lattice-sub 1.5.3__tar.gz → 1.5.4__tar.gz

{lattice_sub-1.5.3/src/lattice_sub.egg-info → lattice_sub-1.5.4}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: lattice-sub
-Version: 1.5.3
+Version: 1.5.4
 Summary: Lattice subtraction for cryo-EM micrographs - removes periodic crystal signals to reveal non-periodic features
 Author-email: George Stephenson <george.stephenson@colorado.edu>, Vignesh Kasinath <vignesh.kasinath@colorado.edu>
 License: MIT
 Project-URL: Homepage, https://github.com/gsstephenson/cryoem-lattice-subtraction
 Project-URL: Documentation, https://github.com/gsstephenson/cryoem-lattice-subtraction#readme
 Project-URL: Repository, https://github.com/gsstephenson/cryoem-lattice-subtraction
-Keywords: cryo-em,electron-microscopy,lattice-subtraction,image-processing,fft
+Keywords: cryo-em,electron-microscopy,lattice-subtraction,image-processing,fft,live-processing,file-watching
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
@@ -57,6 +57,8 @@ Dynamic: license-file
 
 **Remove periodic lattice patterns from cryo-EM micrographs to reveal non-periodic features.**
 
+> **NEW in v1.5.0:** Live watch mode with `--live` flag! Automatically process motion-corrected files as they arrive during data collection.
+
 ![Example Result](https://raw.githubusercontent.com/gsstephenson/cryoem-lattice-subtraction/main/docs/images/example_comparison.png)
 
 ---
@@ -89,6 +91,20 @@ lattice-sub process your_image.mrc -o output.mrc --pixel-size 0.56
 lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56
 ```
 
+### Live Watch Mode (NEW in v1.5.0)
+
+Process files as they arrive during data collection:
+
+```bash
+lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56 --live
+```
+
+In live mode:
+- If files already exist: batch processes them first with all GPUs
+- Then switches to watch mode: monitors for new files with single GPU
+- Press Ctrl+C to stop watching
+- Perfect for processing motion-corrected files as they're generated
+
 ### Generate Comparison Images
 
 ```bash
@@ -118,6 +134,7 @@ lattice-sub batch input_folder/ output_folder/ -p 0.56 --vis comparisons/ -n 10
 | `-t, --threshold` | Peak detection sensitivity (default: **auto** - optimized per image) |
 | `--vis DIR` | Generate 4-panel comparison PNGs in DIR |
 | `-n, --num-vis N` | Limit visualizations to first N images |
+| `--live` | **Watch mode**: continuously monitor directory for new files (Ctrl+C to stop) |
 | `--cpu` | Force CPU processing (GPU is used by default) |
 | `-q, --quiet` | Hide the banner and progress messages |
 | `-v, --verbose` | Show detailed processing information |
@@ -192,6 +209,9 @@ When processing batches on systems with multiple GPUs, files are automatically d
 ```bash
 # Automatically uses all available GPUs
 lattice-sub batch input_folder/ output_folder/ -p 0.56
+
+# Or watch for new files in real-time (live mode)
+lattice-sub batch input_folder/ output_folder/ -p 0.56 --live
 ```
 
 **Example with 2 GPUs and 100 images:**
@@ -220,7 +240,7 @@ lattice-sub batch input/ output/ -p 0.56
 
 **Output:**
 ```
-Phase-preserving FFT inpainting for cryo-EM  |  v1.3.0
+Phase-preserving FFT inpainting for cryo-EM  |  v1.5.3
 
   Configuration
   -------------
@@ -280,6 +300,23 @@ stats = processor.process_directory("raw/", "processed/")
 print(f"Processed {stats.successful}/{stats.total} files")
 ```
 
+### Live Watch Mode
+
+```python
+from lattice_subtraction import LiveBatchProcessor, Config
+
+config = Config(pixel_ang=0.56)
+processor = LiveBatchProcessor(
+    input_dir="raw/",
+    output_dir="processed/",
+    config=config,
+    num_workers=1
+)
+
+# Process existing files, then watch for new ones
+processor.watch_and_process()  # Runs until Ctrl+C
+```
+
 ---
 
