12.1.10.1.3. Gaussian spot centroid detection

This demo shows how the itom.algorithms can be used. In this example a camera DummyGrabber is used to acquire a moving gaussian spot. For the centroid detection the itom.algorithms.centroidxy function is used. Finally, this examples shows how a centroid position marker is added to the gaussian spot image.

Note

For older itom versions the itom.filter function is used for the centroidXY algorithm. By using the itom.algorithms you will get the algorithms information by a pop-up during typing.

from itom import dataIO
from itom import dataObject
from itom import plot2
from itom import timer

try:
    from itom import algorithms

    hasItomAlgo = True
except ImportError:
    from itom import filter

    hasItomAlgo = False
    print(
        "The itom.algorithms module cannot be used because"
        "of an older itom version. Use the itom.filter functions."
    )

Constructor of the live gaussianSpot centroid detection.

class GaussianSpotCentroidDetection:
    def __init__(self):
        """Constructor function of the class."""
        # first initialize the DummyGrabber with a gaussianSpot as private member
        self.__cam = dataIO("DummyGrabber", imageType="gaussianSpot")
        self.__cam.startDevice()

        # define a dataobject for the gaussienSpot image as a public member
        self.dObj = dataObject()
        self.__cam.acquire()
        self.__cam.getVal(self.dObj)
        self.dObj = self.__defineDObj(self.dObj)

        # plot index and handle as private member
        self.__plotHandle = None
        self.__plotIndex = None

        # define timer to update live image
        self.__liveTimer = timer(50, self.__updateTimerCallBack, name="liveTimer")

        return

    ###############################################################################
    # Callback function to update the live image.

    def __updateTimerCallBack(self):
        """Callback function to update the live image."""
        # stop live time if plot window is closed
        if self.__plotHandle:
            if not self.__plotHandle.exists():
                self.__liveTimer.stop()
                return

        # acquire and get image
        self.__cam.acquire()
        self.__cam.getVal(self.dObj)

        # calculate the centroid of the gaussianSpot
        if (
            hasItomAlgo
        ):  # new itom.algorithms with auto completion and docstring in pop-up
            [intensityX, intensityY, centroidX, centroidY] = algorithms.centroidXY(
                self.dObj
            )
        else:  # old itom.filter
            [intensityX, intensityY, centroidX, centroidY] = filter(
                "centroidXY", self.dObj
            )

        print(
            "Centroid (x, y) position: {:.3f} {}, {:.3f} {}".format(
                centroidX, self.dObj.axisUnits[1], centroidY, self.dObj.axisUnits[0]
            )
        )

        # create the centroid xy marker
        centroidMarker = dataObject([2, 1], "float32")
        centroidMarker[0, :] = centroidY
        centroidMarker[1, :] = centroidX

        # plot the camera image with marked centroid position
        if not self.__plotHandle:  # open figure window by first time
            [self.__plotIndex, self.__plotHandle] = plot2(
                self.dObj,
                properties={
                    "keepAspectRatio": True,
                    "colorBarVisible": True,
                    "colorMap": "viridis",
                },
            )

        else:  # replot the figure
            self.__plotHandle.call("replot")

        # delete markers and plot the new one
        if self.__plotHandle:
            self.__plotHandle.call("deleteMarkers")
            self.__plotHandle.call(
                "plotMarkers", centroidMarker, "r+25;2", "centroid", 0
            )

        return

    ###############################################################################
    # Function to defines the dataObject by meta information.

    def __defineDObj(self, dObj: dataObject) -> dataObject:
        """Private function to define the meta information of the image dataObject.

        Args:
            image (dataObject): 2D image

        Returns:
            dataObject: 2D image with define meta information
        """
        # define dataobject
        dObj.setAxisDescription(0, "y axis")
        dObj.setAxisDescription(1, "x axis")
        dObj.setAxisUnit(0, "\xb5m")
        dObj.setAxisUnit(1, "\xb5m")
        dObj.setAxisScale(0, 10e-3)  # pixel pitch of 10 \xb5m
        dObj.setAxisScale(1, 10e-3)  # pixel pitch of 10 \xb5m
        dObj.valueDescription = "intensity"
        dObj.valueUnit = "counts"

        return dObj


if __name__ == "__main__":
    gaussianSpotCentroid = GaussianSpotCentroidDetection()