pulserver 0.1.0__tar.gz

pulserver-0.1.0/.github/workflows/style.yml

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+name: Style
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  PYTHON_VERSION: "3.10"
+
+jobs:
+  linter-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python ${{ env.PYTHON_VERSION }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: pip
+
+      - name: Install Python deps
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install black ruff
+          python -m pip install -e .
+
+      - name: Black Check
+        shell: bash
+        run: black . --diff --color --check
+
+      # - name: ruff Check
+        # shell: bash
+        # run: ruff check src

pulserver-0.1.0/.github/workflows/tags-release.yml

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+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on:
+    push:
+      tags:
+        - 'v[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/<package-name>  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/<package-name>
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

pulserver-0.1.0/.github/workflows/test-cicd.yml

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+name: CI/CD
+
+on: 
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    needs: [test]
+
+    strategy:
+      matrix:
+        python-version: [3.10, 3.12]  # Specify the desired Python versions
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          pip install .[test]
+
+      - name: Run tests
+        run: pytest --cov --cov-report=xml tests
+		
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token:  ${{ secrets.CODECOV_TOKEN }}
+          slug: INFN-MRI/pulserver
+		  
+  docs:
+    runs-on: ubuntu-20.04
+    needs: [test]
+    steps:
+      - name: Get the docs_build artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: docs_final
+          path: docs_build
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+		  
+      - name: Display structure of docs
+        run: ls -R docs_build/
+		  
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs_build
+          destination_dir: .  # Ensure you deploy to the root of the gh-pages branch
+          publish_branch: gh-pages
+          keep_files: false
+		
+	
+		

pulserver-0.1.0/.gitignore

@@ -0,0 +1,26 @@
+*.npy
+build/
+dist/
+*.egg-info/
+**/.ipynb_checkpoints/
+examples/*.ipynb
+*.xml
+.coverage*
+.vscode
+
+
+.idea
+*.log
+tmp/
+
+*_cache/
+*.py[cod]
+*.egg
+*.nbi
+*.nbc
+
+docs/generated/
+docs_build/
+jupyter_execute/
+
+src/pulserver/_version.py

pulserver-0.1.0/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Matteo Cencini
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pulserver-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: pulserver
+Version: 0.1.0
+Summary: A PyPulseq-based client/server MR sequence design toolbox.
+Author-email: Matteo Cencini <matteo.cencini@gmail.com>
+Project-URL: Homepage, https://github.com/INFN-MRI/pulserver
+Project-URL: Bug Reports, https://github.com/INFN-MRI/pulserver/issues
+Project-URL: Source, https://github.com/INFN-MRI/pulserver
+Keywords: pulseq,mri,sequence-design,pulse-sequences,mri-sequences
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+Requires-Dist: numpy<2.0
+Requires-Dist: scipy<1.14
+Requires-Dist: numba
+Requires-Dist: pypulseq
+Requires-Dist: pulpy
+Requires-Dist: mri-nufft
+Requires-Dist: ismrmrd
+Requires-Dist: ipywidgets
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-black; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-sugar; extra == "test"
+Requires-Dist: pytest-xdist; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Requires-Dist: myst-nb; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: mrtwin; extra == "doc"
+
+Pulserver
+=========
+
+Pulserver is a high-level wrapper over PyPulseq. It is designed to 
+improve MR sequence code organization and provide a bridge
+between different Pulseq interpreter representations while providing
+a familiar interface to PyPulseq user.
+
+It also provide a server-based interface to enable online sequence design
+routines, e.g., using the MR scanner as a client.
+
+Features
+--------
+
+
+
+Installation
+------------
+Pulserver can be installed via pip:
+
+.. code-block:: bash
+
+    pip install pulserver
+
+Development
+-----------
+If you want to modifiy the Pulserver code base:
+
+.. code-block:: bash
+
+    git clone https://github.com/INFN-MRI/pulservert.git
+    pip install -e ./pulserver
+
+Usage
+-----
+
+TODO: add quick example
+
+Testing
+-------
+To run the tests, execute the following command in the terminal:
+
+.. code-block:: bash
+
+     pytest .
+
+License
+-------
+This project is licensed under the MIT License.
+
+Contributing
+------------
+Contributions are welcome! Please fork the repository and submit a pull request.

