Merge pull request #575 from tonysyu/feature/viewer-linking

Linked image viewers and docked plugins

skimage/viewer/plugins/base.py

@@ -1,9 +1,12 @@
 """
 Base class for Plugins that interact with ImageViewer.
 """
-from ..qt import QtGui
-from ..qt.QtCore import Qt
+from warnings import warn
 
+import numpy as np
+
+from ..qt import QtGui
+from ..qt.QtCore import Qt, Signal
 from ..utils import RequiredAttr, init_qtapp
 
 
@@ -71,14 +74,24 @@ class Plugin(QtGui.QDialog):
     name = 'Plugin'
     image_viewer = RequiredAttr("%s is not attached to ImageViewer" % name)
 
-    def __init__(self, image_filter=None, height=0, width=400, useblit=True):
+    # Signals used when viewers are linked to the Plugin output.
+    image_changed = Signal(np.ndarray)
+    _started = Signal(int)
+
+    def __init__(self, image_filter=None, height=0, width=400, useblit=True,
+                 dock='bottom'):
         init_qtapp()
         super(Plugin, self).__init__()
 
+        self.dock = dock
+
         self.image_viewer = None
         # If subclass defines `image_filter` method ignore input.
         if not hasattr(self, 'image_filter'):
             self.image_filter = image_filter
+        elif image_filter is not None:
+            warn("If the Plugin class defines an `image_filter` method, "
+                 "then the `image_filter` argument is ignored.")
 
         self.setWindowTitle(self.name)
         self.layout = QtGui.QGridLayout(self)
@@ -109,7 +122,7 @@ class Plugin(QtGui.QDialog):
         self.image_viewer = image_viewer
         self.image_viewer.plugins.append(self)
         #TODO: Always passing image as first argument may be bad assumption.
-        self.arguments.append(self.image_viewer.original_image)
+        self.arguments = [self.image_viewer.original_image]
 
         # Call filter so that filtered image matches widget values
         self.filter_image()
@@ -155,12 +168,22 @@ class Plugin(QtGui.QDialog):
         kwargs = dict([(name, self._get_value(a))
                        for name, a in self.keyword_arguments.items()])
         filtered = self.image_filter(*arguments, **kwargs)
+
         self.display_filtered_image(filtered)
+        self.image_changed.emit(filtered)
 
     def _get_value(self, param):
         # If param is a widget, return its `val` attribute.
         return param if not hasattr(param, 'val') else param.val
 
+    def _update_original_image(self, image):
+        """Update the original image argument passed to the filter function.
+
+        This method is called by the viewer when the original image is updated.
+        """
+        self.arguments[0] = image
+        self.filter_image()
+
     @property
     def filtered_image(self):
         """Return filtered image."""
@@ -183,6 +206,17 @@ class Plugin(QtGui.QDialog):
         """
         setattr(self, name, value)
 
+    def show(self, main_window=True):
+        """Show plugin."""
+        super(Plugin, self).show()
+        self.activateWindow()
+        self.raise_()
+
+        # Emit signal with x-hint so new windows can be displayed w/o overlap.
+        size = self.frameGeometry()
+        x_hint = size.x() + size.width()
+        self._started.emit(x_hint)
+
     def closeEvent(self, event):
         """On close disconnect all artists and events from ImageViewer.
 

skimage/viewer/plugins/color_histogram.py

@@ -10,8 +10,9 @@ from ..canvastools import RectangleTool
 class ColorHistogram(PlotPlugin):
     name = 'Color Histogram'
 
-    def __init__(self, **kwargs):
+    def __init__(self, max_pct=0.99, **kwargs):
         super(ColorHistogram, self).__init__(height=400, **kwargs)
+        self.max_pct = max_pct
 
         print(self.help())
 
@@ -30,7 +31,7 @@ class ColorHistogram(PlotPlugin):
                                                 normed=True)
 
         # Clip bin heights that dominate a-b histogram
-        max_val = pct_total_area(hist, percentile=99)
+        max_val = pct_total_area(hist, percentile=self.max_pct)
         hist = exposure.rescale_intensity(hist, in_range=(0, max_val))
         self.ax.imshow(hist, extent=ab_extents, cmap=plt.cm.gray)
 
@@ -55,12 +56,12 @@ class ColorHistogram(PlotPlugin):
         self.image_viewer.image = color.lab2rgb(lab_masked)
 
 
-def pct_total_area(image, percentile=80):
+def pct_total_area(image, percentile=0.80):
     """Return threshold value based on percentage of total area.
 
     The specified percent of pixels less than the given intensity threshold.
     """
-    idx = int((image.size - 1) * percentile / 100.0)
+    idx = int((image.size - 1) * percentile)
     sorted_pixels = np.sort(image.flat)
     return sorted_pixels[idx]
 

skimage/viewer/plugins/overlayplugin.py

@@ -2,7 +2,7 @@ from warnings import warn
 
 from skimage.util.dtype import dtype_range
 from .base import Plugin
-from ..utils import ClearColormap
+from ..utils import ClearColormap, update_axes_image
 
 
 __all__ = ['OverlayPlugin']
@@ -66,7 +66,8 @@ class OverlayPlugin(Plugin):
             self._overlay_plot = ax.imshow(image, cmap=self.cmap,
                                            vmin=vmin, vmax=vmax)
         else:
-            self._overlay_plot.set_array(image)
+            update_axes_image(self._overlay_plot, image)
+
         self.image_viewer.redraw()
 
     @property

skimage/viewer/plugins/plotplugin.py

@@ -17,6 +17,13 @@ class PlotPlugin(Plugin):
     See base Plugin class for additional details.
     """
 
+    def __init__(self, image_filter=None, height=150, width=400, **kwargs):
+        super(PlotPlugin, self).__init__(image_filter=image_filter,
+                                         height=height, width=width, **kwargs)
+
+        self._height = height
+        self._width = width
+
     def attach(self, image_viewer):
         super(PlotPlugin, self).attach(image_viewer)
         # Add plot for displaying intensity profile.
@@ -26,10 +33,12 @@ class PlotPlugin(Plugin):
         """Redraw plot."""
         self.canvas.draw_idle()
 
-    def add_plot(self, height=4, width=4):
-        self.fig, self.ax = new_plot(figsize=(height, width))
+    def add_plot(self):
+        self.fig, self.ax = new_plot()
+        self.fig.set_figwidth(self._width / float(self.fig.dpi))
+        self.fig.set_figheight(self._height / float(self.fig.dpi))
+
         self.canvas = self.fig.canvas
-        self.canvas.setMinimumHeight(150)
         #TODO: Converted color is slightly different than Qt background.
         qpalette = QtGui.QPalette()
         qcolor = qpalette.color(QtGui.QPalette.Window)