simind-python-connector 1.1.2__tar.gz → 1.2.0__tar.gz

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/MANIFEST.in

@@ -11,12 +11,8 @@ recursive-include tests/fixtures *.smc
 recursive-include examples *.py *.sh
 recursive-include scripts *.py *.sh
 recursive-include docker Dockerfile *.md *.txt *.yaml *.yml *.py *.sh
-exclude AGENTS.md
-exclude opencode.jsonc
-exclude CLAUDE.md
 exclude simind_manual.pdf
 prune simind
-prune docs/superpowers
 prune docs/_build
 prune docs/_generated
 global-exclude __pycache__

{simind_python_connector-1.1.2/simind_python_connector.egg-info → simind_python_connector-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: simind-python-connector
-Version: 1.1.2
+Version: 1.2.0
 Summary: Python SIMIND Monte Carlo connector with STIR/SIRF/PyTomography adaptors
 Author-email: Sam Porter <sam.porter.18@ucl.ac.uk>, Rebecca Gillen <rebecca.gillen.18@ucl.ac.uk>, "Efstathios (Stahis) Varzakis" <efstathios.varzakis.22@ucl.ac.uk>
 Maintainer-email: Sam Porter <sam.porter.18@ucl.ac.uk>
@@ -61,6 +61,9 @@ University.
 SIMIND is **not distributed** with this package. You must separately obtain and
 install a licensed SIMIND installation.
 
+**Supported SIMIND version:** SIMIND V8.0. SIMIND V9.0 is not supported yet;
+V9 support will follow in a later release.
+
 ## Quick Links
 - [Full Documentation](https://simind-python-connector.readthedocs.io/)
 - [Installation](https://simind-python-connector.readthedocs.io/en/latest/installation.html)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/README.md

@@ -19,6 +19,9 @@ University.
 SIMIND is **not distributed** with this package. You must separately obtain and
 install a licensed SIMIND installation.
 
+**Supported SIMIND version:** SIMIND V8.0. SIMIND V9.0 is not supported yet;
+V9 support will follow in a later release.
+
 ## Quick Links
 - [Full Documentation](https://simind-python-connector.readthedocs.io/)
 - [Installation](https://simind-python-connector.readthedocs.io/en/latest/installation.html)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/README.md

@@ -74,6 +74,9 @@ Services
 Notes
 -----
 
+- The container scripts run the `python` service as the invoking host user
+  (`HOST_UID`/`HOST_GID`); direct `docker compose run python` runs as root.
+  The SIRF-based services always run as uid 1000 (`jovyan`).
 - The SIRF container build arg is `SIRF_BASE_IMAGE`.
 - The STIR container build arg is `STIR_BASE_IMAGE`.
 - Install SIMIND by following the official installation instructions on the SIMIND website.

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/compose.yaml

@@ -4,8 +4,12 @@ services:
       context: ..
       dockerfile: docker/python/Dockerfile
     image: simind-python-connector/python:dev
+    # The container scripts run this service as the invoking host user so its
+    # outputs in the shared mount stay writable; direct use runs as root.
+    user: "${HOST_UID:-0}:${HOST_GID:-0}"
     working_dir: /workspace
     environment:
+      HOME: /tmp
       SIMIND_CONNECTOR_BACKEND: python
       SIMIND_ROOT: /workspace/simind
       SIMIND_BIN: ${SIMIND_BIN:-/workspace/simind/simind}

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/constraints.txt

@@ -2,5 +2,7 @@
 # NumPy is capped below 2.x: the STIR/SIRF binaries in the synerbi/sirf base
 # images are compiled against NumPy 1.x and crash with NumPy 2 (see README
 # "NumPy ABI" notes).
+# Backend installs also resolve the base image's imagecodecs and tifffile so
+# their NumPy requirements stay compatible with this cap.
 numpy<2.0
 pytest==8.4.2

