napari-tmidas 0.2.1__py3-none-any.whl → 0.2.4__py3-none-any.whl

napari_tmidas/processing_functions/spotiflow_env_manager.py

@@ -0,0 +1,591 @@
+# processing_functions/spotiflow_env_manager.py
+"""
+This module manages a dedicated virtual environment for Spotiflow.
+"""
+
+import contextlib
+import os
+import subprocess
+import tempfile
+
+import numpy as np
+
+from napari_tmidas._env_manager import BaseEnvironmentManager
+
+try:
+    import tifffile
+except ImportError:
+    tifffile = None
+
+
+class SpotiflowEnvironmentManager(BaseEnvironmentManager):
+    """Environment manager for Spotiflow."""
+
+    def __init__(self):
+        super().__init__("spotiflow")
+
+    def _install_dependencies(self, env_python: str) -> None:
+        """Install Spotiflow-specific dependencies."""
+        # Install PyTorch first for compatibility
+        # Try to detect if CUDA is available and GPU architecture
+        cuda_available = False
+        try:
+            import torch
+
+            cuda_available = torch.cuda.is_available()
+            if cuda_available:
+                print("CUDA is available in main environment")
+                # Try to get GPU info
+                if torch.cuda.device_count() > 0:
+                    gpu_name = torch.cuda.get_device_name(0)
+                    print(f"GPU detected: {gpu_name}")
+            else:
+                print("CUDA is not available in main environment")
+        except ImportError:
+            print("PyTorch not detected in main environment")
+            # Try to detect CUDA from nvidia-smi
+            try:
+                result = subprocess.run(
+                    ["nvidia-smi"], capture_output=True, text=True
+                )
+                if result.returncode == 0:
+                    cuda_available = True
+                    print("NVIDIA GPU detected via nvidia-smi")
+                else:
+                    cuda_available = False
+                    print("No NVIDIA GPU detected")
+            except FileNotFoundError:
+                cuda_available = False
+                print("nvidia-smi not found, assuming no CUDA support")
+
+        if cuda_available:
+            # Try to install PyTorch with CUDA support, but with fallback to CPU-only
+            print("Attempting PyTorch installation with CUDA support...")
+            try:
+                # First try with CUDA 11.8 which supports sm_61 (GTX 1080 Ti) and other older GPUs
+                subprocess.check_call(
+                    [
+                        env_python,
+                        "-m",
+                        "pip",
+                        "install",
+                        "torch==2.0.1",
+                        "torchvision==0.15.2",
+                        "--index-url",
+                        "https://download.pytorch.org/whl/cu118",
+                    ]
+                )
+                print("✓ PyTorch with CUDA 11.8 installed successfully")
+
+                # Test CUDA compatibility
+                test_script = """
+import torch
+try:
+    if torch.cuda.is_available():
+        test_tensor = torch.ones(1).cuda()
+        print("CUDA compatibility test passed")
+    else:
+        print("CUDA not available in PyTorch")
+        exit(1)
+except Exception as e:
+    print(f"CUDA compatibility test failed: {e}")
+    exit(1)
+"""
+                result = subprocess.run(
+                    [env_python, "-c", test_script],
+                    capture_output=True,
+                    text=True,
+                )
+
+                if result.returncode != 0:
+                    print(
+                        "CUDA compatibility test failed, falling back to CPU-only PyTorch..."
+                    )
+                    # Uninstall CUDA version and install CPU version
+                    subprocess.check_call(
+                        [
+                            env_python,
+                            "-m",
+                            "pip",
+                            "uninstall",
+                            "-y",
+                            "torch",
+                            "torchvision",
+                        ]
+                    )
+                    subprocess.check_call(
+                        [
+                            env_python,
+                            "-m",
+                            "pip",
+                            "install",
+                            "torch==2.0.1",
+                            "torchvision==0.15.2",
+                        ]
+                    )
+                    print(
+                        "✓ Switched to CPU-only PyTorch due to CUDA incompatibility"
+                    )
+                else:
+                    print("✓ CUDA compatibility test passed")
+
+            except subprocess.CalledProcessError as e:
+                print(f"CUDA PyTorch installation failed: {e}")
+                print("Falling back to CPU-only PyTorch...")
