mrzerocore 0.3.2__cp37-abi3-win_amd64.whl → 0.4.2__cp37-abi3-win_amd64.whl

{MRzeroCore-0.3.2.dist-info → mrzerocore-0.4.2.dist-info}/METADATA

@@ -1,28 +1,32 @@
-Metadata-Version: 2.3
-Name: MRzeroCore
-Version: 0.3.2
+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-0.4.2.dist-info/RECORD

@@ -0,0 +1,5 @@
+mrzerocore\_prepass.pyd,sha256=UOjZB6opacbWy2UamRQ9dWFmo8R9SBVReCuUN_knEss,401408
+mrzerocore-0.4.2.dist-info\METADATA,sha256=t_KUGUHRYRiEfLDikcp_SEcaAmciBFIQ72PYwHKjHws,5049
+mrzerocore-0.4.2.dist-info\WHEEL,sha256=wIaq5kKGufyzCzRkK9cVMZbLF09Wr1z6BXtkxRsuBGs,95
+mrzerocore-0.4.2.dist-info\licenses\LICENSE,sha256=rd_IFJ484uAluv8CigP2CpXg4l2GJLLKENqB6-RXPp4,35112
+mrzerocore-0.4.2.dist-info\RECORD,,

{MRzeroCore-0.3.2.dist-info → mrzerocore-0.4.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: maturin (1.7.1)
+Generator: maturin (1.11.5)
 Root-Is-Purelib: false
 Tag: cp37-abi3-win_amd64

MRzeroCore/__init__.py

@@ -1,19 +0,0 @@
-import numpy
-if not hasattr(numpy, "int"):
-    numpy.int = int
-if not hasattr(numpy, "float"):
-    numpy.float = float
-if not hasattr(numpy, "complex"):
-    numpy.complex = complex
-
-from .sequence import PulseUsage, Pulse, Repetition, Sequence, chain
-from .phantom.voxel_grid_phantom import VoxelGridPhantom
-from .phantom.custom_voxel_phantom import CustomVoxelPhantom
-from .phantom.sim_data import SimData
-from .phantom.brainweb import generate_brainweb_phantoms
-from .simulation.isochromat_sim import isochromat_sim
-from .simulation.pre_pass import compute_graph, compute_graph_ext, Graph
-from .simulation.main_pass import execute_graph
-from .reconstruction import reco_adjoint
-from .pulseq.exporter import pulseq_write_cartesian
-from . import util

