Move scaling to KTrajectory

src/mrpro/data/KTrajectory.py

@@ -1,13 +1,15 @@
 """KTrajectory dataclass."""
 
 from dataclasses import dataclass
+from typing import Literal
 
 import numpy as np
 import torch
 from typing_extensions import Self
 
 from mrpro.data.enums import TrajType
 from mrpro.data.MoveDataMixin import MoveDataMixin
+from mrpro.data.SpatialDimension import SpatialDimension
 from mrpro.utils import remove_repeat
 from mrpro.utils.summarize_tensorvalues import summarize_tensorvalues
 
@@ -69,8 +71,10 @@ def from_tensor(
         cls,
         tensor: torch.Tensor,
         stack_dim: int = 0,
-        repeat_detection_tolerance: float | None = 1e-8,
+        axes_order: Literal['zxy', 'zyx', 'yxz', 'yzx', 'xyz', 'xzy'] = 'zyx',
+        repeat_detection_tolerance: float | None = 1e-6,
         grid_detection_tolerance: float = 1e-3,
+        encoding_matrix: SpatialDimension | None = None,
     ) -> Self:
         """Create a KTrajectory from a tensor representation of the trajectory.
 
@@ -85,13 +89,33 @@ def from_tensor(
             This should be a 5-dim tensor, with (kz,ky,kx) stacked in this order along stack_dim
         stack_dim
             The dimension in the tensor the directions have been stacked along.
+        axes_order
+            Order of the axes in the tensor. Our convention usually is zyx order.
         repeat_detection_tolerance
             detects if broadcasting can be used, i.e. if dimensions are repeated.
             Set to None to disable.
         grid_detection_tolerance
             tolerance to detect if trajectory points are on integer grid positions
+        encoding_matrix
+            if an encoding matrix is supplied, the trajectory is rescaled to fit
+            within the matrix. Otherwise, it is left as-is.
         """
-        kz, ky, kx = torch.unbind(tensor, dim=stack_dim)
+        ks = tensor.unbind(dim=stack_dim)
+        kz, ky, kx = (ks[axes_order.index(axis)] for axis in 'zyx')
+
+        def normalize(k: torch.Tensor, encoding_size: int) -> torch.Tensor:
+            max_abs_range = 2 * k.abs().max()
+            if encoding_size == 1 or max_abs_range < 1e-6:
+                # a single encoding point should be at zero
+                # avoid division by zero
+                return torch.zeros_like(k)
+            return k * (encoding_size / max_abs_range)
+
+        if encoding_matrix is not None:
+            kz = normalize(kz, encoding_matrix.z)
+            ky = normalize(ky, encoding_matrix.y)
+            kx = normalize(kx, encoding_matrix.x)
+
         return cls(
             kz,
             ky,

src/mrpro/data/KTrajectoryRawShape.py

@@ -1,13 +1,16 @@
 """KTrajectoryRawShape dataclass."""
 
 from dataclasses import dataclass
+from typing import Literal
 
 import numpy as np
 import torch
 from einops import rearrange
+from typing_extensions import Self
 
 from mrpro.data.KTrajectory import KTrajectory
 from mrpro.data.MoveDataMixin import MoveDataMixin
+from mrpro.data.SpatialDimension import SpatialDimension
 
 
 @dataclass(slots=True, frozen=True)
@@ -32,6 +35,56 @@ class KTrajectoryRawShape(MoveDataMixin):
     repeat_detection_tolerance: None | float = 1e-3
     """tolerance for repeat detection. Set to None to disable."""
 
+    @classmethod
+    def from_tensor(
+        cls,
+        tensor: torch.Tensor,
+        stack_dim: int = 0,
+        axes_order: Literal['zxy', 'zyx', 'yxz', 'yzx', 'xyz', 'xzy'] = 'zyx',
+        repeat_detection_tolerance: float | None = 1e-6,
+        encoding_matrix: SpatialDimension | None = None,
+    ) -> Self:
+        """Create a KTrajectoryRawShape from a tensor representation of the trajectory.
+
+        Parameters
+        ----------
+        tensor
+            The tensor representation of the trajectory.
+            This should be a 5-dim tensor, with (kz,ky,kx) stacked in this order along stack_dim
+        stack_dim
+            The dimension in the tensor the directions have been stacked along.
+        axes_order
+            Order of the axes in the tensor. Our convention usually is zyx order.
+        repeat_detection_tolerance
+            detects if broadcasting can be used, i.e. if dimensions are repeated.
+            Set to None to disable.
+        encoding_matrix
+            if an encoding matrix is supplied, the trajectory is rescaled to fit
+            within the matrix. Otherwise, it is left as-is.
+        """
+        ks = tensor.unbind(dim=stack_dim)
+        kz, ky, kx = (ks[axes_order.index(axis)] for axis in 'zyx')
+
+        def normalize(k: torch.Tensor, encoding_size: int) -> torch.Tensor:
+            max_abs_range = 2 * k.abs().max()
+            if encoding_size == 1 or max_abs_range < 1e-6:
+                # a single encoding point should be at zero
+                # avoid division by zero
+                return torch.zeros_like(k)
+            return k * (encoding_size / max_abs_range)
+
+        if encoding_matrix is not None:
+            kz = normalize(kz, encoding_matrix.z)
+            ky = normalize(ky, encoding_matrix.y)
+            kx = normalize(kx, encoding_matrix.x)
+
+        return cls(
+            kz,
+            ky,
+            kx,
+            repeat_detection_tolerance=repeat_detection_tolerance,
+        )
+
     def sort_and_reshape(
         self,
         sort_idx: np.ndarray,