+                # Install PyTorch without CUDA
+                subprocess.check_call(
+                    [
+                        env_python,
+                        "-m",
+                        "pip",
+                        "install",
+                        "torch==2.0.1",
+                        "torchvision==0.15.2",
+                    ]
+                )
+                print("✓ CPU-only PyTorch installed as fallback")
+        else:
+            # Install PyTorch without CUDA
+            print("Installing PyTorch without CUDA support...")
+            subprocess.check_call(
+                [
+                    env_python,
+                    "-m",
+                    "pip",
+                    "install",
+                    "torch==2.0.1",
+                    "torchvision==0.15.2",
+                ]
+            )
+
+        # Install Spotiflow with all dependencies, but force CPU usage to avoid GPU issues
+        print("Installing Spotiflow in the dedicated environment...")
+        subprocess.check_call(
+            [env_python, "-m", "pip", "install", "spotiflow"]
+        )
+
+        # Install additional dependencies for image handling
+        subprocess.check_call(
+            [env_python, "-m", "pip", "install", "tifffile", "numpy"]
+        )
+
+        # Check if installation was successful
+        self._verify_installation(env_python)
+
+    def _verify_installation(self, env_python: str) -> None:
+        """Verify Spotiflow installation."""
+        check_script = """
+import sys
+try:
+    import spotiflow
+    print(f"Spotiflow version: {spotiflow.__version__}")
+    from spotiflow.model import Spotiflow
+    print("Spotiflow model imported successfully")
+    import torch
+    print(f"PyTorch version: {torch.__version__}")
+    print(f"CUDA available: {torch.cuda.is_available()}")
+    if torch.cuda.is_available():
+        print(f"CUDA version: {torch.version.cuda}")
+        print(f"GPU: {torch.cuda.get_device_name(0)}")
+    print("SUCCESS: Spotiflow environment is working correctly")
+except Exception as e:
+    print(f"ERROR: {str(e)}")
+    sys.exit(1)
+"""
+        with tempfile.NamedTemporaryFile(
+            mode="w", suffix=".py", delete=False
+        ) as temp:
+            temp.write(check_script)
+            temp_path = temp.name
+
+        try:
+            result = subprocess.run(
+                [env_python, temp_path],
+                check=True,
+                capture_output=True,
+                text=True,
+            )
+            print(result.stdout)
+            if "SUCCESS" in result.stdout:
+                print(
+                    "Spotiflow environment created and verified successfully."
+                )
+            else:
+                raise RuntimeError(
+                    "Spotiflow environment verification failed."
+                )
+        except subprocess.CalledProcessError as e:
+            print(f"Verification failed: {e.stderr}")
+            raise
+        finally:
+            with contextlib.suppress(FileNotFoundError):
+                os.unlink(temp_path)
+
+    def is_package_installed(self) -> bool:
+        """Check if spotiflow is installed in the current environment."""
+        try:
+            import importlib.util
+
+            return importlib.util.find_spec("spotiflow") is not None
+        except ImportError:
+            return False
+
+
+# Global instance for backward compatibility
+manager = SpotiflowEnvironmentManager()
+
+
+def is_spotiflow_installed():
+    """Check if spotiflow is installed in the current environment."""
+    return manager.is_package_installed()
+
+
+def is_env_created():
+    """Check if the dedicated environment exists."""
+    return manager.is_env_created()
+
+
+def get_env_python_path():
+    """Get the path to the Python executable in the environment."""
+    return manager.get_env_python_path()
+
+
+def create_spotiflow_env():
+    """Create a dedicated virtual environment for Spotiflow."""
+    return manager.create_env()
+
+
+def run_spotiflow_in_env(func_name, args_dict):
+    """
+    Run Spotiflow in a dedicated environment.
