samhitech
diff --git a/‎README.md‎
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diff --git a/‎examples/miEye_scripts/AcquisitionLoopWithIntervals.py‎
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diff --git a/‎src/microEye/_version.py‎
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diff --git a/‎src/microEye/analysis/filters/spatial.py‎
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diff --git a/‎src/microEye/hardware/cams/__init__.py‎
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diff --git a/‎src/microEye/hardware/cams/basler/basler_cam.py‎
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diff --git a/‎src/microEye/hardware/cams/camera_list.py‎
Lines changed: 70 additions & 25 deletions b/‎src/microEye/hardware/cams/camera_list.py‎
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diff --git a/‎src/microEye/hardware/cams/dummy/dummy_panel.py‎
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@@ -7,16 +7,16 @@ The **`microEye`** is a Python toolkit for fluorescence microscopy that supports
 This toolkit is compatible with the [hardware](#hardware) used in our microscope. For further details, refer to the [miEye microscope paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy).
 
 ```bash
-   __  ____              ____                ___  ____  ___       ___ 
-  /  |/  (_)__________  / __/_ _____   _  __|_  |/ / / / _ \___ _|_  |
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __//_  _// // / _ `/ __/
+   __  ____              ____                ___  ____  ___       ____
+  /  |/  (_)__________  / __/_ _____   _  __|_  |/ / / / _ \___ _|_  /
+ / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __//_  _// // / _ `//_ <
 /_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)_/(_)___/\_,_/____/
                           /___/
-         ___   __     __          ___      __
-        / _ | / /__  / /  ___ _  / _ \___ / /__ ___ ____ ___
-       / __ |/ / _ \/ _ \/ _ `/ / , _/ -_) / -_) _ `(_-</ -_)
-      /_/ |_/_/ .__/_//_/\_,_/ /_/|_|\__/_/\__/\_,_/___/\__/
-             /_/
+                         ___   __     __                         
+                        / _ | / /__  / /  ___ _  
+                       / __ |/ / _ \/ _ \/ _ `/ 
+                      /_/ |_/_/ .__/_//_/\_,_/
+                             /_/
 ```
 
 ![Package Health](https://snyk.io/advisor/python/microEye/badge.svg)
 
@@ -1,8 +1,8 @@
-from microEye.hardware.cams import CameraList, Vimba_Panel
+from microEye.hardware.cams import CameraManager, Vimba_Panel
 from microEye.qt import QtCore
 from microEye.utils.thread_worker import QThreadWorker
 
-panel: Vimba_Panel = CameraList.CAMERAS['Vimba'][0]
+panel: Vimba_Panel = CameraManager.CAMERAS['Vimba'][0]
 
 iterations = 5  # number of iterations
 delay = 10  # delay in seconds
 
@@ -1,2 +1,2 @@
 version_info = (2, 4, 0)
-__version__ = '.'.join(map(str, version_info)) + 'a2'
+__version__ = '.'.join(map(str, version_info)) + 'a3'
@@ -3,6 +3,7 @@
 from typing import Optional
 
 import cv2
+import numba as nb
 import numpy as np
 from scipy import signal
 from scipy.fftpack import fft2, fftshift, ifft2, ifftshift
@@ -64,22 +65,8 @@ def gaussian_kernel(dim, sigma):
         return kernel
 
     def run(self, image: np.ndarray) -> np.ndarray:
-        rows, cols = image.shape
-        nrows = cv2.getOptimalDFTSize(rows)
-        ncols = cv2.getOptimalDFTSize(cols)
-        pad_rows = nrows - rows
-        pad_cols = ncols - cols
-
-        # Ensure that pad_cols[1] and pad_rows[1] are at least 1
-        pad_rows = (pad_rows // 2, max(1, pad_rows - pad_rows // 2))
-        pad_cols = (pad_cols // 2, max(1, pad_cols - pad_cols // 2))
-
-        nimg = np.pad(image, (pad_rows, pad_cols), mode='reflect')
-
         res = cv2.normalize(
-            signal.convolve2d(nimg, np.rot90(self.dog), mode='same')[
-                pad_rows[0] : -pad_rows[1], pad_cols[0] : -pad_cols[1]
-            ],
+            signal.fftconvolve(image, np.rot90(self.dog), mode='same'),
             None,
             0,
             255,
@@ -140,17 +127,15 @@ def gaussian_kernel(dim, sigma):
         return kernel
 
     def run(self, image: np.ndarray) -> np.ndarray:
-        point = signal.fftconvolve(image, np.rot90(self.point_kernel), mode='same')
-
-        return cv2.normalize(
-            signal.fftconvolve(point, np.rot90(self.gauss), mode='same'),
-            None,
-            0,
-            255,
-            cv2.NORM_MINMAX,
-            cv2.CV_8U,
+        # precompute combined kernel if possible
+        _combined_kernel = signal.convolve2d(
+            np.rot90(self.gauss), np.rot90(self.point_kernel), mode='full'
         )
 
