mk quick start

config.json

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+{
+  "architectures": [
+    "SegVolModel"
+  ],
+  "auto_map": {
+    "AutoConfig": "model_segvol_single.SegVolConfig",
+    "AutoModel": "model_segvol_single.SegVolModel"
+  },
+  "model_type": "segvol",
+  "patch_size": [
+    4,
+    16,
+    16
+  ],
+  "spatial_size": [
+    32,
+    256,
+    256
+  ],
+  "test_mode": true,
+  "torch_dtype": "float32",
+  "transformers_version": "4.18.0"
+}

model_segvol_single.py

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+from transformers import PreTrainedModel, PretrainedConfig
+import numpy as np
+import monai.transforms as transforms
+import nibabel as nib
+from scipy import sparse
+import ast
+
+class SegVolConfig(PretrainedConfig):
+    model_type = "segvol"
+
+    def __init__(
+        self,
+        test_mode=True,
+        **kwargs,
+    ):
+        self.spatial_size = [32, 256, 256]
+        self.patch_size = [4, 16, 16]
+        self.test_mode = test_mode
+        super().__init__(**kwargs)
+
+class SegVolModel(PreTrainedModel):
+    config_class = SegVolConfig
+
+    def __init__(self, config):
+        super().__init__(config)
+        sam_model = _build_sam(
+            image_encoder_type='vit',
+            embed_dim = 768,
+            patch_size=self.config.patch_size,
+            checkpoint=None,
+            image_size=self.config.spatial_size,
+        )
+        self.model = SegVol(
+            image_encoder=sam_model.image_encoder, 
+            mask_decoder=sam_model.mask_decoder,
+            prompt_encoder=sam_model.prompt_encoder,
+            roi_size=self.config.spatial_size,
+            patch_size=self.config.patch_size,
+            # clip_model=self.config.clip_model,
+            test_mode=self.config.test_mode,
+            )
+        
+        self.processor = SegVolProcessor(spatial_size=self.config.spatial_size)
+
+    def forward_test(self, 
+                image, 
+                zoomed_image=None, 
+                text_prompt=None, 
+                bbox_prompt_group=None, 
+                point_prompt_group=None, 
+                use_zoom=True,):
+        device = image.device
+        assert image.shape[0] == 1 and zoomed_image.shape[0] == 1, 'batch size should be 1'
+        assert not (text_prompt is None and bbox_prompt_group is None and point_prompt_group is None), 'Drive SegVol using at least one type of prompt'
+        bbox_prompt, bbox_prompt_map, point_prompt, point_prompt_map=None, None, None, None
+        if bbox_prompt_group is not None:
+            bbox_prompt, bbox_prompt_map = bbox_prompt_group
+        if point_prompt_group is not None:
+            point_prompt, point_prompt_map = point_prompt_group
+        volume_shape = image[0][0].shape
+
+        with torch.no_grad():
+            logits_global_single = self.model(zoomed_image,
+                                                text=text_prompt, 
+                                                boxes=bbox_prompt, 
+                                                points=point_prompt)
+        logits_global_single = F.interpolate(
+            logits_global_single.cpu(),
+            size=volume_shape, mode='nearest')
+        if not use_zoom:
+            return logits_global_single
+        
+        if point_prompt_map is not None:
+            binary_points = F.interpolate(
+                point_prompt_map.float(),
+                size=volume_shape, mode='nearest')
+        if bbox_prompt_map is not None:
+            binary_cube = F.interpolate(
+                bbox_prompt_map.float(),
+                size=volume_shape, mode='nearest')
+        
+        min_d, min_h, min_w, max_d, max_h, max_w = logits2roi_coor(self.config.spatial_size, logits_global_single[0][0])
+        if min_d is None:
+            print('Fail to detect foreground!')
+            return logits_global_single
+
+        # Crop roi
+        image_single_cropped = image[:, :, min_d:max_d+1, min_h:max_h+1, min_w:max_w+1]
+        global_preds = (torch.sigmoid(logits_global_single[:, :, min_d:max_d+1, min_h:max_h+1, min_w:max_w+1])>0.5).long()
+        
+        assert not (bbox_prompt is not None and point_prompt is not None), 'Do not use point prompt and box prompt at the same time.'
+        prompt_reflection = None
+        if bbox_prompt is not None:
+            binary_cube_cropped = binary_cube[:, :, min_d:max_d+1, min_h:max_h+1, min_w:max_w+1]
+            prompt_reflection = (
+                binary_cube_cropped,
+                global_preds
+            )
+        if point_prompt is not None:
+            binary_points_cropped = binary_points[:, :, min_d:max_d+1, min_h:max_h+1, min_w:max_w+1]
+            prompt_reflection = (
+                binary_points_cropped,
+                global_preds
+            )
+    
+        ## inference
+        with torch.no_grad():
+            logits_single_cropped = sliding_window_inference(
+                    image_single_cropped.to(device), prompt_reflection,
+                    self.config.spatial_size, 1, self.model, 0.5,
+                    text=text_prompt,
+                    use_box=bbox_prompt is not None,
+                    use_point=point_prompt is not None,
+                )
+            logits_single_cropped = logits_single_cropped.cpu().squeeze()
+        logits_global_single[:, :, min_d:max_d+1, min_h:max_h+1, min_w:max_w+1] = logits_single_cropped
+        return logits_global_single
+
+    def forward_train(self, image, train_organs, train_labels):
+        loss = self.model(image, text=None, boxes=None, points=None,
+                 train_organs=train_organs,
+                 train_labels=train_labels)
+        return loss
+
+    def forward(self, **kwargs):
+        if self.config.test_mode:
+            return self.forward_test(kwargs['image'], 
+                                    kwargs['zoomed_image'], 
+                                    kwargs['text_prompt'], 
+                                    kwargs['bbox_prompt_group'], 
+                                    kwargs['point_prompt_group'], 
+                                    kwargs['use_zoom'])
+        else:
+            return self.forward_train(kwargs['image'],
+                                      kwargs['train_organs'],
+                                      kwargs['train_labels'])
+    
+# processor
+class SegVolProcessor():
+    def __init__(self, spatial_size) -> None:
+        self.img_loader = transforms.LoadImage()
+        self.transform4test = transforms.Compose(
+            [
+                DimTranspose(keys=["image", "label"]),
+                MinMaxNormalization(),
+                transforms.CropForegroundd(keys=["image", "label"], source_key="image"),
+                transforms.ToTensord(keys=["image", "label"]),
+            ]
+        )
+        self.zoom_out_transform = transforms.Resized(keys=["image", "label"], spatial_size=spatial_size, mode='nearest-exact')
+        self.transform4train = transforms.Compose(
+        [
+            # transforms.AddChanneld(keys=["image"]),
+            DimTranspose(keys=["image", "label"]),
+            MinMaxNormalization(),
+            transforms.CropForegroundd(keys=["image", "label"], source_key="image"),
+            transforms.SpatialPadd(keys=["image", "label"], spatial_size=spatial_size, mode='constant'),
+            transforms.OneOf(transforms=[
+                transforms.Resized(keys=["image", "label"],spatial_size=spatial_size),
+                transforms.RandCropByPosNegLabeld(
+                    keys=["image", "label"],
+                    label_key="label",
+                    spatial_size=spatial_size,
+                    pos=2,
+                    neg=1,
+                    num_samples=1,
+                    image_key="image",
+                    image_threshold=0,
+                ),
+                ],
+                weights=[1, 3]
+            ),
+            transforms.RandFlipd(keys=["image", "label"], prob=0.2, spatial_axis=0),
+            transforms.RandFlipd(keys=["image", "label"], prob=0.2, spatial_axis=1),
+            transforms.RandFlipd(keys=["image", "label"], prob=0.2, spatial_axis=2),
+            transforms.RandScaleIntensityd(keys="image", factors=0.2, prob=0.2),
+            transforms.RandShiftIntensityd(keys="image", offsets=0.2, prob=0.2),
+            transforms.ToTensord(keys=["image", "label"]),
+        ]
+    )
+    
+    # ct_path is path for a ct scan file with nii.gz format
+    # gt_path is path for a ground truth file with nii.gz format
+    def preprocess_ct_gt(self, ct_path, gt_path, category):
+        item = {}
+        # generate ct_voxel_ndarray
+        ct_voxel_ndarray, _ = self.img_loader(ct_path)
+        ct_voxel_ndarray = np.array(ct_voxel_ndarray).squeeze()
+        ct_shape = ct_voxel_ndarray.shape
+        ct_voxel_ndarray = np.expand_dims(ct_voxel_ndarray, axis=0)
+        ct_voxel_ndarray = self.ForegroundNorm(ct_voxel_ndarray)
+        item['image'] = ct_voxel_ndarray
+
+        # generate gt_voxel_ndarray
+        gt_voxel_ndarray, _ = self.img_loader(gt_path)
+        gt_voxel_ndarray = np.array(gt_voxel_ndarray)
+        present_categories = np.unique(gt_voxel_ndarray)
+        gt_masks = []
+        for cls_idx in range(len(category)):
+            # ignore background
+            cls = cls_idx + 1
+            if cls not in present_categories:
+                gt_voxel_ndarray_category = np.zeros(ct_shape)
+                gt_masks.append(gt_voxel_ndarray_category)
+            else:
+                gt_voxel_ndarray_category = gt_voxel_ndarray.copy()
+                gt_voxel_ndarray_category[gt_voxel_ndarray != cls] = 0
+                gt_voxel_ndarray_category[gt_voxel_ndarray == cls] = 1
+                gt_masks.append(gt_voxel_ndarray_category)
+        gt_voxel_ndarray = np.stack(gt_masks, axis=0)
+        assert gt_voxel_ndarray.shape[0] == len(category) and gt_voxel_ndarray.shape[1:] == ct_voxel_ndarray.shape[1:]
+        item['label'] = gt_voxel_ndarray.astype(np.int32)
+
+        # transform
+        return item['image'], item['label']
+
+    def load_uniseg_case(self, ct_npy_path, gt_npy_path):
+        img_array = np.load(ct_npy_path)
+        allmatrix_sp= sparse.load_npz(gt_npy_path)
+        if 'mask_' in gt_npy_path:
+            gt_shape = ast.literal_eval(gt_npy_path.split('_')[-1].replace('.npz', ''))
+        else:
+            gt_shape = ast.literal_eval(gt_npy_path.split('.')[-2])
+        gt_array=allmatrix_sp.toarray().reshape(gt_shape)
+        return img_array, gt_array
+
+    def ForegroundNorm(self, ct_narray):
+        ct_voxel_ndarray = ct_narray.copy()
+        ct_voxel_ndarray = ct_voxel_ndarray.flatten()
+        thred = np.mean(ct_voxel_ndarray)
+        voxel_filtered = ct_voxel_ndarray[(ct_voxel_ndarray > thred)]
+        upper_bound = np.percentile(voxel_filtered, 99.95)
+        lower_bound = np.percentile(voxel_filtered, 00.05)
+        mean = np.mean(voxel_filtered)
+        std = np.std(voxel_filtered)
+        ct_narray = np.clip(ct_narray, lower_bound, upper_bound)
+        ct_narray = (ct_narray - mean) / max(std, 1e-8)
+        return ct_narray
+
+    def zoom_transform(self, ct_npy, gt_npy):
+        item = {
+            'image': ct_npy,
+            'label': gt_npy
+        }
+        item = self.transform4test(item)
+        item_zoom_out = self.zoom_out_transform(item)
+        item['zoom_out_image'] = item_zoom_out['image']
+        item['zoom_out_label'] = item_zoom_out['label']
+        return item
+
+    def point_prompt_b(self, label_single_resize, num_positive_extra=4, num_negative_extra=0, device='cpu'):
+        point, point_label = select_points(label_single_resize, num_positive_extra=num_positive_extra, num_negative_extra=num_negative_extra)
+        points_single = (point.unsqueeze(0).float().to(device), point_label.unsqueeze(0).float().to(device)) 
+        binary_points_resize = build_binary_points(point, point_label, label_single_resize.shape).unsqueeze(0).unsqueeze(0)
+        return points_single, binary_points_resize
+    
+    def bbox_prompt_b(self, label_single_resize, device='cpu'):
+        box_single = generate_box(label_single_resize).unsqueeze(0).float().to(device)
+        binary_cube_resize = build_binary_cube(box_single, binary_cube_shape=label_single_resize.shape).unsqueeze(0).unsqueeze(0)
+        return box_single, binary_cube_resize
+
+    def dice_score(self, preds, labels, device='cpu'):
+        assert preds.shape[0] == labels.shape[0], "predict & target batch size don't match\n" + str(preds.shape) + str(labels.shape)
+        predict = preds.view(1, -1).to(device)
+        target = labels.view(1, -1).to(device)
+
+        predict = torch.sigmoid(predict)
+        predict = torch.where(predict > 0.5, 1., 0.)
