binary meanings now propagated throughout; plots updated accordingly

README.md

@@ -5,7 +5,7 @@
 
 CodedApertures is a python module that allows one to easily generate and display common coded aperture patterns. Coded apertures are a spatial encoding technique for straight-line optics, wherein traditional lensing (e.g., visible light) is not possible. Even wherein tradiational lensing is possible, there may be other advantages (infinite depth of field). Coded apertures may therefore be used for hard x-ray and gamma-ray imaging for astrophysics, medical imaging, and homeland security applications.
 
-New to coded apertures? Here's a nice article: https://www.paulcarlisle.net/codedaperture/
+New to coded apertures? Here's a nice article: https://www.paulcarlisle.net/codedaperture/.
 
 ### Usage
 

codedapertures/codedapertures.py

@@ -465,11 +465,11 @@ def __init__(self, rank=4, r=5, radius=5, quiet=False):
                 self.l[i,j] = (i_idx + self.r*j_idx) % self.v
 
         # calculate mask
-        self.mask = np.zeros(self.l.shape, dtype=np.int16)
+        self.mask = np.zeros(self.l.shape, dtype=np.int16)+1
         for i in range(self.mask.shape[0]):
             for j in range(self.mask.shape[1]):
                 if self.l[i,j] in self.D:
-                    self.mask[i,j] = 1
+                    self.mask[i,j] = 0
 
         # map to axial matrix
         for i in range(self.diam):
@@ -554,9 +554,9 @@ def show_rhombus(self, labels=False, labelsize=10):
 
                 # add hexagon
                 if self.mask[x_i,y_i] == 1:
-                    facecolor='k'
-                else:
                     facecolor='w'
+                else:
+                    facecolor='k'
                 hex = RegularPolygon((x, y), numVertices=6, radius=hex_radius, 
                               orientation=np.radians(60), 
                                facecolor=facecolor, alpha=0.6, edgecolor='k')
@@ -596,8 +596,8 @@ def show(self, labels=False, labelsize=10):
             row_width = self.diam - abs(self.radius-y)
             start_i   = np.max((self.radius-y,0))
             for x in range(row_width):
-                facecolor = 'k' if self.axial_matrix[x+start_i,y] == 1 else 'w'
-                alpha     = 0.9 if self.axial_matrix[x+start_i,y] == 1 else 0.3
+                facecolor = 'w' if self.axial_matrix[x+start_i,y] == 1 else 'k'
+                alpha     = 0.3 if self.axial_matrix[x+start_i,y] == 1 else 0.9
                 label     = self.l[x+start_i,y]
                 hex = RegularPolygon((x+0.5*abs(y-self.radius)-self.radius,
                                       ((y-self.radius)*((3/2)*hex_vert/2.0))),
@@ -665,11 +665,11 @@ def __init__(self, rank=4, radius=5, quiet=False):
                 self.l[i,j] = (i_idx + self.r*j_idx) % self.v
 
         # calculate mask
-        self.mask = np.zeros(self.l.shape, dtype=np.int16)
+        self.mask = np.zeros(self.l.shape, dtype=np.int16)+1
         for i in range(self.mask.shape[0]):
             for j in range(self.mask.shape[1]):
                 if self.l[i,j] in self.D:
-                    self.mask[i,j] = 1
+                    self.mask[i,j] = 0
 
         # map to axial matrix
         for i in range(self.diam):
@@ -768,9 +768,9 @@ def show_rhombus(self, labels=False, labelsize=10):
 
