simind-python-connector 1.0.0__py3-none-any.whl

simind_python_connector/data/bone.atn

@@ -0,0 +1,187 @@
+<head><title>NIST XCOM database</title><!-- Google Analtyics 4 -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=G-9SLN1VEEJ2"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+  gtag('config', 'G-9SLN1VEEJ2');
+</script>
+<!-- End of Google Analytics 4 -->
+<SCRIPT async type="text/javascript" id="_fed_an_ua_tag" src="https://dap.digitalgov.gov/Universal-Federated-Analytics-Min.js?agency=DOC&subagency=NIST&pua=UA-37115410-46&yt=false&exts=ppsx,pps,f90,sch,rtf,wrl,txz,m1v,xlsm,msi,xsd,f,tif,eps,mpg,xml,pl,xlt,c"></script></head>Photon    
+Energy    Coherent 
+
+1.000E-03 3.442E+03 
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+1.000E+05 2.526E-02     
+

simind_python_connector/data/h2o.atn

@@ -0,0 +1,92 @@
+<head><title>NIST XCOM database</title><!-- Google Analtyics 4 -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=G-9SLN1VEEJ2"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+  gtag('config', 'G-9SLN1VEEJ2');
+</script>
+<!-- End of Google Analytics 4 -->
+<SCRIPT async type="text/javascript" id="_fed_an_ua_tag" src="https://dap.digitalgov.gov/Universal-Federated-Analytics-Min.js?agency=DOC&subagency=NIST&pua=UA-37115410-46&yt=false&exts=ppsx,pps,f90,sch,rtf,wrl,txz,m1v,xlsm,msi,xsd,f,tif,eps,mpg,xml,pl,xlt,c"></script></head>Photon    Tot. w/  
+Energy    Coherent 
+
+1.000E-03 4.077E+03 
+1.500E-03 1.376E+03 
+2.000E-03 6.173E+02 
+3.000E-03 1.928E+02 
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+1.000E+05 2.127E-02 

simind_python_connector/utils/__init__.py

@@ -0,0 +1,120 @@
+"""
+Grab-bag of general utilities shared across modules.
+They are re-exported here for a single, easy import path.
+"""
+
+import contextlib
+import importlib
+
+
+# Lazy imports to avoid SIRF dependencies in CI
+def __getattr__(name):
+    if name in (
+        "interfile_numpy",
+        "io_utils",
+        "simind_utils",
+        "stir_utils",
+        "sirf_stir_utils",
+    ):
+        return importlib.import_module(f".{name}", __name__)
+    raise AttributeError(f"module '{__name__}' has no attribute '{name}'")
+
+
+def get_array(obj):
+    """Return NumPy array from SIRF or STIR object.
+
+    This function works with both SIRF and STIR Python backends:
+    - SIRF: Uses .asarray() or .as_array()
+    - STIR: Uses stirextra.to_numpy()
+    - Backend wrappers: Uses .as_array() method
+
+    Args:
+        obj: Image or acquisition data object (SIRF, STIR, or wrapped)
+
+    Returns:
+        np.ndarray: NumPy array view of the data
+
+    Raises:
+        AttributeError: If object cannot be converted to array
+    """
+    # Check if it's a wrapped backend object
+    if hasattr(obj, "as_array") and callable(obj.as_array):
+        return obj.as_array()
+
+    # Try SIRF native methods
+    if hasattr(obj, "asarray"):
+        try:
+            return obj.asarray()
+        except Exception:
+            return obj.as_array()  # Fallback to as_array if asarray fails
+    if hasattr(obj, "as_array"):
+        return obj.as_array()
+
+    # Try STIR native conversion
+    with contextlib.suppress(ImportError, TypeError, AttributeError):
+        import stirextra
+
+        return stirextra.to_numpy(obj)
+    raise AttributeError(
+        f"Cannot convert {type(obj)} to numpy array. "
+        f"Object must have asarray(), as_array() method, or be a STIR object."
+    )
+
+
+def to_projdata_in_memory(proj_data):
+    """Convert ProjData to ProjDataInMemory for arithmetic operations.
+
+    STIR's ProjData objects don't support arithmetic operations directly.
+    This function converts them to ProjDataInMemory which does.
+
+    Args:
+        proj_data: STIR ProjData object or SIRF AcquisitionData
+
+    Returns:
+        ProjDataInMemory object (STIR) or cloned AcquisitionData (SIRF)
+
+    Note:
+        For SIRF AcquisitionData, this returns a clone since SIRF already
+        supports arithmetic operations.
+    """
+    # Check if it's SIRF (has clone method and supports arithmetic)
+    if hasattr(proj_data, "clone") and not hasattr(proj_data, "get_proj_data_info"):
+        return proj_data.clone()
+
+    # STIR backend: convert to ProjDataInMemory
+    try:
+        import stir
+
+        # Check if already ProjDataInMemory
+        if isinstance(proj_data, stir.ProjDataInMemory):
+            return proj_data
+
+        # Convert ProjData to ProjDataInMemory
+        proj_data_in_mem = stir.ProjDataInMemory(
+            proj_data.get_exam_info(), proj_data.get_proj_data_info()
+        )
+
+        # Copy data segment by segment
+        for seg_num in range(
+            proj_data.get_min_segment_num(), proj_data.get_max_segment_num() + 1
+        ):
+            seg = proj_data.get_segment_by_sinogram(seg_num)
+            proj_data_in_mem.set_segment(seg)
+
+        return proj_data_in_mem
+    except ImportError:
+        # Neither SIRF nor STIR available - return original
+        return proj_data
+
+
+__all__ = [
+    "get_array",
+    "interfile_numpy",
+    "to_projdata_in_memory",
+    "io_utils",
+    "simind_utils",
+    "stir_utils",
+    "sirf_stir_utils",
+    "step_size_rules",
+    "cil_partitioner",
+]

