Saving inv3

tfmoraes
1 parent ce061625
Showing 8 changed files with 126 additions and 64 deletions Show diff stats
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/data/mask.py
invesalius/data/slice_.py
invesalius/data/viewer_slice.py
invesalius/gui/task_slice.py
invesalius/gui/widgets/gradient.py
invesalius/project.py
@@ -236,6 +236,13 @@ class Controller():
         proj = prj.Project()
         proj.OpenPlistProject(path)
         proj.SetAcquisitionModality(proj.modality)
+        self.Slice = sl.Slice()
+        self.Slice._open_image_matrix(proj.matrix_filename,
+                                      tuple(proj.matrix_shape),
+                                      proj.matrix_dtype)
+
+        self.Slice.window_level = proj.level
+        self.Slice.window_width = proj.window
         mask = msk.Mask()
         mask._set_class_index(proj.last_mask_index)
@@ -246,6 +253,8 @@ class Controller():
         self.LoadProject()
+        ps.Publisher().sendMessage('Update threshold limits',
+                                   proj.threshold_range)
         session = ses.Session()
         session.OpenProject(filepath)
         ps.Publisher().sendMessage("Enable state project", True)
@@ -329,8 +338,8 @@ class Controller():
         patients_groups = dcm.GetDicomGroups(directory)
         if len(patients_groups):
             group = dcm.SelectLargerDicomGroup(patients_groups)
-            imagedata, dicom = self.OpenDicomGroup(group, 0, [0,0],gui=True)
-            self.CreateDicomProject(imagedata, dicom)
+            matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0,0],gui=True)
+            self.CreateDicomProject(dicom, matrix, matrix_filename)
         # OPTION 2: ANALYZE?
         else:
             imagedata = analyze.ReadDirectory(directory)
@@ -352,6 +361,9 @@ class Controller():
         const.WINDOW_LEVEL[_('Default')] = (proj.window, proj.level)
         const.WINDOW_LEVEL[_('Manual')] = (proj.window, proj.level)
+        self.Slice = sl.Slice()
+        self.Slice.spacing = proj.spacing
+
         ps.Publisher().sendMessage('Load slice to viewer',
                         (proj.imagedata,
                         proj.mask_dict))
@@ -375,6 +387,11 @@ class Controller():
         if len(proj.mask_dict):
             mask_index = len(proj.mask_dict) -1
+            for m in proj.mask_dict.values():
+                ps.Publisher().sendMessage('Add mask',
+                                           (m.index, m.name,
+                                            m.threshold_range, m.colour))
+            self.Slice.current_mask = proj.mask_dict[mask_index]
             ps.Publisher().sendMessage('Show mask', (mask_index, True))
         ps.Publisher().sendMessage('Load measurement dict',
@@ -419,7 +436,7 @@ class Controller():
         ps.Publisher().sendMessage('Update threshold limits',
                                    proj.threshold_range)
-    def CreateDicomProject(self, imagedata, dicom):
+    def CreateDicomProject(self, dicom, matrix, matrix_filename):
         name_to_const = {"AXIAL":const.AXIAL,
                          "CORONAL":const.CORONAL,
                          "SAGITTAL":const.SAGITAL}
@@ -428,14 +445,17 @@ class Controller():
         proj.name = dicom.patient.name
         proj.modality = dicom.acquisition.modality
         proj.SetAcquisitionModality(dicom.acquisition.modality)
-        proj.imagedata = imagedata
+        proj.matrix_shape = matrix.shape
+        proj.matrix_dtype = matrix.dtype.name
+        proj.matrix_filename = matrix_filename
+        #proj.imagedata = imagedata
         proj.dicom_sample = dicom
         proj.original_orientation =\
                     name_to_const[dicom.image.orientation_label]
