Merge pull request #44 from imr-framework/dev

Release 1.3.1

MANIFEST.in

@@ -1 +1,3 @@
-include pypulseq/utils/SAR/QGlobal.mat
+include VERSION
+include pypulseq/SAR/QGlobal.mat
+recursive-include pypulseq/seq_examples/* *

README.md

@@ -10,45 +10,45 @@ be acquainted with each hardware platform's programming environment.
 PyPulseq enables vendor-neutral pulse sequence design in Python [[1,2]](#references). The pulse sequences can be
 exported as a `.seq` file to be run on Siemens/[GE]/[Bruker] hardware by leveraging their respective
 Pulseq interpreters. This tool is targeted at MRI pulse sequence designers, researchers, students and other interested
-users. It is a translation of the Pulseq framework originally written in Matlab [[3]](#references). Currently, 
+users. It is a translation of the Pulseq framework originally written in Matlab [[3]](#references). Currently,
 PyPulseq is compatible with Pulseq 1.2.0.
 
 It is strongly recommended to first read the [Pulseq specification] before proceeding. The specification
 document defines the concepts required for pulse sequence design using PyPulseq. API docs can be found [here][api-docs].
 
 If you use PyPulseq in your work, cite as:
 ```
-Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design." Journal 
+Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design." Journal
 of Open Source Software 4.42 (2019): 1725.
 
-Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping 
-pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018): 
+Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping
+pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018):
 9-15.
 ```
 
 ## 📢 Pulse sequence development in your browser!
-Design pulse sequences using `pypulseq` in your browser! Check out the [Lightning-start ⚡][lightning-start] section to 
+Design pulse sequences using `pypulseq` in your browser! Check out the [Lightning-start ⚡][lightning-start] section to
 learn how!
 
 ---
 ## [Relevant literature][scholar-citations] (reverse chronological)
 1. Ravi, Keerthi Sravan, and Sairam Geethanath. "Autonomous Magnetic Resonance Imaging." medRxiv (2020).
-2. Nunes, Rita G., et al. "Implementation of a Diffusion-Weighted Echo Planar Imaging sequence using the Open Source 
-Hardware-Independent PyPulseq Tool." ISMRM & SMRT Virtual Conference & Exhibition, International Society for Magnetic 
+2. Nunes, Rita G., et al. "Implementation of a Diffusion-Weighted Echo Planar Imaging sequence using the Open Source
+Hardware-Independent PyPulseq Tool." ISMRM & SMRT Virtual Conference & Exhibition, International Society for Magnetic
 Resonance in Medicine (ISMRM) (2020).
-3. Loktyushin, Alexander, et al. "MRzero--Fully automated invention of MRI sequences using supervised learning." arXiv 
+3. Loktyushin, Alexander, et al. "MRzero--Fully automated invention of MRI sequences using supervised learning." arXiv
 preprint arXiv:2002.04265 (2020).
-4. Jimeno, Marina Manso, et al. "Cross-vendor implementation of a Stack-of-spirals PRESTO BOLD fMRI sequence using 
-TOPPE and Pulseq." ISMRM & SMRT Virtual Conference & Exhibition, International Society for Magnetic Resonance in 
+4. Jimeno, Marina Manso, et al. "Cross-vendor implementation of a Stack-of-spirals PRESTO BOLD fMRI sequence using
+TOPPE and Pulseq." ISMRM & SMRT Virtual Conference & Exhibition, International Society for Magnetic Resonance in
 Medicine (ISMRM) (2020).
 5. Clarke, William T., et al. "Multi-site harmonization of 7 tesla MRI neuroimaging protocols." NeuroImage 206 (2020): 116335.
-6. Geethanath, Sairam, and John Thomas Vaughan Jr. "Accessible magnetic resonance imaging: a review." Journal of 
+6. Geethanath, Sairam, and John Thomas Vaughan Jr. "Accessible magnetic resonance imaging: a review." Journal of
 Magnetic Resonance Imaging 49.7 (2019): e65-e77.
 7. Tong, Gehua, et al. "Virtual Scanner: MRI on a Browser." Journal of Open Source Software 4.43 (2019): 1637.
-8. Archipovas, Saulius, et al. "A prototype of a fully integrated environment for a collaborative work in MR sequence 
-development for a reproducible research." ISMRM 27th Annual Meeting & Exhibition, International Society for 
+8. Archipovas, Saulius, et al. "A prototype of a fully integrated environment for a collaborative work in MR sequence
+development for a reproducible research." ISMRM 27th Annual Meeting & Exhibition, International Society for
 Magnetic Resonance in Medicine (ISMRM) (2019).
-9. Pizetta, Daniel Cosmo. PyMR: a framework for programming magnetic resonance systems. Diss. Universidade de São 
+9. Pizetta, Daniel Cosmo. PyMR: a framework for programming magnetic resonance systems. Diss. Universidade de São
 Paulo (2018).
 ---
 