+        
+        tp = torch.sum(torch.mul(predict, target))
+        den = torch.sum(predict) + torch.sum(target) + 1
+        dice = 2 * tp / den
+        return dice
+    
+    def save_preds(self, ct_path, save_path, logits_mask, start_coord, end_coord):
+        ct = nib.load(ct_path)
+        logits_mask = logits_mask.transpose(-1, -3)
+        start_coord[-1], start_coord[-3] = start_coord[-3], start_coord[-1]
+        end_coord[-1], end_coord[-3] = end_coord[-3], end_coord[-1]
+        preds_save = torch.zeros(ct.shape)
+        preds_save[start_coord[0]:end_coord[0], 
+                        start_coord[1]:end_coord[1], 
+                        start_coord[2]:end_coord[2]] = torch.sigmoid(logits_mask)
+        preds_save = torch.where(preds_save > 0.5, 1., 0.).numpy()
+        preds_nii = nib.Nifti1Image(preds_save, affine=ct.affine, header=ct.header)
+        nib.save(preds_nii, save_path)
+
+    def train_transform(self, ct_npy, gt_npy):
+        item = {
+            'image': ct_npy,
+            'label': gt_npy
+        }
+        item = self.transform4train(item)
+        if type(item) is list:
+            assert len(item) == 1
+            item = item[0]
+        return item
+
+class MinMaxNormalization(transforms.Transform):
+    def __call__(self, data):
+        d = dict(data)
+        k = "image"
+        d[k] = d[k] - d[k].min()
+        d[k] = d[k] / np.clip(d[k].max(), a_min=1e-8, a_max=None)
+        return d
+
+class DimTranspose(transforms.Transform):
+    def __init__(self, keys):
+        self.keys = keys
+    
+    def __call__(self, data):
+        d = dict(data)
+        for key in self.keys:
+            d[key] = np.swapaxes(d[key], -1, -3)
+        return d
+
+# prompts
+def generate_box(pred_pre, bbox_shift=None):
+    meaning_post_label = pred_pre # [h, w, d]
+    ones_idx = (meaning_post_label > 0).nonzero(as_tuple=True)
+    if all(tensor.nelement() == 0 for tensor in ones_idx):
+        bboxes = torch.tensor([-1,-1,-1,-1,-1,-1])
+        return bboxes
+    min_coords = [dim.min() for dim in ones_idx]    # [x_min, y_min, z_min]
+    max_coords = [dim.max() for dim in ones_idx]    # [x_max, y_max, z_max]
+
+
+    if bbox_shift is None:
+        corner_min = []
+        corner_max = []
+        shape = meaning_post_label.shape
+        for coor in min_coords:
+            coor_ = max(0, coor)
+            corner_min.append(coor_)
+        for idx, coor in enumerate(max_coords):
+            coor_ = min(shape[idx], coor)
+            corner_max.append(coor_)
+        corner_min = torch.tensor(corner_min)
+        corner_max = torch.tensor(corner_max)
+        return torch.cat((corner_min, corner_max), dim=0)
+    else:
+        # add perturbation to bounding box coordinates
+        corner_min = []
+        corner_max = []
+        shape = meaning_post_label.shape
+        for coor in min_coords:
+            coor_ = max(0, coor + random.randint(-bbox_shift, bbox_shift))
+            corner_min.append(coor_)
+        for idx, coor in enumerate(max_coords):
+            coor_ = min(shape[idx], coor + random.randint(-bbox_shift, bbox_shift))
+            corner_max.append(coor_)
+        corner_min = torch.tensor(corner_min)
+        corner_max = torch.tensor(corner_max)
+        return torch.cat((corner_min, corner_max), dim=0)
+
+
+def select_points(preds, num_positive_extra=4, num_negative_extra=0, fix_extra_point_num=None):
+    spacial_dim = 3
+    points = torch.zeros((0, 3))
+    labels = torch.zeros((0))
+    pos_thred = 0.9
+    neg_thred = 0.1
+    
+    # get pos/net indices
+    positive_indices = torch.nonzero(preds > pos_thred, as_tuple=True) # ([pos x], [pos y], [pos z])
+    negative_indices = torch.nonzero(preds < neg_thred, as_tuple=True)
+
+    ones_idx = (preds > pos_thred).nonzero(as_tuple=True)
+    if all(tmp.nelement() == 0 for tmp in ones_idx):
+        # all neg
+        num_positive_extra = 0
+        selected_positive_point = torch.tensor([-1,-1,-1]).unsqueeze(dim=0)
+        points = torch.cat((points, selected_positive_point), dim=0)
+        labels = torch.cat((labels, torch.tensor([-1]).reshape(1)))
+    else:
+        # random select a pos point
+        random_idx = torch.randint(len(positive_indices[0]), (1,))
+        selected_positive_point = torch.tensor([positive_indices[i][random_idx] for i in range(spacial_dim)]).unsqueeze(dim=0)
+        points = torch.cat((points, selected_positive_point), dim=0)
+        labels = torch.cat((labels, torch.ones((1))))
+
+    if num_positive_extra > 0:
+        pos_idx_list = torch.randperm(len(positive_indices[0]))[:num_positive_extra]
+        extra_positive_points = []
+        for pos_idx in pos_idx_list:
+            extra_positive_points.append([positive_indices[i][pos_idx] for i in range(spacial_dim)])
+        extra_positive_points = torch.tensor(extra_positive_points).reshape(-1, 3)
+        points = torch.cat((points, extra_positive_points), dim=0)
+        labels = torch.cat((labels, torch.ones((extra_positive_points.shape[0]))))
+
+    if num_negative_extra > 0:
+        neg_idx_list = torch.randperm(len(negative_indices[0]))[:num_negative_extra]
+        extra_negative_points = []
+        for neg_idx in neg_idx_list:
+            extra_negative_points.append([negative_indices[i][neg_idx] for i in range(spacial_dim)])
+        extra_negative_points = torch.tensor(extra_negative_points).reshape(-1, 3)
+        points = torch.cat((points, extra_negative_points), dim=0)
+        labels = torch.cat((labels, torch.zeros((extra_negative_points.shape[0]))))
+    
+    if fix_extra_point_num is None:
+        left_point_num = num_positive_extra + num_negative_extra + 1 - labels.shape[0]
+    else:
+        left_point_num = fix_extra_point_num  + 1 - labels.shape[0]
+
+    for _ in range(left_point_num):
+        ignore_point = torch.tensor([-1,-1,-1]).unsqueeze(dim=0)
+        points = torch.cat((points, ignore_point), dim=0)
+        labels = torch.cat((labels, torch.tensor([-1]).reshape(1)))
+
+    return points, labels
+
+# SegVol
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import numpy as np
+from transformers import CLIPTextModel, CLIPTextConfig
+import random
+
+#%% set up model
+class SegVol(nn.Module):
+    def __init__(self, 
+                image_encoder, 
+                mask_decoder,
+                prompt_encoder,
+                roi_size,
+                patch_size,
+                # clip_model,
+                test_mode=False,
+                ):
+        super().__init__()
+        self.image_encoder = image_encoder
+        self.mask_decoder = mask_decoder
+        self.prompt_encoder = prompt_encoder
+        self.text_encoder = TextEncoder()
+        self.feat_shape = np.array(roi_size)/np.array(patch_size)
+        self.test_mode = test_mode
+        self.dice_loss = BinaryDiceLoss()
+        self.bce_loss = BCELoss()
+        self.decoder_iter = 6
+
+    def forward(self, image, text=None, boxes=None, points=None, **kwargs):
+        bs = image.shape[0]
+        img_shape = (image.shape[2], image.shape[3], image.shape[4])
+        image_embedding, _ = self.image_encoder(image)
+        image_embedding = image_embedding.transpose(1, 2).view(bs, -1, 
+            int(self.feat_shape[0]), int(self.feat_shape[1]), int(self.feat_shape[2]))
+        # test mode
+        if self.test_mode:
+            return self.forward_decoder(image_embedding, img_shape, text, boxes, points)
+        
+        # train mode
+        ## sl
+        sl_loss = self.supervised_forward(image, image_embedding, img_shape, kwargs['train_organs'], kwargs['train_labels'])
+        ## ssl
+        # ssl_loss = self.unsupervised_forward(image, image_embedding, kwargs['pseudo_seg_cleaned'], img_shape)
+        return sl_loss
+
+    def forward_decoder(self, image_embedding, img_shape, text=None, boxes=None, points=None):
+        device = image_embedding.device
+        with torch.no_grad():
+            if boxes is not None:
+                if len(boxes.shape) == 2:
+                    boxes = boxes[:, None, :] # (B, 1, 6)
+            if text is not None:
+                text_embedding = self.text_encoder(text, device)  # (B, 768)
+            else:
+                text_embedding = None
+        sparse_embeddings, dense_embeddings = self.prompt_encoder(
+            points=points,
+            boxes=boxes,
+            masks=None,
+            text_embedding=text_embedding,
+        )
+
+        dense_pe = self.prompt_encoder.get_dense_pe()
+        low_res_masks, _ = self.mask_decoder(
+            image_embeddings=image_embedding,
+            text_embedding = text_embedding,
+            image_pe=dense_pe,
+            sparse_prompt_embeddings=sparse_embeddings,
+            dense_prompt_embeddings=dense_embeddings,
+            multimask_output=False,
+          )
+        logits = F.interpolate(low_res_masks, size=img_shape, mode='trilinear', align_corners=False)
+        return logits
+
+    def supervised_forward(self, image, image_embedding, img_shape, training_organs, train_labels):
+        device = image_embedding.device
+        iter_points, iter_bboxes, iter_organs = self.build_prompt_label(image.shape[0], training_organs, train_labels, device)
+        # select prompt
+        prompt_options = [[None, iter_points, iter_organs], [iter_bboxes, None, iter_organs], 
+                        [None, None, iter_organs], [iter_bboxes, None, None], [None, iter_points, None],
+                        [iter_bboxes, iter_points, None]]
+        sl_loss = 0
+        for prompt in prompt_options:
+            bboxes, points, organs = prompt
+            logits = self.forward_decoder(image_embedding, img_shape, text=organs, boxes=bboxes, points=points)
+            # cal loss
+            sl_loss_dice = self.dice_loss.forward(logits.squeeze().float(), train_labels.squeeze().float())
+            sl_loss_bce = self.bce_loss.forward(logits.squeeze().float(), train_labels.squeeze().float())
+            sl_loss += sl_loss_dice + sl_loss_bce
+        return sl_loss
+    
+    # def unsupervised_forward(self, image, image_embedding, pseudo_seg_cleaned, img_shape):
+    #     sll_loss = 0
+    #     for iter in range(self.decoder_iter):
+    #         if iter % 2 == 0:
+    #             pseudo_labels, pseudo_points_prompt = self.build_pseudo_point_prompt_label(image.shape, pseudo_seg_cleaned)
+    #             logits = self.forward_decoder(image_embedding, img_shape, text=None, boxes=None, points=pseudo_points_prompt)
