goad-py 0.3.0__cp38-abi3-musllinux_1_2_aarch64.whl → 0.4.2__cp38-abi3-musllinux_1_2_aarch64.whl

goad_py/__init__.py

@@ -1,5 +1,7 @@
-from .goad_py import *
+# Re-export everything from the compiled Rust module
+from goad_py._goad_py import *
 
-__doc__ = goad_py.__doc__
-if hasattr(goad_py, "__all__"):
-    __all__ = goad_py.__all__
+# Import Python modules
+from .convergence import Convergence, Convergable, ConvergenceResults
+
+__all__ = ['Convergence', 'Convergable', 'ConvergenceResults']

goad_py/convergence.py

@@ -0,0 +1,382 @@
+from dataclasses import dataclass
+from typing import List, Dict, Optional, Tuple
+import numpy as np
+from . import _goad_py as goad
+
+
+@dataclass
+class Convergable:
+    """Represents a variable to monitor for convergence."""
+    variable: str  # 'asymmetry', 'scatt', 'ext', or 'albedo'
+    tolerance_type: str = 'relative'  # 'relative' or 'absolute'
+    tolerance: float = 0.01
+
+    def __post_init__(self):
+        valid_variables = {'asymmetry', 'scatt', 'ext', 'albedo'}
+        if self.variable not in valid_variables:
+            raise ValueError(f"Invalid variable '{self.variable}'. Must be one of {valid_variables}")
+
+        valid_types = {'relative', 'absolute'}
+        if self.tolerance_type not in valid_types:
+            raise ValueError(f"Invalid tolerance_type '{self.tolerance_type}'. Must be one of {valid_types}")
+
+        if self.tolerance <= 0:
+            raise ValueError(f"Tolerance must be positive, got {self.tolerance}")
+
+
+@dataclass
+class ConvergenceResults:
+    """Results from a convergence study."""
+    converged: bool
+    n_orientations: int
+    values: Dict[str, float]  # Final mean values for each tracked variable
+    sem_values: Dict[str, float]  # Final SEM values for each tracked variable
+    mueller_1d: Optional[np.ndarray] = None
+    mueller_2d: Optional[np.ndarray] = None
+    convergence_history: List[Tuple[int, str, float]] = None  # (n_orientations, variable, sem)
+    warning: Optional[str] = None
+
+
+class Convergence:
+    """Runs multiple MultiProblems until convergence criteria are met."""
+
+    def __init__(
+        self,
+        settings: goad.Settings,
+        convergables: List[Convergable],
+        batch_size: int = 24,
+        max_orientations: int = 100_000,
+        min_batches: int = 10,
+        mueller_1d: bool = True,
+        mueller_2d: bool = False
+    ):
+        """
+        Initialize a convergence study.
+
+        Args:
+            settings: GOAD settings for the simulation
+            convergables: List of variables to monitor for convergence
+            batch_size: Number of orientations per iteration
+            max_orientations: Maximum total orientations before stopping
+            min_batches: Minimum number of batches before allowing convergence
+            mueller_1d: Whether to collect 1D Mueller matrices
+            mueller_2d: Whether to collect 2D Mueller matrices
+        """
+        self.settings = settings
+        self.convergables = convergables
+        self.batch_size = batch_size
+        self.max_orientations = max_orientations
+        self.min_batches = min_batches
+        self.mueller_1d = mueller_1d
+        self.mueller_2d = mueller_2d
+
+        # Validate inputs
+        if not convergables:
+            raise ValueError("Must specify at least one convergable")
+
+        if batch_size <= 0:
+            raise ValueError(f"batch_size must be positive, got {batch_size}")
+
+        if max_orientations <= 0:
+            raise ValueError(f"max_orientations must be positive, got {max_orientations}")
+        
+        if min_batches <= 0:
+            raise ValueError(f"min_batches must be positive, got {min_batches}")
+
+        # Initialize tracking variables
+        self.n_orientations = 0
+        self.convergence_history = []
+
+        # Batch-based statistics tracking for rigorous SEM calculation
+        self.batch_data = []  # List of batch statistics
+
+        # Mueller matrix accumulation
+        self.mueller_1d_sum = None
+        self.mueller_2d_sum = None
+
+    def _update_statistics(self, results: goad.Results, batch_size: int):
+        """Update statistics with new batch results.
+
+        Args:
+            results: Results from a MultiProblem run (pre-averaged over batch_size orientations)
+            batch_size: Number of orientations in this batch
+        """
+        # Check for None values indicating Custom binning
+        if (results.asymmetry is None or results.scat_cross is None or
+            results.ext_cross is None or results.albedo is None):
+            raise ValueError(
+                "Received None values for integrated properties. "
+                "This likely means Custom binning scheme is being used. "
+                "Convergence requires Simple or Interval binning schemes."
+            )
+
+        # Store batch data for proper statistical analysis
+        batch_info = {
+            'batch_size': batch_size,
+            'values': {},
+            'weights': {}
+        }
+
+        # Store values and weights for tracked variables
+        for conv in self.convergables:
+            if conv.variable == 'asymmetry':
+                batch_info['values']['asymmetry'] = results.asymmetry