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/python/Dockerfile

@@ -16,7 +16,7 @@ ENV PATH=${SIMIND_ROOT}/bin:${SIMIND_ROOT}:${PATH}
 # MPICH runtime for SIMIND's MPI binary; the compat script exposes the library
 # names that binary was built against. See docker/python/install_mpich_compat.sh.
 RUN apt-get update \
-    && apt-get install -y --no-install-recommends mpich \
+    && apt-get install -y --no-install-recommends git mpich \
     && rm -rf /var/lib/apt/lists/*
 
 COPY docker/python/install_mpich_compat.sh /usr/local/bin/install_mpich_compat.sh

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/pytomography/Dockerfile

@@ -21,9 +21,8 @@ COPY --chown=1000:100 . /workspace
 
 RUN python -m pip install --upgrade pip \
     && pip install --index-url https://download.pytorch.org/whl/cpu torch \
-    && pip install pytomography --no-deps \
-    && pip install fft-conv-pytorch kornia pydicom rt-utils torchrbf uproot \
-    && pip install --constraint /workspace/docker/constraints.txt -e ".[dev,examples]" \
+    && pip install --constraint /workspace/docker/constraints.txt \
+        -e ".[dev,examples]" pytomography imagecodecs tifffile \
     && python - <<'PY'
 import importlib
 for module in ("torch", "pytomography", "pytest"):

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/sirf/Dockerfile

@@ -20,7 +20,8 @@ WORKDIR /workspace
 COPY --chown=1000:100 . /workspace
 
 RUN python -m pip install --upgrade pip \
-    && pip install --constraint /workspace/docker/constraints.txt -e ".[dev,examples]" \
+    && pip install --constraint /workspace/docker/constraints.txt \
+        -e ".[dev,examples]" imagecodecs tifffile \
     && python - <<'PY'
 import importlib
 for module in ("sirf.STIR", "pytest"):

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docker/stir/Dockerfile

@@ -20,7 +20,8 @@ WORKDIR /workspace
 COPY --chown=1000:100 . /workspace
 
 RUN python -m pip install --upgrade pip \
-    && pip install --constraint /workspace/docker/constraints.txt -e ".[dev,examples]" \
+    && pip install --constraint /workspace/docker/constraints.txt \
+        -e ".[dev,examples]" imagecodecs tifffile \
     && python - <<'PY'
 import stir  # noqa: F401
 import pytest  # noqa: F401

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/changelog.rst

@@ -7,6 +7,64 @@ All notable changes to this project are documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_, and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+1.2.0 - 2026-10-16
+------------------
+
+Changed
+~~~~~~~
+
+- **Breaking:** without the ``CA`` runtime switch, SCATTWIN runs return only
+  the total projection. The energy-window file now holds exactly the requested
+  windows; 1.1.x appended a scatter-order-1 line when every order was 0, which
+  made SIMIND also write ``sca``, ``air`` and a duplicate ``sca_w2``. Code that
+  reads ``outputs["sca_w1"]`` or ``get_scatter_output()`` needs
+  ``add_runtime_switch("CA", 1)``.
+- Internal tidy-up with no behaviour change: type hints use ``X | None`` and
+  built-in generics, ``__all__`` lists are sorted, and redundant ``pass``
+  statements are removed.
+
+Added
+~~~~~
+
+- The ``CA`` runtime switch is accepted (``add_runtime_switch("CA", n)``). It
+  selects the SCATTWIN projections SIMIND V8 writes: without it only ``tot``;
+  ``1`` adds ``sca`` and ``air``; ``2`` adds ``pri``, ``sca`` and ``air``.
+- A SCATTWIN run without the ``CA`` switch, and with every scatter order 0,
+  issues a ``UserWarning`` saying that only total projections will be written.
+- ``get_primary_output()`` returns the primary projection written with
+  ``CA`` = 2.
+- ``get_scatter_output()`` and ``get_primary_output()`` return the total minus
+  the other component when only that one was written, and warn and return
+  ``None`` when neither was.
+
+Fixed
+~~~~~
+
+- ``number - x`` on SIRF image and acquisition wrappers returned wrong values.
+- ``StirImageData`` arithmetic raised ``TypeError`` on STIR 6.2, and
+  ``create_simple_phantom()`` and ``create_attenuation_map()`` failed there.
+- ``StirAcquisitionData.get_info()`` returns STIR's parameter text instead of
+  the SWIG object's address.
+- ``from simind_python_connector.utils import *`` raised ``AttributeError``.
+- Interfile data with a partial trailing pixel is rejected instead of the extra
+  bytes being ignored.
+- The DICOM acquisition builder no longer prints debug lines, and its warnings
+  name the missing ``AcquisitionDate`` and ``AcquisitionTime`` fields.
+
+Deprecated
+~~~~~~~~~~
+
+- STIR 6.2 and earlier, which have no image arithmetic. ``StirImageData``
+  computes it in NumPy there and issues a ``DeprecationWarning``; support will
+  be removed in a future release.
+
+Notes
+~~~~~
+
+- This release supports SIMIND V8.0. SIMIND V9.0 is not supported yet: it
+  changes several output formats and behaviours the connector relies on, so
+  V9 support will follow in a later release.
+
 1.1.2 - 2026-10-15
 ------------------
 

