rename variables and add test

Author: paulhfu

tests/quadStatusBar_test.py

@@ -0,0 +1,220 @@
+###############################################################################
+#   volumina: volume slicing and editing library
+#
+#       Copyright (C) 2011-2019, the ilastik developers
+#                                <[email protected]>
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the Lesser GNU General Public License
+# as published by the Free Software Foundation; either version 2.1
+# 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 Lesser General Public License for more details.
+#
+# See the files LICENSE.lgpl2 and LICENSE.lgpl3 for full text of the
+# GNU Lesser General Public License version 2.1 and 3 respectively.
+# This information is also available on the ilastik web site at:
+# 		   http://ilastik.org/license/
+###############################################################################
+import pytest
+from PyQt5.QtWidgets import QMainWindow
+from PyQt5.QtCore import QPointF, Qt
+from PyQt5.QtGui import QColor
+
+import numpy as np
+import vigra
+from ilastik.applets.layerViewer.layerViewerGui import LayerViewerGui
+from lazyflow.operators.opReorderAxes import OpReorderAxes
+from volumina.volumeEditor import VolumeEditor
+from volumina.volumeEditorWidget import VolumeEditorWidget
+from volumina.layerstack import LayerStackModel
+from volumina.pixelpipeline.datasources import LazyflowSource
+from volumina.layer import AlphaModulatedLayer
+from lazyflow.graph import Operator, InputSlot, OutputSlot, Graph
+
+
+class MainWindow(QMainWindow):
+    def __init__(self):
+        super().__init__()
+        self.volumeEditorWidget = VolumeEditorWidget(parent=self)
+
+
+class OpTestImgaeSlots(Operator):
+    """test operator, containing 3-dim test data"""
+
+    GrayscaleImageIn = InputSlot()
+    Label1ImageIn = InputSlot()
+    Label2ImageIn = InputSlot()
+
+    GrayscaleImageOut = OutputSlot()
+    Label1ImageOut = OutputSlot()
+    Label2ImageOut = OutputSlot()
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        width, height, depth = 300, 200, 40
+
+        # create 2-dimensional images
+        grayscaleImageSource = np.random.randint(0, 255, (depth, height, width, 1))
+        label1ImageSource = np.zeros((depth, height, width, 3), dtype=np.int32)
+        label2ImageSource = np.zeros((depth, height, width, 3), dtype=np.int32)
+
+        for z, set1 in enumerate(grayscaleImageSource[:, :, :, 0]):
+            for y, set2 in enumerate(set1):
+                for x, set3 in enumerate(set2):
+                    if z in range(5, 20) and y in range(20, 30) and x in range(80, 140):
+                        label1ImageSource[z, y, x, :] = [255, 255, 255]
+                    if z in range(25, 37) and y in range(100, 150) and x in range(10, 60):
+                        label2ImageSource[z, y, x, :] = [255, 255, 255]
+
+        self.GrayscaleImageIn.setValue(grayscaleImageSource, notify=False, check_changed=False)
+        self.Label1ImageIn.setValue(label1ImageSource, notify=False, check_changed=False)
+        self.Label2ImageIn.setValue(label2ImageSource, notify=False, check_changed=False)
+
+        self.GrayscaleImageIn.meta.axistags = vigra.defaultAxistags("tzyxc"[5 - len(self.GrayscaleImageIn.meta.shape):])
+        self.Label1ImageIn.meta.axistags = vigra.defaultAxistags("tzyxc"[5 - len(self.Label1ImageIn.meta.shape):])
+        self.Label2ImageIn.meta.axistags = vigra.defaultAxistags("tzyxc"[5 - len(self.Label2ImageIn.meta.shape):])
+
+        self.GrayscaleImageOut.connect(self.GrayscaleImageIn)
+        self.Label1ImageOut.connect(self.Label1ImageIn)
+        self.Label2ImageOut.connect(self.Label2ImageIn)
+
+
+class TestSpinBoxImageView(object):
+
+    def updateAllTiles(self, imageScenes):
+        for scene in imageScenes:
+            scene.joinRenderingAllTiles()
+
+    @pytest.fixture(autouse=True)
+    def setupClass(self, qtbot):
+
+        self.qtbot = qtbot
+        self.main = MainWindow()
+        self.layerStack = LayerStackModel()
+
+        g = Graph()
+        self.op = OpTestImgaeSlots(graph=g)
+
+        self.grayscaleLayer = LayerViewerGui._create_grayscale_layer_from_slot(self.op.GrayscaleImageOut, 1)
+        self.labelLayer1 = AlphaModulatedLayer(LazyflowSource(self.op.Label1ImageOut), tintColor=QColor(Qt.cyan),
+                                               range=(0, 255), normalize=(0, 255))
+        self.labelLayer2 = AlphaModulatedLayer(LazyflowSource(self.op.Label2ImageOut), tintColor=QColor(Qt.yellow),
+                                               range=(0, 255), normalize=(0, 255))
+
+        self.labelLayer1.name = "Segmentation (Label 1)"
+        self.labelLayer2.name = "Segmentation (Label 2)"
+
+        self.layerStack.append(self.grayscaleLayer)
+        self.layerStack.append(self.labelLayer1)
+        self.layerStack.append(self.labelLayer2)
