Add choice of type of attenuation/HU/density map for inpit

README.md

@@ -1,4 +1,4 @@
-# py-smc
+# PySIMIND
 
 Python SIMIND Monte Carlo Connector.
 
@@ -41,7 +41,7 @@ install a licensed SIMIND installation.
 ### Basic Installation
 
 ```bash
-pip install py-smc
+pip install PySIMIND
 ```
 
 Import path remains:
@@ -147,6 +147,7 @@ connector.configure_voxel_phantom(
     source=source,
     mu_map=mu_map,
     voxel_size_mm=4.0,
+    mu_map_type="attenuation",  # or "density" / "hu"
 )
 connector.set_energy_windows([126], [154], [0])  # Tc-99m ± 10%
 connector.add_runtime_switch("FI", "tc99m")
@@ -159,6 +160,13 @@ total = outputs["tot_w1"].projection
 print(total.shape)
 ```
 
+`mu_map_type` controls how `mu_map` is interpreted before writing SIMIND
+density input:
+
+- `"attenuation"`: linear attenuation coefficients (cm^-1), converted to density
+- `"density"`: density map in g/cm^3, used directly
+- `"hu"`: CT HU map, converted with the Schneider model
+
 ### Advanced Density Conversion
 
 ```python

docs/changelog.rst

@@ -10,11 +10,22 @@ The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`
 Unreleased
 ----------
 
