ENH: Updating navigation tools.

vhosouza
1 parent ede9d099
Showing 5 changed files with 352 additions and 328 deletions Show diff stats
invesalius/.idea/dictionaries/Victor.xml
invesalius/.idea/workspace.xml
invesalius/constants.py
invesalius/data/trackers.py
invesalius/gui/task_navigator.py
@@ -5,6 +5,7 @@
       <w>corregistration</w>
       <w>fiducial</w>
       <w>neuronavigation</w>
+      <w>neuronavigator</w>
       <w>trck</w>
     </words>
   </dictionary>
@@ -2,10 +2,11 @@
 <project version="4">
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-      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/gui/dialogs.py" afterPath="$PROJECT_DIR$/gui/dialogs.py" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/dictionaries/Victor.xml" afterPath="$PROJECT_DIR$/.idea/dictionaries/Victor.xml" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/constants.py" afterPath="$PROJECT_DIR$/constants.py" />
       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/gui/task_navigator.py" afterPath="$PROJECT_DIR$/gui/task_navigator.py" />
       <change type="MODIFICATION" beforePath="$PROJECT_DIR$/data/trackers.py" afterPath="$PROJECT_DIR$/data/trackers.py" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
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     <ignored path="invesalius.iws" />
     <ignored path=".idea/workspace.xml" />
@@ -29,120 +30,105 @@
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   <component name="Git.Settings">
     <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$/.." />
@@ -152,11 +138,11 @@
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         <option value="$PROJECT_DIR$/data/coordinates.py" />
         <option value="$PROJECT_DIR$/gui/dialogs.py" />
         <option value="$PROJECT_DIR$/data/trackers.py" />
+        <option value="$PROJECT_DIR$/constants.py" />
+        <option value="$PROJECT_DIR$/gui/task_navigator.py" />
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@@ -164,8 +150,10 @@
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@@ -190,7 +178,6 @@
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@@ -225,6 +212,7 @@
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@@ -465,27 +453,27 @@
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@@ -524,12 +512,29 @@
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@@ -580,7 +582,6 @@
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+            <element signature="e#1008#1023#0" expanded="false" />
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@@ -598,7 +599,6 @@
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@@ -636,7 +631,9 @@
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-          <folding />
+          <folding>
+            <element signature="e#1007#1017#0" expanded="true" />
+          </folding>
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@@ -652,10 +649,6 @@
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@@ -671,10 +663,6 @@
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@@ -693,7 +681,9 @@
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-          <folding />
+          <folding>
+            <element signature="e#1007#1017#0" expanded="true" />
+          </folding>
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       </provider>
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@@ -709,7 +699,6 @@
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-          <folding />
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@@ -717,10 +706,6 @@
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@@ -739,7 +724,6 @@
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-          <folding />
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       </provider>
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@@ -747,10 +731,6 @@
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@@ -769,7 +749,6 @@
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-          <folding />
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@@ -777,10 +756,6 @@
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-          </folding>
         </state>
       </provider>
     </entry>
@@ -805,127 +780,163 @@
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/data/viewer_volume.py">
+    <entry file="file://$PROJECT_DIR$/data/corregistration.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state vertical-scroll-proportion="0.0" vertical-offset="0" max-vertical-offset="1054">
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+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/gui/task_tools.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state vertical-scroll-proportion="0.0" vertical-offset="0" max-vertical-offset="22746">
+        <state vertical-scroll-proportion="-2.9241147" vertical-offset="1734" max-vertical-offset="2397">
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       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/data/corregistration.py">
+    <entry file="file://$PROJECT_DIR$/data/coordinates.py">
       <provider selected="true" editor-type-id="text-editor">
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+        <state vertical-scroll-proportion="0.0" vertical-offset="102" max-vertical-offset="4964">
