ADD: import eeg coordinates plugin

.gitignore

@@ -167,3 +167,5 @@ Sessionx.vim
 [._]*.un~
 
 # End of https://www.gitignore.io/api/vim,tags,python
+
+.idea/

import_eeg_coordinates/gui.py

@@ -0,0 +1,95 @@
+import os
+import wx
+from pubsub import pub as Publisher
+import numpy as np
+import invesalius.constants as const
+import invesalius.data.imagedata_utils as img_utils
+from invesalius.data.markers.marker import MarkerType
+import invesalius.data.slice_ as sl
+import invesalius.gui.dialogs as dlgs
+
+
+class Window(wx.Dialog):
+    def __init__(self, parent):
+        super().__init__(
+            parent,
+            title="Import eeg coordinates",
+            style=wx.DEFAULT_DIALOG_STYLE | wx.FRAME_FLOAT_ON_PARENT,
+        )
+
+        self._init_gui()
+
+    def _init_gui(self):
+        self.position_list = []
+        self.label_list = []
+        wildcard: str = "(*.csv)|*.csv"
+        # Default system path
+        current_dir = os.path.abspath(".")
+
+        dlg_message = "Import Csv EEG"
+        dlg_style = wx.FD_OPEN | wx.FD_CHANGE_DIR
+
+        if sl.Slice().has_affine():
+            dlg = dlgs.FileSelectionDialog(
+                title=dlg_message, wildcard=wildcard, default_dir=current_dir
+            )
+            conversion_radio_box = wx.RadioBox(
+                dlg,
+                -1,
+                _("File csv eeg"),
+                choices=const.SURFACE_SPACE_CHOICES,
+                style=wx.RA_SPECIFY_ROWS,
+            )
+            dlg.sizer.Add(conversion_radio_box, 0, wx.LEFT)
+            dlg.FitSizers()
+        else:
+            dlg = wx.FileDialog(
+                None,
+                message=dlg_message,
+                wildcard=wildcard,
+                default_dir=current_dir,
+                style=dlg_style,
+            )
+            # stl filter is default
+            dlg.SetFilterIndex(0)
+            conversion_radio_box = None
+
+        # Show the dialog and retrieve the user response. If it is the OK response,
+        # process the data.
+        filename = None
+        try:
+            if dlg.ShowModal() == wx.ID_OK:
+                filename = dlg.GetPath()
+                if conversion_radio_box is not None:
+                    data = np.genfromtxt(fname=filename, delimiter=',', encoding=None, dtype=None, skip_header=0)
+                    for i in data:
+                        position_world = [i[1], i[2], i[3]]
+                        convert_to_inv = conversion_radio_box.GetSelection() == const.SURFACE_SPACE_WORLD
+                        if convert_to_inv:
+                            affine = sl.Slice().affine.copy()
+                            affine = np.linalg.inv(affine)
+                            position = img_utils.convert_world_to_voxel(position_world, affine)[0].tolist()
+                            position_voxel = img_utils.convert_invesalius_to_voxel(position).tolist()
+                        else:
+                            position_voxel = position_world
+                            position_voxel[2] = -position_world[2]
+
+                        Publisher.sendMessage(
+                            "Create marker",
+                            marker_type=MarkerType.LANDMARK,
+                            position=position_voxel,
+                            label=i[4],
+                        )
+        except:
+            wx.MessageBox("Invalid EEG coordinates file. \nFile should be structured as ´´electrode,x,y,z,label´´", "InVesalius 3")
+            self._init_gui()
+
+        dlg.Destroy()
+        self.Destroy()
+
+
+if __name__ == "__main__":
+    app = wx.App()
+    window = Window(None)
+    window.Show()
+    app.MainLoop()

import_eeg_coordinates/main.py

@@ -0,0 +1,8 @@
+import wx
+
+from . import gui
+
+
+def load():
+    w = gui.Window(wx.GetApp().GetTopWindow())
+    w.Show()

import_eeg_coordinates/plugin.json

@@ -0,0 +1,5 @@
+{
+    "name": "Import EEG coordinates",
+    "description": "Import EEG coordinates",
+    "enable-startup": false
+}

