diff --git a/cmrsim/analytic/encoding/_from_sequence.py b/cmrsim/analytic/encoding/_from_sequence.py
index f3679999f3be1d78721c323e73bbdbb1d0983aca..c66df44426805aa180d1182a187e2891958cee38 100644
--- a/cmrsim/analytic/encoding/_from_sequence.py
+++ b/cmrsim/analytic/encoding/_from_sequence.py
@@ -81,12 +81,13 @@ class GenericEncoding(BaseSampling):
_, k_adc, t_adc = seq.calculate_kspace()
k_space.append(k_adc.T)
timings.append(t_adc)
-
- # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
- k_space = tf.cast(tf.concat(k_space, axis=0), tf.float32)
- # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
- timings = tf.cast(tf.concat(timings, axis=0), tf.float32)
- return cls(name, k_space, timings, absolute_noise_std, k_space_segments, device)
+ k_space = np.concatenate(k_space, axis=0, dtype=np.float32)
+ timings = np.concatenate(timings, axis=0, dtype=np.float32)
+ # # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
+ # k_space = tf.cast(tf.concat(k_space, axis=0), tf.float32)
+ # # pylint: disable=no-value-for-parameter, unexpected-keyword-arg
+ # timings = tf.cast(tf.concat(timings, axis=0), tf.float32)
+ return cls(name, [k_space, ], [timings, ], absolute_noise_std, k_space_segments, device)
def from_pulseq(self):
raise NotImplementedError("Pulseq interface not yet implemented")
\ No newline at end of file
diff --git a/cmrsim/datasets/_cardiac_mesh.py b/cmrsim/datasets/_cardiac_mesh.py
index 8cae45e42f9ce42f83e41b032d2a4d47cc09ea35..5721fdf9387d32ff3715442ee00da7e3ff9208a0 100644
--- a/cmrsim/datasets/_cardiac_mesh.py
+++ b/cmrsim/datasets/_cardiac_mesh.py
@@ -56,7 +56,7 @@ class MeshDataset:
# pylint: disable=E1101
deformation_mesh = pyvista.UnstructuredGrid(
- {vtk.VTK_TETRA: self.mesh.cell_connectivity.reshape(-1, 4)},
+ {vtk.VTK_TETRA: self.mesh.cells.reshape(-1, 5)[:, 1:]},
reference_positions)
# Apply transformation for all time steps
@@ -200,7 +200,7 @@ class MeshDataset:
# pylint: disable=E1101
probing_mesh = pyvista.UnstructuredGrid(
- {vtk.VTK_TETRA: self.mesh.cell_connectivity.reshape(-1, 4)},
+ {vtk.VTK_TETRA: self.mesh.cells.reshape(-1, 5)[:, 1:]},
reference_positions)
probing_mesh = reference_mesh.probe(probing_mesh)
for name in field_names:
diff --git a/cmrsim/datasets/_flow.py b/cmrsim/datasets/_flow.py
index 3cf201414efd4a63149fb69a5ecf61a5774db59e..305da0d6462fce1b4a9b0509c114ba8ad5b48300 100644
--- a/cmrsim/datasets/_flow.py
+++ b/cmrsim/datasets/_flow.py
@@ -109,20 +109,18 @@ class RefillingFlowDataset(tf.Module):
uniformly gridded mesh
:return: None
"""
+ self.original_mesh = mesh.copy()
image_box = np.max(mesh.points, axis=0) - np.min(mesh.points, axis=0)
dims = (image_box / lookup_map_spacing).astype(int)
resolution = image_box / dims
origin = np.min(mesh.points, axis=0)
- uniform_grid = pyvista.ImageData(dimensions=dims,
- spacing=resolution,
- origin=origin)
+ uniform_grid = pyvista.ImageData(dimensions=dims, spacing=resolution, origin=origin)
self.lookup_map_spacing = lookup_map_spacing
-
- uniform_grid = uniform_grid.sample(mesh)
+ uniform_grid = uniform_grid.sample(mesh, mark_blank=False)
uniform_grid["in_mesh"] = np.array(uniform_grid["vtkValidPointMask"], dtype=np.float64)
self.gridded_mesh = uniform_grid
- self.original_mesh = mesh
+
print("Updated Mesh")
# pylint: disable=multiple-statements
@@ -172,9 +170,9 @@ class RefillingFlowDataset(tf.Module):
resolution = image_box / dims
origin = np.min(r_slice, axis=0)
gridded_seeding_volume = pyvista.ImageData(dimensions=dims + 1,
- spacing=resolution,
- origin=origin)
- self.gridded_seeding_volume = self.gridded_mesh.probe(gridded_seeding_volume)
+ spacing=resolution,
+ origin=origin)
+ self.gridded_seeding_volume = gridded_seeding_volume.sample(self.gridded_mesh, mark_blank=False)
active_indx = np.where(self.gridded_seeding_volume.ptc().cell_data["in_mesh"] > 0.7)
active_cell_centers = self.gridded_seeding_volume.cell_centers().ptc().points[active_indx]
@@ -251,7 +249,7 @@ class RefillingFlowDataset(tf.Module):
# Re-seed particles in un-populated areas with Monte-Carlo rejection:
# 1. Estimate current particle density within slice
self._estimate_particle_density(residual_particle_pos[in_tolerance])
