microeye 2.4.0rc2__tar.gz → 2.4.2__tar.gz

{microeye-2.4.0rc2/src/microeye.egg-info → microeye-2.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microeye
-Version: 2.4.0rc2
+Version: 2.4.2
 Summary: A python toolkit for fluorescence microscopy         that features hardware control, data analysis and vizualization         for super-resolution single-molecule localization microscopy and         single-partical tracking.
 Home-page: https://github.com/samhitech/microEye
 Author: Mohammad Nour Alsamsam
@@ -72,14 +72,15 @@ 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) -->
+
 ![Python Version](https://img.shields.io/badge/Python-3.11-blue)
 ![Package Version](https://img.shields.io/pypi/v/microEye.svg)
 ![Package Version](https://img.shields.io/badge/GUI_Platform-PySide6|PyQt6|PyQt5-navy)
@@ -103,9 +104,132 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Forks](https://img.shields.io/github/forks/samhitech/microEye.svg)
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
+## What's New in microEye 2.4
+
+- **Stage Control Overhaul**
+
+  Stage management has been completely redesigned with a unified controller
+  that handles all stage types through a single, consistent interface. A new
+  Stage Manager lets you add, remove, and assign stages to axes on the fly.
+  Per-axis soft limits, configurable center positions, and a new Calibrate
+  action make setup safer and more repeatable. Dedicated **XY and Z Center
+  buttons** in the Controller dock move stages to their configured center
+  positions in one click.
+
+- **SmarAct MCS2 Support**
+
+  Full support for SmarAct MCS2 multi-channel controllers, including guided
+  setup, calibration, homing, and soft-limit configuration for reliable
+  multi-axis motion.
+
+- **Slides Widget**
+
+  A new Slides dock lets you visualize and navigate multi-channel slide
+  layouts (Sticky-Slide VI, µ-Slide VI, 8/18 Well, and more). Click any
+  channel to move the stage to its center, with live position and delta
+  readouts, position overlays, and context menu options for axis orientation
+  and inversion. Layout settings persist across sessions.
+
+- **Focus Stabilization Improvements**
+
+  The focus stabilizer has been thoroughly refactored. Each axis now has
+  independent PID gains and calibration. New stabilization methods are
+  supported — including Reflection peak fitting, Fiducial/Fourier, and a
+  Hybrid XYZ mode. Frame statistics (count, mean, median) are now tracked
+  and the stabilizer waits for a sufficient number of frames before locking,
+  reducing false engagements. Plots dynamically show only the data relevant
+  to the active method, and all settings persist across sessions.
+
+- **New Analysis & Calibration Tools**
+
+  Three new calibration workflows are available from the Multi-Viewer Tools
+  menu:
+  - **Dark Calibration** — directory-based mean/variance analysis with
+    results cache, import/export, and dataset comparison.
+  - **Photon Transfer Curve (PTC)** — dataset import, run/cache workflows,
+    cache comparison, and Dark-Cal JSON export.
+  - **Sphere Power Calibration** — calibration utilities integrated into
+    the PTC workflow.
+
+  A new **Image Registration** tool for aligning and merging multi-channel
+  stacks (with transformation export/import) is also available in the
+  Multi-Viewer Tools menu.
+
+- **Expanded Camera Support**
+
+  Cameras from Basler, Allied Vision (Vimba X SDK), IDS Peak, Thorlabs,
+  PCO, and PycroManager now share unified ROI, exposure, and framerate
+  handling. Notable additions:
+  - **IDS Peak** is newly supported with binning, flash, and full ROI and
+    acquisition flow.
+  - **Basler** is newly supported.
+  - **Vimba X** gains black level, gain, correction, and binning controls,
+    plus CTI auto-discovery via `VIMBA_X_HOME` / `VIMBA_X_CTI`.
+  - All camera configurations are **automatically saved and restored** on
+    next launch when detected.
+
+- **Laser & Device Controls**
+
+  The Controller dock now shows color-coded, wavelength-aware indicators
+  for each laser and relay. Clicking an indicator toggles the laser state
+  directly from the main UI. Relay mode labels (ON/F1/F2) are shown
+  alongside each laser.
+
+- **Experiment Protocol Designer**
+
+  The protocol action list gains a new **ListLoop** action type for
+  repeating sequences of steps. The parameter adjustment UI now sorts
+  target objects, shows readable labels, and correctly handles integer and
+  float editors.
+
+- **Program-Wide Logging**
+
+  Structured logging replaces scattered print statements across the entire
+  codebase. Log level, file output, and console output are configurable via
+  the launcher UI or CLI flags (`--log-level`, `--no-log-file`,
+  `--no-log-console`). Logs are written per session under `./logs` for
+  easier troubleshooting.
+
+- **Image I/O & Data Handling**
+
+  Image handling has been refactored into a dedicated `microEye.images`
+  package. Zarr V3 is now fully supported for streaming and saving
+  acquisition data, with both zipped and directory store support.
+
+- **Multi-Viewer Improvements**
+
+  The Multi-Viewer gains an **"Opened Files" dock** for quick switching
+  between open datasets, a **Registration Tool** for stack alignment, and
+  new menu entries for the Dark Calibration and PTC tools — all accessible
+  as MDI subwindows.
+
+- **Display & Performance**
+
+  Focus widget plots have been rewritten to eliminate GUI freezes at high
+  framerates (tested at ~165 Hz). A new optional **crosshair overlay** can
+  be enabled on any camera display. OpenGL rendering is now used for image
+  display. Application startup is faster thanks to deferred initialization
+  of heavy components.
+
+- **Stability & Compatibility**
+  - GPU imports are safely guarded on CPU-only systems.
+  - Qt binding selection is configurable at launch via CLI or environment
+    variable.
+  - Spatial filters (DoG, PointGaussFilter, Fourier) are faster via FFT
+    convolution and Numba acceleration.
+  - Qt6 compatibility fixes for mouse event handling.
+  - `PiezoConcept FOC` stage adapter fixes a float/int mismatch that caused
+    random Z jumps.
+
+---
+
+> ⚠️ **Breaking Change:** Zarr V3 support requires **Python 3.11 or
+> newer**. Python 3.9 and 3.10 are no longer supported.
+
 ## Table of Contents
 