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/conf.py

@@ -3,7 +3,8 @@
 import os
 import sys
 from datetime import datetime
-from importlib import metadata as importlib_metadata
+from pathlib import Path
+from runpy import run_path
 
 
 # Add the package to the path
@@ -13,13 +14,9 @@ sys.path.insert(0, os.path.abspath(".."))
 project = "simind-python-connector"
 copyright = f"{datetime.now().year}, Sam Porter, Efstathios Varzakis"
 author = "Sam Porter, Efstathios Varzakis"
-release = "1.1.2"
-for dist_name in ("simind-python-connector",):
-    try:
-        release = importlib_metadata.version(dist_name)
-        break
-    except importlib_metadata.PackageNotFoundError:
-        continue
+release = run_path(
+    str(Path(__file__).resolve().parents[1] / "simind_python_connector/_version.py")
+)["__version__"]
 version = ".".join(release.split(".")[:2])
 
 # General configuration

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/contributing.rst

@@ -44,3 +44,24 @@ If you make changes that affect the documentation:
 .. code-block:: bash
 
     sphinx-build -b html docs docs/_build/html
+
+Preparing a Release
+-------------------
+
+The version is defined once in ``simind_python_connector/_version.py``.
+Package builds, ``simind_python_connector.__version__``, documentation and the
+publishing workflow all read it directly.
+
+Write the release notes for the next version in ``CHANGELOG.md`` and
+``docs/changelog.rst``, then run:
+
+.. code-block:: bash
+
+    bash scripts/release.sh patch
+
+Use ``minor``, ``major`` or an exact version such as ``1.2.0`` instead of
+``patch`` when appropriate. The script updates the shared version and the
+Zenodo and citation metadata, including the citation release date, then creates
+a local release commit and tag. Review your working tree first; the script also
+commits the release notes. It prints the commands for pushing and publishing.
+No other version values need editing by hand.

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/examples/01_basic_simulation.py

@@ -48,10 +48,11 @@ def main() -> None:
     connector.add_config_value(53, 0)
     connector.set_energy_windows([126.0], [154.0], [0])
     add_standard_runtime(connector, photon_multiplier=1, seed=12345, nuclide="tc99m")
+    connector.add_runtime_switch("CA", 1)  # also write scatter and air projections
 
     outputs = connector.run()
     total = outputs["tot_w1"].projection
-    scatter = outputs.get("sca_w1", outputs["tot_w1"]).projection
+    scatter = outputs["sca_w1"].projection
     primary = np.clip(total - scatter, a_min=0.0, a_max=None)
 
     np.save(output_dir / "total.npy", total)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/examples/02_runtime_switch_comparison.py

