fix: path issues tests, rename cslcamera

Author: Alienor134

ControlCamera/CSLcamera.py ControlCamera/ControlCamera.pyControlCamera/CSLcamera.py renamed to ControlCamera/ControlCamera.py

@@ -109,7 +109,7 @@ def __init__(self, config_file, cam_param, downscale=3, mm_dir = "C:/Program Fil
         if key not in ["name", "MMconfig"]:
           try:
             self.mmc.setProperty(self.name, key, config[key])          
-            logger.info(key, self.get_param(key))
+            logger.info("Set config parameter %s=%s", key, self.get_param(key))
           except Exception as e:
             logger.error(f"Failed to update parameter '{key}' with value '{config[key]}': {e}")             
 
@@ -119,7 +119,7 @@ def __init__(self, config_file, cam_param, downscale=3, mm_dir = "C:/Program Fil
       for key in cam_param:
           try:
             self.mmc.setProperty(self.name, key, cam_param[key])
-            logger.info(key, self.get_param(key))
+            logger.info("Set local parameter %s=%s", key, self.get_param(key))
 
           except Exception as e:
             logger.error(f"Failed to update parameter '{key}' with value '{cam_param[key]}': {e}")             
@@ -136,7 +136,7 @@ def update_param(self, key, val):
         """
         try:
             self.mmc.setProperty(self.name, key, val)
-            logger.info(key, self.get_param(key))
+            logger.info("Updated parameter %s=%s", key, self.get_param(key))
 
         except Exception as e:
             logger.error(f"Failed to update parameter '{key}' with value '{val}': {e}")
@@ -161,27 +161,42 @@ def get_param(self, key):
     def continuous_stream(self, transform=None):
       """
       Perform continuous streaming of the camera frames and display them in a window.
+
+      The window is shown at a reduced size so that large sensor
+      images still fit on screen. Press 'q' to close.
       """
-      cv2.namedWindow('live',cv2.WINDOW_AUTOSIZE)
+      cv2.namedWindow('live', cv2.WINDOW_NORMAL)
       self.mmc.startContinuousSequenceAcquisition(1)
       while True:
         if self.mmc.getRemainingImageCount() > 0:
           self.frame = self.mmc.popNextImage()
-          self.image = np.mean(self.frame[:,:,:3], axis =2)
-          #self.image = np.array(Image.fromarray(np.uint8(self.frame)))
-          #self.image[self.image<np.quantile(self.image, 0.99)] = 0
+          # Average RGB channels to get a grayscale image (like original code)
+          self.image = np.mean(self.frame[:, :, :3], axis=2)
+          # self.image = np.array(Image.fromarray(np.uint8(self.frame)))
+          # self.image[self.image<np.quantile(self.image, 0.99)] = 0
+
           if transform is not None:
-                # Apply the transform function here
-                transformed_image = self.image.copy()
-                transformed_image = transform(transformed_image)
-                image = resize(self.image, transformed_image.shape)
-                # Create a combined image by stacking the original and transformed images horizontally
-                combined_image = np.hstack((image, transformed_image))
-                # Display the combined image
-                
-                cv2.imshow('live', cv2.normalize(combined_image, None, 255, 0, cv2.NORM_MINMAX, cv2.CV_8UC1))
+            # Apply the transform function here
+            transformed_image = self.image.copy()
+            transformed_image = transform(transformed_image)
+            image = resize(self.image, transformed_image.shape)
+            # Create a combined image by stacking the original and transformed images horizontally
+            combined_image = np.hstack((image, transformed_image))
+            # Display the combined image (downscaled for the screen)
+            disp = cv2.normalize(combined_image, None, 255, 0, cv2.NORM_MINMAX, cv2.CV_8UC1)
           else:
-                cv2.imshow('live', cv2.normalize(self.image, None, 255,0, cv2.NORM_MINMAX, cv2.CV_8UC1))
+            disp = cv2.normalize(self.image, None, 255, 0, cv2.NORM_MINMAX, cv2.CV_8UC1)
+
+          # Downscale display image if it is larger than a typical window
+          max_h, max_w = 600, 800
+          h, w = disp.shape[:2]
+          scale = min(max_h / h, max_w / w, 1.0)
+          if scale < 1.0:
+            new_size = (int(w * scale), int(h * scale))
+            disp = cv2.resize(disp, new_size, interpolation=cv2.INTER_AREA)
+
+          cv2.imshow('live', disp)
+
         if cv2.waitKey(1) & 0xFF == ord('q'):
           break
 
