Merge branch 'master' of https://github.com/openUC2/ImSwitch

imswitch/imcontrol/controller/controllers/TemperatureController.py

@@ -35,10 +35,12 @@ def __init__(self, *args, **kwargs):
         self.Ki = 0.1
         self.Kd = .5
         self.PIDenabled = False
+        self.pollingPeriod = 5
 
         # get hold on the Temperature Controller
         try:
             self.temperatureController = self._master.rs232sManager["ESP32"]._esp32.temperature
+            self.temperatureController.start_temperature_polling(period=self.pollingPeriod)
         except:
             return
         # Connect TemperatureWidget signals
@@ -130,7 +132,7 @@ def updateSetPointData(self):
     def updateMeasurements(self):
         while self.is_measure:
             self.temperatureValue  = self.temperatureController.get_temperature()
-            if self.temperatureValue > -200: # if not, we have faulty values 
+            if self.temperatureValue and self.temperatureValue > -200: # if not, we have faulty values 
 
                 self._widget.updateTemperature(self.temperatureValue)
 

imswitch/imcontrol/model/interfaces/gxipycamera.py

@@ -14,14 +14,14 @@ class TriggerMode:
     CONTINUOUS = 'Continuous Acqusition'
 
 class CameraGXIPY:
-    def __init__(self,cameraNo=None, exposure_time = 10000, gain = 0, frame_rate=-1, blacklevel=100, binning=1, flipImage=(False, False)):
+    def __init__(self,cameraNo=None, exposure_time = 10000, gain = 0, frame_rate=-1, blacklevel=100, binning=1, flipImage=(False, False), isRGB=False):
         super().__init__()
         self.__logger = initLogger(self, tryInheritParent=True)
 
         # many to be purged
         self.model = "CameraGXIPY"
         self.shape = (0, 0)
-
+        self.isRGB = isRGB
         self.is_connected = False
         self.is_streaming = False
 

imswitch/imcontrol/model/managers/detectors/GXPIPYManager.py

@@ -47,9 +47,15 @@ def __init__(self, detectorInfo, name, **_lowLevelManagers):
         except:
             self.flipY = False
 
+
+        try: 
+            self._isRGB = detectorInfo.managerProperties['gxipycam']['isRGB']
+        except:
+            self._isRGB = False
+
         self.flipImage = (self.flipX, self.flipY)
 
-        self._camera = self._getGXObj(self.cameraId, self.binningValue, self.flipImage)
+        self._camera = self._getGXObj(self.cameraId, self.binningValue, self.flipImage, self._isRGB)
 
         fullShape = (self._camera.SensorWidth,
                 self._camera.SensorHeight)
@@ -305,7 +311,7 @@ def _performSafeCameraAction(self, function):
     def openPropertiesDialog(self):
         self._camera.openPropertiesGUI()
 
-    def _getGXObj(self, cameraId, binning=1, flipImage=(False, False)):
+    def _getGXObj(self, cameraId, binning=1, flipImage=(False, False), isRGB=False):
         try:
             import os
             if os.name == 'darwin':
@@ -314,7 +320,7 @@ def _getGXObj(self, cameraId, binning=1, flipImage=(False, False)):
             else:
                 from imswitch.imcontrol.model.interfaces.gxipycamera import CameraGXIPY
                 self.__logger.debug(f'Trying to initialize Daheng Imaging camera {cameraId}')
-                camera = CameraGXIPY(cameraNo=cameraId, binning=binning, flipImage=flipImage)
+                camera = CameraGXIPY(cameraNo=cameraId, binning=binning, flipImage=flipImage, isRGB=isRGB)
         except Exception as e:
             self.__logger.debug(e)
             self.__logger.warning(f'Failed to initialize CameraGXIPY {cameraId}, loading TIS mocker')

imswitch/imcontrol/model/managers/lasers/ESP32LEDLaserManager.py

@@ -48,7 +48,7 @@ def __init__(self, laserInfo, name, **lowLevelManagers):
         self.enabled = False
         self.setEnabled(self.enabled)
 
-    def setEnabled(self, enabled,  getReturn=True):
+    def setEnabled(self, enabled,  getReturn=False):
         """Turn on (N) or off (F) laser emission"""
         self.enabled = enabled
         if self.channel_index == "LED":
@@ -60,7 +60,7 @@ def setEnabled(self, enabled,  getReturn=True):
                                                 int(self.power*self.enabled),
                                                 despeckleAmplitude = self.laser_despeckle_amplitude,
                                                 despecklePeriod = self.laser_despeckle_period,
-                                                is_blocking=True)
+                                                is_blocking=getReturn)
 
     def setValue(self, power, getReturn=False):
         """Handles output power.
@@ -82,7 +82,7 @@ def setValue(self, power, getReturn=False):
                                     int(self.power),
                                     despeckleAmplitude = self.laser_despeckle_amplitude,
                                     despecklePeriod = self.laser_despeckle_period,
-                                    is_blocking=True)
+                                    is_blocking=getReturn)
 
     def sendTrigger(self, triggerId):
         self._esp32.digital.sendTrigger(triggerId)

tools/loadTimeSeriesStackChannel.py

@@ -0,0 +1,59 @@
+import os
+import re
+import tifffile
+import numpy as np
+import cv2
+
+# Function to extract information from filename
+def parse_filename(filename):
+    # Extract date, Z position, and channel using regex
+    match = re.search(r'(\d{4}_\d{2}_\d{2})-.*_Z_(-?\d+\.\d+).*_(LED|Laser\d)_', filename)
+    if match:
+        return match.group(1), float(match.group(2)), match.group(3)
+    return None, None, None
+
+# Function to load images from a folder
+def load_images_from_folder(folder):
+    images = {}
+    for filename in os.listdir(folder):
+        if filename.endswith(".tif"):
+            date, z_pos, channel = parse_filename(filename)
+            if date and z_pos and channel:
+                key = (date, channel, z_pos)
+                img_path = os.path.join(folder, filename)
+                img = tifffile.imread(img_path)
+                if key in images:
+                    images[key].append(img)
+                else:
+                    images[key] = [img]
+    return images
+
+# Loading images from all folders
+all_images = {}
+
+import os
+# Specify the parent directory
+parent_directory = 'C:\\Users\\user\\Documents\\ImSwitchConfig\\recordings\\2024_01_22-04-43-17_PM'
+# List all subdirectories starting with 't'
+subfolders = [f.name for f in os.scandir(parent_directory) if f.is_dir() and f.name.startswith('t')]
+# Print the list of subfolders
+print(subfolders)
+
+for folder in subfolders:
+    all_images.update(load_images_from_folder(parent_directory+"\\"+folder))
+
+# Organizing and concatenating images for each channel
+timelapses = {}
+for key in sorted(all_images.keys()):
+    date, channel, z_pos = key
+    if channel not in timelapses:
+        timelapses[channel] = []
+    # Assuming that images for the same channel and date are part of the same timeseries
+    timelapses[channel].append(np.concatenate(all_images[key], axis=1))
+
+# Creating timelapse videos
+for channel in timelapses:
+    out = cv2.VideoWriter(f'timelapse_{channel}.avi', cv2.VideoWriter_fourcc(*'DIVX'), 10, (width, height))
+    for img in timelapses[channel]:
+        out.write(img)
+    out.release()