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+            <element signature="e#2#20#0" expanded="true" />
+            <element signature="e#7877#9444#0" expanded="false" />
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         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/data/viewer_slice.py">
+    <entry file="file://$PROJECT_DIR$/gui/dialogs.py">
       <provider selected="true" editor-type-id="text-editor">
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+            <element signature="e#1053#1062#0" expanded="true" />
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     </entry>
-    <entry file="file://$PROJECT_DIR$/gui/task_tools.py">
+    <entry file="file://$PROJECT_DIR$/data/trackers.py">
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+            <element signature="e#0#20#0" expanded="true" />
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-    <entry file="file://$PROJECT_DIR$/data/slice_.py">
+    <entry file="file://$PROJECT_DIR$/project.py">
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     <entry file="file://$PROJECT_DIR$/control.py">
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+    <entry file="file://$PROJECT_DIR$/gui/task_slice.py">
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       <provider selected="true" editor-type-id="text-editor">
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+        <state vertical-scroll-proportion="-0.43265992" vertical-offset="257" max-vertical-offset="3349">
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-    <entry file="file://$PROJECT_DIR$/gui/task_slice.py">
+    <entry file="file://$PROJECT_DIR$/data/viewer_slice.py">
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+    </entry>
+    <entry file="file://$PROJECT_DIR$/data/viewer_volume.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state vertical-scroll-proportion="0.0" vertical-offset="15243" max-vertical-offset="23001">
+          <caret line="24" column="10" selection-start-line="24" selection-start-column="10" selection-end-line="24" selection-end-column="10" />
           <folding />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/gui/task_navigator.py">
+    <entry file="file://$PROJECT_DIR$/data/converters.py">
       <provider selected="true" editor-type-id="text-editor">
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           <folding />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/constants.py">
+    <entry file="file://$PROJECT_DIR$/data/vtk_utils.py">
       <provider selected="true" editor-type-id="text-editor">
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+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/data/volume.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state vertical-scroll-proportion="0.0" vertical-offset="0" max-vertical-offset="13039">
+          <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/data/slice_data.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state vertical-scroll-proportion="0.0" vertical-offset="0" max-vertical-offset="3094">
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+    <entry file="file://$PROJECT_DIR$/data/slice_.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state vertical-scroll-proportion="-14.86027" vertical-offset="9184" max-vertical-offset="22457">
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+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/data/measures.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state vertical-scroll-proportion="0.0" vertical-offset="0" max-vertical-offset="12206">
+          <caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
           <folding />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/data/coordinates.py">
+    <entry file="file://$PROJECT_DIR$/constants.py">
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-          <folding>
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-          </folding>
+        <state vertical-scroll-proportion="0.0" vertical-offset="9521" max-vertical-offset="10115">
+          <caret line="592" column="5" selection-start-line="592" selection-start-column="5" selection-end-line="592" selection-end-column="5" />
+          <folding />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/gui/dialogs.py">
+    <entry file="file://$PROJECT_DIR$/gui/task_surface.py">
       <provider selected="true" editor-type-id="text-editor">
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-          <folding>
-            <element signature="e#1053#1062#0" expanded="true" />
-          </folding>
+        <state vertical-scroll-proportion="0.7607573" vertical-offset="2805" max-vertical-offset="9877">
+          <caret line="204" column="0" selection-start-line="204" selection-start-column="0" selection-end-line="204" selection-end-column="0" />
+          <folding />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/data/trackers.py">
+    <entry file="file://$PROJECT_DIR$/gui/task_navigator.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state vertical-scroll-proportion="0.18106312" vertical-offset="894" max-vertical-offset="3128">