+    #         else:
+    #             pseudo_labels, pseudo_bboxes_prompt = self.build_pseudo_box_prompt_label(image.shape, pseudo_seg_cleaned)
+    #             logits = self.forward_decoder(image_embedding, img_shape, text=None, boxes=pseudo_bboxes_prompt, points=None)
+    #         # cal loss
+    #         sll_loss_dice = self.dice_loss.forward(logits.squeeze().float(), pseudo_labels.squeeze().float())
+    #         sll_loss_bce = self.bce_loss.forward(logits.squeeze().float(), pseudo_labels.squeeze().float())
+    #         sll_loss += sll_loss_dice + sll_loss_bce
+    #     return sll_loss
+
+    def build_prompt_label(self, bs, training_organs, train_labels, device):
+        # generate prompt & label
+        iter_organs = []
+        iter_bboxes = []
+        iter_points_ax = []
+        iter_point_labels = []
+        for sample_idx in range(bs):
+            # organ prompt
+            iter_organs.append(training_organs)
+            # box prompt
+            box = generate_box(train_labels[sample_idx], bbox_shift=10)
+            iter_bboxes.append(box)
+            # point prompt
+            num_positive_extra_max, num_negative_extra_max = 10, 10
+            num_positive_extra = random.randint(0, num_positive_extra_max)
+            num_negative_extra = random.randint(0, num_negative_extra_max)
+            point, point_label = select_points(
+                train_labels[sample_idx],
+                num_positive_extra=num_positive_extra,
+                num_negative_extra=num_negative_extra,
+                fix_extra_point_num=num_positive_extra_max + num_negative_extra_max)
+            iter_points_ax.append(point)
+            iter_point_labels.append(point_label)
+        # batched prompt
+        iter_points_ax = torch.stack(iter_points_ax, dim=0).to(device)
+        iter_point_labels = torch.stack(iter_point_labels, dim=0).to(device)
+        iter_points = (iter_points_ax, iter_point_labels)
+        iter_bboxes = torch.stack(iter_bboxes, dim=0).float().to(device)
+        return iter_points, iter_bboxes, iter_organs
+    
+    # def build_pseudo_point_prompt_label(self, input_shape, seg_labels):
+    #     pseudo_labels = torch.zeros(input_shape).to(self.custom_device)
+    #     # generate points
+    #     points = []
+    #     point_labels = []
+    #     for batch_idx in range(input_shape[0]):
+    #         # generate pseudo label
+    #         unique_ids = torch.unique(seg_labels[batch_idx])
+    #         unique_ids = unique_ids[unique_ids != -1]
+    #         region_id = random.choice(unique_ids).item()
+    #         pseudo_labels[batch_idx][seg_labels[batch_idx]==region_id] = 1
+    #         # generate point prompt
+    #         num_positive_extra_max, num_negative_extra_max = 10, 10
+    #         num_positive_extra = random.randint(4, num_positive_extra_max)
+    #         num_negative_extra = random.randint(0, num_negative_extra_max)
+    #         assert len(pseudo_labels[batch_idx][0].shape) == 3
+    #         point, point_label = select_points(
+    #             pseudo_labels[batch_idx][0],
+    #             num_positive_extra=num_positive_extra,
+    #             num_negative_extra=num_negative_extra,
+    #             fix_extra_point_num=num_positive_extra_max + num_negative_extra_max)
+    #         points.append(point)
+    #         point_labels.append(point_label)
+    #     points = torch.stack(points, dim=0).to(self.custom_device)
+    #     point_labels = torch.stack(point_labels, dim=0).to(self.custom_device)
+    #     pseudo_points_prompt = (points, point_labels)
+    #     return pseudo_labels, pseudo_points_prompt
+
+    # def build_pseudo_box_prompt_label(self, input_shape, seg_labels_cleaned):
+    #     pseudo_labels = torch.zeros(input_shape).to(self.custom_device)
+    #     iter_bboxes = []
+    #     # generate boxes
+    #     for batch_idx in range(input_shape[0]):
+    #         # generate ori pseudo label
+    #         unique_ids = torch.unique(seg_labels_cleaned[batch_idx])
+    #         unique_ids = unique_ids[unique_ids != -1]
+    #         region_id = random.choice(unique_ids).item()
+    #         pseudo_labels[batch_idx][seg_labels_cleaned[batch_idx]==region_id] = 1
+    #         # generate box prompt
+    #         box = generate_box(pseudo_labels[batch_idx][0])
+    #         iter_bboxes.append(box)
+    #         # refine pseudo label
+    #         x_min, y_min, z_min, x_max, y_max, z_max = box
+    #         binary_cube = torch.zeros_like(pseudo_labels[batch_idx][0]).int()
+    #         binary_cube[x_min:x_max+1, y_min:y_max+1, z_min:z_max+1] = 1
+    #         # cal iou
+    #         mask_label = seg_labels_cleaned[batch_idx][0]
+    #         assert binary_cube.shape == mask_label.shape, str(binary_cube.shape) + ' ' + str(mask_label.shape)
+    #         mask_values_in_binary_cube = mask_label[binary_cube == 1]
+    #         unique_mask_values = torch.unique(mask_values_in_binary_cube)
+    #         # print('unique_mask_values ', unique_mask_values)
+    #         for value in unique_mask_values:
+    #             if value == -1: continue
+    #             mask_area = (mask_label == value)
+    #             intersection = (binary_cube & mask_area)
+    #             iou = intersection.float().sum() / mask_area.float().sum()
+    #             if iou > 0.90:
+    #                 # print(f"Mask value {value} has IOU > 0.90 in binary cube.")
+    #                 pseudo_labels[batch_idx][seg_labels_cleaned[batch_idx]==value] = 1
+
+    #     bboxes = torch.stack(iter_bboxes, dim=0).float().to(self.custom_device)
+    #     return pseudo_labels, bboxes
+    
+class TextEncoder(nn.Module):
+    def __init__(self):
+        super().__init__()
+        config = CLIPTextConfig()
+        self.clip_text_model = CLIPTextModel(config)
+        self.tokenizer = None
+        self.dim_align = nn.Linear(512, 768)
+        # freeze text encoder
+        for param in self.clip_text_model.parameters():
+            param.requires_grad = False
+
+    def organ2tokens(self, organ_names, device):
+        text_list = ['A computerized tomography of a {}.'.format(organ_name) for organ_name in organ_names]
+        tokens = self.tokenizer(text_list, padding=True, return_tensors="pt")
+        for key in tokens.keys():
+            tokens[key] = tokens[key].to(device)
+        return tokens
+    
+    def forward(self, text, device):
+        if text is None:
+            return None
+        if type(text) is str:
+            # text is supposed to be list
+            text = [text]
+        tokens = self.organ2tokens(text, device)
+        clip_outputs = self.clip_text_model(**tokens)
+        text_embedding = clip_outputs.pooler_output
+        text_embedding = self.dim_align(text_embedding)
+        return text_embedding
+
+# loss
+import torch
+import torch.nn as nn
+
+class BinaryDiceLoss(nn.Module):
+    def __init__(self, smooth=1, p=2, reduction='mean'):
+        super(BinaryDiceLoss, self).__init__()
+        self.smooth = smooth
+        self.p = p
+        self.reduction = reduction
+
+    def forward(self, predict, target):
+        predict = torch.sigmoid(predict)
+        target_ = target.clone()
+        target_[target == -1] = 0
+        assert predict.shape[0] == target.shape[0], "predict & target batch size don't match\n" + str(predict.shape) + '\n' + str(target.shape[0])
+        predict = predict.contiguous().view(predict.shape[0], -1)
+        target_ = target_.contiguous().view(target_.shape[0], -1)
+
+        num = torch.sum(torch.mul(predict, target_), dim=1)
+        den = torch.sum(predict, dim=1) + torch.sum(target_, dim=1) + self.smooth
+
+        dice_score = 2*num / den
+        dice_loss = 1 - dice_score
+
+        # dice_loss_avg = dice_loss[target[:,0]!=-1].sum() / dice_loss[target[:,0]!=-1].shape[0]
+        dice_loss_avg = dice_loss.sum() / dice_loss.shape[0]
+
+        return dice_loss_avg
+
+class BCELoss(nn.Module):
+    def __init__(self):
+        super(BCELoss, self).__init__()
+        self.criterion = nn.BCEWithLogitsLoss()
+
+    def forward(self, predict, target):
+        assert predict.shape == target.shape, 'predict & target shape do not match\n' + str(predict.shape) + '\n' + str(target.shape)
+        target_ = target.clone()
+        target_[target == -1] = 0
+
+        ce_loss = self.criterion(predict, target_)
+
+        return ce_loss
+
+# monai inference
+
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import warnings
+from typing import Any, Callable, Dict, List, Mapping, Sequence, Tuple, Union
+
+import torch
+import torch.nn.functional as F
+import random
+
+from monai.data.utils import compute_importance_map, dense_patch_slices, get_valid_patch_size
+from monai.transforms import Resize
+from monai.utils import (
+    BlendMode,
+    PytorchPadMode,
+    convert_data_type,
+    ensure_tuple,
+    fall_back_tuple,
+    look_up_option,
+    optional_import,
+)
+
+tqdm, _ = optional_import("tqdm", name="tqdm")
+
+__all__ = ["sliding_window_inference"]
+
+def logits2roi_coor(spatial_size, logits_global_single):
+    # crop predict
+    pred_global_single = torch.sigmoid(logits_global_single) > 0.5
+    ## get all pos idx
+    nonzero_indices = torch.nonzero(pred_global_single)
+    if nonzero_indices.shape[0] == 0:
+        return None, None, None, None, None, None
+    ## get boundary
+    min_d, max_d = nonzero_indices[:, 0].min(), nonzero_indices[:, 0].max()
+    min_h, max_h = nonzero_indices[:, 1].min(), nonzero_indices[:, 1].max()
+    min_w, max_w = nonzero_indices[:, 2].min(), nonzero_indices[:, 2].max()
+    ## padding
+    crop_d, crop_h, crop_w = max_d - min_d + 1, max_h - min_h + 1, max_w - min_w + 1,
+    window_d, window_h, window_w = spatial_size
+    padding_d, padding_h, padding_w = max(0, window_d-crop_d), max(0, window_h-crop_h), max(0, window_w-crop_w)
+    global_d, global_h, global_w = logits_global_single.shape
+    min_d = max(0, min_d - int(padding_d)//2)
+    min_h = max(0, min_h - int(padding_h)//2)
+    min_w = max(0, min_w - int(padding_w)//2)
+    max_d = min(global_d, max_d + int(padding_d)//2)
+    max_h = min(global_h, max_h + int(padding_h)//2)
+    max_w = min(global_w, max_w + int(padding_w)//2)
+    return min_d, min_h, min_w, max_d, max_h, max_w
+
+def build_binary_cube(bbox, binary_cube_shape):
+    min_coord = bbox[0][:3].int().tolist()
+    max_coord = bbox[0][3:].int().tolist()
+    binary_cube = torch.zeros(binary_cube_shape)
