Skip to content

Commit 69059c5

Browse files
pre-commit-ci[bot]pre-commit-ci[bot]
committed
[pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
1 parent dc53d91 commit 69059c5

30 files changed

Lines changed: 248 additions & 199 deletions

‎.github/workflows/build_book.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -57,4 +57,4 @@ jobs:
5757
# Deploy the book's HTML to GitHub Pages
5858
- name: Deploy to GitHub Pages
5959
id: deployment
60-
uses: actions/deploy-pages@v4
60+
uses: actions/deploy-pages@v4

‎docs/01_code_usage/01_toolboxes/demo_analyze_everything.ipynb‎

Lines changed: 15 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -19,21 +19,25 @@
1919
"metadata": {},
2020
"outputs": [],
2121
"source": [
22-
"import napari_stress\n",
23-
"import napari\n",
24-
"import numpy as np\n",
25-
"from napari_stress import reconstruction, measurements, TimelapseConverter, utils, stress_backend, plotting\n",
26-
"import os\n",
2722
"import datetime\n",
23+
"import os\n",
2824
"\n",
29-
"from skimage import io\n",
30-
"\n",
25+
"import matplotlib as mpl\n",
26+
"import matplotlib.pyplot as plt\n",
27+
"import napari\n",
28+
"import numpy as np\n",
3129
"import pandas as pd\n",
3230
"import seaborn as sns\n",
33-
"import matplotlib.pyplot as plt\n",
34-
"import matplotlib as mpl\n",
3531
"\n",
36-
"import yaml"
32+
"import napari_stress\n",
33+
"from napari_stress import (\n",
34+
" TimelapseConverter,\n",
35+
" measurements,\n",
36+
" plotting,\n",
37+
" reconstruction,\n",
38+
" stress_backend,\n",
39+
" utils,\n",
40+
")"
3741
]
3842
},
3943
{
@@ -440,7 +444,7 @@
440444
"if filename is not None:\n",
441445
" filename_without_ending = os.path.basename(filename).split('.')[0]\n",
442446
" save_directory = os.path.join(os.path.dirname(filename), filename_without_ending + '_' + datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S'))\n",
443-
"else: \n",
447+
"else:\n",
444448
" save_directory = os.path.join(os.getcwd(), 'results_' + datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S'))\n",
445449
"\n",
446450
"if not os.path.exists(save_directory):\n",

‎docs/01_code_usage/01_toolboxes/demo_analyze_everything_batch.ipynb‎

Lines changed: 16 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -31,18 +31,24 @@
3131
"metadata": {},
3232
"outputs": [],
3333
"source": [
34-
"import napari\n",
35-
"import numpy as np\n",
36-
"from napari_stress import reconstruction, measurements, utils, stress_backend, TimelapseConverter\n",
3734
"import os\n",
3835
"from pathlib import Path\n",
39-
"from bioio import BioImage\n",
40-
"\n",
41-
"from dask.distributed import Client, get_client\n",
4236
"\n",
37+
"import napari\n",
38+
"import numpy as np\n",
4339
"import pandas as pd\n",
40+
"import vedo\n",
41+
"from bioio import BioImage\n",
42+
"from dask.distributed import Client, get_client\n",
4443
"from skimage import io\n",
45-
"import vedo"
44+
"\n",
45+
"from napari_stress import (\n",
46+
" TimelapseConverter,\n",
47+
" measurements,\n",
48+
" reconstruction,\n",
49+
" stress_backend,\n",
50+
" utils,\n",
51+
")"
4652
]
4753
},
4854
{
@@ -1095,7 +1101,7 @@
10951101
"for job in jobs:\n",
10961102
" try:\n",
10971103
" result = client.gather(job)\n",
1098-
" except Exception as e:\n",
1104+
" except Exception:\n",
10991105
" result = None\n",
11001106
" results_reconstruction.append(result)"
11011107
]
@@ -1228,7 +1234,7 @@
12281234
" n_frames = len(np.unique(result[0][0][:, 0]))\n",
12291235
" df_over_time, df_nearest_pairs, df_all_pairs, df_autocorrelations = utils.compile_data_from_layers(\n",
12301236
" result, n_frames=n_frames, time_step=0)\n",
1231-
" \n",
1237+
"\n",
12321238
" # create folder for results in separate directory with same name as the original data\n",
12331239
" folder_name = os.path.join(root_export, str(Path(row['path']).stem))\n",
12341240
" os.makedirs(folder_name, exist_ok=True)\n",
@@ -1305,7 +1311,7 @@
13051311
"metadata": {},
13061312
"outputs": [],
13071313
"source": [
1308-
"df_to_export.to_csv(os.path.join(root_export, 'results_over_time_all_samples.csv'), index=False) "
1314+
"df_to_export.to_csv(os.path.join(root_export, 'results_over_time_all_samples.csv'), index=False)"
13091315
]
13101316
},
13111317
{

