Changed crop-dims to 1800x1200

camera_alignment_core/constants.py

@@ -37,17 +37,21 @@ def cropping_dimension(self) -> CroppingDimension:
             # The steps by which these dimensions were determined are unknown--they are "inherited constants."
             return CroppingDimension(900, 600)
         elif self == Magnification.SIXTY_THREE:
-            # The cropping dimensions for 63x and 20x were determined by Filip on 8/19/2021 via following steps:
-            #   - Look through a sample of ZSD images at each magnification to determine the minimum FOV dimensions. In both cases it was 1848x1248.
-            #   - Open a minimum-size image with a brightfield channel in FIJI and duplicate one slice of the bright channel.
-            #   - Apply a translation in x and y and a rotation to the image that corresponds to the **assumed worst-case misalignment**:
-            #       - Assumed that the microscope user/bead aligner made a decent attempt to visually align the cameras visually
-            #       - Applied a translation of **5 pixels in both x and y** and a **rotation of 0.5 degrees**
-            #   - Use the line tool to measure the length of the largest regions of black pixels in the resulting image along each axis
-            #   - Multiply those numbers by 2 and subtract from the minimum dimensions
-            return CroppingDimension(1828, 1224)
+            # The cropping dimensions for 63x and 20x were agreed upon by the microscopy committee on 9/4/2021:
+            #   - Ran 180 argolight field of ring images through the generate_alignment_matrix code
+            #   - From the metrics generated from that script, plotted what the crop dimensions would be for each
+            #   argolight images such that no black pixels would exist in the image after alignment ("perfect" crop)
+            #   - Proceeded to look at how much area was lost due to the above cropping, and plotted this as well
+            #   - Matched the area lost from the normal cropping in 100X (~6.3%), and saw how many "perfect" crops
+            #   would fall above or below that threshold
+            #   - Saw that only 5 of the 180 would wall above the 6.3% area lost when cropped "perfectly"
+            #   - Went through these 5 outliers and saw that there were issues with segmentations/SNR/physical
+            #   alignment, shwoing that we should fail the outliers.
+            #   - Agreed that the dimensions that allow loss of 6.3% of total area (1800x1200) for 20X and 63X
+            #   were most suitable for default cropping dimensions
+            return CroppingDimension(1800, 1200)
         elif self == Magnification.TWENTY:
             # See notes re 63X magnification for process by which these cropping dimensions were determined
-            return CroppingDimension(1828, 1224)
+            return CroppingDimension(1800, 1200)
 
         raise ValueError(f"No cropping dimension defined for {self}")