From a1294ceb4819fa91035921b9358775db24b204b0 Mon Sep 17 00:00:00 2001
From: AngusG <premiumdriedfoods@gmail.com>
Date: Tue, 15 Aug 2017 13:50:14 -0400
Subject: [PATCH] add script for cleaning up edges of integer masks

---
 post-process.py | 102 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 post-process.py

diff --git a/post-process.py b/post-process.py
new file mode 100644
index 0000000..81f2945
--- /dev/null
+++ b/post-process.py
@@ -0,0 +1,102 @@
+import argparse
+import numpy as np
+import matplotlib.pyplot as plt
+
+from scipy import ndimage
+
+X_LOW = 80
+X_UPP = 120
+
+Y_LOW = X_LOW
+Y_UPP = X_UPP
+
+MAX_VALID_CLASS = 5
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('mask', help='path to integer mask to clean')
+    parser.add_argument(
+        '--zoom', help="zoom into area bounded by X_LOW, X_UPP, Y_LOW, Y_UPP", action="store_true")
+    args = parser.parse_args()
+
+    orig_mask = plt.imread(args.mask)
+    max_px = orig_mask.max()
+    min_px = orig_mask.min()
+
+    # valid classes are 0 through 5
+    valid_classes = []
+    hist, bin_edges = np.histogram(
+        orig_mask, bins=MAX_VALID_CLASS + 1, range=(0, MAX_VALID_CLASS + 1))
+    class_area_pct = np.zeros(len(hist))
+
+    for i in range(len(hist)):
+        class_area_pct[i] = 100 * float(hist[i] / np.sum(hist))
+        # 1.0% is an arbitrary choice here that seemed to work well
+        if class_area_pct[i] > 1.0:
+            print('class %d is %.2f%% by volume' % (i, class_area_pct[i]))
+            valid_classes.append(i)
+
+    clean_mask = orig_mask.copy()
+    valid_class_arr = np.asarray(valid_classes)
+    print(valid_class_arr)
+    for i in range(len(hist)):
+        if i not in valid_classes:
+            # assign the closest valid class label
+            new_class_label = valid_class_arr[
+                np.argmin(np.abs(valid_class_arr - i))]
+            print('Replacing instances of class %d (area %.2f%%) with valid class %d (area %.2f%%)' % (
+                i, class_area_pct[i], new_class_label, class_area_pct[new_class_label]))
+            clean_mask[orig_mask == i] = new_class_label
+
+        out_of_range_pct = 100 * \
+            float(
+                np.sum(clean_mask[orig_mask > MAX_VALID_CLASS]) / np.sum(hist))
+    print('Replacing out of range classes (area %.2f%%) with top valid class %d (area %.2f%%)' % (
+        out_of_range_pct, MAX_VALID_CLASS, class_area_pct[MAX_VALID_CLASS]))
+    clean_mask[orig_mask > MAX_VALID_CLASS] = MAX_VALID_CLASS
+
+    plt.close('all')
+
+    plt.figure()
+    if args.zoom:
+        plt.imshow(orig_mask[X_LOW:X_UPP, Y_LOW:Y_UPP],
+                   vmin=min_px, vmax=max_px)
+    else:
+        plt.imshow(orig_mask, vmin=min_px, vmax=max_px)
+    plt.title('original mask')
+
+    plt.figure()
+    if args.zoom:
+        plt.imshow(clean_mask[X_LOW:X_UPP, Y_LOW:Y_UPP],
+                   vmin=min_px, vmax=max_px)
+    else:
+        plt.imshow(clean_mask, vmin=min_px, vmax=max_px)
+    plt.title('histogram cleaned mask')
+
+    ### Now median filter the histogram cleaned image ###
+    median_filter_size = 5 # Hyperparameter
+    clean_mask = ndimage.median_filter(clean_mask, size=median_filter_size)
+
+    plt.figure()
+    if args.zoom:
+        plt.imshow(clean_mask[X_LOW:X_UPP,
+                              Y_LOW:Y_UPP], vmin=min_px, vmax=max_px)
+    else:
+        plt.imshow(clean_mask, vmin=min_px, vmax=max_px)
+    plt.title('median filter mask (%dx%d)' %
+              (median_filter_size, median_filter_size))
+
+    morphology_size = 3 # Hyperparameter
+    clean_mask = ndimage.grey_dilation(
+        clean_mask, size=(morphology_size, morphology_size))
+
+    plt.figure()
+    if args.zoom:
+        plt.imshow(clean_mask[X_LOW:X_UPP,
+                              Y_LOW:Y_UPP], vmin=min_px, vmax=max_px)
+    else:
+        plt.imshow(clean_mask, vmin=min_px, vmax=max_px)
+    plt.title('morphology (%dx%d)' % (morphology_size, morphology_size))
+    plt.show()