mrzerocore 0.2.9__cp37-abi3-win32.whl → 0.2.11__cp37-abi3-win32.whl

MRzeroCore/phantom/brainweb/brainweb_data.json

@@ -33,7 +33,7 @@
       "gm": {
         "PD": 0.8,
         "T1": 1.56,
-        "T2": 0.0083,
+        "T2": 0.083,
         "T2'": 0.32,
         "D": 0.83
       },

MRzeroCore/sequence.py

@@ -289,11 +289,11 @@ class Sequence(list):
 
     def cuda(self) -> Sequence:
         """Move this sequence to the specified CUDA device and return it."""
-        return Sequence([rep.cuda() for rep in self])
+        return Sequence([rep.cuda() for rep in self], self.normalized_grads)
 
     def cpu(self) -> Sequence:
         """Move this sequence to the CPU and return it."""
-        return Sequence([rep.cpu() for rep in self])
+        return Sequence([rep.cpu() for rep in self], self.normalized_grads)
 
     @property
     def device(self) -> torch.device:

MRzeroCore/simulation/main_pass.py

@@ -18,12 +18,9 @@ def execute_graph(graph: Graph,
                   min_emitted_signal: float = 1e-2,
                   min_latent_signal: float = 1e-2,
                   print_progress: bool = True,
-                  ) -> torch.Tensor:
-    """Calculate the signal of the sequence by computing the graph.
-
-    This function can optionally return the + or z magnetisation and the
-    encoding of all states, if requested. The encoding consists of the signal
-    of a distribution and its k-t space trajectory.
+                  return_mag_z: int | bool | None = None,
+                  ) -> torch.Tensor | list:
+    """Calculate the signal of the sequence by executing the phase graph.
 
     Parameters
     ----------
@@ -40,11 +37,18 @@ def execute_graph(graph: Graph,
         Should be <= than min_emitted_signal.
     print_progress : bool
         If true, the current repetition is printed while simulating.
+    return_mag_z : int or bool, optional
+        If set, returns the longitudinal magnetisation of either the given
+        repetition (int) or all repetitions (``True``).
+
 
     Returns
     -------
     signal : torch.Tensor
         The simulated signal of the sequence.
+    mag_z : torch.Tensor | list[torch.Tensor]
+        The longitudinal magnetisation of the specified or all repetition(s).
+
     """
     if seq.normalized_grads:
         grad_scale = 1 / data.size
@@ -67,6 +71,7 @@ def execute_graph(graph: Graph,
     # Calculate kt_vec ourselves for autograd
     graph[0][0].kt_vec = torch.zeros(4, device=data.device)
 
+    mag_z = []
     for i, (dists, rep) in enumerate(zip(graph[1:], seq)):
         if print_progress:
             print(f"\rCalculating repetition {i+1} / {len(seq)}", end='')
@@ -129,6 +134,8 @@ def execute_graph(graph: Graph,
         # Use the same adc phase for all coils
         adc_rot = torch.exp(1j * rep.adc_phase).unsqueeze(1)
 
+        mag_z_rep = []
+        mag_z.append(mag_z_rep)
         for dist in dists:
             # Create a list only containing ancestors that were simulated
             ancestors = list(filter(
@@ -141,6 +148,9 @@ def execute_graph(graph: Graph,
                 continue  # skip dists for which no ancestors were simulated
 
             dist.mag = sum([calc_mag(ancestor) for ancestor in ancestors])
+            if dist.dist_type in ['z0', 'z'] and return_mag_z in [i, True]:
+                mag_z_rep.append(dist.mag)
+
             # The pre_pass already calculates kt_vec, but that does not
             # work with autograd -> we need to calculate it with torch
             if dist.dist_type == 'z0':
@@ -154,9 +164,9 @@ def execute_graph(graph: Graph,
             dist_traj = dist.kt_vec + trajectory
 
             # Diffusion
-            k2 = dist_traj[:, :3] * 2 * np.pi
+            k2 = dist_traj[:, :3]
             k1 = torch.empty_like(k2)  # Calculate k-space at start of event
-            k1[0, :] = dist.kt_vec[:3] * 2 * np.pi
+            k1[0, :] = dist.kt_vec[:3]
             k1[1:, :] = k2[:-1, :]
             # Integrate over each event to get b factor (lin. interp. grad)
             b = 1/3 * dt * (k1**2 + k1*k2 + k2**2).sum(1)
@@ -202,7 +212,7 @@ def execute_graph(graph: Graph,
                 dist.mag = dist.mag * r2 * diffusion[-1, :]
                 dist.kt_vec = dist_traj[-1]
             else:  # z or z0
-                k = torch.linalg.vector_norm(dist.kt_vec[:3] * 2 * np.pi)
+                k = torch.linalg.vector_norm(dist.kt_vec[:3])
                 diffusion = torch.exp(-1e-9 * data.D * total_time * k**2)
                 dist.mag = dist.mag * r1 * diffusion
             if dist.dist_type == 'z0':
@@ -223,6 +233,10 @@ def execute_graph(graph: Graph,
         print(" - done")
 
