mrzerocore 0.3.1__tar.gz → 0.4.2__tar.gz

mrzerocore-0.4.2/.github/workflows/deploy_docs.yml

@@ -0,0 +1,38 @@
+name: Deploy
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  # To push a branch 
+      pages: write  # To push to a GitHub Pages site
+      id-token: write # To update the deployment status
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install latest mdbook
+        run: |
+          tag=$(curl 'https://api.github.com/repos/rust-lang/mdbook/releases/latest' | jq -r '.tag_name')
+          url="https://github.com/rust-lang/mdbook/releases/download/${tag}/mdbook-${tag}-x86_64-unknown-linux-gnu.tar.gz"
+          mkdir mdbook
+          curl -sSL $url | tar -xz --directory=./mdbook
+          echo `pwd`/mdbook >> $GITHUB_PATH
+      - name: Build Book
+        run: |
+          cd documentation
+          mdbook build
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload entire repository
+          path: 'documentation/book'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

mrzerocore-0.4.2/.github/workflows/playground_test.yml

@@ -0,0 +1,64 @@
+name: Playground Notebooks Test
+
+on:
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+  schedule:
+    # Run once a week on Sunday at 00:00 UTC
+    - cron: '0 0 * * 0'
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      notebook-matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v3  
+      - name: List all notebooks
+        id: set-matrix
+        run: |
+          NOTEBOOKS=$(printf '%s\n' \
+            documentation/playground_mr0/mr0_FID_seq.ipynb \
+            documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb \
+            documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb \
+            documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb \
+            documentation/playground_mr0/mr0_EPI_2D_seq.ipynb \
+            documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb \
+            documentation/playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb \
+            documentation/playground_mr0/mr0_RARE_2D_seq.ipynb \
+            documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb \
+            documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb \
+            documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb \
+            documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb \
+          | jq -R -s -c 'split("\n")[:-1]')
+          echo "matrix=$NOTEBOOKS" >> $GITHUB_OUTPUT
+
+  test-notebooks:
+    needs: generate-matrix
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        notebook: ${{fromJSON(needs.generate-matrix.outputs.notebook-matrix)}}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+            pip install pypulseq &> /dev/null
+            pip install pydisseqt
+            pip install MRzeroCore --no-deps
+            pip install ismrmrd
+            pip install  torchkbnufft PyWavelets tqdm scikit-image
+            wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null
+            pip install jupyter nbconvert
+      - run: |
+            echo "🧪 Testing ${{ matrix.notebook }}..."
+            python tests/playground_test.py ${{ matrix.notebook }}

mrzerocore-0.4.2/.github/workflows/pypi_publish.yml

@@ -0,0 +1,148 @@
+# This file is a modified version of:
+#
+#    maturin generate-ci github -o .github/workflows/pypi_publish.yml
+#
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+          - runner: ubuntu-22.04
+            target: s390x
+          - runner: ubuntu-22.04
+            target: ppc64le
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+          # - runner: windows-latest
+          #   target: x86
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          # - runner: macos-13
+          #   target: x86_64
+          - runner: macos-14
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    # if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
+    needs: [linux, windows, macos, sdist]
+    permissions:
+      # Use to sign the release artifacts
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v4
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-path: 'wheels-*/*'
+      - name: Publish to PyPI
+        # if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

