feat: add pypulseq reader

Author: paquiteau

pyproject.toml

@@ -27,7 +27,7 @@ pynufft = ["pynufft"]
 pynufft-cpu = ["pynufft"]
 pynufft-gpu = ["pynufft"]
 
-io = ["pymapvbvd"]
+io = ["pymapvbvd", "pypulseq"]
 smaps = ["scikit-image"]
 extra = ["pymapvbvd", "scikit-image", "scikit-learn", "pywavelets"]
 autodiff = ["torch"]

src/mrinufft/io/pulseq.py

@@ -0,0 +1,41 @@
+"""Pulseq Trajectory Reader and writers.
+
+Reads Pulseq `.seq` files to extract k-space trajectory and other parameters. It also provides functionality to create pulseq block and shape objects to
+facilitate the integration of arbitrary k-space trajectories into Pulseq
+sequences. Requires the `pypulseq` package to be installed.
+"""
+
+import numpy as np
+import pypulseq as pp
+
+
+def read_pulseq_traj(filename):
+    """Extract k-space trajectory from a Pulseq sequence file.
+
+    The sequence should be a valid Pulseq `.seq` file, with arbitrary gradient
+    waveforms, which all have the same length.
+
+    Unlike `Sequence.calculate_kspace`, this function returns the k-space
+    trajectory segmented in shots ("blocks" from Pulseq), and works directly
+    from the gradients waveforms stored in the `.seq` file.
+
+    Parameters
+    ----------
+    filename : str
+        Path to the Pulseq `.seq` file.
+
+    Returns
+    -------
+    description : dict
+        the [DESCRIPTION] block from the sequence file.
+    np.ndarray
+        The k-space trajectory as a numpy array of shape (n_shots, n_samples, 3),
+        where the last dimension corresponds to the x, y, and z coordinates in k-space.
+
+    """
+
+    seq = pp.Sequence()
+    seq.read(filename)
+
+
+    gradient_waveforms = seq.waveforms()