Improvements to loading markers files

invesalius/gui/dialogs.py

@@ -99,6 +99,7 @@
 import invesalius.data.polydata_utils as pu
 import invesalius.data.transformations as tr
 import invesalius.data.vtk_utils as vtku
+import invesalius.gui.utils as gui_utils
 import invesalius.gui.widgets.gradient as grad
 import invesalius.session as ses
 import invesalius.utils as utils
@@ -7478,6 +7479,118 @@ def GetPath(self) -> str:
         return self.path
 
 
+def LoadMarkersFile(filename, load_image_fiducials=False, fiducials_only=False):
+    """
+    :param filename: Path to file
+    :param load_image_fiducials: If True, loads image fiducials from the markers file.
+    :param fiducials_only: If True, only loads fiducials, ignoring all other markers in the file.
+    """
+    from invesalius.data.markers.marker import Marker
+    from invesalius.navigation.navigation import NavigationHub
+
+    markers = NavigationHub().markers
+
+    try:
+        with open(filename) as file:
+            magick_line = file.readline()
+            assert magick_line.startswith(const.MARKER_FILE_MAGICK_STRING)
+            version = int(magick_line.split("_")[-1])
+            if version not in const.SUPPORTED_MARKER_FILE_VERSIONS:
+                wx.MessageBox(_("Unknown version of the markers file."), _("InVesalius 3"))
+                return
+
+            # Use the first line after the magick_line as the names for dictionary keys.
+            column_names = file.readline().strip().split("\t")
+            column_names_parsed = [utils.parse_value(name) for name in column_names]
+
+            markers_data = []
+            for line in file:
+                values = line.strip().split("\t")
+                values_parsed = [utils.parse_value(value) for value in values]
+                marker_data = dict(zip(column_names_parsed, values_parsed))
+
+                markers_data.append(marker_data)
+
+        # Create markers from the dictionary.
+        markers_list = []
+        for data in markers_data:
+            marker = Marker(version=version)
+            marker.from_dict(data)
+
+            # When loading markers from file, do not set target based on is_target
+            marker.is_target = False
+
+            markers_list.append(marker)
+            if load_image_fiducials and marker.label in gui_utils.list_fiducial_labels():
+                Publisher.sendMessage(
+                    "Load image fiducials", label=marker.label, position=marker.position
+                )
+        if not fiducials_only:
+            markers.AddMultiple(markers_list)
+
+    except Exception as e:
+        wx.MessageBox(_("Could not import markers"), _("InVesalius 3"))
+        utils.debug(str(e))
+
+
+def ImportMarkers():
+    """
+    Show dialog to load markers from file.
+    Markers are appended to the end of the current marker list.
+    """
+    from invesalius.navigation.navigation import NavigationHub
+
+    markers = NavigationHub().markers
+
+    last_directory = ses.Session().GetConfig("last_directory_3d_surface", "")
+    dialog = FileSelectionDialog(_("Load markers"), last_directory, const.WILDCARD_MARKER_FILES)
+    overwrite_image_checkbox = wx.CheckBox(dialog, -1, _("Overwrite current image fiducials"))
+    clear_checkbox = wx.CheckBox(dialog, -1, _("Clear all previous markers"))
+    options_sizer = wx.StaticBoxSizer(wx.VERTICAL, dialog)
+    options_sizer.Add(overwrite_image_checkbox, 0, wx.LEFT)
+    options_sizer.Add(clear_checkbox, 0, wx.LEFT)
+    dialog.sizer.Add(options_sizer, 0, wx.EXPAND | wx.ALL, 5)
+    dialog.FitSizers()
+
+    if dialog.ShowModal() == wx.ID_OK:
+        filename = dialog.GetPath()
+
+        if clear_checkbox.GetValue():
+            markers.Clear()
+
+        LoadMarkersFile(filename, load_image_fiducials=overwrite_image_checkbox.GetValue())
+
+
+def ImportImageFiducials():
+    """
+    Show dialog to load image fiducials from markers file
+    """
+    from invesalius.navigation.navigation import NavigationHub
+
+    markers = NavigationHub().markers
+
+    last_directory = ses.Session().GetConfig("last_directory_3d_surface", "")
+    dialog = FileSelectionDialog(
+        _("Load image fiducials from markers file"), last_directory, const.WILDCARD_MARKER_FILES
+    )
+    load_markers_checkbox = wx.CheckBox(dialog, -1, _("Load other markers from file"))
+    clear_checkbox = wx.CheckBox(dialog, -1, _("Clear all previous markers"))
+    options_sizer = wx.StaticBoxSizer(wx.VERTICAL, dialog)
+    options_sizer.Add(load_markers_checkbox, 0, wx.LEFT)
+    options_sizer.Add(clear_checkbox, 0, wx.LEFT)
+    dialog.sizer.Add(options_sizer, 0, wx.EXPAND | wx.ALL, 5)
+    dialog.FitSizers()
+
+    if dialog.ShowModal() == wx.ID_OK:
+        filename = dialog.GetPath()
+
+        if clear_checkbox.GetValue():
+            markers.Clear()
+
+        load_fiducials_only = not load_markers_checkbox.GetValue()
+        LoadMarkersFile(filename, load_image_fiducials=True, fiducials_only=load_fiducials_only)
+
+
 class ProgressBarHandler(wx.ProgressDialog):
     def __init__(
         self,