mrzerocore-0.4.2/.github/workflows/simulation_test.yml

@@ -0,0 +1,78 @@
+name: Simulation Test
+
+on:
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      notebook-matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: List all notebooks
+        id: set-matrix
+        run: |
+          python -c "
+          import sys
+          sys.path.append('tests/simulation_test')
+          from config import NOTEBOOKS_TO_TEST
+          import json
+          print(json.dumps(NOTEBOOKS_TO_TEST))
+          " > notebooks.json
+          echo "matrix=$(cat notebooks.json)" >> $GITHUB_OUTPUT
+
+  test-notebooks:
+    needs: generate-matrix
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        notebook: ${{fromJSON(needs.generate-matrix.outputs.notebook-matrix)}}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          pip install pypulseq
+          pip install torchkbnufft
+          pip install nbformat
+
+      - name: Generate sequence file
+        run: |
+          mkdir tests/simulation_test/seq_files
+          python tests/simulation_test/generate_seq_files.py ${{ matrix.notebook }}
+
+      - name: Cloning main branch
+        run: |
+          git clone https://github.com/MRsources/MRzero-Core.git main_branch
+          mkdir tests/simulation_test/ref_files
+
+      - name: Installing main branch version
+        run: |
+          pip install -e ./main_branch
+
+      - name: Generate reference files
+        run: |
+          python tests/simulation_test/generate_ref_files.py
+      
+      - name: Uninstall main branch version and install current version
+        run: |
+          pip uninstall -y MRzeroCore
+          pip install -e .
+
+      - name: Generate actual files
+        run: |
+          mkdir tests/simulation_test/actual_files
+          python tests/simulation_test/generate_actual_files.py
+
+      - name: Run Simulation Test
+        run: |
+          python tests/simulation_test/test_simulation.py

{MRzeroCore-0.3.1 → mrzerocore-0.4.2}/.gitignore

@@ -1,9 +1,9 @@
 /target
-/documentation/_autosummary
-/documentation/_build
+/documentation/book
 out/
 *.seq
 *.env
+*.ipynb_checkpoints
 
 *.pdf
 
@@ -13,6 +13,7 @@ external.seq
 
 # Brainweb files
 *.i8.gz
+*.npz
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -83,4 +84,13 @@ docs/_build/
 .vscode/
 
 # Pyenv
-.python-version
+.python-version
+
+# keep test seq files
+!tests/simulation_test/seq_files/*.seq
+
+# cursor files
+.cursor/
+
+# test venv
+.test_venv/

{MRzeroCore-0.3.1 → mrzerocore-0.4.2}/CHANGELOG.md

@@ -1,3 +1,44 @@
+- 0.4.0
+  - Integrate ISMRMD exporter
+  - Update documentation
+  - Provide option to get PDG graph plotting data without plotting
+  - Helper plotting function that works with all pulseq versions
+- 0.3.13
+  - bugfix: util.load_phantom - B0_polynomial computation used wrong number of dims
+  - default `clear_state_mag` to `True` to avoid memory problems
+  - include optional initial magnetization in execute_graph
+  - fixed numpy version in playground
+- 0.3.12
+  - Changed how to return magnetization from the simulation, see pull request #97
+- 0.3.11
+  - new util functions for phantom loading and simulating
+- 0.3.10
+  - phantom_motion and voxel_motion now also exists in VoxelGridPhantom
+  - new simple simulate function in util, that directly accepts a VoxelGridPhantom
+- 0.3.9
+  - New simple load_default_phantom function in util
+- 0.3.8
+  - Bugfix missing tensor dtype (#82)
+  - Support for 0 shim array shape_id
+  - Default shim in importer for pulses that do not specify any
+  - Deprecated old importer
+- 0.3.7
+  - Support for loading .seq files with pTx rf_shim extension for pulseq
+  - Support for loading .dsv files
+- 0.3.6
+  - Support for complex B1 maps (#80)
+  - Isochromat bugfix (#74)
+- 0.3.5
+  - centered signal on adc samples in `insert_signal_plot()`
+  - ensured `tissue_masks` is never zero to fix remaining bugs
+- 0.3.4
+  - Bugfix: `insert_signal_plot()` now respects adc delay
+- 0.3.3
+  - Bugfix: `VoxelGridPhantom.interpolate()` and `.scale()` now work again
+- 0.3.2
+  - Added tissue maps to phantom and plotting (#68)
+  - Fixed `.plot()`ting of 3D VoxelGridPhantom, added slice parameter
+  - Added `simulate_2D` to util for easy simulation of pypulseq sequences
 - 0.3.1
   - WIP .dsv support with pydisseqt 0.1.5
   - changed type annotation in util.imshow for python 3.9 compatibility

