Add fine-tuned SuperAnimal-Quadruped support and improve demo setup

.github/workflows/codespell.yml

@@ -18,4 +18,4 @@ jobs:
       - name: Codespell
         uses: codespell-project/actions-codespell@v1
         with:
-           ignore_words_list: fmpose, mpjpe, uvd, xyz, hm36, cpn, dbb
+           ignore_words_list: fmpose, mpjpe, uvd, xyz, hm36, cpn, dbb, mot

README.md

@@ -31,7 +31,7 @@ FMPose3D creates a 3D pose from a single 2D image. It leverages fast Flow Matchi
 
 ### Set up an environment
 
-Make sure you have Python 3.10+. You can set this up with:
+Make sure you have Python 3.10. The installation and demos are tested with Python 3.10. You can set this up with:
 ```bash
 conda create -n fmpose_3d python=3.10
 conda activate fmpose_3d
@@ -45,6 +45,8 @@ For the animal pipeline, install the optional DeepLabCut dependency:
 pip install "fmpose3d[animals]"
 ```
 
+> **PyTorch/CUDA note.** FMPose3D pins `torch>=2.4.1,<2.5` and `torchvision>=0.19.1,<0.20`, which use CUDA 12.1 wheels by default on Linux. If your driver does not support CUDA 12.1, or if you need a specific CUDA build, install PyTorch first using the matching command from [pytorch.org](https://pytorch.org/get-started/locally/), then install `fmpose3d`.
+
 ## Demos
 
 ### Testing on in-the-wild images (humans)
@@ -108,7 +110,7 @@ FMPose3D also ships a high-level Python API for end-to-end 3D pose estimation fr
 
 ## Experiments on non-human animals
 
-For animal training/testing and demo scripts, see [animals/README.md](animals/README.md).
+For animal training/testing and demo scripts, see [animals/README.md](animals/README.md). The animal demo **auto-downloads both checkpoints** (a 26-joint SuperAnimal-Quadruped fine-tuned on Animal3D for 2D pose, and the FMPose3D animal flow-matching lifter for 3D) from [Hugging Face](https://huggingface.co/MLAdaptiveIntelligence/FMPose3D) on first run — no manual setup needed.
 
 ## Citation 
 

animals/README.md

@@ -9,8 +9,10 @@ In this part, the FMPose3D model is trained on [Animal3D](https://xujiacong.gith
 
 This visualization script is designed for single-frame based model, allowing you to easily run 3D animal pose estimation on any single image.
 
-Before testing, make sure you have the pre-trained model ready.
-You may either use the model trained by your own or download ours from [here](https://drive.google.com/drive/folders/1kL4aOyWNq0o9zB0rSTRM8KYgkySVmUTk?usp=drive_link) and place it in the `./pre_trained_models` directory.
+Both pre-trained checkpoints are **auto-downloaded from [Hugging Face](https://huggingface.co/MLAdaptiveIntelligence/FMPose3D)** on first run and cached under `~/.cache/huggingface/`. No manual downloads required.
+
+- **3D lifter** (`fmpose3d_animals.pth`) — Animal3D 26-joint flow-matching 2D→3D lifter. Override: set `saved_model_path` in `vis_animals.sh` to a local `.pth`.
+- **2D pose model** (`sa_finetune_hrnet_w32.pt`) — SuperAnimal-Quadruped HRNet-w32 fine-tuned on Animal3D for the 26-joint Animal3D output layout. Override: set `saved_2d_model_path` in `vis_animals.sh` to a local `.pt`.
 
 Next, put your test images into folder `demo/images`. Then run the visualization script:
 ```bash
@@ -49,7 +51,7 @@ Place the downloaded files in the `dataset/` folder of this project:
 ## Training
 The training logs, checkpoints, and related files of each training time will be saved in the './checkpoint' folder.
 
-For trainig on the two datasets:
+For training on the two datasets:
 
 ```bash
 cd animals

animals/demo/vis_animals.py

@@ -23,6 +23,8 @@
 import imageio
 from fmpose3d.animals.common.arguments import opts as parse_args
 from fmpose3d.common.camera import normalize_screen_coordinates, camera_to_world
+from fmpose3d.common.config import SuperAnimalConfig
+from fmpose3d.inference_api.fmpose3d import SuperAnimalEstimator
 
 args = parse_args().parse()
 os.environ["CUDA_VISIBLE_DEVICES"] = args.gpu
@@ -46,21 +48,6 @@
     from fmpose3d.models import get_model
     CFM = get_model(args.model_type)
 
