ENH: Added interface to image reduction

Paulo Henrique Junqueira Amorim
1 parent 5f72b336
Showing 4 changed files with 129 additions and 39 deletions Show diff stats
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/gui/dialogs.py
invesalius/utils.py
@@ -19,12 +19,12 @@
 import math
 import os
 import plistlib
-
+import wx
 import numpy
 from wx.lib.pubsub import pub as Publisher
 import constants as const
-import data.imagedata_utils as utils
+import data.imagedata_utils as image_utils
 import data.mask as msk
 import data.measures
 import data.slice_ as sl
@@ -37,7 +37,7 @@ import reader.dicom_grouper as dg
 import reader.dicom_reader as dcm
 import session as ses
-from utils import debug
+import utils 
 DEFAULT_THRESH_MODE = 0
@@ -171,14 +171,14 @@ class Controller():
         try:
             filename = session.project_path[1]
         except(AttributeError):
-            debug("Project doesn't exist")
+            utils.debug("Project doesn't exist")
             filename = None
         if (filename):
             if (st == const.PROJ_NEW) or (st == const.PROJ_CHANGE):
                 answer = dialog.SaveChangesDialog(filename, self.frame)
                 if not answer:
-                    debug("Close without changes")
+                    utils.debug("Close without changes")
                     self.CloseProject()
                     Publisher.sendMessage("Enable state project", False)
                     Publisher.sendMessage('Set project name')
@@ -186,14 +186,14 @@ class Controller():
                     Publisher.sendMessage("Exit")
                 elif answer == 1:
                     self.ShowDialogSaveProject()
-                    debug("Save changes and close")
+                    utils.debug("Save changes and close")
                     self.CloseProject()
                     Publisher.sendMessage("Enable state project", False)
                     Publisher.sendMessage('Set project name')
                     Publisher.sendMessage("Stop Config Recording")
                     Publisher.sendMessage("Exit")
                 elif answer == -1:
-                    debug("Cancel")
+                    utils.debug("Cancel")
             else:
                 self.CloseProject()
                 Publisher.sendMessage("Enable state project", False)
@@ -347,7 +347,7 @@ class Controller():
                 self.CreateAnalyzeProject(imagedata)
             # OPTION 3: Nothing...
             else:
-                debug("No medical images found on given directory")
+                utils.debug("No medical images found on given directory")
                 return
         self.LoadProject()
         Publisher.sendMessage("Enable state project", True)
@@ -420,7 +420,7 @@ class Controller():
         #TODO: Verify if all Analyse are in AXIAL orientation
         # To get  Z, X, Y (used by InVesaliu), not X, Y, Z
-        matrix, matrix_filename = utils.analyze2mmap(imagedata)
+        matrix, matrix_filename = image_utils.analyze2mmap(imagedata)
         if header['orient'] == 0:
             proj.original_orientation =  const.AXIAL
         elif header['orient'] == 1:
@@ -492,7 +492,7 @@ class Controller():
         interval += 1
         filelist = dicom_group.GetFilenameList()[::interval]
         if not filelist:
-            debug("Not used the IPPSorter")
+            utils.debug("Not used the IPPSorter")
             filelist = [i.image.file for i in dicom_group.GetHandSortedList()[::interval]]
         if file_range != None and file_range[1] > file_range[0]:
@@ -500,9 +500,6 @@ class Controller():
         zspacing = dicom_group.zspacing * interval
-        print "\n======================================="
-        print ">>>>>>>>>>>>>>>>>> zspacing", zspacing, interval
-        print "\n======================================="
         size = dicom.image.size
         bits = dicom.image.bits_allocad
         sop_class_uid = dicom.acquisition.sop_class_uid
@@ -514,16 +511,30 @@ class Controller():
         else:
             use_dcmspacing = 0
-        #imagedata = utils.CreateImageData(filelist, zspacing, xyspacing,size,
-                                          #bits, use_dcmspacing)
-
         imagedata = None
+        
+        sx, sy = size
+        n_slices = len(filelist)
+        resolution_percentage = utils.calculate_resizing_tofitmemory(int(sx), int(sy), n_slices, bits/8)
+        
+        if resolution_percentage < 1.0:
+            re_dialog = dialog.ResizeImageDialog()
+            re_dialog.SetValue(int(resolution_percentage*100))
+            re_dialog_value = re_dialog.ShowModal()  
+            
+            if re_dialog_value == wx.ID_OK:
+                percentage = re_dialog.GetValue()
+                resolution_percentage = percentage / 100.0
+            else:
+                return
-
+            xyspacing = xyspacing[0] / resolution_percentage, xyspacing[1] / resolution_percentage
+       