invesalius/gui/task_navigator.py

@@ -16,7 +16,7 @@
 #    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
 #    detalhes.
 # --------------------------------------------------------------------------
-import itertools
+
 import os
 import time
 from functools import partial
@@ -45,6 +45,7 @@
 import invesalius.constants as const
 import invesalius.data.coordinates as dco
 import invesalius.gui.dialogs as dlg
+import invesalius.gui.utils as gui_utils
 import invesalius.project as prj
 import invesalius.session as ses
 from invesalius import inv_paths, utils
@@ -428,10 +429,14 @@ def __init__(self, parent, nav_hub):
         next_button.Disable()
         self.next_button = next_button
 
+        load_from_file_button = wx.Button(self, label="Load From File")
+        load_from_file_button.Bind(wx.EVT_BUTTON, self.OnLoadFromFile)
+
         top_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        top_sizer.AddMany([(start_button), (reset_button)])
+        top_sizer.AddMany([start_button, reset_button])
 
         bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        bottom_sizer.Add(load_from_file_button)
         bottom_sizer.Add(next_button)
 
         sizer = wx.GridBagSizer(5, 5)
@@ -460,7 +465,7 @@ def __init__(self, parent, nav_hub):
             [
                 (top_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 10),
                 (sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.LEFT | wx.RIGHT, 5),
-                (bottom_sizer, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.TOP, 30),
+                (bottom_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.LEFT | wx.RIGHT | wx.BOTTOM, 30),
             ]
         )
         self.sizer = main_sizer
@@ -564,6 +569,9 @@ def OnResetImageFiducials(self):
         self.start_button.SetValue(False)
         self.OnStartRegistration(self.start_button, self.start_button)
 
+    def OnLoadFromFile(self, evt):
+        dlg.ImportImageFiducials()
+
     def StartRegistration(self):
         Publisher.sendMessage("Enable style", style=const.STATE_REGISTRATION)
         for button in self.btns_set_fiducial:
@@ -2250,6 +2258,7 @@ def __bind_events(self):
         Publisher.subscribe(self._UnsetTarget, "Unset target")
         Publisher.subscribe(self._UnsetPointOfInterest, "Unset point of interest")
         Publisher.subscribe(self._UpdateMarkerLabel, "Update marker label")
+        Publisher.subscribe(self._SetMarkersListRendering, "Set markers list rendering")
         Publisher.subscribe(self._UpdateMEP, "Update marker mep")
 
         Publisher.subscribe(self.SetBrainTarget, "Set brain targets")
@@ -2384,13 +2393,6 @@ def _UpdateMEP(self, marker):
         # Trigger redraw MEP mapping
         Publisher.sendMessage("Redraw MEP mapping")
 
-    @staticmethod
-    def __list_fiducial_labels():
-        """Return the list of marker labels denoting fiducials."""
-        return list(
-            itertools.chain(*(const.BTNS_IMG_MARKERS[i].values() for i in const.BTNS_IMG_MARKERS))
-        )
-
     def UpdateCurrentCoord(self, position):
         self.current_position = list(position[:3])
         self.current_orientation = list(position[3:])
@@ -3291,7 +3293,7 @@ def OnDeleteAllMarkers(self, evt=None):
 
     def OnDeleteFiducialMarker(self, label):
         indexes = []
-        if label and (label in self.__list_fiducial_labels()):
+        if label and (label in gui_utils.list_fiducial_labels()):
             for id_n in range(self.marker_list_ctrl.GetItemCount()):
                 item = self.marker_list_ctrl.GetItem(id_n, const.LABEL_COLUMN)
                 if item.GetText() == label:
@@ -3395,146 +3397,8 @@ def OnCreateMarker(
         )
         self.markers.AddMarker(marker, render=True, focus=True)
 