-try:
-    from deeplabcut.pose_estimation_pytorch.apis import (  # pyright: ignore[reportMissingImports]
-        superanimal_analyze_images,
-    )
-except ImportError:
-    raise ImportError(
-        "DeepLabCut is required for the animal demo. "
-        "Install it with: pip install \"fmpose3d[animals]\""
-    ) from None
-
-superanimal_name = "superanimal_quadruped"
-model_name = "hrnet_w32"
-detector_name = "fasterrcnn_resnet50_fpn_v2"
-max_individuals = 1
-
 def compute_limb_regularization_matrix(gt_3d):
     """
     Compute regularization matrix to align limb directions to vertical (0,0,1).
@@ -145,108 +132,35 @@ def apply_regularization(pose_3d, R):
     """
     return (R @ pose_3d.T).T
 
-def get_pose2D(path, output_dir, type):
+def build_2d_estimator():
+    """Build the 2D pose estimator once.
+
+    Empty --saved_2d_model_path -> auto-download fine-tuned snapshot from HF
+    on first predict.
+    Non-empty path -> use as a local override.
+    """
+    cfg = SuperAnimalConfig(
+        pose_snapshot_path=args.saved_2d_model_path,
+        pytorch_config_path=args.pytorch_config_2d_path,
+        auto_download_finetuned=True,
+    )
+    snapshot = cfg.pose_snapshot_path or "auto-download from HF on first predict"
+    print(f"[2D] pose snapshot = {snapshot}")
+    return SuperAnimalEstimator(cfg)
+
+
+def get_pose2D(estimator, path, output_dir, type):
 
     print('\nGenerating 2D pose...')
-
-    # Check if this is the special debug case for 000000119761_horse
-    filename = Path(path).stem
-    is_debug_case = "000000119761_horse" in filename
-
-    if is_debug_case:
-        print(f"DEBUG MODE: Using provided 2D pose for {filename}")
-        # User provided 2D pose (26 keypoints, x, y coordinates, ignoring the last dimension)
-        provided_pose = np.array([
-            [361, 230], [361, 237], [363, 279], [257, 359], [251, 374],
-            [164, 365], [68, 372], [99, 206], [247, 266], [253, 285],
-            [127, 275], [101, 285], [267, 217], [268, 229], [273, 318],
-            [250, 340], [128, 311], [76, 305], [313, 220], [48, 310],
-            [351, 203], [352, 210], [340, 257], [340, 261], [373, 276],
-            [55, 247]
-        ], dtype=np.float32)
-
-        # Reshape to match expected format: (1, 26, 2) for single individual
-        provided_pose = provided_pose.reshape(1, 26, 2)
-
-        # Create xy_preds dict with the provided pose
-        xy_preds = {path: provided_pose}
-        print(f"Using provided 2D pose with shape: {provided_pose.shape}")
-    else:
-        # Normal prediction flow
-        predictions = superanimal_analyze_images(
-            superanimal_name,
-            model_name,
-            detector_name,
-            path,
-            max_individuals,
-            out_folder=output_dir
-        )
-        print("predictions:", predictions)
-
-        # get the 2D keypoints from the predictions
-        xy_preds = {}
-        # predictions is a dict: {image_path: {"bodyparts": (N, K, 3), "bboxes": ..., "bbox_scores": ...}}
-        for img_path, payload in predictions.items():
-            bodyparts = payload.get("bodyparts")
-            if bodyparts is None:
-                continue
-            # bodyparts shape: (num_individuals, num_keypoints, 3) -> [:, :, :2] keeps x,y
-            xy_preds[img_path] = bodyparts[..., :2]
-
-    print("2D keypoints (x,y) by image:")
-    for img_path, xy in xy_preds.items():
-        print(f"{img_path}: shape {xy.shape}")
-
-    # For debug case, the provided pose is already in Animal3D format (26 keypoints)
-    # So we skip the mapping step
-    if is_debug_case:
-        print("DEBUG MODE: Skipping keypoint mapping (already in Animal3D format)")
-        mapped_keypoints = xy_preds
-    else:
-        # now map the keypoints to a different set of keypoints (used in Animal3D)
-        # keypoint mapping from quadruped80K super keypotints to animal3d keypoints
-        keypoint_mapping = {"quadruped80k":[10, 5, -1, 26, 29, 30, 35, 22, 24, 27, 31, 32, -1, -1, 25, 28, 33, 34, 15, 23, 11, 6, 4, 3, 0, -1]}
-
-        # for the keypoint_mapping, -1 indicates that there is no corresponding keypoint in the source set, but we can interpolate 
-        # for index 2, we can interpolate between keypoints 3 and 4 in the source set to get a better estimate of the missing keypoint
-        # for index 25, we can interpolate between keypoints 22 and 23 in the source set
-        # for index 12, we can interpolate between keypoints 24 and 19 in the source set
-        # for index 13, we can interpolate between keypoints 27 and 19 in the source set
-
-        # Define interpolation rules for -1 indices: {target_idx: (source_idx1, source_idx2)}
-        interpolation_rules = {
-            2: (3, 4),      # interpolate between source keypoints 3 and 4
-            12: (24, 19),   # interpolate between source keypoints 24 and 19
-            13: (27, 19),   # interpolate between source keypoints 27 and 19
-            25: (22, 23),   # interpolate between source keypoints 22 and 23
-        }
-
-        # map the keypoints
-        mapped_keypoints = {}
-        mapping_indices = keypoint_mapping["quadruped80k"]
-
-        for img_path, xy in xy_preds.items():
-            # xy shape: (num_individuals, num_keypoints, 2)
-            num_individuals, num_keypoints, _ = xy.shape
-            num_target_keypoints = len(mapping_indices)
-
-            # Initialize mapped array with NaN or zeros
-            mapped_xy = np.full((num_individuals, num_target_keypoints, 2), np.nan)
-
-            for target_idx, source_idx in enumerate(mapping_indices):
-                if source_idx != -1 and source_idx < num_keypoints:
-                    # Copy the keypoint from source to target position
-                    mapped_xy[:, target_idx, :] = xy[:, source_idx, :]
-                elif source_idx == -1 and target_idx in interpolation_rules:
-                    # Perform interpolation for -1 indices
-                    src1, src2 = interpolation_rules[target_idx]
-                    if src1 < num_keypoints and src2 < num_keypoints:
-                        # Interpolate as the average of the two source keypoints
-                        mapped_xy[:, target_idx, :] = (xy[:, src1, :] + xy[:, src2, :]) / 2.0
-                        print(f"Interpolated keypoint {target_idx} from source keypoints {src1} and {src2}")
-
-            mapped_keypoints[img_path] = mapped_xy
-            print(f"Mapped {img_path}: {xy.shape} -> {mapped_xy.shape}")
+
+    img_bgr = cv2.imread(path)
+    if img_bgr is None:
+        raise FileNotFoundError(f"Failed to read image: {path}")
+
+    # predict() returns (kpts (1, N, 26, 2), scores (1, N, 26), valid_mask (N,)).
+    kpts, _scores, _mask = estimator.predict(img_bgr[None])
+    # Pack into the {img_path: (1, 26, 2)} format expected by the save/vis code below.
+    mapped_keypoints = {path: kpts[:, 0, :, :]}
 