MRzeroCore/phantom/brainweb/__init__.py

@@ -1,171 +0,0 @@
-from typing import Literal
-import json
-import gzip
-import requests
-import os
-import numpy as np
-
-
-# Load the brainweb data file that contains info about tissues, subjects, ...
-brainweb_data_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
-                                  "brainweb_data.json")
-brainweb_data = json.load(open(brainweb_data_path))
-
-
-def load_tissue(subject: int, alias: str, cache_dir: str) -> np.ndarray:
-    download_alias = f"subject{subject:02d}_{alias}"
-    file_name = download_alias + ".i8.gz"  # 8 bit signed int, gnuzip
-    file_path = os.path.join(cache_dir, file_name)
-
-    # Download and cache file if it doesn't exist yet
-    if not os.path.exists(file_path):
-        print(f"Downloading '{download_alias}'", end="", flush=True)
-        response = requests.post(
-            "https://brainweb.bic.mni.mcgill.ca/cgi/brainweb1",
-            data={
-                "do_download_alias": download_alias,
-                "format_value": "raw_byte",
-                "zip_value": "gnuzip"
-            }
-        )
-        with open(file_path, "wb") as f:
-            f.write(response.content)
-        print(" - ", end="")
-
-    # Load the raw BrainWeb data and add it to the return array
-    with gzip.open(file_path) as f:
-        print(f"Loading {os.path.basename(file_path)}", end="", flush=True)
-        # BrainWeb says this data is unsigned, which is a lie
-        tmp = np.frombuffer(f.read(), np.uint8) + 128
-
-    # Vessel bugfix: most of background is 1 instead of zero
-    if alias == "ves":
-        tmp[tmp == 1] = 0
-    data = tmp.reshape(362, 434, 362).swapaxes(0, 2).astype(np.float32)
-
-    print(" - done")
-    return data / 255.0
-
-
-def gen_noise(range: float, res: np.ndarray) -> np.ndarray:
-    if range == 0:
-        return 1
-    else:
-        freq = 20
-        padded_res = (res + freq - 1) // freq * freq
-        try:
-            from perlin_numpy import generate_perlin_noise_3d
-            noise = generate_perlin_noise_3d(padded_res, (freq, freq, freq))
-        except:
-            print("perlin_numpy@git+https://github.com/pvigier/perlin-numpy")
-            print("is not installed, falling back to numpy.random.random()")
-            noise = np.random.random(padded_res)
-        return 1 + range * noise[:res[0], :res[1], :res[2]]
-
-
-def downsample(array: np.ndarray, factor: int) -> np.ndarray:
-    # crop array to multiple of factor
-    shape = (np.array(array.shape) // factor) * factor
-    array = array[:shape[0], :shape[1], :shape[2]]
-
-    tmp = np.zeros(shape // factor)
-    for x in range(factor):
-        for y in range(factor):
-            for z in range(factor):
-                tmp += array[x::factor, y::factor, z::factor]
-
-    return tmp / factor**3
-
-
-def generate_brainweb_phantoms(
-        output_dir: str,
-        config: Literal["3T", "7T-noise", "3T-highres-fat"] = "3T"):
-    """Generate BrainWeb phantom maps for the selected configuration.
-
-    Raw tissue segmentation data is provided by the BrainWeb Database:
-    http://www.bic.mni.mcgill.ca/brainweb/
-
-    All tissue data etc. are stored in [brainweb_data.json](https://github.com/MRsources/MRzero-Core/blob/main/python/MRzeroCore/phantom/brainweb/brainweb_data.json).
-    To ensure consistent configurations and reproducible results, available
-    configs are stored in this file as well. They specify which field strength
-    to use, which tissues to include, and the downsampling and noise levels.
-
-    The emitted files are compressed numpy files, which can be loaded with
-    ``np.load(file_name)``. They contain the following arrays:
-
-     - `PD_map`: Proton Density [a.u.]
-     - `T1_map`: T1 relaxation time [s]
-     - `T2_map`: T2 relaxation time [s]
-     - `T2dash_map`: T2' relaxation time [s]
-     - `D_map`: Isotropic Diffusion coefficient [10^-3 mm² / s]
-     - `tissue_XY`: Tissue segmentation for all included tissues
-
-    Parameters
-    ----------
-    output_dir: str
-        The directory where the generated phantoms will be stored to. In
-        addition, a `cache` folder will be generated there too, which contains
-        all the data downloaded from BrainWeb to avoid repeating the download
-        for all configurations or when generating phantoms again.
-    config: ["3T", "7T-noise", "3T-highres-fat"]
-        The configuration for which the maps are generated.
-    """
-    config_data = brainweb_data["configs"][config]
-    cache_dir = os.path.join(output_dir, "cache")
-
-    try:
-        os.makedirs(cache_dir)
-    except FileExistsError:
-        pass
-
-    # Map resolution:
-    res = np.array([362, 434, 362]) // config_data["downsample"]
-
-    def noise() -> np.ndarray:
-        return gen_noise(config_data["noise"], res)
-
-    for subject in brainweb_data["subjects"]:
-        print(f"Generating '{config}', subject {subject}")
-        maps = {
-            "FOV": np.array([0.181, 0.217, 0.181]),
-            "PD_map": np.zeros(res, dtype=np.float32),
-            "T1_map": np.zeros(res, dtype=np.float32),
-            "T2_map": np.zeros(res, dtype=np.float32),
-            "T2dash_map": np.zeros(res, dtype=np.float32),
-            "D_map": np.zeros(res, dtype=np.float32),
-        }
-
-        for tissue in config_data["tissues"]:
-            tissue_map = sum([
-                load_tissue(subject, alias, cache_dir)
-                for alias in brainweb_data["download-aliases"][tissue]
-            ])
-            tissue_map = downsample(tissue_map, config_data["downsample"])
-            maps["tissue_" + tissue] = tissue_map
-
-            field_strength = config_data["field-strength"]
-            tissue_data = brainweb_data["tissues"][field_strength][tissue]
-
-            # Separate noise maps is slower but uncorrelated.
-            # Might be better for training or worse - could be configurable
-            print("Adding tissue to phantom", end="", flush=True)
-            maps["PD_map"] += tissue_data["PD"] * tissue_map * noise()
-            maps["T1_map"] += tissue_data["T1"] * tissue_map * noise()
-            maps["T2_map"] += tissue_data["T2"] * tissue_map * noise()
-            maps["T2dash_map"] += tissue_data["T2'"] * tissue_map * noise()
-            maps["D_map"] += tissue_data["D"] * tissue_map * noise()
-            print(" - done")
-
-        file = os.path.join(output_dir, f"subject{subject:02d}_{config}.npz")
-        print(f"Saving to '{os.path.basename(file)}'", end="", flush=True)
-        np.savez_compressed(file, **maps)
-        print(" - done\n")
-
-
-if __name__ == "__main__":
-    print("This is for testing only, use generate_brainweb_phantoms directly!")
-    file_dir = os.path.dirname(os.path.realpath(__file__))
-    output_dir = os.path.join(file_dir, "output")
-
-    for config in brainweb_data["configs"].keys():
-        generate_brainweb_phantoms(output_dir, config)