+        point = signal.fftconvolve(image, np.rot90(_combined_kernel), mode='same')
+
+        return cv2.normalize(point, None, 0, 255, cv2.NORM_MINMAX, cv2.CV_8U)
+
     def get_tree_parameters(self):
         '''Return the parameters for the pyqtgraph tree view.'''
         return {
@@ -171,6 +156,30 @@ def get_tree_parameters(self):
         }
 
 
+@nb.njit(parallel=True)
+def radial_coordinates_nb(shape):
+    '''Generates a 2D array with radial cordinates
+    with according to the first two axis of the
+    supplied shape tuple
+
+    Returns
+    -------
+    R, Rsq
+        Radius 2d matrix (R) and radius squared matrix (Rsq)
+    '''
+    R = np.zeros(shape, dtype=np.float32)
+    Rsq = np.zeros(shape, dtype=np.float32)
+
+    center = (shape[0] // 2, shape[1] // 2)
+
+    for i in nb.prange(shape[0]):
+        for j in range(shape[1]):
+            R[i, j] = np.sqrt((i - center[0]) ** 2 + (j - center[1]) ** 2)
+            Rsq[i, j] = R[i, j] ** 2
+
+    return R, Rsq
+
+
 class FourierFilter(SpatialFilter):
     class PROFILES(Enum):
         Gaussian = 1
@@ -241,14 +250,7 @@ def radial_coordinates(self, shape):
         R, Rsq
             Radius 2d matrix (R) and radius squared matrix (Rsq)
         '''
-        y_len = np.arange(-shape[0] // 2, shape[0] // 2)
-        x_len = np.arange(-shape[1] // 2, shape[1] // 2)
-
-        X, Y = np.meshgrid(x_len, y_len)
-
-        Rsq = X**2 + Y**2
-
-        self._radial_coordinates = (np.sqrt(Rsq), Rsq)
+        self._radial_coordinates = radial_coordinates_nb(shape[:2])
 
         return self._radial_coordinates
 
 
@@ -1,5 +1,5 @@
 from microEye.hardware.cams.camera_calibration import dark_calibration
-from microEye.hardware.cams.camera_list import CameraList
+from microEye.hardware.cams.camera_list import CameraList, CameraManager
 from microEye.hardware.cams.camera_panel import Camera_Panel, CamParams
 from microEye.hardware.cams.jobs import AcquisitionJob
 from microEye.hardware.cams.linescan.IR_Cam import (
 
@@ -994,6 +994,9 @@ def GrabOne(self) -> Optional[np.ndarray]:
         if res.GrabSucceeded():
             return res.GetArray()
 
+    def snap_image(self):
+        return self.GrabOne()
+
     def RetrieveResult(self, timeout: int) -> Optional[pylon.GrabResult]:
         '''Retrieve the result of the grabbing
 
 
@@ -80,13 +80,12 @@
     },
 }
 
-class CameraList(QtWidgets.QWidget):
+# singleton camera manager class
+class CameraManager(QtCore.QObject):
     '''
-    A widget for displaying and managing a list of cameras.
+    A singleton class to manage camera instances.
     '''
-
-    cameraAdded = Signal(Camera_Panel, bool)
-    cameraRemoved = Signal(Camera_Panel, bool)
+    _instance = None
 
     CAMERAS : dict[str, list[dict]] = {
         'Basler': [],
@@ -97,6 +96,62 @@ class CameraList(QtWidgets.QWidget):
         'Vimba': [],
     }
 
+    def __new__(cls, *args, **kwargs):
+        if not cls._instance:
+            cls._instance = super().__new__(cls, *args, **kwargs)
+        return cls._instance
+
+    @classmethod
+    def instance(cls):
+        if cls._instance is None:
+            return CameraManager()
+
+        return cls._instance
+
+    def __init__(self):
+        super().__init__()
+
+        self.cam_list = None
+        self.cached_autofocusCam = None
+
+    @property
+    def autofocusCam(self) -> typing.Union[Camera_Panel, None]:
+        '''
+        Get the autofocus camera panel.
+
+        Returns
+        -------
+        Camera_Panel | None
+            The autofocus camera panel, or None if no autofocus camera is available.
+        '''
+        if self.cached_autofocusCam is None:
+            self.cached_autofocusCam = next(
+                (
+                    cam['Panel']
+                    for _, cam_list in CameraManager.CAMERAS.items()
+                    for cam in cam_list
+                    if cam['IR']
+                ),
+                None,
+            )
+        return self.cached_autofocusCam
+
+    @classmethod
+    def snap_ir_image(cls):
+        '''
+        Snap an image on the IR camera if available.
+        '''
+        if cls.instance().autofocusCam is not None:
+            return cls.instance().autofocusCam.cam.snap_image()
+
+class CameraList(QtWidgets.QWidget):
+    '''
+    A widget for displaying and managing a list of cameras.
+    '''
+
+    cameraAdded = Signal(Camera_Panel, bool)
+    cameraRemoved = Signal(Camera_Panel, bool)
+
     def __init__(self, parent: typing.Optional['QtWidgets.QWidget'] = None):
         '''
         Initialize the camera list widget.
@@ -108,9 +163,10 @@ def __init__(self, parent: typing.Optional['QtWidgets.QWidget'] = None):
         '''
         super().__init__(parent=parent)
 