- sampled_particle_pos = self.gridded_seeding_volume.probe(sampled_particle_pos)
+ sampled_particle_pos = pyvista.PointSet(sampled_particle_pos).sample(self.gridded_seeding_volume)
density = np.array(sampled_particle_pos["density"])
decision_boundaries = density / particle_density
# 2. To prevent unintentionally increasing particle density, set the decision boundary
@@ -413,4 +411,4 @@ class RefillingFlowDataset(tf.Module):
smoothed_histogram = gaussian_filter(residual_histogram / sampling_volume,
sigma=sigma, truncate=2.5)
self.gridded_mesh.cell_data["density"] = smoothed_histogram.reshape(-1, order="F")
- return self.gridded_mesh.probe(self.original_mesh)
\ No newline at end of file
+ return self.original_mesh.sample(self.gridded_mesh)
diff --git a/cmrsim/datasets/_regular_grid.py b/cmrsim/datasets/_regular_grid.py
index f46073820700aae74683731c9f09fb6a19f2291b..99f035e6fddf433caf688a50266dea2d1047a00b 100644
--- a/cmrsim/datasets/_regular_grid.py
+++ b/cmrsim/datasets/_regular_grid.py
@@ -103,9 +103,10 @@ class RegularGridDataset:
readout_direction)
nbins = (field_of_view / spacing).m_as("dimensionless").astype(int)
new_slice = pyvista.ImageData(dimensions=nbins, spacing=spacing.m_as("m"),
- origin=-field_of_view.m_as("m") / 2)
+ origin=-field_of_view.m_as("m") / 2)
new_slice = new_slice.transform(total_transform, inplace=False)
- new_slice = self.mesh.probe(new_slice)
+ new_slice = new_slice.sample(self.mesh)
+ # new_slice = self.mesh.probe(new_slice)
if in_mps:
inv_transform = np.eye(4, 4)
@@ -123,7 +124,7 @@ class RegularGridDataset:
Assumes that the main magnetic field is pointing in z-direction of the contained mesh.
The susceptibility os assumed to be specified as parts per million
- (e.g. :math:`\chi_{air} = 0.36ppm`).
+ (e.g. :math:`\\chi_{air} = 0.36ppm`).
The result is store in self.mesh["offres"] and is also returned as Quantity.
@@ -163,8 +164,10 @@ class RegularGridDataset:
# ft_chi_3d_dual = tf.signal.fft3d(chi_3d + 1j * imaginary_channel)
ft_chi_3d_dual = tf.signal.fft3d(chi_3d)
# 2) multiplication with the dipole function
- dipole_kernel = self._compute_fourier_dipole_kernel(field_of_view,
- np.array(ft_chi_3d_dual.shape))
+ dipole_kernel = self._compute_fourier_dipole_kernel(
+ field_of_view,
+ np.array(ft_chi_3d_dual.shape))
+
ft_field_3d = ft_chi_3d_dual * dipole_kernel
# 3) inverse FT to spatial domain
field_3d_dual = tf.signal.ifft3d(ft_field_3d)
@@ -207,7 +210,8 @@ class RegularGridDataset:
r_min = np.min(input_mesh.points, axis=0) - padding.m_as("m") / 2
nbins = (Quantity(r_max - r_min, "m") / pixel_spacing.to("m")).m.astype(int)
mesh = pyvista.ImageData(dimensions=nbins, spacing=pixel_spacing.m_as("m"), origin=r_min)
- mesh = input_mesh.probe(mesh)
+ mesh = mesh.sample(input_mesh)
+ # mesh = input_mesh.probe(mesh)
return cls(mesh)
@classmethod
@@ -248,8 +252,9 @@ class RegularGridDataset:
shape = np.array(shapes[0][0:3])
origin = - pixel_spacing * shape / 2 + origin_offset
- mesh = pyvista.ImageData(dimensions=shape, spacing=pixel_spacing.m_as("m"),
- origin=origin.m_as("m"))
+ mesh = pyvista.ImageData(dimensions=shape,
+ spacing=pixel_spacing.m_as("m"),
+ origin=origin.m_as("m"))
for name, arr in data.items():
mesh[name] = arr.reshape([shape.prod(), *arr.shape[3:]], order="F")
diff --git a/cmrsim/trajectory/_proper_ortho_decomp.py b/cmrsim/trajectory/_proper_ortho_decomp.py
index ce771cde5141a56e49faa9142df2dc7fe70dae70..e9be968c1964e8a9c57098a012c3ee15a242afae 100644
--- a/cmrsim/trajectory/_proper_ortho_decomp.py
+++ b/cmrsim/trajectory/_proper_ortho_decomp.py
@@ -194,7 +194,7 @@ class PODTrajectoryModule(BaseTrajectoryModule):
return tf.ensure_shape(data[:, 0, :3], (None, 3)), additional_data
- @tf.function(jit_compile=False)
+ @tf.function(jit_compile=False, reduce_retracing=True)
def _evaluate_trajectory(self, t: tf.Tensor) -> tf.Tensor:
"""Reconstructs the data state at given times t, by evaluating the taylor series