 - [The microEye](#the-microeye)
+  - [What's New in microEye 2.4](#whats-new-in-microeye-24)
   - [Table of Contents](#table-of-contents)
   - [How to Install microEye](#how-to-install-microeye)
     - [Troubleshooting Installation](#troubleshooting-installation)
@@ -151,7 +275,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
    ```
 
 3. **Install specific hardware drivers: (Optional)**
-
    - Allied Vision CMOS cameras:
 
      Install the [`Vimba X SDK`](https://www.alliedvision.com/en/products/software/vimba-x-sdk/) (_avoid installing it inside the Program Files directory_). After installation, navigate to the `Python API` directory (e.g., `C:\Allied Vision\Vimba X\api\python`) where the `vmbpy` wheel file (`.whl`) is located, and install it using:
@@ -165,7 +288,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
      It has been observed that `vmbpy` can hang when initializing `GenICAM` transport layers (TLs) if the `GENICAM_GENTL64_PATH` environment variable contains `.cti` folders from other providers (e.g., `IDS Peak` or `pylon`). To avoid this, restrict `Vimba X` to load only its own TLs by explicitly specifying the `Vimba X` `.cti` directory in `VmbC.xml`.
 
      **Steps**
-
      1. **Auto (recommended)**
 
         Set the `VIMBA_X_HOME` environment variable to your `Vimba X` installation directory. `microEye` will read `VIMBA_X_HOME` at startup and use it to point the Vimba X transport-layer (`.cti`) configuration (e.g., `VIMBA_X_HOME/cti`).
@@ -178,7 +300,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 
    - Basler CMOS cameras: Install [`pylon`](https://www.baslerweb.com/en/downloads/software/?srsltid=AfmBOoqsMrbQT24hcWiCw-0ptD9PR7nCrPMBZSzi0YlI1CVItNQikMKW&downloadCategory.values.label.data=pylon) (_avoid installing it inside the Program Files directory_).
    - IDS CMOS cameras:
-
      - Install [`IDS Software Suite 4.96.1`](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for Windows 32/64-bit.
      - Alternatively, [`IDS Peak Extended Setup`](https://en.ids-imaging.com/download-peak.html) is prefered as it support old uEye models and the new uEye+ ones.
 