-    # Given a string, try to parse it as an integer, float, or string.
-    #
-    # TODO: This shouldn't be here, but there's currently no good place for the function.
-    #   If csv-related functions are moved to a separate module, this function should be moved there.
-    def ParseValue(self, value):
-        value = value.strip()
-
-        # Handle None, booleans, empty list, and basic types
-        if value == "None":
-            return None
-        if value == "True":
-            return True
-        if value == "False":
-            return False
-        if value == "[]":
-            return []
-
-        # Handle lists and dictionaries
-        if value.startswith("[") and value.endswith("]"):
-            return self._parse_list(value)
-        if value.startswith("{") and value.endswith("}"):
-            return self._parse_dict(value)
-
-        # Try to convert to int or float
-        try:
-            if "." in value or "e" in value.lower():
-                return float(value)
-            return int(value)
-        except ValueError:
-            # Handle quoted strings
-            if (value.startswith('"') and value.endswith('"')) or (
-                value.startswith("'") and value.endswith("'")
-            ):
-                return value[1:-1]
-            return value  # Return as is if not recognized
-
-    def _parse_list(self, list_str):
-        """Parse a list from string format."""
-        return [
-            self.ParseValue(el.strip())
-            for el in self._split_by_outer_commas(list_str[1:-1].strip())
-        ]
-
-    def _parse_dict(self, dict_str):
-        """Parse a dictionary from string format."""
-        items = self._split_by_outer_commas(dict_str[1:-1].strip())
-        return {
-            self.ParseValue(kv.split(":", 1)[0].strip()): self.ParseValue(
-                kv.split(":", 1)[1].strip()
-            )
-            for kv in items
-        }
-
-    def _split_by_outer_commas(self, string):
-        """Split a string by commas that are not inside brackets or braces."""
-        elements = []
-        depth = 0
-        current_element = []
-
-        for char in string:
-            if char in "[{":
-                depth += 1
-            elif char in "]}" and depth > 0:
-                depth -= 1
-
-            if char == "," and depth == 0:
-                elements.append("".join(current_element).strip())
-                current_element = []
-            else:
-                current_element.append(char)
-
-        if current_element:
-            elements.append("".join(current_element).strip())
-
-        return elements
-
-    def GetMarkersFromFile(self, filename, overwrite_image_fiducials):
-        try:
-            with open(filename) as file:
-                magick_line = file.readline()
-                assert magick_line.startswith(const.MARKER_FILE_MAGICK_STRING)
-                version = int(magick_line.split("_")[-1])
-                if version not in const.SUPPORTED_MARKER_FILE_VERSIONS:
-                    wx.MessageBox(_("Unknown version of the markers file."), _("InVesalius 3"))
-                    return
-
-                # Use the first line after the magick_line as the names for dictionary keys.
-                column_names = file.readline().strip().split("\t")
-                column_names_parsed = [self.ParseValue(name) for name in column_names]
-
-                markers_data = []
-                for line in file:
-                    values = line.strip().split("\t")
-                    values_parsed = [self.ParseValue(value) for value in values]
-                    marker_data = dict(zip(column_names_parsed, values_parsed))
-
-                    markers_data.append(marker_data)
-
-            self.marker_list_ctrl.Hide()
-
-            # Create markers from the dictionary.
-            for data in markers_data:
-                marker = Marker(version=version)
-                marker.from_dict(data)
-
-                # When loading markers from file, we first create a marker with is_target set to False, and then call __set_marker_as_target.
-                marker.is_target = False
-
-                # Note that we don't want to render or focus on the markers here for each loop iteration.
-                self.markers.AddMarker(marker, render=False)
-
-                if overwrite_image_fiducials and marker.label in self.__list_fiducial_labels():
-                    Publisher.sendMessage(
-                        "Load image fiducials", label=marker.label, position=marker.position
-                    )
-
-        except Exception as e:
-            wx.MessageBox(_("Invalid markers file."), _("InVesalius 3"))
-            utils.debug(e)
-
-        self.marker_list_ctrl.Show()
-        Publisher.sendMessage("Render volume viewer")
-        Publisher.sendMessage("Update UI for refine tab")
-        self.markers.SaveState()
-
     def OnLoadMarkers(self, evt):
-        """Loads markers from file and appends them to the current marker list.
-        The file should contain no more than a single target marker. Also the
-        file should not contain any fiducials already in the list."""
-
-        last_directory = ses.Session().GetConfig("last_directory_3d_surface", "")
-        dialog = dlg.FileSelectionDialog(
-            _("Load markers"), last_directory, const.WILDCARD_MARKER_FILES
-        )
-        overwrite_checkbox = wx.CheckBox(dialog, -1, _("Overwrite current image fiducials"))
-        dialog.sizer.Add(overwrite_checkbox, 0, wx.CENTER)
-        dialog.FitSizers()
-        if dialog.ShowModal() == wx.ID_OK:
-            filename = dialog.GetPath()
-            self.GetMarkersFromFile(filename, overwrite_checkbox.GetValue())
+        dlg.ImportMarkers()
 
     def OnShowHideAllMarkers(self, evt, ctrl):
         if ctrl.GetValue():
@@ -3714,3 +3578,9 @@ def _AddMarker(self, marker, render, focus):
         # Focus on the added marker.
         if focus:
             self.FocusOnMarker(num_items)
+
+    def _SetMarkersListRendering(self, render):
+        if render:
+            self.marker_list_ctrl.Show()
+        else:
+            self.marker_list_ctrl.Hide()

invesalius/gui/utils.py

@@ -21,7 +21,18 @@
 if TYPE_CHECKING:
     import wx
 
+import itertools
+
+import invesalius.constants as const
+
 
 def calc_width_needed(widget: "wx.Window", num_chars: int) -> int:
     width, height = widget.GetTextExtent("M" * num_chars)
     return width
+
+
+def list_fiducial_labels():
+    """Return the list of marker labels denoting fiducials."""
+    return list(
+        itertools.chain(*(const.BTNS_IMG_MARKERS[i].values() for i in const.BTNS_IMG_MARKERS))
+    )