+ 
         wl = float(dicom.image.level)
         ww = float(dicom.image.window)
-        self.matrix, scalar_range, self.filename = utils.dcm2memmap(filelist, size,
-                                                                    orientation)
+        self.matrix, scalar_range, self.filename = image_utils.dcm2memmap(filelist, size,
+                                                                    orientation, resolution_percentage)
         self.Slice = sl.Slice()
         self.Slice.matrix = self.matrix
@@ -543,10 +554,10 @@ class Controller():
             message = _("Fix gantry tilt applying the degrees below")
             value = -1*tilt_value
             tilt_value = dialog.ShowNumberDialog(message, value)
-            utils.FixGantryTilt(self.matrix, self.Slice.spacing, tilt_value)
+            image_utils.FixGantryTilt(self.matrix, self.Slice.spacing, tilt_value)
         elif (tilt_value) and not (gui):
             tilt_value = -1*tilt_value
-            utils.FixGantryTilt(self.matrix, self.Slice.spacing, tilt_value)
+            image_utils.FixGantryTilt(self.matrix, self.Slice.spacing, tilt_value)
         self.Slice.window_level = wl
         self.Slice.window_width = ww
@@ -57,21 +57,19 @@ def ResampleImage3D(imagedata, value):
     return resample.GetOutput()
-def ResampleImage2D(imagedata, px, py,
+def ResampleImage2D(imagedata, px=None, py=None, resolution_percentage = None,
                         update_progress = None):
     """
     Resample vtkImageData matrix.
     """
+
     extent = imagedata.GetExtent()
     spacing = imagedata.GetSpacing()
+    dimensions = imagedata.GetDimensions()
-
-    #if extent[1]==extent[3]:
-    #    f = extent[1]
-    #elif extent[1]==extent[5]:
-    #    f = extent[1]
-    #elif extent[3]==extent[5]:
-    #    f = extent[3]
+    if resolution_percentage:
+        px = math.ceil(dimensions[0] * resolution_percentage)
+        py = math.ceil(dimensions[1] * resolution_percentage)
     if abs(extent[1]-extent[3]) < abs(extent[3]-extent[5]):
         f = extent[1]
@@ -418,7 +416,7 @@ class ImageCreator:
         return imagedata
-def dcm2memmap(files, slice_size, orientation):
+def dcm2memmap(files, slice_size, orientation, resolution_percentage):
     """
     From a list of dicom files it creates memmap file in the temp folder and
     returns it and its related filename.
@@ -429,21 +427,43 @@ def dcm2memmap(files, slice_size, orientation):
     temp_file = tempfile.mktemp()
     if orientation == 'SAGITTAL':
-        shape = slice_size[0], slice_size[1], len(files)
+        if resolution_percentage == 1.0:
+            shape = slice_size[0], slice_size[1], len(files)
+        else:
+            shape = math.ceil(slice_size[0]*resolution_percentage),\
+                    math.ceil(slice_size[1]*resolution_percentage), len(files)
+
     elif orientation == 'CORONAL':
-        shape = slice_size[1], len(files), slice_size[0]
+        if resolution_percentage == 1.0:
+            shape = slice_size[1], len(files), slice_size[0]
+        else:
+            shape = math.ceil(slice_size[1]*resolution_percentage), len(files),\
+                                        math.ceil(slice_size[0]*resolution_percentage)
     else:
-        shape = len(files), slice_size[1], slice_size[0]
+        if resolution_percentage == 1.0:
+            shape = len(files), slice_size[1], slice_size[0]
+        else:
+            shape = len(files), math.ceil(slice_size[1]*resolution_percentage),\
+                                        math.ceil(slice_size[0]*resolution_percentage)
+
     matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
     dcm_reader = vtkgdcm.vtkGDCMImageReader()
     cont = 0
     max_scalar = None
     min_scalar = None
+
     for n, f in enumerate(files):
         dcm_reader.SetFileName(f)
         dcm_reader.Update()
         image = dcm_reader.GetOutput()
+        if resolution_percentage != 1.0:
+            image_resized = ResampleImage2D(image, px=None, py=None,\
+                                resolution_percentage = resolution_percentage, update_progress = None)
+
+            image = image_resized
+            print ">>>>>>>>>", image.GetDimensions()
+
         min_aux, max_aux = image.GetScalarRange()
         if min_scalar is None or min_aux < min_scalar:
             min_scalar = min_aux
@@ -82,6 +82,65 @@ class NumberDialog(wx.Dialog):
     def GetValue(self):
         return self.num_ctrl.GetValue()
+
+class ResizeImageDialog(wx.Dialog):
+
+    def __init__(self):#, message, value=0):
+        pre = wx.PreDialog()
+        pre.Create(None, -1, "InVesalius 3", size=wx.DefaultSize,
+                   pos=wx.DefaultPosition,
+                   style=wx.DEFAULT_DIALOG_STYLE)
+        self.PostCreate(pre)
+        
+        lbl_message = wx.StaticText(self, -1, _("Your operational system is 32bits or have \nlow memory. It's recommended to reduce the image resolution."))
