mrzerocore 0.4.3__tar.gz → 0.4.4__tar.gz

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/.github/workflows/playground_test.yml

@@ -52,10 +52,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-            pip install pypulseq &> /dev/null
+            pip install pypulseq==1.4.2post1 &> /dev/null
             pip install pydisseqt
-            pip install MRzeroCore --no-deps
             pip install ismrmrd
+            pip install MRzeroCore --no-deps
             pip install  torchkbnufft PyWavelets tqdm scikit-image
             wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null
             pip install jupyter nbconvert

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/.github/workflows/simulation_test.yml

@@ -41,7 +41,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install pypulseq
+          pip install pypulseq==1.4.2post1 &> /dev/null
           pip install torchkbnufft
           pip install nbformat
 

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/CHANGELOG.md

@@ -1,3 +1,13 @@
+- 0.4.4
+  - Fix: support for empty tissue masks in NIfTI phantom
+  - Fix: support for int - constants in NIfTI phantom
+  - Remove unsupported platforms from build (32bit windows, intel mac)
+- 0.4.3
+  - Fix python package normalization
+- 0.4.2
+  - Add NIfTI phantom support
+  - Fix custom voxel phantom plot
+  - Make isochromat sim GPU compatible
 - 0.4.0
   - Integrate ISMRMD exporter
   - Update documentation

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/Cargo.lock

@@ -59,7 +59,7 @@ dependencies = [
 
 [[package]]
 name = "mrzero_core"
-version = "0.4.3"
+version = "0.4.4"
 dependencies = [
  "num-complex",
  "pyo3",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mrzero_core"
-version = "0.4.3"
+version = "0.4.4"
 edition = "2021"
 readme = "README.md"
 

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mrzerocore
-Version: 0.4.3
+Version: 0.4.4
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb

@@ -49,7 +49,7 @@
         }
       ],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb

@@ -46,7 +46,7 @@
         }
       ],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb

@@ -35,7 +35,7 @@
         }
       ],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_FID_seq.ipynb

@@ -21,7 +21,7 @@
       },
       "outputs": [],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb

@@ -49,7 +49,7 @@
         }
       ],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb

@@ -25,7 +25,7 @@
       },
       "outputs": [],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb

@@ -21,7 +21,7 @@
       },
       "outputs": [],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb

@@ -21,7 +21,7 @@
       },
       "outputs": [],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb

@@ -21,7 +21,7 @@
       },
       "outputs": [],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb

@@ -25,7 +25,7 @@
       },
       "outputs": [],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb

@@ -49,7 +49,7 @@
         }
       ],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb

@@ -31,7 +31,7 @@
         }
       ],
       "source": [
-        "!pip install pypulseq &> /dev/null\n",
+        "!pip install pypulseq==1.4.2post1 &> /dev/null\n",
         "!pip install  torchkbnufft --no-deps\n",
         "!pip install ismrmrd\n",
         "!pip install MRzeroCore --no-deps\n",

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/documentation/src/SUMMARY.md

@@ -32,6 +32,12 @@
     - [Reconstruction methods](api-reconstruction.md)
     - [util module](api-util.md)
     - [Other methods](api-unsorted.md)
+  
+
+# 📊 Pulseq-zero
+
+- [Math methods for differentiability](pulseqzero-math.md)
+
 
 ---
 

mrzerocore-0.4.4/documentation/src/pulseqzero-math.md

@@ -0,0 +1,55 @@
+# Differentiable Rounding Helpers for Pulseq Zero Sequences
+
+This module provides **differentiable stand-ins** for common rounding operations (`ceil`, `floor`, `round`) used in **Pulseq sequences**.
+They are designed to keep the optimization pipeline differentiable by **passing gradients through unchanged**, effectively treating these operations as the identity during backpropagation.
+
+
+---
+
+## Design idea
+
+* **Forward pass**: Behaves exactly like the corresponding PyTorch / NumPy rounding operation.
+* **Backward pass**: Returns the incoming gradient unchanged.
+* **Use case**: Allows differentiable optimization of otherwise discrete parameters.
+
+
+---
+
+
+
+## Functional Wrappers
+
+To use the wrapper functions:
+
+```python
+from pulseqzero import round, ceil, floor
+``` 
+
+
+### `ceil(x)`
+
+Differentiable version of `torch.ceil`.
+
+```python
+y = ceil(x)
+```
+
+### `floor(x)`
+
+Differentiable version of `torch.floor`.
+
+```python
+y = floor(x)
+```
+
+### `round(x)`
+
+Differentiable version of `torch.round`.
+
+```python
+y = round(x)
+```
+
+---
+
+

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "mrzerocore"
-version = "0.4.3"
+version = "0.4.4"
 description = "Core functionality of MRzero"
 authors = [
     {name = "Jonathan Endres", email = "jonathan.endres@uk-erlangen.de"},

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/python/MRzeroCore/phantom/nifti_phantom.py

@@ -138,7 +138,7 @@ class NiftiTissue:
 
     def to_dict(self) -> dict:
         def serialize_prop(prop):
-            if isinstance(prop, float):
+            if isinstance(prop, (float, int)):
                 return prop
             elif isinstance(prop, NiftiRef):
                 return prop.to_str()

{mrzerocore-0.4.3 → mrzerocore-0.4.4}/python/MRzeroCore/phantom/tissue_dict.py

@@ -173,21 +173,27 @@ class TissueDict(dict[str, VoxelGridPhantom]):
               ) -> SimData:
         data_list = [self[tissue].build(PD_threshold, voxel_shape) for tissue in self]
 
-        return SimData(
-            PD=torch.cat([obj.PD for obj in data_list]),
-            T1=torch.cat([obj.T1 for obj in data_list]),
-            T2=torch.cat([obj.T2 for obj in data_list]),
-            T2dash=torch.cat([obj.T2dash for obj in data_list]),
-            D=torch.cat([obj.D for obj in data_list]),
-            B0=torch.cat([obj.B0 for obj in data_list]),
-            B1=torch.cat([obj.B1 for obj in data_list], 1),
-            coil_sens=torch.cat([obj.coil_sens for obj in data_list], 1),
-            voxel_pos=torch.cat([obj.voxel_pos for obj in data_list], 0),
-            tissue_masks=torch.stack([obj.tissue_masks for obj in data_list]),
-            size=data_list[0].size,
-            nyquist=data_list[0].nyquist,
-            dephasing_func=data_list[0].dephasing_func,
-        )
+        kwargs = {
+            "PD": torch.cat([obj.PD for obj in data_list]),
+            "T1": torch.cat([obj.T1 for obj in data_list]),
+            "T2": torch.cat([obj.T2 for obj in data_list]),
+            "T2dash": torch.cat([obj.T2dash for obj in data_list]),
+            "D": torch.cat([obj.D for obj in data_list]),
+            "B0": torch.cat([obj.B0 for obj in data_list]),
+            "B1": torch.cat([obj.B1 for obj in data_list], 1),
+            "coil_sens": torch.cat([obj.coil_sens for obj in data_list], 1),
+            "voxel_pos": torch.cat([obj.voxel_pos for obj in data_list], 0),
+            "size": data_list[0].size,
+            "nyquist": data_list[0].nyquist,
+            "dephasing_func": data_list[0].dephasing_func,
+        }
+
+        # Only add tissue_masks if any object has it non-empty
+        if any(obj.tissue_masks for obj in data_list):
+            kwargs["tissue_masks"] = torch.stack([obj.tissue_masks for obj in data_list])
+
+        return SimData(**kwargs)
+
 
 # ============================
 # Helpers for importing NIfTIs