+    binary_cube[min_coord[0]:max_coord[0]+1, min_coord[1]:max_coord[1]+1, min_coord[2]:max_coord[2]+1] = 1
+    return binary_cube
+
+def build_binary_points(points, labels, shape):
+    binary_points = torch.zeros(shape, dtype=torch.int16)
+    binary_points[points[labels == 1, 0].long(), points[labels == 1, 1].long(), points[labels == 1, 2].long()] = 1
+    return binary_points
+
+def sliding_window_inference(
+    inputs: torch.Tensor,
+    prompt_reflection: Union[torch.Tensor, Tuple[torch.Tensor, ...]],
+    roi_size: Union[Sequence[int], int],
+    sw_batch_size: int,
+    predictor: Callable[..., Union[torch.Tensor, Sequence[torch.Tensor], Dict[Any, torch.Tensor]]],
+    overlap: float = 0.25,
+    mode: Union[BlendMode, str] = BlendMode.CONSTANT,
+    sigma_scale: Union[Sequence[float], float] = 0.125,
+    padding_mode: Union[PytorchPadMode, str] = PytorchPadMode.CONSTANT,
+    cval: float = 0.0,
+    sw_device: Union[torch.device, str, None] = None,
+    device: Union[torch.device, str, None] = None,
+    progress: bool = False,
+    roi_weight_map: Union[torch.Tensor, None] = None,
+    *args: Any,
+    **kwargs: Any,
+) -> Union[torch.Tensor, Tuple[torch.Tensor, ...], Dict[Any, torch.Tensor]]:
+    """
+    Sliding window inference on `inputs` with `predictor`.
+
+    The outputs of `predictor` could be a tensor, a tuple, or a dictionary of tensors.
+    Each output in the tuple or dict value is allowed to have different resolutions with respect to the input.
+    e.g., the input patch spatial size is [128,128,128], the output (a tuple of two patches) patch sizes
+    could be ([128,64,256], [64,32,128]).
+    In this case, the parameter `overlap` and `roi_size` need to be carefully chosen to ensure the output ROI is still
+    an integer. If the predictor's input and output spatial sizes are not equal, we recommend choosing the parameters
+    so that `overlap*roi_size*output_size/input_size` is an integer (for each spatial dimension).
+
+    When roi_size is larger than the inputs' spatial size, the input image are padded during inference.
+    To maintain the same spatial sizes, the output image will be cropped to the original input size.
+
+    Args:
+        inputs: input image to be processed (assuming NCHW[D])
+        roi_size: the spatial window size for inferences.
+            When its components have None or non-positives, the corresponding inputs dimension will be used.
+            if the components of the `roi_size` are non-positive values, the transform will use the
+            corresponding components of img size. For example, `roi_size=(32, -1)` will be adapted
+            to `(32, 64)` if the second spatial dimension size of img is `64`.
+        sw_batch_size: the batch size to run window slices.
+        predictor: given input tensor ``patch_data`` in shape NCHW[D],
+            The outputs of the function call ``predictor(patch_data)`` should be a tensor, a tuple, or a dictionary
+            with Tensor values. Each output in the tuple or dict value should have the same batch_size, i.e. NM'H'W'[D'];
+            where H'W'[D'] represents the output patch's spatial size, M is the number of output channels,
+            N is `sw_batch_size`, e.g., the input shape is (7, 1, 128,128,128),
+            the output could be a tuple of two tensors, with shapes: ((7, 5, 128, 64, 256), (7, 4, 64, 32, 128)).
+            In this case, the parameter `overlap` and `roi_size` need to be carefully chosen
+            to ensure the scaled output ROI sizes are still integers.
+            If the `predictor`'s input and output spatial sizes are different,
+            we recommend choosing the parameters so that ``overlap*roi_size*zoom_scale`` is an integer for each dimension.
+        overlap: Amount of overlap between scans.
+        mode: {``"constant"``, ``"gaussian"``}
+            How to blend output of overlapping windows. Defaults to ``"constant"``.
+
+            - ``"constant``": gives equal weight to all predictions.
+            - ``"gaussian``": gives less weight to predictions on edges of windows.
+
+        sigma_scale: the standard deviation coefficient of the Gaussian window when `mode` is ``"gaussian"``.
+            Default: 0.125. Actual window sigma is ``sigma_scale`` * ``dim_size``.
+            When sigma_scale is a sequence of floats, the values denote sigma_scale at the corresponding
+            spatial dimensions.
+        padding_mode: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}
+            Padding mode for ``inputs``, when ``roi_size`` is larger than inputs. Defaults to ``"constant"``
+            See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
+        cval: fill value for 'constant' padding mode. Default: 0
+        sw_device: device for the window data.
+            By default the device (and accordingly the memory) of the `inputs` is used.
+            Normally `sw_device` should be consistent with the device where `predictor` is defined.
+        device: device for the stitched output prediction.
+            By default the device (and accordingly the memory) of the `inputs` is used. If for example
+            set to device=torch.device('cpu') the gpu memory consumption is less and independent of the
+            `inputs` and `roi_size`. Output is on the `device`.
+        progress: whether to print a `tqdm` progress bar.
+        roi_weight_map: pre-computed (non-negative) weight map for each ROI.
+            If not given, and ``mode`` is not `constant`, this map will be computed on the fly.
+        args: optional args to be passed to ``predictor``.
+        kwargs: optional keyword args to be passed to ``predictor``.
+
+    Note:
+        - input must be channel-first and have a batch dim, supports N-D sliding window.
+
+    """
+    print('sliding window inference for ROI')
+    text = kwargs['text']
+    use_box = kwargs['use_box']
+    use_point = kwargs['use_point']
+    assert not (use_box and use_point)
+    compute_dtype = inputs.dtype
+    num_spatial_dims = len(inputs.shape) - 2
+    if overlap < 0 or overlap >= 1:
+        raise ValueError("overlap must be >= 0 and < 1.")
+
+    # determine image spatial size and batch size
+    # Note: all input images must have the same image size and batch size
+    batch_size, _, *image_size_ = inputs.shape
+
+    if device is None:
+        device = inputs.device
+    if sw_device is None:
+        sw_device = inputs.device
+
+    roi_size = fall_back_tuple(roi_size, image_size_)
+    # in case that image size is smaller than roi size
+    image_size = tuple(max(image_size_[i], roi_size[i]) for i in range(num_spatial_dims))
+    pad_size = []
+    for k in range(len(inputs.shape) - 1, 1, -1):
+        diff = max(roi_size[k - 2] - inputs.shape[k], 0)
+        half = diff // 2
+        pad_size.extend([half, diff - half])
+    inputs = F.pad(inputs, pad=pad_size, mode=look_up_option(padding_mode, PytorchPadMode).value, value=cval)
+    #############
+    if use_point or use_box:
+        binary_prompt_map, global_preds = prompt_reflection
+        global_preds = F.pad(global_preds, pad=pad_size, mode=look_up_option(padding_mode, PytorchPadMode).value, value=cval)
+    #############
+    scan_interval = _get_scan_interval(image_size, roi_size, num_spatial_dims, overlap)
+
+    # Store all slices in list
+    slices = dense_patch_slices(image_size, roi_size, scan_interval)
+    num_win = len(slices)  # number of windows per image
+    total_slices = num_win * batch_size  # total number of windows
+
+    # Create window-level importance map
+    valid_patch_size = get_valid_patch_size(image_size, roi_size)
+    if valid_patch_size == roi_size and (roi_weight_map is not None):
+        importance_map = roi_weight_map
+    else:
+        try:
+            importance_map = compute_importance_map(valid_patch_size, mode=mode, sigma_scale=sigma_scale, device=device)
+        except BaseException as e:
+            raise RuntimeError(
+                "Seems to be OOM. Please try smaller patch size or mode='constant' instead of mode='gaussian'."
+            ) from e
+    importance_map = convert_data_type(importance_map, torch.Tensor, device, compute_dtype)[0]  # type: ignore
+    # handle non-positive weights
+    min_non_zero = max(importance_map[importance_map != 0].min().item(), 1e-3)
+    importance_map = torch.clamp(importance_map.to(torch.float32), min=min_non_zero).to(compute_dtype)
+
+    # Perform predictions
+    dict_key, output_image_list, count_map_list = None, [], []
+    _initialized_ss = -1
+    is_tensor_output = True  # whether the predictor's output is a tensor (instead of dict/tuple)
+
+    # for each patch
+    for slice_g in tqdm(range(0, total_slices, sw_batch_size)) if progress else range(0, total_slices, sw_batch_size):
+        slice_range = range(slice_g, min(slice_g + sw_batch_size, total_slices))
+        unravel_slice = [
+            [slice(int(idx / num_win), int(idx / num_win) + 1), slice(None)] + list(slices[idx % num_win])
+            for idx in slice_range
+        ]
+        window_data = torch.cat([inputs[win_slice] for win_slice in unravel_slice]).to(sw_device)
+        #############
+        
+        boxes = None
+        points = None
+        if use_point:
+            window_binary_prompt_map = torch.cat([binary_prompt_map[win_slice] for win_slice in unravel_slice]).to(sw_device)
+            point, point_label = select_points(window_binary_prompt_map.squeeze())
+            points = (point.unsqueeze(0).float().to(device), point_label.unsqueeze(0).float().to(device))  
+            pseudo_label = torch.cat([global_preds[win_slice] for win_slice in unravel_slice]).to(sw_device)
+            boxes = generate_box(pseudo_label.squeeze()).unsqueeze(0).float().to(device)
+        if use_box:
+            if num_win == 1:
+                window_binary_prompt_map = torch.cat([binary_prompt_map[win_slice] for win_slice in unravel_slice]).to(sw_device)
+                boxes = generate_box(window_binary_prompt_map.squeeze()).unsqueeze(0).float().to(device)
+            else:
+                pseudo_label = torch.cat([global_preds[win_slice] for win_slice in unravel_slice]).to(sw_device)
+                boxes = generate_box(pseudo_label.squeeze()).unsqueeze(0).float().to(device)
+        seg_prob_out = predictor(window_data, text, boxes, points)  # batched patch segmentation
+        #############
+        # convert seg_prob_out to tuple seg_prob_tuple, this does not allocate new memory.