pulserver-0.1.0/README.rst

@@ -0,0 +1,53 @@
+Pulserver
+=========
+
+Pulserver is a high-level wrapper over PyPulseq. It is designed to 
+improve MR sequence code organization and provide a bridge
+between different Pulseq interpreter representations while providing
+a familiar interface to PyPulseq user.
+
+It also provide a server-based interface to enable online sequence design
+routines, e.g., using the MR scanner as a client.
+
+Features
+--------
+
+
+
+Installation
+------------
+Pulserver can be installed via pip:
+
+.. code-block:: bash
+
+    pip install pulserver
+
+Development
+-----------
+If you want to modifiy the Pulserver code base:
+
+.. code-block:: bash
+
+    git clone https://github.com/INFN-MRI/pulservert.git
+    pip install -e ./pulserver
+
+Usage
+-----
+
+TODO: add quick example
+
+Testing
+-------
+To run the tests, execute the following command in the terminal:
+
+.. code-block:: bash
+
+     pytest .
+
+License
+-------
+This project is licensed under the MIT License.
+
+Contributing
+------------
+Contributions are welcome! Please fork the repository and submit a pull request.

pulserver-0.1.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

pulserver-0.1.0/docs/_templates/autosummary/base.rst

@@ -0,0 +1,5 @@
+{{ objname  | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

pulserver-0.1.0/docs/_templates/autosummary/class.rst

@@ -0,0 +1,32 @@
+{{ name | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :private-members:
+   :show-inheritance:
+   :special-members: __call__, __add__, __mul__, __matmul__
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

pulserver-0.1.0/docs/_templates/autosummary/function.rst

@@ -0,0 +1,10 @@
+{{ objname  | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+..  _sphx_glr_backref_{{fullname}}:
+
+.. minigallery:: {{fullname}}
+   :add-heading:

pulserver-0.1.0/docs/_templates/autosummary/module.rst

@@ -0,0 +1,64 @@
+{{ "``{}.{}``".format(module.split(".")[-1], objname) | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

pulserver-0.1.0/docs/api.rst

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+API References
+==============
+
+Core
+----
+Core sequence representation.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   pulserver.Sequence
+   pulserver.SequenceParams
+   pulserver.Opts 
+
+Blocks
+------
+Subroutines for the generation of sequence blocks, e.g., 
+preparation modules, rf pulses, phase encoding, readout.
+
+RF Pulses
+^^^^^^^^^
+Non-adiabatic RF pulses blocks, including both the RF events
+and (for spatially-selective pulses), the accompanying gradient event.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   pulserver.blocks.make_hard_pulse
+   pulserver.blocks.make_slr_pulse
+   pulserver.blocks.make_spsp_pulse
+   
+Readout
+^^^^^^^
+Readout blocks, including both the gradient (either trapezoidal or arbitrary, e.g., for spiral imaging), 
+and the accompanying adc events.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   pulserver.blocks.make_line_readout
+   pulserver.blocks.make_spiral_readout
+   
+Phase Encoding
+^^^^^^^^^^^^^^
+Phase encoding blocks, including phase blips for EPI sampling.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   pulserver.blocks.make_phase_encoding
+   
+Miscellaneous
+^^^^^^^^^^^^^
+Miscellaneous blocks such as gradient spoiling.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+
+   pulserver.blocks.make_spoiler_gradient
+   
+
+   

pulserver-0.1.0/docs/binder/apt.txt

@@ -0,0 +1,3 @@
+cmake
+libnfft3-dev
+libgl1-mesa-glx

pulserver-0.1.0/docs/binder/environment.yml

@@ -0,0 +1,9 @@
+name: mrtwin
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip>=19.1.1
+  - jupyter>=1.0.0
+  - pip:
+      - mrtwin