 ## What It Does
@@ -450,6 +487,7 @@ src/lattice_subtraction/
 ├── cli.py                # Command-line interface
 ├── core.py               # LatticeSubtractor main class
 ├── batch.py              # Parallel batch processing
+├── watch.py              # Live watch mode (NEW in v1.5.0)
 ├── config.py             # Configuration dataclass
 ├── io.py                 # MRC file I/O
 ├── masks.py              # FFT mask generation

{lattice_sub-1.5.3 → lattice_sub-1.5.4}/README.md

@@ -15,6 +15,8 @@
 
 **Remove periodic lattice patterns from cryo-EM micrographs to reveal non-periodic features.**
 
+> **NEW in v1.5.0:** Live watch mode with `--live` flag! Automatically process motion-corrected files as they arrive during data collection.
+
 ![Example Result](https://raw.githubusercontent.com/gsstephenson/cryoem-lattice-subtraction/main/docs/images/example_comparison.png)
 
 ---
@@ -47,6 +49,20 @@ lattice-sub process your_image.mrc -o output.mrc --pixel-size 0.56
 lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56
 ```
 
+### Live Watch Mode (NEW in v1.5.0)
+
+Process files as they arrive during data collection:
+
+```bash
+lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56 --live
+```
+
+In live mode:
+- If files already exist: batch processes them first with all GPUs
+- Then switches to watch mode: monitors for new files with single GPU
+- Press Ctrl+C to stop watching
+- Perfect for processing motion-corrected files as they're generated
+
 ### Generate Comparison Images
 
 ```bash
@@ -76,6 +92,7 @@ lattice-sub batch input_folder/ output_folder/ -p 0.56 --vis comparisons/ -n 10
 | `-t, --threshold` | Peak detection sensitivity (default: **auto** - optimized per image) |
 | `--vis DIR` | Generate 4-panel comparison PNGs in DIR |
 | `-n, --num-vis N` | Limit visualizations to first N images |
+| `--live` | **Watch mode**: continuously monitor directory for new files (Ctrl+C to stop) |
 | `--cpu` | Force CPU processing (GPU is used by default) |
 | `-q, --quiet` | Hide the banner and progress messages |
 | `-v, --verbose` | Show detailed processing information |
@@ -150,6 +167,9 @@ When processing batches on systems with multiple GPUs, files are automatically d
 ```bash
 # Automatically uses all available GPUs
 lattice-sub batch input_folder/ output_folder/ -p 0.56
+
+# Or watch for new files in real-time (live mode)
+lattice-sub batch input_folder/ output_folder/ -p 0.56 --live
 ```
 
 **Example with 2 GPUs and 100 images:**
@@ -178,7 +198,7 @@ lattice-sub batch input/ output/ -p 0.56
 
 **Output:**
 ```
-Phase-preserving FFT inpainting for cryo-EM  |  v1.3.0
+Phase-preserving FFT inpainting for cryo-EM  |  v1.5.3
 
   Configuration
   -------------
@@ -238,6 +258,23 @@ stats = processor.process_directory("raw/", "processed/")
 print(f"Processed {stats.successful}/{stats.total} files")
 ```
 
+### Live Watch Mode
+
+```python
+from lattice_subtraction import LiveBatchProcessor, Config
+
+config = Config(pixel_ang=0.56)
+processor = LiveBatchProcessor(
+    input_dir="raw/",
+    output_dir="processed/",
+    config=config,
+    num_workers=1
+)
+
+# Process existing files, then watch for new ones
+processor.watch_and_process()  # Runs until Ctrl+C
+```
+
 ---
 
 ## What It Does
@@ -408,6 +445,7 @@ src/lattice_subtraction/
 ├── cli.py                # Command-line interface
 ├── core.py               # LatticeSubtractor main class
 ├── batch.py              # Parallel batch processing
+├── watch.py              # Live watch mode (NEW in v1.5.0)
 ├── config.py             # Configuration dataclass
 ├── io.py                 # MRC file I/O
 ├── masks.py              # FFT mask generation

