{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Segmentation 3D\n",
    "\n",
    "## 0. Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import openalea.phenomenal.data as phm_data\n",
    "import openalea.phenomenal.display.notebook as phm_display_notebook\n",
    "import openalea.phenomenal.object as phm_obj\n",
    "import openalea.phenomenal.segmentation as phm_seg\n",
    "from openalea.phenotyping_data.fetch import fetch_all_data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Prerequisites\n",
    "\n",
    "### 1.1 Load cloud point of voxel centers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plant_number = 2\n",
    "voxels_size = 16\n",
    "data_dir = fetch_all_data(f\"plant_{plant_number}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "bin_images = phm_data.bin_images(data_dir)\n",
    "calibrations = phm_data.calibrations(data_dir)\n",
    "voxel_grid = phm_data.voxel_grid(data_dir, voxels_size=voxels_size)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1.2 Display voxel grid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "phm_display_notebook.show_voxel_grid(voxel_grid, size=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. Skeletonization\n",
    "\n",
    "### 2.1 Compute Graph and the skeleton\n",
    "Compute the skeleton of the plant voxelgrid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "graph = phm_seg.graph_from_voxel_grid(voxel_grid, connect_all_point=True)\n",
    "voxel_skeleton = phm_seg.skeletonize(voxel_grid, graph)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2.2 Display it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "phm_display_notebook.show_skeleton(voxel_skeleton, with_voxel=True, size=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2.3 Remove not enouth visible segment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Select images\n",
    "image_projection = list()\n",
    "for angle in bin_images[\"side\"]:\n",
    "    projection = calibrations[\"side\"].get_projection(angle)\n",
    "    image_projection.append((bin_images[\"side\"][angle], projection))\n",
    "\n",
    "voxel_skeleton_denoised = phm_seg.segment_reduction(\n",
    "    voxel_skeleton, image_projection, required_visible=5, nb_min_pixel=400\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2.4 Display it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "phm_display_notebook.show_skeleton(voxel_skeleton_denoised, size=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Maize Segmentation\n",
    "\n",
    "### 3.1 Process\n",
    "\n",
    "Voxel skeleton are segmented in several label \"stem\", \"mature_leaf\", \"growing_leaf\" and \"unknow\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "vms = phm_seg.maize_segmentation(voxel_skeleton_denoised, graph)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3.2 Write / Read"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Write\n",
    "vms.write_to_json_gz(\"voxel_maize_segmentation.json\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Load\n",
    "vms = phm_obj.VoxelSegmentation.read_from_json_gz(\"voxel_maize_segmentation.json\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3.3 Display"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "phm_display_notebook.show_segmentation(vms, size=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4. Maize Analysis\n",
    "\n",
    "### 4.1 Process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "vmsi = phm_seg.maize_analysis(vms)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4.2 How to save analysis result :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "vmsi.write_to_json_gz(\"voxel_maize_segmentation_info.json.gz\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "vmsi = phm_obj.VoxelSegmentation.read_from_json_gz(\n",
    "    \"voxel_maize_segmentation_info.json.gz\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4.3 Visualize results: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "phm_display_notebook.show_segmentation(vmsi, size=1)"
   ]
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.17"
  },
  "widgets": {
   "application/vnd.jupyter.widget-state+json": {
    "state": {},
    "version_major": 2,
    "version_minor": 0
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}