         proj.window = float(dicom.image.window)
         proj.level = float(dicom.image.level)
         proj.threshold_range = (-1024, 3033)
-
+        proj.spacing = self.Slice.spacing
         ######
         session = ses.Session()
@@ -448,8 +468,8 @@ class Controller():
     def OnOpenDicomGroup(self, pubsub_evt):
         group, interval, file_range = pubsub_evt.data
-        imagedata, dicom = self.OpenDicomGroup(group, interval, file_range, gui=True)
-        self.CreateDicomProject(imagedata, dicom)
+        matrix, matrix_filename, dicom = self.OpenDicomGroup(group, interval, file_range, gui=True)
+        self.CreateDicomProject(dicom, matrix, matrix_filename)
         self.LoadProject()
         ps.Publisher().sendMessage("Enable state project", True)
@@ -511,12 +531,13 @@ class Controller():
         elif orientation == 'SAGITTAL':
             self.Slice.spacing = zspacing, xyspacing[1], xyspacing[0]
+
         self.Slice.window_level = wl
         self.Slice.window_width = ww
         ps.Publisher().sendMessage('Update threshold limits', scalar_range)
-        return imagedata, dicom
+        return self.matrix, self.filename, dicom
     def LoadImagedataInfo(self):
         proj = prj.Project()
@@ -215,8 +215,8 @@ def Export(imagedata, filename, bin=False):
         writer.SetDataModeToBinary()
     else:
         writer.SetDataModeToAscii()
-    writer.SetInput(imagedata)
-    writer.Write()
+    #writer.SetInput(imagedata)
+    #writer.Write()
 def Import(filename):
     reader = vtk.vtkXMLImageDataReader()
@@ -497,6 +497,7 @@ def dcm2memmap(files, slice_size, orientation):
             array.shape = matrix.shape[0], matrix.shape[1]
             matrix[:, :, n] = array
         else:
+            print array.shape, matrix.shape
             array.shape = matrix.shape[1], matrix.shape[2]
             matrix[n] = array
         update_progress(cont,message)
@@ -20,6 +20,7 @@
 import os
 import plistlib
 import random
+import shutil
 import tempfile
 import numpy
@@ -44,42 +45,46 @@ class Mask():
     def SavePlist(self, filename):
         mask = {}
-        filename = '%s$%s$%d' % (filename, 'mask', self.index)
-        
-        d = self.__dict__
-        for key in d:
-            if isinstance(d[key], vtk.vtkImageData):
-                img_name = '%s_%s.vti' % (filename, key)
-                iu.Export(d[key], img_name, bin=True)
-                mask[key] = {'$vti': os.path.split(img_name)[1]}
-            elif key == 'edited_points':
-                edited_points = {}
-                for p in self.edited_points:
-                    edited_points[str(p)] = self.edited_points[p]
-                mask[key] = edited_points
-            else:
-                mask[key] = d[key]
+        filename = u'%s_%s_%d_%s' % (filename, 'mask', self.index, self.name)
+        img_name = u'%s.dat' % filename
+        self._save_mask(img_name)
+
+        mask['index'] = self.index
+        mask['colour'] = self.colour
+        mask['opacity'] = self.opacity
+        mask['threshold range'] = self.threshold_range
+        mask['name'] = self.name
+        mask['edition threshold range'] = self.edition_threshold_range
+        mask['show'] = self.is_shown
+        mask['mask file'] = os.path.split(img_name)[1]
+        mask['mask shape'] = self.matrix.shape
+
         plistlib.writePlist(mask, filename + '.plist')
         return os.path.split(filename)[1] + '.plist'
     def OpenPList(self, filename):
         mask = plistlib.readPlist(filename)
+
+        self.index = mask['index']
+        self.colour = mask['colour']
+        self.opacity = mask['opacity']
+        self.threshold_range = mask['threshold range']
+        self.name = mask['name']