+        seg_prob_tuple: Tuple[torch.Tensor, ...]
+        if isinstance(seg_prob_out, torch.Tensor):
+            seg_prob_tuple = (seg_prob_out,)
+        elif isinstance(seg_prob_out, Mapping):
+            if dict_key is None:
+                dict_key = sorted(seg_prob_out.keys())  # track predictor's output keys
+            seg_prob_tuple = tuple(seg_prob_out[k] for k in dict_key)
+            is_tensor_output = False
+        else:
+            seg_prob_tuple = ensure_tuple(seg_prob_out)
+            is_tensor_output = False
+
+        # for each output in multi-output list
+        for ss, seg_prob in enumerate(seg_prob_tuple):
+            seg_prob = seg_prob.to(device)  # BxCxMxNxP or BxCxMxN
+
+            # compute zoom scale: out_roi_size/in_roi_size
+            zoom_scale = []
+            for axis, (img_s_i, out_w_i, in_w_i) in enumerate(
+                zip(image_size, seg_prob.shape[2:], window_data.shape[2:])
+            ):
+                _scale = out_w_i / float(in_w_i)
+                if not (img_s_i * _scale).is_integer():
+                    warnings.warn(
+                        f"For spatial axis: {axis}, output[{ss}] will have non-integer shape. Spatial "
+                        f"zoom_scale between output[{ss}] and input is {_scale}. Please pad inputs."
+                    )
+                zoom_scale.append(_scale)
+
+            if _initialized_ss < ss:  # init. the ss-th buffer at the first iteration
+                # construct multi-resolution outputs
+                output_classes = seg_prob.shape[1]
+                output_shape = [batch_size, output_classes] + [
+                    int(image_size_d * zoom_scale_d) for image_size_d, zoom_scale_d in zip(image_size, zoom_scale)
+                ]
+                # allocate memory to store the full output and the count for overlapping parts
+                output_image_list.append(torch.zeros(output_shape, dtype=compute_dtype, device=device))
+                count_map_list.append(torch.zeros([1, 1] + output_shape[2:], dtype=compute_dtype, device=device))
+                _initialized_ss += 1
+
+            # resizing the importance_map
+            resizer = Resize(spatial_size=seg_prob.shape[2:], mode="nearest", anti_aliasing=False)
+
+            # store the result in the proper location of the full output. Apply weights from importance map.
+            for idx, original_idx in zip(slice_range, unravel_slice):
+                # zoom roi
+                original_idx_zoom = list(original_idx)  # 4D for 2D image, 5D for 3D image
+                for axis in range(2, len(original_idx_zoom)):
+                    zoomed_start = original_idx[axis].start * zoom_scale[axis - 2]
+                    zoomed_end = original_idx[axis].stop * zoom_scale[axis - 2]
+                    if not zoomed_start.is_integer() or (not zoomed_end.is_integer()):
+                        warnings.warn(
+                            f"For axis-{axis-2} of output[{ss}], the output roi range is not int. "
+                            f"Input roi range is ({original_idx[axis].start}, {original_idx[axis].stop}). "
+                            f"Spatial zoom_scale between output[{ss}] and input is {zoom_scale[axis - 2]}. "
+                            f"Corresponding output roi range is ({zoomed_start}, {zoomed_end}).\n"
+                            f"Please change overlap ({overlap}) or roi_size ({roi_size[axis-2]}) for axis-{axis-2}. "
+                            "Tips: if overlap*roi_size*zoom_scale is an integer, it usually works."
+                        )
+                    original_idx_zoom[axis] = slice(int(zoomed_start), int(zoomed_end), None)
+                importance_map_zoom = resizer(importance_map.unsqueeze(0))[0].to(compute_dtype)
+                # store results and weights
+                output_image_list[ss][original_idx_zoom] += importance_map_zoom * seg_prob[idx - slice_g]
+                count_map_list[ss][original_idx_zoom] += (
+                    importance_map_zoom.unsqueeze(0).unsqueeze(0).expand(count_map_list[ss][original_idx_zoom].shape)
+                )
+
+    # account for any overlapping sections
+    for ss in range(len(output_image_list)):
+        output_image_list[ss] = (output_image_list[ss] / count_map_list.pop(0)).to(compute_dtype)
+
+    # remove padding if image_size smaller than roi_size
+    for ss, output_i in enumerate(output_image_list):
+        if torch.isnan(output_i).any() or torch.isinf(output_i).any():
+            warnings.warn("Sliding window inference results contain NaN or Inf.")
+
+        zoom_scale = [
+            seg_prob_map_shape_d / roi_size_d for seg_prob_map_shape_d, roi_size_d in zip(output_i.shape[2:], roi_size)
+        ]
+
+        final_slicing: List[slice] = []
+        for sp in range(num_spatial_dims):
+            slice_dim = slice(pad_size[sp * 2], image_size_[num_spatial_dims - sp - 1] + pad_size[sp * 2])
+            slice_dim = slice(
+                int(round(slice_dim.start * zoom_scale[num_spatial_dims - sp - 1])),
+                int(round(slice_dim.stop * zoom_scale[num_spatial_dims - sp - 1])),
+            )
+            final_slicing.insert(0, slice_dim)
+        while len(final_slicing) < len(output_i.shape):
+            final_slicing.insert(0, slice(None))
+        output_image_list[ss] = output_i[final_slicing]
+
+    if dict_key is not None:  # if output of predictor is a dict
+        final_output = dict(zip(dict_key, output_image_list))
+    else:
+        final_output = tuple(output_image_list)  # type: ignore
+    return final_output[0] if is_tensor_output else final_output  # type: ignore
+
+
+def _get_scan_interval(
+    image_size: Sequence[int], roi_size: Sequence[int], num_spatial_dims: int, overlap: float
+) -> Tuple[int, ...]:
+    """
+    Compute scan interval according to the image size, roi size and overlap.
+    Scan interval will be `int((1 - overlap) * roi_size)`, if interval is 0,
+    use 1 instead to make sure sliding window works.
+
+    """
+    if len(image_size) != num_spatial_dims:
+        raise ValueError("image coord different from spatial dims.")
+    if len(roi_size) != num_spatial_dims:
+        raise ValueError("roi coord different from spatial dims.")
+
+    scan_interval = []
+    for i in range(num_spatial_dims):
+        if roi_size[i] == image_size[i]:
+            scan_interval.append(int(roi_size[i]))
+        else:
+            interval = int(roi_size[i] * (1 - overlap))
+            scan_interval.append(interval if interval > 0 else 1)
+    return tuple(scan_interval)
+
+# build 3D SAM
+import torch
+import numpy as np
+from monai.networks.nets import ViT
+
+def _build_sam(
+    image_encoder_type,
+    embed_dim,
+    patch_size,
+    checkpoint,
+    image_size,
+):
+    mlp_dim = 3072
+    num_layers = 12
+    num_heads = 12
+    pos_embed = 'perceptron'
+    dropout_rate = 0.0
+    
+    image_encoder=ViT(
+        in_channels=1,
+        img_size=image_size,
+        patch_size=patch_size,
+        hidden_size=embed_dim,
+        mlp_dim=mlp_dim,
+        num_layers=num_layers,
+        num_heads=num_heads,
+        pos_embed=pos_embed,
+        classification=False,
+        dropout_rate=dropout_rate,
+    )
+    image_embedding_size = [int(item) for item in (np.array(image_size) / np.array(patch_size))]
+
+    if checkpoint is not None:
+        with open(checkpoint, "rb") as f:
+            state_dict = torch.load(f, map_location='cpu')['state_dict']
+            encoder_dict = {k.replace('model.encoder.', ''): v for k, v in state_dict.items() if 'model.encoder.' in k}
+        image_encoder.load_state_dict(encoder_dict)
+        print(f'===> image_encoder.load_param: {checkpoint}')
+    sam = Sam(
+        image_encoder=image_encoder,
+        prompt_encoder=PromptEncoder(
+            embed_dim=embed_dim,
+            image_embedding_size=image_embedding_size,
+            input_image_size=image_size,
+            mask_in_chans=16,
+        ),
+        mask_decoder=MaskDecoder(
+            image_encoder_type=image_encoder_type,
+            num_multimask_outputs=3,
+            transformer=TwoWayTransformer(
+                depth=2,
+                embedding_dim=embed_dim,
+                mlp_dim=2048,
+                num_heads=8,
+            ),
+            transformer_dim=embed_dim,
+            iou_head_depth=3,
+            iou_head_hidden_dim=256,
+            image_size=np.array(image_size),
+            patch_size=np.array(patch_size),
+        ),
+        pixel_mean=[123.675, 116.28, 103.53],
+        pixel_std=[58.395, 57.12, 57.375],
+    )
+    sam.eval()
+    return sam
+
+# mask decoder
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+# All rights reserved.
+
+# This source code is licensed under the license found in the
+# LICENSE file in the root directory of this source tree.
+
+import torch
+from torch import nn
+from torch.nn import functional as F
+
+from typing import List, Tuple, Type, Optional
+
+class MaskDecoder(nn.Module):
+    def __init__(
+        self,
+        *,
+        image_encoder_type: str,
+        transformer_dim: int,
+        transformer: nn.Module,
+        num_multimask_outputs: int = 3,
+        activation: Type[nn.Module] = nn.GELU,
+        iou_head_depth: int = 3,
+        iou_head_hidden_dim: int = 256,
+        image_size,
+        patch_size,
+    ) -> None:
+        """
+        Predicts masks given an image and prompt embeddings, using a
+        transformer architecture.
