scilus · arnaudbore · Feb 23, 2024 · Jan 30, 2024 · Feb 22, 2024 · Feb 23, 2024
diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml
@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: source/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+   - requirements: requirements.txt
diff --git a/docs/source/_static/my_style.css b/docs/source/_static/my_style.css
@@ -1,8 +1,11 @@
+@import url("theme.css");
 /*
 "fix screen width.
 */
+
+
 .wy-nav-content {
-    max-width: 100%;
+    max-width: 80%;
 }
 
 .strike {

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -22,12 +22,13 @@
                         "scilpy.tractanalysis.grid_intersections",
                         "scilpy.tractanalysis.quick_tools",
                         "sklearn", "scilpy.tractanalysis.streamlines_metrics",
-                        "scilpy.tractograms.uncompress", "matplotlib"]
+                        "scilpy.tractograms.uncompress", "matplotlib",
+                        "skimage"]
 
 # -- Project information -----------------------------------------------------
 
 project = 'scilpy'
-copyright = '2020, The SCIL developers'
+copyright = '2024, The SCIL developers'
 author = 'The SCIL developers'
 
 # The short X.Y version
@@ -100,11 +101,9 @@
 
 # To get full width:
 html_static_path = ['_static']
-html_context = {
-    'css_files': [
-        '_static/my_style.css',  # overrides for width size
-    ],
-}
+html_css_files = [
+    'my_style.css',  # overrides for width size
+]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -204,7 +203,7 @@ def setup(app):
         shutil.copyfile(join(path_src, "fake_files", f),
                         join(path_script, "../scilpy/tractanalysis/", f))
 
-    commit_scripts = ["scil_run_commit.py"]
+    commit_scripts = ["scil_tractogram_commit.py"]
 
     amico_scripts = ["scil_NODDI_maps.py",
                      "scil_freewater_maps.py"]
@@ -248,7 +247,7 @@ def setup(app):
                     with open(join(path_src, "scripts", "{}.rst".format(name)),
                               "w") as s:
                         s.write(i + "\n")
-                        s.write("==============\n\n")
+                        s.write("=" * len(i) + "\n\n")
                         help_text = script._build_arg_parser().format_help() \
                             .replace("sphinx-build", i)
                         s.write("::\n\n\t")

diff --git a/docs/source/documentation/construct_participants_tsv_file.rst b/docs/source/documentation/construct_participants_tsv_file.rst
@@ -1,5 +1,5 @@
 Instructions to write the tsv files "participants.tsv" for the script scil_group_comparison.py
-========================================================
+===============================================================================================
 
 The TSV file should follow the BIDS `specification <https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file>`_.
 

diff --git a/docs/source/documentation/create_overlapping_slice_mosaics.rst b/docs/source/documentation/create_overlapping_slice_mosaics.rst
@@ -1,8 +1,6 @@
 Create overlapping slice mosaics
 ================================
 
-::
-
 Screenshots to a series of volume image slices that overlap according to a
 given factor and arranged into a mosaic can be created using the
 `scil_screenshot_volume_mosaic_overlap.py` script. The script takes an input

diff --git a/docs/source/documentation/tractogram_registration.rst b/docs/source/documentation/tractogram_registration.rst
@@ -46,7 +46,7 @@ Complete example
 
 
 Apply back and forth tractogram transformation with the ANTS transformation
------------------
+----------------------------------------------------------------------------
 ::
 
     # The ANTS commands is MOVING->REFERENCE

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -12,5 +12,9 @@ Welcome to the scilpy documentation!
     :maxdepth: 1
     :caption: Documentation
 
