Merge pull request #55 from HiDiHlabs/dev

Fix inconsistent VSI plotting

Author: niklasmueboe

ovrlpy/_plotting.py

@@ -7,6 +7,7 @@
 from matplotlib.axes import Axes
 from matplotlib.colors import Colormap, LinearSegmentedColormap
 from matplotlib.figure import Figure
+from matplotlib.image import AxesImage
 from matplotlib.patches import Rectangle
 from matplotlib.text import Text
 from matplotlib_scalebar.scalebar import ScaleBar
@@ -30,6 +31,7 @@
 )
 
 VSI = "vertical signal integrity"
+_SIGNAL_THRESHOLD = 2
 
 
 def _plot_scalebar(ax: Axes, dx: float = 1, units="um", **kwargs):
@@ -249,10 +251,24 @@ def plot_pseudocells(
     return fig
 
 
+def _plot_signal_integrity(
+    ax: Axes,
+    integrity: np.ndarray,
+    signal: np.ndarray,
+    threshold: float,
+    *,
+    cmap: Colormap = BIH_CMAP,
+) -> AxesImage:
+    # fade out for pixels with signal < threshold
+    alpha = (signal / threshold).clip(0, 1) ** 2
+    img = ax.imshow(integrity, cmap=cmap, alpha=alpha, vmin=0, vmax=1, origin="lower")
+    return img
+
+
 def plot_signal_integrity(
     ovrlp: Ovrlp,
     *,
-    signal_threshold: float = 2.0,
+    signal_threshold: float = _SIGNAL_THRESHOLD,
     cmap: str | Colormap = BIH_CMAP,
     histogram: bool = True,
     scalebar: dict | None = SCALEBAR_PARAMS,
@@ -268,6 +284,7 @@ def plot_signal_integrity(
     signal_threshold : float, optional
         Threshold below which the signal is faded out in the plot,
         to avoid displaying noisy areas with low predictive confidence.
+        Pixels below the threshold are not counted in the histogram.
     cmap : str | matplotlib.colors.Colormap, optional
         Colormap for display.
     histogram : bool, optional
@@ -301,14 +318,10 @@ def plot_signal_integrity(
 
         assert isinstance(ax_im, Axes)
 
-        img = ax_im.imshow(
-            integrity,
-            cmap=cmap,
-            alpha=((signal / signal_threshold).clip(0, 1) ** 2),
-            vmin=0,
-            vmax=1,
+        img = _plot_signal_integrity(
+            ax_im, integrity, signal, signal_threshold, cmap=cmap
         )
-        ax_im.invert_yaxis()
+
         ax_im.spines[["top", "right"]].set_visible(False)
 
         if scalebar is not None:
@@ -343,7 +356,7 @@ def plot_region_of_interest(
     y: float,
     *,
     window_size: int = 30,
-    signal_threshold: float = 5.0,
+    signal_threshold: float = _SIGNAL_THRESHOLD,
     scalebar: dict | None = SCALEBAR_PARAMS,
     figsize: tuple[float, float] = (12, 8),
     **kwargs,
@@ -362,7 +375,8 @@ def plot_region_of_interest(
     window_size : int, optional
         Size of the window to display.
     signal_threshold : float, optional
-        Threshold for the signal plot.
+        Threshold below which the signal is faded out in the VSI plot,
+        to avoid displaying noisy areas with low predictive confidence.
     scalebar : dict[str, typing.Any] | None
         If `None` no scalebar will be plotted. Otherwise a dictionary with
         additional kwargs for ``matplotlib_scalebar.scalebar.ScaleBar``.
@@ -393,18 +407,12 @@ def plot_region_of_interest(
     # integrity map
     ax_integrity = fig.add_subplot(gs[0, 2], label="signal_integrity", facecolor="k")
 
-    img = ax_integrity.imshow(
-        integrity,
-        cmap=BIH_CMAP,
-        alpha=(signal / signal_threshold).clip(0, 1),
-        vmin=0,
-        vmax=1,
+    img = _plot_signal_integrity(
+        ax_integrity, integrity, signal, signal_threshold, cmap=BIH_CMAP
     )
-
-    ax_integrity.set_title("ROI, signal integrity")
-    ax_integrity.invert_yaxis()
     fig.colorbar(img, label=VSI)
 
+    ax_integrity.set_title("ROI, signal integrity")
     ax_integrity.set_xlim(x - window_size, x + window_size)
     ax_integrity.set_ylim(y - window_size, y + window_size)