ENH: Optimized memory in DICOM importation window

Paulo Henrique Junqueira Amorim
1 parent 2c2993a8
Showing 3 changed files with 57 additions and 28 deletions Show diff stats
invesalius/gui/dicom_preview_panel.py
invesalius/reader/dicom.py
invesalius/reader/dicom_reader.py
@@ -22,6 +22,7 @@
  
 #TODO: To create a beautiful API
 import time
+import tempfile
  
 import wx
 import vtk
@@ -34,6 +35,8 @@ from reader import dicom_reader
 import data.vtk_utils as vtku
 import utils
 import vtkgdcm
+
+
 NROWS = 3
 NCOLS = 6
 NUM_PREVIEWS = NCOLS*NROWS
@@ -102,31 +105,18 @@ class DicomInfo(object):
         self.subtitle = subtitle
         self._preview = None
         self.selected = False
+        self.filename = ""
  
     @property
     def preview(self):
-        rdicom = vtkgdcm.vtkGDCMImageReader()
-        if self._preview:
-            return self._preview
-        else:
-            rdicom.SetFileName(self.dicom.image.file)
-            rdicom.Update()
-
-            colorer = vtk.vtkImageMapToWindowLevelColors()
-            colorer.SetInput(rdicom.GetOutput())
-            colorer.SetWindow(float(self.dicom.image.window))
-            colorer.SetLevel(float(self.dicom.image.level))
-            colorer.SetOutputFormatToRGB()
-            colorer.Update()
-
-            width, height, z = colorer.GetOutput().GetDimensions()
-
-            r = colorer.GetOutput().GetPointData().GetScalars()
-            ni = numpy_support.vtk_to_numpy(r)
-            self.img = wx.ImageFromBuffer(width, height, ni)
-            self._preview = self.img.Mirror(False)
-            return self._preview
-
+        
+        if not self._preview:
+            bmp = wx.Bitmap(self.dicom.image.thumbnail_path, wx.BITMAP_TYPE_PNG)
+            self._preview = bmp.ConvertToImage()
+        return self._preview
+        
+    def release_thumbnail(self):
+        self._preview = None
  
 class DicomPaintPanel(wx.Panel):
     def __init__(self, parent):
@@ -238,6 +228,9 @@ class Preview(wx.Panel):
         """
         Set a dicom to preview.
         """
+        if self.dicom_info:
+            self.dicom_info.release_thumbnail()
+
         self.dicom_info = dicom_info
         self.SetTitle(dicom_info.title)
         self.SetSubtitle(dicom_info.subtitle)
@@ -409,7 +402,6 @@ class DicomPreviewSeries(wx.Panel):
     def _display_previews(self):
         initial = self.displayed_position * NCOLS
         final = initial + NUM_PREVIEWS
-
         if len(self.files) < final:
             for i in xrange(final-len(self.files)):
                 try:
@@ -557,7 +549,6 @@ class DicomPreviewSlice(wx.Panel):
     def _display_previews(self):
         initial = self.displayed_position * NCOLS
         final = initial + NUM_PREVIEWS
-
         if len(self.files) < final:
             for i in xrange(final-len(self.files)):
                 try:
@@ -139,9 +139,10 @@ class Parser():
     #    return None#self.vtkgdcm_reader.GetOutput()
  
  
-    def SetDataImage(self, data_image, filename):
+    def SetDataImage(self, data_image, filename, thumbnail_path):
         self.data_image = data_image
         self.filename = self.filepath = filename    
+        self.thumbnail_path = thumbnail_path
  
     def __format_time(self,value):
         sp1 = value.split(".")
@@ -1931,6 +1932,7 @@ class Image(object):
         self.size = (parser.GetDimensionX(), parser.GetDimensionY())
         #self.imagedata = parser.GetImageData()
         self.bits_allocad = parser._GetBitsAllocated()
+        self.thumbnail_path = parser.thumbnail_path
  
         if (parser.GetImageThickness()):
             try:
@@ -19,10 +19,12 @@
 import os
 import Queue
 import threading
+import tempfile
  
 from multiprocessing import cpu_count
  
 import vtk
+import vtkgdcm
 import gdcm
 import wx.lib.pubsub as ps
  
@@ -106,9 +108,8 @@ class LoadDicom(threading.Thread):
             reader.SetFileName(str(filepath))
  
             if (reader.Read()):
-                
                 file = reader.GetFile()
-            
+                 
                 # Retrieve data set
                 dataSet = file.GetDataSet()
  
@@ -173,6 +174,41 @@ class LoadDicom(threading.Thread):
                         data_dict[group][field] = "Invalid Character"
  