-          <caret line="59" column="24" selection-start-line="59" selection-start-column="24" selection-end-line="59" selection-end-column="24" />
+        <state vertical-scroll-proportion="0.6247848" vertical-offset="1524" max-vertical-offset="14892">
+          <caret line="111" column="21" selection-start-line="111" selection-start-column="21" selection-end-line="111" selection-end-column="21" />
           <folding>
-            <element signature="e#0#20#0" expanded="true" />
+            <element signature="e#1007#1017#0" expanded="true" />
           </folding>
         </state>
       </provider>
@@ -578,14 +578,17 @@ ZEBRIS = 4
 DEFAULT_TRACKER = PATRIOT
 #TRACKER = [_("Polhemus PATRIOT"), _("Polhemus PATRIOT"),
 #  _("Polhemus ISOTRAK II"), _("Claron MicronTracker"), _("Zebris CMS20")]
-TRACKER = [_("Claron MicronTracker S40"), _("Polhemus FASTRAK"),
+TRACKER = [_("Claron MicronTracker"), _("Polhemus FASTRAK"),
            _("Polhemus ISOTRAK II"),  _("Polhemus PATRIOT"), _("Zebris CMS20")]
-SINGLE_REF = 0
-DOUBLE_REF = 1
-DEFAULT_REF_MODE = SINGLE_REF
-REF_MODE = [_("Single Ref Mode"), _("Double Ref Mode")]
+STATIC_REF = 0
+DYNAMIC_REF = 1
+DEFAULT_REF_MODE = DYNAMIC_REF
+REF_MODE = [_("Static Reference"), _("Dynamic Reference")]
-OBJECTS = [_("Eigth Coil"),_("Simple Coil")]
+BUTTERFLY_COIL = 0
+CIRCULAR_COIL = 1
+DEFAULT_COIL = BUTTERFLY_COIL
+COILS = [_("Butterfly Coil"),_("Circular Coil")]
 # ------
@@ -8,19 +8,14 @@ import gui.dialogs as dlg
 class Tracker:
     def __init__(self, trck_id):
-        """Initialize spatial trackers for neuronavigation
+        """
+        Initialize spatial trackers for neuronavigation
         :param trck_id: identifier of spatial tracker
-        :return: initialization variable
+        :return: spatial tracker initialization variable
         """
-        trck = {0 : self.ClaronTracker,
-                1 : self.PlhFastrak,
-                2 : self.PlhIsotrakII,
-                3 : self.PlhPatriot,
-                4 : self.ZebrisCMS20}
-
-        self.ReturnTracker(trck, trck_id)
+        self.ReturnTracker(trck_id)
     def ClaronTracker(self):
         trck_init = None
@@ -29,8 +24,8 @@ class Tracker:
             import ClaronTracker
             trck_init = ClaronTracker.ClaronTracker()
-            trck_init.CalibrationDir = "C:\CalibrationFiles"
-            trck_init.MarkerDir = "C:\Markers"
+            trck_init.CalibrationDir = "../objects/mtc_files/CalibrationFiles"
+            trck_init.MarkerDir = "../objects/mtc_files/Markers"
             trck_init.NumberFramesProcessed = 10
             trck_init.FramesExtrapolated = 0
             trck_init.Initialize()
@@ -93,11 +88,24 @@ class Tracker:
         return trck_init
     def ZebrisCMS20(self):
+        trck_init = None
         dlg.TrackerNotConnected(4)
         print 'Zebris device not found.'
-        return None
+        return trck_init
+
+    def DefaultTracker(self):
+        trck_init = None
+
+        try:
+            # import spatial tracker library
+            print 'Trying to connect with spatial tracker.'
+
+        except ImportError:
+            dlg.TrackerNotConnected(5)
+
+        return trck_init  # spatial tracker initialization variable
     def polhemus_serial(self, plh_id):
         trck_init = None
@@ -121,59 +129,66 @@ class Tracker:
         return trck_init
-    def ReturnTracker(self, trck, trck_id):
+    def ReturnTracker(self, trck_id):
         print "Returning"
         print "This is the tracker selected!", trck_id
+        trck = {0 : self.ClaronTracker,
+                1 : self.PlhFastrak,
+                2 : self.PlhIsotrakII,
+                3 : self.PlhPatriot,
+                4 : self.ZebrisCMS20}
+
         return trck[trck_id]()
-class Tracker_Init: 
-    def PolhemusISO_init(self):
-        try:
-            plh = serial.Serial(0, baudrate = 115200, timeout=0.2)
-            return plh
-            
-        except:
-            dlg.TrackerNotConnected(1)
-            raise ValueError('Device not found')
-    
-    def Polhemus_init(self):
-        dev = usb.core.find(idVendor=0x0F44, idProduct=0xEF12)
-        if dev is None:
-            dlg.TrackerNotConnected(1)
-            raise ValueError('Device not found')  
-        try:
-            cfg = dev.get_active_configuration()
-            for i in cfg:
-                for x in i:
-                    x = x        
-            dev.set_configuration()
-        except usb.core.USBError as e:
-            sys.exit("Could not set configuration: %s" % str(e))
-        return dev
-    
-    def Claron_init(self):
-        try:
-            mtc = ClaronTracker.ClaronTracker()
-            mtc.CalibrationDir = "C:\CalibrationFiles"
-            mtc.MarkerDir = "C:\Markers"
-            mtc.NumberFramesProcessed = 10
-            mtc.FramesExtrapolated = 0
-            mtc.Initialize()
-            if mtc.GetIdentifyingCamera():
-                print "Camera Identified."
-                mtc.Run()
-            else:
-                dlg.TrackerNotConnected(2)
-                print "The Claron MicronTracker is not connected!"
