Coverage for ezstitcher/ez/functions.py: 100%

1""" 

2Function-based interface for the EZ module. 

3 

4This module provides simple function-based interfaces for common stitching workflows. 

5""" 

6 

7from pathlib import Path 

8from typing import Optional, Union, List, Dict, Any 

9 

10from .core import EZStitcher 

11 

12 

13def stitch_plate(input_path: Union[str, Path], 

14 output_path: Optional[Union[str, Path]] = None, 

15 **kwargs) -> Path: 

16 """ 

17 One-liner function to stitch a plate of microscopy images. 

18 

19 Args: 

20 input_path: Path to the plate folder 

21 output_path: Path for output (default: input_path + "_stitched") 

22 **kwargs: Additional options passed to EZStitcher 

23 normalize (bool): Whether to apply normalization 

24 flatten_z (bool): Whether to flatten Z-stacks 

25 z_method (str): Method for Z-flattening 

26 channel_weights (List[float]): Weights for channel compositing 

27 well_filter (List[str]): List of wells to process 

28 

29 Returns: 

30 Path: Path to the stitched output 

31 """ 

32 # Pass output_path as a keyword argument 

33 if output_path is not None: 

34 kwargs['output_path'] = output_path 

35 stitcher = EZStitcher(input_path, **kwargs) 

36 return stitcher.stitch()