     print('Generating 2D pose successful!')
 
@@ -259,7 +173,6 @@ def get_pose2D(path, output_dir, type):
         # Save in the same format as vis_in_the_wild.py for compatibility
         output_npz = output_dir_2D + 'keypoints.npz'
         np.savez_compressed(output_npz, reconstruction=mapped_xy)
-        print(f"Saved keypoints to {output_npz}")
 
         # Also save as npy for backup
         img_name = Path(img_path).stem
@@ -275,7 +188,6 @@ def get_pose2D(path, output_dir, type):
                 index=[f'keypoint_{i}' for i in range(mapped_xy.shape[1])]
             )
             df.to_csv(csv_file)
-            print(f"Saved individual {ind_idx} keypoints to {csv_file}")
 
         # Visualize mapped keypoints on image
         img = Image.open(img_path)
@@ -328,39 +240,38 @@ def get_pose2D(path, output_dir, type):
         plt.tight_layout()
         plt.savefig(vis_file, dpi=150, bbox_inches='tight')
         plt.close(fig)
-        print(f"Saved visualization to {vis_file}")
 
 
-def get_pose3D(path, output_dir, type='image'):
-    """
-    Generate 3D pose from 2D keypoints using the model.
-    This function reads the 2D keypoints saved by get_pose2D and generates 3D poses.
+def build_3d_lifter():
+    """Build the 3D lifter once and return (model, device).
+
+    Empty --saved_model_path -> auto-download fmpose3d_animals.pth from HF.
+    Non-empty path is used as a local override.
     """
-    print('\nGenerating 3D pose...')
-    print(f"args.n_joints: {args.n_joints}, args.out_joints: {args.out_joints}")
-
-    ## Reload model
+    from fmpose3d.utils.weights import resolve_weights_path
+
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    model = CFM(args).to(device)
 
