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pre-commit-ci[bot] · pre-commit-ci[bot] · commit 49d504ce2b05 · 2025-11-17T17:55:26.000Z
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diff --git a/docs/01_code_usage/demo_analyze_everything.ipynb b/docs/01_code_usage/demo_analyze_everything.ipynb
@@ -19,21 +19,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import napari_stress\n",
-    "import napari\n",
-    "import numpy as np\n",
-    "from napari_stress import reconstruction, measurements, TimelapseConverter, utils, stress_backend, plotting\n",
-    "import os\n",
     "import datetime\n",
+    "import os\n",
     "\n",
-    "from skimage import io\n",
-    "\n",
+    "import matplotlib as mpl\n",
+    "import matplotlib.pyplot as plt\n",
+    "import napari\n",
+    "import numpy as np\n",
     "import pandas as pd\n",
     "import seaborn as sns\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib as mpl\n",
     "\n",
-    "import yaml"
+    "import napari_stress\n",
+    "from napari_stress import (\n",
+    "    TimelapseConverter,\n",
+    "    measurements,\n",
+    "    plotting,\n",
+    "    reconstruction,\n",
+    "    stress_backend,\n",
+    "    utils,\n",
+    ")"
    ]
   },
   {
@@ -440,7 +444,7 @@
     "if filename is not None:\n",
     "    filename_without_ending = os.path.basename(filename).split('.')[0]\n",
     "    save_directory = os.path.join(os.path.dirname(filename), filename_without_ending + '_' + datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S'))\n",
-    "else: \n",
+    "else:\n",
     "    save_directory = os.path.join(os.getcwd(), 'results_' + datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S'))\n",
     "\n",
     "if not os.path.exists(save_directory):\n",
diff --git a/docs/01_code_usage/demo_analyze_everything_batch.ipynb b/docs/01_code_usage/demo_analyze_everything_batch.ipynb
@@ -31,18 +31,24 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import napari\n",
-    "import numpy as np\n",
-    "from napari_stress import reconstruction, measurements, utils, stress_backend, TimelapseConverter\n",
     "import os\n",
     "from pathlib import Path\n",
-    "from bioio import BioImage\n",
-    "\n",
-    "from dask.distributed import Client, get_client\n",
     "\n",
+    "import napari\n",
+    "import numpy as np\n",
     "import pandas as pd\n",
+    "import vedo\n",
+    "from bioio import BioImage\n",
+    "from dask.distributed import Client, get_client\n",
     "from skimage import io\n",
-    "import vedo"
+    "\n",
+    "from napari_stress import (\n",
+    "    TimelapseConverter,\n",
+    "    measurements,\n",
+    "    reconstruction,\n",
+    "    stress_backend,\n",
+    "    utils,\n",
+    ")"
    ]
   },
   {
@@ -1095,7 +1101,7 @@
     "for job in jobs:\n",
     "    try:\n",
     "        result = client.gather(job)\n",
-    "    except Exception as e:\n",
+    "    except Exception:\n",
     "        result = None\n",
     "    results_reconstruction.append(result)"
    ]
@@ -1228,7 +1234,7 @@
     "        n_frames = len(np.unique(result[0][0][:, 0]))\n",
     "        df_over_time, df_nearest_pairs, df_all_pairs, df_autocorrelations = utils.compile_data_from_layers(\n",
     "            result, n_frames=n_frames, time_step=0)\n",
-    "        \n",
+    "\n",
     "        # create folder for results in separate directory with same name as the original data\n",
     "        folder_name = os.path.join(root_export, str(Path(row['path']).stem))\n",
     "        os.makedirs(folder_name, exist_ok=True)\n",
@@ -1305,7 +1311,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_to_export.to_csv(os.path.join(root_export, 'results_over_time_all_samples.csv'), index=False)    "
+    "df_to_export.to_csv(os.path.join(root_export, 'results_over_time_all_samples.csv'), index=False)"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_droplet_reconstruction_toolbox_code.ipynb b/docs/01_code_usage/demo_droplet_reconstruction_toolbox_code.ipynb
