Upload organ_tumor_mask_box_point_512/config.yaml with huggingface_hub

organ_tumor_mask_box_point_512/config.yaml

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+scratch:
+  resolution: 512
+  batch_size: 8
+  num_workers: 10
+  num_frames: 8
+  max_num_objects: 1
+  base_lr: 5.0e-05
+  vision_lr: 3.0e-05
+  phases_per_epoch: 1
+  num_epochs: 40
+dataset:
+  organ_data_folder: /mnt/bn/bes-nas-zqz-lq-v6arnold6/mlx/users/zhangqizhe/data/TumorSegDB/v2.0/organ/internal/train
+  organ_metadata_file: /mnt/bn/bes-nas-zqz-lq-v6arnold6/mlx/users/zhangqizhe/data/TumorSegDB/v2.0/organ.jsonl
+  tumor_data_folder: /mnt/bn/bes-nas-zqz-lq-v6arnold6/mlx/users/zhangqizhe/data/TumorSegDB/v2.0/tumor/internal/train
+  tumor_metadata_file: /mnt/bn/bes-nas-zqz-lq-v6arnold6/mlx/users/zhangqizhe/data/TumorSegDB/v2.0/tumor.jsonl
+  multiplier: 1
+vos:
+  transforms:
+  - _target_: training.dataset.transforms.ComposeAPI
+    transforms:
+    - _target_: training.dataset.transforms.RandomResizeAPI
+      sizes: ${scratch.resolution}
+      square: true
+      consistent_transform: true
+    - _target_: training.dataset.transforms.ToTensorAPI
+    - _target_: training.dataset.transforms.NormalizeAPI
+      mean:
+      - 0.485
+      - 0.456
+      - 0.406
+      std:
+      - 0.229
+      - 0.224
+      - 0.225
+trainer:
+  _target_: training.trainer.Trainer
+  mode: train_only
+  max_epochs: ${times:${scratch.num_epochs},${scratch.phases_per_epoch}}
+  accelerator: cuda
+  seed_value: 123
+  data:
+    train:
+      _target_: training.dataset.sam2_datasets.TorchTrainMixedDataset
+      phases_per_epoch: ${scratch.phases_per_epoch}
+      batch_sizes:
+      - ${scratch.batch_size}
+      datasets:
+      - _target_: training.dataset.utils.RepeatFactorWrapper
+        dataset:
+          _target_: training.dataset.utils.ConcatDataset
+          datasets:
+          - _target_: training.dataset.vos_dataset.VOSDataset
+            transforms: ${vos.transforms}
+            training: true
+            video_dataset:
+              _target_: training.dataset.vos_raw_dataset.NPZRawDataset
+              data_folder: ${dataset.organ_data_folder}
+              metadata_file: ${dataset.organ_metadata_file}
+              dimension: 3
+              num_frames: ${scratch.num_frames}
+            sampler:
+              _target_: training.dataset.vos_sampler.RandomUniformSampler
+              num_frames: ${scratch.num_frames}
+              max_num_objects: ${scratch.max_num_objects}
+            multiplier: ${dataset.multiplier}
+          - _target_: training.dataset.vos_dataset.VOSDataset
+            transforms: ${vos.transforms}
+            training: true
+            video_dataset:
+              _target_: training.dataset.vos_raw_dataset.NPZRawDataset
+              data_folder: ${dataset.tumor_data_folder}
+              metadata_file: ${dataset.tumor_metadata_file}
+              dimension: 3
+              num_frames: ${scratch.num_frames}
+            sampler:
+              _target_: training.dataset.vos_sampler.RandomUniformSampler
+              num_frames: ${scratch.num_frames}
+              max_num_objects: ${scratch.max_num_objects}
+            multiplier: ${dataset.multiplier}
+      shuffle: true
+      num_workers: ${scratch.num_workers}
+      pin_memory: true
+      drop_last: true
+      collate_fn:
+        _target_: training.utils.data_utils.collate_fn
+        _partial_: true
+        dict_key: all
+  model:
+    _target_: training.model.sam2.SAM2Train
+    image_encoder:
+      _target_: sam2.modeling.backbones.image_encoder.ImageEncoder
+      scalp: 1