+
+    Parameters:
+    -----------
+    func_name : str
+        Name of the Spotiflow function to run
+    args_dict : dict
+        Dictionary of arguments for Spotiflow prediction
+
+    Returns:
+    --------
+    numpy.ndarray or tuple
+        Detection results (points coordinates and optionally heatmap/flow)
+    """
+    # Ensure the environment exists
+    if not is_env_created():
+        create_spotiflow_env()
+
+    # Prepare temporary files
+    with (
+        tempfile.NamedTemporaryFile(suffix=".tif", delete=False) as input_file,
+        tempfile.NamedTemporaryFile(
+            suffix=".npy", delete=False
+        ) as output_file,
+        tempfile.NamedTemporaryFile(
+            mode="w", suffix=".py", delete=False
+        ) as script_file,
+    ):
+
+        # Save input image
+        tifffile.imwrite(input_file.name, args_dict["image"])
+
+        # Prepare a temporary script to run Spotiflow
+        script = f"""
+import numpy as np
+import os
+import sys
+print("Starting Spotiflow detection script...")
+print(f"Python version: {{sys.version}}")
+
+try:
+    from spotiflow.model import Spotiflow
+    print("✓ Spotiflow model imported successfully")
+except Exception as e:
+    print(f"✗ Failed to import Spotiflow model: {{e}}")
+    sys.exit(1)
+
+try:
+    import tifffile
+    print("✓ tifffile imported successfully")
+except Exception as e:
+    print(f"✗ Failed to import tifffile: {{e}}")
+    sys.exit(1)
+
+try:
+    # Load image
+    print(f"Loading image from: {input_file.name}")
+    image = tifffile.imread('{input_file.name}')
+    print(f"✓ Image loaded successfully, shape: {{image.shape}}, dtype: {{image.dtype}}")
+except Exception as e:
+    print(f"✗ Failed to load image: {{e}}")
+    sys.exit(1)
+
+try:
+    # Load the model
+    if '{args_dict.get('model_path', '')}' and os.path.exists('{args_dict.get('model_path', '')}'):
+        # Load custom model from folder
+        print(f"Loading custom model from {args_dict.get('model_path', '')}")
+        model = Spotiflow.from_folder('{args_dict.get('model_path', '')}')
+    else:
+        # Load pretrained model
+        print(f"Loading pretrained model: {args_dict.get('pretrained_model', 'general')}")
+        model = Spotiflow.from_pretrained('{args_dict.get('pretrained_model', 'general')}')
+    print("✓ Model loaded successfully")
+
+    # Handle device selection and force_cpu parameter
+    import torch
+    force_cpu = {args_dict.get('force_cpu', False)}
+
+    if force_cpu:
+        print("Forcing CPU execution as requested")
+        device = torch.device("cpu")
+        # Set environment variable to ensure CPU usage
+        import os
+        os.environ["CUDA_VISIBLE_DEVICES"] = ""
+    else:
+        # Use CUDA if available and compatible
+        if torch.cuda.is_available():
+            try:
+                # Test CUDA compatibility by creating a small tensor
+                test_tensor = torch.ones(1).cuda()
+                device = torch.device("cuda")
+                print("Using CUDA (GPU) for inference")
+            except Exception as cuda_e:
+                print(f"CUDA incompatible ({{cuda_e}}), falling back to CPU")
+                device = torch.device("cpu")
+                force_cpu = True
+        else:
+            print("CUDA not available, using CPU")
+            device = torch.device("cpu")
+            force_cpu = True
+
+    # Move model to appropriate device
+    try:
+        model = model.to(device)
+        print(f"Model moved to device: {{device}}")
+    except Exception as device_e:
+        if not force_cpu:
+            print(f"Failed to move model to GPU ({{device_e}}), falling back to CPU")
+            device = torch.device("cpu")
+            model = model.to(device)
+        else:
+            raise
+
+except Exception as e:
+    print(f"✗ Failed to load model: {{e}}")
+    sys.exit(1)
+
+# Utility functions for input preparation
+def _validate_axes(img, axes):
+    if img.ndim != len(axes):
+        raise ValueError(f"Image has {{img.ndim}} dimensions, but axes has {{len(axes)}} dimensions")
+
+def _prepare_input(img, axes):
+    _validate_axes(img, axes)
+    if axes in {{"YX", "ZYX", "TYX", "TZYX"}}:
+        return img[..., None]
+    elif axes in {{"YXC", "ZYXC", "TYXC", "TZYXC"}}:
+        return img
+    elif axes == "CYX":
+        return img.transpose(1, 2, 0)
+    elif axes == "CZYX":
+        return img.transpose(1, 2, 3, 0)
+    elif axes == "ZCYX":
+        return img.transpose(0, 2, 3, 1)
+    elif axes == "TCYX":
+        return img.transpose(0, 2, 3, 1)
+    elif axes == "TZCYX":
+        return img.transpose(0, 1, 3, 4, 2)
+    elif axes == "TCZYX":
+        return img.transpose(0, 2, 3, 4, 1)
+    else:
+        raise ValueError(f"Invalid axes: {{axes}}")
+
+try:
+    # Handle axes and input preparation
+    axes = '{args_dict.get('axes', 'auto')}'
+    if axes == 'auto':
+        # Auto-infer axes
+        ndim = image.ndim
+        if ndim == 2:
+            axes = "YX"
+        elif ndim == 3:
+            axes = "ZYX"
+        elif ndim == 4:
+            if image.shape[-1] <= 4:
+                axes = "ZYXC"
+            else:
+                axes = "TZYX"
+        elif ndim == 5:
+            axes = "TZYXC"
+        else:
+            raise ValueError(f"Cannot infer axes for {{ndim}}D image")
+
+    print(f"Using axes: {{axes}}")
+
+    # Prepare input
+    prepared_img = _prepare_input(image, axes)
+    print(f"Prepared image shape: {{prepared_img.shape}}")
+
+    # Check model compatibility
+    is_3d_image = len(image.shape) == 3 and "Z" in axes
+    if is_3d_image and not model.config.is_3d:
+        print("Warning: Using a 2D model on 3D data. Consider using a 3D model.")
+
+except Exception as e:
+    print(f"✗ Failed to prepare input: {{e}}")
+    # Fallback to original image
+    prepared_img = image
+    axes = "YX" if image.ndim == 2 else "ZYX"
+
+try:
+    # Parse string parameters
+    def parse_param(param_str, default_val):
+        if param_str == "auto":
+            return default_val
+        try:
+            return eval(param_str) if param_str.startswith("(") else param_str
+        except:
+            return default_val
+
+    n_tiles_parsed = parse_param('{args_dict.get('n_tiles', 'auto')}', None)
+    scale_parsed = parse_param('{args_dict.get('scale', 'auto')}', None)
+
+    # Handle normalization manually (similar to napari-spotiflow)
+    normalizer_type = '{args_dict.get('normalizer', 'percentile')}'
+    if normalizer_type == "percentile":
+        normalizer_low = {args_dict.get('normalizer_low', 1.0)}
+        normalizer_high = {args_dict.get('normalizer_high', 99.8)}
+        print(f"Applying percentile normalization: {{normalizer_low}}% to {{normalizer_high}}%")
+        p_low, p_high = np.percentile(prepared_img, [normalizer_low, normalizer_high])
+        normalized_img = np.clip((prepared_img - p_low) / (p_high - p_low), 0, 1)
+    elif normalizer_type == "minmax":
+        print("Applying min-max normalization")
+        img_min, img_max = prepared_img.min(), prepared_img.max()
+        normalized_img = (prepared_img - img_min) / (img_max - img_min) if img_max > img_min else prepared_img
+    else:
+        normalized_img = prepared_img
+
+    print(f"Normalized image range: {{normalized_img.min():.3f}} to {{normalized_img.max():.3f}}")
+
+    # Prepare prediction parameters (following napari-spotiflow style)
+    predict_kwargs = {{
+        'subpix': {args_dict.get('subpixel', True)},  # Note: Spotiflow API uses 'subpix', not 'subpixel'
+        'peak_mode': '{args_dict.get('peak_mode', 'fast')}',
+        'normalizer': None,  # We handle normalization manually
+        'exclude_border': {args_dict.get('exclude_border', True)},
+        'min_distance': {args_dict.get('min_distance', 2)},
+        'verbose': True,
+    }}
+
+    # Set probability threshold - use automatic or provided value
+    prob_thresh = {args_dict.get('prob_thresh', None)}
+    if prob_thresh is not None and prob_thresh > 0.0:
+        predict_kwargs['prob_thresh'] = prob_thresh
+    # If prob_thresh is None or 0.0, don't set it - let spotiflow use automatic threshold
+
+    if n_tiles_parsed is not None:
+        predict_kwargs['n_tiles'] = n_tiles_parsed
+    if scale_parsed is not None:
+        predict_kwargs['scale'] = scale_parsed
+
+    print(f"Prediction parameters: {{predict_kwargs}}")
+except Exception as e:
+    print(f"✗ Failed to prepare parameters: {{e}}")
+    sys.exit(1)
+
+try:
+    # Perform spot detection
+    print("Running Spotiflow prediction...")
