwhere(scribble_mask_bg)[:, 1:].unsqueeze(0)[:, random_number: random_number + limit_num, :] else: bg_coors = torch.argwhere(scribble_mask_bg)[:, 1:].unsqueeze(0) bg_coors_label = torch.zeros(1, bg_coors.size(1)) bp_list.append(bg_coors) bl_list.append(bg_coors_label) batch_points.append(torch.cat(bp_list, dim=1)) batch_labels.append(torch.cat(bl_list, dim=1)) # for scribble if self.args.use_scribble: smallest_n = min(tensor.size(1) for tensor in batch_labels) batch_points = [tensor[:, :smallest_n] if tensor.size(1) > smallest_n else tensor for tensor in batch_points] batch_labels = [tensor[:, :smallest_n] if tensor.size(1) > smallest_n else tensor for tensor in batch_labels] # # Check the shapes of the adjusted tensors # for i, tensor in enumerate(batch_points): # print(f"Tensor {i + 1} shape: {tensor.shape}") print('First batch: fn: {:.4f}, fp: {:.4f}, label 0: {}, label 1: {}'.format( torch.count_nonzero(fn_masks[0]) / torch.count_nonzero(true_masks[0]), torch.count_nonzero(fp_masks[0]) / torch.count_nonzero(true_masks[0]), str(batch_labels[0].numel() - torch.count_nonzero(batch_labels[0])), str(torch.count_nonzero(batch_labels[0])) ) ) print('--- ===================================== ---') print('--- above before model, below after model ---') print('--- ===================================== ---') return batch_points, batch_labels def iteration_forward(self, sam_model, features, image_embedding, prev_masks, points=None, boxes=None): prev_masks = F.interpolate(prev_masks, scale_factor=0.25) features = [features[i].to(self.args.device) for i in range(0, len(features))] new_point_embedding, new_image_embedding = sam_model.prompt_encoder( points=points, boxes=boxes, masks=prev_masks, image_embeddings=image_embedding.to(self.args.device) ) mask, dice_pred = sam_model.mask_decoder( prompt_embeddings=new_point_embedding, # (B, 2, 256) image_embeddings=new_image_embedding, # (B, 256, 64, 64) feature_list=features, ) return mask, dice_pred