notebook: update notebooks

refactor notebooks to comply with ruff rules

Author: lukasbehammer

notebooks/Image_Comparison.ipynb

@@ -111,6 +111,7 @@
     "import os\n",
     "\n",
     "import skimage.transform as skt\n",
+    "\n",
     "import viqa\n",
     "from viqa import MultipleMetrics, load_data"
    ]
@@ -137,7 +138,9 @@
    "outputs": [],
    "source": [
     "# Change the project name and results folder\n",
-    "results_path = \"/path/to/results\"  # make sure this path exists before running the notebook\n",
+    "results_path = (\n",
+    "    \"/path/to/results\"  # make sure this path exists before running the notebook\n",
+    ")\n",
     "project_name = \"image_comparison\"\n",
     "\n",
     "# Choose the slice to visualize in the report, only one slice should be chosen\n",
@@ -173,10 +176,10 @@
    ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "## Data Loading",
-   "id": "4fe1f2f0327339a1"
+   "id": "4fe1f2f0327339a1",
+   "metadata": {},
+   "source": "## Data Loading"
   },
   {
    "cell_type": "code",
@@ -225,46 +228,46 @@
    ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "## Image Statistics",
-   "id": "4a434d2014297e90"
+   "id": "4a434d2014297e90",
+   "metadata": {},
+   "source": "## Image Statistics"
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "### Reference Image",
-   "id": "aa0db190908d6b4"
+   "id": "aa0db190908d6b4",
+   "metadata": {},
+   "source": "### Reference Image"
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "outputs": [],
    "execution_count": null,
+   "id": "b487df468724b444",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# Calculate and print statistics for reference image\n",
     "img_r.calculate_statistics()\n",
     "img_r.describe()"
-   ],
-   "id": "b487df468724b444"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "### Modified Image",
-   "id": "a4866d4774a074b3"
+   "id": "a4866d4774a074b3",
+   "metadata": {},
+   "source": "### Modified Image"
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "outputs": [],
    "execution_count": null,
+   "id": "2938c602ee3be7ea",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# Calculate and print statistics for modified image\n",
     "img_m.calculate_statistics()\n",
     "img_m.describe()"
-   ],
-   "id": "2938c602ee3be7ea"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -328,7 +331,12 @@
     "# Run this to visualize centers\n",
     "if calc_cnr:\n",
     "    metric_cnr = viqa.CNR(**cnr_load_parameters)\n",
-    "    metric_cnr.set_centers(img=img_m, signal_center=cnr_calc_parameters[\"signal_center\"], background_center=cnr_calc_parameters[\"background_center\"], radius=cnr_calc_parameters[\"radius\"])"
+    "    metric_cnr.set_centers(\n",
+    "        img=img_m,\n",
+    "        signal_center=cnr_calc_parameters[\"signal_center\"],\n",
+    "        background_center=cnr_calc_parameters[\"background_center\"],\n",
+    "        radius=cnr_calc_parameters[\"radius\"],\n",
+    "    )"
    ]
   },
   {
@@ -370,7 +378,11 @@
     "# Run this to visualize center\n",
     "if calc_snr:\n",
     "    metric_snr = viqa.SNR(**snr_load_parameters)\n",
-    "    metric_snr.set_centers(img=img_m, signal_center=snr_calc_parameters[\"signal_center\"], radius=snr_calc_parameters[\"radius\"])"
+    "    metric_snr.set_centers(\n",
+    "        img=img_m,\n",
+    "        signal_center=snr_calc_parameters[\"signal_center\"],\n",
+    "        radius=snr_calc_parameters[\"radius\"],\n",
+    "    )"
    ]
   },
   {
@@ -754,7 +766,18 @@
    "source": [
     "# Change types of reports you want to generate\n",
     "# img_r, img_m are for parameter ``image``.\n",
-    "multiple.report(csv=True, metadata=True, text=True, image=True, file_path=results_path, project_name=project_name, export_image=True, img_r=img_r, img_m=img_m, **slice_vis)"
+    "multiple.report(\n",
+    "    csv=True,\n",
+    "    metadata=True,\n",
+    "    text=True,\n",
+    "    image=True,\n",
+    "    file_path=results_path,\n",
+    "    project_name=project_name,\n",
+    "    export_image=True,\n",
+    "    img_r=img_r,\n",
+    "    img_m=img_m,\n",
+    "    **slice_vis,\n",
+    ")"
    ]
   }
  ],