microlive 1.0.12__py3-none-any.whl → 1.0.19__py3-none-any.whl

microlive/utils/__init__.py

@@ -2,6 +2,12 @@
 
 from .device import get_device, is_gpu_available, get_device_info, check_gpu_status
 from .resources import get_icon_path, get_model_path
+from .model_downloader import (
+    get_frap_nuclei_model_path,
+    cache_model,
+    list_cached_models,
+    MODEL_DIR,
+)
 
 __all__ = [
     "get_device",
@@ -10,4 +16,9 @@ __all__ = [
     "check_gpu_status",
     "get_icon_path",
     "get_model_path",
+    # Model downloader
+    "get_frap_nuclei_model_path",
+    "cache_model",
+    "list_cached_models",
+    "MODEL_DIR",
 ]

microlive/utils/model_downloader.py

@@ -0,0 +1,293 @@
+"""
+Model download utilities for MicroLive.
+
+This module provides functions to download and cache pretrained models from
+the MicroLive GitHub repository. It follows the same patterns used by Cellpose
+for robust model provisioning.
+
+Models are downloaded on first use and cached locally in ~/.microlive/models/
+to avoid repeated downloads.
+"""
+
+import os
+import ssl
+import shutil
+import tempfile
+import logging
+from pathlib import Path
+from urllib.request import urlopen
+from urllib.error import URLError, HTTPError
+
+logger = logging.getLogger(__name__)
+
+# =============================================================================
+# Configuration
+# =============================================================================
+
+# Base URL for raw GitHub content
+_GITHUB_RAW_BASE = "https://raw.githubusercontent.com/ningzhaoAnschutz/microlive/main"
+
+# Model URLs - Add new models here
+MODEL_URLS = {
+    "frap_nuclei": f"{_GITHUB_RAW_BASE}/modeling/cellpose_models/cellpose_models/FRAP_nuclei_model/models/cellpose_1728581750.581418",
+}
+
+# Local cache directory (similar to Cellpose's ~/.cellpose/models/)
+_MODEL_DIR_ENV = os.environ.get("MICROLIVE_LOCAL_MODELS_PATH")
+_MODEL_DIR_DEFAULT = Path.home() / ".microlive" / "models"
+MODEL_DIR = Path(_MODEL_DIR_ENV) if _MODEL_DIR_ENV else _MODEL_DIR_DEFAULT
+
+
+# =============================================================================
+# Download Utilities (adapted from Cellpose)
+# =============================================================================
+
+def download_url_to_file(url: str, dst: str, progress: bool = True) -> None:
+    """
+    Download object at the given URL to a local path.
+    
+    Adapted from Cellpose/torch implementation for robustness.
+    
+    Args:
+        url: URL of the object to download.
+        dst: Full path where object will be saved.
+        progress: Whether to display a progress bar. Default: True.
+    
+    Raises:
+        HTTPError: If the server returns an error status.
+        URLError: If the URL cannot be reached.
+    """
+    try:
+        from tqdm import tqdm
+        HAS_TQDM = True
+    except ImportError:
+        HAS_TQDM = False
+        progress = False
+    
+    file_size = None
+    
+    # Handle SSL certificate verification issues
+    ssl_context = ssl.create_default_context()
+    ssl_context.check_hostname = False
+    ssl_context.verify_mode = ssl.CERT_NONE
+    
+    try:
+        u = urlopen(url, context=ssl_context)
+    except URLError as e:
+        raise URLError(f"Failed to connect to {url}: {e}")
+    
+    meta = u.info()
+    if hasattr(meta, "getheaders"):
+        content_length = meta.getheaders("Content-Length")
+    else:
+        content_length = meta.get_all("Content-Length")
+    
+    if content_length is not None and len(content_length) > 0:
+        file_size = int(content_length[0])
+    
+    # Save to temp file first, then move (atomic operation)
+    dst = os.path.expanduser(dst)
+    dst_dir = os.path.dirname(dst)
+    os.makedirs(dst_dir, exist_ok=True)
+    
+    f = tempfile.NamedTemporaryFile(delete=False, dir=dst_dir)
+    try:
+        if HAS_TQDM and progress:
+            with tqdm(total=file_size, disable=not progress, unit="B", 
+                      unit_scale=True, unit_divisor=1024,
+                      desc=f"Downloading {Path(dst).name}") as pbar:
+                while True:
+                    buffer = u.read(8192)
+                    if len(buffer) == 0:
+                        break
+                    f.write(buffer)
+                    pbar.update(len(buffer))
+        else:
+            # Simple download without progress bar
+            while True:
+                buffer = u.read(8192)
+                if len(buffer) == 0:
+                    break
+                f.write(buffer)
+        
+        f.close()
+        shutil.move(f.name, dst)
+        logger.info(f"Successfully downloaded model to {dst}")
+        
+    except Exception as e:
+        f.close()
+        if os.path.exists(f.name):
+            os.remove(f.name)
+        raise RuntimeError(f"Download failed: {e}")
+    finally:
+        if os.path.exists(f.name):
+            try:
+                os.remove(f.name)
+            except OSError:
+                pass
+
+
+# =============================================================================
+# Model Cache Functions
+# =============================================================================
+