‎docs/01_code_usage/01_toolboxes/demo_anisotropic_stresses.ipynb‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -29,12 +29,11 @@
2929
}
3030
],
3131
"source": [
32-
"import napari\n",
33-
"import napari_stress\n",
34-
"from napari_stress import measurements, approximation\n",
3532
"import matplotlib.pyplot as plt\n",
33+
"import napari\n",
3634
"\n",
37-
"import numpy as np"
35+
"import napari_stress\n",
36+
"from napari_stress import approximation, measurements"
3837
]
3938
},
4039
{

‎docs/01_code_usage/01_toolboxes/demo_droplet_reconstruction_toolbox_code.ipynb‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,9 +18,10 @@
1818
"metadata": {},
1919
"outputs": [],
2020
"source": [
21-
"from napari_stress import sample_data, reconstruction\n",
2221
"import napari\n",
23-
"import numpy as np"
22+
"import numpy as np\n",
23+
"\n",
24+
"from napari_stress import reconstruction, sample_data"
2425
]
2526
},
2627
{

‎docs/01_code_usage/02_example_workflows/demo_fit_ellipsoid_code.ipynb‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -24,12 +24,11 @@
2424
"metadata": {},
2525
"outputs": [],
2626
"source": [
27-
"import napari_stress\n",
28-
"from napari_stress import approximation, measurements, vectors\n",
27+
"import matplotlib.pyplot as plt\n",
2928
"import napari\n",
30-
"import numpy as np\n",
3129
"\n",
32-
"import matplotlib.pyplot as plt"
30+
"import napari_stress\n",
31+
"from napari_stress import approximation, measurements, vectors"
3332
]
3433
},
3534
{

‎docs/01_code_usage/02_example_workflows/demo_measure_intensity_on_surface.ipynb‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -18,11 +18,12 @@
1818
"metadata": {},
1919
"outputs": [],
2020
"source": [
21-
"from napari_stress import sample_data, reconstruction, measurements, vectors, sample_data\n",
22-
"import numpy as np\n",
2321
"import napari\n",
22+
"import numpy as np\n",
2423
"import vedo\n",
25-
"from skimage import transform"
24+
"from skimage import transform\n",
25+
"\n",
26+
"from napari_stress import measurements, sample_data"
2627
]
2728
},
2829
{

‎docs/01_code_usage/02_example_workflows/demo_measure_intensity_on_vectors.ipynb‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -18,11 +18,12 @@
1818
"metadata": {},
1919
"outputs": [],
2020
"source": [
21-
"from napari_stress import vectors, sample_data, measurements, frame_by_frame\n",
22-
"from skimage import transform, filters, measure\n",
2321
"import napari\n",
22+
"import numpy as np\n",
2423
"import vedo\n",
25-
"import numpy as np"
24+
"from skimage import filters, measure, transform\n",
25+
"\n",
26+
"from napari_stress import frame_by_frame, measurements, sample_data, vectors"
2627
]
2728
},
2829
{

