Accept mask and bg keyworks to get_rgb/imshow.

Author: tboggs

spectral/algorithms/spymath.py

@@ -80,7 +80,7 @@ def matrix_sqrt(X=None, symmetric=False, inverse=False, eigs=None):
         return V.dot(SRV).dot(np.linalg.inv(V))
 
 
-def get_histogram_cdf_points(data, cdf_vals, ignore=None):
+def get_histogram_cdf_points(data, cdf_vals, ignore=None, mask=None):
     '''Returns input values corresponding to the data's CDF values.
 
     Arguments:
@@ -108,11 +108,13 @@ def get_histogram_cdf_points(data, cdf_vals, ignore=None):
         associated CDF values in `cdf_vals`.
     '''
     data = data.ravel()
+    if mask is not None:
+        data = data[mask.ravel() != 0]
     if ignore is not None and ignore in data:
         data = data[np.where(data != ignore)]
     isort = np.argsort(data)
     N = len(data)
-    return[data[isort[int(x * (N - 1))]] for x in cdf_vals]
+    return [data[isort[int(x * (N - 1))]] for x in cdf_vals]
 
 
 class NaNValueWarning(UserWarning):

spectral/graphics/graphics.py

@@ -556,6 +556,12 @@ def get_rgb(source, bands=None, **kwargs):
     '''
     return get_rgb_meta(source, bands, **kwargs)[0]
 
+def _fill_mask(arr, mask, fill_value):
+    if mask is None:
+        return arr
+    arr[mask == 0] = np.array(fill_value) / 255.
+    return arr
+
 def get_rgb_meta(source, bands=None, **kwargs):
     '''Same as get_rgb but also returns some metadata.
 
@@ -579,6 +585,8 @@ def get_rgb_meta(source, bands=None, **kwargs):
 
     meta = {}
     monochrome = False
+    mask = kwargs.get('mask', None)
+    bg = kwargs.get('bg', settings.imshow_background_color)
 
     if isinstance(source, Image) and len(source.shape) == 3:
         # Figure out which bands to display
@@ -637,7 +645,7 @@ def get_rgb_meta(source, bands=None, **kwargs):
             rgb = rgb.astype(int)
             pal = kwargs["colors"]
             rgb = pal[rgb[:,:,0]] / 255.
-            return (rgb, meta)
+            return (_fill_mask(rgb, mask, bg), meta)
         elif color_scale is not None:
             # Colors should be generated from the supplied color scale
             # This section assumes rgb colors in the range 0-255.
@@ -648,7 +656,7 @@ def get_rgb_meta(source, bands=None, **kwargs):
             rgb3 = np.zeros((s[0], s[1], 3), int)
             rgb3 = np.apply_along_axis(scale, 2, rgb)
             rgb = rgb3.astype(np.float) / 255.
-            return (rgb, meta)
+            return (_fill_mask(rgb, mask, bg), meta)
         else:
             # Only one band of data to display but still need to determine how
             # to scale the data values
@@ -732,11 +740,11 @@ def get_rgb_meta(source, bands=None, **kwargs):
             rgb[:, :, i] = 0
         else:
             rgb[:, :, i] = np.clip((rgb[:, :, i] - lower) / span, 0, 1)
-    return (rgb, meta)
+    return (_fill_mask(rgb, mask, bg), meta)
 
 # For checking if valid keywords were supplied
 _get_rgb_kwargs = ('stretch', 'stretch_all', 'bounds', 'colors', 'color_scale',
-                   'auto_scale', 'ignore')
+                   'auto_scale', 'ignore', 'mask', 'bg')
 
 def running_ipython():
     '''Returns True if ipython is running.'''

spectral/graphics/spypylab.py

@@ -1280,7 +1280,8 @@ def plot(data, source=None):
 
     set_mpl_interactive()
 
-    if source is not None and hasattr(source, 'bands'):
+    if source is not None and hasattr(source, 'bands') and \
+       source.bands.centers is not None:
         xvals = source.bands.centers
     else:
         xvals = list(range(data.shape[-1]))

spectral/spectral.py

@@ -70,6 +70,10 @@ class SpySettings:
             Width and height (in inches) of windows opened with `imshow`. If
             this value is `None`, matplotlib's default size is used.
     
+        `imshow_background_color` (3-tuple of integers, default (0,0,0)):
+
+            Default color to use for masked pixels in `imshow` displays.
+
         `imshow_interpolation` (str, default `None`):
 
             Pixel interpolation to be used in imshow windows. If this value
@@ -136,6 +140,7 @@ class SpySettings:
 
     # imshow settings
     imshow_figure_size = None
+    imshow_background_color = (0, 0, 0)
     imshow_interpolation = None
     imshow_stretch = (0.0, 1.0)
     imshow_stretch_all = True