@@ -18,9 +18,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import sample_data, reconstruction\n",
     "import napari\n",
-    "import numpy as np"
+    "import numpy as np\n",
+    "\n",
+    "from napari_stress import reconstruction, sample_data"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_fit_ellipsoid_code.ipynb b/docs/01_code_usage/demo_fit_ellipsoid_code.ipynb
@@ -24,11 +24,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import napari_stress\n",
-    "from napari_stress import approximation, measurements, vectors\n",
+    "import matplotlib.pyplot as plt\n",
     "import napari\n",
     "\n",
-    "import matplotlib.pyplot as plt"
+    "import napari_stress\n",
+    "from napari_stress import approximation, measurements, vectors"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_measure_intensity_on_surface.ipynb b/docs/01_code_usage/demo_measure_intensity_on_surface.ipynb
@@ -18,11 +18,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import sample_data, reconstruction, measurements, vectors, sample_data\n",
-    "import numpy as np\n",
     "import napari\n",
+    "import numpy as np\n",
     "import vedo\n",
-    "from skimage import transform"
+    "from skimage import transform\n",
+    "\n",
+    "from napari_stress import measurements, sample_data"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_measure_intensity_on_vectors.ipynb b/docs/01_code_usage/demo_measure_intensity_on_vectors.ipynb
@@ -18,11 +18,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import vectors, sample_data, measurements, frame_by_frame\n",
-    "from skimage import transform, filters, measure\n",
     "import napari\n",
+    "import numpy as np\n",
     "import vedo\n",
-    "import numpy as np"
+    "from skimage import filters, measure, transform\n",
+    "\n",
+    "from napari_stress import frame_by_frame, measurements, sample_data, vectors"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_measure_patch_fitted_curvature.ipynb b/docs/01_code_usage/demo_measure_patch_fitted_curvature.ipynb
@@ -17,15 +17,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import measurements, sample_data, approximation\n",
-    "import vedo\n",
-    "from skimage import filters, measure\n",
+    "import matplotlib.pyplot as plt\n",
+    "import napari\n",
     "import numpy as np\n",
     "import pandas as pd\n",
+    "import vedo\n",
+    "from skimage import filters, measure\n",
     "\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "import napari"
+    "from napari_stress import approximation, measurements, sample_data"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_patch_fitting_reconstruction.ipynb b/docs/01_code_usage/demo_patch_fitting_reconstruction.ipynb
@@ -16,12 +16,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import reconstruction, frame_by_frame, extract_vertex_points\n",
     "import napari\n",
-    "import vedo\n",
     "import numpy as np\n",
-    "from skimage import transform, filters, measure\n",
-    "from napari_timelapse_processor import frame_by_frame"
+    "import vedo\n",
+    "from napari_timelapse_processor import frame_by_frame\n",
+    "from skimage import filters, measure, transform\n",
+    "\n",
+    "from napari_stress import extract_vertex_points, frame_by_frame, reconstruction"
    ]
   },
   {
@@ -236,13 +237,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress._reconstruction.patches import (_estimate_patch_radii,\n",
-    "                                                   _find_neighbor_indices,\n",
-    "                                                   _orient_patch,\n",
-    "                                                   _fit_quadratic_surface, \n",
-    "                                                   _create_fitted_coordinates,\n",
-    "                                                   compute_orientation_matrix,\n",
-    "                                                   _calculate_mean_curvature_on_patch)"
+    "from napari_stress._reconstruction.patches import (\n",