  
+
+                # -------------- To Create DICOM Thumbnail -----------
+                rvtk = vtkgdcm.vtkGDCMImageReader()
+                rvtk.SetFileName(str(filepath))
+                rvtk.Update()
+                
+                try:
+                    data = data_dict['0028']['1050']
+                    level = [float(value) for value in data.split('\\')][0]
+                    data = data_dict['0028']['1051']
+                    window =  [float(value) for value in data.split('\\')][0]
+                except(KeyError):
+                    level = 300.0
+                    window = 2000.0 
+         
+                colorer = vtk.vtkImageMapToWindowLevelColors()
+                colorer.SetInput(rvtk.GetOutput())
+                colorer.SetWindow(float(window))
+                colorer.SetLevel(float(level))
+                colorer.SetOutputFormatToRGB()
+                colorer.Update()           
+                
+                resample = vtk.vtkImageResample()
+                resample.SetInput(colorer.GetOutput())
+                resample.SetAxisMagnificationFactor ( 0, 0.25 )
+                resample.SetAxisMagnificationFactor ( 1, 0.25 )
+                resample.SetAxisMagnificationFactor ( 2, 1 )    
+                resample.Update()
+ 
+                thumbnail_path = tempfile.mktemp()
+
+                write_png = vtk.vtkPNGWriter()
+                write_png.SetInput(resample.GetOutput())
+                write_png.SetFileName(thumbnail_path)
+                write_png.Write()
  
                 # ----------   Refactory --------------------------------------
                 data_dict['invesalius'] = {'orientation_label' : GetImageOrientationLabel(str(filepath))}
@@ -190,7 +226,7 @@ class LoadDicom(threading.Thread):
  
                 if not(is_dicom_dir):
                     parser = dicom.Parser()
-                    parser.SetDataImage(dict_file[filepath], filepath)
+                    parser.SetDataImage(dict_file[filepath], filepath, thumbnail_path)
  