+
+        activeOutSlot = self.op.GrayscaleImageOut  # take any out slot here
+        if activeOutSlot.ready() and activeOutSlot.meta.axistags is not None:
+            # Use an OpReorderAxes adapter to transpose the shape for us.
+            op5 = OpReorderAxes(graph=g)
+            op5.Input.connect(activeOutSlot)
+            op5.AxisOrder.setValue('txyzc')
+            shape = op5.Output.meta.shape
+
+            # We just needed the op to determine the transposed shape.
+            # Disconnect it so it can be garbage collected.
+            op5.Input.disconnect()
+            op5.cleanUp()
+
+        self.editor = VolumeEditor(self.layerStack, self.main)
+        self.editorWidget = self.main.volumeEditorWidget
+        self.editorWidget.init(self.editor)
+
+        self.editor.dataShape = shape
+
+        # Find the xyz midpoint
+        midpos5d = [x // 2 for x in shape]
+        # center viewer there
+        # set xyz position
+        midpos3d = midpos5d[1:4]
+        self.editor.posModel.slicingPos = midpos3d
+        self.editor.navCtrl.panSlicingViews(midpos3d, [0, 1, 2])
+        for i in range(3):
+            self.editor.navCtrl.changeSliceAbsolute(midpos3d[i], i)
+
+        self.main.setCentralWidget(self.editorWidget)
+        self.main.show()
+        self.qtbot.addWidget(self.main)
+
+    def testAddingAndRemovingPosVal(self):
+        assert 0 == len(self.editorWidget.quadViewStatusBar.layerValueWidgets)
+
+        for layer in self.layerStack:
+            if not layer.showPosValue:
+                layer.showPosValue = True
+            if not layer.visible:
+                layer.visible = True
+
+        for layer in self.layerStack:
+            assert layer in self.editorWidget.quadViewStatusBar.layerValueWidgets
+
+        self.layerStack[0].showPosValue = False
+        assert self.layerStack[0] not in self.editorWidget.quadViewStatusBar.layerValueWidgets
+        self.layerStack[2].showPosValue = False
+        assert self.layerStack[2] not in self.editorWidget.quadViewStatusBar.layerValueWidgets
+        self.layerStack[1].showPosValue = False
+        assert self.layerStack[1] not in self.editorWidget.quadViewStatusBar.layerValueWidgets
+        self.layerStack[2].showPosValue = True
+        assert self.layerStack[2] in self.editorWidget.quadViewStatusBar.layerValueWidgets
+
+    def testLayerPositionValueStrings(self):
+        for layer in self.layerStack:
+            if not layer.showPosValue:
+                layer.showPosValue = True
+            if not layer.visible:
+                layer.visible = True
+
+        x, y, z = 90, 25, 10
+
+        posVal = 255-int(self.op.GrayscaleImageIn.value[z, y, x, 0])
+        grayValidationStrings = ["Gray:" + str(posVal), "Gray:" + str(posVal+1), "Gray:" + str(posVal-1)]
+        label1ValidationString = "Label 1"
+        label2ValidationString = "Label 2"
+
+        signal = self.editor.posModel.cursorPositionChanged
+        with self.qtbot.waitSignal(signal, timeout=1000):
+            self.editor.navCtrl.changeSliceAbsolute(z, 2)
+
+        # After change of crosshair positions tiles are marked dirty.
+        self.updateAllTiles(self.editor.imageScenes)  # Wait for all tiles being refreshed
+
+        signals = [self.editorWidget.quadViewStatusBar.layerValueWidgets[self.grayscaleLayer].textChanged,
+                   self.editorWidget.quadViewStatusBar.layerValueWidgets[self.labelLayer1].textChanged]
+        with self.qtbot.waitSignals(signals, timeout=1000):
+            self.editor.navCtrl.positionDataCursor(QPointF(x, y), 2)
+
+        self.updateAllTiles(self.editor.imageScenes)  # Wait for all tiles being refreshed
+
+        assert self.editorWidget.quadViewStatusBar.layerValueWidgets[
+                   self.grayscaleLayer].text() in grayValidationStrings
+        assert self.editorWidget.quadViewStatusBar.layerValueWidgets[self.labelLayer1].text() == label1ValidationString
+
+        x, y, z = 39, 130, 30
+
+        posVal = 255-int(self.op.GrayscaleImageIn.value[z, y, x, 0])
+        grayValidationStrings = ["Gray:" + str(posVal), "Gray:" + str(posVal+1), "Gray:" + str(posVal-1)]
+
+        with self.qtbot.waitSignal(signal, timeout=1000):
+            self.editor.navCtrl.changeSliceAbsolute(y, 1)
+
+        self.updateAllTiles(self.editor.imageScenes)  # Wait for all tiles being refreshed
+
+        with self.qtbot.waitSignals(signals, timeout=1000):
+            self.editor.navCtrl.positionDataCursor(QPointF(x, z), 1)
+
+        self.updateAllTiles(self.editor.imageScenes)  # Wait for all tiles being refreshed
+
+        assert self.editorWidget.quadViewStatusBar.layerValueWidgets[
+                   self.grayscaleLayer].text() in grayValidationStrings
+        assert self.editorWidget.quadViewStatusBar.layerValueWidgets[self.labelLayer2].text() == label2ValidationString
+

