napari-tmidas 0.2.2__py3-none-any.whl → 0.2.5__py3-none-any.whl

napari_tmidas/processing_functions/cellpose_env_manager.py

@@ -5,152 +5,439 @@ Updated to support Cellpose 4 (Cellpose-SAM) installation.
 """
 
 import os
-import platform
-import shutil
 import subprocess
+import sys
 import tempfile
-import venv
+import threading
+from contextlib import suppress
 
 import tifffile
 
-# Define the environment directory in user's home folder
-ENV_DIR = os.path.join(
-    os.path.expanduser("~"), ".napari-tmidas", "envs", "cellpose"
-)
+from napari_tmidas._env_manager import BaseEnvironmentManager
+
+# Global variable to track running processes for cancellation
+_running_processes = []
+_process_lock = threading.Lock()
+
+
+def cancel_all_processes():
+    """Cancel all running cellpose processes."""
+    with _process_lock:
+        for process in _running_processes[
+            :
+        ]:  # Copy list to avoid modification during iteration
+            try:
+                if process.poll() is None:  # Process is still running
+                    process.terminate()
+                    # Give it a moment to terminate gracefully
+                    try:
+                        process.wait(timeout=5)
+                    except subprocess.TimeoutExpired:
+                        # Force kill if it doesn't terminate gracefully
+                        process.kill()
+                        process.wait()
+                _running_processes.remove(process)
+            except (OSError, subprocess.SubprocessError) as e:
+                print(f"Error terminating process: {e}")
+
+
+def _add_process(process):
+    """Add a process to the tracking list."""
+    with _process_lock:
+        _running_processes.append(process)
+
+
+def _remove_process(process):
+    """Remove a process from the tracking list."""
+    with _process_lock:
+        if process in _running_processes:
+            _running_processes.remove(process)
+
+
+class CellposeEnvironmentManager(BaseEnvironmentManager):
+    """Environment manager for Cellpose."""
+
+    def __init__(self):
+        super().__init__("cellpose")
+
+    def _install_dependencies(self, env_python: str) -> None:
+        """Install Cellpose-specific dependencies."""
+        # Install cellpose 4 and other dependencies
+        print(
+            "Installing Cellpose 4 (Cellpose-SAM) in the dedicated environment..."
+        )
+
+        # Install packages one by one with error checking
+        packages = ["cellpose", "zarr", "tifffile"]
+        for package in packages:
+            print(f"Installing {package}...")
+            try:
+                subprocess.check_call(
+                    [env_python, "-m", "pip", "install", package]
+                )
+                print(f"✓ {package} installed successfully")
+            except subprocess.CalledProcessError as e:
+                print(f"✗ Failed to install {package}: {e}")
+                raise
+
+        # Verify installations
+        print("Verifying installations...")
+
+        # Check cellpose
+        try:
+            result = subprocess.run(
+                [
+                    env_python,
+                    "-c",
+                    "from cellpose import core; print(f'GPU available: {core.use_gpu()}')",
+                ],
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            print("✓ Cellpose installation verified:")
+            print(result.stdout)
+        except subprocess.CalledProcessError as e:
+            print(f"✗ Cellpose verification failed: {e}")
+            raise
+
+        # Check zarr
+        try:
+            result = subprocess.run(
+                [
+                    env_python,
+                    "-c",
+                    "import zarr; print(f'Zarr version: {zarr.__version__}')",
+                ],
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            print("✓ Zarr installation verified:")
+            print(result.stdout)
+        except subprocess.CalledProcessError as e:
+            print(f"✗ Zarr verification failed: {e}")
+            raise
+
+        # Check tifffile
+        try:
+            result = subprocess.run(
+                [
+                    env_python,
+                    "-c",
+                    "import tifffile; print(f'Tifffile version: {tifffile.__version__}')",
+                ],
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            print("✓ Tifffile installation verified:")
+            print(result.stdout)
+        except subprocess.CalledProcessError as e:
+            print(f"✗ Tifffile verification failed: {e}")
+            raise
+
+    def is_package_installed(self) -> bool:
+        """Check if cellpose is installed in the current environment."""
+        try:
+            import importlib.util
+
+            return importlib.util.find_spec("cellpose") is not None
+        except ImportError:
+            return False
+
+    def are_all_packages_installed(self) -> bool:
+        """Check if all required packages are installed in the dedicated environment."""
+        if not self.is_env_created():
+            return False
+
+        env_python = self.get_env_python_path()
+        required_packages = ["cellpose", "zarr", "tifffile"]
+
+        for package in required_packages:
+            try:
+                subprocess.run(
+                    [env_python, "-c", f"import {package}"],
+                    capture_output=True,
+                    text=True,
+                    check=True,
+                )
+            except subprocess.CalledProcessError:
+                print(f"Missing package in cellpose environment: {package}")
+                return False
+
+        return True
+
+    def reinstall_packages(self) -> None:
+        """Force reinstall all packages in the dedicated environment."""
+        if not self.is_env_created():
+            print("Environment not created. Creating new environment...")
+            self.create_env()
+            return
+
+        env_python = self.get_env_python_path()
+        print("Force reinstalling packages in cellpose environment...")
+        self._install_dependencies(env_python)
+
+
+# Global instance for backward compatibility
+manager = CellposeEnvironmentManager()
 