@@ -47,6 +47,7 @@ def _run_case(
     connector.add_config_value(53, 0)
     connector.set_energy_windows([75.0], [225.0], [0])
     add_standard_runtime(connector, photon_multiplier=1, seed=seed)
+    connector.add_runtime_switch("CA", 0)  # total projections only
     outputs = connector.run()
     return outputs["tot_w1"].projection
 

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/examples/03_multi_window.py

@@ -51,6 +51,7 @@ def main() -> None:
     connector.set_energy_windows(lowers, uppers, orders)
     connector.add_config_value(1, 208.0)
     add_standard_runtime(connector, photon_multiplier=1, seed=12345, nuclide="lu177")
+    connector.add_runtime_switch("CA", 0)  # total projections only
 
     outputs = connector.run()
 

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/examples/05_scattwin_vs_penetrate_comparison.py

@@ -47,6 +47,10 @@ def _run_case(
     connector.add_config_value(53, 1)
     connector.set_energy_windows([75.0], [225.0], [0])
     add_standard_runtime(connector, photon_multiplier=1, seed=12345)
+    # CA = 1 makes SCATTWIN write scatter and air projections; PENETRATE would
+    # drop its per-component outputs with it.
+    if scoring_routine == 1:
+        connector.add_runtime_switch("CA", 1)
 
     results = connector.run()
     return {key: value.projection for key, value in results.items()}
@@ -401,8 +405,8 @@ def main() -> None:
     )
     pen_outputs = _run_case(pen_dir, "pen_case01", source, mu_map, scoring_routine=4)
 
-    scatt_total = scatt_outputs.get("tot_w1", scatt_outputs[sorted(scatt_outputs)[0]])
-    scatt_scatter = scatt_outputs.get("sca_w1", np.zeros_like(scatt_total))
+    scatt_total = scatt_outputs["tot_w1"]
+    scatt_scatter = scatt_outputs["sca_w1"]
     scatt_primary = np.clip(scatt_total - scatt_scatter, a_min=0.0, a_max=None)
     scatt_primary_sum = float(scatt_primary.sum())
     scatt_scatter_sum = float(scatt_scatter.sum())

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/examples/07A_stir_adaptor_osem.py

@@ -177,6 +177,7 @@ def main() -> None:
     adaptor.add_runtime_switch("CC", "ma-megp")
     adaptor.add_runtime_switch("NN", 1)
     adaptor.add_runtime_switch("RR", 12345)
+    adaptor.add_runtime_switch("CA", 0)  # total projections only
     adaptor.add_config_value(1, 140.0)
     adaptor.add_config_value(19, 2)
     adaptor.add_config_value(53, 0)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0/docs}/examples/07B_sirf_adaptor_osem.py

@@ -159,6 +159,7 @@ def main() -> None:
     adaptor.add_runtime_switch("CC", "ma-megp")
     adaptor.add_runtime_switch("NN", 1)
     adaptor.add_runtime_switch("RR", 12345)
+    adaptor.add_runtime_switch("CA", 0)  # total projections only
     adaptor.add_config_value(1, 140.0)
     adaptor.add_config_value(19, 2)
     adaptor.add_config_value(53, 0)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/examples/07C_pytomography_adaptor_osem.py

@@ -127,6 +127,7 @@ def main() -> None:
     adaptor.add_runtime_switch("CC", "ma-megp")
     adaptor.add_runtime_switch("NN", 1)
     adaptor.add_runtime_switch("RR", 12345)
+    adaptor.add_runtime_switch("CA", 0)  # total projections only
     adaptor.add_config_value(1, 140.0)
     adaptor.add_config_value(19, 2)
     adaptor.add_config_value(53, 0)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/installation.rst

@@ -65,6 +65,16 @@ maintained by** the SIMIND project or Lund University.
 SIMIND is **not** distributed with this package (or on PyPI) and must be
 installed separately.
 