+                batch_info['weights']['asymmetry'] = results.scat_cross
+            elif conv.variable == 'scatt':
+                batch_info['values']['scatt'] = results.scat_cross
+                batch_info['weights']['scatt'] = 1.0  # Equal weighting
+            elif conv.variable == 'ext':
+                batch_info['values']['ext'] = results.ext_cross
+                batch_info['weights']['ext'] = 1.0  # Equal weighting
+            elif conv.variable == 'albedo':
+                batch_info['values']['albedo'] = results.albedo
+                batch_info['weights']['albedo'] = results.ext_cross + results.scat_cross
+
+        self.batch_data.append(batch_info)
+
+        # Update Mueller matrices if enabled
+        if self.mueller_1d and results.mueller_1d is not None:
+            mueller_1d_array = np.array(results.mueller_1d)
+            if self.mueller_1d_sum is None:
+                self.mueller_1d_sum = mueller_1d_array * batch_size
+            else:
+                self.mueller_1d_sum += mueller_1d_array * batch_size
+
+        if self.mueller_2d and results.mueller is not None:
+            mueller_2d_array = np.array(results.mueller)
+            if self.mueller_2d_sum is None:
+                self.mueller_2d_sum = mueller_2d_array * batch_size
+            else:
+                self.mueller_2d_sum += mueller_2d_array * batch_size
+
+        # Update total orientation count
+        self.n_orientations += batch_size
+
+    def _calculate_mean_and_sem(self, variable: str) -> Tuple[float, float]:
+        """Calculate mean and standard error of the mean for a variable using batch data.
+
+        Args:
+            variable: Variable name
+
+        Returns:
+            Tuple of (mean, sem)
+        """
+        if not self.batch_data:
+            return 0.0, float('inf')
+
+        # Extract batch values and weights
+        batch_values = []
+        batch_weights = []
+        batch_sizes = []
+
+        for batch in self.batch_data:
+            if variable in batch['values']:
+                batch_values.append(batch['values'][variable])
+                batch_weights.append(batch['weights'][variable])
+                batch_sizes.append(batch['batch_size'])
+
+        if not batch_values:
+            return 0.0, float('inf')
+
+        batch_values = np.array(batch_values)
+        batch_weights = np.array(batch_weights)
+        batch_sizes = np.array(batch_sizes)
+
+        # For weighted variables (asymmetry, albedo), use weighted statistics
+        if variable in ['asymmetry', 'albedo']:
+            # Calculate weighted mean across batches
+            # Each batch contributes: weight * batch_size * value
+            total_weighted_sum = np.sum(batch_weights * batch_sizes * batch_values)
+            total_weight = np.sum(batch_weights * batch_sizes)
+            weighted_mean = total_weighted_sum / total_weight
+
+            # Calculate weighted variance between batches
+            if len(batch_values) < 2:
+                return weighted_mean, float('inf')  # Cannot estimate variance with < 2 batches
+
+            # For batch means, we need to account for the effective weight of each batch
+            effective_weights = batch_weights * batch_sizes
+            weighted_variance_batch_means = np.sum(effective_weights * (batch_values - weighted_mean)**2) / np.sum(effective_weights)
+
+            # Scale up to estimate population variance
+            # Batch means have variance = population_variance / average_batch_size
+            # So population_variance ≈ batch_means_variance * average_batch_size
+            avg_batch_size = np.average(batch_sizes, weights=effective_weights)
+            estimated_population_variance = weighted_variance_batch_means * avg_batch_size
+
+            # Calculate SEM for the total sample (using n-1 for sample standard error)
+            total_n = np.sum(batch_sizes)
+            sem = np.sqrt(estimated_population_variance / (total_n - 1))
+
+            return weighted_mean, sem
+
+        else:
+            # For unweighted variables (scatt, ext), use simple batch statistics
+            # Calculate mean of batch means, weighted by batch size
+            total_sum = np.sum(batch_sizes * batch_values)
+            total_n = np.sum(batch_sizes)
+            mean = total_sum / total_n
+
+            # Calculate variance between batch means
+            if len(batch_values) < 2:
+                return mean, float('inf')
+
+            batch_means_variance = np.var(batch_values, ddof=1)
+
+            # Scale up to estimate population variance
+            # Batch means have variance = population_variance / average_batch_size
+            # So population_variance ≈ batch_means_variance * average_batch_size
+            avg_batch_size = np.mean(batch_sizes)
+            estimated_population_variance = batch_means_variance * avg_batch_size
+
+            # Calculate SEM for the total sample (using n-1 for sample standard error)
+            sem = np.sqrt(estimated_population_variance / (total_n - 1))
+
+            return mean, sem
+
+    def _check_convergence(self) -> Dict[str, bool]:
+        """Check if all convergence criteria are met.
+
+        Returns:
+            Dict mapping variable names to convergence status
+        """
+        converged = {}
+
+        for conv in self.convergables:
+            mean, sem = self._calculate_mean_and_sem(conv.variable)
+
+            # Calculate tolerance based on type
+            if conv.tolerance_type == 'relative':
+                # Relative tolerance: SEM / |mean| < tolerance
+                if mean != 0:
+                    relative_sem = sem / abs(mean)
+                    converged[conv.variable] = relative_sem < conv.tolerance
+                else:
+                    # If mean is zero, use absolute comparison
+                    converged[conv.variable] = sem < conv.tolerance
+            else:
+                # Absolute tolerance: SEM < tolerance
+                converged[conv.variable] = sem < conv.tolerance
+
+        return converged
+
+    def _all_converged(self) -> bool:
+        """Check if all variables have converged.
+
+        Returns:
+            True if all variables meet their convergence criteria and minimum batches completed
+        """
+        # Check minimum batches requirement first
+        if len(self.batch_data) < self.min_batches:
+            return False
+            
+        converged_status = self._check_convergence()
+        return all(converged_status.values())
+
+    def _print_progress(self, iteration: int):
+        """Print convergence progress.
+
+        Args:
+            iteration: Current iteration number
+        """
+        print(f"\nIteration {iteration} ({self.n_orientations} orientations):")
+
+        converged_status = self._check_convergence()
+
+        for conv in self.convergables:
+            mean, sem = self._calculate_mean_and_sem(conv.variable)
+
+            # Calculate 95% CI
+            ci_lower = mean - 1.96 * sem
+            ci_upper = mean + 1.96 * sem
+
+            # Format based on tolerance type
+            if conv.tolerance_type == 'relative':
+                if mean != 0:
+                    relative_sem = sem / abs(mean)
+                    target_str = f"{conv.tolerance*100:.1f}%"
+                    current_str = f"{relative_sem*100:.2f}%"
+                else:
+                    target_str = f"{conv.tolerance} (abs, mean=0)"
+                    current_str = f"{sem:.4g}"
+            else:
+                target_str = f"{conv.tolerance}"
+                current_str = f"{sem:.4g}"
+
+            # Status indicator
+            status = "✓" if converged_status[conv.variable] else "❌"
+
+            # Print line with mean, SEM, CI, and convergence status
+            print(f"  {conv.variable:<10}: {mean:.6f} ± {sem:.6f} [{ci_lower:.6f}, {ci_upper:.6f}] | SEM: {current_str} (target: {target_str}) {status}")
+
+            # Add to convergence history
+            self.convergence_history.append((self.n_orientations, conv.variable, sem))
+
+    def run(self) -> ConvergenceResults:
+        """Run the convergence study.
+
+        Returns:
+            ConvergenceResults containing final values and convergence status
+        """
+        iteration = 0
+        converged = False
+        warning = None
+
+        while not converged and self.n_orientations < self.max_orientations:
+            iteration += 1
+
+            # Determine batch size for this iteration
+            remaining = self.max_orientations - self.n_orientations
+            batch_size = min(self.batch_size, remaining)
+
+            # Set batch size
+            orientations = goad.create_uniform_orientation(batch_size)
+
+            # Set the orientations for the settings
+            self.settings.orientation = orientations
+
+            mp = goad.MultiProblem(self.settings)
+            mp.py_solve()
+
+            # Update statistics
+            self._update_statistics(mp.results, batch_size)
+
+            # Print progress
+            self._print_progress(iteration)
+
+            # Check convergence
+            converged = self._all_converged()
+
+        # Prepare final results
+        if converged:
+            print(f"\nConverged after {self.n_orientations} orientations.")
+        else:
+            warning = f"Maximum orientations ({self.max_orientations}) reached without convergence"
+            print(f"\nWarning: {warning}")
+
+        # Calculate final values and SEMs
+        final_values = {}
+        final_sems = {}
+        for conv in self.convergables:
+            mean, sem = self._calculate_mean_and_sem(conv.variable)
+            final_values[conv.variable] = mean
+            final_sems[conv.variable] = sem
+
+        # Prepare Mueller matrices
+        mueller_1d = None
+        mueller_2d = None
+        if self.mueller_1d and self.mueller_1d_sum is not None:
+            mueller_1d = self.mueller_1d_sum / self.n_orientations
+        if self.mueller_2d and self.mueller_2d_sum is not None:
+            mueller_2d = self.mueller_2d_sum / self.n_orientations
+
+        return ConvergenceResults(
+            converged=converged,
+            n_orientations=self.n_orientations,
+            values=final_values,
+            sem_values=final_sems,
+            mueller_1d=mueller_1d,
+            mueller_2d=mueller_2d,
+            convergence_history=self.convergence_history,
+            warning=warning
+        )