                 # add hexagon
                 if self.mask[x_i,y_i] == 1:
-                    facecolor='k'
-                else:
                     facecolor='w'
+                else:
+                    facecolor='k'
                 hex = RegularPolygon((x, y), numVertices=6, radius=hex_radius, 
                               orientation=np.radians(60), 
                                facecolor=facecolor, alpha=0.6, edgecolor='k')
@@ -810,8 +810,8 @@ def show(self, labels=False, labelsize=10):
             row_width = self.diam - abs(self.radius-y)
             start_i   = np.max((self.radius-y,0))
             for x in range(row_width):
-                facecolor = 'k' if self.axial_matrix[x+start_i,y] == 1 else 'w'
-                alpha     = 0.9 if self.axial_matrix[x+start_i,y] == 1 else 0.3
+                facecolor = 'w' if self.axial_matrix[x+start_i,y] == 1 else 'k'
+                alpha     = 0.3 if self.axial_matrix[x+start_i,y] == 1 else 0.9
                 label     = self.l[x+start_i,y]
                 hex = RegularPolygon((x+0.5*abs(y-self.radius)-self.radius,
                                       ((y-self.radius)*((3/2)*hex_vert/2.0))),
@@ -852,7 +852,7 @@ def __init__(self, radius=3, fill=0.5, quiet=False):
         self.radius       = radius
         self.diam         = self.radius*2+1
         self.side_width   = radius + 1
-        self.axial_matrix = np.zeros((self.diam,self.diam))
+        self.axial_matrix = np.zeros((self.diam,self.diam))+1
         self.loc_matrix   = np.zeros((2,self.diam,self.diam))
         self.fill         = fill
 
@@ -861,12 +861,12 @@ def __init__(self, radius=3, fill=0.5, quiet=False):
             for j in range(self.diam):
                 if (i+j > (self.radius-1)) and (i+j < (self.diam+self.radius)):
                     if random.random() < self.fill:
-                        self.axial_matrix[i,j] = 1
+                        self.axial_matrix[i,j] = 0
                 else:
                     self.axial_matrix[i,j] = np.nan
 
         # determine actual fill factor
-        self.actual_fill = np.sum(self.axial_matrix == 1) / np.sum(~np.isnan(self.axial_matrix))
+        self.actual_fill = 1- (np.sum(self.axial_matrix == 1) / np.sum(~np.isnan(self.axial_matrix)))
 
         # generate locations
         for i in range(self.diam):
@@ -904,8 +904,8 @@ def show(self):
             row_width = self.diam - abs(self.radius-y)
             start_i   = np.max((self.radius-y,0))
             for x in range(row_width):
-                facecolor = 'k' if self.axial_matrix[x+start_i,y] == 1 else 'w'
-                alpha     = 0.6 if self.axial_matrix[x+start_i,y] == 1 else 0.3
+                facecolor = 'w' if self.axial_matrix[x+start_i,y] == 1 else 'k'
+                alpha     = 0.3 if self.axial_matrix[x+start_i,y] == 1 else 0.9
                 hex = RegularPolygon((x+0.5*abs(y-self.radius)-self.radius,
                                       ((y-self.radius)*((3/2)*hex_vert/2.0))),
                                      numVertices=6, radius=hex_vert/2.0, 
@@ -981,8 +981,8 @@ def show(self, inverse=False, size=5):
             size of the plot (default 8)
         """
         plt.rcParams['figure.figsize'] = [size,size]
-        cmap = "binary_r" if inverse else "binary"
-        plt.imshow(self.mask, cmap="gray", origin='lower', aspect=1)
+        cmap = "binary" if inverse else "binary_r"
+        plt.imshow(self.mask, cmap=cmap, origin='lower', aspect=1)
         plt.axis('off')
         plt.title(f"Pseudo-Noise Product Array [m: {self.m}, n: {self.n}]")
         plt.show()

setup.py

@@ -1,7 +1,7 @@
 import setuptools
 
 setuptools.setup(name='codedapertures',
-      version='0.7.1',
+      version='0.8',
       description='a python package for generating coded apertures',
       long_description='CodedApertures is a python package that allows one to easily generate and display common coded aperture patterns. Coded apertures are a spatial encoding technique for straight-line optics, wherein traditional lensing (e.g., visible light) is not possible. Even wherein tradiational lensing is possible, there may be other advantages (infinite depth of field). Coded apertures may therefore be used for hard x-ray and gamma-ray imaging for astrophysics, medical imaging, and homeland security applications.',
       url='https://github.com/bpops/codedapertures',