Merge pull request #131 from gauzias/remove_visbrain_from_doc

refresh doc manual
brain-slam · Nov 29, 2024 · ca54d10 · ca54d10
2 parents 9cf1e49 + 57b62e4
commit ca54d10
Show file tree

Hide file tree

Showing 15 changed files with 346 additions and 363 deletions.
diff --git a/.gitignore b/.gitignore
@@ -144,7 +144,3 @@ venv.bak/
 # modules.xml
 # .idea/misc.xml 
 # *.ipr
-
-curv_py.py
-.gitignore
-slam/plot.py
diff --git a/doc/conf.py b/doc/conf.py
@@ -20,13 +20,10 @@
 import sys
 from datetime import date
 
-from visbrain.config import CONFIG
 import sphinx_gallery  # noqa
 from sphinx_gallery.sorting import FileNameSortKey
 import sphinx_bootstrap_theme
 
-CONFIG["MPL_RENDER"] = True
-
 
 curdir = os.path.dirname(__file__)
 sys.path.append(os.path.abspath(os.path.join(curdir, "..")))
@@ -200,11 +197,5 @@
     "filename_pattern": "^((?!sgskip).)*$",
     "backreferences_dir": "generated",
     "within_subsection_order": FileNameSortKey,
-    "reference_url": {
-        "numpy": "http://docs.scipy.org/doc/numpy-1.9.1",
-        "scipy": "http://docs.scipy.org/doc/scipy-0.17.0/reference",
-        "trimesh": "https://github.com/mikedh/trimesh",
-        "visbrain": "https://github.com/EtienneCmb/visbrain",
-        "nibabel": "https://nipy.org/nibabel",
-    },
+    "reference_url": {},
 }
diff --git a/examples/example_basics.py b/examples/example_basics.py
@@ -23,7 +23,7 @@
 
 # loading a mesh stored on the disc as a gifti file,
 # this is a feature of SLAM
-mesh = sio.load_mesh("examples/data/example_mesh.gii")
+mesh = sio.load_mesh("../examples/data/example_mesh.gii")
 
 ###############################################################################
 # affine transformations can be applied to mesh objects

diff --git a/examples/example_curvature.py b/examples/example_curvature.py
@@ -27,7 +27,7 @@
 
 ###############################################################################
 # loading an examplar mesh
-mesh_file = "examples/data/example_mesh.gii"
+mesh_file = "../examples/data/example_mesh.gii"
 mesh = sio.load_mesh(mesh_file)
 
 ###############################################################################

diff --git a/examples/example_differential_geometry.py b/examples/example_differential_geometry.py
@@ -24,8 +24,8 @@
 
 ###############################################################################
 # loading an examplar mesh and corresponding texture
-mesh_file = "examples/data/example_mesh.gii"
-texture_file = "examples/data/example_texture.gii"
+mesh_file = "../examples/data/example_mesh.gii"
+texture_file = "../examples/data/example_texture.gii"
 mesh = sio.load_mesh(mesh_file)
 tex = sio.load_texture(texture_file)
 

diff --git a/examples/example_distortion.py b/examples/example_distortion.py
@@ -29,7 +29,7 @@
 ###############################################################################
 # Loading an example mesh and a smoothed copy of it
 
-mesh = sio.load_mesh("examples/data/example_mesh.gii")
+mesh = sio.load_mesh("../examples/data/example_mesh.gii")
 mesh_s = sdg.laplacian_mesh_smoothing(mesh, nb_iter=50, dt=0.1)
 
 ###############################################################################

diff --git a/examples/example_geodesic.py b/examples/example_geodesic.py
@@ -28,7 +28,7 @@
 
 ###############################################################################
 # Mesh importation
-mesh = sio.load_mesh("examples/data/example_mesh.gii")
+mesh = sio.load_mesh("../examples/data/example_mesh.gii")
 
 ###############################################################################
 # Getting the vertex index in specified geo_distance of vert

diff --git a/examples/example_profile_texture.py b/examples/example_profile_texture.py
@@ -24,8 +24,8 @@
 
 ###############################################################################
 # loading an example mesh and its texture
-mesh_file = "examples/data/example_mesh.gii"
-texture_file = "examples/data/example_texture.gii"
+mesh_file = "../examples/data/example_mesh.gii"
+texture_file = "../examples/data/example_texture.gii"
 mesh = sio.load_mesh(mesh_file)
 texture = sio.load_texture(texture_file)
 

diff --git a/examples/example_registration.py b/examples/example_registration.py
@@ -24,8 +24,8 @@
 
 ###############################################################################
 # loading an two unregistered meshes
-mesh_1 = sio.load_mesh("examples/data/example_mesh.gii")
-mesh_2 = sio.load_mesh("examples/data/example_mesh_2.gii")
+mesh_1 = sio.load_mesh("../examples/data/example_mesh.gii")
+mesh_2 = sio.load_mesh("../examples/data/example_mesh_2.gii")
 
 ###############################################################################
 # compute ICP registration

diff --git a/examples/example_remeshing.py b/examples/example_remeshing.py
@@ -26,14 +26,14 @@
 
 ###############################################################################
 # Source object files
-source_mesh_file = "examples/data/example_mesh.gii"
-source_texture_file = "examples/data/example_texture.gii"
-source_spherical_mesh_file = "examples/data/example_mesh_spherical.gii"
+source_mesh_file = "../examples/data/example_mesh.gii"
+source_texture_file = "../examples/data/example_texture.gii"
+source_spherical_mesh_file = "../examples/data/example_mesh_spherical.gii"
 
 ###############################################################################
 # Target object files
-target_mesh_file = "examples/data/example_mesh_2.gii"
-target_spherical_mesh_file = "examples/data/example_mesh_2_spherical.gii"
+target_mesh_file = "../examples/data/example_mesh_2.gii"
+target_spherical_mesh_file = "../examples/data/example_mesh_2_spherical.gii"
 
 source_mesh = sio.load_mesh(source_mesh_file)
 source_tex = sio.load_texture(source_texture_file)