-    model = {}
-    model['CFM'] = CFM(args).to(device)
-
-    model_dict = model['CFM'].state_dict()
-    model_path = args.saved_model_path
-    print(f"Loading model from: {model_path}")
+    model_path = resolve_weights_path(args.saved_model_path, f"{args.model_type}.pth")
+    print(f"[3D] lifter weights = {model_path}")
     pre_dict = torch.load(model_path, map_location=device, weights_only=True)
-    for name, key in model_dict.items():
+    model_dict = model.state_dict()
+    for name in model_dict:
         model_dict[name] = pre_dict[name]
-    model['CFM'].load_state_dict(model_dict)
-    print("Model loaded successfully!")
-
-    model = model['CFM'].eval()
+    model.load_state_dict(model_dict)
+    return model.eval()
+
+
+def get_pose3D(model, path, output_dir, type='image'):
+    """
+    Generate 3D pose from 2D keypoints using the model.
+    Reads the 2D keypoints saved by get_pose2D and generates 3D poses.
+    """
+    print('\nGenerating 3D pose...')
 
-    ## Load input 2D keypoints
     keypoints = np.load(output_dir + 'input_2D/keypoints.npz', allow_pickle=True)['reconstruction']
-    print(f"Loaded keypoints shape: {keypoints.shape}")
 
-    ## Generate 3D poses
     if type == "image":
         i = 0
         img = cv2.imread(path)
@@ -422,9 +333,6 @@ def euler_sample(c_2d, y_local, steps, model_3d):
         return y_local
 
     ## Estimation (without TTA for better results)
-    print("input_2D.shape:", input_2D.shape)
-    print("input_2D:", input_2D[0, 0])
-
     # Single inference without flip augmentation
     # Create 3D random noise with shape (1, 1, J, 3)
     y = torch.randn(input_2D.size(0), input_2D.size(1), input_2D.size(2), 3, device=device)
@@ -492,7 +400,6 @@ def euler_sample(c_2d, y_local, steps, model_3d):
         output_dir_2D_img = output_dir + 'pose2D_on_image/'
         os.makedirs(output_dir_2D_img, exist_ok=True)
         cv2.imwrite(f'{output_dir_2D_img}{i:04d}_2d.png', img_copy)
-        print(f"Saved 2D pose on image to {output_dir_2D_img}{i:04d}_2d.png")
 
     ## Save 3D pose as npz
     output_dir_3D = output_dir + 'pose3D/'
@@ -603,46 +510,46 @@ def img2gif(video_path, name, output_dir, duration=0.25):
 
 
 if __name__ == "__main__":
-    
+
     os.environ["CUDA_VISIBLE_DEVICES"] = args.gpu
 
     path = args.path # file path or folder path
-
-    # Check if path is a directory
+
+    # Build the 2D estimator and 3D lifter ONCE; reuse across all images/frames.
+    # This avoids redundant HF resolution and DLC/torch model reloads.
+    estimator_2d = build_2d_estimator()
+    model_3d = build_3d_lifter()
+
     if os.path.isdir(path):
-        # Get all image files in the directory
         image_extensions = ['*.jpg', '*.jpeg', '*.png', '*.bmp', '*.JPG', '*.JPEG', '*.PNG', '*.BMP']
         image_files = []
         for ext in image_extensions:
             image_files.extend(glob.glob(os.path.join(path, ext)))
         image_files.sort()
-        
+
         if len(image_files) == 0:
             print(f"No image files found in {path}")
             exit(0)
-        
+
         print(f"Found {len(image_files)} images in {path}")
-
-        # Process each image
+
         for img_path in tqdm(image_files, desc="Processing images"):
             filename = img_path.split('/')[-1].split('.')[0]
             output_dir = './predictions/' + filename + '/'
-            
+
             print(f"\nProcessing: {img_path}")
-            get_pose2D(img_path, output_dir, args.type)
-            get_pose3D(img_path, output_dir, args.type)
-        
+            get_pose2D(estimator_2d, img_path, output_dir, args.type)
+            get_pose3D(model_3d, img_path, output_dir, args.type)
+
         print(f'\nAll {len(image_files)} images processed successfully!')
     else:
         # Single file processing
         filename = path.split('/')[-1].split('.')[0]
         output_dir = './predictions/' + filename + '/'
 
-        get_pose2D(path, output_dir, args.type)
-        get_pose3D(path, output_dir, args.type)
+        get_pose2D(estimator_2d, path, output_dir, args.type)
+        get_pose3D(model_3d, path, output_dir, args.type)
 
-        if args.type=="video":
+        if args.type == "video":
             img2video(path, filename, output_dir)
             img2gif(path, filename, output_dir)
-
-        print('Generating demo successful!')