{
 "cells": [
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   "cell_type": "markdown",
   "id": "e5d0bcbc-c479-4f71-88a3-8c44e8e0ac0b",
   "metadata": {},
   "source": [
    "# Colormaps \n",
    "stackview supports colormaps as defined in [Matplotlib](https://matplotlib.org/stable/tutorials/colors/colormaps.html) and aims at compatibility with [microfilm](https://github.com/guiwitz/microfilm)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "f58d68f7-e838-4e3d-9b35-f3e4907d7fb7",
   "metadata": {},
   "outputs": [],
   "source": [
    "import stackview\n",
    "import numpy as np\n",
    "from skimage.io import imread"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4d6da998-1568-4f45-a9c1-2f652973bc6e",
   "metadata": {},
   "outputs": [],
   "source": [
    "image = imread(\"data/blobs.tif\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4e4876c3-110b-4830-926f-0f67583ce409",
   "metadata": {},
   "source": [
    "You can show images with colormaps such as `pure_green`, `pure_red`, `pure_magenta_r`. The `_r` by the end specifies that low values correspond to high intensity."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ca9d0724-cd07-442e-aef2-48f3dbc12afc",
   "metadata": {},
   "outputs": [
    {
     "data": {
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      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.slice(image, colormap=\"pure_magenta_r\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "b4c776de-44bc-42a4-9866-b880e8700b32",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "546ca66bf9624102abea16807d7769e4",
       "version_major": 2,
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      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.curtain(image, image, colormap=\"pure_green\", curtain_colormap=\"pure_green_r\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6c7d246f-b11d-416a-9228-1fe5a1971f3c",
   "metadata": {},
   "source": [
    "As `imswitch()` shows a list (or dictionary) of images, you can also specify a list of colormaps."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "1e3fa547-72e3-4698-bac3-39e8199a6a57",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "model_id": "cb279be343c64f658adffe442e310d01",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), HBox(children=(Button(d…"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.switch(\n",
    "    [image, image, image],\n",
    "    colormap=[\"pure_magenta\", \"pure_green\", \"pure_cyan\"]\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3e5721d7-afa4-4e61-8466-a047614c786c",
   "metadata": {},
   "source": [
    "You can also specify a single colormap for all images."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "155539c5-c5cb-47f9-b31b-39a6b434c473",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "1aa7b4ee3b294edeb664ff7ffb31bfd3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), HBox(children=(Button(d…"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.switch(\n",
    "    [image, image[::-1], image[:,::-1]],\n",
    "    colormap=\"pure_green\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "82244820-743e-488d-bf8f-db0145b65054",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a69de38ad115442b9482a761a27c560c",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "_Cropper(children=(IntRangeSlider(value=(0, 254), description='Y', max=254), IntRangeSlider(value=(0, 256), de…"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.crop(image, colormap='pure_green')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "49eca120-2264-4c75-af7e-574dd9d3293c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c9f63bc2196b4d69bb647d73b885ce3f",
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       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), VBox(chi…"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "labels = np.zeros_like(image, dtype=np.uint32)\n",
    "labels[10:20, 10:20] = 1\n",
    "\n",
    "stackview.annotate(image, labels, colormap=\"pure_magenta\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "8e91b5fc-7a83-4b68-8108-223189851467",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "model_id": "47029cef3e474605a13cb948d6c07992",
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      "text/plain": [
       "VBox(children=(interactive(children=(Checkbox(value=False, description='flip_x'), Checkbox(value=False, descri…"
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     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def flip(image, flip_x:bool, flip_y:bool):\n",
    "    if flip_x:\n",
    "        image = image[...,::-1]\n",
    "    if flip_y:\n",
    "        image = image[::-1]\n",
    "    return image\n",
    "    \n",
    "stackview.interact(flip, image, colormap=\"pure_magenta\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b8906f7f-e528-4a8d-bf47-4b6845e805ed",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d40f0dc45bea47359a06d38f4ea52c48",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=160, width=160),)),)), IntSlide…"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mri = imread(\"data/Haase_MRT_tfl3d1.tif\")\n",
    "\n",
    "stackview.orthogonal(mri, colormap=\"pure_green\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "20573447-6987-4629-97bc-bbe1c8627660",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f809f3d25c9549d8aaa3ec980071fe92",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=160, width=160),)),)), IntSlider(value=60, des…"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.picker(mri, colormap=\"pure_green\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c7bdd4b7-aafa-44af-8425-8d7f799f23d0",
   "metadata": {},
   "source": [
    "## Display range\n",
    "One can also tune the display range by providing the minimum and maximum intensity that should be shown."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "988ffba9-343c-499f-a999-99f8d99a306a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "bfc296fdc26d4940a9e8f3685016351f",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.slice(image, display_max=100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "281da7ba-f7c3-4e88-a076-136f78ac4528",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f90e182baaa4492bbf1e49f236a7ebd4",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stackview.slice(image, display_min=50)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2f94b703-36f2-4580-910e-19521e8d6d62",
   "metadata": {},
   "source": [
    "## Muliti-channel images\n",
    "To overlay multi-channel images with defined colormaps per channel, you can also `stackview.switch()` with `toggleable=True`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "785762f3-64a2-425f-a159-79508b665496",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "7b4b4741b7514625af32d44043961d7c",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=512, width=672),)),)), HBox(children=(ToggleBu…"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hela_cells = imread(\"data/hela-cells.tif\")\n",
    "\n",
    "stackview.switch(\n",
    "    {\"lysosomes\":   hela_cells[:,:,0],\n",
    "     \"mitochondria\":hela_cells[:,:,1],\n",
    "     \"nuclei\":      hela_cells[:,:,2]\n",
    "    },\n",
    "    colormap=[\"pure_magenta\", \"pure_green\", \"pure_blue\"],\n",
    "    toggleable=True\n",
    ")"
   ]
  }
 ],
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