Pixel Replication Demo fully running

SRC/Python/.idea/Python.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.5.1 (C:\Users\angeline\Anaconda3\python.exe)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
+  </component>
+</module>
\ No newline at end of file

SRC/Python/.idea/misc.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
+    <OptionsSetting value="true" id="Add" />
+    <OptionsSetting value="true" id="Remove" />
+    <OptionsSetting value="true" id="Checkout" />
+    <OptionsSetting value="true" id="Update" />
+    <OptionsSetting value="true" id="Status" />
+    <OptionsSetting value="true" id="Edit" />
+    <ConfirmationsSetting value="0" id="Add" />
+    <ConfirmationsSetting value="0" id="Remove" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.5.1 (C:\Users\angeline\Anaconda3\python.exe)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file

SRC/Python/.idea/modules.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/Python.iml" filepath="$PROJECT_DIR$/.idea/Python.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file

SRC/Python/GenerateEllipseLib.py → SRC/Python/GENERATE_ELLIPSE_LIB.py

@@ -32,13 +32,13 @@ def GetRandomEllipseImage(K):
     import numpy as np
     IMSIZE = 1000
     mu1 = [500, 500]
-    bw = np.zeros([IMSIZE, IMSIZE], dtype=bool)
+    bw = np.zeros([IMSIZE, IMSIZE])
     ptsCombined = np.empty([1,2])
     pts = []
     ptsEdge = []
     bValidEllipse = False
 
-    while ~bValidEllipse:
+    while bValidEllipse == False:
         for k in np.arange(0, K, 1, dtype=int):
             pts_tmp, ptsEdge_tmp = GetRandomEllipsePts(mu1, IMSIZE)
             ptsCombined = np.append(ptsCombined, pts_tmp, axis=0)
@@ -66,8 +66,16 @@ def GetRandomEllipseImage(K):
 
     ptsCombined = np.concatenate(pts[0:K])
     bw[np.array([ptsCombined[0:,0]]), np.array([ptsCombined[0:,1]])] = 1
-    return bw
 
+    ellipseBounds = np.where(bw == 1)
+    minx = np.min(ellipseBounds[1]) - 10
+    maxx = np.max(ellipseBounds[1]) + 10
+    miny = np.min(ellipseBounds[0]) - 10
+    maxy = np.max(ellipseBounds[0]) + 10
+
+    bw = bw[miny:maxy, minx:maxx]
+    bw = np.uint8(bw)
+    return bw
 
 def genEllipse(mu, cv, c, bFill):
     import numpy as np
@@ -103,7 +111,6 @@ def genEllipse(mu, cv, c, bFill):
     idx = np.where(bw==1)
     pts = np.transpose(np.vstack((idx[0], idx[1])))
 
-    pts = np.array(pts)
     return pts, bw
 
 
@@ -112,8 +119,6 @@ def GetRandomEllipsePts(mu, IMSIZE):
     import numpy as np
     from numpy.matlib import repmat
     import scipy.ndimage.morphology as bwmorph
-    pts = []
-    ptsEdge = []
 
     RADII_0 = 10
     RADII_1 = 20
@@ -128,6 +133,9 @@ def GetRandomEllipsePts(mu, IMSIZE):
     pts = genEllipse(mu, cv, 1, 1)
     ptsEdge = genEllipse(mu, cv, 1, 0)
 
+    pts = pts[0]
+    ptsEdge = ptsEdge[0]
+
     theta = 2 * np.pi * np.random.rand()
 
     pts = pts - np.matlib.repmat(mu, pts.shape[0], 1)
@@ -176,3 +184,5 @@ def GetOverlap(idxPts):
                 break
 
     return bNoFullOverlap
+
+bwim = GetRandomEllipseImage(2)
\ No newline at end of file

SRC/Python/PixelRepLib.py → SRC/Python/PIXEL_REPLICATION_LIB.py

@@ -36,16 +36,21 @@
 #   and label is used to select the component to replicate
 
 def PixelReplicate(bwim):
-    from numpy.matlib import repmat
     import numpy as np
     import cv2
 
     print("Computing distance transform...")
-    bwd = cv2.distanceTransform(bwim, distanceType=cv2.DIST_L2, maskSize=5)
+    bwd = cv2.distanceTransform(bwim, distanceType=cv2.DIST_L2, maskSize=3)
     bwd = np.asmatrix(bwd, dtype=float)
     roundBwd = np.round(bwd)
     nPtsRep = np.sum(roundBwd, dtype=int)
 
+    # for debugging --
+    import matplotlib.pyplot as plt
+    plt.figure()
+    plt.imshow(bwd)
+    # ----------------
+
     ptsRep = np.zeros((nPtsRep.astype(int), 2))
     r, c = np.where(bwim == 1)
     pts = np.asarray([r, c], dtype=int)
@@ -91,6 +96,7 @@ def drawClusters(gmmfit, bwim):
     clusters = gmmfit.predict(pts)
     print("Clusters Found: ", np.unique(clusters)+1)
 
+    plt.figure()
     plt.imshow(bwim, cmap='gray')
     plt.hold(True)
     print("Plotting...")
@@ -98,7 +104,6 @@ def drawClusters(gmmfit, bwim):
     for h in np.unique(clusters):
         clustIdx = np.where(clusters == h)
         clustIdx = clustIdx[0]
-        print("Cluster ", h + 1, "Indices: ", clustIdx)
         plt.scatter(x=pts[clustIdx, 1], y=pts[clustIdx, 0], c=colors[h])
     plt.show()
     plt.hold(False)

SRC/Python/PixelReplication.py → SRC/Python/PixelRep_Demo.py

@@ -27,14 +27,13 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-import cv2
-import PixelRepLib as PR
-import GenerateEllipseLib as GenEllipse
+import PIXEL_REPLICATION_LIB as PR
+import GENERATE_ELLIPSE_LIB as GenEllipse
 
 # Generate random ellipse image
 print("Generating Ellipse...")
-K = 5 # number of ellipse to fit
-# bwim = GenEllipse.GetRandomEllipseImage(K)
+K = 2 # number of ellipse to fit
+bwim = GenEllipse.GetRandomEllipseImage(K)
 
 # You may import an image for demo by uncommenting the following code:
 # im = cv2.imread('filename',cv2.CV_8UC1)
@@ -42,9 +41,6 @@ K = 5 # number of ellipse to fit
 # plt.imshow(im)
 # plt.show()
 
-im = cv2.imread('U:\Angeline\PixelRep\Ellipse.tif',cv2.CV_8UC1)
-th, bwim = cv2.threshold(im, 0, 1, cv2.THRESH_BINARY)
-
 # IMPORTANT NOTE:
 # bwim only has 1 connected component. if bwim has multiple connected
 # components, process each one separately
@@ -60,8 +56,7 @@ gmmfit = PR.fitGMM(ptsRep, K)
 
 PR.drawClusters(gmmfit, bwim)
 
-# Draw Gaussian isocontours for triangular elliptical approximation (see online methods).
-# These are exact for circles and approximate for ellipticals.
+