+        self.edition_threshold_range = mask['edition threshold range']
+        self.is_shown = mask['show']
+        mask_file = mask['mask file']
+        shape = mask['mask shape']
         dirpath = os.path.abspath(os.path.split(filename)[0])
-        for key in mask:
-            print "Key", key
-            if key == 'imagedata':
-                filepath = os.path.split(mask[key]["$vti"])[-1]
-                path = os.path.join(dirpath, filepath)
-                self.imagedata = iu.Import(path)
-            elif key == 'edited_points':
-                edited_points = {}
-                for p in mask[key]:
-                    k = [float(i) for i in p.replace('(', '').replace(')', '').split(',')]
-                    edited_points[tuple(k)] = mask[key][p]
-                    
-                setattr(self, key, edited_points)
-            else:
-                setattr(self, key, mask[key])
+        path = os.path.join(dirpath, mask_file)
+        self._open_mask(path, tuple(shape))
+
+    def _save_mask(self, filename):
+        shutil.copyfile(self.temp_file, filename)
+
+    def _open_mask(self, filename, shape, dtype='uint8'):
+        print ">>", filename, shape
+        self.temp_file = filename
+        self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype, mode="r+")
     def _set_class_index(self, index):
         Mask.general_index = index
@@ -75,6 +75,7 @@ class Slice(object):
         self.current_mask = None
         self.blend_filter = None
         self.matrix = None
+        self.spacing = (1.0, 1.0, 1.0)
         self.number_of_colours = 256
         self.saturation_range = (0, 0)
@@ -542,6 +543,7 @@ class Slice(object):
     def ShowMask(self, index, value):
         "Show a mask given its index and 'show' value (0: hide, other: show)"
+        print "Showing Mask"
         proj = Project()
         proj.mask_dict[index].is_shown = value
         if (index == self.current_mask.index):
@@ -946,6 +948,12 @@ class Slice(object):
         return imagedata_mask
+    def _open_image_matrix(self, filename, shape, dtype):
+        self.matrix_filename = filename
+        print ">>>", filename
+        self.matrix = numpy.memmap(filename, shape=shape, dtype=dtype,
+                                   mode='r+')
+
     def OnExportMask(self, pubsub_evt):
         #imagedata = self.current_mask.imagedata
         imagedata = self.imagedata
@@ -1172,7 +1172,7 @@ class Viewer(wx.Panel):
                                  max_slice_number)
         self.slice_data = self.create_slice_window()
-        self.slice_data.actor.SetInput(imagedata)
+        #self.slice_data.actor.SetInput(imagedata)
         self.slice_data.SetCursor(self.__create_cursor())
         self.cam = self.slice_data.renderer.GetActiveCamera()
         self.__build_cross_lines(imagedata)
@@ -479,6 +479,7 @@ class MaskProperties(wx.Panel):
         (thresh_min, thresh_max) = Project().threshold_modes[evt.GetString()]
         self.gradient.SetMinValue(thresh_min)
         self.gradient.SetMaxValue(thresh_max)
+        self.OnSlideChanging(None)
         self.OnSlideChanged(None)
     def OnSlideChanged(self, evt):
@@ -320,6 +320,7 @@ class GradientCtrl(wx.Panel):
         self.minimun = minValue
         self.maximun = maxValue
         self.colour = colour
+        self.changed = False
         self._draw_controls()
         self._bind_events_wx()
         self.SetBackgroundColour((0, 255, 0))
@@ -353,13 +354,15 @@ class GradientCtrl(wx.Panel):
         self.gradient_slider.Bind(EVT_SLIDER_CHANGED, self.OnSlider)
         # self.spin_min.Bind(wx.lib.intctrl.EVT_INT, self.ChangeMinValue)
-        self.spin_min.Bind(wx.EVT_KILL_FOCUS, self._FireSpinMinChange)
