Methods to stitch a position grid

mantis/analysis/AnalysisSettings.py

@@ -1,3 +1,5 @@
+import warnings
+
 from typing import Literal, Optional, Union
 
 import numpy as np
@@ -10,6 +12,11 @@ class MyBaseModel(BaseModel, extra=Extra.forbid):
     pass
 
 
+class ProcessingSettings(MyBaseModel):
+    fliplr: Optional[bool] = False
+    flipud: Optional[bool] = False
+
+
 class DeskewSettings(MyBaseModel):
     pixel_size_um: PositiveFloat
     ls_angle_deg: PositiveFloat
@@ -87,3 +94,27 @@ def check_affine_transform_list(cls, v):
                 raise ValueError("Each element in affine_transform_list must be a 4x4 ndarray")
 
         return v
+
+
+class StitchSettings(MyBaseModel):
+    channels: Optional[list[str]] = None
+    preprocessing: Optional[ProcessingSettings] = None
+    postprocessing: Optional[ProcessingSettings] = None
+    column_translation: Optional[list[float, float]] = None
+    row_translation: Optional[list[float, float]] = None
+    total_translation: Optional[dict[str, list[float, float]]] = None
+
+    def __init__(self, **data):
+        if data.get("total_translation") is None:
+            if any(
+                (data.get("column_translation") is None, data.get("row_translation") is None)
+            ):
+                raise ValueError(
+                    "If total_translation is not provided, both column_translation and row_translation must be provided"
+                )
+            else:
+                warnings.warn(
+                    "column_translation and row_translation are deprecated. Use total_translation instead.",
+                    DeprecationWarning,
+                )
+        super().__init__(**data)

mantis/analysis/settings/example_stitch_settings.yml

@@ -0,0 +1,28 @@
+channels: [Phase3D] # may be null in which case all channels will be stitched
+preprocessing:
+  fliplr: true
+  flipud: false
+postprocessing:
+  fliplr: false
+  flipud: true
+total_translation: # translation distance in (x, y) in pixels for each image
+  0/2/000000:
+  - 0.0
+  - 39.7
+  0/2/000001:
+  - 883.75
+  - 39.7
+  0/2/001000:
+  - 1.8
+  - 920.5
+  0/2/001001:
+  - 885.55
+  - 920.7
+# Instead of computing a total (x, y) shift for each image using estimate-stitch
+# you can also supply column_translation and row_translation as (x, y) lists
+# that will be applied to all images. column_translation and row_translation
+# should be approximately (950, 0) and (0, 950) for 1000x1000 images with 5% overlap.
+# This method of stitching images is being deprecated as the stage often does not
+# make reproducible movements.
+column_translation:
+row_translation: