mrzerocore 0.2.6__tar.gz → 0.2.7__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (90) hide show
  1. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/Cargo.lock +1 -1
  2. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/Cargo.toml +1 -1
  3. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/PKG-INFO +1 -1
  4. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/overview.md +81 -81
  5. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/brainweb/__init__.py +3 -2
  6. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/.github/workflows/pypi_publish.yml +0 -0
  7. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/.gitignore +0 -0
  8. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/.readthedocs.yaml +0 -0
  9. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/EULA.txt +0 -0
  10. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/LICENSE +0 -0
  11. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/README.md +0 -0
  12. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/_config.yml +0 -0
  13. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/_toc.yml +0 -0
  14. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api/phantom.md +0 -0
  15. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api/reco.md +0 -0
  16. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api/sequence.md +0 -0
  17. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api/simulation/isochromat_sim.md +0 -0
  18. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api/simulation/pdg_sim.md +0 -0
  19. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api/simulation.md +0 -0
  20. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/api.md +0 -0
  21. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/intro.md +0 -0
  22. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/logo.png +0 -0
  23. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/phantom_generation.md +0 -0
  24. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/AdjDataUser2gB0_transversal_0.08moving_average.mat +0 -0
  25. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/flash.ipynb +0 -0
  26. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr00_FLASH_2D_ernstAngle_opt.ipynb +0 -0
  27. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_CS_cartesian_seq.ipynb +0 -0
  28. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_CS_radial_seq.ipynb +0 -0
  29. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb +0 -0
  30. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb +0 -0
  31. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_DWI_GRE_2D_seq.ipynb +0 -0
  32. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb +0 -0
  33. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_FID_seq.ipynb +0 -0
  34. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb +0 -0
  35. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb +0 -0
  36. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb +0 -0
  37. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb +0 -0
  38. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb +0 -0
  39. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb +0 -0
  40. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_burst_TSE.ipynb +0 -0
  41. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_opt_FLASH_2D_IR_Fit_T1.ipynb +0 -0
  42. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_opt_FLASH_2D_IR_voxelNN_T1.ipynb +0 -0
  43. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_pypulseq_exmpls_seq.ipynb +0 -0
  44. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/mr0_upload_seq.ipynb +0 -0
  45. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/numerical_brain_cropped.mat +0 -0
  46. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/ptx_phantom.p +0 -0
  47. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/pulseq_flash.ipynb +0 -0
  48. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/pulseq_rf_shim.ipynb +0 -0
  49. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/pulseq_sim_pTx.ipynb +0 -0
  50. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/seqs/flash pTx CP.seq +0 -0
  51. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/seqs/flash pTx EP.seq +0 -0
  52. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/seqs/flash pTx QM.seq +0 -0
  53. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/subject05.npz +0 -0
  54. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/util.py +0 -0
  55. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/requirements.txt +0 -0
  56. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/resources/logo.blend +0 -0
  57. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/resources/logo.png +0 -0
  58. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/resources/studio_small_09_2k.hdr +0 -0
  59. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/pyproject.toml +0 -0
  60. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/__init__.py +0 -0
  61. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/brainweb/brainweb_data.json +0 -0
  62. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/brainweb/brainweb_data_sources.txt +0 -0
  63. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/brainweb/output/.gitkeep +0 -0
  64. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/custom_voxel_phantom.py +0 -0
  65. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/sim_data.py +0 -0
  66. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/voxel_grid_phantom.py +0 -0
  67. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/exporter.py +0 -0
  68. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/exporter_v2.py +0 -0
  69. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/helpers.py +0 -0
  70. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_exporter.py +0 -0
  71. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/__init__.py +0 -0
  72. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/adc.py +0 -0
  73. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/helpers.py +0 -0
  74. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulse.py +0 -0
  75. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/__init__.py +0 -0
  76. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/adc.py +0 -0
  77. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/block.py +0 -0
  78. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/definitons.py +0 -0
  79. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/gradient.py +0 -0
  80. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/helpers.py +0 -0
  81. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/rf.py +0 -0
  82. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/pulseq_file/trap.py +0 -0
  83. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/pulseq/pulseq_loader/spoiler.py +0 -0
  84. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/reconstruction.py +0 -0
  85. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/sequence.py +0 -0
  86. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/simulation/isochromat_sim.py +0 -0
  87. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/simulation/main_pass.py +0 -0
  88. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/simulation/pre_pass.py +0 -0
  89. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/src/lib.rs +0 -0
  90. {MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/src/pre_pass.rs +0 -0
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/Cargo.lock RENAMED
@@ -53,7 +53,7 @@ dependencies = [
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  [[package]]
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  name = "mrzero_core"
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- version = "0.2.6"
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+ version = "0.2.7"
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  dependencies = [
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  "num-complex",
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  "pyo3",
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/Cargo.toml RENAMED
@@ -1,6 +1,6 @@
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  [package]
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  name = "mrzero_core"
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- version = "0.2.6"
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+ version = "0.2.7"
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  edition = "2021"
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  # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/PKG-INFO RENAMED
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  Metadata-Version: 2.1
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  Name: MRzeroCore
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- Version: 0.2.6
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+ Version: 0.2.7
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  Classifier: Programming Language :: Rust
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  Classifier: Programming Language :: Python :: Implementation :: CPython
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  Classifier: Programming Language :: Python :: Implementation :: PyPy
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/documentation/playground_mr0/overview.md RENAMED
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- (playground_mr0)=
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- # Playground MR0
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-
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- Welcome to Playground MR0, a playground to share, vary and simulate MR sequences.
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- MR sequences are written in the Pulseq standard using the pypulseq library.
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- Pulseq files are simulated with the efficient Phase Distribution Graph Bloch simulation.
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- Here we share links to example colabs that contain various MR sequences or let you upload your own seq file for simulation.
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-
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- Many of the examples are build using [PyPulseq](https://github.com/imr-framework/pypulseq) and simulate the resulting .seq files with `MR0`.
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- These .seq files could also be measured on any MRI scanner using a Pulseq interpreter.
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-
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-
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- ## Code and simulate PyPulseq
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-
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- | Sequence | Google Colab |
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- | -------- | ------------ |
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- | [Free Induction Decay](FID_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_FID_seq.ipynb">mr0_FID_seq.ipynb</a> |
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- | [Spin Echo CPMG](SE_CPMG_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb">mr0_SE_CPMG_seq.ipynb</a> |
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- | [Stimulated Echo 3 pulses - 5 echoes](STE_3pulses_5echoes_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb">mr0_STE_3pulses_5echoes_seq.ipynb</a> |
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- | [FLASH 2D sequence](FLASH_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb">mr0_FLASH_2D_seq.ipynb</a> |
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- | [EPI 2D sequence](EPI_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb">mr0_EPI_2D_seq.ipynb</a> |
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- | [RARE 2D sequence](RARE_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb">mr0_RARE_2D_seq.ipynb</a> |
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- | [bSSFP 2D sequence](bSSFP_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb">mr0_bSSFP_2D_seq.ipynb</a> |
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- | [Diffusion weighted Gradient Echo](DWI_GRE_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_DWI_GRE_2D_seq.ipynb">mr0_DWI_GRE_2D_seq.ipynb</a> |
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- | [Interactive GRE to FLASH](GRE2FLASH_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb">mr0_GRE_to_FLASH.ipynb</a> |
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- | [DREAM STE for B0, B1, TxRx mapping](DREAM_STE_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb">mr0_DREAM_STE_seq.ipynb</a> |
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- | [DREAM STID for B0, B1, TxRx mapping](DREAM_STID_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb">mr0_DREAM_STID_seq.ipynb</a> |
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- | [Burst TSE](burst_TSE_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_burst_TSE.ipynb">mr0_burst_TSE.ipynb</a> |
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- | [Compressed Sensing cartesian](mr0_CS_cartesian_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_CS_cartesian_seq.ipynb">mr0_CS_cartesian_seq.ipynb</a> |
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- | [Compressed Sensing radial](mr0_CS_radial_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_CS_radial_seq.ipynb">mr0_CS_radial_seq.ipynb</a> |
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- | [Pulseq with RF shimming](pulseq_ptx) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/pulseq_rf_shim.ipynb">pulseq_rf_shim.ipynb</a> |
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- ## Plot and simulate predifined .seq files
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- | Sequence | Google Colab |
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- | -------- | ------------ |
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- | [Simulate pypulseq example sequences](mr0_pypulseq_example) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_pypulseq_exmpls_seq.ipynb">mr0_pypulseq_exmpls_seq.ipynb</a> |
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- | [Simulate own uploaded seq files](mr0_upload_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_upload_seq.ipynb">mr0_upload_seq.ipynb</a> |
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- ## MR-zero optimization
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- Gradient descent optimizations using automatic differentiation by backpropagation
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- | Sequence | Google Colab |
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- | -------- | ------------ |
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- | [IR FLASH 2D sequence for T1 mapping using a fit](IR_FLASH_fit) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_opt_FLASH_2D_IR_Fit_T1.ipynb">mr0_opt_FLASH_2D_IR_Fit_T1.ipynb</a> |
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- | [IR FLASH 2D sequence for T1 mapping using a NN](IR_FLASH_NN) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_opt_FLASH_2D_IR_voxelNN_T1.ipynb">mr0_opt_FLASH_2D_IR_voxelNN_T1.ipynb</a> |
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- ## MR-double-zero optimization
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- Gradient-free optimization with [nevergrad](https://github.com/facebookresearch/nevergrad)
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- | Sequence | Google Colab |
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- | -------- | ------------ |
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- | [Ernst angle optimization](mr00_FLASH_2D_ernstAngle_opt) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr00_FLASH_2D_ernstAngle_opt.ipynb">mr00_FLASH_2D_ernstAngle_opt.ipynb</a> |
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- ## MR plot wall of fame
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- famous historic plots recreated
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- ## FLASH (temporary notebooks)
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- | Sequence | Google Colab |
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- | -------- | ------------ |
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- | [Pure `MR0` FLASH](flash) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/examples/flash.ipynb">flash.ipynb</a> |
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- | [pulseq FLASH](pulseq_flash) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/examples/pulseq_flash.ipynb">pulseq_flash.ipynb</a> |
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- | [pulseq pTx FLASH](pulseq_pTx) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/examples/pulseq_sim_pTx.ipynb">pulseq_sim_pTx.ipynb</a> |
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- ## Notebook execution results
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- ::::{toggle}
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- :::{nb-exec-table}
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- :::
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- ::::
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+ (playground_mr0)=
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+ # Playground MR0
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+
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+ Welcome to Playground MR0, a playground to share, vary and simulate MR sequences.
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+ MR sequences are written in the Pulseq standard using the pypulseq library.
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+ Pulseq files are simulated with the efficient Phase Distribution Graph Bloch simulation.
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+ Here we share links to example colabs that contain various MR sequences or let you upload your own seq file for simulation.
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+
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+ Many of the examples are build using [PyPulseq](https://github.com/imr-framework/pypulseq) and simulate the resulting .seq files with `MR0`.
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+ These .seq files could also be measured on any MRI scanner using a Pulseq interpreter.
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+
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+
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+ ## Code and simulate PyPulseq
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+
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+ | Sequence | Google Colab |
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+ | -------- | ------------ |
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+ | [Free Induction Decay](FID_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_FID_seq.ipynb">mr0_FID_seq.ipynb</a> |
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+ | [Spin Echo CPMG](SE_CPMG_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb">mr0_SE_CPMG_seq.ipynb</a> |
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+ | [Stimulated Echo 3 pulses - 5 echoes](STE_3pulses_5echoes_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb">mr0_STE_3pulses_5echoes_seq.ipynb</a> |
20
+ | [FLASH 2D sequence](FLASH_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb">mr0_FLASH_2D_seq.ipynb</a> |
21
+ | [EPI 2D sequence](EPI_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb">mr0_EPI_2D_seq.ipynb</a> |
22
+ | [RARE 2D sequence](RARE_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb">mr0_RARE_2D_seq.ipynb</a> |
23
+ | [bSSFP 2D sequence](bSSFP_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb">mr0_bSSFP_2D_seq.ipynb</a> |
24
