{
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    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "%matplotlib inline"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "# Cameras and images\n\nThis demo shows with the example of the ``DummyGrabber``\nhow you acquire an image and apply some filters.\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "from itom import dataIO\nfrom itom import dataObject\nfrom itom import algorithms\nfrom itom import liveImage\nfrom itom import saveIDC\nfrom itom import loadIDC\nfrom itom import plot"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Initialize a ``DummyGrabber`` camera\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "cam = dataIO(\"DummyGrabber\")\ncam.setParam(\"bpp\", 8)\n# start camera (only once)\ncam.startDevice()\n\n# show live image of camera\nliveImage(cam)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        ".. hint:: The live images tries to acquire and get up to 50 images per second\n    from the camera. If you want to acquire images by yourself in a script, you need\n    to stop the timer of the live images for a certain amount of time. After you are\n    done with your manual acquisition, you can restart the timer again.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "currentStatus = cam.getAutoGrabbing()\nprint(\"Current value of auto grabbing property of the camera:\", currentStatus)\n\ncam.setAutoGrabbing(False)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Acquire 10 images in a list of dataObjects\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "result = []\nd = dataObject()  # empty data object where the image should be put in\n\nfor i in range(0, 10):\n    cam.acquire()\n    cam.getVal(d)  # d is a shallow copy of the camera image\n    result.append(d.copy())"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the list of images to the **image1.idc** file (idc is a file format for the python pickle module)\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "saveIDC(\"image1.idc\", {\"result\": result, \"description\": \"sample 1\"})"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Load the list of images\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "loaded_objects = loadIDC(\"image1.idc\")\nresult2 = loaded_objects[\"result\"]\n\n# plot the 3rd image from the list\nplot(result2[2])"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Acquire 10 images in an image stack\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "num = 10\nsizex = cam.getParam(\"sizex\")\nsizey = cam.getParam(\"sizey\")\nbpp = cam.getParam(\"bpp\")\n\nif bpp == 8:\n    d = dataObject([num, sizey, sizex], \"uint8\")\nelse:\n    d = dataObject([num, sizey, sizex], \"uint16\")\n\nfor idx in range(num):\n    cam.acquire()\n    cam.copyVal(d[idx, :, :])  # partial deep copy into one part of the 3d object d\n\nplot(d)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Calculate mean value of image stack in z-direction.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "result_mean = dataObject()\n\nalgorithms.calcMeanZ(d, result_mean, ignoreInf=0, calcStd=0)\n# result_mean is a 3d Object with [1 x sizey x sizex] dimensions.\n# We squeeze it to get a 2D Object\nresult_mean = result_mean.squeeze()\n\nresult_mean.setTag(\"title\", \"mean value of {} acquisitions\".format(num))\nresult_mean.axisUnits = (\"px\", \"px\")\nresult_mean.axisDescriptions = (\"y\", \"x\")\nplot(result_mean)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "<img src=\"file://../../_static/demoCameraAndImages_1.png\" width=\"100%\">\n\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Apply Gaussian filter onto the mean image.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "result_filter = dataObject()\nkernelVal = 9\nalgorithms.gaussianFilter(result_mean, result_filter, kernelx=kernelVal, kernely=kernelVal)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Copy meta information from source ``dataObject``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "result_filter.copyMetaInfo(result_mean)\nresult_filter.setTag(\"title\", \"Gaussian filter with kernel {}\".format(kernelVal))\nplot(result_filter)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "<img src=\"file://../../_static/demoCameraAndImages_2.png\" width=\"100%\">\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "# reset the auto grabbing functionality of possibly connected live images\ncam.setAutoGrabbing(currentStatus)\n\n# end camera\ncam.stopDevice()"
      ]
    }
  ],
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