+
+        Arguments:
+          transformer_dim (int): the channel dimension of the transformer
+          transformer (nn.Module): the transformer used to predict masks
+          num_multimask_outputs (int): the number of masks to predict
+            when disambiguating masks
+          activation (nn.Module): the type of activation to use when
+            upscaling masks
+          iou_head_depth (int): the depth of the MLP used to predict
+            mask quality
+          iou_head_hidden_dim (int): the hidden dimension of the MLP
+            used to predict mask quality
+        """
+        super().__init__()
+        self.transformer_dim = transformer_dim
+        self.transformer = transformer
+
+        self.num_multimask_outputs = num_multimask_outputs
+
+        self.iou_token = nn.Embedding(1, transformer_dim)
+        self.num_mask_tokens = num_multimask_outputs + 1
+        self.mask_tokens = nn.Embedding(self.num_mask_tokens, transformer_dim)
+
+        if image_encoder_type == 'swin_vit':
+            self.feat_shape = image_size/patch_size
+            self.output_upscaling = nn.Sequential(
+                nn.ConvTranspose3d(transformer_dim, transformer_dim // 4, kernel_size=2, stride=2),
+                nn.LayerNorm((transformer_dim // 4, int(self.feat_shape[0]), int(self.feat_shape[1]), int(self.feat_shape[2]))),    # swin
+                activation(),
+                nn.ConvTranspose3d(transformer_dim // 4, transformer_dim // 8, kernel_size=2, stride=2),        # swin
+                # nn.Conv3d(transformer_dim // 4, transformer_dim // 8, kernel_size=3, stride=1, padding=1),    # vit
+                activation(),
+            )
+        else:
+            self.feat_shape = image_size/patch_size * 2
+            self.output_upscaling = nn.Sequential(
+                nn.ConvTranspose3d(transformer_dim, transformer_dim // 4, kernel_size=2, stride=2),
+                nn.LayerNorm((transformer_dim // 4, int(self.feat_shape[0]), int(self.feat_shape[1]), int(self.feat_shape[2]))), # vit
+                activation(),
+                nn.ConvTranspose3d(transformer_dim // 4, transformer_dim // 8, kernel_size=2, stride=2),
+                # nn.Conv3d(transformer_dim // 4, transformer_dim // 8, kernel_size=3, stride=1, padding=1),
+                activation(),
+            )
+        self.output_hypernetworks_mlps = nn.ModuleList(
+            [
+                MLP(transformer_dim, transformer_dim, transformer_dim // 8, 3)
+                for i in range(self.num_mask_tokens)
+            ]
+        )
+
+        self.iou_prediction_head = MLP(
+            transformer_dim, iou_head_hidden_dim, self.num_mask_tokens, iou_head_depth
+        )
+
+        self.txt_align_upscaled_embedding = nn.Linear(768, 96)
+
+    def forward(
+        self,
+        image_embeddings: torch.Tensor,
+        text_embedding: Optional[torch.Tensor],
+        image_pe: torch.Tensor,
+        sparse_prompt_embeddings: torch.Tensor,
+        dense_prompt_embeddings: torch.Tensor,
+        multimask_output: bool,
+    ) -> Tuple[torch.Tensor, torch.Tensor]:
+        """
+        Predict masks given image and prompt embeddings.
+
+        Returns:
+          torch.Tensor: batched predicted masks
+        """
+        # print('--------------decoder here--------------')
+        masks, iou_pred = self.predict_masks(
+            image_embeddings=image_embeddings,
+            text_embedding=text_embedding,
+            image_pe=image_pe,
+            sparse_prompt_embeddings=sparse_prompt_embeddings,
+            dense_prompt_embeddings=dense_prompt_embeddings,
+        )
+
+        # Select the correct mask or masks for output
+        if multimask_output:
+            mask_slice = slice(1, None)
+        else:
+            mask_slice = slice(0, 1)
+        masks = masks[:, mask_slice, :, :, :]
+        iou_pred = iou_pred[:, mask_slice]
+
+        # Prepare output
+        return masks, iou_pred
+
+    def predict_masks(
+        self,
+        image_embeddings: torch.Tensor,
+        text_embedding: torch.Tensor,
+        image_pe: torch.Tensor,
+        sparse_prompt_embeddings: torch.Tensor,
+        dense_prompt_embeddings: torch.Tensor,
+    ) -> Tuple[torch.Tensor, torch.Tensor]:
+        """Predicts masks. See 'forward' for more details."""
+        # Concatenate output tokens
+        output_tokens = torch.cat([self.iou_token.weight, self.mask_tokens.weight], dim=0)
+        output_tokens = output_tokens.unsqueeze(0).expand(sparse_prompt_embeddings.size(0), -1, -1)
+        tokens = torch.cat((output_tokens, sparse_prompt_embeddings), dim=1)
+        # Expand per-image data in batch direction to be per-mask
+        if image_embeddings.shape[0] != tokens.shape[0]:
+            src = torch.repeat_interleave(image_embeddings, tokens.shape[0], dim=0)
+        else:
+            src = image_embeddings
+        src = src + dense_prompt_embeddings
+        pos_src = torch.repeat_interleave(image_pe, tokens.shape[0], dim=0)
+        b, c, h, w, d = src.shape
+
+        # Run the transformer
+        hs, src = self.transformer(src, pos_src, tokens)
+        iou_token_out = hs[:, 0, :]
+        mask_tokens_out = hs[:, 1 : (1 + self.num_mask_tokens), :]
+
+        # Upscale mask embeddings and predict masks using the mask tokens
+        src = src.transpose(1, 2).view(b, c, h, w, d)
+        upscaled_embedding = self.output_upscaling(src)
+        hyper_in_list: List[torch.Tensor] = []
+        for i in range(self.num_mask_tokens):
+            hyper_in_list.append(self.output_hypernetworks_mlps[i](mask_tokens_out[:, i, :]))
+        hyper_in = torch.stack(hyper_in_list, dim=1)
+        b, c, h, w, d = upscaled_embedding.shape
+        masks = (hyper_in @ upscaled_embedding.view(b, c, h * w * d)).view(b, -1, h, w, d)
+        
+        if text_embedding is not None:
+            text_embedding_down = self.txt_align_upscaled_embedding(text_embedding).unsqueeze(dim=1)
+            upscaled_embedding = upscaled_embedding.view(b, c, h * w * d)
+            sim = (text_embedding_down @ upscaled_embedding).view(b, -1, h, w, d)
+            sim = sim.repeat(1, masks.shape[1], 1, 1, 1)
+            masks = masks + sim
+        iou_pred = self.iou_prediction_head(iou_token_out)
+
+        return masks, iou_pred
+
+# Lightly adapted from
+# https://github.com/facebookresearch/MaskFormer/blob/main/mask_former/modeling/transformer/transformer_predictor.py # noqa
+class MLP(nn.Module):
+    def __init__(
+        self,
+        input_dim: int,
+        hidden_dim: int,
+        output_dim: int,
+        num_layers: int,
+        sigmoid_output: bool = False,
+    ) -> None:
+        super().__init__()
+        self.num_layers = num_layers
+        h = [hidden_dim] * (num_layers - 1)
+        self.layers = nn.ModuleList(
+            nn.Linear(n, k) for n, k in zip([input_dim] + h, h + [output_dim])
+        )
+        self.sigmoid_output = sigmoid_output
+
+    def forward(self, x):
+        for i, layer in enumerate(self.layers):
+            x = F.relu(layer(x)) if i < self.num_layers - 1 else layer(x)
+        if self.sigmoid_output:
+            x = F.sigmoid(x)
+        return x
+
+# prompt encoder
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+# All rights reserved.
+
+# This source code is licensed under the license found in the
+# LICENSE file in the root directory of this source tree.
+
+import numpy as np
+import torch
+from torch import nn
+
+from typing import Any, Optional, Tuple, Type
+
+class PromptEncoder(nn.Module):
+    def __init__(
+        self,
+        embed_dim: int,
+        image_embedding_size: Tuple[int, int, int],
+        input_image_size: Tuple[int, int, int],
+        mask_in_chans: int,
+        activation: Type[nn.Module] = nn.GELU,
+    ) -> None:
+        """
+        Encodes prompts for input to SAM's mask decoder.
+
+        Arguments:
+          embed_dim (int): The prompts' embedding dimension
+          image_embedding_size (tuple(int, int)): The spatial size of the
+            image embedding, as (H, W).
+          input_image_size (int): The padded size of the image as input
+            to the image encoder, as (H, W).
+          mask_in_chans (int): The number of hidden channels used for
+            encoding input masks.
+          activation (nn.Module): The activation to use when encoding
+            input masks.
+        """
+        super().__init__()
+        self.embed_dim = embed_dim
+        self.input_image_size = input_image_size
+        self.image_embedding_size = image_embedding_size
+        self.pe_layer = PositionEmbeddingRandom(embed_dim // 2)
+
+        self.num_point_embeddings: int = 4  # pos/neg point + 2 box corners
+        point_embeddings = [nn.Embedding(1, embed_dim) for i in range(self.num_point_embeddings)]
+        self.point_embeddings = nn.ModuleList(point_embeddings)
+        self.not_a_point_embed = nn.Embedding(1, embed_dim)
+
+        self.mask_input_size = (4 * image_embedding_size[0], 4 * image_embedding_size[1], 4 * image_embedding_size[2])
+        self.mask_downscaling = nn.Sequential(
+            nn.Conv2d(1, mask_in_chans // 4, kernel_size=2, stride=2),
+            LayerNorm2d(mask_in_chans // 4),
+            activation(),
+            nn.Conv2d(mask_in_chans // 4, mask_in_chans, kernel_size=2, stride=2),
+            LayerNorm2d(mask_in_chans),
+            activation(),
+            nn.Conv2d(mask_in_chans, embed_dim, kernel_size=1),
+        )
+        self.no_mask_embed = nn.Embedding(1, embed_dim)
+
+    def get_dense_pe(self) -> torch.Tensor:
+        """
+        Returns the positional encoding used to encode point prompts,
+        applied to a dense set of points the shape of the image encoding.
+
+        Returns:
+          torch.Tensor: Positional encoding with shape
+            1x(embed_dim)x(embedding_h)x(embedding_w)
+        """
+        return self.pe_layer(self.image_embedding_size).unsqueeze(0)
+
+    def _embed_points(
+        self,
+        points: torch.Tensor,
+        labels: torch.Tensor,
+        pad: bool,
+    ) -> torch.Tensor:
+        """Embeds point prompts."""
+        points = points + 0.5  # Shift to center of pixel
+        if pad:
+            padding_point = torch.zeros((points.shape[0], 1, 3), device=points.device)
+            padding_label = -torch.ones((labels.shape[0], 1), device=labels.device)
+            points = torch.cat([points, padding_point], dim=1)
+            labels = torch.cat([labels, padding_label], dim=1)
+        point_embedding = self.pe_layer.forward_with_coords(points, self.input_image_size)
+        point_embedding[labels == -1] = 0.0
+        point_embedding[labels == -1] += self.not_a_point_embed.weight
+        point_embedding[labels == 0] += self.point_embeddings[0].weight
+        point_embedding[labels == 1] += self.point_embeddings[1].weight
+        return point_embedding
+
+    def _embed_boxes(self, boxes: torch.Tensor) -> torch.Tensor:
+        """Embeds box prompts."""