 
 def is_cellpose_installed():
     """Check if cellpose is installed in the current environment."""
-    try:
-        import importlib.util
-
-        return importlib.util.find_spec("cellpose") is not None
-    except ImportError:
-        return False
+    return manager.is_package_installed()
 
 
 def is_env_created():
     """Check if the dedicated environment exists."""
-    env_python = get_env_python_path()
-    return os.path.exists(env_python)
+    return manager.is_env_created()
 
 
 def get_env_python_path():
     """Get the path to the Python executable in the environment."""
-    if platform.system() == "Windows":
-        return os.path.join(ENV_DIR, "Scripts", "python.exe")
-    else:
-        return os.path.join(ENV_DIR, "bin", "python")
+    return manager.get_env_python_path()
 
 
 def create_cellpose_env():
     """Create a dedicated virtual environment for Cellpose."""
-    # Ensure the environment directory exists
-    os.makedirs(os.path.dirname(ENV_DIR), exist_ok=True)
-
-    # Remove existing environment if it exists
-    if os.path.exists(ENV_DIR):
-        shutil.rmtree(ENV_DIR)
-
-    print(f"Creating Cellpose environment at {ENV_DIR}...")
+    return manager.create_env()
 
-    # Create a new virtual environment
-    venv.create(ENV_DIR, with_pip=True)
 
-    # Path to the Python executable in the new environment
-    env_python = get_env_python_path()
-
-    # # Install numpy first to ensure correct version
-    # print("Installing NumPy...")
-    # subprocess.check_call(
-    #     [env_python, "-m", "pip", "install", "--upgrade", "pip"]
-    # )
-    # subprocess.check_call(
-    #     [env_python, "-m", "pip", "install", "numpy>=1.24,<1.25"]
-    # )
-
-    # Install cellpose 4 and other dependencies
-    print(
-        "Installing Cellpose 4 (Cellpose-SAM) in the dedicated environment..."
-    )
-    subprocess.check_call([env_python, "-m", "pip", "install", "cellpose"])
+def check_cellpose_packages():
+    """Check if all required packages are installed in the cellpose environment."""
+    return manager.are_all_packages_installed()
 
-    # # Install PyTorch - needed for GPU acceleration
-    # print("Installing PyTorch for GPU acceleration...")
-    # subprocess.check_call([
-    #     env_python, "-m", "pip", "install",
-    #     "torch", "torchvision"
-    # ])
 
-    # # Install tifffile for image handling
-    # subprocess.check_call([env_python, "-m", "pip", "install", "tifffile"])
+def reinstall_cellpose_packages():
+    """Force reinstall all packages in the cellpose environment."""
+    return manager.reinstall_packages()
 
