temporary fixes, non working solution

ramancom/simulatedraman.py

@@ -21,6 +21,8 @@ If not, see <https://www.gnu.org/licenses/>.
 Simualted Raman interface module for testing without actual raman system connected
 """
 
+import sys
+stdout = sys.stdout
 from time import sleep
 import numpy as np
 from shutil import copyfile
@@ -35,9 +37,9 @@ class SimulatedRaman(RamanBase):
         self.currentpos = None, 0., 0.
         self.currentZ = 0.
         # some plausible data to simulate consecutively changing positions
-        self.positionlist = np.array([[ 1526. , -1379.9,  -131. ],
-                                      [ 3762.5, -1197.7,  -138.1],
-                                      [ 2313.7, -2627.2,  -138.1],
+        self.positionlist = np.array([[ -12012,  13716,  -1290],
+                                      [ -11955,  -9200,  -1279],
+                                      [  10978,  -9254,  -1297],
                                       [ 2704.1, -1788.2,  -138.1],
                                       [ 3884. , -2650.8,  -138.1]])
         self.znum = 4
@@ -77,6 +79,7 @@ class SimulatedRaman(RamanBase):
         
     def moveToAbsolutePosition(self, x, y, z=None, epsxy=0.11, epsz=0.011, debugReturn=False, measurementRunning=False):
         assert self.connected
+        print('moving to:', x, y, z, file=stdout)
         if z is None:
             self.currentpos = x, y, self.currentpos[2]        
         else:

viewitems.py

@@ -113,49 +113,51 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
             self.update()
     
     def contextMenuEvent(self, event):
-        contextMenu = QtWidgets.QMenu("Particle options")
-
-        combineMenu = QtWidgets.QMenu("Combine Particles into")
-        
-        combineActs = []
-        assignments = []
-        for index in self.selectedContours:
-#            partIndex = int(np.where(self.parent.dataset.ramanscansortindex == index)[0])
-            partIndex = index
-            assignments.append(self.parent.analysiswidget.datastats.particleResults[partIndex])
-        assignments.append("other")
-        for assignment in np.unique(np.array(assignments)):
-            combineActs.append(combineMenu.addAction(assignment))
-        
-        reassignActs = []
-        reassignMenu = QtWidgets.QMenu("Reassign particle(s) into")
-        for polymer in self.parent.analysiswidget.datastats.getUniquePolymers():
-            reassignActs.append(reassignMenu.addAction(polymer))
-        reassignActs.append(reassignMenu.addAction("other"))
-        
-        contextMenu.addMenu(combineMenu)        
-        contextMenu.addMenu(reassignMenu)
-        deleteAct = contextMenu.addAction("Delete Particle(s)")
-
-        numParticles = len(self.selectedContours)
-        if numParticles == 0:
-            reassignMenu.setDisabled(True)
-            combineMenu.setDisabled(True)
-            deleteAct.setDisabled(True)
-        elif numParticles == 1:
-            combineMenu.setDisabled(True)
-
-        action = contextMenu.exec_(event.screenPos())
-
-        if action == deleteAct:
-            print('deleting')
-        elif action in combineActs:
-            newAssignment = action.text()
-            self.parent.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)
+        if self.parent.analysiswidget is not None:
+            contextMenu = QtWidgets.QMenu("Particle options")
+    
+            combineMenu = QtWidgets.QMenu("Combine Particles into")
+            
+            combineActs = []
+            assignments = []
+            for index in self.selectedContours:
+    #            partIndex = int(np.where(self.parent.dataset.ramanscansortindex == index)[0])
+                partIndex = index
+                assignments.append(self.parent.analysiswidget.datastats.particleResults[partIndex])
+            assignments.append("other")
+            for assignment in np.unique(np.array(assignments)):
+                combineActs.append(combineMenu.addAction(assignment))
+            
+            reassignActs = []
+            reassignMenu = QtWidgets.QMenu("Reassign particle(s) into")
+            
+            for polymer in self.parent.analysiswidget.datastats.getUniquePolymers():
+                reassignActs.append(reassignMenu.addAction(polymer))
+            reassignActs.append(reassignMenu.addAction("other"))
             
-        elif action in reassignActs:
-            newAssignment = action.text()                
-            self.parent.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)
+            contextMenu.addMenu(combineMenu)        
+            contextMenu.addMenu(reassignMenu)
+            deleteAct = contextMenu.addAction("Delete Particle(s)")
+    
+            numParticles = len(self.selectedContours)
+            if numParticles == 0:
+                reassignMenu.setDisabled(True)
+                combineMenu.setDisabled(True)
+                deleteAct.setDisabled(True)
+            elif numParticles == 1:
+                combineMenu.setDisabled(True)
+    
+            action = contextMenu.exec_(event.screenPos())
+    
+            if action == deleteAct:
+                print('deleting')
+            elif action in combineActs:
+                newAssignment = action.text()
+                self.parent.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)
+                
+            elif action in reassignActs:
+                newAssignment = action.text()                
+                self.parent.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)
             
     
 class FitPosIndicator(QtWidgets.QGraphicsItem):

zeissimporter.py

@@ -186,10 +186,12 @@ class ZeissImporter(QtWidgets.QDialog):
         dataset.coordinatetransform = T, pc
         
         # set image center as reference point in data set (use Zeiss coordinates)
-        p0 = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
+        p0center = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
+        p0 = p0center-.5*np.array((self.region.width, self.region.height))
+        p1 = p0center+.5*np.array((self.region.width, self.region.height))
         dataset.readin = False
         dataset.lastpos = p0
-        dataset.maxdim = p0 + p0
+        dataset.maxdim = p0 + p1
         
         zmin, zmax = dataset.zpositions.min(), dataset.zpositions.max()
         blur = (blur)*(255.)