volumina/layer.py

@@ -60,7 +60,7 @@ class Layer(QObject):
     somethingChanged signals is emitted."""
     changed = pyqtSignal()
 
-    showValueChanged = pyqtSignal(object, bool)
+    showPosValueChanged = pyqtSignal(object, bool)
     visibleChanged = pyqtSignal(bool)
     opacityChanged = pyqtSignal(float)
     nameChanged = pyqtSignal(object)  # sends a python str object, not unicode!
@@ -82,13 +82,13 @@ def visible(self, value):
             self.visibleChanged.emit(value)
 
     @property
-    def showValue(self):
-        return self._showValue
+    def showPosValue(self):
+        return self._showPosValue
 
-    @showValue.setter
-    def showValue(self, value):
-        self._showValue = value
-        self.showValueChanged.emit(self, value)
+    @showPosValue.setter
+    def showPosValue(self, value):
+        self._showPosValue = value
+        self.showPosValueChanged.emit(self, value)
 
     def toggleVisible(self):
         """Convenience function."""
@@ -175,17 +175,17 @@ def toolTip(self):
     def setToolTip(self, tip):
         self._toolTip = tip
 
-    def setValueWidget(self, value):
+    def getPosInfo(self, value):
         """
         This function needs to be overwritten by every layer.
-        This function is called by QuadStatusBar.setMouseCoords. It is expected to return a tuple of information for
-        the position widgets, showing current pixelvalues of respective layer.
+        It is called by QuadStatusBar.setLayerPosIfos and is expected to return a tuple of information for
+        the position widgets, showing current pixelvalues at cursor position of respective layer.
         :param val: layer value at current cursor position
         :return: ((String)text, (QColor)foregroundcolor, (QColor)backgroundcolor) for respective widget
         """
         if value is not None:
-            return self.name + str(value), QColor(255, 255, 255), QColor(0, 0, 0)
-        return None, QColor(255, 255, 255), QColor(0, 0, 0)
+            return self.name + str(value), QColor(0, 0, 0), QColor(255, 255, 255)
+        return None, QColor(0, 0, 0), QColor(255, 255, 255)
 
     def isDifferentEnough(self, other_layer):
         """This ugly function is here to support the updateAllLayers function in the layerViewerGui in ilastik"""
@@ -201,7 +201,7 @@ def __init__(self, datasources, direct=False):
         super(Layer, self).__init__()
         self._name = u"Unnamed Layer"
         self._visible = True
-        self._showValue = False
+        self._showPosValue = False
         self._opacity = 1.0
         self._datasources = datasources
         self._layerId = None
@@ -429,10 +429,16 @@ def isDifferentEnough(self, other_layer):
             return True
         return self._window_leveling != other_layer._window_leveling
 