+    "    _calculate_mean_curvature_on_patch,\n",
+    "    _create_fitted_coordinates,\n",
+    "    _estimate_patch_radii,\n",
+    "    _find_neighbor_indices,\n",
+    "    _fit_quadratic_surface,\n",
+    "    _orient_patch,\n",
+    ")"
    ]
   },
   {
@@ -283,7 +285,7 @@
     "# Initialize fitted point cloud and find neighbors\n",
     "fitted_point_cloud = np.copy(point_cloud)\n",
     "search_radii = _estimate_patch_radii(point_cloud)\n",
-    "    \n",
+    "\n",
     "neighbor_indices = _find_neighbor_indices(point_cloud, search_radii)\n",
     "mean_curvatures = [np.nan] * len(point_cloud)\n",
     "principal_curvatures = [np.nan] * len(point_cloud)\n",
@@ -309,10 +311,10 @@
     "    fitted_point_cloud[idx, :] = fitted_query_point[None, :] @ orient_matrix.T +\\\n",
     "        patch_center\n",
     "    fitted_patch_transformed = fitted_patch @ orient_matrix.T + patch_center\n",
-    "    \n",
+    "\n",
     "    mean_curv, principal_curv = _calculate_mean_curvature_on_patch(\n",
     "        fitted_query_point, fitting_params)\n",
-    "    \n",
+    "\n",
     "    mean_curvatures[idx] = mean_curv\n",
     "    principal_curvatures[idx] = principal_curv"
    ]
diff --git a/docs/01_code_usage/demo_spherical_harmonics_code.ipynb b/docs/01_code_usage/demo_spherical_harmonics_code.ipynb
@@ -19,10 +19,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import approximation\n",
-    "import vedo\n",
+    "import matplotlib.pyplot as plt\n",
     "import napari\n",
-    "import matplotlib.pyplot as plt"
+    "import vedo\n",
+    "\n",
+    "from napari_stress import approximation"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_surface_reconstruction_code.ipynb b/docs/01_code_usage/demo_surface_reconstruction_code.ipynb
@@ -19,9 +19,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import napari_stress\n",
+    "import napari\n",
     "import vedo\n",
-    "import napari"
+    "\n",
+    "import napari_stress"
    ]
   },
   {
diff --git a/docs/01_code_usage/demo_surface_tracing.ipynb b/docs/01_code_usage/demo_surface_tracing.ipynb
@@ -19,16 +19,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from napari_stress import reconstruction\n",
-    "from napari_stress._reconstruction.fit_utils import _sigmoid, _function_args_to_list\n",
-    "import napari\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
+    "import napari\n",
     "import numpy as np\n",
+    "import vedo\n",
     "from scipy.interpolate import RegularGridInterpolator\n",
     "from scipy.optimize import curve_fit\n",
-    "from skimage import filters, morphology, measure\n",
-    "import vedo"
+    "from skimage import filters, measure, morphology\n",
+    "\n",
+    "from napari_stress import reconstruction\n",
+    "from napari_stress._reconstruction.fit_utils import (\n",
+    "      _function_args_to_list,\n",
+    "      _sigmoid,\n",
+    ")"
    ]
   },
   {
@@ -480,7 +483,7 @@
     "\n",
     "ax.plot(x, _sigmoid(np.arange(0, len(intensity_values), 1), *popt), linestyle = 'dotted', linewidth=5, label= 'Fitted curve')\n",
     "ax.vlines(x[len(x)//2], 0, 1, label = f'Initial boundary: {x[len(x)//2]}', color='orange')\n",
-    "ax.vlines(sampling_distance * popt[0], 0, 1, label = 'New surface boundary: {:.2f}'.format(popt[0] * sampling_distance))\n",
+    "ax.vlines(sampling_distance * popt[0], 0, 1, label = f'New surface boundary: {popt[0] * sampling_distance:.2f}')\n",
     "\n",
     "ax.legend(fontsize=14)\n",
     "ax.set_ylabel('Intensity', fontsize=16)\n",
diff --git a/docs/04_FAQ/bulk_vs_surface.ipynb b/docs/04_FAQ/bulk_vs_surface.ipynb
@@ -27,15 +27,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from aicsimageio import AICSImage\n",
-    "from napari_stress import measurements, reconstruction, plotting, utils, vectors\n",
+    "import matplotlib.pyplot as plt\n",
     "import napari\n",
     "import numpy as np\n",
-    "from scipy.interpolate import griddata\n",
-    "import vedo\n",
-    "import matplotlib.pyplot as plt\n",