+def get_model_path(model_name: str) -> Path:
+    """
+    Get the local cache path for a model.
+    
+    Args:
+        model_name: Name of the model (e.g., "frap_nuclei").
+        
+    Returns:
+        Path to the cached model file.
+    """
+    return MODEL_DIR / model_name
+
+
+def is_model_cached(model_name: str) -> bool:
+    """
+    Check if a model is already cached locally.
+    
+    Args:
+        model_name: Name of the model.
+        
+    Returns:
+        True if the model exists locally, False otherwise.
+    """
+    return get_model_path(model_name).exists()
+
+
+def cache_model(model_name: str, force_download: bool = False) -> str:
+    """
+    Ensure a model is cached locally, downloading if necessary.
+    
+    This function follows the Cellpose pattern:
+    1. Check if model exists in local cache
+    2. If not (or force_download=True), download from GitHub
+    3. Return the local path
+    
+    Args:
+        model_name: Name of the model (must be in MODEL_URLS).
+        force_download: If True, re-download even if cached.
+        
+    Returns:
+        String path to the cached model file.
+        
+    Raises:
+        ValueError: If model_name is not recognized.
+        RuntimeError: If download fails.
+    """
+    if model_name not in MODEL_URLS:
+        available = ", ".join(MODEL_URLS.keys())
+        raise ValueError(f"Unknown model '{model_name}'. Available: {available}")
+    
+    MODEL_DIR.mkdir(parents=True, exist_ok=True)
+    cached_file = get_model_path(model_name)
+    
+    if not cached_file.exists() or force_download:
+        url = MODEL_URLS[model_name]
+        logger.info(f"Downloading model '{model_name}' from {url}")
+        print(f"Downloading MicroLive model '{model_name}' (first time only)...")
+        
+        try:
+            download_url_to_file(url, str(cached_file), progress=True)
+        except (HTTPError, URLError) as e:
+            raise RuntimeError(
+                f"Failed to download model '{model_name}' from GitHub. "
+                f"Error: {e}\n\n"
+                f"If this persists, you can manually download from:\n"
+                f"  {url}\n"
+                f"And place it at:\n"
+                f"  {cached_file}"
+            )
+    else:
+        logger.debug(f"Model '{model_name}' already cached at {cached_file}")
+    
+    return str(cached_file)
+
+
+# =============================================================================
+# Convenience Functions for Specific Models
+# =============================================================================
+
+def get_frap_nuclei_model_path() -> str:
+    """
+    Get the path to the FRAP nuclei segmentation model.
+    
+    Downloads the model from GitHub if not already cached locally.
+    The model is stored in ~/.microlive/models/frap_nuclei
+    
+    Returns:
+        String path to the FRAP nuclei model file.
+        
+    Example:
+        >>> from microlive.utils.model_downloader import get_frap_nuclei_model_path
+        >>> model_path = get_frap_nuclei_model_path()
+        >>> # Use with Cellpose
+        >>> from cellpose import models
+        >>> model = models.CellposeModel(pretrained_model=model_path)
+    """
+    return cache_model("frap_nuclei")
+
+
+# =============================================================================
+# Verification and Diagnostics
+# =============================================================================
+
+def verify_model_integrity(model_name: str) -> bool:
+    """
+    Verify that a cached model file exists and has non-zero size.
+    
+    Args:
+        model_name: Name of the model to verify.
+        
+    Returns:
+        True if the model file exists and is valid.
+    """
+    model_path = get_model_path(model_name)
+    if not model_path.exists():
+        return False
+    
+    # Check file size (should be > 1MB for a real model)
+    size_bytes = model_path.stat().st_size
+    if size_bytes < 1_000_000:
+        logger.warning(f"Model file seems too small ({size_bytes} bytes): {model_path}")
+        return False
+    
+    return True
+
+
+def list_cached_models() -> dict:
+    """
+    List all cached models and their status.
+    
+    Returns:
+        Dictionary mapping model names to their cache status and size.
+    """
+    result = {}
+    for name in MODEL_URLS:
+        path = get_model_path(name)
+        if path.exists():
+            size_mb = path.stat().st_size / (1024 * 1024)
+            result[name] = {"cached": True, "size_mb": round(size_mb, 2), "path": str(path)}
+        else:
+            result[name] = {"cached": False, "size_mb": 0, "path": str(path)}
+    return result
+
+
+def clear_model_cache(model_name: str = None) -> None:
+    """
+    Clear cached models.
+    
+    Args:
+        model_name: Specific model to clear, or None to clear all.
+    """
+    if model_name:
+        path = get_model_path(model_name)
+        if path.exists():
+            path.unlink()
+            logger.info(f"Cleared cached model: {model_name}")
+    else:
+        if MODEL_DIR.exists():
+            shutil.rmtree(MODEL_DIR)
+            logger.info(f"Cleared all cached models from {MODEL_DIR}")

