Merge branch 'main' into plot_source

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.8"
     # You can also specify other tool versions:
     # nodejs: "16"
     # rust: "1.55"

README.md

@@ -1,6 +1,8 @@
 OHBA Software Library (OSL)
 ===========================
 
+Documentation: https://osl.readthedocs.io/en/latest/.
+
 Install from Source Code
 ------------------------
 The recommended installation depends on your operating system. OSL can be installed from source using:
@@ -14,11 +16,10 @@ pip install -e .
 where the environment file `<os>.yml` can be:
 
 - `linux.yml` for a generic linux machine.
-- `m1_mac.yml` if you are using a modern Mac computer.
 - `hbaws.yml` if you are using an OHBA workstation at Oxford.
 - `bmrc.yml` if you are using the BMRC at Oxford.
 
-Note, all of the above environments come with Jupyter Notebook installed. The `hbaws.yml` and `m1_mac.yml` environments also comes with Spyder installed.
+Note, all of the above environments come with Jupyter Notebook installed. The `hbaws.yml` environment also comes with Spyder installed.
 
 Deleting osl
 ------------

doc/source/api.rst

@@ -1,5 +1,5 @@
 API
-================
+===
 
 This page is the reference for the functions in OSL.
 
@@ -162,9 +162,11 @@ Utility functions for running an OSL Preprocessing pipeline.
 
 
 GLM
-******
+***
+
 GLM Base
 ++++++++
+
 Modality specific wrappers for glmtools.
 
 .. currentmodule:: osl.glm.glm_base
@@ -193,7 +195,7 @@ Modality specific wrappers for glmtools.
    SensorClusterPerm.get_sig_clusters
 
 GLM Epochs
-++++++++++++++++++++++++
+++++++++++
 
 .. currentmodule:: osl.glm.glm_epochs
 
@@ -227,7 +229,7 @@ GLM Epochs
 
 
 GLM Spectrum
-++++++++++++++++++++++++
+++++++++++++
 
 GLM-Spectrum classes and functions designed to work with GLM-Spectra computed from  MNE format sensorspace data
 
@@ -284,11 +286,13 @@ GLM-Spectrum classes and functions designed to work with GLM-Spectra computed fr
 
 
 RHINO
-********************
+*****
+
 Tools for Coregistration and forward modeling 
 
 Coregistration
 ++++++++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.coreg
@@ -309,6 +313,7 @@ Deep-level RHINO functions used by wrappers
 
 Forward modeling
 ++++++++++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.forward_model
@@ -324,7 +329,8 @@ Deep-level RHINO functions used by wrappers
 
 
 FSL-utils
-+++++++++++
++++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.fsl_utils
@@ -342,7 +348,8 @@ Deep-level RHINO functions used by wrappers
 
 
 Polhemus
-+++++++++++
+++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.polhemus
@@ -358,7 +365,8 @@ Deep-level RHINO functions used by wrappers
 
 
 Surfaces
-+++++++++++
+++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.surfaces
@@ -378,7 +386,8 @@ Deep-level RHINO functions used by wrappers
 
 
 Utils
-+++++++++++
++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.utils
@@ -448,7 +457,7 @@ Deep-level RHINO functions used by wrappers
 
 
 Source Reconstruction
-**********************
+*********************
 
 Pipeline Functions
 ++++++++++++++++++
@@ -467,6 +476,7 @@ Primary user-level functions for running OSL coregistration and source_recon fun
 
 Wrappers
 ++++++++
+
 Primary wrapper functions to use in a source_recon configuration
 
 .. currentmodule:: osl.source_recon.wrappers
@@ -499,6 +509,7 @@ Primary wrapper functions to use in a source_recon configuration
 
 Beamforming
 +++++++++++
+
 Second-level beamforming functions used by wrappers
 
 .. currentmodule:: osl.source_recon.beamforming
@@ -533,9 +544,9 @@ Second-level beamforming functions used by wrappers
     _prepare_beamformer_input
 
 
-
 Sign-flipping
 +++++++++++++
+
 Second-level sign-flipping functions used by wrappers
 
 .. currentmodule:: osl.source_recon.sign_flipping
@@ -566,6 +577,7 @@ Second-level sign-flipping functions used by wrappers
 
 Utils
 +++++
+
 Utility functions for running an OSL Source Recon pipeline.
 
 .. currentmodule:: osl.source_recon.batch
@@ -580,6 +592,7 @@ Utility functions for running an OSL Source Recon pipeline.
 