                     dcm = dicom.Dicom()
                     self.l.acquire()
...	...	@@ -22,6 +22,7 @@
22	22
23	23	#TODO: To create a beautiful API
24	24	import time
	25	+import tempfile
25	26
26	27	import wx
27	28	import vtk
...	...	@@ -34,6 +35,8 @@ from reader import dicom_reader
34	35	import data.vtk_utils as vtku
35	36	import utils
36	37	import vtkgdcm
	38	+
	39	+
37	40	NROWS = 3
38	41	NCOLS = 6
39	42	NUM_PREVIEWS = NCOLS*NROWS
...	...	@@ -102,31 +105,18 @@ class DicomInfo(object):
102	105	self.subtitle = subtitle
103	106	self._preview = None
104	107	self.selected = False
	108	+ self.filename = ""
105	109
106	110	@property
107	111	def preview(self):
108		- rdicom = vtkgdcm.vtkGDCMImageReader()
109		- if self._preview:
110		- return self._preview
111		- else:
112		- rdicom.SetFileName(self.dicom.image.file)
113		- rdicom.Update()
114		-
115		- colorer = vtk.vtkImageMapToWindowLevelColors()
116		- colorer.SetInput(rdicom.GetOutput())
117		- colorer.SetWindow(float(self.dicom.image.window))
118		- colorer.SetLevel(float(self.dicom.image.level))
119		- colorer.SetOutputFormatToRGB()
120		- colorer.Update()
121		-
122		- width, height, z = colorer.GetOutput().GetDimensions()
123		-
124		- r = colorer.GetOutput().GetPointData().GetScalars()
125		- ni = numpy_support.vtk_to_numpy(r)
126		- self.img = wx.ImageFromBuffer(width, height, ni)
127		- self._preview = self.img.Mirror(False)
128		- return self._preview
129		-
	112	+
	113	+ if not self._preview:
	114	+ bmp = wx.Bitmap(self.dicom.image.thumbnail_path, wx.BITMAP_TYPE_PNG)
	115	+ self._preview = bmp.ConvertToImage()
	116	+ return self._preview
	117	+
	118	+ def release_thumbnail(self):
	119	+ self._preview = None
130	120
131	121	class DicomPaintPanel(wx.Panel):
132	122	def __init__(self, parent):
...	...	@@ -238,6 +228,9 @@ class Preview(wx.Panel):
238	228	"""
239	229	Set a dicom to preview.
240	230	"""
	231	+ if self.dicom_info:
	232	+ self.dicom_info.release_thumbnail()
	233	+
241	234	self.dicom_info = dicom_info
242	235	self.SetTitle(dicom_info.title)
243	236	self.SetSubtitle(dicom_info.subtitle)
...	...	@@ -409,7 +402,6 @@ class DicomPreviewSeries(wx.Panel):
409	402	def _display_previews(self):
410	403	initial = self.displayed_position * NCOLS
411	404	final = initial + NUM_PREVIEWS
412		-
413	405	if len(self.files) < final:
414	406	for i in xrange(final-len(self.files)):
415	407	try:
...	...	@@ -557,7 +549,6 @@ class DicomPreviewSlice(wx.Panel):
557	549	def _display_previews(self):
558	550	initial = self.displayed_position * NCOLS
559	551	final = initial + NUM_PREVIEWS
560		-
561	552	if len(self.files) < final:
562	553	for i in xrange(final-len(self.files)):
563	554	try:
...	...
...	...	@@ -139,9 +139,10 @@ class Parser():
139	139	# return None#self.vtkgdcm_reader.GetOutput()
140	140
141	141
142		- def SetDataImage(self, data_image, filename):
	142	+ def SetDataImage(self, data_image, filename, thumbnail_path):
143	143	self.data_image = data_image
144	144	self.filename = self.filepath = filename
	145	+ self.thumbnail_path = thumbnail_path
145	146
146	147	def __format_time(self,value):
147	148	sp1 = value.split(".")
...	...	@@ -1931,6 +1932,7 @@ class Image(object):
1931	1932	self.size = (parser.GetDimensionX(), parser.GetDimensionY())
1932	1933	#self.imagedata = parser.GetImageData()
1933	1934	self.bits_allocad = parser._GetBitsAllocated()
	1935	+ self.thumbnail_path = parser.thumbnail_path
1934	1936
1935	1937	if (parser.GetImageThickness()):
1936	1938	try:
...	...
...	...	@@ -19,10 +19,12 @@
19	19	import os
20	20	import Queue
21	21	import threading
	22	+import tempfile
22	23
23	24	from multiprocessing import cpu_count
24	25
25	26	import vtk
	27	+import vtkgdcm
26	28	import gdcm
27	29	import wx.lib.pubsub as ps
28	30
...	...	@@ -106,9 +108,8 @@ class LoadDicom(threading.Thread):
106	108	reader.SetFileName(str(filepath))
107	109
108	110	if (reader.Read()):
109		-
110	111	file = reader.GetFile()
111		-
	112	+
112	113	# Retrieve data set
113	114	dataSet = file.GetDataSet()
114	115
...	...	@@ -173,6 +174,41 @@ class LoadDicom(threading.Thread):
173	174	data_dict[group][field] = "Invalid Character"
174	175
175	176
	177	+
	178	+ # -------------- To Create DICOM Thumbnail -----------
	179	+ rvtk = vtkgdcm.vtkGDCMImageReader()
	180	+ rvtk.SetFileName(str(filepath))
	181	+ rvtk.Update()
	182	+
	183	+ try:
	184	+ data = data_dict['0028']['1050']
	185	+ level = [float(value) for value in data.split('\\')][0]
	186	+ data = data_dict['0028']['1051']
	187	+ window = [float(value) for value in data.split('\\')][0]
	188	+ except(KeyError):
	189	+ level = 300.0
	190	+ window = 2000.0
	191	+
	192	+ colorer = vtk.vtkImageMapToWindowLevelColors()
	193	+ colorer.SetInput(rvtk.GetOutput())
	194	+ colorer.SetWindow(float(window))
	195	+ colorer.SetLevel(float(level))
	196	+ colorer.SetOutputFormatToRGB()
	197	+ colorer.Update()
	198	+
	199	+ resample = vtk.vtkImageResample()
	200	+ resample.SetInput(colorer.GetOutput())
	201	+ resample.SetAxisMagnificationFactor ( 0, 0.25 )
	202	+ resample.SetAxisMagnificationFactor ( 1, 0.25 )
	203	+ resample.SetAxisMagnificationFactor ( 2, 1 )
	204	+ resample.Update()
	205	+
	206	+ thumbnail_path = tempfile.mktemp()
	207	+
	208	+ write_png = vtk.vtkPNGWriter()
	209	+ write_png.SetInput(resample.GetOutput())
	210	+ write_png.SetFileName(thumbnail_path)
	211	+ write_png.Write()
176	212
177	213	# ---------- Refactory --------------------------------------
178	214	data_dict['invesalius'] = {'orientation_label' : GetImageOrientationLabel(str(filepath))}
...	...	@@ -190,7 +226,7 @@ class LoadDicom(threading.Thread):
190	226
191	227	if not(is_dicom_dir):
192	228	parser = dicom.Parser()
193		- parser.SetDataImage(dict_file[filepath], filepath)
	229	+ parser.SetDataImage(dict_file[filepath], filepath, thumbnail_path)
194	230
195	231	dcm = dicom.Dicom()
196	232	self.l.acquire()
...	...