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Merge branch 'master' into modif_github_actions
# Conflicts: # setup.py
2 parents 6ec1677 + ca54d10 commit a5b7937

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‎.github/workflows/continuous_integration.yml‎

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@@ -7,7 +7,7 @@ jobs:
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strategy:
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matrix:
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os: ['ubuntu-20.04','ubuntu-22.04']
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python-version: ["3.8", "3.9", "3.10"]
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python-version: ["3.8", "3.9"]
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exclude:
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- os: 'ubuntu-22.04'
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python-version: '3.6'

‎.github/workflows/publish.yml‎

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@@ -3,15 +3,33 @@ on:
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release:
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types: [published]
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jobs:
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pypi:
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build-n-publish-pypi:
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name: Build and publish Python to PyPI
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- run: python3 -m pip install --upgrade build && python3 -m build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}
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- uses: actions/checkout@master
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- name: Set up Python 3.10.5
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uses: actions/setup-python@v2
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with:
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python-version: 3.10.5
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- name: Install pypa/build
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run: >-
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python -m
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pip install
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build
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--user
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- name: Build a binary wheel and a source tarball
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run: >-
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python -m
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build
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--sdist
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--wheel
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--outdir dist/
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- name: Publish distribution to PyPI
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if: startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@master
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.gitignore‎

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@@ -144,7 +144,3 @@ venv.bak/
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# modules.xml
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# .idea/misc.xml
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# *.ipr
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curv_py.py
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.gitignore
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slam/plot.py

‎doc/conf.py‎

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@@ -20,13 +20,10 @@
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import sys
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from datetime import date
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from visbrain.config import CONFIG
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import sphinx_gallery # noqa
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from sphinx_gallery.sorting import FileNameSortKey
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import sphinx_bootstrap_theme
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CONFIG["MPL_RENDER"] = True
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curdir = os.path.dirname(__file__)
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sys.path.append(os.path.abspath(os.path.join(curdir, "..")))
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"filename_pattern": "^((?!sgskip).)*$",
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"backreferences_dir": "generated",
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"within_subsection_order": FileNameSortKey,
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"reference_url": {
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"numpy": "http://docs.scipy.org/doc/numpy-1.9.1",
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"scipy": "http://docs.scipy.org/doc/scipy-0.17.0/reference",
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"trimesh": "https://github.com/mikedh/trimesh",
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"visbrain": "https://github.com/EtienneCmb/visbrain",
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"nibabel": "https://nipy.org/nibabel",
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},
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"reference_url": {},
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}

‎environment.yml‎

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@@ -2,8 +2,9 @@ name: base
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dependencies:
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- pip:
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- numpy
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- numpy==1.19.5
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- scipy
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- trimesh
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- nibabel>=2.1
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- networkx
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- networkx
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- tvb-gdist

‎examples/example_basics.py‎

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# Authors: Guillaume Auzias <[email protected]>
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# License: BSD (3-clause)
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# License: MIT
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# sphinx_gallery_thumbnail_number = 2
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###############################################################################
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# boundary of the mesh or list of faces
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# this functionnality requires to install the optional package shapely
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mesh.outline()
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# mesh.outline()
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###############################################################################
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# the convex hull is another Trimesh object that is available as a property

‎examples/example_curvature.py‎

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# Authors: Guillaume Auzias <[email protected]>
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# Julien Barrès <[email protected]>
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# License: BSD (3-clause)
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# License: MIT
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# sphinx_gallery_thumbnail_number = 2
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###############################################################################
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# NOTE: there is no visualization tool in slam, but we provide at the
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# end of this script exemplare code to do the visualization with
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# an external solution
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###############################################################################
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# importation of slam modules
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import slam.utils as ut
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import numpy as np
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import slam.generate_parametric_surfaces as sgps
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import slam.io as sio
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import slam.plot as splt
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import slam.curvature as scurv
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###############################################################################
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###############################################################################
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# Comptue estimations of principal curvatures
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PrincipalCurvatures, PrincipalDir1, PrincipalDir2 = scurv.curvatures_and_derivatives(
33-
mesh
34-
)
35+
PrincipalCurvatures, PrincipalDir1, PrincipalDir2 \
36+
= scurv.curvatures_and_derivatives(mesh)
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3638
###############################################################################
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# Comptue Gauss curvature from principal curvatures
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4143
# Comptue mean curvature from principal curvatures
4244
mean_curv = 0.5 * (PrincipalCurvatures[0, :] + PrincipalCurvatures[1, :])
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44-
###############################################################################
45-
# Plot mean curvature
46-
visb_sc = splt.visbrain_plot(
47-
mesh=mesh, tex=mean_curv, caption="mean curvature", cblabel="mean curvature"
48-
)
49-
visb_sc.preview()
50-
51-
###############################################################################
52-
# Plot Gauss curvature
53-
visb_sc = splt.visbrain_plot(
54-
mesh=mesh,
55-
tex=gaussian_curv,
56-
caption="Gaussian curvature",
57-
cblabel="Gaussian curvature",
58-
cmap="hot",
59-
)
60-
visb_sc.preview()
61-
6246
###############################################################################
6347
# Decomposition of the curvatures into ShapeIndex and Curvedness
6448
# Based on 'Surface shape and curvature scales
6549
# Jan JKoenderink & Andrea Jvan Doorn'
6650
shapeIndex, curvedness = scurv.decompose_curvature(PrincipalCurvatures)
6751