-        self.spin_min.Bind(wx.EVT_TEXT_ENTER, self._FireSpinMinChange)
+        self.spin_min.Bind(wx.EVT_LEAVE_WINDOW, self._FireSpinMinChanged)
+        self.spin_min.Bind(wx.EVT_KILL_FOCUS, self._FireSpinMinChanged)
+        self.spin_min.Bind(wx.EVT_KEY_DOWN, self._FireSpinMinChange)
         self.spin_min.Bind(wx.EVT_MOUSEWHEEL, self.OnMinMouseWheel)
         # self.spin_max.Bind(wx.lib.intctrl.EVT_INT, self.ChangeMaxValue)
-        self.spin_max.Bind(wx.EVT_KILL_FOCUS, self._FireSpinMaxChange)
-        self.spin_max.Bind(wx.EVT_TEXT_ENTER, self._FireSpinMaxChange)
+        self.spin_max.Bind(wx.EVT_LEAVE_WINDOW, self._FireSpinMaxChanged)
+        self.spin_max.Bind(wx.EVT_KILL_FOCUS, self._FireSpinMaxChanged)
+        self.spin_max.Bind(wx.EVT_KEY_DOWN, self._FireSpinMaxChange)
         self.spin_max.Bind(wx.EVT_MOUSEWHEEL, self.OnMaxMouseWheel)
     def OnSlider(self, evt):
@@ -377,17 +380,27 @@ class GradientCtrl(wx.Panel):
         self._GenerateEvent(myEVT_THRESHOLD_CHANGING)
     def _FireSpinMinChange(self, evt):
+        evt.Skip()
         value = int(self.spin_min.GetValue())
         if value != self.GetMinValue():
             self.SetMinValue(value)
             self._GenerateEvent(myEVT_THRESHOLD_CHANGING)
+    def _FireSpinMinChanged(self, evt):
+        if self.changed:
+            self._GenerateEvent(myEVT_THRESHOLD_CHANGED)
+
     def _FireSpinMaxChange(self, evt):
+        evt.Skip()
         value = int(self.spin_max.GetValue())
         if value != self.GetMaxValue():
             self.SetMaxValue(value)
             self._GenerateEvent(myEVT_THRESHOLD_CHANGING)
+    def _FireSpinMaxChanged(self, evt):
+        if self.changed:
+            self._GenerateEvent(myEVT_THRESHOLD_CHANGED)
+
     def OnMinMouseWheel(self, e):
         """ 
         When the user wheel the mouse over min texbox
@@ -464,6 +477,13 @@ class GradientCtrl(wx.Panel):
         return self.minimun
     def _GenerateEvent(self, event):
+        if event == myEVT_THRESHOLD_CHANGING:
+            self.changed = True
+            print 'changing'
+        elif event == myEVT_THRESHOLD_CHANGED :
+            self.changed = False
+            print 'changed'
+
         evt = SliderEvent(event, self.GetId(), self.min_range,
                           self.max_range, self.minimun, self.maximun)
         self.GetEventHandler().ProcessEvent(evt)
@@ -211,7 +211,7 @@ class Project(object):
         # that we encode in utf-8.
         filename = filename.encode('utf-8')
         dir_temp = tempfile.mkdtemp(filename)
-        filename_tmp = os.path.join(dir_temp, filename)
+        filename_tmp = os.path.join(dir_temp, 'matrix.dat')
         project = {}
@@ -220,18 +220,21 @@ class Project(object):
                 project[key] = {'#plist':
                                 self.__dict__[key].SavePlist(filename_tmp).decode('utf-8')}
             elif key == 'dicom_sample':
-                sample_path = os.path.join(dir_temp, 'sample.dcm')
-                shutil.copy(self.dicom_sample.parser.filename,sample_path)
-                os.chmod(sample_path, stat.S_IREAD|stat.S_IWRITE)
+                #sample_path = os.path.join(dir_temp, 'sample.dcm')
+                #shutil.copy(self.dicom_sample.parser.filename,sample_path)
+                #os.chmod(sample_path, stat.S_IREAD|stat.S_IWRITE)
-                project[key] = 'sample.dcm'
+                #project[key] = 'sample.dcm'
+                pass
+            elif key.startswith('matrix'):
+                continue
             else:
                 project[key] = self.__dict__[key]
         masks = {}
         for index in self.mask_dict:
             masks[str(index)] = {'#mask':\
