{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "735ff639-5973-4493-bca8-db49f7b91209",
   "metadata": {},
   "outputs": [],
   "source": [
    "import qim3d\n",
    "import os\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "16f0056a-83a3-4741-8386-1d20fa2e190e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Define the base directory and file name\n",
    "base_dir = '/data/cinemax/wood/wood_Zoom_polaris'\n",
    "file_name = 'wood_32.tiff'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "1fe8809c-db81-421c-8e44-089ae33fb85c",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Construct the full file path\n",
    "file_path = os.path.join(base_dir, file_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "af53a518-4583-4def-ad67-27b6a136e3ef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "67b7c3ed50e649ce81bfe74f01580534",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Loading:   0%|          | 0.00B/258MB  [00:00<?, ?B/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Loaded shape: (30, 2125, 2125)\n",
      "Volume using 258.4 MB of memory\n",
      "\n",
      "System memory:\n",
      " • Total.: 125.2 GB\n",
      " • Used..: 85.7 GB (68.4%)\n",
      " • Free..: 39.5 GB (31.6%)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Successfully loaded image. Shape: (30, 2125, 2125)\n",
      "An error occurred: name 'log' is not defined\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    # Load the image\n",
    "    vol = qim3d.io.load(file_path)\n",
    "    print(f\"Successfully loaded image. Shape: {vol.shape}\")\n",
    "    \n",
    "    # Compute structure tensor with custom parameters\n",
    "    val, vec = qim3d.processing.structure_tensor(\n",
    "        vol, \n",
    "        sigma=2.0, \n",
    "        rho=10.0, \n",
    "        base_noise=True, \n",
    "        full=False, \n",
    "        visualize=True  # Set to True to generate visualizations\n",
    "    )\n",
    "    \n",
    "    print(\"Structure tensor computation completed.\")\n",
    "    print(f\"Eigenvalues shape: {val.shape}\")\n",
    "    print(f\"Eigenvectors shape: {vec.shape}\")\n",
    "except Exception as e:\n",
    "    print(f\"An error occurred: {e}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "3d25bb99-dccd-40fe-9626-9c78ffa3f0cc",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'val' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[12], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# Display the middle slice of the eigenvalue volume\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m middle_slice \u001b[38;5;241m=\u001b[39m val\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m2\u001b[39m] \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m2\u001b[39m\n\u001b[1;32m      3\u001b[0m plt\u001b[38;5;241m.\u001b[39mfigure(figsize\u001b[38;5;241m=\u001b[39m(\u001b[38;5;241m12\u001b[39m, \u001b[38;5;241m10\u001b[39m))\n\u001b[1;32m      4\u001b[0m plt\u001b[38;5;241m.\u001b[39mimshow(val[:, :, middle_slice, \u001b[38;5;241m0\u001b[39m], cmap\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mviridis\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
      "\u001b[0;31mNameError\u001b[0m: name 'val' is not defined"
     ]
    }
   ],
   "source": [
    "# Display the middle slice of the eigenvalue volume\n",
    "middle_slice = val.shape[2] // 2\n",
    "plt.figure(figsize=(12, 10))\n",
    "plt.imshow(val[:, :, middle_slice, 0], cmap='viridis')\n",
    "plt.colorbar()\n",
    "plt.title(f'First Eigenvalue (Middle Slice: {middle_slice})')\n",
    "plt.show()\n",
    "\n",
    "# Display the middle slice of the original volume\n",
    "plt.figure(figsize=(12, 10))\n",
    "plt.imshow(vol[:, :, middle_slice], cmap='gray')\n",
    "plt.colorbar()\n",
    "plt.title(f'Original Volume (Middle Slice: {middle_slice})')\n",
    "plt.show()\n",
    "\n",
    "# Error handling\n",
    "try:\n",
    "    # Your code here\n",
    "    pass\n",
    "except FileNotFoundError:\n",
    "    print(f\"Error: File not found at {file_path}\")\n",
    "    print(\"Please check if the file exists and the path is correct.\")\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c9af27d8-e309-4446-894b-982adef96440",
   "metadata": {},
   "outputs": [],
   "source": [
    "    # List contents of the directory to help debugging\n",
    "    try:\n",
    "        print(f\"\\nContents of {base_dir}:\")\n",
    "        for item in os.listdir(base_dir):\n",
    "            print(item)\n",
    "    except Exception as e:\n",
    "        print(f\"Could not list directory contents: {e}\")\n",
    "\n",
    "except AttributeError as e:\n",
    "    print(f\"Error: {e}\")\n",
    "    print(\"This might be due to an incompatibility with the qim3d version you're using.\")\n",
    "    print(\"Please check the qim3d documentation for the correct usage of structure_tensor function.\")\n",
    "\n",
    "except Exception as e:\n",
    "    print(f\"An unexpected error occurred: {e}\")\n",
    "\n",
    "print(f\"\\nQIM3D version: {qim3d.__version__}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "b47fb9e3-3cd0-4354-aa6e-116300575f99",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b2a68c5b002743419402fea3f69eb8f5",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Loading:   0%|          | 0.00B/258MB  [00:00<?, ?B/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Loaded shape: (30, 2125, 2125)\n",
      "Volume using 258.4 MB of memory\n",
      "\n",
      "System memory:\n",
      " • Total.: 125.2 GB\n",
      " • Used..: 118.7 GB (94.8%)\n",
      " • Free..: 6.5 GB (5.2%)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Successfully loaded image. Original shape: (30, 2125, 2125)\n",
      "Cut to middle 1/8th along y-axis. New shape: (30, 1062, 2125)\n",
      "Saved cut volume to: /data/cinemax/wood/wood_Zoom_polaris/wood_32_y4.tiff\n",
      "\n",
      "QIM3D version: 0.4.1\n"
     ]
    }
   ],
   "source": [
    "import qim3d\n",
    "import os\n",
    "import numpy as np\n",
    "\n",
    "# Define the base directory and file name\n",
    "base_dir = '/data/cinemax/wood/wood_Zoom_polaris'\n",
    "input_file_name = 'wood_32.tiff'\n",
    "output_file_name = 'wood_32_y4.tiff'\n",
    "\n",
    "# Construct the full file paths\n",
    "input_file_path = os.path.join(base_dir, input_file_name)\n",
    "output_file_path = os.path.join(base_dir, output_file_name)\n",
    "\n",
    "def cut_middle_eighth_y(volume):\n",
    "    \"\"\"Cut the volume to 1/8th of its length along the y-axis from the middle.\"\"\"\n",
    "    z, y, x = volume.shape\n",
    "    y_start = y // 2 - y // 4\n",
    "    y_end = y // 2 + y // 4\n",
    "    return volume[:, y_start:y_end, :]\n",
    "\n",
    "try:\n",
    "    # Load the image\n",
    "    vol = qim3d.io.load(input_file_path)\n",
    "    print(f\"Successfully loaded image. Original shape: {vol.shape}\")\n",
    "    \n",
    "    # Cut the volume\n",
    "    cut_vol = cut_middle_eighth_y(vol)\n",
    "    print(f\"Cut to middle 1/8th along y-axis. New shape: {cut_vol.shape}\")\n",
    "    \n",
    "    # Save the cut volume\n",
    "    qim3d.io.save(output_file_path, cut_vol)\n",
    "    print(f\"Saved cut volume to: {output_file_path}\")\n",
    "\n",
    "except Exception as e:\n",
    "    print(f\"An error occurred: {e}\")\n",
    "\n",
    "print(f\"\\nQIM3D version: {qim3d.__version__}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "93a77bd6-3263-468d-9860-2e46ae05dea5",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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