.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "11_demos\itom\basics\demo_GaussianSpotCentroidDetection.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_11_demos_itom_basics_demo_GaussianSpotCentroidDetection.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_11_demos_itom_basics_demo_GaussianSpotCentroidDetection.py:

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.

.. GENERATED FROM PYTHON SOURCE LINES 15-33

.. code-block:: default


    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."
        )








.. GENERATED FROM PYTHON SOURCE LINES 35-36

Constructor of the live gaussianSpot centroid detection.

.. GENERATED FROM PYTHON SOURCE LINES 36-136

.. code-block:: default



    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()








.. GENERATED FROM PYTHON SOURCE LINES 137-139

.. image:: ../../_static/demoGaussianSpotCentroidDetection_1.png
   :width: 100%


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** ( 0 minutes  0.016 seconds)


.. _sphx_glr_download_11_demos_itom_basics_demo_GaussianSpotCentroidDetection.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example


    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: demo_GaussianSpotCentroidDetection.py <demo_GaussianSpotCentroidDetection.py>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: demo_GaussianSpotCentroidDetection.ipynb <demo_GaussianSpotCentroidDetection.ipynb>`