diff --git a/src/m2stitch/_stage_model.py b/src/m2stitch/_stage_model.py index 8a27b23..970b245 100644 --- a/src/m2stitch/_stage_model.py +++ b/src/m2stitch/_stage_model.py @@ -1,5 +1,6 @@ import itertools from typing import Callable +from typing import Optional from typing import Tuple import numpy as np @@ -11,7 +12,11 @@ def compute_image_overlap2( - grid: pd.DataFrame, direction: str, sizeY: Int, sizeX: Int, predictor: Callable + grid: pd.DataFrame, + direction: str, + sizeY: Int, + sizeX: Int, + predictor: Optional[Callable], ) -> Tuple[Float, ...]: """Compute the value of the image overlap. @@ -25,6 +30,8 @@ def compute_image_overlap2( the image width sizeX : Int the image height + predictor : Optional[Callable], optional + the predictor function of outliers Returns ------- @@ -43,8 +50,12 @@ def compute_image_overlap2( ] ) translation = translation[:, np.all(np.isfinite(translation), axis=0)] - c = predictor(translation.T) - res = np.median(translation[:, c == 1], axis=1) + if predictor is not None: + c = predictor(translation.T) + ind = c == 1 + else: + ind = np.ones(translation.shape[1], dtype=bool) + res = np.median(translation[:, ind], axis=1) assert len(res) == 2 return tuple(res) diff --git a/src/m2stitch/stitching.py b/src/m2stitch/stitching.py index f1b0a39..5479f3d 100644 --- a/src/m2stitch/stitching.py +++ b/src/m2stitch/stitching.py @@ -30,7 +30,7 @@ @dataclass -class ElipticEnvelopPredictor: +class EllipticEnvelopePredictor: contamination: float epsilon: float random_seed: int @@ -55,6 +55,7 @@ def stitch_images( full_output: bool = False, row_col_transpose: bool = True, ncc_threshold: Float = 0.5, + outlier_predictor_name: str = "elliptic_envelope", ) -> Tuple[pd.DataFrame, dict]: """Compute image positions for stitching. @@ -95,6 +96,10 @@ def stitch_images( the threshold of the normalized cross correlation used to select the initial stitched pairs. + outlier_predictor_name : str, default "elliptic_envelope" + the name of the outlier predictor. + "elliptic_envelope" or "none" are supported. + Returns ------- grid : pd.DataFrame @@ -104,6 +109,14 @@ def stitch_images( prop_dict : dict the dict of estimated parameters. (to be documented) """ + + if outlier_predictor_name == "elliptic_envelope": + outlier_predictor = EllipticEnvelopePredictor(0.1, 0.1, 0) + elif outlier_predictor_name == "none": + outlier_predictor = None + else: + raise ValueError(f"Unknown outlier_predictor_name: {outlier_predictor_name}") + images = np.array(images) assert (position_indices is not None) or (rows is not None and cols is not None) if position_indices is None: @@ -202,12 +215,19 @@ def get_lims(dimension, size): assert np.any( grid["left_ncc_first"] > ncc_threshold ), "there is no good left pair, (try lowering the ncc_threshold)" - predictor = ElipticEnvelopPredictor(contamination=0.4, epsilon=0.01, random_seed=0) left_displacement = compute_image_overlap2( - grid[grid["left_ncc_first"] > ncc_threshold], "left", sizeY, sizeX, predictor + grid[grid["left_ncc_first"] > ncc_threshold], + "left", + sizeY, + sizeX, + outlier_predictor, ) top_displacement = compute_image_overlap2( - grid[grid["top_ncc_first"] > ncc_threshold], "top", sizeY, sizeX, predictor + grid[grid["top_ncc_first"] > ncc_threshold], + "top", + sizeY, + sizeX, + outlier_predictor, ) overlap_top = np.clip(100 - top_displacement[0] * 100, pou, 100 - pou) overlap_left = np.clip(100 - left_displacement[1] * 100, pou, 100 - pou)