{MRzeroCore-0.3.1 → mrzerocore-0.4.2}/Cargo.lock

@@ -1,6 +1,6 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
+version = 4
 
 [[package]]
 name = "autocfg"
@@ -59,7 +59,7 @@ dependencies = [
 
 [[package]]
 name = "mrzero_core"
-version = "0.3.1"
+version = "0.4.2"
 dependencies = [
  "num-complex",
  "pyo3",

{MRzeroCore-0.3.1 → mrzerocore-0.4.2}/Cargo.toml

@@ -1,11 +1,13 @@
 [package]
 name = "mrzero_core"
-version = "0.3.1"
+version = "0.4.2"
 edition = "2021"
+readme = "README.md"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
 crate-type = ["cdylib"]
+name = "MRzeroCore"
 
 [dependencies]
 pyo3 = { version = "0.21.2", features = ["abi3-py37", "extension-module", "num-complex"] }

{MRzeroCore-0.3.1 → mrzerocore-0.4.2}/PKG-INFO

@@ -1,28 +1,32 @@
-Metadata-Version: 2.3
-Name: MRzeroCore
-Version: 0.3.1
+Metadata-Version: 2.4
+Name: mrzerocore
+Version: 0.4.2
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: License :: OSI Approved :: GNU Affero General Public License v3
-Requires-Dist: torch >=1.12
+Requires-Dist: ismrmrd
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: pydisseqt>=0.1.13
 Requires-Dist: pypulseq
-Requires-Dist: matplotlib >=3.5
-Requires-Dist: scipy >=1.7
-Requires-Dist: requests >=2.20
+Requires-Dist: requests>=2.20
 Requires-Dist: scikit-image
+Requires-Dist: scipy>=1.7
 Requires-Dist: torchkbnufft
-Requires-Dist: pydisseqt >=0.1.4
+Requires-Dist: torch>=1.12
+Requires-Dist: tqdm
+Requires-Dist: nibabel
 License-File: LICENSE
 Summary: Core functionality of MRzero
 Author-email: Jonathan Endres <jonathan.endres@uk-erlangen.de>
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
-Project-URL: Repository, https://github.com/MRsources/MRzero-Core
-Project-URL: Documentation, https://mrzero-core.readthedocs.io/
+Project-URL: Documentation, https://mrsources.github.io/MRzero-Core/
 Project-URL: MRzero-Paper, https://arxiv.org/abs/2002.04265
+Project-URL: Repository, https://github.com/MRsources/MRzero-Core
 
 [![Documentation Status](https://readthedocs.org/projects/mrzero-core/badge/?version=latest)](https://mrzero-core.readthedocs.io/en/latest/?badge=latest)
+![PyPI - Version](https://img.shields.io/pypi/v/MRzeroCore)
 
 # MRzero Core
 
@@ -43,7 +47,29 @@ The typical way of using it is like the following:
 import MRzeroCore as mr0
 ```
 
-Examples on how to use can be found in the [Playground](https://mrzero-core.readthedocs.io/en/latest/playground_mr0/overview.html).
+Examples on how to use MR-zero can be found in the [Playground](https://mrzero-core.readthedocs.io/en/latest/playground_mr0/overview.html).
+
+## Pulseq Integration
+
+**MRzero Core makes Pulseq simulation incredibly easy** - simulate any .seq file in just one line:
+
+```python
+import MRzeroCore as mr0
+
+# Simulate any Pulseq file
+seq = mr0.Sequence.import_file("your_sequence.seq")
+signal = mr0.util.simulate(seq)  # That's it!
+```
+
+### Key Features:
+- **One-line simulation** of any Pulseq .seq file
+- **PyPulseq integration** - write sequences in Python, simulate with MR-zero
+- **Google Colab ready** - [13+ ready-to-run examples](https://mrzero-core.readthedocs.io/en/latest/playground_mr0/overview.html#code-and-simulate-pypulseq)
+- **MATLAB ↔ Python workflow** - create in MATLAB Pulseq, simulate in Python
+- **No dependencies** - fully self-contained Pulseq parser included
+- **Scanner-ready export** - export MR-zero sequences as .seq files
+
+Try it now: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_upload_seq.ipynb)
 
 ## Links
 
@@ -69,11 +95,18 @@ maturin build --interpreter python
 docker run --rm -v <path-to-repo>/MRzero-Core:/io ghcr.io/pyo3/maturin build
 ```
 