@@ -389,14 +510,12 @@ The following table lists the hardware devices that are integrated and supported
 ### How to Use
 
 1. **Headless Manager**:
-
    - Open the `miEye_module` and navigate to `Tools -> Micro-Manager Headless Manager` in the main menu.
    - Start a new headless instance using a specific configuration file.
    - Stop individual running instances or terminate all instances simultaneously.
    - Save configurations for future use or load previously saved configurations for headless instances.
 
 2. **Core Instances**:
-
    - Open the `miEye_module` and navigate to `Tools -> Micro-Manager Core Bridges` in the main menu.
    - Click on `Add Core Bridge` and provide the port address in the dialog box.
    - A list of connected devices will be displayed, allowing you to view each device's properties.

{microeye-2.4.0rc2 → microeye-2.4.2}/README.md

@@ -7,14 +7,15 @@ 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) -->
+
 ![Python Version](https://img.shields.io/badge/Python-3.11-blue)
 ![Package Version](https://img.shields.io/pypi/v/microEye.svg)
 ![Package Version](https://img.shields.io/badge/GUI_Platform-PySide6|PyQt6|PyQt5-navy)
@@ -38,9 +39,132 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Forks](https://img.shields.io/github/forks/samhitech/microEye.svg)
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
+## What's New in microEye 2.4
+
+- **Stage Control Overhaul**
+
+  Stage management has been completely redesigned with a unified controller
+  that handles all stage types through a single, consistent interface. A new
+  Stage Manager lets you add, remove, and assign stages to axes on the fly.
+  Per-axis soft limits, configurable center positions, and a new Calibrate
+  action make setup safer and more repeatable. Dedicated **XY and Z Center
+  buttons** in the Controller dock move stages to their configured center
+  positions in one click.
+
+- **SmarAct MCS2 Support**
+
+  Full support for SmarAct MCS2 multi-channel controllers, including guided
+  setup, calibration, homing, and soft-limit configuration for reliable
+  multi-axis motion.
+
+- **Slides Widget**
+
+  A new Slides dock lets you visualize and navigate multi-channel slide
+  layouts (Sticky-Slide VI, µ-Slide VI, 8/18 Well, and more). Click any
+  channel to move the stage to its center, with live position and delta
+  readouts, position overlays, and context menu options for axis orientation
+  and inversion. Layout settings persist across sessions.
+
+- **Focus Stabilization Improvements**
+
+  The focus stabilizer has been thoroughly refactored. Each axis now has
+  independent PID gains and calibration. New stabilization methods are
+  supported — including Reflection peak fitting, Fiducial/Fourier, and a
+  Hybrid XYZ mode. Frame statistics (count, mean, median) are now tracked
+  and the stabilizer waits for a sufficient number of frames before locking,
+  reducing false engagements. Plots dynamically show only the data relevant
+  to the active method, and all settings persist across sessions.
+
+- **New Analysis & Calibration Tools**
+
+  Three new calibration workflows are available from the Multi-Viewer Tools
+  menu:
+  - **Dark Calibration** — directory-based mean/variance analysis with
+    results cache, import/export, and dataset comparison.
+  - **Photon Transfer Curve (PTC)** — dataset import, run/cache workflows,
+    cache comparison, and Dark-Cal JSON export.
+  - **Sphere Power Calibration** — calibration utilities integrated into
+    the PTC workflow.
+
+  A new **Image Registration** tool for aligning and merging multi-channel
+  stacks (with transformation export/import) is also available in the
+  Multi-Viewer Tools menu.
+
+- **Expanded Camera Support**
+
+  Cameras from Basler, Allied Vision (Vimba X SDK), IDS Peak, Thorlabs,
+  PCO, and PycroManager now share unified ROI, exposure, and framerate
+  handling. Notable additions:
+  - **IDS Peak** is newly supported with binning, flash, and full ROI and
+    acquisition flow.
+  - **Basler** is newly supported.
+  - **Vimba X** gains black level, gain, correction, and binning controls,
+    plus CTI auto-discovery via `VIMBA_X_HOME` / `VIMBA_X_CTI`.
+  - All camera configurations are **automatically saved and restored** on
+    next launch when detected.
+
+- **Laser & Device Controls**
+
+  The Controller dock now shows color-coded, wavelength-aware indicators
+  for each laser and relay. Clicking an indicator toggles the laser state
+  directly from the main UI. Relay mode labels (ON/F1/F2) are shown
+  alongside each laser.
+
+- **Experiment Protocol Designer**
+
+  The protocol action list gains a new **ListLoop** action type for
+  repeating sequences of steps. The parameter adjustment UI now sorts
+  target objects, shows readable labels, and correctly handles integer and
+  float editors.
+
+- **Program-Wide Logging**
+
+  Structured logging replaces scattered print statements across the entire
+  codebase. Log level, file output, and console output are configurable via
+  the launcher UI or CLI flags (`--log-level`, `--no-log-file`,
+  `--no-log-console`). Logs are written per session under `./logs` for
+  easier troubleshooting.
+
+- **Image I/O & Data Handling**
+
+  Image handling has been refactored into a dedicated `microEye.images`
+  package. Zarr V3 is now fully supported for streaming and saving
+  acquisition data, with both zipped and directory store support.
+
+- **Multi-Viewer Improvements**
+
+  The Multi-Viewer gains an **"Opened Files" dock** for quick switching
+  between open datasets, a **Registration Tool** for stack alignment, and
+  new menu entries for the Dark Calibration and PTC tools — all accessible
+  as MDI subwindows.
+
+- **Display & Performance**
+
+  Focus widget plots have been rewritten to eliminate GUI freezes at high
+  framerates (tested at ~165 Hz). A new optional **crosshair overlay** can
+  be enabled on any camera display. OpenGL rendering is now used for image
+  display. Application startup is faster thanks to deferred initialization
+  of heavy components.
+
+- **Stability & Compatibility**
+  - GPU imports are safely guarded on CPU-only systems.
+  - Qt binding selection is configurable at launch via CLI or environment
+    variable.
+  - Spatial filters (DoG, PointGaussFilter, Fourier) are faster via FFT
+    convolution and Numba acceleration.
+  - Qt6 compatibility fixes for mouse event handling.
+  - `PiezoConcept FOC` stage adapter fixes a float/int mismatch that caused
+    random Z jumps.
+
+---
+
+> ⚠️ **Breaking Change:** Zarr V3 support requires **Python 3.11 or
+> newer**. Python 3.9 and 3.10 are no longer supported.
+
 ## Table of Contents
 