goad_py/{__init__.pyi → goad_py.pyi}

@@ -20,27 +20,18 @@ Default behavior (minimal setup):
 Example (minimal setup):
     import goad_py as goad
     
-    # Ultra-simple single orientation
     settings = goad.Settings("particle.obj")
-    problem = goad.Problem(settings)
-    problem.py_solve()
-    print(f"Extinction: {problem.results.ext_cross}")
-    
-    # Multi-orientation averaging (100 random orientations)
-    orientations = goad.create_uniform_orientation(100)
-    settings = goad.Settings("particle.obj", orientation=orientations)
     mp = goad.MultiProblem(settings)
     mp.py_solve()
-    print(f"Average extinction: {mp.results.ext_cross}")
     
-    # Truly minimal (just geometry path)
-    settings = goad.Settings("particle.obj")  # Everything else uses defaults!
-    mp = goad.MultiProblem(settings)
-    mp.py_solve()
-    print(f"Results: {mp.results.scat_cross}")
+    results = mp.results
+    print(f"Scattering cross-section: {results.scat_cross}")
+    print(f"Extinction cross-section: {results.ext_cross}")
+    print(f"Asymmetry parameter: {results.asymmetry}")
 """
 
-from typing import Optional, List, Dict, Any, Union
+from typing import Optional, List, Dict, Any, Union, Tuple
+import numpy as np
 
 class Euler:
     """Euler angles for rotations."""
@@ -342,4 +333,121 @@ def create_discrete_orientation(eulers: List[Euler], euler_convention: Optional[
 
 def sum_as_string(a: int, b: int) -> str: ...
 