+    "import pandas as pd\n",
     "import seaborn as sns\n",
-    "import pandas as pd"
+    "import vedo\n",
+    "from aicsimageio import AICSImage\n",
+    "from scipy.interpolate import griddata\n",
+    "\n",
+    "from napari_stress import (\n",
+    "    measurements,\n",
+    "    reconstruction,\n",
+    "    utils,\n",
+    ")"
    ]
   },
   {
@@ -325,7 +330,7 @@
     "\n",
     "fig.colorbar(pcm1, ax=axes[0], label='Radius (surface labelled)', location='top')\n",
     "fig.colorbar(pcm2, ax=axes[1], label='Radius (bulk labelled)', location='top')\n",
-    "fig.colorbar(pcm3, ax=axes[2], label='Difference (absolute), avg={:.5f}'.format(np.nanmean(difference)), location='top')\n",
+    "fig.colorbar(pcm3, ax=axes[2], label=f'Difference (absolute), avg={np.nanmean(difference):.5f}', location='top')\n",
     "\n",
     "for ax in axes:\n",
     "    ax.set_xticks([0, 100, 200])\n",
@@ -378,9 +383,9 @@
     "difference_cell = df_surface_over_time[\"stress_cell_anisotropy\"].values[0] - df_bulk_over_time[\"stress_cell_anisotropy\"].values[0]\n",
     "difference_total = df_surface_over_time[\"stress_total_anisotropy\"].values[0] - df_bulk_over_time[\"stress_total_anisotropy\"].values[0]\n",
     "\n",
-    "print('Difference tissue stress anisotropy: {:.4} kPa'.format(difference_tissue))\n",
-    "print('Difference cell stress anisotropy: {:.4} kPa'.format(difference_cell))\n",
-    "print('Difference total stress anisotropy: {:.4} kPa'.format(difference_total))"
+    "print(f'Difference tissue stress anisotropy: {difference_tissue:.4} kPa')\n",
+    "print(f'Difference cell stress anisotropy: {difference_cell:.4} kPa')\n",
+    "print(f'Difference total stress anisotropy: {difference_total:.4} kPa')"
    ]
   },
   {
diff --git a/docs/04_FAQ/geodesics_tools.ipynb b/docs/04_FAQ/geodesics_tools.ipynb
@@ -20,18 +20,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import vedo\n",
-    "import pygeodesic.geodesic as geodesic\n",
-    "import gdist\n",
-    "import potpourri3d as pp3d\n",
+    "import time\n",
     "\n",
+    "import gdist\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import tqdm\n",
-    "\n",
+    "import potpourri3d as pp3d\n",
+    "import pygeodesic.geodesic as geodesic\n",
     "import seaborn as sns\n",
-    "import matplotlib.pyplot as plt\n",
-    "import time"
+    "import tqdm\n",
+    "import vedo"
    ]
   },
   {
@@ -259,7 +258,7 @@
     "g = sns.catplot(data=df, x='n_vertices', y='time', hue='method', kind='bar')\n",
     "\n",
     "# set x-labels\n",
-    "g.set_axis_labels('Number of vertices', 'Time [s]') "
+    "g.set_axis_labels('Number of vertices', 'Time [s]')"
    ]
   },
   {
diff --git a/docs/04_FAQ/validation/analyze_validation.ipynb b/docs/04_FAQ/validation/analyze_validation.ipynb
diff --git a/docs/04_FAQ/validation/benchmark_spherical_droplet.ipynb b/docs/04_FAQ/validation/benchmark_spherical_droplet.ipynb
diff --git a/docs/04_FAQ/validation/create_validation_data.ipynb b/docs/04_FAQ/validation/create_validation_data.ipynb
diff --git a/docs/04_FAQ/validation/validation_stress_paper.ipynb b/docs/04_FAQ/validation/validation_stress_paper.ipynb
diff --git a/readthedocs.yaml b/readthedocs.yaml

Original file line number	Diff line number	Diff line change
`@@ -18,9 +18,10 @@`
`18`	`18`	`"metadata": {},`
`19`	`19`	`"outputs": [],`
`20`	`20`	`"source": [`
`21`		`- "from napari_stress import sample_data, reconstruction\n",`
`22`	`21`	`"import napari\n",`
`23`		`- "import numpy as np"`
	`22`	`+ "import numpy as np\n",`
	`23`	`+ "\n",`
	`24`	`+ "from napari_stress import reconstruction, sample_data"`
`24`	`25`	`]`
`25`	`26`	`},`
`26`	`27`	`{`
Original file line number	Diff line number	Diff line change
`@@ -19,9 +19,10 @@`
`19`	`19`	`"metadata": {},`
`20`	`20`	`"outputs": [],`
`21`	`21`	`"source": [`
`22`		`- "import napari_stress\n",`
	`22`	`+ "import napari\n",`
`23`	`23`	`"import vedo\n",`
`24`		`- "import napari"`
	`24`	`+ "\n",`
	`25`	`+ "import napari_stress"`
`25`	`26`	`]`
`26`	`27`	`},`
`27`	`28`	`{`