+Supported SIMIND Versions
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release supports and is tested with **SIMIND V8.0**.
+
+**SIMIND V9.0 is not supported yet.** V9 changes several output formats and
+behaviours the connector relies on, so runs can fail or return incorrect
+projections. V9 support will follow in a later release; until then, use
+SIMIND V8.0.
+
 Use the official SIMIND resources for installation and manual/reference
 documentation:
 

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/testing.rst

@@ -29,14 +29,15 @@ Automatic Dependency Detection
 
 The test suite automatically detects available dependencies:
 
-* **SIRF detection**: Attempts to ``import sirf``
+* **SIRF detection**: Attempts to ``import sirf.STIR``
 * **STIR detection**: Attempts to ``import stir``, then imports the STIR
   conversion helpers the way the package itself does (``stir.extra`` preferred,
   the legacy ``stirextra`` module only as a fallback), so a broken
   ``stir.extra`` dependency is reported as unavailable instead of being masked
   by the legacy module
 * **PyTomography detection**: Attempts to ``import pytomography``
-* **SIMIND detection**: Checks if ``simind`` command is available
+* **SIMIND detection**: Uses ``$SIMIND_BIN`` when set, otherwise looks for
+  ``simind`` on ``PATH``
 * **CI detection**: Checks ``CI`` or ``GITHUB_ACTIONS`` environment variables
 
 Tests requiring unavailable dependencies are automatically skipped with informative messages.
@@ -118,17 +119,6 @@ the official SIMIND site and manual:
 The container suite includes ``tests/test_container_library_isolation.py``,
 which asserts that each container can import only its target backend library.
 
-Alternative CI Configuration
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-The dependency-exclusion selection lives in ``.github/workflows/tests.yml`` so it
-applies to CI only; the default ``pytest`` run keeps every available test.
-
-.. code-block:: bash
-
-    # Run only the CI-friendly selection locally
-    pytest -m "not integration and not requires_sirf and not requires_stir and not requires_simind and not requires_pytomography and not requires_cil and not requires_setr and not ci_skip"
-
 Test Categories
 ---------------
 
@@ -140,8 +130,8 @@ The default CI job runs the tests that avoid heavyweight dependencies. These foc
 * **Conversion maths** – ``tests/test_schneider_density.py`` exercises the HU-to-density pipelines.
 * **Configuration & builders** – ``tests/test_simulation_config.py`` and ``tests/test_acquisition_builder_unit.py`` validate YAML/SMC handling plus Interfile header generation without a SIRF runtime.
 * **Connector behavior** – ``tests/test_python_connector.py`` and ``tests/test_connector_backend_separation.py`` cover the connector-first API without requiring reconstruction packages.
-* **Utility helpers** – ``tests/test_utils.py``, ``tests/test_utils_small.py``, ``tests/test_interfile_parser.py``, and ``tests/test_interfile_numpy.py`` cover file parsing and small helper functions.
-* **Backend guards** – ``tests/test_backends.py`` ensures optional backend imports remain isolated.
+* **Utility helpers** – ``tests/test_utils_small.py``, ``tests/test_interfile_parser.py``, and ``tests/test_interfile_numpy.py`` cover file parsing and small helper functions.
+* **Backend dispatch** – ``tests/test_backends.py`` covers backend detection and dispatch with stand-in backends.
 
 Backend-Dependent Suites
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -149,15 +139,16 @@ Backend-Dependent Suites
 Tests that construct real STIR/SIRF/PyTomography objects carry dependency
 markers and are skipped when those packages are unavailable. These include:
 
-* ``tests/test_native_adaptors.py`` for STIR/SIRF adaptor behavior.
+* ``tests/test_native_geometry_real.py`` for native STIR/SIRF image geometry.
+* ``tests/test_utils.py`` for phantom, image and acquisition helpers on SIRF and STIR.
 * ``tests/test_pytomography_adaptor.py`` for PyTomography tensor and output adaptation.
-* ``tests/test_arithmetic_operations.py`` and ``tests/test_sirf_stir_utils.py`` for backend wrapper/helper behavior.
+* ``tests/test_arithmetic_operations.py`` and ``tests/test_stir_backend_arithmetic.py`` for arithmetic on real backend objects.
 