of mode-weights and computing the weighted sum.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 299aecddd854488a9a9f8a5863f85ced995f3ad6..f3728a7b820042d34ace998b711764360ceac6e8 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -177,7 +177,7 @@ nbsphinx_thumbnails = {
'example_gallery/analytic_simulation/3_multiple_coils': '_static/notebook_thumbnails/analytic_multiple_coils.png',
'example_gallery/analytic_simulation/BSSFP_offresonance': '_static/notebook_thumbnails/analytic_static_bssfp.png',
'example_gallery/analytic_simulation/cardiac_dti_with_background': '_static/notebook_thumbnails/analytic_cdti_stylized.png',
- 'example_gallery/analytic_simulation/simulate_mrxcat_cmrsim': '_static/notebook_thumbnails/analytic_bssfp.svg',
+ 'example_gallery/analytic_simulation/slice_profile_weighting': '_static/notebook_thumbnails/analytic_slice_select.png',
# Bloch
'example_gallery/bloch_simulation/static_cartesian_SEEPI_shepp': '_static/notebook_thumbnails/static_bloch_epi.svg',
'example_gallery/bloch_simulation/static_cartesian_sGRE_shepp': '_static/notebook_thumbnails/static_bloch_spoiled_gre.svg',
diff --git a/notebooks/analytic_simulation/1_basic_functionality.ipynb b/notebooks/analytic_simulation/1_basic_functionality.ipynb
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--- a/notebooks/analytic_simulation/1_basic_functionality.ipynb
+++ b/notebooks/analytic_simulation/1_basic_functionality.ipynb
@@ -1,3 +1,3 @@
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--- a/notebooks/analytic_simulation/2_motion.ipynb
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--- a/notebooks/analytic_simulation/BSSFP_offresonance.ipynb
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--- a/notebooks/analytic_simulation/slice_profile_weighting.ipynb
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--- a/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
+++ b/notebooks/bloch_simulation/flow_bssfp_submodules_aorta.ipynb
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index a0e472c25eaf680975b56fea8f4e7cde025dc072..5e6d5ab47f9f267aa8a0ca9db4064671bda848b0 100644
--- a/notebooks/bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb
+++ b/notebooks/bloch_simulation/flow_mvenc_sGRE_ubend_parallel.ipynb
@@ -1,3 +1,3 @@
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index c03839575be4659e5016e6d842334affada11727..cb544a28ddcd5df089e503314beb75c962d7a854 100644
--- a/notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb
+++ b/notebooks/bloch_simulation/flow_venc_sGRE_turbUBend.ipynb
@@ -1,3 +1,3 @@
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--- a/notebooks/bloch_simulation/movmesh_bssfp.ipynb
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diff --git a/notebooks/local_functions.py b/notebooks/local_functions.py
index d0997809f94a39a51784f3801333c7a468ac0877..c37a4f5b765762ebe5e1581ddb4222f582d47516 100644
--- a/notebooks/local_functions.py
+++ b/notebooks/local_functions.py
@@ -68,7 +68,7 @@ def create_cylinder_phantom(dimensions=(200, 200, 4), spacing=(0.001, 0.001, 0.0
:return: pyvista.UnstructuredGrid
"""
- raster = pyvista.UniformGrid(dimensions=dimensions, spacing=spacing, origin=-np.array(dimensions) * np.array(spacing) / 2)
+ raster = pyvista.ImageData(dimensions=dimensions, spacing=spacing, origin=-np.array(dimensions) * np.array(spacing) / 2)
cylinders = [pyvista.Cylinder(center=(*xy_positions[i].m_as("m"), 0.), direction=(0., 0., 1.), radius=radii[i].m_as("m"),)
for i in range(len(radii))]
max_radius = np.max(np.array(dimensions[0:2]) * np.array(spacing[0:2])) / 2
@@ -110,7 +110,7 @@ def create_spherical_phantom(dimensions=(120, 120, 120), spacing=(0.002, 0.002,
:param big_radius: float in meter
:return: pyvista.UnstructuredGrid
"""
- raster = pyvista.UniformGrid(dimensions=dimensions, spacing=spacing,
+ raster = pyvista.ImageData(dimensions=dimensions, spacing=spacing,
origin=-np.array(dimensions) * np.array(spacing) / 2)
sphere_big = pyvista.Sphere(radius=big_radius).extract_surface()
box = pyvista.Box(bounds=(-big_radius * 0.3, big_radius * 0.3, -big_radius/5,
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