+        self.__camera_manager = CameraManager.instance()
+
         self.cam_list = None
         self.item_model = QtGui.QStandardItemModel()
-        self.cached_autofocusCam = None
 
         #  Layout
         self.InitLayout()
@@ -172,17 +228,7 @@ def autofocusCam(self) -> typing.Union[Camera_Panel, None]:
         Camera_Panel | None
             The autofocus camera panel, or None if no autofocus camera is available.
         '''
-        if self.cached_autofocusCam is None:
-            self.cached_autofocusCam = next(
-                (
-                    cam['Panel']
-                    for _, cam_list in CameraList.CAMERAS.items()
-                    for cam in cam_list
-                    if cam['IR']
-                ),
-                None,
-            )
-        return self.cached_autofocusCam
+        return self.__camera_manager.autofocusCam
 
     def add_camera_clicked(self):
         '''
@@ -244,7 +290,6 @@ def add_camera(self, cam, mini=False):
         else:
             self._display_warning_message('Device is in use or already added.')
 
-
     def _add_camera_generic(self, cam, mini, config):
         '''
         Generic camera/panel adder.
@@ -277,7 +322,7 @@ def _add_camera_generic(self, cam, mini, config):
         panel : Camera_Panel = panel_class(*args)
 
         # Add to CAMERAS dict
-        CameraList.CAMERAS[driver].append(
+        CameraManager.CAMERAS[driver].append(
             {'Camera': panel.cam, 'Panel': panel, 'IR': mini, 'Info': cam}
         )
         return panel
@@ -344,7 +389,7 @@ def remove_camera(self, cam):
         cam : dict
             The camera information dictionary.
         '''
-        cams: list[dict] = CameraList.CAMERAS.get(cam['Driver'], [])
+        cams: list[dict] = CameraManager.CAMERAS.get(cam['Driver'], [])
         if cams:
             for item in cams:
                 pan: Camera_Panel = item['Panel']
@@ -377,7 +422,7 @@ def removeAllCameras(self):
         Remove all cameras.
         Stops any active acquisitions and properly disposes of camera resources.
         '''
-        for _, camera_list in self.CAMERAS.items():
+        for _, camera_list in CameraManager.CAMERAS.items():
             # Create a copy of the list since we'll be modifying it during iteration
             for camera_info in camera_list[:]:
                 panel: Camera_Panel = camera_info['Panel']
@@ -485,22 +530,22 @@ def update_list(self):
         self.cam_table.setModel(self.item_model)
 
         # Update the cached_autofocusCam value
-        self.cached_autofocusCam = None
+        self.__camera_manager.cached_autofocusCam = None
 
     @classmethod
     def update_gui(cls):
         '''
         Update the GUI of all added cameras.
         '''
-        for _, cam_list in cls.CAMERAS.items():
+        for _, cam_list in CameraManager.CAMERAS.items():
             for cam in cam_list:
                 cam['Panel'].updateInfo()
 
     def snap_image(self):
         '''
         Snap an image on all non IR cameras.
         '''
-        for _, cam_list in CameraList.CAMERAS.items():
+        for _, cam_list in CameraManager.CAMERAS.items():
             for cam in cam_list:
                 if not cam['IR']:
                     cam['Panel'].capture_image()
@@ -518,7 +563,7 @@ def get_config(self):
         '''
         config : list[dict] = []
 
-        for _, cam_list in CameraList.CAMERAS.items():
+        for _, cam_list in CameraManager.CAMERAS.items():
             for cam in cam_list:
                 cam_config : dict = cam['Info'].copy()
                 cam_config['IR'] = cam['IR']
 
@@ -133,7 +133,7 @@ def cam_capture(self, *args, **kwargs):
 
                 self._buffer.put(
                     self._cam.get_dummy_image_from_pattern(
-                        self.acq_job.frames_captured / 100
+                        cycle_time * 1e-9
                     ).tobytes()
                 )
                 # add sensor temperature to the stack
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`version_info = (2, 4, 0)`
`2`		`-__version__ = '.'.join(map(str, version_info)) + 'a2'`
	`2`	`+__version__ = '.'.join(map(str, version_info)) + 'a3'`
Original file line number	Diff line number	Diff line change
`@@ -133,7 +133,7 @@ def cam_capture(self, args, *kwargs):`
`133`	`133`
`134`	`134`	`self._buffer.put(`
`135`	`135`	`self._cam.get_dummy_image_from_pattern(`
`136`		`- self.acq_job.frames_captured / 100`
	`136`	`+ cycle_time * 1e-9`
`137`	`137`	`).tobytes()`
`138`	`138`	`)`
`139`	`139`	`# add sensor temperature to the stack`