 SIMIND and Container Diagnostics
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-SIMIND-dependent tests use ``requires_simind`` and are skipped unless the
-``simind`` command is available. Container and geometry diagnostics include:
+SIMIND-dependent tests use ``requires_simind`` and are skipped unless SIMIND
+is found. Container and geometry diagnostics include:
 
 * ``tests/test_integration.py`` for full workflow checks.
 * ``tests/test_container_library_isolation.py`` for backend container import isolation.
@@ -168,13 +159,6 @@ latter two are provided by ``docker/python/Dockerfile``, which installs MPICH
 and exposes the ``libmpi.so.12``/``libmpifort.so.12`` names SIMIND links
 against. They never run in GitHub CI because the SIMIND binary is not tracked.
 
-Integration Test
-~~~~~~~~~~~~~~~~
-
-``tests/test_integration.py`` orchestrates a full example run and needs
-external runtime dependencies. It is marked with dependency markers so it is
-skipped in lightweight CI environments.
-
 Configuration Files
 -------------------
 
@@ -195,34 +179,19 @@ tests/conftest.py
 Adding New Tests
 ----------------
 
-When adding new tests, use appropriate markers:
-
-.. code-block:: python
-
-    import pytest
-
-    @pytest.mark.unit
-    def test_pure_python_logic():
-        """Test that doesn't need external dependencies."""
-        assert True
+Use ``unit`` for isolated behavior and ``integration`` for workflows involving
+external systems. Add the relevant dependency markers whenever a test needs a
+reconstruction library or SIMIND. The distribution build check runs once in
+the CI build job, separately from the unit test matrix.
 
-    @pytest.mark.requires_sirf  
-    def test_sirf_functionality():
-        """Test that uses SIRF objects."""
-        from sirf.STIR import ImageData
-        # ... test code
+Assert observable results: array values and orientation, saved file contents,
+metadata or a useful failure. Stub external I/O at the boundary when needed.
+Tests that only check whether a function exists, repeat its implementation or
+assert private storage details do not establish that a workflow works.
 
-    @pytest.mark.requires_simind
-    def test_simind_execution():
-        """Test that calls SIMIND command."""
-        # ... test code that runs simind
-
-    @pytest.mark.requires_pytomography
-    def test_pytomography_path():
-        """Test that uses PyTomography APIs."""
-        # ... test code that imports pytomography
-
-This ensures your tests will be properly categorized and run in the appropriate environments.
+SIMIND geometry comparisons use Flag 8 set to false for a repeatable initial
+random state. Choose photon statistics to support the numerical tolerance;
+setting ``RR`` alone does not make V8 simulations reproducible.
 
 Continuous Integration
 ----------------------
@@ -234,5 +203,3 @@ GitHub Actions is used to run tests automatically. The CI workflow:
 3. **Executes CI-friendly tests** using dependency markers
 4. **Generates coverage reports** for the tested code
 5. **Builds and validates the package**
-
-This approach ensures reliable CI while maintaining comprehensive test coverage for local development.

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/docs/usage.rst

@@ -61,12 +61,10 @@ SPECT header remains. Measured on a real SIMIND V8.0 run, 49 characters is the
 exact maximum prefix for ``{prefix}_tot_w1.a00``; a 50-character prefix
 truncates it. The 47-character cap is a conservative policy with a small margin
 below that measured boundary, not an engine-measured limit. The longest
-engine-written name adds a ``_tot_w{N}.a00`` suffix (10 characters plus the
-digits of the window number), and when every scatter order is below 1 the
-window file gains the required extra line, which adds one more output set, so
-the suffix can reach 13 characters and a 47-character prefix plus that suffix
-uses the 60-character buffer exactly. To stay inside that budget, at most 99
-energy windows are accepted; a larger set raises ``ValueError``.
+engine-written name adds a ``_tot_w{N}.a00`` suffix. With at most 99 energy
+windows this suffix is 12 characters long, leaving a margin inside the
+60-character buffer. Window files contain exactly the requested windows;
+more than 99 windows raises ``ValueError``.
 