simind_python_connector/utils/backend_access.py

@@ -0,0 +1,121 @@
+"""
+Centralized backend import and access helpers.
+
+This module provides a single source of truth for backend imports, eliminating
+the need for duplicate try/except import blocks scattered throughout the codebase.
+
+All backend-related imports (factory functions, interfaces, detection utilities,
+and wrappers) are centralized here, with proper fallback handling when backends
+are unavailable.
+"""
+
+from types import SimpleNamespace
+from typing import Any, Dict
+
+
+def get_backend_interfaces() -> tuple[bool, Dict[str, Any]]:
+    """Get all backend interfaces and utilities with fallback handling.
+
+    This is the single source of truth for backend imports. When backends are
+    unavailable, it returns stub values (None or type(None)) so calling code
+    can check BACKEND_AVAILABLE and handle the missing dependencies gracefully.
+
+    Returns:
+        Tuple of (BACKEND_AVAILABLE, interfaces_dict) where interfaces_dict contains:
+        - 'factories': Backend factory functions
+          (create_acquisition_data, create_image_data)
+        - 'types': Interface type hints (AcquisitionDataInterface, ImageDataInterface)
+        - 'wrappers': Wrapping utilities
+          (ensure_acquisition_interface, ensure_image_interface, etc.)
+        - 'detection': Backend detection functions (detect_*_backend, get/set_backend)
+
+    Example:
+        >>> BACKEND_AVAILABLE, backends = get_backend_interfaces()
+        >>> if BACKEND_AVAILABLE:
+        >>>     create_acq = backends['factories']['create_acquisition_data']
+        >>>     data = create_acq('template.hs')
+    """
+    try:
+        from simind_python_connector.backends import (
+            AcquisitionDataInterface,
+            ImageDataInterface,
+            create_acquisition_data,
+            create_image_data,
+            detect_acquisition_backend,
+            detect_backend_from_interface,
+            detect_image_backend,
+            get_backend,
+            set_backend,
+        )
+        from simind_python_connector.utils.sirf_stir_utils import (
+            ensure_acquisition_interface,
+            ensure_image_interface,
+            to_native_acquisition,
+            to_native_image,
+        )
+
+        return True, {
+            "factories": {
+                "create_acquisition_data": create_acquisition_data,
+                "create_image_data": create_image_data,
+            },
+            "types": {
+                "AcquisitionDataInterface": AcquisitionDataInterface,
+                "ImageDataInterface": ImageDataInterface,
+            },
+            "wrappers": {
+                "ensure_acquisition_interface": ensure_acquisition_interface,
+                "ensure_image_interface": ensure_image_interface,
+                "to_native_acquisition": to_native_acquisition,
+                "to_native_image": to_native_image,
+            },
+            "detection": {
+                "detect_acquisition_backend": detect_acquisition_backend,
+                "detect_image_backend": detect_image_backend,
+                "detect_backend_from_interface": detect_backend_from_interface,
+                "get_backend": get_backend,
+                "set_backend": set_backend,
+            },
+        }
+    except ImportError:
+        # Return fallback stubs when backends are unavailable
+        return False, {
+            "factories": {
+                "create_acquisition_data": None,
+                "create_image_data": None,
+            },
+            "types": {
+                "AcquisitionDataInterface": type(None),
+                "ImageDataInterface": type(None),
+            },
+            "wrappers": {
+                "ensure_acquisition_interface": None,
+                "ensure_image_interface": None,
+                "to_native_acquisition": None,
+                "to_native_image": None,
+            },
+            "detection": {
+                "detect_acquisition_backend": None,
+                "detect_image_backend": None,
+                "detect_backend_from_interface": None,
+                "get_backend": None,
+                "set_backend": None,
+            },
+        }
+
+
+def _to_namespace(mapping: Dict[str, Any]) -> SimpleNamespace:
+    """Convert a dictionary to a SimpleNamespace (handles None gracefully)."""
+    return SimpleNamespace(**(mapping or {}))
+
+
+BACKEND_AVAILABLE, _interfaces = get_backend_interfaces()
+BACKENDS = SimpleNamespace(
+    factories=_to_namespace(_interfaces.get("factories", {})),
+    types=_to_namespace(_interfaces.get("types", {})),
+    wrappers=_to_namespace(_interfaces.get("wrappers", {})),
+    detection=_to_namespace(_interfaces.get("detection", {})),
+)
+
+
+__all__ = ["get_backend_interfaces", "BACKEND_AVAILABLE", "BACKENDS"]

