clear DS_Store

bluemindai · Jun 23, 2024 · aea1ac8 · aea1ac8
1 parent a8ee944
commit aea1ac8
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/scripts/del_npy.ipynb b/scripts/del_npy.ipynb
@@ -8,7 +8,7 @@
    "source": [
     "import os\n",
     "\n",
-    "dir = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_preprocessed/Dataset101_mosaic_skelet_spine/nnUNetPlans_3d_fullres\"\n",
+    "dir = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_preprocessed/Dataset102_mosaic_skelet_ribs/nnUNetPlans_3d_fullres\"\n",
     "files = os.listdir(dir)\n",
     "\n",
     "for file in files:\n",

diff --git a/scripts/evaluate.ipynb b/scripts/evaluate.ipynb
@@ -10,9 +10,9 @@
     "from nnunetv2.imageio.nibabel_reader_writer import NibabelIOWithReorient\n",
     "import json\n",
     "\n",
-    "folder_ref = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones/labelsTr'\n",
-    "model_folder = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset904_mosaic_kidney_stones/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres_mosaic_spacing_stdres_NoRsmp'\n",
-    "folder_pred = f'{model_folder}/fold_3/validation'\n",
+    "folder_ref = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset102_mosaic_skelet_ribs/labelsTr'\n",
+    "model_folder = '/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_results/Dataset102_mosaic_skelet_ribs/nnUNetTrainerNoMirroring__Mosaic_nnUNetPlannerResEncL_stdres_NoRsmp_24G__3d_fullres'\n",
+    "folder_pred = f'{model_folder}/fold_0/validation'\n",
     "output_file = f'{folder_pred}/summary.json'\n",
     "dataset_json = f'{model_folder}/dataset.json'\n",
     "image_reader_writer = NibabelIOWithReorient()\n",

diff --git a/scripts/generate_json.ipynb b/scripts/generate_json.ipynb
@@ -11,21 +11,23 @@
     "from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json\n",
     "import os\n",
     "\n",
-    "dataset = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset904_mosaic_kidney_stones\"\n",
+    "dataset = \"/home/eolika/Desktop/BlueMind/nnUNet/trains/nnUNet_raw/Dataset903_mosaic_head_pathology\"\n",
     "\n",
     "generate_dataset_json(output_folder=dataset,\n",
     "                      channel_names={0: \"CT\"},\n",
     "                      labels={\n",
     "                          'background': 0,\n",
-    "                          \"kidney_stone\": 1\n",
+    "                          \"brain\": 1,\n",
+    "                          \"ischemic_stroke\": 2,\n",
+    "                          \"intracerebral_hemorrhage\": 3\n",
     "                        },\n",
     "                        num_training_cases=len(os.listdir(f'{dataset}/imagesTr')), \n",
     "                        file_ending='.nii.gz',\n",
     "                        dataset_name=dataset.split('/')[-1], \n",
     "                        reference='BlueMind AI Inc',\n",
     "                        release='1.0.0',\n",
     "                        overwrite_image_reader_writer='NibabelIOWithReorient',\n",
-    "                        description=\"kidney_stones\")"
+    "                        description=\"head_pathology\")"
    ]
   },
   {