@@ -126,7 +126,7 @@ Contributing guidelines can be found [here][contrib-guidelines].
 
 ---
 ## References
-1. Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design." 
+1. Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design."
 Journal of Open Source Software 4.42 (2019): 1725.
 2. Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping
 pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018):
@@ -142,7 +142,7 @@ resonance in medicine 77.4 (2017): 1544-1552.
 [google-colab]: https://colab.research.google.com/
 [installation]: #installation
 [lightning-start]: #lightning-start----pypulseq-in-your-browser
-[notebook-examples]: https://github.com/imr-framework/pypulseq/tree/master/pypulseq/seq_examples/notebooks
+[notebook-examples]: https://github.com/imr-framework/pypulseq/tree/dev/pypulseq/seq_examples/notebooks
 [Pulseq specification]: https://pulseq.github.io/specification.pdf
 [scholar-citations]: https://scholar.google.com/scholar?oi=bibs&hl=en&cites=16703093871665262997
 [script-examples]: https://github.com/imr-framework/pypulseq/tree/master/pypulseq/seq_examples/scripts

VERSION

@@ -0,0 +1 @@
+1.3.1

doc/source/conf.py

@@ -2,7 +2,7 @@
 #
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
-# http:https://www.sphinx-doc.org/en/master/config
+# https:https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
 
@@ -12,45 +12,53 @@
 #
 import os
 import sys
-
 sys.path.insert(0, os.path.abspath('../../'))
 
+
 # -- Project information -----------------------------------------------------
 
 project = 'pypulseq'
-copyright = '2019, Keerthi Sravan Ravi'
+copyright = '2021, Keerthi Sravan Ravi'
 author = 'Keerthi Sravan Ravi'
 
 # The full version, including alpha/beta/rc tags
-release = '1.2.1rev1'
+release = '1.3.1'
+
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
+extensions = [
+'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'recommonmark'
+]
 
-master_doc = 'index'
+source_suffix = {
+ '.rst': 'restructuredtext',
+ '.txt': 'restructuredtext',
+ '.md': 'markdown',
+}
+
+source_parsers = {'.md': 'recommonmark.parser.CommonMarkParser'}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = ['setup*']
 
 autodoc_mock_imports = ['numpy', 'matplotlib', 'scipy']
 
-add_module_names = False
-
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages. See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'classic'
+html_theme = 'furo'
+html_logo = '../../logo_transparent.png'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

doc/source/index.rst

@@ -3,30 +3,23 @@ pypulseq
 .. image:: ../../logo.png
  :align: center
 
-`pypulseq <https://github.com/imr-framework/pypulseq>`_ enables vendor-neutral pulse sequence design in Python [1]_. The pulse sequences can be
-exported as a `.seq` file to be run on Siemens/`GE <https://toppemri.github.io>`_/
-`Bruker <https://github.com/pulseq/bruker_interpreter>`_ hardware by leveraging their respective Pulseq interpreters.
-This tool is targeted at MR pulse sequence designers, MRI researchers and other interested users. It is a translation
-of the Pulseq framework originally written in Matlab [2]_.
+Introduction
+============
+`pypulseq <https://github.com/imr-framework/pypulseq>`_ enables vendor-neutral pulse sequence design in Python [1]_ [2]_. The pulse sequences can be exported as a `.seq` file to be run on Siemens/`GE <https://toppemri.github.io>`_/`Bruker <https://github.com/pulseq/bruker_interpreter>`_ hardware by leveraging their respective Pulseq interpreters. This tool is targeted at MR pulse sequence designers, MRI researchers and other interested users. It is a translation of the Pulseq framework originally written in Matlab [3]_.
 