+    try:
+        points, details = model.predict(normalized_img, **predict_kwargs)
+    except (RuntimeError, Exception) as pred_e:
+        if "CUDA" in str(pred_e) and not force_cpu:
+            print(f"CUDA error during prediction ({{pred_e}}), retrying with CPU")
+            # Move model to CPU and retry
+            device = torch.device("cpu")
+            model = model.to(device)
+            # Set environment to force CPU
+            import os
+            os.environ["CUDA_VISIBLE_DEVICES"] = ""
+            points, details = model.predict(normalized_img, **predict_kwargs)
+        else:
+            raise
+
+    print(f"✓ Initial detection: {{len(points)}} spots")
+
+    # Only apply minimal additional filtering if we still have too many detections
+    # This should rarely be needed now that we use proper automatic thresholding
+    if len(points) > 500:  # Only if we have an excessive number of spots
+        print(f"Applying additional filtering for {{len(points)}} spots")
+
+        # Check if we can apply probability filtering
+        if hasattr(details, 'prob'):
+            # Use a more stringent threshold
+            auto_thresh = 0.7
+            prob_mask = details.prob > auto_thresh
+            points = points[prob_mask]
+            print(f"After additional probability thresholding ({{auto_thresh}}): {{len(points)}} spots")
+
+    print(f"Final detection: {{len(points)}} spots")
+
+    if len(points) > 0:
+        print(f"✓ Points shape: {{points.shape}}")
+        print(f"✓ Points dtype: {{points.dtype}}")
+        print(f"✓ First few points: {{points[:3]}}")
+
+except Exception as e:
+    print(f"✗ Failed during spot detection: {{e}}")
+    import traceback
+    traceback.print_exc()
+    sys.exit(1)
+
+try:
+    # Prepare output data
+    output_data = {{
+        'points': points,
+    }}
+
+    # Save results
+    print(f"Saving results to: {output_file.name}")
+    np.save('{output_file.name}', output_data)
+    print(f"✓ Results saved successfully")
+    print(f"Detected {{len(points)}} spots")
+except Exception as e:
+    print(f"✗ Failed to save results: {{e}}")
+    sys.exit(1)
+"""
+
+        # Write script
+        script_file.write(script)
+        script_file.flush()
+
+        # Execute the script in the dedicated environment
+        env_python = get_env_python_path()
+        result = subprocess.run(
+            [env_python, script_file.name],
+            capture_output=True,
+            text=True,
+        )
+
+        # Check for errors
+        if result.returncode != 0:
+            print("Error in Spotiflow environment execution:")
+            print(f"STDOUT: {result.stdout}")
+            print(f"STDERR: {result.stderr}")
+            raise subprocess.CalledProcessError(
+                result.returncode, result.args, result.stdout, result.stderr
+            )
+
+        print(result.stdout)
+
+        # Load and return results
+        output_data = np.load(output_file.name, allow_pickle=True).item()
+
+        # Clean up temporary files
+        with contextlib.suppress(FileNotFoundError):
+            os.unlink(input_file.name)
+            os.unlink(output_file.name)
+            os.unlink(script_file.name)
+
+        return output_data