+Added
+~~~~~
+
+- ``mu_map_type`` input selection for SIMIND phantom setup, supporting
+  attenuation maps, density maps, and HU maps in
+  ``SimindPythonConnector.configure_voxel_phantom()``.
+
 Changed
 ~~~~~~~
 
-- Updated user-facing branding to ``py-smc`` and added explicit non-affiliation
+- Updated user-facing branding to ``PySIMIND`` and added explicit non-affiliation
   and external-SIMIND-install disclaimers in README/docs.
+- STIR/SIRF/PyTomography adaptors now forward ``mu_map_type`` so input-map
+  interpretation is configurable across connector and adaptor workflows.
+- Usage docs now describe ``mu_map_type`` options and example calls for
+  connector/adaptor setup.
 
 [0.5.0] - 2026-03-05
 --------------------

docs/conf.py

@@ -1,4 +1,4 @@
-"""Sphinx configuration file for py-smc documentation."""
+"""Sphinx configuration file for PySIMIND documentation."""
 
 import os
 import sys
@@ -10,11 +10,11 @@
 sys.path.insert(0, os.path.abspath(".."))
 
 # Project information
-project = "py-smc"
+project = "PySIMIND"
 copyright = f"{datetime.now().year}, Sam Porter, Efstathios Varzakis"
 author = "Sam Porter, Efstathios Varzakis"
 release = "0.5.0"
-for dist_name in ("py-smc", "sirf-simind-connection"):
+for dist_name in ("PySIMIND", "py-smc", "sirf-simind-connection"):
     try:
         release = importlib_metadata.version(dist_name)
         break

docs/index.rst

@@ -1,5 +1,5 @@
-py-smc Documentation
-====================
+PySIMIND Documentation
+======================
 
 .. toctree::
    :maxdepth: 2

docs/intro.rst

@@ -3,7 +3,7 @@
 Introduction
 ============
 
-py-smc is a Python toolkit for SIMIND SPECT workflows.
+PySIMIND is a Python toolkit for SIMIND SPECT workflows.
 
 Disclaimer
 ----------

docs/testing.rst

@@ -3,7 +3,7 @@
 Testing
 =======
 
-This document explains the testing strategy for py-smc, which handles the
+This document explains the testing strategy for PySIMIND, which handles the
 challenge of testing code that depends on optional external dependencies (SIRF,
 STIR, SIMIND, and PyTomography) that may not be available in every
 environment.

docs/usage.rst

@@ -42,6 +42,26 @@ inputs/outputs without any reconstruction-package dependency.
     total = outputs["tot_w1"].projection
     print(total.shape)
 
+Map Input Types
+---------------
+
+``configure_voxel_phantom()`` supports three ``mu_map`` input conventions via
+``mu_map_type``:
+
+- ``"attenuation"``: linear attenuation coefficients (cm^-1), converted to
+  density before SIMIND input writing.
+- ``"density"``: density map in g/cm^3, passed through directly.
+- ``"hu"``: CT HU map, converted to density with the Schneider model.
+
+.. code-block:: python
+
+    connector.configure_voxel_phantom(
+        source=source,
+        mu_map=mu_map,
+        voxel_size_mm=4.0,
+        mu_map_type="attenuation",  # or "density" / "hu"
+    )
+
 Adaptor Workflows
 -----------------
 
@@ -60,6 +80,7 @@ STIR adaptor
         config_source=get("Example.yaml"),
         output_dir="output/stir_adaptor",
         output_prefix="stir_case01",
+        mu_map_type="attenuation",  # or "density" / "hu"
     )
     adaptor.set_source(stir_source)
     adaptor.set_mu_map(stir_mu_map)
@@ -83,6 +104,7 @@ SIRF adaptor
         config_source=get("Example.yaml"),
         output_dir="output/sirf_adaptor",
         output_prefix="sirf_case01",
+        mu_map_type="attenuation",  # or "density" / "hu"
     )
     adaptor.set_source(sirf_source)
     adaptor.set_mu_map(sirf_mu_map)
@@ -113,6 +135,7 @@ Build the system matrix directly with PyTomography APIs.
         config_source=get("Example.yaml"),
         output_dir="output/pytomo_adaptor",
         output_prefix="pytomo_case01",
+        mu_map_type="attenuation",  # or "density" / "hu"
     )
     adaptor.set_source(source_tensor_xyz)
     adaptor.set_mu_map(mu_tensor_xyz)

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "py-smc"
+name = "PySIMIND"
 version = "0.5.0"
 description = "Python SIMIND Monte Carlo connector with STIR/SIRF/PyTomography adaptors"
 readme = "README.md"

sirf_simind_connection/__init__.py

@@ -1,13 +1,13 @@
 """
-py-smc connector/adaptor API.
+PySIMIND connector/adaptor API.
 """
 
 import importlib
 from importlib import metadata as _meta
 from typing import Any
 
 
-for _dist_name in ("py-smc", "sirf-simind-connection", __name__):
+for _dist_name in ("PySIMIND", "py-smc", "sirf-simind-connection", __name__):
     try:  # installed (pip/poetry)
         __version__ = _meta.version(_dist_name)
         break

sirf_simind_connection/connectors/python_connector.py

@@ -10,12 +10,15 @@
 import shutil
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Any, Dict, Optional, Union
+from typing import Any, Dict, Literal, Optional, Union
 
 import numpy as np
 
 from sirf_simind_connection.connectors.base import BaseConnector
-from sirf_simind_connection.converters.attenuation import attenuation_to_density
+from sirf_simind_connection.converters.attenuation import (
+    attenuation_to_density,
+    hu_to_density_schneider,
+)
 from sirf_simind_connection.converters.simind_to_stir import SimindToStirConverter
 from sirf_simind_connection.core.config import RuntimeSwitches, SimulationConfig
 from sirf_simind_connection.core.executor import SimindExecutor
@@ -31,6 +34,7 @@
 
 ConfigSource = Union[str, os.PathLike[str], SimulationConfig]
 PathLike = Union[str, os.PathLike[str]]
+MuMapType = Literal["attenuation", "density", "hu"]
 
 
 @dataclass(frozen=True)
@@ -108,15 +112,31 @@ def configure_voxel_phantom(
         mu_map: np.ndarray,
         voxel_size_mm: float = 4.0,
         scoring_routine: Union[ScoringRoutine, int] = ScoringRoutine.SCATTWIN,
+        mu_map_type: MuMapType = "attenuation",
     ) -> tuple[Path, Path]:
         """
         Configure voxel geometry and write source/density input files.
 
+        Args:
+            source: Source activity array in SIMIND image axes (z, y, x).
+            mu_map: Input volume interpreted according to ``mu_map_type``.
+            voxel_size_mm: Isotropic voxel size in mm.
+            scoring_routine: SIMIND scoring routine identifier.
