Add folder with micromanager config file and add stop/start function …

…for loghthouse plus solve bug in movement

__init__.py

@@ -36,8 +36,10 @@ def __init__(self):
         try:
             self.core = Core()
             print(self.core)
+            print("micromanager connection established succesfully!")
         except:
             print("Did you open uManager with the proper configuration?")
+            return -1
 
 
         # Init arduino serial communication
@@ -63,8 +65,8 @@ def initUI(self):
         self.current_slider, self.current_text = self.create_slider_with_text('Current', -300, 300, 0, self.change_optotune_current)
 
         # Sliders for motor frequency and amplitude
-        self.frequency_slider, self.frequency_text = self.create_slider_with_text('Acceleration', 1000, 15000, 1000, self.send_acc_serial_command)
-        self.amplitude_slider, self.amplitude_text = self.create_slider_with_text('Amplitude', 10, 100, 100, self.send_width_serial_command)
+        self.acceleration_slider, self.acceleration_text = self.create_slider_with_text('Acceleration', 1000, 15000, 5000, self.send_acc_serial_command)
+        self.amplitude_slider, self.amplitude_text = self.create_slider_with_text('Amplitude', 20, 100, 100, self.send_width_serial_command)
 
         # Main layout setup
         main_layout = QVBoxLayout()
@@ -81,7 +83,7 @@ def initUI(self):
         main_layout.addLayout(self.y_slider)
         main_layout.addLayout(self.z_slider)
         main_layout.addLayout(self.current_slider)
-        main_layout.addLayout(self.frequency_slider)
+        main_layout.addLayout(self.acceleration_slider)
         main_layout.addLayout(self.amplitude_slider)
 
         self.setLayout(main_layout)
@@ -165,7 +167,7 @@ def print_values(self):
         print("Y Position:", self.y_text.text())
         print("Z Position:", self.z_text.text())
         print("Current:", self.current_text.text())
-        print("Frequency:", self.frequency_text.text())
+        print("Frequency:", self.acceleration_text.text())
         print("Amplitude:", self.amplitude_text.text())
         print("Exposure:", self.exposure_text.itemAt(1).widget().text())
         print("Alpha:", self.alpha_text.itemAt(1).widget().text())

arduino/step_motor_LSM/src/motor.cpp

@@ -4,18 +4,14 @@ TMC2130Stepper driver = TMC2130Stepper(EN_PIN, DIR_PIN, STEP_PIN, CS_PIN);
 AccelStepper stepper = AccelStepper(stepper.DRIVER, STEP_PIN, DIR_PIN);
 
 bool dir = true;
-int sheet_width = 200;
+int sheet_width = 100;
 long headAcceleration = 5000;
-long cero_position = 0;
 
 void init_motor() {
 
     pinMode(CS_PIN, OUTPUT);
     digitalWrite(CS_PIN, HIGH);
-
-    // Grab the initial position and set it as the cero position
-    cero_position = stepper.currentPosition();
-
+
     driver.begin();           
     driver.rms_current(600);    // Set stepper current to 600mA
     driver.stealthChop(1);      // Enable extremely quiet stepping
@@ -26,49 +22,54 @@ void init_motor() {
     stepper.setAcceleration(headAcceleration); 
     stepper.setEnablePin(EN_PIN);
     stepper.setPinsInverted(false, false, true);
-    stepper.enableOutputs();
+    //stepper.enableOutputs();
+    // Grab the initial position and set it as the cero position
+    //stepper.setCurrentPosition(0);
 }
 
 void task_move_motor(void *pvParameters) {
   command_t received_command;
-  long current_position;
-  int new_sheet_width = sheet_width;
-  int first_move = true;
+  bool first_move = true;
+  bool start_movement = false;
 
   while(1)
   {
     // If there is an element in the queue...
     if(x_received_commands_queue != NULL && xQueueReceive(x_received_commands_queue, (void *)&received_command, 0) == pdTRUE){
-      if(received_command.command == "w"){
-        new_sheet_width = received_command.value;
-      }else if (received_command.command == "a"){
+      if(received_command.command == "w"){ // change width
+        sheet_width = received_command.value;
+      }else if (received_command.command == "a"){ // Change amplitude
         stepper.setAcceleration(received_command.value); 
+      }else if(received_command.command == "s"){  // Start the stepper motor movement
+        stepper.enableOutputs();
+        stepper.setCurrentPosition(0);
+        start_movement = true;
+        first_move = true;
+      }else if(received_command.command == "h"){  // Stop the stepper motor
+        stepper.stop();
+        stepper.disableOutputs();
+        start_movement = false;
       }
 
     }
 
-    current_position = stepper.currentPosition();
-
-    if (stepper.distanceToGo() == 0) {
-      if (first_move){
-        stepper.move(sheet_width/2);
-        first_move = false;
-      }
-      else if (dir){
-        stepper.move(sheet_width);  
-      }else{
-        stepper.move(-1*sheet_width);
+    if(start_movement){
+      if (stepper.distanceToGo() == 0) {
+        if (first_move){
+          stepper.moveTo(sheet_width/2);
+          first_move = false;
+        }
+        else if (dir){
+          stepper.moveTo(sheet_width);  
+        }else{
+          stepper.moveTo(-1*sheet_width);
+        }
+        dir = !dir;
       }
-      dir = !dir;
-    }
 
-    // Update the sheet width only when it cross the cero position
-    if(current_position == cero_position){
-      sheet_width = new_sheet_width;
+      stepper.run();
     }
-    stepper.run();
-
-    vTaskDelay(2/ portTICK_PERIOD_MS);
+    vTaskDelay(1/ portTICK_PERIOD_MS);
   }
 
 }

micro_manager_config_files/MMConfig_cameraTest.cfg

@@ -0,0 +1,48 @@
+# Generated by Configurator on Mon Apr 29 17:41:10 CEST 2024
+
+# Reset
+Property,Core,Initialize,0
+
+
+# PixelSize settings
+# Resolution preset: Res20x
+ConfigPixelSize,Res20x,Objective,Label,Mitutoyo 20x Plan Apo L
+PixelSize_um,Res20x,1.2
+
+# Resolution preset: Res40x
+ConfigPixelSize,Res40x,Objective,Label,Nikon 40X Plan Fluor ELWD
+PixelSize_um,Res40x,0.25
+
+
+# Devices
+Device,pco_camera,PCO_Camera,pco_camera
+
+# Pre-init settings for devices
+Property,pco_camera,DemoMode,Off
+
+# Pre-init settings for COM ports
+
+# Hub (parent) references
+
+# Initialize
+Property,Core,Initialize,1
+
+# Delays
+
+# Focus directions
+
+# Roles
+Property,Core,Camera,pco_camera
+Property,Core,AutoShutter,1
+
+# Camera-synchronized devices
+
+# Labels
+
+# Configuration presets
+# Group: Channel
+
+# Group: System
+# Preset: Startup
+
+

test_code/pycromanager_test.py

@@ -4,7 +4,7 @@
     # Check if Micro-Manager is running and ZMQ server is enabled on port 4827
     with Acquisition(directory='/', name='acquisition_name') as acq:
         # Create events for acquisition
-        events = multi_d_acquisition_events(num_time_points=0)
+        events = multi_d_acquisition_events(num_time_points=5)
         print(f"Acquisition events created: {events}")
 
         # Start the acquisition