-            return mtc
-        
-        except:
-            dlg.TrackerNotConnected(2)
-            raise ValueError('Device not found') 
-         
-        
-    def Zebris_init(self):
-        dlg.TrackerNotConnected(3)
-        return
 \ No newline at end of file
+
+# class Tracker_Init:
+#     def PolhemusISO_init(self):
+#         try:
+#             plh = serial.Serial(0, baudrate = 115200, timeout=0.2)
+#             return plh
+#
+#         except:
+#             dlg.TrackerNotConnected(1)
+#             raise ValueError('Device not found')
+#
+#     def Polhemus_init(self):
+#         dev = usb.core.find(idVendor=0x0F44, idProduct=0xEF12)
+#         if dev is None:
+#             dlg.TrackerNotConnected(1)
+#             raise ValueError('Device not found')
+#         try:
+#             cfg = dev.get_active_configuration()
+#             for i in cfg:
+#                 for x in i:
+#                     x = x
+#             dev.set_configuration()
+#         except usb.core.USBError as e:
+#             sys.exit("Could not set configuration: %s" % str(e))
+#         return dev
+#
+#     def Claron_init(self):
+#         try:
+#             mtc = ClaronTracker.ClaronTracker()
+#             mtc.CalibrationDir = "C:\CalibrationFiles"
+#             mtc.MarkerDir = "C:\Markers"
+#             mtc.NumberFramesProcessed = 10
+#             mtc.FramesExtrapolated = 0
+#             mtc.Initialize()
+#             if mtc.GetIdentifyingCamera():
+#                 print "Camera Identified."
+#                 mtc.Run()
+#             else:
+#                 dlg.TrackerNotConnected(2)
+#                 print "The Claron MicronTracker is not connected!"
+#             return mtc
+#
+#         except:
+#             dlg.TrackerNotConnected(2)
+#             raise ValueError('Device not found')
+#
+#
+#     def Zebris_init(self):
+#         dlg.TrackerNotConnected(3)
+#         return
 \ No newline at end of file
@@ -18,24 +18,19 @@
 #--------------------------------------------------------------------------
 import sys
-from numpy import *
-import serial
+import numpy as np
 import wx
 import wx.lib.masked.numctrl
-import wx.lib.platebtn as pbtn
 from wx.lib.pubsub import pub as Publisher
 import constants as const
 import data.bases as db
 import data.corregistration as dcr
-import data.trackers as dtrk
+import data.trackers as dt
 import data.coordinates as dco
 import gui.dialogs as dlg
 import gui.widgets.foldpanelbar as fpb
 import gui.widgets.colourselect as csel
-import gui.widgets.platebtn as pbtn
-import project as prj
-import utils as utl
 class TaskPanel(wx.Panel):
@@ -45,7 +40,7 @@ class TaskPanel(wx.Panel):
         inner_panel = InnerTaskPanel(self)
         sizer = wx.BoxSizer(wx.HORIZONTAL)
-        sizer.Add(inner_panel, 1, wx.EXPAND | wx.GROW | wx.BOTTOM | wx.RIGHT |
+        sizer.Add(inner_panel, 1, wx.EXPAND|wx.GROW|wx.BOTTOM|wx.RIGHT |
                   wx.LEFT, 7)
         sizer.Fit(self)
@@ -53,35 +48,31 @@ class TaskPanel(wx.Panel):
         self.Update()
         self.SetAutoLayout(1)
+
 class InnerTaskPanel(wx.Panel):
     def __init__(self, parent):
         wx.Panel.__init__(self, parent)
-        default_colour = self.GetBackgroundColour()
-        self.SetBackgroundColour(wx.Colour(255,255,255))
+        default_color = self.GetBackgroundColour()
+        self.SetBackgroundColour(wx.Colour(255, 255, 255))
         self.SetAutoLayout(1)
-        # Neuronavigator Title
-        text = wx.StaticText(self, -1, 'Choose the tracker, ref mode, select the reference points, coregistrate and neuronavigate',
-                              size = wx.Size(90, 30))
+        text_nav = wx.StaticText(self, -1, 'Configure spatial tracker and '
+                                           'coregistrate for neuronavigation.',
+                                 size=wx.Size(90, 30))
-        # Create horizontal sizers to represent lines in the panel
+        # Create horizontal sizer to represent lines in the panel
         line_new = wx.BoxSizer(wx.HORIZONTAL)
-        line_new.Add(text, 1, wx.EXPAND|wx.GROW| wx.TOP|wx.CENTER, 0)
-        #line_new.SetDimension(1, 1, width = 25, height = 25)
-        #line_new.Add(button_new_surface, 0, wx.ALL|wx.EXPAND|wx.GROW, 0)
+        line_new.Add(text_nav, 1, wx.EXPAND|wx.GROW|wx.TOP|wx.RIGHT, 4)
-        # Folde panel which contains surface properties and quality
+        # Fold panel which contains navigation configurations
         fold_panel = FoldPanel(self)
-        fold_panel.SetBackgroundColour(default_colour)
-
-        # Button to fold to select region task
-        line_inutil = wx.StaticText(self, -1, 'Linha sem sentido')
+        fold_panel.SetBackgroundColour(default_color)
-        # Add line sizers into main sizer
+        # Add line sizer into main sizer
         main_sizer = wx.BoxSizer(wx.VERTICAL)
-        main_sizer.Add(line_new, 0,wx.GROW|wx.EXPAND|wx.ALIGN_CENTER|wx.TOP, 5)
+        main_sizer.Add(line_new, 0,
+                       wx.GROW|wx.EXPAND|wx.LEFT|wx.RIGHT|wx.TOP, 5)
         main_sizer.Add(fold_panel, 1, wx.GROW|wx.EXPAND|wx.ALL, 5)
-        main_sizer.Add(line_inutil, 0, wx.ALIGN_RIGHT|wx.RIGHT|wx.BOTTOM, 5)
         main_sizer.Fit(self)
         self.SetSizer(main_sizer)
@@ -106,6 +97,7 @@ class FoldPanel(wx.Panel):
         self.Update()
         self.SetAutoLayout(1)
+
 class InnerFoldPanel(wx.Panel):
     def __init__(self, parent):
         wx.Panel.__init__(self, parent)
@@ -119,7 +111,7 @@ class InnerFoldPanel(wx.Panel):