 ``RuntimeOperator`` carries per-run switches, an orbit file and an optional
 timeout in seconds. A run that exceeds the timeout stops and raises
@@ -116,6 +114,11 @@ supported by the Interfile connector. LIST_MODE (2) and FORCED_COLLIMATION (3)
 write outputs the connector cannot read, so they are rejected at preflight;
 they remain available through lower-level use of the package.
 
+For repeatable diagnostic runs on SIMIND V8, set
+``connector.get_config().set_flag(8, False)`` to reuse the same initial random
+state. The bundled configurations enable Flag 8 for independent simulations.
+The ``RR`` switch alone does not make repeated runs reproducible.
+
 A literal 1x1x1 voxel phantom is rejected (SIMIND does not support it), so pad
 the source and mu map to at least two voxels in one dimension. A non-zero
 source that ``quantization_scale`` rounds to all zeros is also rejected;
@@ -136,12 +139,28 @@ Adaptor Workflows
 Use adaptors when you want connector-managed SIMIND execution plus native
 objects for a target reconstruction package.
 
-Primary projections are unsupported by these adaptors. ``get_primary_output()``
-raises ``NotImplementedError`` once outputs exist and ``RuntimeError`` before a
-successful run. The adaptors consume SIMIND's standard SPECT output, which has
-no standalone primary file; primary projections can still be produced through
-lower-level SIMIND use with ``/CA:2``. Use ``get_total_output()`` and
-``get_scatter_output()`` instead.
+Enabling ``keep_all_views_in_cache`` in SIRF/STIR can cause memory errors on
+large acquisitions. Disable it if view caching exhausts available memory.
+
+With the SCATTWIN scoring routine, SIMIND V8 writes only the total projection
+unless the ``CA`` runtime switch asks for more: ``CA`` = 1 adds scatter
+(``sca``) and air (``air``) projections, ``CA`` = 2 adds primary (``pri``),
+scatter and air projections. A SCATTWIN run without ``CA`` issues a
+``UserWarning``; set ``CA`` = 0 to keep total-only output without it.
+
+Keep energy-window scatter orders at 0 unless you need SIMIND's per-order
+behaviour. On V8, a window with scatter order above 0 produces only
+``sca_wN`` (no ``tot_wN``), and its presence makes SIMIND also write ``sca``
+and ``air`` for the order-0 windows whatever ``CA`` is set to.
+
+.. code-block:: python
+
+    adaptor.add_runtime_switch("CA", 1)
+
+``get_scatter_output()`` and ``get_primary_output()`` return the written
+projection, or the total minus the other one when only that was written
+(``tot = pri + sca``). When neither was written they warn and return ``None``.
+Before a successful run they raise ``RuntimeError``.
 
