mrzerocore 0.2.10__tar.gz → 0.2.11__tar.gz

{MRzeroCore-0.2.10 → MRzeroCore-0.2.11}/CHANGELOG.md

@@ -1,3 +1,5 @@
+- 0.2.11
+  - (re-)introduced return_mag_z parameter in pdg simulation
 - 0.2.10
   - change default FOV in all notebooks to phantom size (200 mm)
   - Use Open in Colab badges in the playground instead of links

{MRzeroCore-0.2.10 → MRzeroCore-0.2.11}/Cargo.lock

@@ -53,7 +53,7 @@ dependencies = [
 
 [[package]]
 name = "mrzero_core"
-version = "0.2.10"
+version = "0.2.11"
 dependencies = [
  "num-complex",
  "pyo3",

{MRzeroCore-0.2.10 → MRzeroCore-0.2.11}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mrzero_core"
-version = "0.2.10"
+version = "0.2.11"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

{MRzeroCore-0.2.10 → MRzeroCore-0.2.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MRzeroCore
-Version: 0.2.10
+Version: 0.2.11
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -18,9 +18,9 @@ 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: Repository, https://github.com/MRsources/MRzero-Core
 Project-URL: MRzero-Paper, https://arxiv.org/abs/2002.04265
+Project-URL: Repository, https://github.com/MRsources/MRzero-Core
+Project-URL: Documentation, https://mrzero-core.readthedocs.io/
 
 [![Documentation Status](https://readthedocs.org/projects/mrzero-core/badge/?version=latest)](https://mrzero-core.readthedocs.io/en/latest/?badge=latest)
 

{MRzeroCore-0.2.10 → MRzeroCore-0.2.11}/documentation/_toc.yml

@@ -42,5 +42,6 @@ chapters:
   - file: playground_mr0/mr00_FLASH_2D_ernstAngle_opt.ipynb
 
   - file: playground_mr0/flash
+  - file: playground_mr0/flash_DWI
   - file: playground_mr0/pulseq_flash
   - file: playground_mr0/pulseq_sim_pTx

{MRzeroCore-0.2.10 → MRzeroCore-0.2.11}/python/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-0.2.10 → MRzeroCore-0.2.11}/python/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='')
@@ -129,7 +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(
@@ -142,6 +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':
@@ -224,6 +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