{lattice_sub-1.5.3 → lattice_sub-1.5.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lattice-sub"
-version = "1.5.3"
+version = "1.5.4"
 description = "Lattice subtraction for cryo-EM micrographs - removes periodic crystal signals to reveal non-periodic features"
 readme = "README.md"
 license = {text = "MIT"}
@@ -23,7 +23,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
-keywords = ["cryo-em", "electron-microscopy", "lattice-subtraction", "image-processing", "fft"]
+keywords = ["cryo-em", "electron-microscopy", "lattice-subtraction", "image-processing", "fft", "live-processing", "file-watching"]
 dependencies = [
     "numpy>=1.24",
     "scipy>=1.11",

{lattice_sub-1.5.3 → lattice_sub-1.5.4/src/lattice_sub.egg-info}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: lattice-sub
-Version: 1.5.3
+Version: 1.5.4
 Summary: Lattice subtraction for cryo-EM micrographs - removes periodic crystal signals to reveal non-periodic features
 Author-email: George Stephenson <george.stephenson@colorado.edu>, Vignesh Kasinath <vignesh.kasinath@colorado.edu>
 License: MIT
 Project-URL: Homepage, https://github.com/gsstephenson/cryoem-lattice-subtraction
 Project-URL: Documentation, https://github.com/gsstephenson/cryoem-lattice-subtraction#readme
 Project-URL: Repository, https://github.com/gsstephenson/cryoem-lattice-subtraction
-Keywords: cryo-em,electron-microscopy,lattice-subtraction,image-processing,fft
+Keywords: cryo-em,electron-microscopy,lattice-subtraction,image-processing,fft,live-processing,file-watching
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
@@ -57,6 +57,8 @@ Dynamic: license-file
 
 **Remove periodic lattice patterns from cryo-EM micrographs to reveal non-periodic features.**
 
+> **NEW in v1.5.0:** Live watch mode with `--live` flag! Automatically process motion-corrected files as they arrive during data collection.
+
 ![Example Result](https://raw.githubusercontent.com/gsstephenson/cryoem-lattice-subtraction/main/docs/images/example_comparison.png)
 
 ---
@@ -89,6 +91,20 @@ lattice-sub process your_image.mrc -o output.mrc --pixel-size 0.56
 lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56
 ```
 
+### Live Watch Mode (NEW in v1.5.0)
+
+Process files as they arrive during data collection:
+
+```bash
+lattice-sub batch input_folder/ output_folder/ --pixel-size 0.56 --live
+```
+
+In live mode:
+- If files already exist: batch processes them first with all GPUs
+- Then switches to watch mode: monitors for new files with single GPU
+- Press Ctrl+C to stop watching
+- Perfect for processing motion-corrected files as they're generated
+
 ### Generate Comparison Images
 
 ```bash
@@ -118,6 +134,7 @@ lattice-sub batch input_folder/ output_folder/ -p 0.56 --vis comparisons/ -n 10
 | `-t, --threshold` | Peak detection sensitivity (default: **auto** - optimized per image) |
 | `--vis DIR` | Generate 4-panel comparison PNGs in DIR |
 | `-n, --num-vis N` | Limit visualizations to first N images |
+| `--live` | **Watch mode**: continuously monitor directory for new files (Ctrl+C to stop) |
 | `--cpu` | Force CPU processing (GPU is used by default) |
 | `-q, --quiet` | Hide the banner and progress messages |
 | `-v, --verbose` | Show detailed processing information |
@@ -192,6 +209,9 @@ When processing batches on systems with multiple GPUs, files are automatically d
 ```bash
 # Automatically uses all available GPUs
 lattice-sub batch input_folder/ output_folder/ -p 0.56
+
+# Or watch for new files in real-time (live mode)
+lattice-sub batch input_folder/ output_folder/ -p 0.56 --live
 ```
 
 **Example with 2 GPUs and 100 images:**
@@ -220,7 +240,7 @@ lattice-sub batch input/ output/ -p 0.56
 
 **Output:**
 ```
-Phase-preserving FFT inpainting for cryo-EM  |  v1.3.0
+Phase-preserving FFT inpainting for cryo-EM  |  v1.5.3
 
   Configuration
   -------------
@@ -280,6 +300,23 @@ stats = processor.process_directory("raw/", "processed/")
 print(f"Processed {stats.successful}/{stats.total} files")
 ```
 
