Automated delay

src/pymicroscope/base/mapcontroller.py

@@ -0,0 +1,55 @@
+from mytk import *
+import math
+from typing import Tuple, Optional
+from typing import Any
+
+class MapController(Bindable):
+    '''Giving all the position to create a map of all the sample'''
+    def __init__(self, device, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.device = device
+
+        self.z_image_number = 1
+        self.microstep_pixel = 0.16565
+        self.z_range = 1
+        self.x_dimension = 1000
+        self.y_dimension = 500
+
+        self.parameters: dict[str, Optional[Tuple[int, int, int]]] = {
+            "Upper left corner": None,
+            "Upper right corner": None,
+            "Lower left corner": None,
+            "Lower right corner": None,
+        }
+
+    def create_positions_for_map(self):
+        '''Giving all the deplacement position according to the x and y image dimension'''
+        positions_list = []
+
+        corner1 = self.parameters["Upper left corner"]
+        corner2 = self.parameters["Upper right corner"]
+        corner3 = self.parameters["Lower left corner"]
+        corner4 = self.parameters["Lower right corner"]
+
+        x_image_dimension = self.x_dimension*self.microstep_pixel
+        y_image_dimension = self.y_dimension*self.microstep_pixel
+        z_image_dimension = self.z_range*self.microstep_pixel
+
+        if all(x != (0.0, 0.0, 0.0) for x in self.parameters.values()): 
+            number_of_x_image = math.ceil((corner2[0] - corner1[0]) / (0.9*x_image_dimension))
+            number_of_y_image = math.ceil((corner2[1] - corner4[1])/ (0.9*y_image_dimension))
+        else:
+             number_of_x_image = 1
+             number_of_y_image = 1
+
+
+        for z in range(self.z_image_number):
+                z_position = z*z_image_dimension
+                for y in range(number_of_y_image):
+                    y_position = y*y_image_dimension*0.9
+                    for x in range(number_of_x_image):
+                        x_position = x*x_image_dimension*0.9
+                        positions_list.append((x_position, y_position, z_position))
+
+
+        return positions_list

src/pymicroscope/experiment/actions.py

@@ -150,6 +150,19 @@ def __init__(
     def do_perform(self, results=None) -> dict[str, Any] | None:
         self.device.moveInMicronsBy(self.d_position)
         return {"displacement": self.d_position}
+
+class ActionHome(Action):
+    def __init__(
+        self,
+        linear_motion_device: LinearMotionDevice,
+        *args,
+        **kwargs,
+    ):
+        super().__init__(*args, **kwargs)
+        self.device: LinearMotionDevice = linear_motion_device
+
+    def do_perform(self, results=None) -> None:
+        self.device.home()
 
 
 class ActionFunctionCall(Action):
@@ -296,10 +309,3 @@ def do_perform(self, results=None) -> dict[str, Any] | None:
 
         self.output = filepath
 
-
-class ActionClear(Action):
-    def __init__(self, filepath: Path, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.filepath = filepath
-        for file in self.filepath:
-            self.filepath[file] = None

src/pymicroscope/hardware/kinesisdevice.py

@@ -0,0 +1,82 @@
+from hardwarelibrary.physicaldevice import *
+from hardwarelibrary.motion.linearmotiondevice import *
+from hardwarelibrary.communication.communicationport import *
+from hardwarelibrary.communication.usbport import USBPort
+from hardwarelibrary.communication.serialport import SerialPort
+from hardwarelibrary.communication.commands import DataCommand
+from hardwarelibrary.communication.debugport import DebugPort
+
+import time
+from struct import *
+
+from pyftdi.ftdi import Ftdi #FIXME: should not be here.
+from mytk import *
+from pylablib.devices.Thorlabs import kinesis
+
+class KinesisDevice(LinearMotionDevice):
+    #SERIAL_NUMBER = "83849018"
+
+    def __init__(self, serialNumber: str = None, channel: int = 1):
+        super().__init__(serialNumber=serialNumber, idVendor=self.classIdVendor, idProduct=self.classIdProduct)
+        self.thorlabs_device = None
+        self.channel =channel
+        self.nativeStepsPerMicrons = 128
+
+
+        # All values are in native units (i.e. microsteps)
+        self.xMinLimit = 0
+        self.xMaxLimit = 857599
+
+    def __del__(self):
+        try:
+            self.thorlabs_device.close()
+        except:
+            return
+
+    def doInitializeDevice(self):
+        available_devices = kinesis.KinesisDevice.list_devices()
+        available_serial_numbers = [ device[0] for device in available_devices]
+
+        if self.serialNumber not in available_serial_numbers:
+            raise RuntimeError("Kinesis Device with serial number {0} not found.".format(self.serialNumber))
+
+        '''Connect the right Kinesis Motor, open the port, set the channel and the reference position'''
+        self.thorlabs_device = kinesis.KinesisMotor(conn=self.serialNumber)
+        if self.thorlabs_device is None:
+            raise PhysicalDevice.UnableToInitialize("Cannot allocate port {0}".format(self.thorlabs_device))
+        else:
+            self.thorlabs_device.open()
+            self.thorlabs_device.set_supported_channels(channels= self.channel)
+            self.thorlabs_device.set_position_reference() #set the initilal point
+
+    def doShutdownDevice(self):
+        self.thorlabs_device.close()
+        self.thorlabs_device = None
+
+    def position(self) -> int:  # for 1D compatibility
+        position_tuple = super().position()
+        return position_tuple[0]
+
+    def doGetPosition(self) -> tuple:
+        return (self.thorlabs_device.get_position(),)
+
+    def doMoveTo(self, position):
+        self.thorlabs_device.move_to(position=position[0])
+        if self.thorlabs_device.is_moving() is False:
+            raise Exception("unable to move the device.")
+        else:
+            self.thorlabs_device.wait_move()
+
+    def doMoveBy(self, displacement):
+        self.thorlabs_device.move_by(distance=displacement[0])
+        if self.thorlabs_device.is_moving() is False:
+                raise Exception("unable to move the device.")
+        else:
+            self.thorlabs_device.wait_move()
+
+    def doHome(self):
+        self.thorlabs_device.move_to(position=0)
+        if self.thorlabs_device.is_moving() is False:
+            raise Exception("unable to move the device to home.")
+        else:
+            self.thorlabs_device.wait_for_stop()