 - [The microEye](#the-microeye)
+  - [What's New in microEye 2.4](#whats-new-in-microeye-24)
   - [Table of Contents](#table-of-contents)
   - [How to Install microEye](#how-to-install-microeye)
     - [Troubleshooting Installation](#troubleshooting-installation)
@@ -86,7 +210,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
    ```
 
 3. **Install specific hardware drivers: (Optional)**
-
    - Allied Vision CMOS cameras:
 
      Install the [`Vimba X SDK`](https://www.alliedvision.com/en/products/software/vimba-x-sdk/) (_avoid installing it inside the Program Files directory_). After installation, navigate to the `Python API` directory (e.g., `C:\Allied Vision\Vimba X\api\python`) where the `vmbpy` wheel file (`.whl`) is located, and install it using:
@@ -100,7 +223,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
      It has been observed that `vmbpy` can hang when initializing `GenICAM` transport layers (TLs) if the `GENICAM_GENTL64_PATH` environment variable contains `.cti` folders from other providers (e.g., `IDS Peak` or `pylon`). To avoid this, restrict `Vimba X` to load only its own TLs by explicitly specifying the `Vimba X` `.cti` directory in `VmbC.xml`.
 
      **Steps**
-
      1. **Auto (recommended)**
 
         Set the `VIMBA_X_HOME` environment variable to your `Vimba X` installation directory. `microEye` will read `VIMBA_X_HOME` at startup and use it to point the Vimba X transport-layer (`.cti`) configuration (e.g., `VIMBA_X_HOME/cti`).
@@ -113,7 +235,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 
    - Basler CMOS cameras: Install [`pylon`](https://www.baslerweb.com/en/downloads/software/?srsltid=AfmBOoqsMrbQT24hcWiCw-0ptD9PR7nCrPMBZSzi0YlI1CVItNQikMKW&downloadCategory.values.label.data=pylon) (_avoid installing it inside the Program Files directory_).
    - IDS CMOS cameras:
-
      - Install [`IDS Software Suite 4.96.1`](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for Windows 32/64-bit.
      - Alternatively, [`IDS Peak Extended Setup`](https://en.ids-imaging.com/download-peak.html) is prefered as it support old uEye models and the new uEye+ ones.
 