simind_python_connector/utils/import_helpers.py

@@ -0,0 +1,74 @@
+"""
+Centralized import helpers for SIRF/STIR backends.
+
+This module provides reusable functions for importing backend types with
+proper fallback handling. This eliminates the need for duplicate try/except
+import blocks scattered throughout the codebase.
+"""
+
+from typing import Tuple, Type
+
+
+def get_sirf_types() -> Tuple[Type, Type, bool]:
+    """Import SIRF types with fallback.
+
+    Returns:
+        Tuple of (ImageData, AcquisitionData, SIRF_AVAILABLE)
+        If SIRF is not available, returns (type(None), type(None), False)
+    """
+    try:
+        from sirf.STIR import AcquisitionData, ImageData
+
+        return ImageData, AcquisitionData, True
+    except ImportError:
+        return type(None), type(None), False
+
+
+def get_stir_types() -> Tuple[Type, Type, bool]:
+    """Import STIR Python types with fallback.
+
+    Returns:
+        Tuple of (FloatVoxelsOnCartesianGrid, ProjData, STIR_AVAILABLE)
+        If STIR is not available, returns (type(None), type(None), False)
+    """
+    try:
+        import stir
+
+        return stir.FloatVoxelsOnCartesianGrid, stir.ProjData, True
+    except ImportError:
+        return type(None), type(None), False
+
+
+def get_backend_types() -> Tuple[Type, Type, Type, Type, str]:
+    """Import backend-agnostic types (tries SIRF first, then STIR).
+
+    Returns:
+        Tuple of (ImageData, AcquisitionData, ImageType, AcqType, backend_name)
+        where ImageType/AcqType are the native backend types
+
+    Raises:
+        ImportError: If neither SIRF nor STIR is available
+    """
+    # Try SIRF first
+    ImageData, AcquisitionData, sirf_available = get_sirf_types()
+    if sirf_available:
+        return ImageData, AcquisitionData, ImageData, AcquisitionData, "sirf"
+
+    # Fall back to STIR
+    StirImage, StirProj, stir_available = get_stir_types()
+    if stir_available:
+        return StirImage, StirProj, StirImage, StirProj, "stir"
+
+    raise ImportError(
+        "Neither SIRF nor STIR Python is available. "
+        "Please install one of:\n"
+        "  - SIRF (sirf.STIR)\n"
+        "  - STIR Python (stir + stirextra)"
+    )
+
+
+__all__ = [
+    "get_sirf_types",
+    "get_stir_types",
+    "get_backend_types",
+]