 STIR adaptor
 ~~~~~~~~~~~~

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/examples/01_basic_simulation.py

@@ -48,10 +48,11 @@ def main() -> None:
     connector.add_config_value(53, 0)
     connector.set_energy_windows([126.0], [154.0], [0])
     add_standard_runtime(connector, photon_multiplier=1, seed=12345, nuclide="tc99m")
+    connector.add_runtime_switch("CA", 1)  # also write scatter and air projections
 
     outputs = connector.run()
     total = outputs["tot_w1"].projection
-    scatter = outputs.get("sca_w1", outputs["tot_w1"]).projection
+    scatter = outputs["sca_w1"].projection
     primary = np.clip(total - scatter, a_min=0.0, a_max=None)
 
     np.save(output_dir / "total.npy", total)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/examples/02_runtime_switch_comparison.py

@@ -47,6 +47,7 @@ def _run_case(
     connector.add_config_value(53, 0)
     connector.set_energy_windows([75.0], [225.0], [0])
     add_standard_runtime(connector, photon_multiplier=1, seed=seed)
+    connector.add_runtime_switch("CA", 0)  # total projections only
     outputs = connector.run()
     return outputs["tot_w1"].projection
 

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/examples/03_multi_window.py

@@ -51,6 +51,7 @@ def main() -> None:
     connector.set_energy_windows(lowers, uppers, orders)
     connector.add_config_value(1, 208.0)
     add_standard_runtime(connector, photon_multiplier=1, seed=12345, nuclide="lu177")
+    connector.add_runtime_switch("CA", 0)  # total projections only
 
     outputs = connector.run()
 

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/examples/05_scattwin_vs_penetrate_comparison.py

@@ -47,6 +47,10 @@ def _run_case(
     connector.add_config_value(53, 1)
     connector.set_energy_windows([75.0], [225.0], [0])
     add_standard_runtime(connector, photon_multiplier=1, seed=12345)
+    # CA = 1 makes SCATTWIN write scatter and air projections; PENETRATE would
+    # drop its per-component outputs with it.
+    if scoring_routine == 1:
+        connector.add_runtime_switch("CA", 1)
 
     results = connector.run()
     return {key: value.projection for key, value in results.items()}
@@ -401,8 +405,8 @@ def main() -> None:
     )
     pen_outputs = _run_case(pen_dir, "pen_case01", source, mu_map, scoring_routine=4)
 
-    scatt_total = scatt_outputs.get("tot_w1", scatt_outputs[sorted(scatt_outputs)[0]])
-    scatt_scatter = scatt_outputs.get("sca_w1", np.zeros_like(scatt_total))
+    scatt_total = scatt_outputs["tot_w1"]
+    scatt_scatter = scatt_outputs["sca_w1"]
     scatt_primary = np.clip(scatt_total - scatt_scatter, a_min=0.0, a_max=None)
     scatt_primary_sum = float(scatt_primary.sum())
     scatt_scatter_sum = float(scatt_scatter.sum())

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/examples/07A_stir_adaptor_osem.py

@@ -177,6 +177,7 @@ def main() -> None:
     adaptor.add_runtime_switch("CC", "ma-megp")
     adaptor.add_runtime_switch("NN", 1)
     adaptor.add_runtime_switch("RR", 12345)
+    adaptor.add_runtime_switch("CA", 0)  # total projections only
     adaptor.add_config_value(1, 140.0)
     adaptor.add_config_value(19, 2)
     adaptor.add_config_value(53, 0)

{simind_python_connector-1.1.2/docs → simind_python_connector-1.2.0}/examples/07B_sirf_adaptor_osem.py

@@ -159,6 +159,7 @@ def main() -> None:
     adaptor.add_runtime_switch("CC", "ma-megp")
     adaptor.add_runtime_switch("NN", 1)
     adaptor.add_runtime_switch("RR", 12345)
+    adaptor.add_runtime_switch("CA", 0)  # total projections only
     adaptor.add_config_value(1, 140.0)
     adaptor.add_config_value(19, 2)
     adaptor.add_config_value(53, 0)

{simind_python_connector-1.1.2 → simind_python_connector-1.2.0}/examples/07C_pytomography_adaptor_osem.py

@@ -127,6 +127,7 @@ def main() -> None:
     adaptor.add_runtime_switch("CC", "ma-megp")
     adaptor.add_runtime_switch("NN", 1)
     adaptor.add_runtime_switch("RR", 12345)
+    adaptor.add_runtime_switch("CA", 0)  # total projections only
     adaptor.add_config_value(1, 140.0)
     adaptor.add_config_value(19, 2)
     adaptor.add_config_value(53, 0)