{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "ada4b32a-8077-4e9e-bc02-6d6ba1b10282",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Attempting to load file: /data/cinemax/wood/wood_Zoom_polaris/wood_zoom.tiff\n",
      "Will save cropped file as: /data/cinemax/wood/wood_Zoom_polaris/wood_32.tiff\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c3ed408ae873460db622377a6d9a60a0",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Loading:   0%|          | 0.00B/8.41GB  [00:00<?, ?B/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Loaded shape: (1000, 2125, 2125)\n",
      "Volume using 8.4 GB of memory\n",
      "\n",
      "System memory:\n",
      " • Total.: 125.2 GB\n",
      " • Used..: 124.6 GB (99.5%)\n",
      " • Free..: 635.4 MB (0.5%)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Successfully loaded image. Original shape: (1000, 2125, 2125)\n",
      "Cropped to middle 1/64th. New shape: (30, 2125, 2125)\n",
      "Saved cropped volume to: /data/cinemax/wood/wood_Zoom_polaris/wood_32.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",
    "file_name = 'wood_zoom.tiff'\n",
    "output_file_name = 'wood_32.tiff'\n",
    "\n",
    "# Construct the full file paths\n",
    "input_file_path = os.path.join(base_dir, file_name)\n",
    "output_file_path = os.path.join(base_dir, output_file_name)\n",
    "\n",
    "# Print the file paths to verify\n",
    "print(f\"Attempting to load file: {input_file_path}\")\n",
    "print(f\"Will save cropped file as: {output_file_path}\")\n",
    "\n",
    "def crop_middle_64th(volume):\n",
    "    \"\"\"Crop the volume to 1/32th of its length from the middle.\"\"\"\n",
    "    z, y, x = volume.shape\n",
    "    z_start = z // 2 - z // 64\n",
    "    z_end = z // 2 + z // 64\n",
    "    return volume[z_start:z_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",
    "    # Crop the volume\n",
    "    cropped_vol = crop_middle_64th(vol)\n",
    "    print(f\"Cropped to middle 1/64th. New shape: {cropped_vol.shape}\")\n",
    "    \n",
    "    # Save the cropped volume\n",
    "    qim3d.io.save(output_file_path, cropped_vol)\n",
    "    print(f\"Saved cropped volume to: {output_file_path}\")\n",
    "\n",
    "except FileNotFoundError:\n",
    "    print(f\"Error: File not found at {input_file_path}\")\n",
    "    print(\"Please check if the file exists and the path is correct.\")\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": null,
   "id": "69ba8103-6ad8-49a3-8d97-20e8bf66437d",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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