Merge branch dev into gat1

Server/resources/js/mapInspector.js

@@ -88,7 +88,7 @@ var imageObj = undefined; //the stitched map image
         if(toolTipBead){
             const canvas = $('#mapCanvas');
             const location = `(${Math.round(toolTipBead[2][0])}, ${Math.round(toolTipBead[2][1])})`;
-            const radius = Math.round(toolTipBead[2][2]);
+            let radius = Math.round(toolTipBead[2][2]);
             let type = '';
             let rgb = `(${Math.round(toolTipBead[0][0])}, ${Math.round(toolTipBead[0][1])}, ${Math.round(toolTipBead[0][2])})`;
             var rectWidth = 325,
@@ -114,6 +114,7 @@ var imageObj = undefined; //the stitched map image
                 type = 'Crushed Bead';
                 rgb = 'N/A';
                 ctx.fillStyle = $('#crushedBeadOutline').val();
+                radius = 'N/A';
             } else if (toolTipBead[1] === 'waterBead') {
                 type = 'Water Bead';
                 ctx.fillStyle = $('#waterBeadOutline').val();

lib/color_labeler.py

@@ -0,0 +1,45 @@
+import cv2
+import numpy as np
+from collections import OrderedDict
+from scipy.spatial import distance as dist
+
+class ColorLabeler:
+	def __init__(self):
+		self.colorsToIgnore = ['darkgray', 'darkblue', 'black']
+
+		colors = OrderedDict({
+			"red": (255, 0, 0),
+			"green": (0, 255, 0),
+			"blue": (0, 0, 255),
+            "black": (0, 0, 0),
+            "yellow": (255, 255, 0),
+            "darkblue": (0, 0, 71),
+            "gray": (96, 96, 96),
+            "darkgray": (70, 70, 70),
+            "white": (255, 255, 255),
+            })
+
+		self.lab = np.zeros((len(colors), 1, 3), dtype="uint8")
+		self.colorNames = []
+
+		for (i, (name, rgb)) in enumerate(colors.items()):
+			self.lab[i] = rgb
+			self.colorNames.append(name)
+
+		self.lab = cv2.cvtColor(self.lab, cv2.COLOR_RGB2LAB)
+
+	def label(self, img, c):
+		mask = np.zeros(img.shape[:2], dtype="uint8")
+		cv2.drawContours(mask, [c], -1, 255, -1)
+		mask = cv2.erode(mask, None, iterations=2)
+		mean = cv2.mean(img, mask=mask)[:3]
+
+		minDist = (np.inf, None)
+
+		for (i, row) in enumerate(self.lab):
+			d = dist.euclidean(row[0], mean)
+
+			if d < minDist[0]:
+				minDist = (d, i)
+
+		return self.colorNames[minDist[1]]

lib/counting.py

@@ -36,6 +36,7 @@
 from enum import Enum
 from os import listdir, path
 from . import util
+from . import color_labeler
 
 """
     Description: an enum class to handle the HoughCircle configuration values that are used in cv2.HoughCircles().
@@ -76,7 +77,6 @@ def getColorBeads(self, houghConfig, detectionParams):
         circles = cv2.HoughCircles(blur,cv2.HOUGH_GRADIENT,dp=houghConfig["dp"],minDist=houghConfig["minDist"],
                             param1=houghConfig["param1"],param2=houghConfig["param2"],minRadius=houghConfig["minRadius"],maxRadius=houghConfig["maxRadius"])
 
-
         circles = np.uint16(np.around(circles))
         for i in circles[0,:]:
             # i[0] is x coordinate, i[1] is y coordinate, i[2] is radius
@@ -134,32 +134,37 @@ def isWater(self, RGB):
 
     def getCrushedBeads(self, image, circles):
         temp_img = self.grayScaleMap.copy()
+
         for i in circles[0,:]:
             # fills in the circle
             cv2.circle(temp_img, (i[0],i[1]) ,i[2], (255,255,255), -1)
             #fills the outer edges of the circle
             cv2.circle(temp_img,(i[0], i[1]), i[2], (255,255,255), 17)
 
+
         blur = cv2.GaussianBlur(temp_img, (19, 19), 0)
+        lab = cv2.cvtColor(self.colorMap, cv2.COLOR_BGR2LAB)
         thresh = cv2.threshold(blur, 225, 255, cv2.THRESH_BINARY_INV)[1]
         img_output, contours, hierarchy = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
 
