Merge pull request #1072 from blink1073/add-viewer-tests

Add Viewer Tests

skimage/viewer/canvastools/base.py

@@ -115,7 +115,7 @@ def _on_key_press(self, event):
     @property
     def geometry(self):
         """Geometry information that gets passed to callback functions."""
-        raise NotImplementedError
+        return None
 
 
 class ToolHandles(object):

skimage/viewer/canvastools/linetool.py

@@ -69,7 +69,7 @@ def on_enter(pts):
 
     @property
     def end_points(self):
-        return self._end_pts
+        return self._end_pts.astype(int)
 
     @end_points.setter
     def end_points(self, pts):
@@ -191,7 +191,7 @@ def _shrink_scan_line(self):
             self.callback_on_change(self.geometry)
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     import matplotlib.pyplot as plt
     from skimage import data
 

skimage/viewer/canvastools/painttool.py

@@ -198,7 +198,7 @@ def at(self, row, col):
         return [slice(ymin, ymax), slice(xmin, xmax)]
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     np.testing.rundocs()
     from skimage import data
 

skimage/viewer/canvastools/recttool.py

@@ -201,7 +201,7 @@ def geometry(self):
         return self.extents
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     import matplotlib.pyplot as plt
     from skimage import data
 

skimage/viewer/plugins/base.py

@@ -239,7 +239,8 @@ def closeEvent(self, event):
 
     def clean_up(self):
         self.remove_image_artists()
-        self.image_viewer.plugins.remove(self)
+        if self in self.image_viewer.plugins:
+            self.image_viewer.plugins.remove(self)
         self.image_viewer.reset_image()
         self.image_viewer.redraw()
 

skimage/viewer/plugins/lineprofile.py

@@ -46,7 +46,7 @@ def attach(self, image_viewer):
         if self._limit_type == 'image':
             self.limits = (np.min(image), np.max(image))
         elif self._limit_type == 'dtype':
-            self._limit_type = dtype_range[image.dtype.type]
+            self.limits = dtype_range[image.dtype.type]
         elif self._limit_type is None or len(self._limit_type) == 2:
             self.limits = self._limit_type
         else:
@@ -91,6 +91,7 @@ def get_profiles(self):
         profile: list of 1d arrays
             Profile of intensity values. Length 1 (grayscale) or 3 (rgb).
         """
+        self._update_data()
         profiles = [data.get_ydata() for data in self.profile]
         return self.line_tool.end_points, profiles
 
@@ -103,8 +104,15 @@ def _autoscale_view(self):
     def line_changed(self, end_points):
         x, y = np.transpose(end_points)
         self.line_tool.end_points = end_points
-        scan = measure.profile_line(self.image_viewer.original_image,
-                                    *end_points[:, ::-1],
+        self._update_data()
+        self.ax.relim()
+
+        self._autoscale_view()
+        self.redraw()
+
+    def _update_data(self):
+        scan = measure.profile_line(self.image_viewer.image,
+                                    *self.line_tool.end_points[:, ::-1],
                                     linewidth=self.line_tool.linewidth)
         self.scan_data = scan
         if scan.ndim == 1:
@@ -117,11 +125,6 @@ def line_changed(self, end_points):
             self.profile[i].set_xdata(np.arange(scan.shape[0]))
             self.profile[i].set_ydata(scan[:, i])
 
-        self.ax.relim()
-
-        self._autoscale_view()
-        self.redraw()
-
     def reset_axes(self, scan_data):
         # Clear lines out
         for line in self.ax.lines:
@@ -147,7 +150,7 @@ def output(self):
             The line scan values across the image.
         """
         end_points = self.line_tool.end_points
-        line_image = np.zeros(self.image_viewer.original_image.shape[:2],
+        line_image = np.zeros(self.image_viewer.image.shape[:2],
                               np.uint8)
         width = self.line_tool.linewidth
         if width > 1:
@@ -162,4 +165,3 @@ def output(self):
         rr, cc = draw.line(y1, x1, y2, x2)
         line_image[rr, cc] = 255
         return line_image, self.scan_data
-

