Ximea Updates

src/navigate/controller/sub_controllers/acquire_bar.py

@@ -541,7 +541,7 @@ def toggle_bdv_widgets(self, main_widget: str, dependent_widgets: list) -> None:
         state = self.acquire_pop.tab_frame.inputs[main_widget].get_variable().get()
         for widget in dependent_widgets:
             self.acquire_pop.tab_frame.inputs[widget].widget.config(
-                state="readonly" if state else "disabled"
+                state="normal" if state else "disabled"
             )
 
     def update_microscope_mode(self, *args: Iterable) -> None:

src/navigate/model/devices/camera/base.py

@@ -126,7 +126,7 @@ def __init__(
         # readout time in model and controller
         self.camera_parameters["trigger_source"] = 2.0 # external trigger
         self.camera_parameters["readout_speed"] = 1.0
-        self.camera_parameters["pixel_size_in_microns"] = 6.5
+        # self.camera_parameters["pixel_size_in_microns"] = 6.5
         self.camera_parameters["trigger_active"] = 1.0
         self.camera_parameters["trigger_mode"] = 1.0 # standard trigger mode
         self.camera_parameters["trigger_polarity"] = 2.0

src/navigate/model/devices/camera/ximea.py

@@ -36,6 +36,7 @@
 
 # Third Party Imports
 from ximea import xiapi
+import numpy as np
 
 # Local Imports
 from navigate.model.devices.camera.base import CameraBase
@@ -73,6 +74,7 @@ def __init__(
         super().__init__(microscope_name, device_connection, configuration)
 
         #: str: Name of the microscope
+        self._frames_received = None
         self.microscope_name = microscope_name
 
         #: object: Camera Object
@@ -81,6 +83,15 @@ def __init__(
         #: dict: Configuration settings
         self.configuration = configuration
 
+        #: bool: Auto restart flag
+        self.auto_restart = True
+
+        #: int: Auto restart counter
+        self.auto_restart_counter = 0
+
+        #: int: Timeout counter
+        self.timeout_counter = 0
+
         #: dict: Camera parameters
         self.camera_parameters["x_pixels"] = self.cam.get_param("width:max")
         self.camera_parameters["y_pixels"] = self.cam.get_param("height:max")
@@ -379,7 +390,7 @@ def set_ROI_and_binning(self, roi_width=2048, roi_height=2048, center_x=1024, ce
         result = self.set_ROI(roi_width, roi_height, center_x, center_y)
         return result
 
-    def initialize_image_series(self, data_buffer=None, number_of_frames=100):
+    def initialize_image_series(self, data_buffer=None, number_of_frames=1000):
         """Initialize Ximea Camera image series.
 
         Parameters
@@ -395,8 +406,12 @@ def initialize_image_series(self, data_buffer=None, number_of_frames=100):
         self._number_of_frames = number_of_frames
         self._frames_received = 0
 
-        # set buffer policy: XI_BP_SAFE
-        self.cam.set_param("buffer_policy", "XI_BP_SAFE")
+        # # set buffer policy: XI_BP_SAFE
+        # self.cam.set_param("buffer_policy", "XI_BP_SAFE")
+
+        # *** use UNSAFE
+        self.cam.set_param("buffer_policy", "XI_BP_UNSAFE")
+
         # set image data format to XI_MONO16, this value can be set only if acquisition is stopped.
         self.cam.set_param('imgdataformat', "XI_MONO16")
         #imgpayloadsize changes automatically after setting imgdataformat
@@ -422,15 +437,29 @@ def get_new_frame(self):
         frame : numpy.ndarray
             Frame ids from Ximea camera.
         """
-        # attach buffer to image object
-        self._image.bp = self._data_buffer[self._frames_received].ctypes.data
-        self._image.bp_size = self._data_buffer[self._frames_received].nbytes
+        # # attach buffer to image object
+        # self._image.bp = self._data_buffer[self._frames_received].ctypes.data
+        # self._image.bp_size = self._data_buffer[self._frames_received].nbytes
         # get data from camera
         try:
             self.cam.get_image(self._image, 500)
         except xiapi.Xi_error as e:
+            if e.status == 10:  # XI_ERR_TIMEOUT
+                self.timeout_counter += 1
+                if self.auto_restart and self.timeout_counter >= 5 and self.auto_restart_counter < 3:
+                    self.auto_restart_counter += 1
+                    logger.warning(f"Timeout error while getting image. Restarting acquisition. Auto restart it {self.auto_restart_counter}")
+                    self.cam.stop_acquisition()
+                    self.cam.start_acquisition()
+                    return [-1]
             logger.error(f"Error getting image from camera: {e}")
             return []
+        self.auto_restart_counter = 0
+        self.timeout_counter = 0
+        # *** copy image to data buffer
+        self._data_buffer[self._frames_received][:, :] = np.copy(
+            self._image.get_image_data_numpy()
+        )
 
         frames_received = [self._frames_received]
 

src/navigate/model/features/common_features.py

@@ -37,6 +37,7 @@
 from threading import Lock
 import logging
 from multiprocessing.managers import ListProxy
+from queue import Queue, Empty
 