{microlive-1.0.12.dist-info → microlive-1.0.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microlive
-Version: 1.0.12
+Version: 1.0.19
 Summary: Live-cell microscopy image analysis and single-molecule measurements
 Project-URL: Homepage, https://github.com/ningzhaoAnschutz/microlive
 Project-URL: Documentation, https://github.com/ningzhaoAnschutz/microlive/blob/main/docs/user_guide.md
@@ -67,6 +67,7 @@ Requires-Dist: scipy==1.13.1
 Requires-Dist: seaborn==0.13.2
 Requires-Dist: snapgene-reader>=0.1
 Requires-Dist: statsmodels==0.14.4
+Requires-Dist: tasep-models
 Requires-Dist: tifffile>=2024.1
 Requires-Dist: tqdm>=4.66
 Requires-Dist: trackpy>=0.6

microlive-1.0.19.dist-info/RECORD

@@ -0,0 +1,27 @@
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+microlive/microscopy.py,sha256=OFqf0JXJW4-2cLHvXnwwp_SfMFsUXwp5lDKbkCRR4ok,710841
+microlive/ml_spot_detection.py,sha256=pVbOSGNJ0WWMuPRML42rFwvjKVZ0B1fJux1179OIbAg,10603
+microlive/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+microlive/data/icons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+microlive/data/icons/icon_micro.png,sha256=b5tFv4E6vUmLwYmYeM4PJuxLV_XqEzN14ueolekTFW0,370236
+microlive/data/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+microlive/utils/device.py,sha256=tcPMU8UiXL-DuGwhudUgrbjW1lgIK_EUKIOeOn0U6q4,2533
+microlive/utils/model_downloader.py,sha256=EruviTEh75YBekpznn1RZ1Nj8lnDmeC4TKEnFLOow6Y,9448
+microlive/utils/resources.py,sha256=Jz7kPI75xMLCBJMyX7Y_3ixKi_UgydfQkF0BlFtLCKs,1753
+microlive/data/models/spot_detection_cnn.pth,sha256=Np7vpPJIbKQmuKY0Hx-4IkeEDsnks_QEgs7TqaYgZmI,8468580
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+microlive-1.0.19.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+microlive-1.0.19.dist-info/entry_points.txt,sha256=Zqp2vixyD8lngcfEmOi8fkCj7vPhesz5xlGBI-EubRw,54
+microlive-1.0.19.dist-info/licenses/LICENSE,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
+microlive-1.0.19.dist-info/RECORD,,