+### Live Watch Mode
+
+```python
+from lattice_subtraction import LiveBatchProcessor, Config
+
+config = Config(pixel_ang=0.56)
+processor = LiveBatchProcessor(
+    input_dir="raw/",
+    output_dir="processed/",
+    config=config,
+    num_workers=1
+)
+
+# Process existing files, then watch for new ones
+processor.watch_and_process()  # Runs until Ctrl+C
+```
+
 ---
 
 ## What It Does
@@ -450,6 +487,7 @@ src/lattice_subtraction/
 ├── cli.py                # Command-line interface
 ├── core.py               # LatticeSubtractor main class
 ├── batch.py              # Parallel batch processing
+├── watch.py              # Live watch mode (NEW in v1.5.0)
 ├── config.py             # Configuration dataclass
 ├── io.py                 # MRC file I/O
 ├── masks.py              # FFT mask generation

{lattice_sub-1.5.3 → lattice_sub-1.5.4}/src/lattice_subtraction/__init__.py

@@ -19,7 +19,7 @@ Example:
     >>> result.save("output.mrc")
 """
 
-__version__ = "1.5.3"
+__version__ = "1.5.4"
 __author__ = "George Stephenson & Vignesh Kasinath"
 
 from .config import Config

{lattice_sub-1.5.3 → lattice_sub-1.5.4}/src/lattice_subtraction/cli.py

@@ -313,9 +313,9 @@ def setup_gpu(yes: bool, force: bool):
 )
 @click.option(
     "--pixel-size", "-p",
-    type=float,
-    required=True,
-    help="Pixel size in Angstroms",
+    type=click.FloatRange(min=0.0, min_open=True),
+    required=False,
+    help="Pixel size in Angstroms (must be positive). Required unless --config provides pixel_ang.",
 )
 @click.option(
     "--threshold", "-t",
@@ -397,7 +397,23 @@ def process(
     if config:
         logger.info(f"Loading config from {config}")
         cfg = Config.from_yaml(config)
+        # Override with command-line options if provided
+        if pixel_size is not None:
+            cfg.pixel_ang = pixel_size
+        if threshold is not None:
+            cfg.threshold = threshold
+        if inside_radius != 90.0:  # Non-default value
+            cfg.inside_radius_ang = inside_radius
+        if outside_radius is not None:
+            cfg.outside_radius_ang = outside_radius
+        if cpu:
+            cfg.backend = "numpy"
     else:
+        # No config file - pixel_size is required
+        if pixel_size is None:
+            raise click.UsageError(
+                "--pixel-size is required when --config is not provided"
+            )
         # Use "auto" threshold if not specified (GPU-optimized per-image)
         thresh_value = threshold if threshold is not None else "auto"
         cfg = Config(
@@ -462,9 +478,9 @@ def process(
 @click.argument("output_dir", type=click.Path(file_okay=False))
 @click.option(
     "--pixel-size", "-p",
-    type=float,
-    required=True,
-    help="Pixel size in Angstroms",
+    type=click.FloatRange(min=0.0, min_open=True),
+    required=False,
+    help="Pixel size in Angstroms (must be positive). Required unless --config provides pixel_ang.",
 )
 @click.option(
     "--threshold", "-t",
@@ -571,7 +587,19 @@ def batch(
     # Load or create config
     if config:
         cfg = Config.from_yaml(config)
+        # Override with command-line options if provided
+        if pixel_size is not None:
+            cfg.pixel_ang = pixel_size
+        if threshold is not None:
+            cfg.threshold = threshold
+        if cpu:
+            cfg.backend = "numpy"
     else:
+        # No config file - pixel_size is required
+        if pixel_size is None:
+            raise click.UsageError(
+                "--pixel-size is required when --config is not provided"
+            )
         # Use "auto" threshold if not specified (GPU-optimized per-image)
         thresh_value = threshold if threshold is not None else "auto"
         cfg = Config(