import_world_coordinates/gui.py

@@ -0,0 +1,233 @@
+import wx
+from pubsub import pub as Publisher
+import numpy as np
+
+import invesalius.data.coordinates as dco
+import invesalius.data.imagedata_utils as img_utils
+from invesalius.data.markers.marker import MarkerType
+import invesalius.data.slice_ as sl
+
+
+class Window(wx.Dialog):
+    def __init__(
+        self,
+        parent,
+        title="Import World Coordinates into InVesalius",
+        style=wx.DEFAULT_DIALOG_STYLE | wx.FRAME_FLOAT_ON_PARENT | wx.STAY_ON_TOP,
+    ):
+        wx.Dialog.__init__(self, parent, -1, title=title, style=style)
+
+        self.x = -48.48
+        self.y = -28.06
+        self.z = 60.10
+        self.rx = -2.44
+        self.ry = -0.14
+        self.rz = -1.48
+
+        self.arx = 0
+        self.ary = 180
+        self.arz = 0
+
+        self._init_gui()
+
+        self.set_original_coordinates(
+            self.x, self.y, self.z, self.rx, self.ry, self.rz, self.arx, self.ary, self.arz
+        )
+
+        self._bind_events()
+
+    def set_original_coordinates(self, sx, sy, sz, srx, sry, srz, arx, ary, arz):
+        self.x = sx
+        self.y = sy
+        self.z = sz
+        self.rx = srx
+        self.ry = sry
+        self.rz = srz
+
+        self.apply_rx = arx
+        self.apply_ry = ary
+        self.apply_rz = arz
+
+        self.txt_x.ChangeValue(str(sx))
+        self.txt_y.ChangeValue(str(sy))
+        self.txt_z.ChangeValue(str(sz))
+        self.txt_rx.ChangeValue(str(srx))
+        self.txt_ry.ChangeValue(str(sry))
+        self.txt_rz.ChangeValue(str(srz))
+
+        self.txt_apply_rx.ChangeValue(str(arx))
+        self.txt_apply_ry.ChangeValue(str(ary))
+        self.txt_apply_rz.ChangeValue(str(arz))
+
+    def _init_gui(self):
+        self.txt_x = wx.TextCtrl(self, -1)
+        self.txt_y = wx.TextCtrl(self, -1)
+        self.txt_z = wx.TextCtrl(self, -1)
+        self.txt_rx = wx.TextCtrl(self, -1)
+        self.txt_ry = wx.TextCtrl(self, -1)
+        self.txt_rz = wx.TextCtrl(self, -1)
+
+        self.txt_apply_rx = wx.TextCtrl(self, -1)
+        self.txt_apply_ry = wx.TextCtrl(self, -1)
+        self.txt_apply_rz = wx.TextCtrl(self, -1)
+
+        self.check_rotation = wx.CheckBox(self, -1, "Rotation")
+        self.check_rotation.SetValue(True)
+
+        self.button_create_marker = wx.Button(self, wx.ID_OK, label="Create Marker")
+        self.button_close = wx.Button(self, wx.ID_CLOSE)
+
+        button_sizer = wx.StdDialogButtonSizer()
+        button_sizer.AddButton(self.button_create_marker)
+        button_sizer.AddButton(self.button_close)
+        button_sizer.Realize()
+
+        sizer_original = wx.FlexGridSizer(3, 2, 5, 5)
+        sizer_original.AddMany(
+            (
+                (wx.StaticText(self, -1, "X"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_x, 0, wx.EXPAND),
+                (wx.StaticText(self, -1, "Y"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_y, 0, wx.EXPAND),
+                (wx.StaticText(self, -1, "Z"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_z, 0, wx.EXPAND),
+            )
+        )
+
+        original_sbox = wx.StaticBoxSizer(wx.HORIZONTAL, self, "Translation")
+        original_sbox.Add(sizer_original, 0, wx.EXPAND | wx.ALL, 5)
+
+        sizer_new = wx.FlexGridSizer(3, 2, 5, 5)
+        sizer_new.AddMany(
+            (
+                (wx.StaticText(self, -1, "RX"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_rx, 0, wx.ALIGN_CENTER_VERTICAL),
+                (wx.StaticText(self, -1, "RY"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_ry, 0, wx.ALIGN_CENTER_VERTICAL),
+                (wx.StaticText(self, -1, "RZ"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_rz, 0, wx.ALIGN_CENTER_VERTICAL),
+            )
+        )
+        new_sbox = wx.StaticBoxSizer(wx.HORIZONTAL, self, "Orientation (rad)")
+        new_sbox.Add(sizer_new, 0, wx.EXPAND | wx.ALL, 5)
+
+        content_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        content_sizer.Add(original_sbox, 1, wx.EXPAND | wx.ALL, 5)
+        content_sizer.Add(new_sbox, 1, wx.EXPAND | wx.ALL, 5)
+
+        sizer_apply = wx.FlexGridSizer(2, 3, 5, 5)
+        sizer_apply.AddMany(
+            (