-def goad_py_add() -> None: ...
+def goad_py_add() -> None: ...
+
+# Convergence Analysis Classes
+
+class Convergable:
+    """Represents a variable to monitor for convergence.
+    
+    Defines convergence criteria for integrated scattering parameters
+    including asymmetry parameter, scattering cross-section, extinction
+    cross-section, and single-scattering albedo.
+    """
+    
+    variable: str
+    tolerance_type: str
+    tolerance: float
+    
+    def __init__(
+        self,
+        variable: str,
+        tolerance_type: str = 'relative',
+        tolerance: float = 0.01
+    ) -> None:
+        """Initialize convergence criterion.
+        
+        Args:
+            variable: Variable to monitor ('asymmetry', 'scatt', 'ext', 'albedo')
+            tolerance_type: 'relative' or 'absolute' tolerance
+            tolerance: Tolerance value (relative as fraction, absolute as value)
+            
+        Raises:
+            ValueError: If variable name or tolerance_type is invalid
+        """
+        ...
+
+class ConvergenceResults:
+    """Results from a convergence study.
+    
+    Contains final convergence status, parameter values with uncertainties,
+    and complete convergence history for analysis.
+    """
+    
+    converged: bool
+    n_orientations: int
+    values: Dict[str, float]
+    sem_values: Dict[str, float]
+    mueller_1d: Optional[np.ndarray]
+    mueller_2d: Optional[np.ndarray]
+    convergence_history: List[Tuple[int, str, float]]
+    warning: Optional[str]
+    
+    def __init__(
+        self,
+        converged: bool,
+        n_orientations: int,
+        values: Dict[str, float],
+        sem_values: Dict[str, float],
+        mueller_1d: Optional[np.ndarray] = None,
+        mueller_2d: Optional[np.ndarray] = None,
+        convergence_history: List[Tuple[int, str, float]] = None,
+        warning: Optional[str] = None
+    ) -> None: ...
+
+class Convergence:
+    """Runs multiple MultiProblems until convergence criteria are met.
+    
+    Implements statistical convergence analysis for scattering parameters
+    using batch-based standard error estimation. Monitors multiple variables
+    simultaneously and stops when all meet their convergence criteria.
+    
+    Example:
+        convergence = Convergence(
+            settings=goad.Settings("particle.obj"),
+            convergables=[
+                Convergable('asymmetry', 'absolute', 0.005),
+                Convergable('scatt', 'relative', 0.01),
+            ],
+            batch_size=100
+        )
+        results = convergence.run()
+    """
+    
+    def __init__(
+        self,
+        settings: Settings,
+        convergables: List[Convergable],
+        batch_size: int = 24,
+        max_orientations: int = 100_000,
+        min_batches: int = 10,
+        mueller_1d: bool = True,
+        mueller_2d: bool = False
+    ) -> None:
+        """Initialize convergence study.
+        
+        Args:
+            settings: GOAD settings for the simulation
+            convergables: List of variables to monitor for convergence
+            batch_size: Number of orientations per iteration
+            max_orientations: Maximum total orientations before stopping
+            min_batches: Minimum number of batches before allowing convergence
+            mueller_1d: Whether to collect 1D Mueller matrices
+            mueller_2d: Whether to collect 2D Mueller matrices
+            
+        Raises:
+            ValueError: If parameters are invalid or no convergables specified
+        """
+        ...
+    
+    def run(self) -> ConvergenceResults:
+        """Run the convergence study.
+        
+        Executes batches of orientations until all convergence criteria
+        are met or maximum orientations reached. Provides progress updates
+        and rigorous statistical analysis.
+        
+        Returns:
+            ConvergenceResults containing final values and convergence status
+        """
+        ...

{goad_py-0.3.0.dist-info → goad_py-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: goad-py
-Version: 0.3.0
+Version: 0.4.2
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Physics
@@ -43,14 +43,38 @@ pip install goad-py
 import goad_py
 
 # Create a problem with minimal setup
-problem = goad_py.Problem("path/to/geometry.obj")
-
-# Solve and get results
-results = problem.py_solve()
+settings = goad_py.Settings("path/to/geometry.obj")
+mp = goad_py.MultiProblem(settings)
+mp.py_solve()
 