skimage/viewer/tests/test_plugins.py

@@ -0,0 +1,185 @@
+# -*- coding: utf-8 -*-
+import numpy as np
+import skimage
+import skimage.data as data
+from skimage.filter.rank import median
+from skimage.morphology import disk
+from numpy.testing import assert_equal, assert_allclose, assert_almost_equal
+from numpy.testing.decorators import skipif
+
+try:
+    from skimage.viewer.qt import qt_api
+    from skimage.viewer import ImageViewer
+    from skimage.viewer.plugins import (
+        LineProfile, Measure, CannyPlugin, LabelPainter, Crop, ColorHistogram,
+        PlotPlugin)
+    from skimage.viewer.plugins.base import Plugin
+    from skimage.viewer.widgets import Slider
+    viewer_available = not qt_api is None
+except ImportError:
+    viewer_available = False
+
+
+def setup_line_profile(image, limits='image'):
+    viewer = ImageViewer(skimage.img_as_float(image))
+    plugin = LineProfile(limits=limits)
+    viewer += plugin
+    return plugin
+
+
+@skipif(not viewer_available)
+def test_line_profile():
+    """ Test a line profile using an ndim=2 image"""
+    plugin = setup_line_profile(data.camera())
+    line_image, scan_data = plugin.output()
+    for inp in [line_image.nonzero()[0].size,
+                line_image.sum() / line_image.max(),
+                scan_data.size]:
+        assert_equal(inp, 172)
+    assert_equal(line_image.shape, (512, 512))
+    assert_allclose(scan_data.max(), 0.9176, rtol=1e-3)
+    assert_allclose(scan_data.mean(), 0.2812, rtol=1e-3)
+
+
+@skipif(not viewer_available)
+def test_line_profile_rgb():
+    """ Test a line profile using an ndim=3 image"""
+    plugin = setup_line_profile(data.chelsea(), limits=None)
+    for i in range(6):
+        plugin.line_tool._thicken_scan_line()
+    line_image, scan_data = plugin.output()
+    assert_equal(line_image[line_image == 128].size, 750)
+    assert_equal(line_image[line_image == 255].size, 151)
+    assert_equal(line_image.shape, (300, 451))
+    assert_equal(scan_data.shape, (151, 3))
+    assert_allclose(scan_data.max(), 0.772, rtol=1e-3)
+    assert_allclose(scan_data.mean(), 0.4359, rtol=1e-3)
+
+
+@skipif(not viewer_available)
+def test_line_profile_dynamic():
+    """Test a line profile updating after an image transform"""
+    image = data.coins()[:-50, :]  # shave some off to make the line lower
+    image = skimage.img_as_float(image)
+    viewer = ImageViewer(image)
+
+    lp = LineProfile(limits='dtype')
+    viewer += lp
+
+    line = lp.get_profiles()[-1][0]
+    assert line.size == 129
+    assert_almost_equal(np.std(viewer.image), 0.208, 3)
+    assert_almost_equal(np.std(line), 0.229, 3)
+    assert_almost_equal(np.max(line) - np.min(line), 0.725, 1)
+
+    viewer.image = skimage.img_as_float(median(image,
+                                               selem=disk(radius=3)))
+
+    line = lp.get_profiles()[-1][0]
+    assert_almost_equal(np.std(viewer.image), 0.198, 3)
+    assert_almost_equal(np.std(line), 0.220, 3)
+    assert_almost_equal(np.max(line) - np.min(line), 0.639, 1)
+
+
+@skipif(not viewer_available)
+def test_measure():
+    image = data.camera()
+    viewer = ImageViewer(image)
+    m = Measure()
+    viewer += m
+
+    m.line_changed([(0, 0), (10, 10)])
+    assert_equal(str(m._length.text), '14.1')
+    assert_equal(str(m._angle.text[:5]), '135.0')
+
+
+@skipif(not viewer_available)
+def test_canny():
+    image = data.camera()
+    viewer = ImageViewer(image)
+    c = CannyPlugin()
+    viewer += c
+
+    canny_edges = viewer.show(False)
+    viewer.close()
+    edges = canny_edges[0][0]
+    assert edges.sum() == 2852
+
+
+@skipif(not viewer_available)
+def test_label_painter():
+    image = data.camera()
+    moon = data.moon()
+    viewer = ImageViewer(image)
+    lp = LabelPainter()
+    viewer += lp
+
+    assert_equal(lp.radius, 5)
+    lp.label = 1
+    assert_equal(str(lp.label), '1')
+    lp.label = 2
+    assert_equal(str(lp.paint_tool.label), '2')
+    assert_equal(lp.paint_tool.radius, 5)
+    lp._on_new_image(moon)
+    assert_equal(lp.paint_tool.shape, moon.shape)
+
+
+@skipif(not viewer_available)
+def test_crop():
+    image = data.camera()
+    viewer = ImageViewer(image)
+    c = Crop()
+    viewer += c
+
+    c.crop((0, 100, 0, 100))
+    assert_equal(viewer.image.shape, (101, 101))
+
+
+@skipif(not viewer_available)
+def test_color_histogram():
+    image = skimage.img_as_float(data.load('color.png'))
+    viewer = ImageViewer(image)
+    ch = ColorHistogram(dock='right')
+    viewer += ch
+
+    assert_almost_equal(viewer.image.std(), 0.352, 3),
+    ch.ab_selected((0, 100, 0, 100)),
+    assert_almost_equal(viewer.image.std(), 0.325, 3)
+
+
+@skipif(not viewer_available)
+def test_plot_plugin():
+    viewer = ImageViewer(data.moon())
+    plugin = PlotPlugin(image_filter=lambda x: x)
+    viewer += plugin
+
+    assert_equal(viewer.image, data.moon())
+    plugin._update_original_image(data.coins())
+    assert_equal(viewer.image, data.coins())
+    viewer.close()
+
+
+@skipif(not viewer_available)
+def test_plugin():
+    img = skimage.img_as_float(data.moon())
+    viewer = ImageViewer(img)
+
+    def median_filter(img, radius=3):
+        return median(img, selem=disk(radius=radius))
+
+    plugin = Plugin(image_filter=median_filter)
+    viewer += plugin
+
+    plugin += Slider('radius', 1, 5)
+
+    assert_almost_equal(np.std(viewer.image), 12.556, 3)
+
+    plugin.filter_image()
+
+    assert_almost_equal(np.std(viewer.image), 12.931, 3)
+
+    plugin.show()
+    plugin.close()
+    plugin.clean_up()
+    img, _ = plugin.output()
+    assert_equal(img, viewer.image)