 Parcellation
 ************
+
 Second-level Parcellation functions used by wrappers
 
 .. currentmodule:: osl.source_recon.parcellation.parcellation
@@ -620,6 +633,7 @@ Second-level Parcellation functions used by wrappers
 
 Nifti Utils
 ++++++++++++
+
 Second-level Parcellation functions used by wrappers
 
 .. currentmodule:: osl.source_recon.parcellation.nii
@@ -638,9 +652,11 @@ Second-level Parcellation functions used by wrappers
 
 Report
 ******
+
 Sensor level
 ++++++++++++
-.. currentmodule:: osl.report.raw_report
+
+.. currentmodule:: osl.report.preproc_report
 
 .. autosummary::
    :toctree: stubs
@@ -656,6 +672,7 @@ Sensor level
 
 Source level
 ++++++++++++
+
 .. currentmodule:: osl.report.src_report
 
 .. autosummary::
@@ -685,7 +702,7 @@ File handling
 
 
 Logger
-++++++++++++
+++++++
 
 .. currentmodule:: osl.utils.logger
 
@@ -735,4 +752,4 @@ OPM Utilities
 
     convert_notts
 
-    correct_mri
+    correct_mri

doc/source/conf.py

@@ -6,23 +6,27 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import os
+import sys
+import inspect
+
+__location__ = os.path.join(
+    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
+)
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
+sys.path.insert(0, os.path.join(__location__, "../.."))
 
 # -- Project information -----------------------------------------------------
 
-project = 'osl'
-copyright = '2023, OMG'
-author = 'OMG'
+project = 'OSL'
+copyright = '2023, OHBA Analysis Group'
+author = 'OHBA Analysis Group'
 
 # The full version, including alpha/beta/rc tags
-release = '0.0.1dev'
+release = '0.5.1'
 
 
 # -- General configuration ---------------------------------------------------

doc/source/install.rst

@@ -1,12 +1,28 @@
 Installation
 ============
 
-First, make sure you have conda (or miniconda) installed: https://docs.conda.io/en/latest. Then oslpy can be installed from source using the following:
+We recommend installing OSL within a virtual environment. You can do this with `Anaconda <https://docs.anaconda.com/free/anaconda/install/index.html>`_ (or `miniconda <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_).
 
-::
-    
-    git clone https://github.com/OHBA-analysis/oslpy.git
-    cd oslpy
+Linux
+-----
+
+1. Install FSL using the instructions `here <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux>`_.
+
+2. Install OSL either via pip using::
+
+    pip install osl
+
+or from source (in editable mode) using::
+
+    git clone https://github.com/OHBA-analysis/osl.git
+    cd osl
     conda env create -f envs/linux.yml
     conda activate osl
     pip install -e .
+
+Windows
+-------
+
+If you're using a Windows machine, we recommend you install FSL within a `Ubuntu <https://ubuntu.com/wsl>`_ (linux) subsystem following the instructions `here <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows>`_.
+
+Then install OSL using the instructions above.

envs/windows.yml

@@ -0,0 +1,46 @@
+name: osl
+channels:
+- conda-forge
+dependencies:
+- python=3.8.16
+- pip=23.0.1
+- vtk=9.1.0=*osmesa*
+- pyvista=0.38.5
+- pip:
+  - jupyter==1.0.0
+  - ipympl==0.9.3
+  - ipywidgets==8.0.5
+  - ipyevents==2.0.1
+  - ipyvtklink==0.2.2
+  - jupyter-client==8.1.0
+  - numpy==1.23.5
+  - scipy==1.10.1
+  - matplotlib==3.7.1
+  - mne==1.3.1
+  - scikit-learn==1.2.2
+  - fslpy==3.11.3
+  - sails==1.4.0
+  - tabulate==0.9.0
+  - pyyaml==6.0
+  - neurokit2==0.2.3
+  - jinja2==3.1.2
+  - glmtools==0.2.1
+  - numba==0.56.4
+  - nilearn==0.10.2
+  - dask==2023.3.2
+  - distributed==2023.3.2
+  - parse==1.19.0
+  - opencv-python==4.7.0.72
+  - h5io==0.1.7
+  - mat73==0.60
+  - nibabel==5.0.1
+  - pandas==1.5.3
+  - panel==1.2.3
+  - pqdm==0.2.0
+  - seaborn==0.12.2
+  - tensorflow==2.9.1
+  - tensorflow_probability==0.17.0
+  - tqdm==4.65.0
+  - osfclient==0.0.5
+  - osl==0.5.1
+  - osl-dynamics==1.2.11