-    # Check if installation was successful
-    try:
-        # Run a command to check if cellpose can be imported and GPU is available
-        result = subprocess.run(
-            [
-                env_python,
-                "-c",
-                "from cellpose import core; print(f'GPU available: {core.use_gpu()}')",
-            ],
-            capture_output=True,
-            text=True,
-            check=True,
-        )
-        print(f"Cellpose environment check: {result.stdout.strip()}")
-    except subprocess.CalledProcessError as e:
-        print(f"Warning: Cellpose installation check failed: {e.stderr}")
 
-    print("Cellpose environment created successfully.")
-    return env_python
+def cancel_cellpose_processing():
+    """Cancel all running cellpose processes."""
+    cancel_all_processes()
 
 
 def run_cellpose_in_env(func_name, args_dict):
     """
-    Run Cellpose in a dedicated environment with minimal complexity.
-
-    Parameters:
-    -----------
-    func_name : str
-        Name of the Cellpose function to run (currently unused)
-    args_dict : dict
-        Dictionary of arguments for Cellpose segmentation
-
-    Returns:
-    --------
-    numpy.ndarray
-        Segmentation masks
+    Run Cellpose in a dedicated environment with optimized zarr support.
     """
     # Ensure the environment exists
     if not is_env_created():
         create_cellpose_env()
 
-    # Prepare temporary files
-    with tempfile.NamedTemporaryFile(
-        suffix=".tif", delete=False
-    ) as input_file, tempfile.NamedTemporaryFile(
-        suffix=".tif", delete=False
-    ) as output_file, tempfile.NamedTemporaryFile(
-        mode="w", suffix=".py", delete=False
-    ) as script_file:
+    # Check if all required packages are installed
+    if not manager.are_all_packages_installed():
+        print("Missing packages detected. Reinstalling...")
+        manager.reinstall_packages()
+
+    # Check for zarr optimization
+    use_zarr_direct = "zarr_path" in args_dict
+
+    if use_zarr_direct:
+        zarr_path = args_dict["zarr_path"]
+        print(f"Using optimized zarr processing for: {zarr_path}")
+        return run_zarr_processing(zarr_path, args_dict)
+    else:
+        return run_legacy_processing(args_dict)
 
-        # Save input image
-        tifffile.imwrite(input_file.name, args_dict["image"])
 
-        # Prepare a temporary script to run Cellpose
-        # Updated to use Cellpose 4 parameters
+def run_zarr_processing(zarr_path, args_dict):
+    """Process zarr files directly without temporary input files."""
+
+    with (
+        tempfile.NamedTemporaryFile(
+            suffix=".tif", delete=False
+        ) as output_file,
+        tempfile.NamedTemporaryFile(
+            mode="w", suffix=".py", delete=False
+        ) as script_file,
+    ):
+
+        # Create zarr processing script (similar to working TIFF script)
         script = f"""
 import numpy as np
+import sys
 from cellpose import models, core
 import tifffile
+import zarr
+
+# Force output to flush immediately for real-time progress
+import sys
+sys.stdout.flush()
+
+print("=== Cellpose Environment Info ===")
+print(f"GPU available in dedicated environment: {{core.use_gpu()}}")
+sys.stdout.flush()
+
+def process_volume(image, name=""):
+    print(f"\\nProcessing {{name}}: shape={{image.shape}}, range={{np.min(image):.1f}}-{{np.max(image):.1f}}")
+    sys.stdout.flush()
+
+    # GPU detection IN THE DEDICATED ENVIRONMENT (not main environment)
+    gpu_available = core.use_gpu()
+    use_gpu_requested = {str(args_dict.get('use_gpu', True))}  # Convert to string for f-string
+    actual_use_gpu = use_gpu_requested and gpu_available
+
+    print(f"GPU: requested={{use_gpu_requested}}, available={{gpu_available}}, using={{actual_use_gpu}}")
+    sys.stdout.flush()
+
+    # Create model with explicit GPU setting
+    print("Creating Cellpose model...")
+    sys.stdout.flush()
+    model = models.CellposeModel(gpu=actual_use_gpu)
+    print(f"Model created (GPU={{model.gpu}})")
+    sys.stdout.flush()
+
+    print("Running segmentation...")
+    sys.stdout.flush()
+
+    # Remove deprecated channels parameter for Cellpose v4.0.1+
+    masks, flows, styles = model.eval(
+        image,
+        # channels parameter removed - deprecated in v4.0.1+
+        flow_threshold={args_dict.get('flow_threshold', 0.4)},
+        cellprob_threshold={args_dict.get('cellprob_threshold', 0.0)},
+        batch_size={args_dict.get('batch_size', 32)},
+        normalize={args_dict.get('normalize', {'tile_norm_blocksize': 128})},
+        do_3D={args_dict.get('do_3D', False)},
+        flow3D_smooth={args_dict.get('flow3D_smooth', 0)},
+        anisotropy={args_dict.get('anisotropy', None)},
+        z_axis={args_dict.get('z_axis', 0)} if {args_dict.get('do_3D', False)} else None,
+        channel_axis={args_dict.get('channel_axis', None)}
+    )
 