MRzeroCore/phantom/brainweb/brainweb_data.json

@@ -1,93 +0,0 @@
-{
-  "configs": {
-    "3T": {
-      "field-strength": "3T",
-      "tissues": ["gm", "wm", "csf"],
-      "downsample": 3,
-      "noise": 0
-    },
-    "7T-noise": {
-      "field-strength": "7T",
-      "tissues": ["gm", "wm", "csf"],
-      "downsample": 3,
-      "noise": 0.2
-    },
-    "3T-highres-fat": {
-      "field-strength": "3T",
-      "tissues": ["gm", "wm", "csf", "fat"],
-      "downsample": 1,
-      "noise": 0
-    }
-  },
-  "subjects": [
-    4, 5, 6, 18, 20, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54
-  ],
-  "download-aliases": {
-    "gm": ["gry"],
-    "wm": ["wht"],
-    "csf": ["csf", "ves"],
-    "fat": ["fat", "mus", "m-s", "dura", "fat2"]
-  },
-  "tissues": {
-    "3T": {
-      "gm": {
-        "PD": 0.8,
-        "T1": 1.56,
-        "T2": 0.083,
-        "T2'": 0.32,
-        "D": 0.83
-      },
-      "wm": {
-        "PD": 0.7,
-        "T1": 0.83,
-        "T2": 0.075,
-        "T2'": 0.18,
-        "D": 0.65
-      },
-      "csf": {
-        "PD": 1,
-        "T1": 4.16,
-        "T2": 1.65,
-        "T2'": 0.059,
-        "D": 3.19
-      },
-      "fat": {
-        "PD": 1,
-        "T1": 0.37,
-        "T2": 0.125,
-        "T2'": 0.012,
-        "D": 0.1
-      }
-    },
-    "7T": {
-      "gm": {
-        "PD": 0.8,
-        "T1": 1.67,
-        "T2": 0.043,
-        "T2'": 0.82,
-        "D": 0.83
-      },
-      "wm": {
-        "PD": 0.7,
-        "T1": 1.22,
-        "T2": 0.037,
-        "T2'": 0.65,
-        "D": 0.65
-      },
-      "csf": {
-        "PD": 1,
-        "T1": 4.0,
-        "T2": 0.8,
-        "T2'": 0.204,
-        "D": 3.19
-      },
-      "fat": {
-        "PD": 1,
-        "T1": 0.374,
-        "T2": 0.125,
-        "T2'": 0.0117,
-        "D": 0.1
-      }
-    }
-  }
-}

MRzeroCore/phantom/brainweb/brainweb_data_sources.txt

@@ -1,74 +0,0 @@
-! NOTE
-7T maps are not checked as thrououghly. Only source so far:
-https://cds.ismrm.org/protected/14MProceedings/PDFfiles/3208.pdf
-
-
-# T1 and T2 times, taken from:
-# https://mri-q.com/uploads/3/4/5/7/34572113/normal_relaxation_times_at_3t.pdf
-# Value taken from paper with most participants (draw: closest to mean of all)
-# Studies that are outliers are ignored (WM T2 time)
-
-# T2' calculated from T2 and T2*, taken from:
-# https://www.sciencedirect.com/science/article/pii/S0730725X07001701?via%3Dihub
-
-# Water / Fat T2': https://link.springer.com/article/10.1007/s00723-015-0737-5 (4.7 T)
-
-# Errors are uncertenties of studies, not data on variation in one measurement
-
-Brainweb Tissues:
- - CSF
-   T1: 4163 ± 263
-	T2: 1650 (approx, taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973950/)
-	T2*: 57.1 -> T2': 59.1
-
- - Gray Matter
-   T1: 1558 ± 88
-	T2: 83 ± 4
-   T2*: 66.0 ± 1.4 -> T2': 322
-
- - White Matter
-   T1: 830 ± 0
-	T2: 75 ± 3
-   T2*: 53.2 ± 1.2 -> T2': 183
-	T2': 56 ± 1
-
- - Fat
-   T1: 374 ± 45
-	T2: 125
-	T2* = 10.7 -> T2': 11.7
-
-# The following values are not used for phantom generation
-
- - Muscle
-   T1: 1100 ± 59
-	T2: 40
-
- - Muscle/Skin
-
- - Skull
-    Probably similar to Bone marrow, but they don't overlap in the images
-
- - Blood vessels
-    Probably similar to CSF (mostly water)
-
- - Connective (region around fat)
-    Overlaps nearly fully with Fat
-
- - Dura matter
-    Very little volume, probably not noticable at lower resolutions
-
- - Bone marrow
-    T1: 586 ± 73
-	T2: 127
-
-
-Diffusion:
-Values taken from https://onlinelibrary.wiley.com/doi/10.1002/jmri.1076
-10^-3 mm² / s
-CSF: 3.19 ± 0.10
-WM:  0.65 ± 0.03
-GM:  0.83 ± 0.05
-
-No great source for fat, https://onlinelibrary.wiley.com/doi/10.1002/mrm.24535
-says it barely diffuses
-FAT: ~0.1