Watershed workflow

volumina/colortables.py

@@ -113,6 +113,7 @@ def partlyJetTransparent(N=256, ratio = 2./3):
             QColor(240, 230, 140).rgba(), #khaki
             QColor(69, 69, 69).rgba()]    # dark grey
 
+
 random256 = [             
             QColor(201, 200, 200).rgba(),
             QColor(0, 0, 255).rgba(),
@@ -392,7 +393,25 @@ def create_random_8bit():
     '''Create a colortable suitable for 8bit data.
 
     Creates a pseudo-random colortable in the 8bit range'''
-    return random256;
+
+    # don't return random256 directly. Otherwise the list will be changed by some code directly, 
+    # and everything gets messed up.
+    # use a creator instead
+    #return random256;
+    return [color for color in random256]
+
+def create_random_8bit_zero_transparent():
+    '''Create a colortable suitable for 8bit data.
+
+    Creates a pseudo-random colortable in the 8bit range
+    Replace zero(th) Color with transparent'''
+    temp = random256
+    temp[0] = QColor(0, 0, 0, 0).rgba()
+
+    # don't return random256 directly. Otherwise the list will be changed by some code directly, 
+    # and everything gets messed up.
+    # use a creator instead
+    return [color for color in temp]
 
 def create_random_16bit():
     '''Create a colortable suitable for 16bit data.

volumina/pixelpipeline/imagesources.py

@@ -418,11 +418,14 @@ def toImage( self ):
             tImg = time.time()
             img = QImage(a.shape[1], a.shape[0], QImage.Format_ARGB32)
             if not issubclass( a.dtype.type, np.integer ):
-                raise NotImplementedError()
                 #FIXME: maybe this should be done in a better way using an operator before the colortable request which properly handles 
                 #this problem 
                 warnings.warn("Data for colortable layers cannot be float, casting",RuntimeWarning)
                 a = np.asanyarray(a, dtype=np.uint32)
+                warnings.warn("As a workaround, volumina/volumina/pixelpipeline/imagesource.py, comment the raise NotImplementedError; Or adjust your data-set to be np.integer conform",RuntimeWarning)
+                #TODO raise Error just stopped but doesn't handle anything. 
+                # The Warning and conversion did the job
+                raise NotImplementedError()
 
             # If we have a masked array with a non-trivial mask, ensure that mask is made transparent.
             _colorTable = self._colorTable

volumina/sliceSelectorHud.py

@@ -434,6 +434,7 @@ def _get_pos_widget(name, backgroundColor, foregroundColor):
 
     spinbox = DelayedSpinBox(750)
     spinbox.setAlignment(Qt.AlignCenter)
+    #set the information that will be viewed, if hovered over the Coordination Box
     spinbox.setToolTip("{0} Spin Box".format(name))
     spinbox.setButtonSymbols(QAbstractSpinBox.NoButtons)
     spinbox.setMaximumHeight(20)
@@ -490,6 +491,16 @@ def createQuadViewStatusBar(self,
                                 xbackgroundColor, xforegroundColor,
                                 ybackgroundColor, yforegroundColor,
                                 zbackgroundColor, zforegroundColor):
+        """
+        adds the following properties to the lower part of the view
+        X value (X Spin Box)
+        Y value
+        Z value
+        Busy-waiting box (invisible)
+        Position
+        Time Spin Box
+
+        """
         self.xLabel, self.xSpinBox = _get_pos_widget('X',
                                                      xbackgroundColor,
                                                      xforegroundColor)
@@ -500,6 +511,11 @@ def createQuadViewStatusBar(self,
                                                      zbackgroundColor,
                                                      zforegroundColor)
 
+        #partial connection means:
+        #The partial object is created by definition of the connection, 
+        #not when the event is triggered. 
+        #That means: _handlePositionBoxValueChanged() is called when connecting, so that it will 
+        #always handle the contents that have changed in the viewer.
         self.xSpinBox.delayedValueChanged.connect( partial(self._handlePositionBoxValueChanged, 'x') )
         self.ySpinBox.delayedValueChanged.connect( partial(self._handlePositionBoxValueChanged, 'y') )
         self.zSpinBox.delayedValueChanged.connect( partial(self._handlePositionBoxValueChanged, 'z') )
@@ -640,6 +656,11 @@ def _onTimeSliderChanged(self):
                 self.timeSpinBox.setValue(self.timeSlider.value())
 
     def _handlePositionBoxValueChanged(self, axis, value):
+        """
+        Take the old values of the spinBoxes
+        and change the value of the given axis
+        Emit the signal with the new position
+        """
         new_position = [self.xSpinBox.value(), self.ySpinBox.value(), self.zSpinBox.value()]
         changed_axis = ord(axis) - ord('x')
         new_position[changed_axis] = value

volumina/widgets/.gitignore

@@ -0,0 +1 @@
+session.vim