v0.6.1

CHANGELOG.md

@@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.6.1] - 2021-10-19
+
+Fixed bug related to positioning of acquisitions from old MCD files
+
 ## [v0.6.0] - 2021-10-18
 
 Replaced imctools by readimc
@@ -28,6 +32,7 @@ Updated documentation
 Last release before introducing this changelog
 
 
+[v0.6.1]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.6.0...v0.6.1
 [v0.6.0]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.6...v0.6.0
 [v0.5.6]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.4...v0.5.6
 [v0.5.4]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.3...v0.5.4

napari_imc/io/mcd.py

@@ -51,10 +51,10 @@ def read_acquisition(self, acquisition_id: int, channel_label: str) -> Tuple[Ima
             if acquisition.id == acquisition_id
         )
         channel_index = acquisition.channel_labels.index(channel_label)
-        xs_physical = [acquisition.start_x_um, acquisition.end_x_um]
-        ys_physical = [acquisition.start_y_um, acquisition.end_y_um]
-        x_physical, y_physical = min(xs_physical), min(ys_physical)
-        w_physical, h_physical = max(xs_physical) - x_physical, max(ys_physical) - y_physical
+        x_physical = min(acquisition.start_x_um, acquisition.end_x_um)
+        y_physical = min(acquisition.start_y_um, acquisition.end_y_um)
+        w_physical = x_physical + acquisition.width_um
+        h_physical = y_physical + acquisition.height_um
         channel_img = self._mcd_file.read_acquisition(acquisition)[channel_index]
         if x_physical != acquisition.start_x_um:
             channel_img = channel_img[:, ::-1]