+                (wx.StaticText(self, -1, "RX"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (wx.StaticText(self, -1, "RY"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (wx.StaticText(self, -1, "RZ"), 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_apply_rx, 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_apply_ry, 0, wx.ALIGN_CENTER_VERTICAL),
+                (self.txt_apply_rz, 0, wx.ALIGN_CENTER_VERTICAL),
+            )
+        )
+        new_abox = wx.StaticBoxSizer(wx.HORIZONTAL, self, "Apply rotation (degree)")
+        new_abox.Add(sizer_apply, 0, wx.EXPAND | wx.ALL, 5)
+
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.Add(content_sizer, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+        main_sizer.Add(self.check_rotation, 0, wx.LEFT | wx.ALIGN_LEFT, 7)
+        main_sizer.Add(new_abox, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 7)
+        main_sizer.Add(button_sizer, 0, wx.EXPAND | wx.TOP | wx.BOTTOM, 5)
+
+        self.SetSizer(main_sizer)
+        main_sizer.Fit(self)
+        self.Layout()
+
+    def _bind_events(self):
+        self.button_create_marker.Bind(wx.EVT_BUTTON, self.OnCreateMarker)
+        self.button_close.Bind(wx.EVT_BUTTON, self.OnClose)
+        self.Bind(wx.EVT_CLOSE, self.OnClose)
+        self.check_rotation.Bind(wx.EVT_CHECKBOX, self.OnEnableRotation)
+
+    def OnCreateMarker(self, evt):
+        try:
+            x = float(self.txt_x.GetValue())
+        except ValueError:
+            x = self.x
+
+        try:
+            y = float(self.txt_y.GetValue())
+        except ValueError:
+            y = self.y
+
+        try:
+            z = float(self.txt_z.GetValue())
+        except ValueError:
+            z = self.z
+
+        try:
+            rx = float(self.txt_rx.GetValue())
+        except ValueError:
+            rx = self.rx
+
+        try:
+            ry = float(self.txt_ry.GetValue())
+        except ValueError:
+            ry = self.ry
+
+        try:
+            rz = float(self.txt_rz.GetValue())
+        except ValueError:
+            rz = self.rz
+
+        m_coord = dco.coordinates_to_transformation_matrix(
+            position=[x, y, z],
+            orientation=[np.rad2deg(rx), np.rad2deg(ry), np.rad2deg(rz)],
+            axes="sxyz",
+        )
+        affine = sl.Slice().affine.copy()
+        m_coord_transformed = affine @ m_coord
+        position, orientation = dco.transformation_matrix_to_coordinates(
+            m_coord_transformed,
+            axes="sxyz",
+        )
+
+        if self.check_rotation.GetValue():
+            try:
+                arx = float(self.txt_apply_rx.GetValue())
+            except ValueError:
+                arx = self.apply_rx
+            try:
+                ary = float(self.txt_apply_ry.GetValue())
+            except ValueError:
+                ary = self.apply_ry
+            try:
+                arz = float(self.txt_apply_rz.GetValue())
+            except ValueError:
+                arz = self.apply_rz
+            m_displacement = dco.coordinates_to_transformation_matrix(
+                position=[0, 0, 0],
+                orientation=[arx, ary, arz],
+                axes="sxyz",
+            )
+            position, orientation = dco.transformation_matrix_to_coordinates(
+                m_coord_transformed @ m_displacement,
+                axes="sxyz",
+            )
+
+        position_voxel = img_utils.convert_invesalius_to_voxel(position)
+        Publisher.sendMessage(
+            "Create marker",
+            marker_type=MarkerType.COIL_TARGET,
+            position=position_voxel.tolist(),
+            orientation=orientation.tolist(),
+        )
+
+    def OnEnableRotation(self, evt):
+        if evt.IsChecked():
+            self.txt_apply_rx.Enable()
+            self.txt_apply_ry.Enable()
+            self.txt_apply_rz.Enable()
+        else:
+            self.txt_apply_rx.Disable()
+            self.txt_apply_ry.Disable()
+            self.txt_apply_rz.Disable()
+
+    def OnClose(self, evt):
+        self.Destroy()

import_world_coordinates/main.py

@@ -0,0 +1,8 @@
+import wx
+
+from . import gui
+
+
+def load():
+    w = gui.Window(wx.GetApp().GetTopWindow())
+    w.Show()

import_world_coordinates/plugin.json

@@ -0,0 +1,5 @@
+{
+    "name": "Import world coordinates",
+    "description": "Import world coordinates into invesalius coordinate system",
+    "enable-startup": false
+}