Converted particleAreas into particleSize for filtering of components

segmentation.py

@@ -82,9 +82,9 @@ class Segmentation(QtCore.QObject):
                               'upThresh': 0.5,
                               'invertThresh': False,
                               'maxholebrightness': 0.5,
-                              'minparticlearea': 20,
+                              'minparticlesize': 20,
                               'enableMaxArea': False,
-                              'maxparticlearea': 100000,
+                              'maxparticlesize': 100000,
                               'minparticledistance': 20,
                               'closeBackground': False,
                               'fuzzycluster': False,
@@ -113,9 +113,9 @@ class Segmentation(QtCore.QObject):
                    Parameter("activateUpThresh", np.bool, self.detectParams['activateUpThresh'], helptext="activate upper threshold", show=False, linkedParameter='upThresh'),
                    Parameter("upThresh", float, self.detectParams['upThresh'], .01, 1.0, 2, .02, helptext="Upper threshold", show=False),
                    Parameter("maxholebrightness", float, self.detectParams['maxholebrightness'], 0, 1, 2, 0.02, helptext="Close holes brighter than..", show = True),
-                   Parameter("minparticlearea", int, self.detectParams['minparticlearea'], 1, 1000, 0, 50, helptext="Min. particle pixel area", show=False),
-                   Parameter("enableMaxArea", np.bool, self.detectParams['enableMaxArea'], helptext="enable filtering for maximal pixel area", show=False, linkedParameter='maxparticlearea'),
-                   Parameter("maxparticlearea", int, self.detectParams['maxparticlearea'], 10, 1E9, 0, 50, helptext="Max. particle pixel area", show=False),
+                   Parameter("minparticlesize", int, self.detectParams['minparticlesize'], 1, 1000, 0, 50, helptext="Min. particle size (µm)", show=False),
+                   Parameter("enableMaxArea", np.bool, self.detectParams['enableMaxArea'], helptext="enable filtering for maximal particle size", show=False, linkedParameter='maxparticlearea'),
+                   Parameter("maxparticlesize", int, self.detectParams['maxparticlesize'], 10, 1E9, 0, 50, helptext="Max. particle size (µm)", show=False),
                    Parameter("minparticledistance", int, self.detectParams['minparticledistance'], 5, 1000, 0, 5, helptext="Min. distance between particles", show=False),
                    Parameter("measurefrac", float, self.detectParams['measurefrac'], 0, 1, 2, stepsize = 0.05, helptext="measure fraction of particles", show=False),
                    Parameter("closeBackground", np.bool, self.detectParams['closeBackground'], helptext="close holes in sure background", show=False),
@@ -238,10 +238,7 @@ class Segmentation(QtCore.QObject):
         if self.cancelcomputation:
             return None, None
         
-        if self.enableMaxArea:
-            maxArea = self.maxparticlearea
-        else:
-            maxArea = np.inf
+        minArea, maxArea = self.getMinMaxParticleArea(dataset)
         
         ##get sure_fg
         '''the peak_local_max function takes the min distance between peaks. Unfortunately, that means that individual 
@@ -265,7 +262,7 @@ class Segmentation(QtCore.QObject):
         
         for label in range(1, n):
             area = stats[label, cv2.CC_STAT_AREA]
-            if self.minparticlearea < area < maxArea:
+            if minArea < area < maxArea:
                 up = stats[label, cv2.CC_STAT_TOP]
                 left = stats[label, cv2.CC_STAT_LEFT]
                 width = stats[label, cv2.CC_STAT_WIDTH]
@@ -339,7 +336,7 @@ class Segmentation(QtCore.QObject):
 
                 for cnt in tmpcontours:
                     contourArea = cv2.contourArea(cnt) * scaleFactor**2
-                    if contourArea >= self.minparticlearea:
+                    if contourArea >= minArea:
                         tmplabel = markers[cnt[0,0,1],cnt[0,0,0]]
                         if tmplabel ==0:
                             continue
@@ -404,6 +401,24 @@ class Segmentation(QtCore.QObject):
         self.detectionState.emit(f'finished particle detection after {total_time} seconds')
         return measurementPoints, finalcontours
     
+    def getMinMaxParticleArea(self, dataset):
+        """
+        Converts specified particle sizes into particle areas that are used for filtering detection results.
+        Size is interpreted as sphere equivalent diameter.
+        a = pi*(d/2)²
+        :return:
+        """
+        pixelscale = dataset.getPixelScale()
+        minRadius = (self.minparticlesize / pixelscale) / 2
+        minArea = np.pi * minRadius**2
+        
+        if self.enableMaxArea:
+            maxRadius = (self.maxparticlesize / pixelscale) / 2
+            maxArea = np.pi * maxRadius**2
+        else:
+            maxArea = np.inf
+        
+        return minArea, maxArea
     
     def addToPreviewImage(self, subimg, up, left, previewImage):
         """