TrueMatch Import reworked

analysis/analysisview.py

@@ -301,8 +301,11 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
             self.refSelector.setDisabled(False)
             
     def importTrueMatchResults(self):
+        if self.importWindow is not None:
+            del self.importWindow
+        
         self.importWindow = LoadTrueMatchResults(self.particleContainer, self)
-        self.importWindow.exec()
+#        self.importWindow.exec()
         
     @QtCore.pyqtSlot()
     def applyHQIThresholdToResults(self):
@@ -622,8 +625,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
     
     def closeEvent(self, event):
         for window in [self.importWindow, self.dbWin]:
-            try: window.close()
-            except: pass
+            if window is not None:
+                window.close()
+                
         self.viewparent.imparent.particelAnalysisAct.setChecked(False)
         event.accept()
 

analysis/particleCharacterization.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program, see COPYING.  
+If not, see <https://www.gnu.org/licenses/>.
+"""
+
+import numpy as np
+import cv2
+
+def getContourStatsWithPixelScale(cnt, pixelscale):
+        long, short, longellipse, shortellipse, area = getContourStats(cnt)
+        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2
+
+def getContourStats(cnt):
+    ##characterize particle
+        longellipse, shortellipse = np.nan, np.nan
+        
+        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...
+            ellipse = cv2.fitEllipse(cnt)
+            shortellipse, longellipse = ellipse[1]
+
+        rect = cv2.minAreaRect(cnt)
+        long, short = rect[1]
+        if short>long:
+            long, short = short, long
+        
+        area = cv2.contourArea(cnt)
+    
+        return long, short, longellipse, shortellipse, area
\ No newline at end of file

analysis/particleEditor.py

@@ -31,25 +31,8 @@ from PyQt5 import QtWidgets, QtCore
 from copy import deepcopy
 
 from .particlePainter import ParticlePainter
+from .particleCharacterization import getContourStatsWithPixelScale
 
-def getContourStatsWithPixelScale(contours, pixelscale):
-        ##characterize particle
-        longellipse, shortellipse = np.nan, np.nan
-        
-        cnt = contours
-        
-        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...
-            ellipse = cv2.fitEllipse(cnt)
-            shortellipse, longellipse = ellipse[1]
-
-        rect = cv2.minAreaRect(cnt)
-        long, short = rect[1]
-        if short>long:
-            long, short = short, long
-        
-        area = cv2.contourArea(cnt)
-    
-        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2
 
 
 class ParticleContextMenu(QtWidgets.QMenu):

segmentation.py

@@ -28,6 +28,8 @@ from skimage.feature import peak_local_max
 from skimage.morphology import watershed
 from random import random
 
+from .analysis.particleCharacterization import getContourStats
+
 class Parameter(object):
     def __init__(self, name, dtype, value=None, minval=None, maxval=None, 
                  decimals=0, stepsize=1, helptext=None, show=False, linkedParameter=None):
@@ -282,21 +284,6 @@ class Segmentation(object):
             
         sure_fg = cv2.dilate(sure_fg, np.ones((3, 3)))
         return sure_fg
-
-    def characterizeParticle(self, contours):
-        longellipse, shortellipse = np.nan, np.nan
-        
-        cnt = contours
-        
-        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...
-            ellipse = cv2.fitEllipse(cnt)
-            shortellipse, longellipse = ellipse[1]
-        rect = cv2.minAreaRect(cnt)
-        long, short = rect[1]
-        if short>long:
-            long, short = short, long
-    
-        return long, short, longellipse, shortellipse, cv2.contourArea(cnt)
     
     def getMeasurementPoints(self, binParticle, numPoints=1):
         binParticle = cv2.copyMakeBorder(binParticle, 1, 1, 1, 1, 0)
@@ -449,7 +436,6 @@ class Segmentation(object):
             img[np.nonzero(sure_bg)] |= 2
             return img, 1        
         
-        
         dist_transform = cv2.distanceTransform(thresh, cv2.DIST_L2,5)
         print("distanceTransform")
         if self.cancelcomputation:
@@ -464,7 +450,7 @@ class Segmentation(object):
             return None, None, None
         if return_step=="watershed":
             return np.uint8(255*(markers!=0)), 0  
-
+        
         if cv2.__version__ > '3.5':        
             contours, hierarchy = cv2.findContours(markers, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
         else:
@@ -484,7 +470,8 @@ class Segmentation(object):
             label = markers[cnt[0,0,1],cnt[0,0,0]]
             if label==0:
                 continue
-            particlestats.append(self.characterizeParticle(cnt))
+            stats = getContourStats(cnt)
+            particlestats.append(stats)
             x0, x1 = cnt[:,0,0].min(), cnt[:,0,0].max()
             y0, y1 = cnt[:,0,1].min(), cnt[:,0,1].max()
             subimg = (markers[y0:y1+1,x0:x1+1]).copy()