+ | [Diffusion weighted Gradient Echo](DWI_GRE_2D_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_DWI_GRE_2D_seq.ipynb">mr0_DWI_GRE_2D_seq.ipynb</a> |
25
+ | [Interactive GRE to FLASH](GRE2FLASH_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb">mr0_GRE_to_FLASH.ipynb</a> |
26
+ | [DREAM STE for B0, B1, TxRx mapping](DREAM_STE_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb">mr0_DREAM_STE_seq.ipynb</a> |
27
+ | [DREAM STID for B0, B1, TxRx mapping](DREAM_STID_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb">mr0_DREAM_STID_seq.ipynb</a> |
28
+ | [Burst TSE](burst_TSE_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_burst_TSE.ipynb">mr0_burst_TSE.ipynb</a> |
29
+ | [Compressed Sensing cartesian](mr0_CS_cartesian_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_CS_cartesian_seq.ipynb">mr0_CS_cartesian_seq.ipynb</a> |
30
+ | [Compressed Sensing radial](mr0_CS_radial_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_CS_radial_seq.ipynb">mr0_CS_radial_seq.ipynb</a> |
31
+ | [Pulseq with RF shimming](pulseq_ptx) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/pulseq_rf_shim.ipynb">pulseq_rf_shim.ipynb</a> |
32
+
33
+ ## Plot and simulate predifined .seq files
34
+
35
+ | Sequence | Google Colab |
36
+ | -------- | ------------ |
37
+ | [Simulate pypulseq example sequences](mr0_pypulseq_example) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_pypulseq_exmpls_seq.ipynb">mr0_pypulseq_exmpls_seq.ipynb</a> |
38
+ | [Simulate own uploaded seq files](mr0_upload_seq) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_upload_seq.ipynb">mr0_upload_seq.ipynb</a> |
39
+
40
+
41
+ ## MR-zero optimization
42
+
43
+ Gradient descent optimizations using automatic differentiation by backpropagation
44
+
45
+ | Sequence | Google Colab |
46
+ | -------- | ------------ |
47
+ | [IR FLASH 2D sequence for T1 mapping using a fit](IR_FLASH_fit) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_opt_FLASH_2D_IR_Fit_T1.ipynb">mr0_opt_FLASH_2D_IR_Fit_T1.ipynb</a> |
48
+ | [IR FLASH 2D sequence for T1 mapping using a NN](IR_FLASH_NN) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr0_opt_FLASH_2D_IR_voxelNN_T1.ipynb">mr0_opt_FLASH_2D_IR_voxelNN_T1.ipynb</a> |
49
+
50
+
51
+ ## MR-double-zero optimization
52
+
53
+ Gradient-free optimization with [nevergrad](https://github.com/facebookresearch/nevergrad)
54
+
55
+ | Sequence | Google Colab |
56
+ | -------- | ------------ |
57
+ | [Ernst angle optimization](mr00_FLASH_2D_ernstAngle_opt) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/mr00_FLASH_2D_ernstAngle_opt.ipynb">mr00_FLASH_2D_ernstAngle_opt.ipynb</a> |
58
+
59
+
60
+ ## MR plot wall of fame
61
+
62
+ famous historic plots recreated
63
+
64
+
65
+ ## FLASH (pure MR0 example notebooks)
66
+
67
+ | Sequence | Google Colab |
68
+ | -------- | ------------ |
69
+ | [Pure `MR0` FLASH](flash) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/flash.ipynb">flash.ipynb</a> |
70
+ | [pulseq FLASH](pulseq_flash) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/pulseq_flash.ipynb">pulseq_flash.ipynb</a> |
71
+ | [pulseq pTx FLASH](pulseq_pTx) | <a target="_blank" href="https://colab.research.google.com/github/MRsources/MRzero-Core/blob/main/documentation/playground_mr0/pulseq_sim_pTx.ipynb">pulseq_sim_pTx.ipynb</a> |
72
+
73
+
74
+ ## Notebook execution results
75
+
76
+ ::::{toggle}
77
+
78
+ :::{nb-exec-table}
79
+ :::
80
+
81
+ ::::
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/python/MRzeroCore/phantom/brainweb/__init__.py RENAMED
@@ -4,7 +4,7 @@ import gzip
4
4
  import requests
5
5
  import os
6
6
  import numpy as np
7
- from perlin_numpy import generate_perlin_noise_3d
7
+ # from perlin_numpy import generate_perlin_noise_3d
8
8
 
9
9
 
10
10
  # Load the brainweb data file that contains info about tissues, subjects, ...
@@ -54,7 +54,8 @@ def gen_noise(range: float, res: np.ndarray) -> np.ndarray:
54
54
  else:
55
55
  freq = 20
56
56
  padded_res = (res + freq - 1) // freq * freq
57
- noise = generate_perlin_noise_3d(padded_res, (freq, freq, freq))
57
+ # noise = generate_perlin_noise_3d(padded_res, (freq, freq, freq))
58
+ noise = np.random.random(padded_res)
58
59
  return 1 + range * noise[:res[0], :res[1], :res[2]]
59
60
 
60
61
 
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/.gitignore RENAMED
File without changes
{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/.readthedocs.yaml RENAMED
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{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/EULA.txt RENAMED
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{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/LICENSE RENAMED
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{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/README.md RENAMED
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{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/pyproject.toml RENAMED
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{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/src/lib.rs RENAMED
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{MRzeroCore-0.2.6 → MRzeroCore-0.2.7}/src/pre_pass.rs RENAMED
File without changes