@@ -324,14 +445,12 @@ The following table lists the hardware devices that are integrated and supported
 ### How to Use
 
 1. **Headless Manager**:
-
    - Open the `miEye_module` and navigate to `Tools -> Micro-Manager Headless Manager` in the main menu.
    - Start a new headless instance using a specific configuration file.
    - Stop individual running instances or terminate all instances simultaneously.
    - Save configurations for future use or load previously saved configurations for headless instances.
 
 2. **Core Instances**:
-
    - Open the `miEye_module` and navigate to `Tools -> Micro-Manager Core Bridges` in the main menu.
    - Click on `Add Core Bridge` and provide the port address in the dialog box.
    - A list of connected devices will be displayed, allowing you to view each device's properties.

microeye-2.4.2/src/microEye/_version.py

@@ -0,0 +1,2 @@
+version_info = (2, 4, 2)
+__version__ = '.'.join(map(str, version_info))

{microeye-2.4.0rc2 → microeye-2.4.2}/src/microEye/hardware/cams/basler/basler_panel.py

@@ -1,10 +1,16 @@
 import logging
 import traceback
 from time import perf_counter_ns
+from typing import Optional
 
 from microEye.hardware.cams.basler.basler_cam import BaslerParams, basler_cam, pylon
 from microEye.hardware.cams.camera_options import CamParams
-from microEye.hardware.cams.camera_panel import AcquisitionJob, Camera_Panel, Queue
+from microEye.hardware.cams.camera_panel import (
+    AcquisitionJob,
+    Camera_Panel,
+    Parameter,
+    Queue,
+)
 from microEye.qt import (
     QDateTime,
     QtCore,
@@ -164,7 +170,7 @@ class Basler_Panel(Camera_Panel):
         # start a timer to update the camera params
         self.timer = QtCore.QTimer(self)
         self.timer.setSingleShot(True)
-        self.timer.setInterval(1000)
+        self.timer.setInterval(250)  # Update every 250 ms after a change
         self.timer.timeout.connect(self.update_params)
         self.timer.start()
 
@@ -192,10 +198,6 @@ class Basler_Panel(Camera_Panel):
                     )
 
                     with param.treeChangeBlocker():
-                        if value != param.value():
-                            param.setValue(value)
-                        if enabled != param.opts.get('enabled', True):
-                            param.setOpts(enabled=enabled)
                         if limits and (
                             len(limits) != len(param.opts.get('limits', []))
                             or any(
@@ -206,6 +208,10 @@ class Basler_Panel(Camera_Panel):
                             )
                         ):
                             param.setLimits(limits)
+                        if value != param.value():
+                            param.setValue(value)
+                        if enabled != param.opts.get('enabled', True):
+                            param.setOpts(enabled=enabled)
                 except Exception as e:
                     logging.getLogger(__name__).error(
                         f"Error updating parameter {prop.get('name', 'unknown')}: {e}"
@@ -215,12 +221,22 @@ class Basler_Panel(Camera_Panel):
             self.refresh_exposure()
 
         worker = QThreadWorker(update)
-        worker.signals.finished.connect(
-            self.timer.start
-        )  # Restart the timer after fetching stats
+        # worker.signals.finished.connect(
+        #     self.timer.start
+        # )  # Restart the timer after fetching stats
 
         QtCore.QThreadPool.globalInstance().start(worker)
 
+    def update_cam(self, param: Optional[Parameter], param_value):
+        path = super().update_cam(param, param_value)
+
+        # Restart the timer to update the camera params after a change
+        if hasattr(self, 'timer') and self.timer is not None:
+            self.timer.start()
+
+        if path is None:
+            return
+
     @property
     def cam(self):
         '''The basler_cam property.