+        boxes = boxes + 0.5  # Shift to center of pixel
+        coords = boxes.reshape(-1, 2, 3)
+        corner_embedding = self.pe_layer.forward_with_coords(coords, self.input_image_size)
+        corner_embedding[:, 0, :] += self.point_embeddings[2].weight
+        corner_embedding[:, 1, :] += self.point_embeddings[3].weight
+        return corner_embedding
+
+    def _embed_masks(self, masks: torch.Tensor) -> torch.Tensor:
+        """Embeds mask inputs."""
+        mask_embedding = self.mask_downscaling(masks)
+        return mask_embedding
+
+    def _get_batch_size(
+        self,
+        points: Optional[Tuple[torch.Tensor, torch.Tensor]],
+        boxes: Optional[torch.Tensor],
+        masks: Optional[torch.Tensor],
+        text_embedding: Optional[torch.Tensor],
+    ) -> int:
+        """
+        Gets the batch size of the output given the batch size of the input prompts.
+        """
+        if points is not None:
+            return points[0].shape[0]
+        elif boxes is not None:
+            return boxes.shape[0]
+        elif masks is not None:
+            return masks.shape[0]
+        elif text_embedding is not None:
+            return text_embedding.shape[0]
+        else:
+            return 1
+
+    def _get_device(self) -> torch.device:
+        return self.point_embeddings[0].weight.device
+
+    def forward(
+        self,
+        points: Optional[Tuple[torch.Tensor, torch.Tensor]],
+        boxes: Optional[torch.Tensor],
+        masks: Optional[torch.Tensor],
+        text_embedding: Optional[torch.Tensor],
+    ) -> Tuple[torch.Tensor, torch.Tensor]:
+        
+        bs = self._get_batch_size(points, boxes, masks, text_embedding)
+        sparse_embeddings = torch.empty((bs, 0, self.embed_dim), device=self._get_device())
+
+        if points is not None:
+            coords, labels = points
+            point_embeddings = self._embed_points(coords, labels, pad=(boxes is None))
+            sparse_embeddings = torch.cat([sparse_embeddings, point_embeddings], dim=1)
+        
+        if boxes is not None:
+            box_embeddings = self._embed_boxes(boxes)
+            sparse_embeddings = torch.cat([sparse_embeddings, box_embeddings], dim=1)
+        
+        if text_embedding is not None:
+            sparse_embeddings = torch.cat([sparse_embeddings, text_embedding.unsqueeze(dim=1)], dim=1)
+        
+        if masks is not None:
+            dense_embeddings = self._embed_masks(masks)
+        else:
+            dense_embeddings = self.no_mask_embed.weight.reshape(1, -1, 1, 1, 1).expand(
+                bs, -1, int(self.image_embedding_size[0]), int(self.image_embedding_size[1]), int(self.image_embedding_size[2])
+            )
+
+        return sparse_embeddings, dense_embeddings
+
+
+class PositionEmbeddingRandom(nn.Module):
+    """
+    Positional encoding using random spatial frequencies.
+    """
+
+    def __init__(self, num_pos_feats: int = 64, scale: Optional[float] = None) -> None:
+        super().__init__()
+        if scale is None or scale <= 0.0:
+            scale = 1.0
+        self.register_buffer(
+            "positional_encoding_gaussian_matrix",
+            scale * torch.randn((3, num_pos_feats)),
+        )
+
+    def _pe_encoding(self, coords: torch.Tensor) -> torch.Tensor:
+        """Positionally encode points that are normalized to [0,1]."""
+        # assuming coords are in [0, 1]^2 square and have d_1 x ... x d_n x 2 shape
+        coords = 2 * coords - 1
+        coords = coords @ self.positional_encoding_gaussian_matrix
+        coords = 2 * np.pi * coords
+        # outputs d_1 x ... x d_n x C shape
+        return torch.cat([torch.sin(coords), torch.cos(coords)], dim=-1)
+
+    def forward(self, size: Tuple[int, int, int]) -> torch.Tensor:
+        """Generate positional encoding for a grid of the specified size."""
+        h, w, d = size
+        device: Any = self.positional_encoding_gaussian_matrix.device
+        grid = torch.ones((h, w, d), device=device, dtype=torch.float32)
+        y_embed = grid.cumsum(dim=0) - 0.5
+        x_embed = grid.cumsum(dim=1) - 0.5
+        z_embed = grid.cumsum(dim=2) - 0.5
+        y_embed = y_embed / h
+        x_embed = x_embed / w
+        z_embed = z_embed / d
+
+        pe = self._pe_encoding(torch.stack([x_embed, y_embed, z_embed], dim=-1))
+        return pe.permute(3, 0, 1, 2)  # C x H x W x D
+
+    def forward_with_coords(
+        self, coords_input: torch.Tensor, image_size: Tuple[int, int]
+    ) -> torch.Tensor:
+        """Positionally encode points that are not normalized to [0,1]."""
+        coords = coords_input.clone()
+        coords[:, :, 0] = coords[:, :, 0] / image_size[1]
+        coords[:, :, 1] = coords[:, :, 1] / image_size[0]
+        coords[:, :, 2] = coords[:, :, 2] / image_size[2]
+        return self._pe_encoding(coords.to(torch.float))  # B x N x C
+
+# two way transformer
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+# All rights reserved.
+
+# This source code is licensed under the license found in the
+# LICENSE file in the root directory of this source tree.
+
+import torch
+from torch import Tensor, nn
+
+import math
+from typing import Tuple, Type
+
+class TwoWayTransformer(nn.Module):
+    def __init__(
+        self,
+        depth: int,
+        embedding_dim: int,
+        num_heads: int,
+        mlp_dim: int,
+        activation: Type[nn.Module] = nn.ReLU,
+        attention_downsample_rate: int = 2,
+    ) -> None:
+        """
+        A transformer decoder that attends to an input image using
+        queries whose positional embedding is supplied.
+
+        Args:
+          depth (int): number of layers in the transformer
+          embedding_dim (int): the channel dimension for the input embeddings
+          num_heads (int): the number of heads for multihead attention. Must
+            divide embedding_dim
+          mlp_dim (int): the channel dimension internal to the MLP block
+          activation (nn.Module): the activation to use in the MLP block
+        """
+        super().__init__()
+        self.depth = depth
+        self.embedding_dim = embedding_dim
+        self.num_heads = num_heads
+        self.mlp_dim = mlp_dim
+        self.layers = nn.ModuleList()
+
+        for i in range(depth):
+            self.layers.append(
+                TwoWayAttentionBlock(
+                    embedding_dim=embedding_dim,
+                    num_heads=num_heads,
+                    mlp_dim=mlp_dim,
+                    activation=activation,
+                    attention_downsample_rate=attention_downsample_rate,
+                    skip_first_layer_pe=(i == 0),
+                )
+            )
+
+        self.final_attn_token_to_image = Attention(
+            embedding_dim, num_heads, downsample_rate=attention_downsample_rate
+        )
+        self.norm_final_attn = nn.LayerNorm(embedding_dim)
+
+    def forward(
+        self,
+        image_embedding: Tensor,
+        image_pe: Tensor,
+        point_embedding: Tensor,
+    ) -> Tuple[Tensor, Tensor]:
+        """
+        Args:
+          image_embedding (torch.Tensor): image to attend to. Should be shape
+            B x embedding_dim x h x w for any h and w.
+          image_pe (torch.Tensor): the positional encoding to add to the image. Must
+            have the same shape as image_embedding.
+          point_embedding (torch.Tensor): the embedding to add to the query points.
+            Must have shape B x N_points x embedding_dim for any N_points.
+
+        Returns:
+          torch.Tensor: the processed point_embedding
+          torch.Tensor: the processed image_embedding
+        """
+        # BxCxHxW -> BxHWxC == B x N_image_tokens x C
+        bs, c, h, w, d = image_embedding.shape
+        image_embedding = image_embedding.flatten(2).permute(0, 2, 1)
+        image_pe = image_pe.flatten(2).permute(0, 2, 1)
+
+        # Prepare queries
+        queries = point_embedding
+        keys = image_embedding
+
+        # Apply transformer blocks and final layernorm
+        for layer in self.layers:
+            queries, keys = layer(
+                queries=queries,
+                keys=keys,
+                query_pe=point_embedding,
+                key_pe=image_pe,
+            )
+
+        # Apply the final attention layer from the points to the image
+        q = queries + point_embedding
+        k = keys + image_pe
+        attn_out = self.final_attn_token_to_image(q=q, k=k, v=keys)
+        queries = queries + attn_out
+        queries = self.norm_final_attn(queries)
+
+        return queries, keys
+
+
+class TwoWayAttentionBlock(nn.Module):
+    def __init__(
+        self,
+        embedding_dim: int,
+        num_heads: int,
+        mlp_dim: int = 2048,
+        activation: Type[nn.Module] = nn.ReLU,
+        attention_downsample_rate: int = 2,
+        skip_first_layer_pe: bool = False,
+    ) -> None:
+        """
+        A transformer block with four layers: (1) self-attention of sparse
+        inputs, (2) cross attention of sparse inputs to dense inputs, (3) mlp
+        block on sparse inputs, and (4) cross attention of dense inputs to sparse
+        inputs.
+
+        Arguments:
+          embedding_dim (int): the channel dimension of the embeddings
+          num_heads (int): the number of heads in the attention layers
+          mlp_dim (int): the hidden dimension of the mlp block
+          activation (nn.Module): the activation of the mlp block
+          skip_first_layer_pe (bool): skip the PE on the first layer
+        """
+        super().__init__()
+        self.self_attn = Attention(embedding_dim, num_heads)
+        self.norm1 = nn.LayerNorm(embedding_dim)
+
+        self.cross_attn_token_to_image = Attention(
+            embedding_dim, num_heads, downsample_rate=attention_downsample_rate
+        )
+        self.norm2 = nn.LayerNorm(embedding_dim)
+
+        self.mlp = MLPBlock(embedding_dim, mlp_dim, activation)
+        self.norm3 = nn.LayerNorm(embedding_dim)
+
+        self.norm4 = nn.LayerNorm(embedding_dim)
+        self.cross_attn_image_to_token = Attention(
+            embedding_dim, num_heads, downsample_rate=attention_downsample_rate
+        )
+
+        self.skip_first_layer_pe = skip_first_layer_pe
+
+    def forward(
+        self, queries: Tensor, keys: Tensor, query_pe: Tensor, key_pe: Tensor
+    ) -> Tuple[Tensor, Tensor]:
+        # Self attention block
+        if self.skip_first_layer_pe:
+            queries = self.self_attn(q=queries, k=queries, v=queries)
+        else:
+            q = queries + query_pe
+            attn_out = self.self_attn(q=q, k=q, v=queries)
+            queries = queries + attn_out
+        queries = self.norm1(queries)
+
+        # Cross attention block, tokens attending to image embedding
+        q = queries + query_pe
+        k = keys + key_pe
+        attn_out = self.cross_attn_token_to_image(q=q, k=k, v=keys)
+        queries = queries + attn_out
+        queries = self.norm2(queries)
+
+        # MLP block
+        mlp_out = self.mlp(queries)
+        queries = queries + mlp_out
+        queries = self.norm3(queries)
+
+        # Cross attention block, image embedding attending to tokens
+        q = queries + query_pe
+        k = keys + key_pe
+        attn_out = self.cross_attn_image_to_token(q=k, k=q, v=queries)
+        keys = keys + attn_out
+        keys = self.norm4(keys)
+
+        return queries, keys
+
+
+class Attention(nn.Module):
+    """
+    An attention layer that allows for downscaling the size of the embedding
+    after projection to queries, keys, and values.
