Display slice by slice

Wrappers/Python/ccpi/viewer/CILViewer2D.py

@@ -245,7 +245,10 @@ def InitialiseBox(self, clickPosition):
     def OnMouseWheelForward(self, interactor, event):
         if self.GetInputData() is None:
             return
-        maxSlice = self.GetInputData().GetExtent()[self.GetSliceOrientation() * 2 + 1]
+        if self._viewer._reader is None:
+            maxSlice = self.GetInputData().GetExtent()[self.GetSliceOrientation() * 2 + 1]
+        else:
+            maxSlice = self._viewer._reader.GetWholeExtent()[self.GetSliceOrientation() * 2 + 1]
         shift = interactor.GetShiftKey()
         advance = 1
         if shift:
@@ -265,6 +268,10 @@ def OnMouseWheelBackward(self, interactor, event):
         if self.GetInputData() is None:
             return
         minSlice = self.GetInputData().GetExtent()[self.GetSliceOrientation() * 2]
+        if self._viewer._reader is None:
+            minSlice = self.GetInputData().GetExtent()[self.GetSliceOrientation() * 2]
+        else:
+            minSlice = self._viewer._reader.GetWholeExtent()[self.GetSliceOrientation() * 2]
         shift = interactor.GetShiftKey()
         advance = 1
         if shift:
@@ -1140,6 +1147,9 @@ def __init__(self, dimx=600, dimy=600, ren=None, renWin=None, iren=None, debug=T
         self.imageTracer.AutoCloseOn()
         self.imageTracer.AddObserver(vtk.vtkWidgetEvent.Select, self.style.OnTracerModifiedEvent, 1.0)
 
+        # input reader
+        self._reader = None
+
         self.__vis_mode = CILViewer2D.IMAGE_WITH_OVERLAY
         self.setVisualisationToImageWithOverlay()
 
@@ -1153,10 +1163,23 @@ def setInput3DData(self, imageData):
 
     def setInputData(self, imageData):
         self.log("setInputData")
-        self.img3D = imageData
+        self._img3D = imageData
+        self.installPipeline()
+        self.axes_initialised = True
+
+    def setInputDataReader(self, reader):
+        self._reader = reader
         self.installPipeline()
         self.axes_initialised = True
 
+    @property
+    def img3D(self):
+        if self._reader is None:
+            return self._img3D
+        else:
+            self._reader.Update()
+            return self._reader.GetOutput()
+
     def setInputData2(self, imageData):
         self.image2 = imageData
         # TODO resample on image1
@@ -1196,9 +1219,9 @@ def setInputAsNumpy(self,
             shiftScaler.SetShift(-iMin)
             shiftScaler.SetOutputScalarType(dtype)
             shiftScaler.Update()
-            self.img3D = shiftScaler.GetOutput()
+            self._img3D = shiftScaler.GetOutput()
         else:
-            self.img3D = importer.GetOutput()
+            self._img3D = importer.GetOutput()
 
         self.installPipeline()
 
@@ -1228,6 +1251,9 @@ def updateMainVOI(self):
         extent = [i for i in self.img3D.GetExtent()]
         extent[self.sliceOrientation * 2] = self.getActiveSlice()
         extent[self.sliceOrientation * 2 + 1] = self.getActiveSlice()
+        if self._reader is not None:
+            self._reader.SetTargetZExtent((extent[4], extent[5]))
+            self._reader.Update()
         self.voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4], extent[5])
         self.log("extent {0}".format(extent))
         self.voi.Update()
@@ -1352,8 +1378,6 @@ def installImageWithOverlayPipeline(self):
 
         self.voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4], extent[5])
 
-        self.voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4], extent[5])
-
         self.voi.Update()
 
         # set window/level for slice based on values in entire volume:

Wrappers/Python/ccpi/viewer/utils/conversion.py

@@ -22,7 +22,7 @@
 import os
 import math
 import numpy
-import vtk
+import vtkmodules.all as vtk
 from vtk.util.vtkAlgorithm import VTKPythonAlgorithmBase
 from vtk.util import numpy_support
 
@@ -1421,6 +1421,21 @@ def GetTargetZExtent(self):
         Get the target extent to crop to on the z axis.
         '''
         return self._TargetZExtent
+
+    def GetShape(self):
+        readshape = self.GetStoredArrayShape()
+        is_fortran = self.GetIsFortran()
+
+        if is_fortran:
+            shape = list(readshape)
+        else:
+            shape = list(readshape)[::-1]
+        return shape
+
+    def GetWholeExtent(self):
+        shape = self.GetShape()
+        extent = (0, shape[0] - 1, 0, shape[1] - 1, 0, shape[2] - 1)
+        return extent
 
     def RequestData(self, request, inInfo, outInfo):
         outData = vtk.vtkImageData.GetData(outInfo)
@@ -1429,14 +1444,8 @@ def RequestData(self, request, inInfo, outInfo):
 
         # get basic info
         big_endian = self.GetBigEndian()
-        readshape = self.GetStoredArrayShape()
         file_header_length = self.GetFileHeaderLength()
-        is_fortran = self.GetIsFortran()
-
-        if is_fortran:
-            shape = list(readshape)
-        else:
-            shape = list(readshape)[::-1]
+        shape = self.GetShape()
 
         tmpdir = tempfile.mkdtemp()
         header_filename = os.path.join(tmpdir, "header.mhd")

Wrappers/Python/examples/display_full_slice.py

@@ -0,0 +1,26 @@
+from ccpi.viewer import viewer2D
+from ccpi.viewer.utils.conversion import cilTIFFCroppedReader, cilNumpyCroppedReader
+import os, glob
+
+
+data_dir = os.path.abspath('C:/Users/ofn77899/Data/dvc/')
+
+ftype = 'tiff'
+
+if ftype == 'npy':
+    fname = os.path.abspath('C:/Users/ofn77899/Data/dvc/frame_000_f.npy')
+    reader = cilNumpyCroppedReader()
+    reader.SetFileName(fname)
+elif ftype == 'tiff':
+    reader = cilTIFFCroppedReader()
+    data_dir = os.path.abspath('C:/Users/ofn77899/Data/dvc/frame_000')
+    fnames = glob.glob(os.path.join(data_dir, '*.tiff'))
+    reader.SetFileName(fnames)
+
+
+v = viewer2D()
+
+v.setInputDataReader(reader)
+
+v.startRenderLoop()
+