+            mu_map_type: Interpretation of ``mu_map`` values:
+                - ``"attenuation"``: linear attenuation (cm^-1), converted to density.
+                - ``"density"``: density (g/cm^3), written directly.
+                - ``"hu"``: CT Hounsfield Units, converted via Schneider model.
+
         Returns:
             Tuple of (source_file_path, density_file_path).
         """
         source_array = np.asarray(source, dtype=np.float32)
         mu_map_array = np.asarray(mu_map, dtype=np.float32)
+        normalized_map_type = str(mu_map_type).strip().lower()
+        if normalized_map_type not in {"attenuation", "density", "hu"}:
+            raise ValueError(
+                "mu_map_type must be one of: 'attenuation', 'density', 'hu'"
+            )
 
         if source_array.ndim != 3 or mu_map_array.ndim != 3:
             raise ValueError("source and mu_map must both be 3D arrays")
@@ -176,8 +196,11 @@ def configure_voxel_phantom(
         cfg.set_data_file(6, src_prefix)
 
         if cfg.get_flag(11):
-            photon_energy = float(cfg.get_value("photon_energy"))
-            density = attenuation_to_density(mu_map_array, photon_energy) * 1000.0
+            density = self._convert_mu_input_to_density(
+                mu_map_array=mu_map_array,
+                mu_map_type=normalized_map_type,
+                photon_energy=float(cfg.get_value("photon_energy")),
+            )
         else:
             density = np.zeros_like(mu_map_array)
 
@@ -191,6 +214,21 @@ def configure_voxel_phantom(
 
         return source_path, density_path
 
+    @staticmethod
+    def _convert_mu_input_to_density(
+        mu_map_array: np.ndarray,
+        mu_map_type: MuMapType,
+        photon_energy: float,
+    ) -> np.ndarray:
+        """Convert attenuation/HU/density map input to density in mg/cm^3."""
+        if mu_map_type == "attenuation":
+            density_g_cm3 = attenuation_to_density(mu_map_array, photon_energy)
+        elif mu_map_type == "density":
+            density_g_cm3 = mu_map_array
+        else:  # mu_map_type == "hu"
+            density_g_cm3 = hu_to_density_schneider(mu_map_array)
+        return density_g_cm3 * 1000.0
+
     def set_energy_windows(
         self,
         lower_bounds: Union[float, list[float]],

sirf_simind_connection/connectors/pytomography_adaptor.py

@@ -17,6 +17,7 @@
 from sirf_simind_connection.connectors.base import BaseConnector
 from sirf_simind_connection.connectors.python_connector import (
     ConfigSource,
+    MuMapType,
     RuntimeOperator,
     SimindPythonConnector,
 )
@@ -56,6 +57,7 @@ def __init__(
         voxel_size_mm: float = 4.0,
         quantization_scale: float = 1.0,
         scoring_routine: Union[ScoringRoutine, int] = ScoringRoutine.SCATTWIN,
+        mu_map_type: MuMapType = "attenuation",
     ) -> None:
         if torch is None:
             raise ImportError(
@@ -80,6 +82,7 @@ def __init__(
             if isinstance(scoring_routine, int)
             else scoring_routine
         )
+        self._mu_map_type: MuMapType = mu_map_type
 
         self._source: Optional[torch.Tensor] = None
         self._mu_map: Optional[torch.Tensor] = None
@@ -146,6 +149,7 @@ def run(
             mu_map=mu_map_zyx,
             voxel_size_mm=self.voxel_size_mm,
             scoring_routine=self._scoring_routine,
+            mu_map_type=self._mu_map_type,
         )
         self.python_connector.set_energy_windows(*self._energy_windows)
 

sirf_simind_connection/connectors/sirf_adaptor.py

@@ -10,6 +10,7 @@
 from sirf_simind_connection.connectors.base import BaseConnector
 from sirf_simind_connection.connectors.python_connector import (
     ConfigSource,
+    MuMapType,
     RuntimeOperator,
     SimindPythonConnector,
 )
@@ -35,6 +36,7 @@ def __init__(
         photon_multiplier: int = 1,
         quantization_scale: float = 1.0,
         scoring_routine: ScoringRoutine | int = ScoringRoutine.SCATTWIN,
+        mu_map_type: MuMapType = "attenuation",
     ) -> None:
         if sirf is None:
             raise ImportError("SirfSimindAdaptor requires the SIRF Python package.")
@@ -53,6 +55,7 @@ def __init__(
         self._source: Any = None
         self._mu_map: Any = None
         self._outputs: Optional[dict[str, Any]] = None
+        self._mu_map_type: MuMapType = mu_map_type
 
         self.add_runtime_switch("NN", photon_multiplier)
 
@@ -92,6 +95,7 @@ def run(self, runtime_operator: Optional[RuntimeOperator] = None) -> dict[str, A
             mu_map=mu_arr,
             voxel_size_mm=voxel_size_mm,
             scoring_routine=self._scoring_routine,
+            mu_map_type=self._mu_map_type,
         )
         raw_outputs = self.python_connector.run(runtime_operator=runtime_operator)
         self._outputs = {

sirf_simind_connection/connectors/stir_adaptor.py

@@ -10,6 +10,7 @@
 from sirf_simind_connection.connectors.base import BaseConnector
 from sirf_simind_connection.connectors.python_connector import (
     ConfigSource,
+    MuMapType,
     RuntimeOperator,
     SimindPythonConnector,
 )
@@ -35,6 +36,7 @@ def __init__(
         photon_multiplier: int = 1,
         quantization_scale: float = 1.0,
         scoring_routine: ScoringRoutine | int = ScoringRoutine.SCATTWIN,
+        mu_map_type: MuMapType = "attenuation",
     ) -> None:
         if stir is None:
             raise ImportError("StirSimindAdaptor requires the STIR Python package.")
@@ -53,6 +55,7 @@ def __init__(
         self._source: Any = None
         self._mu_map: Any = None
         self._outputs: Optional[dict[str, Any]] = None
+        self._mu_map_type: MuMapType = mu_map_type
 
         self.add_runtime_switch("NN", photon_multiplier)
 
@@ -92,6 +95,7 @@ def run(self, runtime_operator: Optional[RuntimeOperator] = None) -> dict[str, A
             mu_map=mu_arr,
             voxel_size_mm=voxel_size_mm,
             scoring_routine=self._scoring_routine,
+            mu_map_type=self._mu_map_type,
         )
         raw_outputs = self.python_connector.run(runtime_operator=runtime_operator)
         self._outputs = {