+    """
+
+    def __init__(
+        self,
+        embedding_dim: int,
+        num_heads: int,
+        downsample_rate: int = 1,
+    ) -> None:
+        super().__init__()
+        self.embedding_dim = embedding_dim
+        self.internal_dim = embedding_dim // downsample_rate
+        self.num_heads = num_heads
+        assert self.internal_dim % num_heads == 0, "num_heads must divide embedding_dim."
+
+        self.q_proj = nn.Linear(embedding_dim, self.internal_dim)
+        self.k_proj = nn.Linear(embedding_dim, self.internal_dim)
+        self.v_proj = nn.Linear(embedding_dim, self.internal_dim)
+        self.out_proj = nn.Linear(self.internal_dim, embedding_dim)
+
+    def _separate_heads(self, x: Tensor, num_heads: int) -> Tensor:
+        b, n, c = x.shape
+        x = x.reshape(b, n, num_heads, c // num_heads)
+        return x.transpose(1, 2)  # B x N_heads x N_tokens x C_per_head
+
+    def _recombine_heads(self, x: Tensor) -> Tensor:
+        b, n_heads, n_tokens, c_per_head = x.shape
+        x = x.transpose(1, 2)
+        return x.reshape(b, n_tokens, n_heads * c_per_head)  # B x N_tokens x C
+
+    def forward(self, q: Tensor, k: Tensor, v: Tensor) -> Tensor:
+        # Input projections
+        q = self.q_proj(q)
+        k = self.k_proj(k)
+        v = self.v_proj(v)
+
+        # Separate into heads
+        q = self._separate_heads(q, self.num_heads)
+        k = self._separate_heads(k, self.num_heads)
+        v = self._separate_heads(v, self.num_heads)
+
+        # Attention
+        _, _, _, c_per_head = q.shape
+        attn = q @ k.permute(0, 1, 3, 2)  # B x N_heads x N_tokens x N_tokens
+        attn = attn / math.sqrt(c_per_head)
+        attn = torch.softmax(attn, dim=-1)
+
+        # Get output
+        out = attn @ v
+        out = self._recombine_heads(out)
+        out = self.out_proj(out)
+
+        return out
+
+# From https://github.com/facebookresearch/detectron2/blob/main/detectron2/layers/batch_norm.py # noqa
+# Itself from https://github.com/facebookresearch/ConvNeXt/blob/d1fa8f6fef0a165b27399986cc2bdacc92777e40/models/convnext.py#L119  # noqa
+class LayerNorm2d(nn.Module):
+    def __init__(self, num_channels: int, eps: float = 1e-6) -> None:
+        super().__init__()
+        self.weight = nn.Parameter(torch.ones(num_channels))
+        self.bias = nn.Parameter(torch.zeros(num_channels))
+        self.eps = eps
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        u = x.mean(1, keepdim=True)
+        s = (x - u).pow(2).mean(1, keepdim=True)
+        x = (x - u) / torch.sqrt(s + self.eps)
+        x = self.weight[:, None, None] * x + self.bias[:, None, None]
+        return x
+
+class MLPBlock(nn.Module):
+    def __init__(
+        self,
+        embedding_dim: int,
+        mlp_dim: int,
+        act: Type[nn.Module] = nn.GELU,
+    ) -> None:
+        super().__init__()
+        self.lin1 = nn.Linear(embedding_dim, mlp_dim)
+        self.lin2 = nn.Linear(mlp_dim, embedding_dim)
+        self.act = act()
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        return self.lin2(self.act(self.lin1(x)))
+    
+
+# sam
+class Sam(nn.Module):
+    mask_threshold: float = 0.0
+    image_format: str = "RGB"
+
+    def __init__(
+        self,
+        image_encoder,
+        prompt_encoder,
+        mask_decoder,
+        pixel_mean: List[float] = [123.675, 116.28, 103.53],
+        pixel_std: List[float] = [58.395, 57.12, 57.375],
+    ) -> None:
+        """
+        SAM predicts object masks from an image and input prompts.
+
+        Arguments:
+          image_encoder (ImageEncoderViT): The backbone used to encode the
+            image into image embeddings that allow for efficient mask prediction.
+          prompt_encoder (PromptEncoder): Encodes various types of input prompts.
+          mask_decoder (MaskDecoder): Predicts masks from the image embeddings
+            and encoded prompts.
+          pixel_mean (list(float)): Mean values for normalizing pixels in the input image.
+          pixel_std (list(float)): Std values for normalizing pixels in the input image.
+        """
+        super().__init__()
+        self.image_encoder = image_encoder
+        self.prompt_encoder = prompt_encoder
+        self.mask_decoder = mask_decoder
+        self.register_buffer("pixel_mean", torch.Tensor(pixel_mean).view(-1, 1, 1), False)
+        self.register_buffer("pixel_std", torch.Tensor(pixel_std).view(-1, 1, 1), False)
+
+    @property
+    def device(self) -> Any:
+        return self.pixel_mean.device
+
+    @torch.no_grad()
+    def forward(
+        self,
+        batched_input: List[Dict[str, Any]],
+        multimask_output: bool,
+    ) -> List[Dict[str, torch.Tensor]]:
+        """
+        Predicts masks end-to-end from provided images and prompts.
+        If prompts are not known in advance, using SamPredictor is
+        recommended over calling the model directly.
+
+        Arguments:
+          batched_input (list(dict)): A list over input images, each a
+            dictionary with the following keys. A prompt key can be
+            excluded if it is not present.
+              'image': The image as a torch tensor in 3xHxW format,
+                already transformed for input to the model.
+              'original_size': (tuple(int, int)) The original size of
+                the image before transformation, as (H, W).
+              'point_coords': (torch.Tensor) Batched point prompts for
+                this image, with shape BxNx2. Already transformed to the
+                input frame of the model.
+              'point_labels': (torch.Tensor) Batched labels for point prompts,
+                with shape BxN.
+              'boxes': (torch.Tensor) Batched box inputs, with shape Bx4.
+                Already transformed to the input frame of the model.
+              'mask_inputs': (torch.Tensor) Batched mask inputs to the model,
+                in the form Bx1xHxW.
+          multimask_output (bool): Whether the model should predict multiple
+            disambiguating masks, or return a single mask.
+
+        Returns:
+          (list(dict)): A list over input images, where each element is
+            as dictionary with the following keys.
+              'masks': (torch.Tensor) Batched binary mask predictions,
+                with shape BxCxHxW, where B is the number of input prompts,
+                C is determined by multimask_output, and (H, W) is the
+                original size of the image.
+              'iou_predictions': (torch.Tensor) The model's predictions
+                of mask quality, in shape BxC.
+              'low_res_logits': (torch.Tensor) Low resolution logits with
+                shape BxCxHxW, where H=W=256. Can be passed as mask input
+                to subsequent iterations of prediction.
+        """
+        input_images = torch.stack([self.preprocess(x["image"]) for x in batched_input], dim=0)
+        image_embeddings = self.image_encoder(input_images)
+
+        outputs = []
+        for image_record, curr_embedding in zip(batched_input, image_embeddings):
+            if "point_coords" in image_record:
+                points = (image_record["point_coords"], image_record["point_labels"])
+            else:
+                points = None
+            sparse_embeddings, dense_embeddings = self.prompt_encoder(
+                points=points,
+                boxes=image_record.get("boxes", None),
+                masks=image_record.get("mask_inputs", None),
+            )
+            low_res_masks, iou_predictions = self.mask_decoder(
+                image_embeddings=curr_embedding.unsqueeze(0),
+                image_pe=self.prompt_encoder.get_dense_pe(),
+                sparse_prompt_embeddings=sparse_embeddings,
+                dense_prompt_embeddings=dense_embeddings,
+                multimask_output=multimask_output,
+            )
+            masks = self.postprocess_masks(
+                low_res_masks,
+                input_size=image_record["image"].shape[-2:],
+                original_size=image_record["original_size"],
+            )
+            masks = masks > self.mask_threshold
+            outputs.append(
+                {
+                    "masks": masks,
+                    "iou_predictions": iou_predictions,
+                    "low_res_logits": low_res_masks,
+                }
+            )
+        return outputs
+
+    def postprocess_masks(
+        self,
+        masks: torch.Tensor,
+        input_size: Tuple[int, ...],
+        original_size: Tuple[int, ...],
+    ) -> torch.Tensor:
+        """
+        Remove padding and upscale masks to the original image size.
+
+        Arguments:
+          masks (torch.Tensor): Batched masks from the mask_decoder,
+            in BxCxHxW format.
+          input_size (tuple(int, int)): The size of the image input to the
+            model, in (H, W) format. Used to remove padding.
+          original_size (tuple(int, int)): The original size of the image
+            before resizing for input to the model, in (H, W) format.
+
+        Returns:
+          (torch.Tensor): Batched masks in BxCxHxW format, where (H, W)
+            is given by original_size.
+        """
+        masks = F.interpolate(
+            masks,
+            (self.image_encoder.img_size, self.image_encoder.img_size),
+            mode="bilinear",
+            align_corners=False,
+        )
+        masks = masks[..., : input_size[0], : input_size[1]]
+        masks = F.interpolate(masks, original_size, mode="bilinear", align_corners=False)
+        return masks
+
+    def preprocess(self, x: torch.Tensor) -> torch.Tensor:
+        """Normalize pixel values and pad to a square input."""
+        # Normalize colors
+        # TODO
+        x = (x - self.pixel_mean) / self.pixel_std
+
+        # Pad
+        h, w = x.shape[-2:]
+        padh = self.image_encoder.img_size - h
+        padw = self.image_encoder.img_size - w
+        x = F.pad(x, (0, padw, 0, padh))
+        return x

SegVol_v1.pth → pytorch_model.bin

@@ -1,3 +1,3 @@
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+size 723726667

special_tokens_map.json

@@ -0,0 +1 @@
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tokenizer_config.json

@@ -0,0 +1 @@
+{"unk_token": {"content": "<|endoftext|>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "bos_token": {"content": "<|startoftext|>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "eos_token": {"content": "<|endoftext|>", "single_word": false, "lstrip": false, "rstrip": false, "normalized": true, "__type": "AddedToken"}, "pad_token": "<|endoftext|>", "add_prefix_space": false, "errors": "replace", "do_lower_case": true, "name_or_path": "/home/yuxin/BAAI/code_release/segvol_transformers/config/clip", "special_tokens_map_file": "/home/yuxin/BAAI/code_release/segvol_transformers/config/clip/special_tokens_map.json", "tokenizer_class": "CLIPTokenizer"}