     # Only return measured samples
-    return torch.cat([
+    measured = torch.cat([
         sig[rep.adc_usage > 0, :] for sig, rep in zip(signal, seq)
     ])
+    if return_mag_z is not None:
+        return measured, mag_z
+    else:
+        return measured

{MRzeroCore-0.2.9.dist-info → MRzeroCore-0.2.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MRzeroCore
-Version: 0.2.9
+Version: 0.2.11
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -18,8 +18,8 @@ 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: Documentation, https://mrzero-core.readthedocs.io/
 Project-URL: MRzero-Paper, https://arxiv.org/abs/2002.04265
+Project-URL: Documentation, https://mrzero-core.readthedocs.io/
 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)

{MRzeroCore-0.2.9.dist-info → MRzeroCore-0.2.11.dist-info}/RECORD

@@ -1,7 +1,7 @@
-MRzeroCore-0.2.9.dist-info/METADATA,sha256=GtzqfojjCDeKCeEHW2vxJr8gciCl4W89M2fyCHfB_Rc,3800
-MRzeroCore-0.2.9.dist-info/WHEEL,sha256=gXYpX75r-fJLXR2RD6r-k3EXD66bMIXTAL43kNqJgxg,92
-MRzeroCore-0.2.9.dist-info/license_files/LICENSE,sha256=rd_IFJ484uAluv8CigP2CpXg4l2GJLLKENqB6-RXPp4,35112
-MRzeroCore/phantom/brainweb/brainweb_data.json,sha256=HETnXgLJndWbqeL4yfm8N-f9t0EwO-v6HzRA46f4VPU,1795
+MRzeroCore-0.2.11.dist-info/METADATA,sha256=U4oPS2MmczYLu2kn73X5CrJ4h42STauc_kIgTlTiQb0,3801
+MRzeroCore-0.2.11.dist-info/WHEEL,sha256=gXYpX75r-fJLXR2RD6r-k3EXD66bMIXTAL43kNqJgxg,92
+MRzeroCore-0.2.11.dist-info/license_files/LICENSE,sha256=rd_IFJ484uAluv8CigP2CpXg4l2GJLLKENqB6-RXPp4,35112
+MRzeroCore/phantom/brainweb/brainweb_data.json,sha256=El9J5dfEIwGi4_SoRif6ic6IVSMKh01jK0hNRbBYNqA,1794
 MRzeroCore/phantom/brainweb/brainweb_data_sources.txt,sha256=Sh6NFLU1bhdaD0pp12D_Hc70cA_UC1s7KdHcuoGTKuA,1853
 MRzeroCore/phantom/brainweb/output/.gitkeep,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 MRzeroCore/phantom/brainweb/__init__.py,sha256=R48NlkMNpMgyKKwFm-5iUlhxBKctQ6dXx7yCmyVwm6E,6828
@@ -26,11 +26,11 @@ MRzeroCore/pulseq/pulseq_loader/pulseq_file/__init__.py,sha256=VzN3j7pirpI8zJdfv
 MRzeroCore/pulseq/pulseq_loader/spoiler.py,sha256=R6Hjfno3U-fuICjLUUxmDk_7-Z1HjZYmE55mXTWTIAI,1007
 MRzeroCore/pulseq/pulseq_loader/__init__.py,sha256=6OLwC3k9LSjl8aRin9pV4-Rb-Q3YSbToayyeKbXnUdQ,2812
 MRzeroCore/reconstruction.py,sha256=LGk5EdgQ4AkhWN-7Q81YMkIEEW0T9Q37O2Pat0d-d4o,4277
-MRzeroCore/sequence.py,sha256=DRWdCwTZseDQjL8FGfy36I7inrX1Viuv1TRzInr50z8,27601
+MRzeroCore/sequence.py,sha256=wqRwpUIKdX9mgmctmIL2Ttr3eZPJ_H1ACLamkzPp7sY,27647
 MRzeroCore/simulation/isochromat_sim.py,sha256=u6KbN7S8REOHiKqzDGMma7937cKX4bnmj3gXoAiNLi0,9185
-MRzeroCore/simulation/main_pass.py,sha256=VqM_83740KONxvFHPZAdTwcutZDeKGMViU9lB3xRLjw,9395
+MRzeroCore/simulation/main_pass.py,sha256=DNXEJmN7AEWuqNbMma6AWqJpHH4ihhC3YRJKRhoi4RU,9830
 MRzeroCore/simulation/pre_pass.py,sha256=5wmXKxgFeGwA7yrqTkOjcWoFuGuRYEPzedRGqkx2Evg,5117
 MRzeroCore/util.py,sha256=39TPselHu7f218BRdjHB4_kCSPnFuCC45YmdGotc4uA,11460
 MRzeroCore/__init__.py,sha256=8WViV9GQRwnksnopAAfKWRmtRYk75DC3ke4OQwLx-fU,850
-MRzeroCore/_prepass.pyd,sha256=CKvRp3WHK4J2AUZesqDSKb_dLtqZK4Cj3-HI-GPlOiw,355840
-MRzeroCore-0.2.9.dist-info/RECORD,,
+MRzeroCore/_prepass.pyd,sha256=IBPl4RZknTboJuiJZDiAuFzc9kMr0a8KwEPicF_B3b4,351232
+MRzeroCore-0.2.11.dist-info/RECORD,,