+    object_count = np.max(masks)
+    print(f"Found {{object_count}} objects in {{name}}")
+    sys.stdout.flush()
+    return masks
+
+print("Opening zarr: {zarr_path}")
+sys.stdout.flush()
+zarr_root = zarr.open('{zarr_path}', mode='r')
+
+if hasattr(zarr_root, 'shape'):
+    image = np.array(zarr_root)
+    result = process_volume(image, "zarr")
+else:
+    arrays = list(zarr_root.array_keys())
+    print(f"Arrays: {{arrays}}")
+    sys.stdout.flush()
+    zarr_array = zarr_root[arrays[0]]
+    print(f"Selected: {{arrays[0]}}, shape={{zarr_array.shape}}")
+    sys.stdout.flush()
+
+    if len(zarr_array.shape) == 5:  # TCZYX
+        T, C, Z, Y, X = zarr_array.shape
+        print(f"5D TCZYX: T={{T}}, C={{C}}, Z={{Z}}, Y={{Y}}, X={{X}}")
+        print(f"Will process {{T*C}} T,C combinations")
+        sys.stdout.flush()
+        result = np.zeros((T, C, Z, Y, X), dtype=np.uint32)
+
+        for t in range(T):
+            for c in range(C):
+                print(f"\\n=== T={{t+1}}/{{T}}, C={{c+1}}/{{C}} ===")
+                sys.stdout.flush()
+                image = np.array(zarr_array[t, c, :, :, :])
+                masks = process_volume(image, f"T{{t+1}}C{{c+1}}")
+                result[t, c] = masks
+
+    elif len(zarr_array.shape) == 4:  # 4D
+        dim1, Z, Y, X = zarr_array.shape
+        print(f"4D array: dim1={{dim1}}, Z={{Z}}, Y={{Y}}, X={{X}}")
+        sys.stdout.flush()
+        result = np.zeros((dim1, Z, Y, X), dtype=np.uint32)
+
+        for i in range(dim1):
+            print(f"\\n=== Volume {{i+1}}/{{dim1}} ===")
+            sys.stdout.flush()
+            image = np.array(zarr_array[i, :, :, :])
+            masks = process_volume(image, f"Vol{{i+1}}")
+            result[i] = masks
+    else:
+        image = np.array(zarr_array)
+        result = process_volume(image, "3D")
+
+print(f"Saving results: shape={{result.shape}}, total objects={{np.max(result)}}")
+sys.stdout.flush()
+tifffile.imwrite('{output_file.name}', result.astype(np.uint32))
+print("Complete!")
+sys.stdout.flush()
+"""
 
