Merge pull request #136 from ianhi/segment-cmaps

more kwarg options for image segmenter

Author: ianhi

examples/image-segmentation.ipynb

@@ -171,6 +171,53 @@
     "display(preloaded)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Styling\n",
+    "\n",
+    "\n",
+    "### imshow parameters\n",
+    "\n",
+    "You can modify the display of the image using any kwargs accepted the [imshow](https://matplotlib.org/api/_as_gen/matplotlib.pyplot.imshow.html) command. For example if we convert our example image to gray-scale then we can choose the colormap with the `cmap` argument."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ipywidgets import HBox\n",
+    "\n",
+    "grayscale_image = image.mean(axis=-1)\n",
+    "gray = image_segmenter(grayscale_image, nclasses=3, mask=mask, figsize=(5, 5), cmap=\"gray\")\n",
+    "display(gray)\n",
+    "plasma = image_segmenter(grayscale_image, nclasses=3, mask=mask, figsize=(5, 5), cmap=\"plasma\")\n",
+    "display(plasma)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## LassoSelector line\n",
+    "\n",
+    "You can change the appearance of the LassoSelector line using the `lineprops` kwarg. So to make the line very thick and red:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lineprops = {\"color\":\"red\", \"linewidth\":10}\n",
+    "gray = image_segmenter(grayscale_image, nclasses=3, mask=mask, figsize=(5, 5), cmap=\"gray\",lineprops = lineprops)\n",
+    "display(gray)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -195,7 +242,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,

mpl_interactions/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 10, 1)
+version_info = (0, 11, 0)
 __version__ = ".".join(map(str, version_info))

mpl_interactions/generic.py

@@ -393,10 +393,14 @@ def __init__(
         mask=None,
         mask_colors=None,
         mask_alpha=0.75,
+        lineprops=None,
         figsize=(10, 10),
-        cmap="viridis",
+        **kwargs,
     ):
         """
+        Create an image segmenter. Any ``kwargs`` will be passed through to the ``imshow``
+        call that displays *img*.
+
         parameters
         ----------
         img : array_like
@@ -409,12 +413,14 @@ def __init__(
         mask_alpha : float, default .75
             The alpha values to use for selected regions. This will always override the alpha values
             in mask_colors if any were passed
+        lineprops : dict, default: None
+            lineprops passed to LassoSelector. If None the default values are:
+            {"color": "black", "linewidth": 1, "alpha": 0.8}
         figsize : (float, float), optional
             passed to plt.figure
-        cmap : 'string'
-            the colormap to use if img has shape (X,Y)
+        **kwargs:
+            All other kwargs will passed to the imshow command for the image
         """
-
         # ensure mask colors is iterable and the same length as the number of classes
         # choose colors from default color cycle?
 
@@ -450,10 +456,11 @@ def __init__(
         with ioff:
             self.fig = figure(figsize=figsize)
             self.ax = self.fig.gca()
-            self.displayed = self.ax.imshow(self._img)
+            self.displayed = self.ax.imshow(self._img, **kwargs)
             self._mask = self.ax.imshow(self._overlay)
 
-        lineprops = {"color": "black", "linewidth": 1, "alpha": 0.8}
+        if lineprops is None:
+            lineprops = {"color": "black", "linewidth": 1, "alpha": 0.8}
         useblit = False if "ipympl" in get_backend().lower() else True
         self.lasso = LassoSelector(self.ax, self._onselect, lineprops=lineprops, useblit=useblit)
         self.lasso.set_visible(True)

mpl_interactions/mpl_kwargs.py

@@ -0,0 +1,58 @@
+# this is a list of options to Line2D partially taken from
+# https://github.com/matplotlib/matplotlib/blob/f9d29189507cfe4121a231f6ab63539d216c37bd/lib/matplotlib/lines.py#L271
+# many of these can also be made into functions
+plot_kwargs_list = [
+    "alpha",
+    "linewidth",
+    "linestyle",
+    "color",
+    "marker",
+    "markersize",
+    "markeredgewidth",
+    "markeredgecolor",
+    "markerfacecolor",
+    "markerfacecoloralt",
+    "fillstyle",
+    "antialiased",
+    "dash_capstyle",
+    "solid_capstyle",
+    "dash_joinstyle",
+    "solid_joinstyle",
+    "pickradius",
+    "drawstyle",
+    "markevery",
+    "label",
+]
+
+imshow_kwargs_list = [
+    "cmap",
+    "norm",
+    "aspect",
+    "interpolation",
+    "alpha",
+    "vmin",
+    "vmax",
+    "origin",
+    "extent",
+    "filternorm",
+    "filterrad",
+    "resample",
+    "url",
+]
+
+
+def kwarg_popper(kwargs, mpl_kwargs):
+    """
+    This will not modify kwargs for you.
+
+    Usage
+    -----
+
+    kwargs, plot_kwargs = kwarg_popper(kwargs, plot_kwargs_list)
+    """
+    kwargs = dict(kwargs)
+    passthrough = {}
+    for k in mpl_kwargs:
+        if k in kwargs:
+            passthrough[k] = kwargs.pop(k)
+    return kwargs, passthrough

mpl_interactions/pyplot.py

@@ -24,6 +24,7 @@
     notebook_backend,
     update_datalim_from_bbox,
 )
+from .mpl_kwargs import plot_kwargs_list, imshow_kwargs_list, kwarg_popper
 
 # functions that are methods
 __all__ = [
@@ -128,35 +129,7 @@ def f(x, tau):
         interactive_plot(x, f, tau=(0, np.pi, 1000))
 
     """
-    # this is a list of options to Line2D partially taken from
-    # https://github.com/matplotlib/matplotlib/blob/f9d29189507cfe4121a231f6ab63539d216c37bd/lib/matplotlib/lines.py#L271
-    # many of these can also be made into functions
-    plot_kwargs_list = [
-        "alpha",
-        "linewidth",
-        "linestyle",
-        "color",
-        "marker",
-        "markersize",
-        "markeredgewidth",
-        "markeredgecolor",
-        "markerfacecolor",
-        "markerfacecoloralt",
-        "fillstyle",
-        "antialiased",
-        "dash_capstyle",
-        "solid_capstyle",
-        "dash_joinstyle",
-        "solid_joinstyle",
-        "pickradius",
-        "drawstyle",
-        "markevery",
-        "label",
-    ]
-    plot_kwargs = {}
-    for k in plot_kwargs_list:
-        if k in kwargs:
-            plot_kwargs[k] = kwargs.pop(k)
+    kwargs, plot_kwargs = kwarg_popper(kwargs, plot_kwargs_list)
     x_and_y = False
     x = None
     fmt = None