finalized the preliminary functions for classification

David Mayerich
1 parent fad1a72c
Showing 2 changed files with 63 additions and 49 deletions Show diff stats
python/classify.py
python/envi.py
@@ -9,31 +9,37 @@ import numpy
 import colorsys
 import sklearn
 import sklearn.metrics
-from scipy import misc
-from envi import envi
+import scipy
+import scipy.misc
+import envi
 #generate a 2D color class map using a stack of binary class images
+#input: C is a C x Y x X binary image
+#output: an RGB color image with a unique color for each class
 def classcolor2(C):
     #determine the number of classes
-    nc = C.shape[-1]
+    nc = C.shape[0]
+    
+    s = C.shape[1:]
+    s = numpy.append(s, 3)
     #generate an RGB image
-    RGB = numpy.zeros((C.shape[0], C.shape[1], 3), dtype=numpy.ubyte)
+    RGB = numpy.zeros(s, dtype=numpy.ubyte)
     #for each class
     for c in range(0, nc):
         hsv = (c * 1.0 / nc, 1, 1)
         color = numpy.asarray(colorsys.hsv_to_rgb(hsv[0], hsv[1], hsv[2])) * 255
-        RGB[C[:, :, c], :] = color
+        RGB[C[c, ...], :] = color
     return RGB
 #create a function that loads a set of class images as a stack of binary masks
 #input: list of class image names
-#output: X x Y x C stack of binary mask images
+#output: C x Y x X binary image specifying class/pixel membership
 #example: image2class(("class_coll.bmp", "class_epith.bmp"))
-def image2class(*masks):
+def image2class(masks):
     #get num of mask file names
     num_masks = len(masks)
@@ -42,53 +48,26 @@ def image2class(*masks):
         print("Usage example: image2class(('class_coll.bmp', 'class_epith.bmp'))")
         return
-    #load first mask to get dimensions -- assuming all masks have same dimensions
-    mask = misc.imread(masks[0], flatten=True).astype(numpy.bool)
-
-    mask_stack = numpy.zeros((mask.shape[0], mask.shape[1], num_masks), dtype=numpy.bool)
-    mask_stack[:,:,0] = mask
-
-    #load the rest of masks
-    for i in range(1, num_masks):
-        mask_stack[:,:,i] = misc.imread(masks[i], flatten=True).astype(numpy.bool)
-
-    return mask_stack
-
+    classimages = []
+    for m in masks:
+        img = scipy.misc.imread(m, flatten=True).astype(numpy.bool)
+        classimages.append(img)
-#create a set of feature/target pairs for classification
-#input: envi file object, stack of class masks, list of class names
-#output: feature matrix (features x pixels), target matrix (1 x pixels)
-#example: generate_training(("class_coll.bmp", "class_epith.bmp"), (1, 2))
-def generate_training(filename, mask_stack):
-    #create envi file object
-    E = envi(filename)
+    result = numpy.stack(classimages)
+    sum_images = numpy.sum(result.astype(numpy.uint32), 0)
-    # get number of classes
-    C = mask_stack.shape[2]
+    #identify and remove redundant pixels
+    bad_idx = sum_images > 1
+    result[:, bad_idx] = 0
-    #get number of annotated pixels
-    num_pixels = 0
-    for i in range(0,C):
-        num_pixels += numpy.count_nonzero(mask_stack[:,:,i])
+    return result
-    feature_matrix = numpy.zeros((E.header.bands, num_pixels), dtype=E.header.data_type)
-    target_matrix = numpy.zeros((1, num_pixels))
-    #load masks and append the corresponding pixels to feature matrix and labels to target_matrix
-    idx = 0
-    for i in range(0,C):
-        mask = E.loadmask(mask_stack[:,:,i])
-        feature_matrix[:, idx:idx + mask.shape[1]] = mask
-        target_matrix[idx:idx+mask.shape[1]] = (i+1)
-        idx += mask.shape[1]
-
-    return feature_matrix, target_matrix
-
-#create a class mask stack from an X x Y x C probability image
-#input: X x Y x C image giving the probability P(c |x,y)
-#output: X x Y x C binary class image
+#create a class mask stack from an C x Y x X probability image
+#input: C x Y x X image giving the probability P(c |x,y)
+#output: C x Y x X binary class image
 def prob2class(prob_image):
-    class_image = numpy.zeros_like(prob_image)
+    class_image = numpy.zeros(prob_image.shape, dtype=numpy.bool)
     #get nonzero indices
     nnz_idx = numpy.transpose(numpy.nonzero(numpy.sum(prob_image, axis=0)))
@@ -98,8 +77,20 @@ def prob2class(prob_image):
         class_image[idx_max_prob, idx[0], idx[1]] = 1
     return class_image
+
 #calculate an ROC curve given a probability image and mask of "True" values
-def image2roc(P, t_vals, mask=[]):
+#input:
+#       P is a Y x X probability image specifying P(c | x,y)
+#       t_vals is a Y x X binary image specifying points where x,y = c
+#       mask is a mask specifying all pixels to be considered (positives and negatives)
+#           use this mask to limit analysis to regions of the image that have been classified
+#output: fpr, tpr, thresholds
+#       fpr is the false-positive rate (x-axis of an ROC curve)
+#       tpr is the true-positive rate (y-axis of an ROC curve)
+#       thresholds stores the threshold associated with each point on the ROC curve
+#
+#note: the AUC can be calculated as auc = sklearn.metrics.auc(fpr, tpr)
+def prob2roc(P, t_vals, mask=[]):
     if not P.shape == t_vals.shape:
         print("ERROR: the probability and mask images must be the same shape")
@@ -127,3 +118,7 @@ def image2roc(P, t_vals, mask=[]):
     labels = numpy.concatenate((Lp, Ln))
     return sklearn.metrics.roc_curve(labels, scores)
+
+#Function to convert a set of class labels to a matrix of neuron responses for an ANN
+
+#Function CNN extraction function
 \ No newline at end of file
@@ -278,6 +278,25 @@ class envi:
         return band
+    #create a set of feature/target pairs for classification
+    #input: envi file object, stack of class masks C x Y x X
+    #output: feature matrix (features x pixels), target matrix (1 x pixels)
+    #example: generate_training(("class_coll.bmp", "class_epith.bmp"), (1, 2))
+    def loadtrain(self, classimages):
+
+        # get number of classes
+        C = classimages.shape[0]
+
+        F = []
+        T = []
+        for c in range(0, C):
+            f = self.loadmask(classimages[c, :, :])            #load the feature matrix for class c
+            t = numpy.ones((f.shape[1])) * (c+1)         #generate a target array                 
+            F.append(f)
+            T.append(t)
+
+        return numpy.concatenate(F, 1).transpose(), numpy.concatenate(T)
+
     def __del__(self):
         self.file.close()
 \ No newline at end of file