68-
###############################################################################
69-
# Plot of ShapeIndex and Curvedness
70-
visb_sc = splt.visbrain_plot(
71-
mesh=mesh,
72-
tex=shapeIndex,
73-
caption="ShapeIndex",
74-
cblabel="ShapeIndex",
75-
cmap="coolwarm",
76-
)
77-
visb_sc.preview()
78-
79-
visb_sc = splt.visbrain_plot(
80-
mesh=mesh, tex=curvedness, caption="Curvedness", cblabel="Curvedness", cmap="hot"
81-
)
82-
visb_sc.preview()
83-
84-
8552
###############################################################################
8653
# Estimation error on the principal curvature length
8754
K = [1, 0]
@@ -137,17 +104,6 @@
137104
k1_relative_change = abs((k1_analytic - k1_estim) / k1_analytic)
138105
k1_absolute_change = abs((k1_analytic - k1_estim))
139106

140-
###############################################################################
141-
# Error plot
142-
143-
visb_sc = splt.visbrain_plot(
144-
mesh=quadric,
145-
tex=k_mean_absolute_change,
146-
caption="K_mean absolute error",
147-
cblabel="K_mean absolute error",
148-
)
149-
visb_sc.preview()
150-
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###############################################################################
152108
# Estimation error on the curvature directions
153109
# commented because there is a bug:
@@ -190,21 +146,70 @@
190146
)
191147
angular_error_1 = 180 * angular_error_1 / np.pi
192148

149+
#############################################################################
150+
# VISUALIZATION USING EXTERNAL TOOLS
151+
#############################################################################
152+
# import visbrain # visu using visbrain
153+
# Plot mean curvature
154+
# visb_sc = splt.visbrain_plot(
155+
# mesh=mesh,
156+
# tex=mean_curv,
157+
# caption="mean curvature",
158+
# cblabel="mean curvature"
159+
# )
160+
# visb_sc.preview()
161+
#############################################################################
162+
# # Plot Gauss curvature
163+
# visb_sc = splt.visbrain_plot(
164+
# mesh=mesh,
165+
# tex=gaussian_curv,
166+
# caption="Gaussian curvature",
167+
# cblabel="Gaussian curvature",
168+
# cmap="hot",
169+
# )
170+
# visb_sc.preview()
171+
###############################################################################
172+
# Plot of ShapeIndex and Curvedness
173+
# visb_sc = splt.visbrain_plot(
174+
# mesh=mesh,
175+
# tex=shapeIndex,
176+
# caption="ShapeIndex",
177+
# cblabel="ShapeIndex",
178+
# cmap="coolwarm",
179+
# )
180+
# visb_sc.preview()
181+
#
182+
# visb_sc = splt.visbrain_plot(
183+
# mesh=mesh,
184+
# tex=curvedness,
185+
# caption="Curvedness",
186+
# cblabel="Curvedness",
187+
# cmap="hot"
188+
# )
189+
# visb_sc.preview()
193190
###############################################################################
194191
# Error plot
195-
196-
visb_sc = splt.visbrain_plot(
197-
mesh=quadric,
198-
tex=angular_error_0,
199-
caption="Angular error 0",
200-
cblabel="Angular error 0",
201-
)
202-
visb_sc.preview()
203-
204-
visb_sc = splt.visbrain_plot(
205-
mesh=quadric,
206-
tex=angular_error_1,
207-
caption="Angular error 1",
208-
cblabel="Angular error 1",
209-
)
210-
visb_sc.preview()
192+
# visb_sc = splt.visbrain_plot(
193+
# mesh=quadric,
194+
# tex=k_mean_absolute_change,
195+
# caption="K_mean absolute error",
196+
# cblabel="K_mean absolute error",
197+
# )
198+
# visb_sc.preview()
199+
# ###############################################################################
200+
# # Error plot
201+
# visb_sc = splt.visbrain_plot(
202+
# mesh=quadric,
203+
# tex=angular_error_0,
204+
# caption="Angular error 0",
205+
# cblabel="Angular error 0",
206+
# )
207+
# visb_sc.preview()
208+
#
209+
# visb_sc = splt.visbrain_plot(
210+
# mesh=quadric,
211+
# tex=angular_error_1,
212+
# caption="Angular error 1",
213+
# cblabel="Angular error 1",
214+
# )
215+
# visb_sc.preview()

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