Probe_angle (5DOF) & Consensus of TransM

parallax/__init__.py

@@ -4,7 +4,7 @@
 
 import os
 
-__version__ = "1.12.0"
+__version__ = "1.13.0"
 
 # allow multiple OpenMP instances
 os.environ["KMP_DUPLICATE_LIB_OK"] = "True"

parallax/control_panel/probe_calibration_handler.py

@@ -13,6 +13,8 @@
 from parallax.probe_calibration.probe_calibration import ProbeCalibration
 from parallax.handlers.calculator import Calculator
 from parallax.handlers.reticle_metadata import ReticleMetadata
+from parallax.utils.coords_converter import get_transMs_bregma_to_local
+from parallax.utils.probe_angles import find_probe_angle, find_probe_angles_dict
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.WARNING)
@@ -25,6 +27,9 @@ class StageCalibrationInfo:
     """
     detection_status: str = "default"  # options: default, process, accepted
     transM: Optional[np.ndarray] = None
+    transM_bregma: Optional[dict] = None
+    arc_angle_global: Optional[tuple] = None
+    arc_angle_bregma: Optional[dict] = None
     L2_err: Optional[float] = None
     dist_travel: Optional[np.ndarray] = None
     status_x: Optional[str] = None
@@ -500,6 +505,10 @@ def probe_detect_accepted_status(self, switch_probe=False):
             return
 
         self.probe_detection_status = "accepted"
+
+        # Update reticle selector
+        self.reticle_metadata.load_metadata_from_file()
+
         # Update into model
         self.update_stage_info_to_model(self.selected_stage_id)
         self.model.set_calibration_status(self.selected_stage_id, True)
@@ -536,9 +545,6 @@ def probe_detect_accepted_status(self, switch_probe=False):
             self.filter = "no_filter"
             logger.debug(f"filter: {self.filter}")
 
-        # Update reticle selector
-        self.reticle_metadata.load_metadata_from_file()
-
 
     def update_probe_calib_status_transM(self, transformation_matrix):
         """
@@ -607,6 +613,7 @@ def display_probe_calib_status(self, transM, L2_err, dist_travel):
 
     def update_probe_calib_status(self, moving_stage_id, transM, L2_err, dist_travel):
         """
+        Handler for the signal emitted when the probe calibration. (transM_info)
         Updates the probe calibration status based on the moving stage ID and the provided calibration data.
         If the selected stage matches the moving stage, the calibration data is displayed on the UI.
         """
@@ -786,6 +793,14 @@ def update_stage_info_to_model(self, stage_id) -> None:
         stage_info.status_y = self.calib_status_y
         stage_info.status_z = self.calib_status_z
 
+        # Update transM from bregma if available
+        transMbs = get_transMs_bregma_to_local(self.model, stage_id)
+        stage_info.transM_bregma = transMbs
+
+        # Get 3D angle
+        stage_info.arc_angle_global = find_probe_angle(self.transM)
+        stage_info.arc_angle_bregma = find_probe_angles_dict(transMbs)
+
     def update_stage_info(self, info):
         if isinstance(info, StageCalibrationInfo):
             self.transM = info.transM

parallax/handlers/calculator.py

@@ -11,7 +11,7 @@
 from PyQt6.uic import loadUi
 from PyQt6.QtCore import Qt
 
-from parallax.utils.coords_converter import CoordsConverter
+from parallax.utils.coords_converter import local_to_global, global_to_local
 from parallax.stages.stage_controller import StageController
 from parallax.config.config_path import ui_dir
 
@@ -167,11 +167,11 @@ def _convert(self, sn):
         logger.debug(f"User Input (Local): {self.reticle}")
         trans_type, local_pts, global_pts = self._get_transform_type(globalX, globalY, globalZ, localX, localY, localZ)
         if trans_type == "global_to_local":
-            local_pts_ret = CoordsConverter.global_to_local(self.model, sn, global_pts, self.reticle)
+            local_pts_ret = global_to_local(self.model, sn, global_pts, self.reticle)
             if local_pts_ret is not None:
                 self._show_local_pts_result(sn, local_pts_ret)
         elif trans_type == "local_to_global":
-            global_pts_ret = CoordsConverter.local_to_global(self.model, sn, local_pts, self.reticle)
+            global_pts_ret = local_to_global(self.model, sn, local_pts, self.reticle)
             if global_pts_ret is not None:
                 self._show_global_pts_result(sn, global_pts_ret)
         else:
@@ -434,8 +434,8 @@ def _is_z_safe_pos(self, stage_sn, x, y, z):
                 continue
             try:
                 # Apply transformations to get global points for Z=15 and Z=0
-                global_pts_z15 = CoordsConverter.local_to_global(self.model, stage_sn, local_pts_z15)
-                global_pts_z0 = CoordsConverter.local_to_global(self.model, stage_sn, local_pts_z0)
+                global_pts_z15 = local_to_global(self.model, stage_sn, local_pts_z15)
+                global_pts_z0 = local_to_global(self.model, stage_sn, local_pts_z0)
 
                 if global_pts_z15 is None or global_pts_z0 is None:
                     return False  # Transformation failed, return False

parallax/handlers/reticle_metadata.py

@@ -72,6 +72,7 @@ def __init__(self, model, reticle_selector):
         self.ui.add_btn.clicked.connect(self._add_groupbox)
         self.ui.update_btn.clicked.connect(self._update_reticle_info)
 
+        # Update reticle selector
         self.model.add_reticle_metadata_instance(self)
 
     def load_metadata_from_file(self):
@@ -87,7 +88,7 @@ def load_metadata_from_file(self):
             Exception: If there is an error reading the metadata file, logs the error.
         """
         if not os.path.exists(reticle_metadata_file):
-            logger.info("No existing metadata file found. Starting fresh.")
+            logger.debug("No existing metadata file found. Starting fresh.")
             return
 
         try:
@@ -98,7 +99,8 @@ def load_metadata_from_file(self):
                 for group_box in self.groupboxes.values():
                     self._update_reticles(group_box)
                 self._update_to_reticle_selector()
-
+            else:
+                logger.debug("Metadata json file is empty. Starting fresh.")
         except Exception as e:
             logger.error(f"Error reading metadata file: {e}")
 
@@ -111,6 +113,7 @@ def _create_groupbox_from_metadata(self, reticle_data):
                 return  # Do not add a new groupbox if it already exists
 
             self._populate_groupbox(name, reticle_info)
+            logger.debug(f"Created groupbox for reticle: {name}")
 
     def _add_groupbox(self):
         """This method creates new groupboxes with an alphabet name."""

parallax/model.py

@@ -360,7 +360,7 @@ def get_reticle_metadata(self, reticle_name):
         Returns:
             dict: Metadata information for the reticle.
         """
-        return self.reticle_metadata.get(reticle_name)
+        return self.reticle_metadata.get(reticle_name, None)
 
     def remove_reticle_metadata(self, reticle_name):
         """Remove reticle metadata.