+
+        icon = wx.ArtProvider.GetBitmap(wx.ART_WARNING, wx.ART_MESSAGE_BOX, (32,32))
+        bmp = wx.StaticBitmap(self, -1, icon)
+
+        btn_ok = wx.Button(self, wx.ID_OK)
+        btn_ok.SetHelpText("Value will be applied.")
+        btn_ok.SetDefault()
+
+        btn_cancel = wx.Button(self, wx.ID_CANCEL)
+        btn_cancel.SetHelpText("Value will not be applied.")
+
+        btn_sizer = wx.StdDialogButtonSizer()
+        btn_sizer.AddButton(btn_ok)
+        btn_sizer.AddButton(btn_cancel)
+        btn_sizer.Realize()
+
+        lbl_message_percent = wx.StaticText(self, -1, _("Resolution percentage"))
+
+        num_ctrl_percent = wx.SpinCtrl(self, -1, "", (30, 50))
+        num_ctrl_percent.SetRange(20,100) 
+        self.num_ctrl_porcent = num_ctrl_percent
+
+        sizer_percent = wx.BoxSizer(wx.HORIZONTAL)
+        sizer_percent.Add(lbl_message_percent, 0, wx.ALIGN_CENTRE|wx.ALL, 5)
+        sizer_percent.Add(num_ctrl_percent, 0, wx.ALIGN_CENTRE|wx.ALL, 5)
+
+        sizer_itens = wx.BoxSizer(wx.VERTICAL)
+        sizer_itens.Add(lbl_message, 0, wx.ALIGN_CENTRE_VERTICAL|wx.ALL|wx.EXPAND, 5)
+        sizer_itens.AddSizer(sizer_percent, 0, wx.ALIGN_CENTRE|wx.ALL, 5)
+        sizer_itens.Add(btn_sizer, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 25)
+
+        sizer_general = wx.BoxSizer(wx.HORIZONTAL)
+        sizer_general.Add(bmp, 0, wx.ALIGN_CENTRE|wx.ALL, 15)
+        sizer_general.AddSizer(sizer_itens, 90, wx.ALIGN_CENTRE|wx.ALL, 10)
+
+        self.SetSizer(sizer_general)
+        sizer_itens.Fit(self)
+        self.Layout()
+        self.SetAutoLayout(True)
+        self.Centre()
+    
+    def SetValue(self, value):
+        self.num_ctrl_porcent.SetValue(value)
+
+    def GetValue(self):
+        return self.num_ctrl_porcent.GetValue()
+
+
 def ShowNumberDialog(message, value=0):
     dlg = NumberDialog(message, value)
     dlg.SetValue(value)
@@ -213,7 +213,7 @@ def calculate_resizing_tofitmemory(x_size,y_size,n_slices,byte):
         n_slices: number of slices
         byte: bytes allocated for each pixel sample
     """
-    imagesize = x_size * y_size * n_slices * byte  
+    imagesize = x_size * y_size * n_slices * byte * 17 
     sg = sigar.open()
     ram_free = sg.mem().actual_free()
@@ -221,6 +221,9 @@ def calculate_resizing_tofitmemory(x_size,y_size,n_slices,byte):
     swap_free = sg.swap().free()
     sg.close()
+    print "RAM FREE", ram_free
+    print "RAM_TOTAL", ram_total
+
     if (sys.platform == 'win32'):
         if (platform.architecture()[0] == '32bit'):
             if ram_free>1400000000:
@@ -237,14 +240,11 @@ def calculate_resizing_tofitmemory(x_size,y_size,n_slices,byte):
     if (swap_free>ram_total):
         swap_free=ram_total
-    resize = (float((ram_free+0.5*swap_free)/imagesize))       
+    resize = (float((ram_free+0.5*swap_free)/imagesize))      
     resize=math.sqrt(resize)  # this gives the "resize" for each axis x and y
     if (resize>1): 
         resize=1
-    return (100*resize)
-
-
-
+    return round(resize,2)
 def predict_memory(nfiles, x, y, p):
	@@ -82,6 +82,65 @@ class NumberDialog(wx.Dialog):		@@ -82,6 +82,65 @@ class NumberDialog(wx.Dialog):
82	def GetValue(self):	82	def GetValue(self):
83	return self.num_ctrl.GetValue()	83	return self.num_ctrl.GetValue()
84		84
		85	+
		86	+class ResizeImageDialog(wx.Dialog):
		87	+
		88	+ def __init__(self):#, message, value=0):
		89	+ pre = wx.PreDialog()
		90	+ pre.Create(None, -1, "InVesalius 3", size=wx.DefaultSize,
		91	+ pos=wx.DefaultPosition,
		92	+ style=wx.DEFAULT_DIALOG_STYLE)
		93	+ self.PostCreate(pre)
		94	+
		95	+ lbl_message = wx.StaticText(self, -1, _("Your operational system is 32bits or have \nlow memory. It's recommended to reduce the image resolution."))
