fix(eyepy.core): fixes bscan_region and bscan_position plotting when …

…plotting only a part of the fundus

also adds new header_gif to the README

README.md

@@ -3,7 +3,7 @@
 Use Python to import, analyse and visualize retinal imaging data.
 </p>
 
-![header_gif](https://user-images.githubusercontent.com/5720058/218448527-d0477fa3-0cb6-4a3e-88e8-e10a60cc7a91.gif)
+![header_gif](https://user-images.githubusercontent.com/5720058/228815448-4b561246-dac9-4f8f-abde-e0dd5457a72b.gif)
 
 [![Documentation](https://img.shields.io/badge/docs-eyepy-blue)](https://MedVisBonn.github.io/eyepy)
 [![PyPI version](https://badge.fury.io/py/eyepie.svg)](https://badge.fury.io/py/eyepie)

src/eyepy/core/eyeenface.py

@@ -135,7 +135,10 @@ def plot(
 
         """
         ax = plt.gca() if ax is None else ax
-        ax.imshow(self.data[region], cmap='gray')
+        vmin = np.min(self.data)
+        vmax = np.max(self.data)
+
+        ax.imshow(self.data[region], cmap='gray', vmin=vmin, vmax=vmax)
 
         # Make sure tick labels match the image region
         y_start = region[0].start if region[0].start is not None else 0

src/eyepy/core/eyevolume.py

@@ -721,13 +721,15 @@ def _plot_bscan_positions(
         for i in bscan_positions:
             scale = np.array([self.localizer.scale_x, self.localizer.scale_y])
 
-            start = self[i].meta['start_pos'] / scale
-            end = self[i].meta['end_pos'] / scale
+            start = self[i].meta['start_pos'] / scale - np.array(
+                [region[1].start, region[0].start])
+            end = self[i].meta['end_pos'] / scale - np.array(
+                [region[1].start, region[0].start])
 
             for pos in [start, end]:
                 # Check for both axis if pos is in region
-                if not (region[0].start <= pos[0] <= region[0].stop
-                        and region[1].start <= pos[1] <= region[1].stop):
+                if not (0 <= pos[0] <= region[0].stop - region[0].start
+                        and 0 <= pos[1] <= region[1].stop - region[1].start):
                     logger.warning(
                         'B-scan position can not be plotted because the visualized region does not contain the complete B-scan.'
                     )
@@ -755,15 +757,19 @@ def _plot_bscan_region(self,
 
         scale = np.array([self.localizer.scale_x, self.localizer.scale_y])
 
-        upper_left = self[-1].meta['start_pos'] / scale
-        lower_left = self[0].meta['start_pos'] / scale
-        lower_right = self[0].meta['end_pos'] / scale
-        upper_right = self[-1].meta['end_pos'] / scale
+        upper_left = np.array(self[-1].meta['start_pos']) / scale - np.array(
+            [region[1].start, region[0].start])
+        lower_left = np.array(self[0].meta['start_pos']) / scale - np.array(
+            [region[1].start, region[0].start])
+        lower_right = np.array(self[0].meta['end_pos']) / scale - np.array(
+            [region[1].start, region[0].start])
+        upper_right = np.array(self[-1].meta['end_pos']) / scale - np.array(
+            [region[1].start, region[0].start])
 
         for pos in [upper_left, lower_left, lower_right, upper_right]:
             # Check for both axis if pos is in region
-            if not (region[0].start <= pos[0] <= region[0].stop
-                    and region[1].start <= pos[1] <= region[1].stop):
+            if not (0 <= pos[0] < region[0].stop - region[0].start
+                    and 0 <= pos[1] < region[1].stop - region[1].start):
                 logger.warning(
                     'B-scan region can not be plotted because the visualized region does not contain the complete B-scan region.'
                 )