+      trunk:
+        _target_: sam2.modeling.backbones.hieradet.Hiera
+        embed_dim: 96
+        num_heads: 1
+        stages:
+        - 1
+        - 2
+        - 7
+        - 2
+        global_att_blocks:
+        - 5
+        - 7
+        - 9
+        window_pos_embed_bkg_spatial_size:
+        - 7
+        - 7
+      neck:
+        _target_: sam2.modeling.backbones.image_encoder.FpnNeck
+        position_encoding:
+          _target_: sam2.modeling.position_encoding.PositionEmbeddingSine
+          num_pos_feats: 256
+          normalize: true
+          scale: null
+          temperature: 10000
+        d_model: 256
+        backbone_channel_list:
+        - 768
+        - 384
+        - 192
+        - 96
+        fpn_top_down_levels:
+        - 2
+        - 3
+        fpn_interp_model: nearest
+    memory_attention:
+      _target_: sam2.modeling.memory_attention.MemoryAttention
+      d_model: 256
+      pos_enc_at_input: true
+      layer:
+        _target_: sam2.modeling.memory_attention.MemoryAttentionLayer
+        activation: relu
+        dim_feedforward: 2048
+        dropout: 0.1
+        pos_enc_at_attn: false
+        self_attention:
+          _target_: sam2.modeling.sam.transformer.RoPEAttention
+          rope_theta: 10000.0
+          feat_sizes:
+          - 32
+          - 32
+          embedding_dim: 256
+          num_heads: 1
+          downsample_rate: 1
+          dropout: 0.1
+        d_model: 256
+        pos_enc_at_cross_attn_keys: true
+        pos_enc_at_cross_attn_queries: false
+        cross_attention:
+          _target_: sam2.modeling.sam.transformer.RoPEAttention
+          rope_theta: 10000.0
+          feat_sizes:
+          - 32
+          - 32
+          rope_k_repeat: true
+          embedding_dim: 256
+          num_heads: 1
+          downsample_rate: 1
+          dropout: 0.1
+          kv_in_dim: 64
+      num_layers: 4
+    memory_encoder:
+      _target_: sam2.modeling.memory_encoder.MemoryEncoder
+      out_dim: 64
+      position_encoding:
+        _target_: sam2.modeling.position_encoding.PositionEmbeddingSine
+        num_pos_feats: 64
+        normalize: true
+        scale: null
+        temperature: 10000
+      mask_downsampler:
+        _target_: sam2.modeling.memory_encoder.MaskDownSampler
+        kernel_size: 3
+        stride: 2
+        padding: 1
+      fuser:
+        _target_: sam2.modeling.memory_encoder.Fuser
+        layer:
+          _target_: sam2.modeling.memory_encoder.CXBlock
+          dim: 256
+          kernel_size: 7
+          padding: 3
+          layer_scale_init_value: 1.0e-06
+          use_dwconv: true
+        num_layers: 2
+    num_maskmem: 7
+    image_size: ${scratch.resolution}
+    num_semantic_tokens: 14
+    semantic_prompt_level: 2
+    sigmoid_scale_for_mem_enc: 20.0
+    sigmoid_bias_for_mem_enc: -10.0
+    use_mask_input_as_output_without_sam: true
+    directly_add_no_mem_embed: true
+    no_obj_embed_spatial: true
+    use_high_res_features_in_sam: true
+    multimask_output_in_sam: true
+    iou_prediction_use_sigmoid: true
+    use_obj_ptrs_in_encoder: true
+    add_tpos_enc_to_obj_ptrs: true
+    proj_tpos_enc_in_obj_ptrs: true
+    use_signed_tpos_enc_to_obj_ptrs: true
+    only_obj_ptrs_in_the_past_for_eval: true
+    pred_obj_scores: true
+    pred_obj_scores_mlp: true
+    fixed_no_obj_ptr: true
+    multimask_output_for_tracking: true
+    use_multimask_token_for_obj_ptr: true
+    multimask_min_pt_num: 0
+    multimask_max_pt_num: 1
+    use_mlp_for_obj_ptr_proj: true
+    prob_to_use_pt_input_for_train: 0.5
+    prob_to_use_pt_input_for_eval: 0.0