-It is strongly recommended to first read the `Pulseq specification <https://pulseq.github.io/specification.pdf>`_
-before proceeding. The specification document defines the concepts required for pulse sequence design using `pypulseq`.
+It is strongly recommended to first read the `Pulseq specification <https://pulseq.github.io/specification.pdf>`_ before proceeding. The specification document defines the concepts required for pulse sequence design using `pypulseq`.
 
-.. [1] Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018): 9-15.
+.. [1] Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design." Journal of Open Source Software 4.42 (2019): 1725.
 
-.. [2] Layton, Kelvin J., et al. "Pulseq: a rapid and hardware‐independent pulse sequence prototyping framework." Magnetic resonance in medicine 77.4 (2017): 1544-1552.
+.. [2] Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018): 9-15.
+
+.. [3] Layton, Kelvin J., et al. "Pulseq: a rapid and hardware‐independent pulse sequence prototyping framework." Magnetic resonance in medicine 77.4 (2017): 1544-1552.
 
-.. automodule:: pypulseq
- :members:
 
 API documentation
 ==================
 
 .. toctree::
- :maxdepth: 7
+ :maxdepth: 2
 
  modules
-
-Tools
-======
-* :ref:`search`

doc/source/modules.rst

@@ -5,3 +5,4 @@ pypulseq
  :maxdepth: 4
 
  pypulseq
+ setup

doc/source/pypulseq.SAR.rst

@@ -0,0 +1,21 @@
+pypulseq.SAR package
+====================
+
+Submodules
+----------
+
+pypulseq.SAR.SAR\_calc module
+-----------------------------
+
+.. automodule:: pypulseq.SAR.SAR_calc
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pypulseq.SAR
+ :members:
+ :undoc-members:
+ :show-inheritance:

doc/source/pypulseq.Sequence.rst

@@ -12,6 +12,14 @@ pypulseq.Sequence.block module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.Sequence.parula module
+-------------------------------
+
+.. automodule:: pypulseq.Sequence.parula
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.Sequence.read\_seq module
 ----------------------------------
 
@@ -44,7 +52,6 @@ pypulseq.Sequence.write\_seq module
  :undoc-members:
  :show-inheritance:
 
-
 Module contents
 ---------------
 

doc/source/pypulseq.rst

@@ -5,9 +5,10 @@ Subpackages
 -----------
 
 .. toctree::
+ :maxdepth: 4
 
+ pypulseq.SAR
  pypulseq.Sequence
- pypulseq.utils
 
 Submodules
 ----------
@@ -36,6 +37,14 @@ pypulseq.align module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.block\_to\_events module
+---------------------------------
+
+.. automodule:: pypulseq.block_to_events
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.calc\_duration module
 ------------------------------
 
@@ -140,6 +149,14 @@ pypulseq.make\_delay module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.make\_digital\_output\_pulse module
+--------------------------------------------
+
+.. automodule:: pypulseq.make_digital_output_pulse
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.make\_extended\_trapezoid module
 -----------------------------------------
 
@@ -148,6 +165,14 @@ pypulseq.make\_extended\_trapezoid module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.make\_extended\_trapezoid\_area module
+-----------------------------------------------
+
+.. automodule:: pypulseq.make_extended_trapezoid_area
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.make\_gauss\_pulse module
 ----------------------------------
 
@@ -156,6 +181,14 @@ pypulseq.make\_gauss\_pulse module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.make\_label module
+---------------------------
+
+.. automodule:: pypulseq.make_label
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.make\_sinc\_pulse module
 ---------------------------------
 
@@ -172,6 +205,14 @@ pypulseq.make\_trap\_pulse module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.make\_trigger module
+-----------------------------
+
+.. automodule:: pypulseq.make_trigger
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.opts module
 --------------------
 
@@ -204,6 +245,14 @@ pypulseq.split\_gradient\_at module
  :undoc-members:
  :show-inheritance:
 
+pypulseq.supported\_labels module
+---------------------------------
+
+.. automodule:: pypulseq.supported_labels
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 pypulseq.traj\_to\_grad module
 ------------------------------
 
@@ -212,7 +261,6 @@ pypulseq.traj\_to\_grad module
  :undoc-members:
  :show-inheritance:
 
-
 Module contents
 ---------------