src/mrpro/data/traj_calculators/KTrajectoryPulseq.py

@@ -2,7 +2,6 @@
 
 from pathlib import Path
 
-import pypulseq as pp
 import torch
 from einops import rearrange
 
@@ -40,8 +39,10 @@ def __call__(self, kheader: KHeader) -> KTrajectoryRawShape:
         -------
             trajectory of type KTrajectoryRawShape
         """
+        from pypulseq import Sequence
+
         # create PyPulseq Sequence object and read .seq file
-        seq = pp.Sequence()
+        seq = Sequence()
         seq.read(file_path=str(self.seq_path))
 
         # calculate k-space trajectory using PyPulseq
@@ -52,20 +53,11 @@ def __call__(self, kheader: KHeader) -> KTrajectoryRawShape:
         n_samples = torch.unique(n_samples)
         if len(n_samples) > 1:
             raise ValueError('We currently only support constant number of samples')
-        n_k0 = int(n_samples.item())
-
-        def rescale_and_reshape_traj(k_traj: torch.Tensor, encoding_size: int):
-            if encoding_size > 1 and torch.max(torch.abs(k_traj)) > 0:
-                k_traj = k_traj * encoding_size / (2 * torch.max(torch.abs(k_traj)))
-            else:
-                # We force k_traj to be 0 if encoding_size = 1. This is typically the case for kz in 2D sequences.
-                # However, it happens that seq.calculate_kspace() returns values != 0 (numerical noise) in such cases.
-                k_traj = torch.zeros_like(k_traj)
-            return rearrange(k_traj, '(other k0) -> other k0', k0=n_k0)
-
-        # rearrange k-space trajectory to match MRpro convention
-        kx = rescale_and_reshape_traj(k_traj_adc[0], kheader.encoding_matrix.x)
-        ky = rescale_and_reshape_traj(k_traj_adc[1], kheader.encoding_matrix.y)
-        kz = rescale_and_reshape_traj(k_traj_adc[2], kheader.encoding_matrix.z)
 
-        return KTrajectoryRawShape(kz, ky, kx, self.repeat_detection_tolerance)
+        k_traj_reshaped = rearrange(k_traj_adc, 'xyz (other k0) -> xyz other k0', k0=int(n_samples.item()))
+        return KTrajectoryRawShape.from_tensor(
+            k_traj_reshaped,
+            axes_order='xyz',
+            encoding_matrix=kheader.encoding_matrix,
+            repeat_detection_tolerance=self.repeat_detection_tolerance,
+        )

tests/data/_PulseqRadialTestSeq.py

@@ -29,7 +29,9 @@ def __init__(self, seq_filename: str, n_x=256, n_spokes=10):
 
         system = pypulseq.Opts()
         rf, gz, _ = pypulseq.make_sinc_pulse(flip_angle=0.1, slice_thickness=1e-3, system=system, return_gz=True)
-        gx = pypulseq.make_trapezoid(channel='x', flat_area=n_x * delta_k, flat_time=2e-3, system=system)
+        gx = pypulseq.make_trapezoid(
+            channel='x', flat_area=n_x * delta_k, flat_time=n_x * system.grad_raster_time, system=system
+        )
         adc = pypulseq.make_adc(num_samples=n_x, duration=gx.flat_time, delay=gx.rise_time, system=system)
         gx_pre = pypulseq.make_trapezoid(channel='x', area=-gx.area / 2 - delta_k / 2, duration=2e-3, system=system)
         gz_reph = pypulseq.make_trapezoid(channel='z', area=-gz.area / 2, duration=2e-3, system=system)

tests/data/test_traj_calculators.py

@@ -260,11 +260,11 @@ def test_KTrajectoryPulseq_validseq_random_header(pulseq_example_rad_seq, valid_
     trajectory_calculator = KTrajectoryPulseq(seq_path=pulseq_example_rad_seq.seq_filename)
     trajectory = trajectory_calculator(kheader=valid_rad2d_kheader)
 
-    kx_test = pulseq_example_rad_seq.traj_analytical.kx.squeeze(0).squeeze(0)
-    kx_test *= valid_rad2d_kheader.encoding_matrix.x / (2 * torch.max(torch.abs(kx_test)))
+    kx_test = pulseq_example_rad_seq.traj_analytical.kx.squeeze()
+    kx_test = kx_test * valid_rad2d_kheader.encoding_matrix.x / (2 * kx_test.abs().max())
 
-    ky_test = pulseq_example_rad_seq.traj_analytical.ky.squeeze(0).squeeze(0)
-    ky_test *= valid_rad2d_kheader.encoding_matrix.y / (2 * torch.max(torch.abs(ky_test)))
+    ky_test = pulseq_example_rad_seq.traj_analytical.ky.squeeze()
+    ky_test = ky_test * valid_rad2d_kheader.encoding_matrix.y / (2 * ky_test.abs().max())
 
     torch.testing.assert_close(trajectory.kx.to(torch.float32), kx_test.to(torch.float32), atol=1e-2, rtol=1e-3)
     torch.testing.assert_close(trajectory.ky.to(torch.float32), ky_test.to(torch.float32), atol=1e-2, rtol=1e-3)