-                                 self.mask_dict[index].SavePlist(filename_tmp).decode('utf-8')}
+                                 self.mask_dict[index].SavePlist(filename_tmp)}
         surfaces = {}
         for index in self.surface_dict:
@@ -241,9 +244,10 @@ class Project(object):
         project['surface_dict'] = surfaces
         project['mask_dict'] = masks
         project['measurement_dict'] = self.GetMeasuresDict()
-        img_file = '%s_%s.vti' % (filename_tmp, 'imagedata')
-        iu.Export(self.imagedata, img_file, bin=True)
-        project['imagedata'] = {'$vti':os.path.split(img_file)[1].decode('utf-8')}
+        shutil.copyfile(self.matrix_filename, filename_tmp)
+        project['matrix'] = {'filename':os.path.split(filename_tmp)[1].decode('utf-8'),
+                             'shape': self.matrix_shape,
+                             'dtype': self.matrix_dtype}
         plistlib.writePlist(project, filename_tmp + '.plist')
@@ -268,23 +272,25 @@ class Project(object):
         dirpath = os.path.abspath(os.path.split(filelist[0])[0])
         for key in project:
-            if key == 'imagedata':
-                filepath = os.path.split(project[key]["$vti"])[-1]
+            if key == 'matrix':
+                filepath = os.path.split(project[key]["filename"])[-1]
                 path = os.path.join(dirpath, filepath)
-                self.imagedata = iu.Import(path)
+                self.matrix_filename = path
+                self.matrix_shape = project[key]['shape']
+                self.matrix_dtype = project[key]['dtype']
             elif key == 'presets':
                 filepath = os.path.split(project[key]["#plist"])[-1]
                 path = os.path.join(dirpath, filepath)
                 p = Presets()
                 p.OpenPlist(path)
                 self.presets = p
-            elif key == 'dicom_sample':
-                path = os.path.join(dirpath, project[key])
-                p = dicom.Parser()
-                p.SetFileName(path)
-                d = dicom.Dicom()
-                d.SetParser(p)
-                self.dicom_sample = d
+            #elif key == 'dicom_sample':
+                #path = os.path.join(dirpath, project[key])
+                #p = dicom.Parser()
+                #p.SetFileName(path)
+                #d = dicom.Dicom()
+                #d.SetParser(p)
+                #self.dicom_sample = d
             elif key == 'mask_dict':
                 self.mask_dict = {}
	@@ -1172,7 +1172,7 @@ class Viewer(wx.Panel):		@@ -1172,7 +1172,7 @@ class Viewer(wx.Panel):
1172	max_slice_number)	1172	max_slice_number)
1173		1173
1174	self.slice_data = self.create_slice_window()	1174	self.slice_data = self.create_slice_window()
1175	- self.slice_data.actor.SetInput(imagedata)	1175	+ #self.slice_data.actor.SetInput(imagedata)
1176	self.slice_data.SetCursor(self.__create_cursor())	1176	self.slice_data.SetCursor(self.__create_cursor())
1177	self.cam = self.slice_data.renderer.GetActiveCamera()	1177	self.cam = self.slice_data.renderer.GetActiveCamera()
1178	self.__build_cross_lines(imagedata)	1178	self.__build_cross_lines(imagedata)
	@@ -479,6 +479,7 @@ class MaskProperties(wx.Panel):		@@ -479,6 +479,7 @@ class MaskProperties(wx.Panel):
479	(thresh_min, thresh_max) = Project().threshold_modes[evt.GetString()]	479	(thresh_min, thresh_max) = Project().threshold_modes[evt.GetString()]
480	self.gradient.SetMinValue(thresh_min)	480	self.gradient.SetMinValue(thresh_min)
481	self.gradient.SetMaxValue(thresh_max)	481	self.gradient.SetMaxValue(thresh_max)
		482	+ self.OnSlideChanging(None)
482	self.OnSlideChanged(None)	483	self.OnSlideChanged(None)
483		484
484	def OnSlideChanged(self, evt):	485	def OnSlideChanged(self, evt):