Merge pull request #2 from StrokaLab/feature/axis-angle

Feature/axis angle

Author: thomaskcr

README.md

@@ -47,3 +47,7 @@ $ pip install -r bin/requirements.txt
 ```
 $ jupyter nbextension enable --py widgetsnbextension
 ```
+
+### Checking for Errors
+
+In order to check for errors after running jobs, navigate to your main repository, then go to: data / projects / 'your project name' / system / job errors

code/cells/shapes.py

@@ -165,3 +165,59 @@ def get_hull_aspect_ratios(self):
         ls = min([float(a), float(b)]) / max([float(a), float(b)])
 
         return ab, ls
+    
+    def get_angle(self):
+        sorted_hull_points = self.get_convex_hull()
+        hull_point_array = numpy.asarray(sorted_hull_points)
+
+        ellipse_hull = skimage.measure.EllipseModel()
+        success = ellipse_hull.estimate(hull_point_array)
+        
+        if not success:
+            add_points = 10
+
+            while not success and add_points < 100:
+                add_points_skip = int(math.floor(len(self.path) / add_points))
+
+                path = numpy.asarray(self.path)
+                add_points_arr = path[::add_points_skip]
+
+                new_arr = numpy.append(hull_point_array, add_points_arr, 0)
+                hull_point_array = new_arr.copy()
+                
+
+                ellipse_hull = skimage.measure.EllipseModel()
+                success = ellipse_hull.estimate(hull_point_array)
+                
+                add_points += 10
+        
+        xc, yc, a, b, phi = ellipse_hull.params
+        # need to calculate the slope of the line relative to the image, not the x,y axis.
+        a_p1 = xc + a*math.cos(phi), yc + a*math.sin(phi)
+        a_p2 = xc - a*math.cos(phi), yc - a*math.sin(phi)
+        b_p1 = xc - b*math.sin(phi), yc + b*math.cos(phi)
+        b_p2 = xc + b*math.sin(phi), yc - b*math.cos(phi)
+
+        # we need to invert only the apparent y-axis 
+        x_max, y_max = self.image.shape
+        m = ((y_max - a_p1[0]) - (y_max - a_p2[0])) / (a_p1[1] - a_p2[1])
+        image_angle = math.atan(m)
+        image_angle_deg = math.degrees(image_angle)
+        if image_angle_deg < 0:
+            image_angle_deg += 180
+
+        #import matplotlib.pyplot
+         
+        #matplotlib.pyplot.figure(15)
+        #matplotlib.pyplot.imshow(self.image)
+        #for hp in hull_point_array:
+        #   r, c = hp
+        #   matplotlib.pyplot.plot(r, c, 'o')
+        #   matplotlib.pyplot.scatter([c], [r], color='#AA3C39', marker=',')
+
+        #matplotlib.pyplot.plot([a_p1[1], a_p2[1]], [a_p1[0], a_p2[0]], 'y') #Change y to change color 
+        #matplotlib.pyplot.plot([b_p1[1], b_p2[1]], [b_p1[0], b_p2[0]], 'c') #Change c to change color 
+        #matplotlib.pyplot.savefig('/Users/adamlanda/Documents/JAnaP/data/testfig.png')
+        #matplotlib.pyplot.close()
+
+        return image_angle_deg

code/cli/jobs/shapes.py

@@ -130,5 +130,8 @@ def __calculate_shape_data(self, image_path, perimeter_path, job_entity_row):
 
         shape_data["hull_aspect_ratio_ab"], shape_data["hull_aspect_ratio"] = \
             shape_calculator.get_hull_aspect_ratios()
+            
+        #adding angle
+        shape_data["angle"] = shape_calculator.get_angle()
 
         return shape_data

code/cli/output.py

@@ -91,6 +91,7 @@ def generate_cell_data_file(project):
     #                   "Hull Aspect Ratio (< 1)"])
 
     output_row.extend(["Hull Aspect Ratio (< 1)"])
+    output_row.extend(["Angle of Major Axis wrt X-Axis (degrees)"])
 
 
 
@@ -167,7 +168,8 @@ def generate_cell_data_file(project):
             output_row.extend([shape_data.get("solidity", ""),
                                shape_data.get("circularity", ""),
                                shape_data.get("convex_area", ""),
-                               shape_data.get("hull_aspect_ratio", "")])
+                               shape_data.get("hull_aspect_ratio", ""), 
+                               shape_data.get("angle", "")])
                                #shape_data.get("aspect_ratio", "")])
         else:
             # Perimeter

web/application.py

@@ -2,6 +2,10 @@
 import inspect
 import sys
 
+# TODO: Determine why this change was made
+import matplotlib
+matplotlib.use('TkAgg')
+
 import werkzeug.serving
 import thread