{microeye-2.4.0rc2 → microeye-2.4.2}/src/microEye/hardware/cams/camera_panel.py

@@ -4,7 +4,7 @@ import re
 import threading
 import traceback
 from queue import Queue
-from typing import Union
+from typing import Optional, Union
 
 import numpy as np
 from pyqtgraph.parametertree import Parameter
@@ -520,14 +520,16 @@ class Camera_Panel(QtWidgets.QGroupBox):
 
         self.camera_options.set_roi_info(x, y, w, h)
 
-    def update_cam(self, param: Union[Parameter, None], param_value):
+    def update_cam(self, param: Optional[Parameter], param_value):
         path = self.camera_options.param_tree.childPath(param)
 
         if path is None:
-            return
+            return None
 
         self.cam.update_cam(param, path, param_value)
 
+        return path
+
     def refresh_framerate(self, value=None):
         pass
 

{microeye-2.4.0rc2 → microeye-2.4.2}/src/microEye/hardware/cams/micam.py

@@ -781,32 +781,48 @@ class miDummy(miCamera):
         '''
         noise = kwargs.get('noise', 0)  # noise to add to fiducial positions
         drift = kwargs.get('drift', [0, 0, 0])  # drift in x, y, z
+        psf_model = kwargs.get('psf_model', 'airy').lower()
+        airy_scale = kwargs.get('airy_scale', 1.22)
         kernel_size = int(6 * max(sigma_x, sigma_y)) | 1  # odd size, covers >99% of PSF
 
-        x = np.arange(self.width)
-        y = np.arange(self.height)
-        X, Y = np.meshgrid(x, y)
-
-        pattern = np.zeros((self.width, self.height), dtype=np.float64)
+        pattern = np.zeros((self.height, self.width), dtype=np.float64)
 
-        ax, ay = 1 / (2 * sigma_x**2), 1 / (2 * sigma_y**2)
+        eps = np.finfo(np.float64).eps
+        ax, ay = 1 / (2 * sigma_x**2 + eps), 1 / (2 * sigma_y**2 + eps)
         for fid in fiducials:
             x = fid[0]
             y = fid[1]
 
             x += drift[0] + (np.random.random_sample() - 0.5) * noise
             y += drift[1] + (np.random.random_sample() - 0.5) * noise
-            x_slice = slice(
-                int(max(x - kernel_size, 0)), int(min(x + kernel_size, self.width))
-            )
-            y_slice = slice(
-                int(max(y - kernel_size, 0)), int(min(y + kernel_size, self.height))
-            )
+            x0 = int(max(x - kernel_size, 0))
+            x1 = int(min(x + kernel_size, self.width))
+            y0 = int(max(y - kernel_size, 0))
+            y1 = int(min(y + kernel_size, self.height))
+
+            if x1 <= x0 or y1 <= y0:
+                continue
+
+            x_local = np.arange(x0, x1, dtype=np.float64) - x
+            y_local = np.arange(y0, y1, dtype=np.float64) - y
+
+            if psf_model == 'airy':
+                # Airy-like approximation using sinc^2 radial profile.
+                r = np.sqrt(
+                    np.add.outer(
+                        (y_local / (sigma_y + np.random.random_sample() * 0.1 + eps))
+                        ** 2,
+                        (x_local / (sigma_x + np.random.random_sample() * 0.1 + eps))
+                        ** 2,
+                    )
+                )
+                patch = np.sinc(r / (airy_scale + eps)) ** 2
+            else:
+                gx = np.exp(-(x_local**2) * ax)
+                gy = np.exp(-(y_local**2) * ay)
+                patch = np.multiply.outer(gy, gx)
 
-            pattern[y_slice, x_slice] += self.drift_amplitude * np.exp(
-                -((X[y_slice, x_slice] - x) ** 2) * ax
-                - ((Y[y_slice, x_slice] - y) ** 2) * ay
-            )
+            pattern[y0:y1, x0:x1] += self.drift_amplitude * patch
 
         if pattern.min() < 0:
             pattern += abs(pattern.min())

{microeye-2.4.0rc2 → microeye-2.4.2}/src/microEye/hardware/mieye/acquisition_manager.py

