dataset processing jupiter

Author: robert-graf

tutorials/tutorial_Dataset_processing.ipynb

@@ -71,7 +71,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from TPTBox.core.bids_files import formats,entities_keys\n",
+    "from TPTBox.core.bids_files import entities_keys, formats\n",
+    "\n",
     "print('Known formats:\\n','\\n'.join(formats))\n",
     "print()\n",
     "print()\n",
@@ -104,6 +105,7 @@
    "outputs": [],
    "source": [
     "from pathlib import Path\n",
+    "\n",
     "from TPTBox.core.dicom.dicom_extract import extract_dicom_folder\n",
     "\n",
     "path_to_dicom_dataset = \"TODO\"\n",
@@ -123,6 +125,7 @@
    "outputs": [],
    "source": [
     "from pathlib import Path\n",
+    "\n",
     "path_to_dicom_dataset = \"/media/data/robert/datasets/dicom_example/VR-DICOM/\"\n",
     "dataset_name = 'VR-DICOM2'\n",
     "target_folder = Path(path_to_dicom_dataset).parent\n",
@@ -142,8 +145,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from TPTBox import BIDS_Global_info,BIDS_FILE\n",
+    "from TPTBox import BIDS_FILE, BIDS_Global_info\n",
     "from TPTBox.core.bids_constants import sequence_splitting_keys\n",
+    "\n",
     "print(\"if one of the values of these keys is diffrent, than it is considered a other sequence:\", sequence_splitting_keys)\n",
     "print(\"sub will alway split\")\n",
     "\n",
@@ -215,10 +219,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from TPTBox.stitching import stitching\n",
-    "from TPTBox import to_nii\n",
     "from concurrent.futures import ProcessPoolExecutor\n",
     "\n",
+    "from TPTBox import to_nii\n",
+    "from TPTBox.stitching import stitching\n",
+    "\n",
     "derivative_folder = \"derivative_stiched\"\n",
     "\n",
     "def process_files(files):\n",
@@ -269,14 +274,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from TPTBox.segmentation import run_totalvibeseg\n",
     "from TPTBox import BIDS_FILE\n",
+    "from TPTBox.segmentation import run_totalvibeseg\n",
+    "\n",
     "# run_totalvibeseg\n",
     "# You can alos use a string/Path if you want to set the path yourself.\n",
     "dataset = \"/media/data/robert/datasets/dicom_example/dataset-VR-DICOM2/\"\n",
     "in_file = BIDS_FILE(f\"{dataset}/derivative_stiched/sub-111168222/T2w/sub-111168222_sequ-301-stiched_acq-ax_part-water_T2w.nii.gz\",dataset)\n",
     "out_file = in_file.get_changed_path(\"nii.gz\",\"msk\",parent=\"derivative\",info={\"seg\":\"TotalVibeSegmentator\",\"mod\":in_file.bids_format})\n",
-    "run_totalvibeseg(in_file,out_file)"
+    "run_totalvibeseg(in_file,out_file,True)"
    ]
   },
   {
@@ -309,7 +315,8 @@
    "outputs": [],
    "source": [
     "# Pick a fitting model:\n",
-    "from spineps.models import modelid2folder_semantic,modelid2folder_instance\n",
+    "from spineps.models import modelid2folder_instance, modelid2folder_semantic\n",
+    "\n",
     "print('Available Semantic Models',modelid2folder_semantic())\n",
     "print('Available Instance Models',modelid2folder_instance())\n",
     "\n",
@@ -331,6 +338,7 @@
    "outputs": [],
    "source": [
     "from TPTBox.segmentation.spineps import run_spineps_single\n",
+    "\n",
     "#With 'ignore_compatibility_issues = True' you can force to rund\n",
     "out_paths = run_spineps_single(\n",
     "    file_path,\n",