Change order of arguments for show_positions, fix arguments

docs/tutorials/basics.ipynb

@@ -256,7 +256,7 @@
     "positions = [(127, 147), (130, 209), (202, 136)]\n",
     "\n",
     "fig, axs = plt.subplots(1,2, figsize=(11,4))\n",
-    "om.trace.show_positions(video[0], positions, ax=axs[0])\n",
+    "om.trace.show_positions(positions, video[0], ax=axs[0])\n",
     "traces = om.trace.extract_traces(video, positions, size=5, ax=axs[1], show=True, fps=500)\n",
     "plt.show()"
    ]
@@ -292,7 +292,7 @@
    "source": [
     "fig, axs = plt.subplots(1, 2, figsize=(10,5))\n",
     "\n",
-    "om.trace.show_positions(video[0], positions, ax=axs[0])\n",
+    "om.trace.show_positions(positions, video[0], ax=axs[0])\n",
     "\n",
     "x_axis_ms = (np.arange(video.shape[0]) / 500.0) * 1000\n",
     "traces = om.extract_traces(video[:300],\n",

docs/tutorials/ratiometry.ipynb

@@ -173,7 +173,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "om.show_positions(video_green[0], positions)"
+    "om.show_positions(positions, video_green[0])"
    ]
   },
   {

optimap/trace/_core.py

@@ -1,3 +1,5 @@
+import warnings
+
 import matplotlib.pyplot as plt
 import numpy as np
 
@@ -114,19 +116,21 @@ def rect_mask(video, x, y):
     return traces
 
 
-def show_positions(image, positions, size=None, cmap="gray", vmin=None, vmax=None, ax=None, **kwargs):
+def show_positions(positions, image=None, size=None, color=None, cmap="gray", vmin=None, vmax=None, ax=None, **kwargs):
     """Overlay positions on an image.
 
     Parameters
     ----------
-    image : 2D array
-        Image to overlay positions on
     positions : list of tuples
         List of positions to overlay
+    image : 2D array
+        Image to overlay positions on, optional
     size : float or array-like, shape (n, ), optional
         Size of the points, see `s` parameter in :py:func:`matplotlib.pyplot.scatter` for more information
+    color : str or list of str, optional
+        Color of the points, by default None
     cmap : str, optional
-        Colormap to use, by default 'gray'
+        Colormap to use for image, by default 'gray'
     vmin : float, optional
         Minimum value for the colormap, by default None
     vmax : float, optional
@@ -145,11 +149,21 @@ def show_positions(image, positions, size=None, cmap="gray", vmin=None, vmax=Non
         show = True
     else:
         show = False
-
-    ax.imshow(image, cmap=cmap, vmin=vmin, vmax=vmax, interpolation="none")
-    ax.axis("off")
-    for pos in positions:
-        ax.scatter(pos[0], pos[1], s=size, **kwargs)
+
+    if isinstance(image, np.ndarray) and image.ndim == 2 and image.shape[1] == 2:
+        image, positions = positions, image
+        warnings.warn("The order of arguments for optimap.show_positions() has changed.", DeprecationWarning)
+
+    if image is not None:
+        ax.imshow(image, cmap=cmap, vmin=vmin, vmax=vmax, interpolation="none")
+        ax.axis("off")
+
+    if isinstance(color, str) or color is None:
+        color = [color, ] * len(positions)
+    if isinstance(size, (int, float)) or size is None:
+        size = [size, ] * len(positions)
+    for pos, s, c in zip(positions, size, color):
+        ax.scatter(pos[0], pos[1], s=s, c=c, **kwargs)
     if show:
         plt.show()
     return ax