@@ -366,9 +366,13 @@ def z_stack_acquisition(
 
                     if (
                         FocusStabilizer.instance().isFocusStabilized(Axis.Z)
-                        and FocusStabilizer.instance().useCal()
+                        and FocusStabilizer.instance().isAdjustSetPoint()
                     ):
-                        value = FocusStabilizer.instance().calCoeff(Axis.Z) * step_size
+                        value = step_size
+                        if not FocusStabilizer.instance().useCal():
+                            value /= FocusStabilizer.instance().calCoeff(
+                                Axis.Z
+                            )
                         if reverse:
                             value *= -1
                         FocusStabilizer.instance().setParameter(value, True)
@@ -463,9 +467,7 @@ def z_calibration(
                 QtCore.QThread.msleep(delay * nFrames)
                 positions[x, 0] = x * step_size
                 _, snapshot = FocusStabilizer.instance().tracker_snapshot
-                positions[x, 1] = np.mean(
-                    snapshot[-nFrames:, 2]
-                )
+                positions[x, 1] = np.mean(snapshot[-nFrames:, 2])
         else:
             logger.warning('Z-calibration failed!')
             info = [{'Z-Stage Open': stage_manager.z_stage().is_open()}]

{microeye-2.4.0rc2 → microeye-2.4.2}/src/microEye/hardware/stages/kinesis/kinesis.py

@@ -1,3 +1,4 @@
+import logging
 import traceback
 from typing import Optional
 
@@ -16,6 +17,8 @@ from microEye.qt import QtCore, QtSerialPort, QtWidgets, Signal
 from microEye.utils.parameter_tree import Tree
 from microEye.utils.thread_worker import QThreadWorker
 
+logger = logging.getLogger(__name__)
+
 
 class KinesisXY(AbstractStage):
     '''Class for controlling Two Kinesis Devices as an XY Stage'''
@@ -30,6 +33,7 @@ class KinesisXY(AbstractStage):
             axes=(Axis.X, Axis.Y),
             readyRead=None,
             center=kwargs.get('center', [17, 13]),
+            min_factor=kwargs.get('min_factor', 0),
         )
 
         self.X = KDC101Controller(portName=x_port)
@@ -58,8 +62,11 @@ class KinesisXY(AbstractStage):
         force = kwargs.get('force', False)
         is_async = kwargs.get('is_async', True)
 
-        x = round(max(0, min(self.x_max, x)), self.prec)
-        y = round(max(0, min(self.y_max, y)), self.prec)
+        x = self._clamp(Axis.X, x)
+        y = self._clamp(Axis.Y, y)
+
+        x = round(x, self.prec)
+        y = round(y, self.prec)
         if x != self.X.position or force:
             self.run_async(self.X.move_absolute, x, is_async=is_async)
         if y != self.Y.position or force:
@@ -71,6 +78,7 @@ class KinesisXY(AbstractStage):
 
         x = round(x, self.prec)
         y = round(y, self.prec)
+
         if x != 0:
             self.run_async(self.X.move_relative, x, is_async=is_async)
         if y != 0:
@@ -120,18 +128,23 @@ class KinesisXY(AbstractStage):
         if not isinstance(config, dict):
             raise ValueError('Config must be a dictionary.')
 
-        super().load_config(config)
-
-        x_config = config.get('X', {})
-        y_config = config.get('Y', {})
-
-        if isinstance(x_config, dict):
-            self.X.setBaudRate(x_config.get('baudrate', 115200))
-            self.X.setPortName(x_config.get('port', 'COM12'))
-
-        if isinstance(y_config, dict):
-            self.Y.setBaudRate(y_config.get('baudrate', 115200))
-            self.Y.setPortName(y_config.get('port', 'COM13'))
+        try:
+            x_config = config.get('X', {})
+            y_config = config.get('Y', {})
+
+            if isinstance(x_config, dict):
+                self.X.setBaudRate(x_config.get('baudrate', 115200))
+                self.X.setPortName(x_config.get('port', 'COM12'))
+
+            if isinstance(y_config, dict):
+                self.Y.setBaudRate(y_config.get('baudrate', 115200))
+                self.Y.setPortName(y_config.get('port', 'COM13'))
+        except Exception as e:
+            logger.error(
+                f'Error loading KinesisXY config: {e}\n{traceback.format_exc()}'
+            )
+        finally:
+            super().load_config(config)
 
 
 if __name__ == '__main__':