-        for c in contours:
-            # calculate moments for each contour
-            M = cv2.moments(c)
+        cl = color_labeler.ColorLabeler()
 
-           # calculate x,y coordinate of center
-            if M["m00"] != 0:
-                cX = int(M["m10"] / M["m00"])
-                cY = int(M["m01"] / M["m00"])
-            else:
-                cX, cY = 0, 0
+        for c in contours:
+            color = cl.label(lab, c)
 
-            x = self.getBrightestColor([cX, cY, 10])
-            print(x)
+            if color not in cl.colorsToIgnore:
+                cv2.drawContours(image, [c], -1, (0, 255, 0), 2)
 
-            cv2.circle(image, (cX, cY), 5, (0, 0, 255), -1)
-            self.crushedBeads.append([[0, 0, 0], 'crushedBead', [cX, cY, 35]])
+                # compute the center of the contour
+                M = cv2.moments(c)
+                if M['m00'] > 0:
+                    cX = int((M["m10"] / M["m00"]))
+                    cY = int((M["m01"] / M["m00"]))
+                    self.crushedBeads.append([[0, 0, 0], 'crushedBead', [cX, cY, 35]])
+                else:
+                    cX = 0
+                    cY = 0
+                cv2.circle(image, (cX, cY), 2, (0, 255, 0), 3)
 
     """
         Description: a function that takes an array representing a circle's[x-coord of center, y-coord of center, radius]
@@ -232,7 +237,7 @@ def getAverageColor(self, circleInfo):
         isWater = self.isWater(average)
         type = 'waterBead' if isWater else 'bead'
         return [[average[0],average[1],average[2]], type, [circleInfo[0],circleInfo[1],circleInfo[2]]] #[[R,G,B], isWater, [x,y,radius]]
-    
+
     def getMiddleColor(self, circleInfo):
         img = self.colorMap
         imgY = img.shape[0]
@@ -253,7 +258,7 @@ def getMiddleColor(self, circleInfo):
                 reds.append(bgrValue[2])
                 greens.append(bgrValue[1])
                 blues.append(bgrValue[0])
-        
+
         average = (round(np.mean(reds), 2), round(np.mean(greens), 2), round(np.mean(blues), 2))
         isWater = self.isWater(average)
         type = 'waterBead' if isWater else 'bead'
@@ -282,8 +287,8 @@ def getRadiusAverageColor(self, circleInfo):
         isWater = self.isWater(average)
         type = 'waterBead' if isWater else 'bead'
         return [[average[0],average[1],average[2]], type, [circleInfo[0],circleInfo[1],circleInfo[2]]] #[[R,G,B], isWater, [x,y,radius]]
-            
-        
+
+
     def getFourQuadrantColor(self, circleInfo):
         img = self.colorMap
         imgY = img.shape[0]
@@ -305,18 +310,11 @@ def getFourQuadrantColor(self, circleInfo):
                     reds.append(bgrValue[2])
                     greens.append(bgrValue[1])
                     blues.append(bgrValue[0])
-        
+
         average = (round(np.mean(reds), 2), round(np.mean(greens), 2), round(np.mean(blues), 2))
         isWater = self.isWater(average)
         type = 'waterBead' if isWater else 'bead'
         return [[average[0],average[1],average[2]], type, [circleInfo[0],circleInfo[1],circleInfo[2]]] #[[R,G,B], isWater, [x,y,radius]]
-
-
-
-
-
-
-
 
     """
         Description: a function that takes a bead's radius and x and y coordinates of the center and returns coordinates of every point in
@@ -334,10 +332,10 @@ def getPointsInCircle(self, radius, centerX, centerY):
 
 
     """
-        Description: 
+        Description:
         @param colorFormat: a string that is either 'rgb', 'hsv', 'cmyk', or 'grayscale'
         @return void, writes file directly from class attributes
-    """ 
+    """
     def makeBeadsCSV(self, colorFormat):
         newPath = self.imagePath
         endIndex = newPath.rfind("/")

requirements.txt

@@ -4,4 +4,5 @@ Flask==1.0.2
 gevent==1.3.6
 pillow==5.3.0
 imutils==0.5.3
+scipy==1.3.1
 matplotlib