         # parent panel. Perhaps we need to insert the item into the sizer also...
         # Study this.
         fold_panel = fpb.FoldPanelBar(self, -1, wx.DefaultPosition,
-                                      (10, 300), 0,fpb.FPB_SINGLE_FOLD)
+                                      (10, 320), 0,fpb.FPB_SINGLE_FOLD)
         # Fold panel style
         style = fpb.CaptionBarStyle()
@@ -493,7 +485,7 @@ class NeuronavigationTools(wx.Panel):
         trck_id = evt.GetSelection()
         # self.trk_init = dco.Tracker().ReturnTracker(trck_id)
-        self.trk_init = dco.Tracker(trck_id)
+        self.trk_init = dt.Tracker(trck_id)
         # if self.tracker_id == 0:
         #     self.trk_init = dtrk.Tracker_Init().PolhemusISO_init()
@@ -549,7 +541,7 @@ class ObjectWNeuronavigation(wx.Panel):
         self.SetBackgroundColour(default_colour)
         self.SetAutoLayout(1)
-        self.object_id = const.OBJECTS
+        self.object_id = const.COILS
 #         self.aux_img__INO_ref=0
         self.showObj = None
@@ -558,10 +550,12 @@ class ObjectWNeuronavigation(wx.Panel):
         #Line 1      
         text_choice = wx.StaticText(self, -1, _("Select the Object:"))  
         #Line 2      
-        self.choice_object = wx.ComboBox(self, -1, "Select the Object:", size=(97, 23),
-                                     choices = const.OBJECTS, style = wx.CB_DROPDOWN|wx.CB_READONLY|wx.CB_SORT)
-#        choice_object.SetSelection(0)
-        self.choice_object.Bind(wx.EVT_COMBOBOX,self.OnChoiseObject)  
+        choice_object = wx.ComboBox(self, -1, "Select the Object:",
+                                         size=(97, 23),
+                                         choices = const.COILS,
+                                         style = wx.CB_DROPDOWN|wx.CB_READONLY|wx.CB_SORT)
+        choice_object.SetSelection(const.DEFAULT_COIL)
+        choice_object.Bind(wx.EVT_COMBOBOX, self.OnChoiceObject)
         #Line 3        
         correg_object= wx.Button(self, -1, label='Corregistrate object', size = wx.Size(125,23))
@@ -582,7 +576,7 @@ class ObjectWNeuronavigation(wx.Panel):
 #             name='numCtrl3I', parent=self, integerWidth = 4, fractionWidth = 1)
         line2 = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
-        line2.AddMany([(self.choice_object, 1,wx.EXPAND|wx.LEFT|wx.TOP),
+        line2.AddMany([(choice_object, 1,wx.EXPAND|wx.LEFT|wx.TOP),
                        (correg_object, 1, wx.GROW|wx.EXPAND|wx.RIGHT|wx.TOP)])
 #         line3 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
@@ -626,7 +620,7 @@ class ObjectWNeuronavigation(wx.Panel):
         self.coord3a=pubsub_evt.data[8]   
         self.img_inio=pubsub_evt.data[9]       
-    def OnChoiseObject(self, evt):
+    def OnChoiceObject(self, evt):
         self.object_id = evt.GetSelection()  
         self.object_name = self.choice_object.GetValue()
 ##        if self.object_name == " Add new object...":