feat(eyepy.core): reflect plotted region in x and y axis for both loc…

…alizer and B-scan; check if bscan_region bscan position indicators are in plotting region

src/eyepy/core/annotations.py

@@ -236,6 +236,9 @@ def projection(self):
         Returns:
 
         """
+
+        # The flip is required because in the volume the bottom most B-scan has the lowest index
+        # while in the enface projection the bottom most position should have the biggest index.
         return np.flip(np.nansum(self.data, axis=1), axis=0)
 
     @property

src/eyepy/core/eyebscan.py

@@ -103,23 +103,12 @@ def plot(
             ax = plt.gca()
 
         # Complete region index expression
-        if region[0].start is None:
-            r0_start = 0
-        else:
-            r0_start = region[0].start
-        if region[1].start is None:
-            r1_start = 0
-        else:
-            r1_start = region[1].start
-        if region[0].stop is None:
-            r0_stop = self.shape[0]
-        else:
-            r0_stop = region[0].stop
-        if region[1].stop is None:
-            r1_stop = self.shape[1]
-        else:
-            r1_stop = region[1].stop
-        region = np.s_[r0_start:r0_stop, r1_start:r1_stop]
+        y_start = region[0].start if region[0].start is not None else 0
+        y_stop = region[0].stop if region[0].stop is not None else self.shape[0]
+        x_start = region[1].start if region[1].start is not None else 0
+        x_stop = region[1].stop if region[1].stop is not None else self.shape[1]
+
+        region = np.s_[y_start:y_stop, x_start:x_stop]
 
         if not layers:
             layers = []
@@ -202,3 +191,11 @@ def plot(
                 label=layer,
                 **layer_kwargs,
             )
+
+        # Hack to avoid a warning when setting the tick labels later
+        # Warning: FixedFormatter should only be used together with FixedLocator
+        ax.set_yticks(ax.get_yticks())
+        ax.set_xticks(ax.get_xticks())
+
+        ax.set_yticklabels((ax.get_yticks() + y_start).astype(int))
+        ax.set_xticklabels((ax.get_xticks() + x_start).astype(int))

src/eyepy/core/eyeenface.py

@@ -118,3 +118,12 @@ def plot(self,
         if ax is None:
             ax = plt.gca()
         ax.imshow(self.data[region], cmap="gray")
+
+        ax.set_yticks(ax.get_yticks())
+        ax.set_xticks(ax.get_xticks())
+
+        y_start = region[0].start if region[0].start is not None else 0
+        x_start = region[1].start if region[1].start is not None else 0
+
+        ax.set_yticklabels((ax.get_yticks() + y_start).astype(int))
+        ax.set_xticklabels((ax.get_xticks() + x_start).astype(int))

src/eyepy/core/eyevolume.py

@@ -630,6 +630,16 @@ def plot(
 
         """
 
+        # Complete region index expression
+        y_start = region[0].start if region[0].start is not None else 0
+        y_stop = region[0].stop if region[
+            0].stop is not None else self.localizer.shape[0]
+        x_start = region[1].start if region[1].start is not None else 0
+        x_stop = region[1].stop if region[
+            1].stop is not None else self.localizer.shape[1]
+
+        region = np.s_[y_start:y_stop, x_start:x_stop]
+
         if ax is None:
             ax = plt.gca()
 
@@ -694,9 +704,15 @@ def _plot_bscan_positions(
             start = self[i].meta["start_pos"] / scale
             end = self[i].meta["end_pos"] / scale
 
-            # x = [start[0], end[0]]
-            # y = [start[1], end[1]]
-            # ax.plot(x, y, **line_kwargs)
+            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):
+                    logger.warning(
+                        "B-scan position can not be plotted because the visualized region does not contain the complete B-scan."
+                    )
+                    return
+
             polygon = patches.Polygon(
                 [start, end],
                 closed=False,
@@ -727,6 +743,15 @@ def _plot_bscan_region(self,
         lower_right = self[0].meta["end_pos"] / scale
         upper_right = self[-1].meta["end_pos"] / scale
 
+        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):
+                logger.warning(
+                    "B-scan region can not be plotted because the visualized region does not contain the complete B-scan region."
+                )
+                return
+
         polygon = patches.Polygon(
             [upper_left, lower_left, lower_right, upper_right],
             closed=True,