 # Third party imports
 
@@ -1119,7 +1120,7 @@ def __init__(
         # TODO: distance > 1000 should not be hardcoded and somehow related to
         #  different kinds of stage devices.
         #: int: The stage distance threshold for pausing the data thread.
-        self.stage_distance_threshold = 1000
+        self.stage_distance_threshold = 200
 
         #: dict: A dictionary of the previous position in the multi-position table.
         self.pre_position = None
@@ -1156,6 +1157,7 @@ def __init__(
 
         self.prepare_next_channel = PrepareNextChannel(model)
 
+
         #: dict: A dictionary defining the configuration for the z-stack acquisition
         self.config_table = {
             "signal": {
@@ -1172,6 +1174,12 @@ def __init__(
             "node": {"node_type": "multi-step", "device_related": True},
         }
 
+        if self.model.active_microscope_name == "Macroscale":
+            self.data_queue = Queue()
+            self.config_table["signal"]["response"] = self.signal_response_func
+
+        self.resend_trigger = False
+
     def get_microscope_state(self, microscope_state: dict) -> None:
         """Get the microscope state from the configuration.
 
@@ -1313,6 +1321,9 @@ def signal_func(self):
             A boolean value indicating whether to continue the z-stack acquisition
             process.
         """
+        if self.resend_trigger:
+            return True
+
         if self.model.stop_acquisition:
             return False
         data_thread_is_paused = False
@@ -1414,6 +1425,8 @@ def signal_end(self) -> bool:
         bool
             A boolean value indicating whether to end the current node.
         """
+        if self.resend_trigger:
+            return False
 
         # end this node
         if self.model.stop_acquisition:
@@ -1483,6 +1496,21 @@ def signal_end(self) -> bool:
 
         return False
 
+    def signal_response_func(self, *args) -> bool:
+        try:
+            r = self.data_queue.get(timeout=100)
+            if r == -1:
+                self.resend_trigger = True
+            else:
+                self.resend_trigger = False
+        except Empty:
+            logger.warning(
+                "ZStackAcquisition: No data received within the timeout period."
+            )
+            return False
+
+        return True
+
     def update_channel(self) -> None:
         """Update the active channel during multichannel acquisition.
 
@@ -1519,10 +1547,18 @@ def in_data_func(self, frame_ids: list) -> None:
             A list of frame IDs received during data acquisition.
 
         """
+
+        if -1 in frame_ids and hasattr(self, "data_queue"):
+            self.data_queue.put(-1)
+            self.received_frames += frame_ids.index(-1)
+            return
         self.received_frames += len(frame_ids)
         if self.image_writer is not None:
             self.image_writer.save_image(frame_ids)
 
+        if hasattr(self, "data_queue"):
+            self.data_queue.put(True)
+
     def end_data_func(self) -> bool:
         """Check if all expected data frames have been received.
 

src/navigate/view/popups/acquire_popup.py

@@ -426,7 +426,7 @@ def __init__(self, parent: AcquirePopUp, frame: ttk.Frame) -> None:
             input_class=ValidatedSpinbox,
             input_var=tk.StringVar(),
             input_args={
-                "from_": 0,
+                "from_": -360,
                 "to": 360,
                 "increment": 1,
             },
@@ -443,7 +443,7 @@ def __init__(self, parent: AcquirePopUp, frame: ttk.Frame) -> None:
             input_class=ValidatedSpinbox,
             input_var=tk.StringVar(),
             input_args={
-                "from_": 0,
+                "from_": -360,
                 "to": 360,
                 "increment": 1,
             },
@@ -455,11 +455,11 @@ def __init__(self, parent: AcquirePopUp, frame: ttk.Frame) -> None:
         self.inputs["rotate_angle_z"] = LabelInput(
             parent=rotate_notebook,
             label_pos="top",
-            label="Y Angle",
+            label="Z Angle",
             input_class=ValidatedSpinbox,
             input_var=tk.StringVar(),
             input_args={
-                "from_": 0,
+                "from_": -360,
                 "to": 360,
                 "increment": 1,
             },