 # Access scattering data
-print(f"Number of angles: {results.num_angles}")
-print(f"Scattering cross section: {results.sca_cross_section}")
+results = mp.results
+print(f"Scattering cross-section: {results.scat_cross}")
+print(f"Extinction cross-section: {results.ext_cross}")
+print(f"Asymmetry parameter: {results.asymmetry}")
+```
+
+### Convergence Analysis
+
+For statistical error estimation, use the convergence analysis functionality:
+
+```python
+from goad_py import Convergence, Convergable
+
+# Set up convergence analysis
+convergence = Convergence(
+    settings=goad_py.Settings(geom_path="path/to/geometry.obj"),
+    convergables=[
+        Convergable('asymmetry', 'absolute', 0.005),  # absolute SEM < 0.005
+        Convergable('scatt', 'relative', 0.01),       # relative SEM < 1%
+    ],
+    batch_size=100
+)
+
+# Run until convergence
+results = convergence.run()
+print(f"Converged: {results.converged}")
+print(f"Final values: {results.values}")
 ```
 
 ## Features
@@ -59,6 +83,7 @@ print(f"Scattering cross section: {results.sca_cross_section}")
 - Support for various 3D geometry formats
 - Configurable wavelength, refractive index, and orientations
 - Multi-orientation averaging capabilities
+- Convergence analysis for statistical error estimation
 - Efficient parallel computation with GIL release
 
 ## Documentation

goad_py-0.4.2.dist-info/RECORD

@@ -0,0 +1,9 @@
+goad_py-0.4.2.dist-info/METADATA,sha256=JWxD4wctGOJzIWAWzjEpHPrdKbEgabqBjqGbgAptSR4,3181
+goad_py-0.4.2.dist-info/WHEEL,sha256=dOnalb29euhUK3FRsG9PGb9HBYXnNGRGVeKIPHUwibU,106
+goad_py.libs/libgcc_s-e52197c3.so.1,sha256=vkPW1Auw6CH9Bjk7frmX3hry_1H9c0tRI0Ncyg71WUI,724137
+goad_py.libs/libstdc++-405035b3.so.6,sha256=dhdlt148awG0mZDLGM8wZy1R4PeU5HXvi8l9pgv4DiY,22443689
+goad_py/__init__.py,sha256=vZn5zZZdTgm1qTQFYCqgNKBKDAoheMo5OvwdLIIl3Dk,242
+goad_py/_goad_py.abi3.so,sha256=Kl6jqv2uEB2RiXY-SlvUlpLzBtelJTIYW-DdA60aeys,2166617
+goad_py/convergence.py,sha256=8HTlrpv3RLD8FfmZuT_2mySVtnpHaPLKx6Rcw-jDgB0,14930
+goad_py/goad_py.pyi,sha256=Ue33wS-DLeI2JTwpKyPXNk4D-Trt9S5MBQSO8qW5XGc,14922
+goad_py-0.4.2.dist-info/RECORD,,

{goad_py-0.3.0.dist-info → goad_py-0.4.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: maturin (1.9.0)
+Generator: maturin (1.9.1)
 Root-Is-Purelib: false
 Tag: cp38-abi3-musllinux_1_2_aarch64

goad_py-0.3.0.dist-info/RECORD

@@ -1,9 +0,0 @@
-goad_py-0.3.0.dist-info/METADATA,sha256=_QAoI_pML6HmYtVhYwEzjAjrZ1ieYWmib0Hk0QRvDGI,2434
-goad_py-0.3.0.dist-info/WHEEL,sha256=XrXtO6TC5d8ini6lhMZhY6K70cqp9-og79F-C64Ik-M,106
-goad_py.libs/libgcc_s-e52197c3.so.1,sha256=vkPW1Auw6CH9Bjk7frmX3hry_1H9c0tRI0Ncyg71WUI,724137
-goad_py.libs/libstdc++-405035b3.so.6,sha256=dhdlt148awG0mZDLGM8wZy1R4PeU5HXvi8l9pgv4DiY,22443689
-goad_py/__init__.py,sha256=YW_7ejLyMUb8grQQmBo-vpbgTYF2xRruw6x7UxAerIg,111
-goad_py/__init__.pyi,sha256=Fc4JBBbKMYZ0MA_DzycbC2v19YARzGKNg0bfmTkNhPQ,11489
-goad_py/goad_py.abi3.so,sha256=4bAY6AE8Uxh-g_sgtHEZG5-JsUu5P0lDb47rk0PnKd4,2035593
-goad_py/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-goad_py-0.3.0.dist-info/RECORD,,