@@ -293,4 +308,3 @@ def save_video(self, save_folder,  _run=None):
           _run.add_artifact(fname, "video.tiff")
           _run.add_artifact(fname, "video_timing.csv")
         return result, timing
-

ControlCamera/__init__.py

@@ -1 +1 @@
-from .CSLcamera import ControlCamera
+from .ControlCamera import ControlCamera

README.md

@@ -5,7 +5,7 @@
 [![Python Version](https://img.shields.io/badge/python-3.8%2B-blue.svg)](https://www.python.org/downloads/)
 [![License: GPL-3.0](https://img.shields.io/badge/License-GPL%203.0-blue.svg)](LICENSE)
 [![DOI](https://img.shields.io/badge/DOI-pending%20Zenodo-orange.svg)](https://zenodo.org)
-[![Platform](https://img.shields.io/badge/platform-Windows%20%7C%20Linux%20%7C%20macOS-lightgrey.svg)](https://github.com/Alienor134/UC2_Fluorescence_microscope)
+[![Platform](https://img.shields.io/badge/platform-Windows-lightgrey.svg)](https://github.com/Alienor134/UC2_Fluorescence_microscope)
 [![Arduino Compatible](https://img.shields.io/badge/Arduino-Compatible-00979D?logo=Arduino&logoColor=white)](https://www.arduino.cc/)
 
 ---

Tests/unit/test_camera_params.py Tests/test_camera_params.pyTests/unit/test_camera_params.py renamed to Tests/test_camera_params.py

@@ -1,14 +1,15 @@
 import unittest
 from unittest.mock import patch
 from pathlib import Path
+import importlib
 
 from ControlCamera import ControlCamera
+cc_module = importlib.import_module("ControlCamera.ControlCamera")
 
 
-TESTS_DIR = Path(__file__).resolve().parent
 # MMconfig directory lives alongside Tests/, not inside unit/
-MMCONFIG_DIR = TESTS_DIR.parent / "MMconfig"
-CONFIG_FILE = MMCONFIG_DIR / "Daheng.json"
+MMCONFIG_DIR = "MMconfig"
+CONFIG_FILE = MMCONFIG_DIR + "/Daheng.json"
 
 
 class FakeCore:
@@ -36,24 +37,24 @@ class TestControlCameraParams(unittest.TestCase):
     """Hardware‑free tests focusing on camera parameter handling."""
 
     def setUp(self):
-        # Patch CMMCorePlus.instance() used inside CSLcamera to return our fake core
-        patch_target = "ControlCamera.CSLcamera.CMMCorePlus"
-        self._patcher = patch(patch_target)
+        # Patch CMMCorePlus.instance() as used in the ControlCamera implementation
+        # module so that it returns our FakeCore instead of real hardware.
+        self._patcher = patch.object(cc_module, "CMMCorePlus")
         MockCoreClass = self._patcher.start()
 
         self.fake_core = FakeCore()
         MockCoreClass.instance.return_value = self.fake_core
 
-        cam_params = {"Exposure": "10"}
+        cam_params = {"Exposure(us)": "10"}
         self.camera = ControlCamera(str(CONFIG_FILE), cam_params)
 
     def tearDown(self):
         self._patcher.stop()
 
     def test_update_and_get_param_roundtrip(self):
         # Changing a parameter should be visible via get_param
-        self.camera.update_param("Exposure", "20")
-        value = self.camera.get_param("Exposure")
+        self.camera.update_param("Exposure(us)", "20")
+        value = self.camera.get_param("Exposure(us)")
         self.assertEqual(value, "20")
 
     def test_initial_config_applies_some_properties(self):

Tests/test_daheng.py

@@ -6,7 +6,9 @@
 # Define test configuration file and parameters
 
 CAM_PARAMS = {"TriggerMode": "On", #off
-             "TriggerSource": "Line0"} #Software
+             "TriggerSource": "Line0",
+              "SensorHeight":2048,
+                "SensorWidth":2448} #Software
 CONFIG_FILE = "MMconfig/Daheng.json"
 
 # Initialize the camera controller

Tests/test_output/video.tiff

@@ -1,11 +1,3 @@
 ,0
-0,1768221226.2650905
-1,1768221226.328556
-2,1768221226.390074
-3,1768221226.4594235
-4,1768221226.5228765
-5,1768221226.583436
-6,1768221226.6459248
-7,1768221226.7025583
-8,1768221226.7591913
-9,1768221226.8148563
+0,1769184539.625449
+1,1769184539.973073