-    documentation/tractogram_registration
+    documentation/btensor_scripts
+    documentation/bundle_diameter_fitting_function
+    documentation/construct_participants_tsv_file
+    documentation/create_overlapping_slice_mosaics
     documentation/devcontainer
+    documentation/tractogram_registration
diff --git a/docs/source/modules/scilpy.connectivity.rst b/docs/source/modules/scilpy.connectivity.rst
@@ -0,0 +1,10 @@
+scilpy.connectivity package
+===============================
+
+scilpy.connectivity.connectivity\_tools module
+------------------------------------------------------
+
+.. automodule:: scilpy.connectivity.connectivity_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/modules/scilpy.denoise.rst b/docs/source/modules/scilpy.denoise.rst
@@ -0,0 +1,10 @@
+scilpy.denoise package
+===============================
+
+scilpy.denoise.asym\_filtering module
+------------------------------------------------------
+
+.. automodule:: scilpy.denoise.asym_filtering
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/modules/scilpy.dwi.rst b/docs/source/modules/scilpy.dwi.rst
@@ -0,0 +1,19 @@
+scilpy.dwi package
+===============================
+
+scilpy.dwi.operations module
+------------------------------------------------------
+
+.. automodule:: scilpy.dwi.operations
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.dwi.utils module
+------------------------------------------------------
+
+.. automodule:: scilpy.dwi.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
diff --git a/docs/source/modules/scilpy.gpuparallel.rst b/docs/source/modules/scilpy.gpuparallel.rst
@@ -0,0 +1,10 @@
+scilpy.gpuparallel package
+===============================
+
+scilpy.gpuparallel.opencl\_utils module
+------------------------------------------------------
+
+.. automodule:: scilpy.gpuparallel.opencl_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/modules/scilpy.gradients.rst b/docs/source/modules/scilpy.gradients.rst
@@ -0,0 +1,34 @@
+scilpy.gradients package
+===============================
+
+scilpy.gradients.bvec\_bval\_tools module
+------------------------------------------------------
+
+.. automodule:: scilpy.gradients.bvec_bval_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.gradients.gen\_gradient\_sampling module
+------------------------------------------------------
+
+.. automodule:: scilpy.gradients.gen_gradient_sampling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.gradients.optimize\_gradient\_sampling module
+-----------------------------------------------------------
+
+.. automodule:: scilpy.gradients.optimize_gradient_sampling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.gradients.utils module
+-------------------------------------------------------
+
+.. automodule:: scilpy.gradients.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/modules/scilpy.gradientsampling.rst b/docs/source/modules/scilpy.gradientsampling.rst
diff --git a/docs/source/modules/scilpy.image.rst b/docs/source/modules/scilpy.image.rst
@@ -1,24 +1,16 @@
 scilpy.image package
 ====================
 
-scilpy.image.operations module
-------------------------------
+scilpy.image.labels module
+--------------------------
 
-.. automodule:: scilpy.image.operations
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-scilpy.image.resample\_volume module
-------------------------------------
-
-.. automodule:: scilpy.image.resample_volume
+.. automodule:: scilpy.image.labels
    :members:
    :undoc-members:
    :show-inheritance:
 
 scilpy.image.reslice module
----------------------------
+----------------------------
 
 .. automodule:: scilpy.image.reslice
    :members:
@@ -33,3 +25,26 @@ scilpy.image.utils module
    :undoc-members:
    :show-inheritance:
 
+scilpy.image.volume\_math module
+--------------------------------
+
+.. automodule:: scilpy.image.volume_math
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.image.volume\_operations module
+--------------------------------------
+
+.. automodule:: scilpy.image.volume_operations
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.image.volume\_space\_management module
+---------------------------------------------
+
+.. automodule:: scilpy.image.volume_space_management
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/modules/scilpy.io.rst b/docs/source/modules/scilpy.io.rst
@@ -1,6 +1,38 @@
 scilpy.io package
 =================
 
+scilpy.io.btensor module
+------------------------
+
+.. automodule:: scilpy.io.btensor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.io.deprecator module
+---------------------------
+
+.. automodule:: scilpy.io.deprecator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.io.fetcher module
+------------------------
+
+.. automodule:: scilpy.io.fetcher
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scilpy.io.gradients module
+--------------------------
+
+.. automodule:: scilpy.io.gradients
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 scilpy.io.image module
 ----------------------
 
@@ -17,10 +49,26 @@ scilpy.io.streamlines module
    :undoc-members:
    :show-inheritance:
 
+scilpy.io.tensor module
+-----------------------
+
+.. automodule:: scilpy.io.tensor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 scilpy.io.utils module
 ----------------------
 
 .. automodule:: scilpy.io.utils
    :members:
    :undoc-members:
    :show-inheritance:
+
+scilpy.io.varian\_fdf module
+----------------------------
+
+.. automodule:: scilpy.io.varian_fdf
+   :members:
+   :undoc-members:
+   :show-inheritance:
-Original file line number
+Diff line change
@@ Expand Up / @@ -46,7 +46,7 @@ Complete example @@
     Apply back and forth tractogram transformation with the ANTS transformation
-    -----------------
+    ----------------------------------------------------------------------------
     ::
         # The ANTS commands is MOVING->REFERENCE
@@ Expand Down @@