-    def setValueWidget(self, value):
+    def getPosInfo(self, value):
+        """overwrites Layer.getPosInfo"""
         if value is not None:
-            return 'Gray:' + str(value.black()), QColor(value.black(), value.black(), value.black()), value
-        return None, QColor(255, 255, 255), QColor(0, 0, 0)
+            gray_val = 255
+            if value.value() in range(int(gray_val/2-10), int(gray_val/2+10)):
+                gray_val = value.black() + 20 * numpy.sign(value.black() - value.value())
+            else:
+                gray_val = value.black()
+            return 'Gray:' + str(value.black()), QColor(gray_val, gray_val, gray_val), value
+        return None, QColor(0, 0, 0), QColor(255, 255, 255)
 
     def __init__(self, datasource, range=None, normalize=None, direct=False, window_leveling=False):
         assert isinstance(datasource, SourceABC)
@@ -458,15 +464,16 @@ def tintColor(self, c):
             self._tintColor = c
             self.tintColorChanged.emit()
 
-    def setValueWidget(self, value):
+    def getPosInfo(self, value):
+        """overwrites Layer.getPosInfo"""
         if value is None:
-            return None, QColor(255, 255, 255), QColor(0, 0, 0)
+            return None, QColor(0, 0, 0), QColor(255, 255, 255)
         elif "Segmentation (Label " in self.name:
             if value.getRgb() == (0,0,0,0):
-                return None, QColor(255, 255, 255), QColor(0, 0, 0)
+                return None, QColor(0, 0, 0), QColor(255, 255, 255)
             return self.name[self.name.find("(") + 1:self.name.find(")")], QColor(255, 255, 255), self.tintColor
         else:
-            return self.name + str(value.getRgb()), QColor(255, 255, 255), QColor(0, 0, 0)
+            return self.name + str(value.getRgb()), QColor(0, 0, 0), QColor(255, 255, 255)
 
     def __init__(self, datasource, tintColor=QColor(255, 0, 0), range=(0, 255), normalize=None):
         assert isinstance(datasource, SourceABC)

volumina/patchAccessor.py

@@ -94,36 +94,28 @@ def patchRectF(self, blockNum, overlap=0):
         return QRectF(QPointF(startx, starty), QPointF(endx, endy))
 
     def getPatchesForRect(self, startx, starty, endx, endy):
-        """returns patchnumbers for patches that are intersecting with the normalized rectangle defined by upper left
-        corner (staŕtx/y) and lower right corner (endx/y)
         """
-        if endy < 0 or endx < 0:
-            # allowing no inverted start/end -positions, there should be no negative end-positions
-            return []
+        Looks up patches for specified block
+        x in [startx, endx)
+        y in [starty, endy)
+        :returns: list of patch ids
+        """
+        assert startx < endx
+        assert starty < endy
+
         sx = int(numpy.floor(1.0 * startx / self._blockSize))
         ex = int(numpy.ceil(1.0 * endx / self._blockSize))
         sy = int(numpy.floor(1.0 * starty / self._blockSize))
         ey = int(numpy.ceil(1.0 * endy / self._blockSize))
 
-        # Clip to rect to upper bounds
+        # Clip to rect bounds
+        sx = max(sx, 0)
+        sy = max(sy, 0)
         ex = min(ex, self._cX)
         ey = min(ey, self._cY)
 
-        # return an index also, when start and end are equal
-        if sx == ex:
-            if ex >= self._cX:
-                sx = sx - 1
-            else:
-                ex = ex + 1
-        if sy == ey:
-            if ey >= self._cY:
-                sy = sy - 1
-            else:
-                ey = ey + 1
-
-        # Clip to rect to lower bounds
-        sx = max(sx, 0)
-        sy = max(sy, 0)
+        sx = max(min(sx, ex - 1), 0)
+        sy = max(min(sy, ey - 1), 0)
 
         nums = []
         for y in range(sy, ey):

volumina/quadsplitter.py

@@ -270,8 +270,8 @@ def addStatusBar(self, bar):
     def setGrayScaleToQuadStatusBar(self, gray):
         self.quadViewStatusBar.setGrayScale(gray)
 
-    def setMouseCoordsToQuadStatusBar(self, x, y, z):
-        self.quadViewStatusBar.setMouseCoords(x, y, z)
+    def setLayerPosIfosToQuadStatusBar(self, x, y, z):
+        self.quadViewStatusBar.setMousePosInfos(x, y, z)
 
     def ensureMaximized(self, axis):
         """