		96	+
		97	+ icon = wx.ArtProvider.GetBitmap(wx.ART_WARNING, wx.ART_MESSAGE_BOX, (32,32))
		98	+ bmp = wx.StaticBitmap(self, -1, icon)
		99	+
		100	+ btn_ok = wx.Button(self, wx.ID_OK)
		101	+ btn_ok.SetHelpText("Value will be applied.")
		102	+ btn_ok.SetDefault()
		103	+
		104	+ btn_cancel = wx.Button(self, wx.ID_CANCEL)
		105	+ btn_cancel.SetHelpText("Value will not be applied.")
		106	+
		107	+ btn_sizer = wx.StdDialogButtonSizer()
		108	+ btn_sizer.AddButton(btn_ok)
		109	+ btn_sizer.AddButton(btn_cancel)
		110	+ btn_sizer.Realize()
		111	+
		112	+ lbl_message_percent = wx.StaticText(self, -1, _("Resolution percentage"))
		113	+
		114	+ num_ctrl_percent = wx.SpinCtrl(self, -1, "", (30, 50))
		115	+ num_ctrl_percent.SetRange(20,100)
		116	+ self.num_ctrl_porcent = num_ctrl_percent
		117	+
		118	+ sizer_percent = wx.BoxSizer(wx.HORIZONTAL)
		119	+ sizer_percent.Add(lbl_message_percent, 0, wx.ALIGN_CENTRE\|wx.ALL, 5)
		120	+ sizer_percent.Add(num_ctrl_percent, 0, wx.ALIGN_CENTRE\|wx.ALL, 5)
		121	+
		122	+ sizer_itens = wx.BoxSizer(wx.VERTICAL)
		123	+ sizer_itens.Add(lbl_message, 0, wx.ALIGN_CENTRE_VERTICAL\|wx.ALL\|wx.EXPAND, 5)
		124	+ sizer_itens.AddSizer(sizer_percent, 0, wx.ALIGN_CENTRE\|wx.ALL, 5)
		125	+ sizer_itens.Add(btn_sizer, 0, wx.ALIGN_CENTER_VERTICAL\|wx.ALL, 25)
		126	+
		127	+ sizer_general = wx.BoxSizer(wx.HORIZONTAL)
		128	+ sizer_general.Add(bmp, 0, wx.ALIGN_CENTRE\|wx.ALL, 15)
		129	+ sizer_general.AddSizer(sizer_itens, 90, wx.ALIGN_CENTRE\|wx.ALL, 10)
		130	+
		131	+ self.SetSizer(sizer_general)
		132	+ sizer_itens.Fit(self)
		133	+ self.Layout()
		134	+ self.SetAutoLayout(True)
		135	+ self.Centre()
		136	+
		137	+ def SetValue(self, value):
		138	+ self.num_ctrl_porcent.SetValue(value)
		139	+
		140	+ def GetValue(self):
		141	+ return self.num_ctrl_porcent.GetValue()
		142	+
		143	+
85	def ShowNumberDialog(message, value=0):	144	def ShowNumberDialog(message, value=0):
86	dlg = NumberDialog(message, value)	145	dlg = NumberDialog(message, value)
87	dlg.SetValue(value)	146	dlg.SetValue(value)