‎docs/01_code_usage/02_example_workflows/demo_measure_patch_fitted_curvature.ipynb‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -17,15 +17,14 @@
1717
"metadata": {},
1818
"outputs": [],
1919
"source": [
20-
"from napari_stress import measurements, sample_data, approximation\n",
21-
"import vedo\n",
22-
"from skimage import filters, measure\n",
20+
"import matplotlib.pyplot as plt\n",
21+
"import napari\n",
2322
"import numpy as np\n",
2423
"import pandas as pd\n",
24+
"import vedo\n",
25+
"from skimage import filters, measure\n",
2526
"\n",
26-
"import matplotlib.pyplot as plt\n",
27-
"\n",
28-
"import napari"
27+
"from napari_stress import approximation, measurements, sample_data"
2928
]
3029
},
3130
{

‎docs/01_code_usage/02_example_workflows/demo_patch_fitting_reconstruction.ipynb‎

Lines changed: 16 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -16,12 +16,13 @@
1616
"metadata": {},
1717
"outputs": [],
1818
"source": [
19-
"from napari_stress import reconstruction, frame_by_frame, extract_vertex_points\n",
2019
"import napari\n",
21-
"import vedo\n",
2220
"import numpy as np\n",
23-
"from skimage import transform, filters, measure\n",
24-
"from napari_timelapse_processor import frame_by_frame"
21+
"import vedo\n",
22+
"from napari_timelapse_processor import frame_by_frame\n",
23+
"from skimage import filters, measure, transform\n",
24+
"\n",
25+
"from napari_stress import extract_vertex_points, frame_by_frame, reconstruction"
2526
]
2627
},
2728
{
@@ -236,13 +237,14 @@
236237
"metadata": {},
237238
"outputs": [],
238239
"source": [
239-
"from napari_stress._reconstruction.patches import (_estimate_patch_radii,\n",
240-
" _find_neighbor_indices,\n",
241-
" _orient_patch,\n",
242-
" _fit_quadratic_surface, \n",
243-
" _create_fitted_coordinates,\n",
244-
" compute_orientation_matrix,\n",
245-
" _calculate_mean_curvature_on_patch)"
240+
"from napari_stress._reconstruction.patches import (\n",
241+
" _calculate_mean_curvature_on_patch,\n",
242+
" _create_fitted_coordinates,\n",
243+
" _estimate_patch_radii,\n",
244+
" _find_neighbor_indices,\n",
245+
" _fit_quadratic_surface,\n",
246+
" _orient_patch,\n",
247+
")"
246248
]
247249
},
248250
{
@@ -283,7 +285,7 @@
283285
"# Initialize fitted point cloud and find neighbors\n",
284286
"fitted_point_cloud = np.copy(point_cloud)\n",
285287
"search_radii = _estimate_patch_radii(point_cloud)\n",
286-
" \n",
288+
"\n",
287289
"neighbor_indices = _find_neighbor_indices(point_cloud, search_radii)\n",
288290
"mean_curvatures = [np.nan] * len(point_cloud)\n",
289291
"principal_curvatures = [np.nan] * len(point_cloud)\n",
@@ -309,10 +311,10 @@
309311
" fitted_point_cloud[idx, :] = fitted_query_point[None, :] @ orient_matrix.T +\\\n",
310312
" patch_center\n",
311313
" fitted_patch_transformed = fitted_patch @ orient_matrix.T + patch_center\n",
312-
" \n",
314+
"\n",
313315
" mean_curv, principal_curv = _calculate_mean_curvature_on_patch(\n",
314316
" fitted_query_point, fitting_params)\n",
315-
" \n",
317+
"\n",
316318
" mean_curvatures[idx] = mean_curv\n",
317319
" principal_curvatures[idx] = principal_curv"
318320
]

0 commit comments

Comments
 (0)