OBF loading fixes (and info display enhancement)

PYME/IO/DataSources/OBFDataSource.py

@@ -47,13 +47,20 @@ def __init__(self, obf, stack_number=None):
         self.stack = stack
 
     def getSlice(self, ind):
-        return self.stack.data[:,:,ind].squeeze()
+        if len(self.stack.data.shape) == 2:
+            assert(ind == 0)
+            return self.stack.data[:,:]
+        else:
+            return self.stack.data[:,:,ind].squeeze()
 
     def getSliceShape(self):
         return self.stack.data.shape[:2]
 
-    def getNumSlices(self):
-        return self.stack.data.shape[2]
+    def getNumSlices(self): # we allow for 2D
+        if len(self.stack.data.shape) > 2:
+            return self.stack.data.shape[2]
+        else:
+            return 1
 
     def getEvents(self):
         return []

PYME/IO/image.py

@@ -803,8 +803,10 @@ def _loadOBF(self, filename):
         logger.debug('file: {}'.format(filename))
         if len(obf.stacks) > 1 and stack_number is None and self.haveGUI:
                 import wx
-                options = ['%d: %s' % (ind, stack.name) for (ind, stack) in enumerate(obf.stacks)]
-
+                def format_stack_info(ind, stack):
+                    return '%d: %s (shape %s)' % (ind, stack.name, stack.shape)
+
+                options = [format_stack_info(ind, stack) for (ind, stack) in enumerate(obf.stacks)]                
                 dlg = wx.SingleChoiceDialog(None, 'Stack', 'Select a stack', options)
                 if dlg.ShowModal() == wx.ID_OK:
                     stack_number = dlg.GetSelection()
@@ -821,7 +823,8 @@ def _loadOBF(self, filename):
             raise NotImplementedError('Scale factors other than 1 not yet supported for OBF metadata')
         self.mdh['voxelsize.x'] = voxel_sizes[0] / 1E-6 # [m -> um]
         self.mdh['voxelsize.y'] = voxel_sizes[1] / 1E-6 # [m -> um]
-        self.mdh['voxelsize.z'] = voxel_sizes[2] / 1E-6 # [m -> um]
+        if len(voxel_sizes) > 2:
+            self.mdh['voxelsize.z'] = voxel_sizes[2] / 1E-6 # [m -> um]
 
 
 

PYME/LMVis/visCore.py

@@ -889,7 +889,8 @@ def OnSaveSession(self, event):
                                    #nameUtils.genResultDirectoryPath(), 
                                    extension='.pvs')
         if not filename == '':
-            self.save_session(filename)
+            from pathlib import Path
+            self.save_session(Path(filename).with_suffix('.pvs'))
 
     def load_session(self, filename):
         import yaml