+        script_file.write(script)
+        script_file.flush()
+
+        try:
+            # Run with REAL-TIME output (don't capture, let it stream)
+            env_python = get_env_python_path()
+            print("=== Starting Cellpose Processing ===")
+
+            # Use Popen for real-time progress and cancellation support
+            process = subprocess.Popen(
+                [env_python, script_file.name],
+                cwd=os.getcwd(),
+                stdout=sys.stdout,
+                stderr=sys.stderr,
+                text=True,
+            )
+
+            # Track the process for cancellation
+            _add_process(process)
+
+            try:
+                # Wait for completion
+                returncode = process.wait()
+
+                if returncode != 0:
+                    raise RuntimeError(
+                        f"Cellpose failed with return code {returncode}"
+                    )
+
+            finally:
+                # Remove from tracking regardless of outcome
+                _remove_process(process)
+
+            # Check if output file was created
+            if not os.path.exists(output_file.name):
+                raise RuntimeError("Output file was not created")
+
+            return tifffile.imread(output_file.name)
+
+        finally:
+            # Cleanup
+            for fname in [output_file.name, script_file.name]:
+                with suppress(OSError, FileNotFoundError):
+                    os.unlink(fname)
+
+
+def run_legacy_processing(args_dict):
+    """Legacy processing for numpy arrays (original working TIFF approach)."""
+
+    with (
+        tempfile.NamedTemporaryFile(suffix=".tif", delete=False) as input_file,
+        tempfile.NamedTemporaryFile(
+            suffix=".tif", delete=False
+        ) as output_file,
+        tempfile.NamedTemporaryFile(
+            mode="w", suffix=".py", delete=False
+        ) as script_file,
+    ):
+
+        # Save input image (exactly like original working code)
+        tifffile.imwrite(input_file.name, args_dict["image"])
+
+        # Create script (exactly like original working code)
+        script = f"""
+import numpy as np
+from cellpose import models, core
+import tifffile
 
 # Load image
 image = tifffile.imread('{input_file.name}')
 
-# Create and run model
+# Create and run model (exactly like original working code)
 model = models.CellposeModel(
     gpu={args_dict.get('use_gpu', True)})
 
@@ -166,7 +453,10 @@ masks, flows, styles = model.eval(
     batch_size={args_dict.get('batch_size', 32)},
     normalize=normalize,
     do_3D={args_dict.get('do_3D', False)},
-    z_axis={args_dict.get('z_axis', 0)} if {args_dict.get('do_3D', False)} else None
+    flow3D_smooth={args_dict.get('flow3D_smooth', 0)},
+    anisotropy={args_dict.get('anisotropy', None)},
+    z_axis={args_dict.get('z_axis', 0)} if {args_dict.get('do_3D', False)} else None,
+    channel_axis={args_dict.get('channel_axis', None)}
 )
 
 # Save results
@@ -178,18 +468,33 @@ tifffile.imwrite('{output_file.name}', masks)
         script_file.flush()
 
     try:
-        # Run the script in the dedicated environment
+        # Run the script with cancellation support
         env_python = get_env_python_path()
-        result = subprocess.run(
-            [env_python, script_file.name], capture_output=True, text=True
+
+        # Use Popen for cancellation support
+        process = subprocess.Popen(
+            [env_python, script_file.name],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
         )
-        print("Stdout:", result.stdout)
-        # Check for errors
-        if result.returncode != 0:
-            print("Stderr:", result.stderr)
-            raise RuntimeError(
-                f"Cellpose segmentation failed: {result.stderr}"
-            )
+
+        # Track the process for cancellation
+        _add_process(process)
+
+        try:
+            # Wait for completion and get output
+            stdout, stderr = process.communicate()
+            print("Stdout:", stdout)
+
+            # Check for errors
+            if process.returncode != 0:
+                print("Stderr:", stderr)
+                raise RuntimeError(f"Cellpose segmentation failed: {stderr}")
+
+        finally:
+            # Remove from tracking regardless of outcome
+            _remove_process(process)
 
         # Read and return the results
         return tifffile.imread(output_file.name)
@@ -199,9 +504,7 @@ tifffile.imwrite('{output_file.name}', masks)
         raise
 
     finally:
-        # Clean up temporary files using contextlib.suppress
-        from contextlib import suppress
-
+        # Clean up temporary files
         for fname in [input_file.name, output_file.name, script_file.name]:
             with suppress(OSError, FileNotFoundError):
                 os.unlink(fname)