resolves #192 by checking for non-existent labels in the bounding box computation

scripts/spam-ereg-discrete

@@ -83,9 +83,15 @@ class MainWindow(QWidget):
         self.Phi = numpy.eye(4)
         self.mainWindowGrid = QGridLayout(self)
 
-        self.nonConvergedGrains = numpy.where(DDIC['returnStatus'] < args.RETURN_STAT_THRESHOLD)[0][1:]
+        # Issue #192 will be fixed here, by making sure the loew return stat list also has real boundin boxes
+        #   (i.e., grains are really defined)
+        nonConvergedGrains = DDIC['returnStatus'] < args.RETURN_STAT_THRESHOLD
+        presentGrains      = REFlabBB[:,1]>REFlabBB[:,0]
+        print(numpy.where(nonConvergedGrains), presentGrains)
+        self.nonConvergedGrains = numpy.where(numpy.logical_and(nonConvergedGrains, presentGrains))[0][0:]
+
         self.N = 0 # Number of the current nonConvergedGrain that's being studied
-        print("Going to work on these labels:\n", self.nonConvergedGrains)
+        print("Going to work on these labels:\n", self.nonConvergedGrains, "(p.s. I removed non-existent labels:", numpy.where(~presentGrains)[0][1:]," )")
         if len(self.nonConvergedGrains) > 0:
             self.alignOneLabel()
             self.labAndPhi = []
@@ -113,7 +119,7 @@ class MainWindow(QWidget):
                                     labelDilate=args.LABEL_DILATE, margin=args.margin,
                                     maskOtherLabels=args.MASK)
 
-        if REGgl is not None:
+        if REFgl is not None:
             # 2020-10-23: EA on Issue #186: using spam.helpers.slicePadded
             REFsubvol = spam.helpers.slicePadded(REFgrey, REFgl['boundingBox']+numpy.array([0,1,0,1,0,1]))
 
@@ -136,18 +142,21 @@ class MainWindow(QWidget):
             self.nextLabelButton.clicked.connect(self.nextLabel)
             self.mainWindowGrid.addWidget(self.nextLabelButton, 2, 1)
         else:
-            nextLabel()
-
-    def nextLabel(self):
-        #print("Phi:", self.eregWidget.output())
-        self.eregWidget.close()
-
-        # Get Phi output from graphical
-        PhiTmp = self.eregWidget.output()
-        # Add back in int displacement
-        PhiTmp[0:3, -1] += self.diplacementInt
-        #                       nonConvergedGrain label number, eye-Phi
-        self.labAndPhi.append([self.nonConvergedGrains[self.N], PhiTmp])
+            self.nextLabel(widgetOpen=False)
+
+    def nextLabel(self, widgetOpen=True):
+        if widgetOpen:
+            self.eregWidget.close()
+
+            # Get Phi output from graphical
+            PhiTmp = self.eregWidget.output()
+            # Add back in int displacement
+            PhiTmp[0:3, -1] += self.diplacementInt
+            #                       nonConvergedGrain label number, eye-Phi
+            self.labAndPhi.append([self.nonConvergedGrains[self.N], PhiTmp])
+        else:
+            # This grain was skipped, let's add nothing in its place
+            self.labAndPhi.append([self.nonConvergedGrains[self.N], numpy.eye(4)])
 
         # Move onto next grain, otherwise write and quit
         self.N += 1