+    prob_to_use_box_input_for_train: 0.5
+    prob_to_use_box_input_for_eval: 1.0
+    prob_to_use_mask_input_for_train: 0.5
+    prob_to_use_mask_input_for_eval: 0.0
+    prob_to_sample_from_gt_for_train: 0.1
+    num_frames_to_correct_for_train: 2
+    num_frames_to_correct_for_eval: 1
+    rand_frames_to_correct_for_train: true
+    add_all_frames_to_correct_as_cond: true
+    num_init_cond_frames_for_train: 2
+    rand_init_cond_frames_for_train: true
+    num_correction_pt_per_frame: 7
+    use_act_ckpt_iterative_pt_sampling: false
+    num_init_cond_frames_for_eval: 1
+    forward_backbone_per_frame_for_eval: false
+  logging:
+    tensorboard_writer:
+      _target_: training.utils.logger.make_tensorboard_logger
+      log_dir: ${launcher.experiment_log_dir}/tensorboard
+      flush_secs: 120
+      should_log: true
+    log_dir: ${launcher.experiment_log_dir}/logs
+    log_freq: 10
+  checkpoint:
+    save_dir: ${launcher.experiment_log_dir}/checkpoints
+    save_freq: 5
+    model_weight_initializer:
+      _partial_: true
+      _target_: training.utils.checkpoint_utils.load_state_dict_into_model
+      strict: true
+      ignore_unexpected_keys: null
+      ignore_missing_keys:
+      - sam_mask_decoder.semantic_tokens.weight
+      state_dict:
+        _target_: training.utils.checkpoint_utils.load_checkpoint_and_apply_kernels
+        checkpoint_path: /mnt/bn/bes-nas-zqz-lq-v6arnold6/mlx/users/zhangqizhe/model/SAM2.1/sam2.1_hiera_tiny.pt
+        ckpt_state_dict_keys:
+        - model
+  distributed:
+    backend: nccl
+    find_unused_parameters: true
+  optim:
+    amp:
+      enabled: true
+      amp_dtype: bfloat16
+    optimizer:
+      _target_: torch.optim.AdamW
+    gradient_clip:
+      _target_: training.optimizer.GradientClipper
+      max_norm: 0.1
+      norm_type: 2
+    param_group_modifiers:
+    - _target_: training.optimizer.layer_decay_param_modifier
+      _partial_: true
+      layer_decay_value: 0.9
+      apply_to: image_encoder.trunk
+      overrides:
+      - pattern: '*pos_embed*'
+        value: 1.0
+    options:
+      lr:
+      - scheduler:
+          _target_: fvcore.common.param_scheduler.CosineParamScheduler
+          start_value: ${scratch.base_lr}
+          end_value: ${divide:${scratch.base_lr},10}
+      - scheduler:
+          _target_: fvcore.common.param_scheduler.CosineParamScheduler
+          start_value: ${scratch.vision_lr}
+          end_value: ${divide:${scratch.vision_lr},10}
+        param_names:
+        - image_encoder.*
+      weight_decay:
+      - scheduler:
+          _target_: fvcore.common.param_scheduler.ConstantParamScheduler
+          value: 0.1
+      - scheduler:
+          _target_: fvcore.common.param_scheduler.ConstantParamScheduler
+          value: 0.0
+        param_names:
+        - '*bias*'
+        module_cls_names:
+        - torch.nn.LayerNorm
+  loss:
+    all:
+      _target_: training.loss_fns.MultiStepMultiMasksAndIous
+      weight_dict:
+        loss_mask: 20
+        loss_dice: 1
+        loss_iou: 1
+        loss_class: 1
+      supervise_all_iou: true
+      iou_use_l1_loss: true
+      pred_obj_scores: true
+      focal_alpha_obj_score: -1.0
+      focal_gamma_obj_score: 0
+launcher:
+  num_nodes: 1
+  gpus_per_node: 8
+  experiment_log_dir: /mnt/bn/bes-nas-zqz-lq-v6arnold6/mlx/users/zhangqizhe/code/Med/TumorSeg/logs/train/sam2.1/hiera_t/organ_tumor_mask_box_point_512
+submitit:
+  partition: null
+  account: null
+  qos: null
+  cpus_per_task: 10
+  use_cluster: false
+  timeout_hour: 24
+  name: null
+  port_range:
+  - 10000
+  - 65000