Peter Sobolewski psobolewskiPhD
psobolewskiPhD
/ napari_line_profile_layer.py
Last active
August 23, 2021 12:23
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| #%% | |
| import matplotlib.pyplot as plt | |
| from matplotlib.backends.backend_qt5agg import FigureCanvas | |
| from skimage import measure | |
| from skimage import io | |
| import numpy as np | |
| import os | |
| import napari | |
| #%% |
psobolewskiPhD
/ napari_line_profile_widget.py
Last active
August 26, 2021 15:19
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| import matplotlib.pyplot as plt | |
| from matplotlib.backends.backend_qt5agg import FigureCanvas | |
| from skimage import measure | |
| import numpy as np | |
| import napari | |
| def profile_line(viewer): | |
| def get_image_layer(): | |
| for layer in viewer.layers.selection: |
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| #%% | |
| from aicsimageio import AICSImage | |
| import napari | |
| import dask.array as da | |
| import numpy as np | |
| from vispy.color import Colormap | |
| import os | |
| from qtpy.QtWidgets import QListWidget | |
| from qtpy.QtCore import Qt |
psobolewskiPhD
/ napari_crop.py
Created
September 23, 2021 11:12
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| # %% | |
| import napari | |
| from skimage import data | |
| # %% | |
| viewer = napari.Viewer() | |
| image = viewer.add_image(data.astronaut(), rgb=True) | |
| image.data.shape | |
| # %% | |
| viewer.camera.zoom = 2.5 |
psobolewskiPhD
/ gist:635f70cc5a1814ddbf5988fd419d126e
Created
November 30, 2021 09:16
scikit-image 0.20.0dev: python -c "import skimage; skimage.test()"
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| skimage version 0.20.0.dev0 | |
| ==================================== ERRORS ==================================== | |
| _ ERROR collecting miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/feature/tests/test_basic_features.py _ | |
| ImportError while importing test module '/Users/piotrsobolewski/Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/feature/tests/test_basic_features.py'. | |
| Hint: make sure your test modules/packages have valid Python names. | |
| Traceback: | |
| miniforge3/envs/test-scik/lib/python3.9/importlib/__init__.py:127: in import_module | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/feature/__init__.py:4: in <module> |
psobolewskiPhD
/ gist:a01f8e5692d3b812621eb7fd73b42e4d
Created
November 30, 2021 15:42
scikit-image wheel with fixed openmp
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| ================================ warnings summary ================================ | |
| miniforge3/envs/test-scik/lib/python3.9/importlib/__init__.py:127 | |
| /Users/piotrsobolewski/Dev/miniforge3/envs/test-scik/lib/python3.9/importlib/__init__.py:127: UserWarning: Viewer requires Qt | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/filters/tests/test_ridges.py::test_3d_null_matrix | |
| miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/filters/tests/test_ridges.py::test_3d_linearity | |
| miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/filters/tests/test_ridges.py::test_3d_cropped_camera_image | |
| /Users/piotrsobolewski/Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/_shared/utils.py:214: RuntimeWarning: Images with dimensions (M, N, 3) are interpreted as 2D+RGB by default. Use `multichannel=False` to interpret as 3D image with last dimension of length 3. | |
| return func(*args, **kwargs) |
psobolewskiPhD
/ gist:7253e0ef964b13710814240744944e0c
Last active
December 4, 2021 09:25
scikit-image 0.19.0 tests macOS 12 Apple M1
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| skimage version 0.19.0 | |
| ==================================== ERRORS ==================================== | |
| _ ERROR collecting Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/feature/tests/test_basic_features.py _ | |
| ImportError while importing test module '/Users/piotrsobolewski/Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/feature/tests/test_basic_features.py'. | |
| Hint: make sure your test modules/packages have valid Python names. | |
| Traceback: | |
| Dev/miniforge3/envs/test-scik/lib/python3.9/importlib/__init__.py:127: in import_module | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/feature/__init__.py:4: in <module> |
psobolewskiPhD
/ gist:38dcd662ad9a7e6e17ab8ee3db5f81a9
Created
December 4, 2021 09:35
conda-forge scikit-image 0.18.3 macOS 12 Apple M1 tests
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| ============================= test session starts ============================== | |
| platform darwin -- Python 3.9.7, pytest-6.2.5, py-1.11.0, pluggy-1.0.0 | |
| rootdir: /Users/piotrsobolewski | |
| plugins: localserver-0.5.1 | |
| collected 6245 items / 3 skipped / 6242 selected | |
| Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/_shared/tests/test_coord.py . [ 0%] | |
| ......................................... [ 0%] | |
| Dev/miniforge3/envs/test-scik/lib/python3.9/site-packages/skimage/_shared/tests/test_fast_exp.py . [ 0%] | |
| [ 0%] |
psobolewskiPhD
/ gist:cc1e43727cd316cc2cfdd6f06990e06d
Created
December 5, 2021 17:47
Fresh scikit 0.19 why, python 3.9.7
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| =============================== warnings summary =============================== | |
| Dev/miniforge3/envs/test-scik-9/lib/python3.9/importlib/__init__.py:127 | |
| /Users/piotrsobolewski/Dev/miniforge3/envs/test-scik-9/lib/python3.9/importlib/__init__.py:127: UserWarning: Viewer requires Qt | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| Dev/miniforge3/envs/test-scik-9/lib/python3.9/site-packages/skimage/filters/tests/test_ridges.py::test_3d_null_matrix | |
| Dev/miniforge3/envs/test-scik-9/lib/python3.9/site-packages/skimage/filters/tests/test_ridges.py::test_3d_linearity | |
| Dev/miniforge3/envs/test-scik-9/lib/python3.9/site-packages/skimage/filters/tests/test_ridges.py::test_3d_cropped_camera_image | |
| /Users/piotrsobolewski/Dev/miniforge3/envs/test-scik-9/lib/python3.9/site-packages/skimage/_shared/utils.py:293: RuntimeWarning: Images with dimensions (M, N, 3) are interpreted as 2D+RGB by default. Use `multichannel=False` to interpret as 3D image with last dimension of length 3. | |
| return func(*args, **kwarg |
psobolewskiPhD
/ gist:4f867c589218882276da93345f2836f9
Created
December 5, 2021 17:55
fresh scikit-image 0.19 on python 3.10
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| =============================== warnings summary =============================== | |
| Dev/miniforge3/envs/test-scik/lib/python3.10/importlib/__init__.py:126 | |
| /Users/piotrsobolewski/Dev/miniforge3/envs/test-scik/lib/python3.10/importlib/__init__.py:126: UserWarning: Viewer requires Qt | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| Dev/miniforge3/envs/test-scik/lib/python3.10/site-packages/skimage/filters/tests/test_ridges.py::test_3d_null_matrix | |
| Dev/miniforge3/envs/test-scik/lib/python3.10/site-packages/skimage/filters/tests/test_ridges.py::test_3d_linearity | |
| Dev/miniforge3/envs/test-scik/lib/python3.10/site-packages/skimage/filters/tests/test_ridges.py::test_3d_cropped_camera_image | |
| /Users/piotrsobolewski/Dev/miniforge3/envs/test-scik/lib/python3.10/site-packages/skimage/_shared/utils.py:293: RuntimeWarning: Images with dimensions (M, N, 3) are interpreted as 2D+RGB by default. Use `multichannel=False` to interpret as 3D image with last dimension of length 3. | |
| return func(*args, **kwargs) |
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