data loading ok, need to convert RGBA to RGB

MontpellierRessourcesImagerie · Jan 20, 2025 · 013b851 · 013b851
1 parent 49f9cda
commit 013b851
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diff --git a/volker/toolsets/tree_ring_segmentation/pythonProject/tree_rings_prepare_data.ipynb b/volker/toolsets/tree_ring_segmentation/pythonProject/tree_rings_prepare_data.ipynb
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "1f72240e-c42a-4a54-81d7-5c3eafd59002",
    "metadata": {},
    "outputs": [],
@@ -248,22 +248,36 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "1eb53565-e3e1-46a1-8330-8646b8f06649",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "FileNotFoundError",
+     "evalue": "[Errno 2] No such file or directory: '/media/baecker/6b38a953-6650-4da5-94d9-57bd718df733/2025/in/2007_tree_rings/input_images/masks/patches'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[4], line 29\u001b[0m\n\u001b[1;32m     26\u001b[0m         os\u001b[38;5;241m.\u001b[39mrename(imagePath, os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(imageOutFolder, imageName))\n\u001b[1;32m     27\u001b[0m         counter \u001b[38;5;241m=\u001b[39m counter \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m\n\u001b[0;32m---> 29\u001b[0m \u001b[43mmain\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+      "Cell \u001b[0;32mIn[4], line 8\u001b[0m, in \u001b[0;36mmain\u001b[0;34m()\u001b[0m\n\u001b[1;32m      6\u001b[0m image_patches_folder \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(input_folder, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpatches\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      7\u001b[0m mask_patches_folder \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(masks_folder, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpatches\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 8\u001b[0m masks \u001b[38;5;241m=\u001b[39m \u001b[43mos\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlistdir\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmask_patches_folder\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      9\u001b[0m mask_paths \u001b[38;5;241m=\u001b[39m [os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(mask_patches_folder, file) \u001b[38;5;28;01mfor\u001b[39;00m file \u001b[38;5;129;01min\u001b[39;00m masks \u001b[38;5;28;01mif\u001b[39;00m file\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m.tif\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m file\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m.jpg\u001b[39m\u001b[38;5;124m\"\u001b[39m)]\n\u001b[1;32m     10\u001b[0m image_paths \u001b[38;5;241m=\u001b[39m [os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mjoin(image_patches_folder, file) \u001b[38;5;28;01mfor\u001b[39;00m file \u001b[38;5;129;01min\u001b[39;00m masks \u001b[38;5;28;01mif\u001b[39;00m file\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m.tif\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m file\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m.jpg\u001b[39m\u001b[38;5;124m\"\u001b[39m)]\n",
+      "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '/media/baecker/6b38a953-6650-4da5-94d9-57bd718df733/2025/in/2007_tree_rings/input_images/masks/patches'"
+     ]
+    }
+   ],
    "source": [
     "import random \n",
     "import numpy as np\n",
+    "import os\n",
     "\n",
     "def main():\n",
     "    image_patches_folder = os.path.join(input_folder, \"patches\")\n",
     "    mask_patches_folder = os.path.join(masks_folder, \"patches\")\n",
     "    masks = os.listdir(mask_patches_folder)\n",
     "    mask_paths = [os.path.join(mask_patches_folder, file) for file in masks if file.endswith(\".tif\") or file.endswith(\".jpg\")]\n",
     "    image_paths = [os.path.join(image_patches_folder, file) for file in masks if file.endswith(\".tif\") or file.endswith(\".jpg\")]\n",
-    "    maskOutFolder = os.path.join(masks_folder, \"validation_patches\")\n",
-    "    imageOutFolder = os.path.join(input_folder, \"validation_patches\")\n",
+    "    maskOutFolder = os.path.join(masks_folder, \"test_patches\")\n",
+    "    imageOutFolder = os.path.join(input_folder, \"test_patches\")\n",
     "    os.makedirs(maskOutFolder, exist_ok=True)\n",
     "    os.makedirs(imageOutFolder, exist_ok=True)\n",
     "    N = len(mask_paths)\n",
@@ -286,7 +300,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "aea50a10-165f-4c8d-9218-14e612fb0d89",
+   "id": "bddee775-b7f5-477f-996b-79a1e675d8a5",
    "metadata": {},
    "outputs": [],
    "source": []