-To **build the documentation**, run
+**Building the documentation**
+
+Install newest (beta) version of mdBook:
+```bash
+cargo install --git https://github.com/rust-lang/mdBook.git mdbook
 ```
-jupyter-book build documentation/
+
+Run a live-preview server:
+```bash
+# in the root directory:
+mdbook serve documentation
 ```
-in the root folder of this project. This requires jupyter-book as well as MRzeroCore itself to be installed.
 
 
 ## Official builds

{MRzeroCore-0.3.1 → mrzerocore-0.4.2}/README.md

@@ -1,4 +1,5 @@
 [![Documentation Status](https://readthedocs.org/projects/mrzero-core/badge/?version=latest)](https://mrzero-core.readthedocs.io/en/latest/?badge=latest)
+![PyPI - Version](https://img.shields.io/pypi/v/MRzeroCore)
 
 # MRzero Core
 
@@ -19,7 +20,29 @@ The typical way of using it is like the following:
 import MRzeroCore as mr0
 ```
 
-Examples on how to use can be found in the [Playground](https://mrzero-core.readthedocs.io/en/latest/playground_mr0/overview.html).
+Examples on how to use MR-zero can be found in the [Playground](https://mrzero-core.readthedocs.io/en/latest/playground_mr0/overview.html).
+
+## Pulseq Integration
+
+**MRzero Core makes Pulseq simulation incredibly easy** - simulate any .seq file in just one line:
+
+```python
+import MRzeroCore as mr0
+
+# Simulate any Pulseq file
+seq = mr0.Sequence.import_file("your_sequence.seq")
+signal = mr0.util.simulate(seq)  # That's it!
+```
+
+### Key Features:
+- **One-line simulation** of any Pulseq .seq file
+- **PyPulseq integration** - write sequences in Python, simulate with MR-zero
+- **Google Colab ready** - [13+ ready-to-run examples](https://mrzero-core.readthedocs.io/en/latest/playground_mr0/overview.html#code-and-simulate-pypulseq)
+- **MATLAB ↔ Python workflow** - create in MATLAB Pulseq, simulate in Python
+- **No dependencies** - fully self-contained Pulseq parser included
+- **Scanner-ready export** - export MR-zero sequences as .seq files
+
+Try it now: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_upload_seq.ipynb)
 
 ## Links
 
@@ -45,11 +68,18 @@ maturin build --interpreter python
 docker run --rm -v <path-to-repo>/MRzero-Core:/io ghcr.io/pyo3/maturin build
 ```
 
-To **build the documentation**, run
+**Building the documentation**
+
+Install newest (beta) version of mdBook:
+```bash
+cargo install --git https://github.com/rust-lang/mdBook.git mdbook
 ```
-jupyter-book build documentation/
+
+Run a live-preview server:
+```bash
+# in the root directory:
+mdbook serve documentation
 ```
-in the root folder of this project. This requires jupyter-book as well as MRzeroCore itself to be installed.
 
 
 ## Official builds

mrzerocore-0.4.2/documentation/book.toml

@@ -0,0 +1,12 @@
+[book]
+title = "MR-zero"
+description = "Documentation for MR-zero Core and some of its adjacent projects."
+authors = ["Madga Duarte", "Jonathan Endres", "Moritz Zaiss"]
+language = "en"
+src = "src"
+
+[output.html]
+mathjax-support = true
+git-repository-url = "https://github.com/MRsources/MRzero-Core"
+edit-url-template = "https://github.com/MRsources/MRzero-Core/edit/main/documentation/{path}"
+site-url = "/mrzero-core/"