{
  "cells": [
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "%matplotlib inline"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "# Load and save dataObject\n\nThis demo shows how to **save** and **load** ``dataObjects``\nto/from image formats as well as native itom formats.\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "from itom import dataObject\nfrom itom import algorithms\nfrom itom import rgba\nfrom itom import plot\nfrom itom import saveIDC\nfrom itom import loadIDC"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Create a colored dataObject of type ``rgba32``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "rgba32 = dataObject([100, 100], \"rgba32\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Set all pixels to a gray value.\nTherefore ``red=green=blue`` with no transparency,\nwhat means that alpha has to be set to the maximal value of ``255``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "rgba32[0:100, 0:100] = rgba(150, 150, 150, 255)\n\n\"\"\"insert a red, green and blue bar in the picture wich are not complete intransparent\"\"\"\nrgba32[10:30, :] = rgba(255, 0, 0, 150)\nrgba32[50:70, :] = rgba(0, 255, 0, 150)\nrgba32[80:100, :] = rgba(0, 0, 255, 150)\n\"\"\"show the image\"\"\"\nplot(rgba32)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the ``dataObject`` as a *.tiff file with a rgba color palette.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "algorithms.saveTiff(rgba32, \"pic_rgba.tiff\", \"rgba\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Reload the picture as it was, that is of type ``rgba32``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "reload_tiff_rgba = dataObject()\nalgorithms.loadAnyImage(reload_tiff_rgba, \"pic_rgba.tiff\", \"asIs\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the ``dataObject`` as a *.tiff file with a rgb color palette,\nwhich causes that the transparency of the bars will be ignored. \nIf ``gray`` or ``gray16`` is choosen as color palette the colored\n``dataObject`` will be converted to a gray image \n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "algorithms.saveTiff(rgba32, \"pic_rgb.tiff\", \"rgb\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Reload the picture as it was, that is of type ``rgba32``\nwith all alpha values set to ``255`` (no transparency).\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "reload_tiff_rgb = dataObject()\nalgorithms.loadAnyImage(reload_tiff_rgb, \"pic_rgb.tiff\", \"asIs\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the ``dataObject`` as a *.png file with a ``gray`` color palette\n(also ``gray16`` and all colored palettes are supportted).\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "algorithms.savePNG(rgba32, \"pic_gray.png\", \"gray\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Reload the picture as it was, that is of type ``gray`` (type ``uint8``) \n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "reload_png_gray = dataObject()\nalgorithms.loadAnyImage(reload_png_gray, \"pic_gray.png\", \"asIs\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the ``dataObject`` as a *.pgm with a 16bit grayscale\n(``gray`` and ``gray16`` are only supported for gray images).\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "algorithms.savePGM(rgba32, \"pic_gray.pgm\", \"gray16\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Load the *.pgm file as it was, that is of type ``gray``\n(type ``uint16`` due to the 16bit gray color palette) \n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "reload_pgm_gray16 = dataObject()\nalgorithms.loadAnyImage(reload_pgm_gray16, \"pic_gray.pgm\", \"asIs\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the ``dataObject`` as an *.idc file (itom data collection,\nsaved using Python module ``pickle``) therefore it must be wrapped into a ``dictionary``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "dataDict = {\"data\": rgba32}\nsaveIDC(\"pic_idc.idc\", dataDict)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Load the *.idc file as it was, that is of type ``dictionary``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "loaded_dic = loadIDC(\"pic_idc.idc\")\nreload_img = loaded_dic[\"data\"]"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Copy the dataObject\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "rgba32_1 = rgba32"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save both (also more possible) in one *.idc file.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "dic_1 = {\"data_1\": rgba32, \"data_2\": rgba32_1}\nloaded_dic_1 = saveIDC(\"multi_pic_idc.idc\", dic_1)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "In this section a ``uint8`` ``dataObject`` is created and saved in false colors.\ncreate a gray image of type uint8\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "uint8 = dataObject([100, 100], \"uint8\")\n\n# insert blocks with values of 0.0, 1.0, 50 and 100\nuint8[0:25, :] = 0\nuint8[25:50, :] = 1\nuint8[50:75, :] = 50\nuint8[75:100, :] = 100"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save as *.tiff file colored in the ``hotIron`` color palette.\nOther palettes are for example ``grayMarked`` or ``falseColor``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "algorithms.saveTiff(uint8, \"pic_uint8.tiff\", \"hotIron\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "This section shows how to save floating point ``dataObjects`` as a image.\ncreate a gray image of type float32\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "float32 = dataObject([100, 100], \"float32\")\n\n# insert blocks with values of 0.0, 1.0, 50 and 100\nfloat32[0:25, :] = 0.0\nfloat32[25:50, :] = 1.0\nfloat32[50:75, :] = 50.0\nfloat32[75:100, :] = 100.0"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Save the ``float32`` ``dataObject`` as a *.png file\nwith a ``falseColor`` palette (here ``hotIron`` is used,\nothers are for example ``grayMarked`` or ``falseColor``).\nIf you save a ``dataObject`` of type float the color palette is spaced between\n``[0, 1]`` ->all values above ``1.0`` will be clipped to the maximum value.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "algorithms.savePNG(float32, \"pic_falseColor.png\", \"hotIron\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Reload the saved *.png as a ``uint8`` ``dataObject``\n->all steps with values above 1.0 have the same gray value.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "reload_png_falseColor = dataObject()\nalgorithms.loadAnyImage(reload_png_falseColor, \"pic_falseColor.png\", \"GRAY\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "To get rid of the problem above you need to normalize your\n``dataObject`` between ``0.0`` and ``1.0`` using the function ``normalize``.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "normfloat32 = float32.normalize(0.0, 1.0, \"float32\")\nalgorithms.savePNG(normfloat32, \"pic_normalized_falseColor.png\", \"hotIron\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Reload the image as a ``uint8`` ``dataObject``\n->all steps are included.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "reload_normalized_falseColor = dataObject()\nalgorithms.loadAnyImage(\n    reload_normalized_falseColor,\n    \"pic_normalized_falseColor.png\",\n    \"GRAY\",\n)"
      ]
    }
  ],
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