Merge pull request #7 from bamf-health/aimi2

Aimi2-kidney-ct

.pre-commit-config.yaml

@@ -1,27 +1,26 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
-        exclude_types: [jupyter, csv]
       - id: check-yaml
       - id: check-merge-conflict
       - id: debug-statements
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: ["--profile", "black", "--filter-files"]
-        additional_dependencies: [toml]
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black-jupyter
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.11.1
     hooks:
       - id: mypy
-        args: ["--implicit-optional"]
-        additional_dependencies:
-          [numpy, pydicom, SimpleITK, types-requests, segmentationmetrics]
+        args: [--implicit-optional]
+        additional_dependencies: [pydicom, SimpleITK, types-requests]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.5.6
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--select, I, --fix]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]

model_performance.ipynb

@@ -38,22 +38,24 @@
     "\n",
     "warnings.filterwarnings(\"ignore\")\n",
     "\n",
-    "from pathlib import Path\n",
-    "import requests\n",
-    "import zipfile\n",
     "import io\n",
+    "import zipfile\n",
+    "from pathlib import Path\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import skimage.measure\n",
-    "import scipy.stats as stats\n",
     "import pydicom\n",
     "import pydicom_seg\n",
-    "import SimpleITK as sitk\n",
+    "import requests\n",
+    "import scipy.stats as stats\n",
+    "import seaborn as sns\n",
     "import segmentationmetrics as sm\n",
+    "import SimpleITK as sitk\n",
+    "import skimage.measure\n",
     "from segmentationmetrics.surface_distance import compute_surface_dice_at_tolerance\n",
+    "\n",
     "from kits_metrics import compute_metrics_for_case\n",
-    "import matplotlib.pyplot as plt\n",
-    "import seaborn as sns\n",
     "\n",
     "sns.set_theme(style=\"whitegrid\")\n",
     "%matplotlib inline"
@@ -101,9 +103,9 @@
    "outputs": [],
    "source": [
     "def download_inference(\n",
-    "    extract_dir=\"qa-results\",record='13244892',filename = 'kidney-ct.zip'\n",
+    "    extract_dir=\"qa-results\", record=\"13244892\", filename=\"kidney-ct.zip\"\n",
     "):\n",
-    "    url=f\"https://zenodo.org/record/{record}/files/{filename}\"\n",
+    "    url = f\"https://zenodo.org/record/{record}/files/{filename}\"\n",
     "    # download the zip file and extract it\n",
     "    r = requests.get(url)\n",
     "    z = zipfile.ZipFile(io.BytesIO(r.content))\n",
@@ -1160,7 +1162,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,