config

type AlgorithmConfig struct {
	// NIPALS algorithm parameters
	NIPALS NIPALSConfig `json:"nipals"`

	// Kernel PCA algorithm parameters
	KernelPCA KernelPCAConfig `json:"kernel_pca"`
}

type AnalysisConfig struct {
	// Default number of components if not specified
	DefaultComponents int `json:"default_components"`

	// Whether to show preview of transformed data
	ShowPreview bool `json:"show_preview"`

	// Maximum number of rows to show in preview
	PreviewMaxRows int `json:"preview_max_rows"`
}

type CLIConfig struct {
	// CSV parsing configuration
	CSV CSVConfig `json:"csv"`

	// Output configuration
	Output OutputConfig `json:"output"`

	// Analysis configuration
	Analysis AnalysisConfig `json:"analysis"`
}

type CSVConfig struct {
	// Number of rows to sample for column type detection
	TypeDetectionSampleSize int `json:"type_detection_sample_size"`

	// Default null value strings
	DefaultNullValues []string `json:"default_null_values"`
}

type GUIConfig struct {
	// Visualization configuration
	Visualization VisualizationConfig `json:"visualization"`

	// UI configuration
	UI UIConfig `json:"ui"`
}

type KernelPCAConfig struct {
	// Minimum eigenvalue: eigenvalues below this threshold are clamped to it
	// to avoid division-by-zero when normalizing eigenvectors.
	// This is a numerical stability guard, not a truncation criterion.
	MinEigenvalue float64 `json:"min_eigenvalue"`
}

type NIPALSConfig struct {
	// Convergence tolerance: iteration stops when the change in the score vector
	// (Euclidean norm of t_new - t_old) falls below this threshold.
	// Smaller values give more precise components at the cost of more iterations.
	Tolerance float64 `json:"tolerance"`

	// Maximum number of power iterations per component.
	// For well-conditioned data, convergence typically occurs in <50 iterations.
	// Increase only if you see "did not converge" warnings on ill-conditioned data.
	MaxIterations int `json:"max_iterations"`
}

type OutputConfig struct {
	// Suffix for output files
	FileSuffix string `json:"file_suffix"`

	// Whether to create output directory if it doesn't exist
	CreateOutputDir bool `json:"create_output_dir"`
}

type UIConfig struct {
	// Maximum rows to show in data preview
	DataPreviewMaxRows int `json:"data_preview_max_rows"`

	// Maximum columns to show in data preview
	DataPreviewMaxCols int `json:"data_preview_max_cols"`

	// Default zoom factor for plots
	DefaultZoomFactor float64 `json:"default_zoom_factor"`
}

type VisualizationConfig struct {
	// Threshold for showing variables in loadings plot
	LoadingsVariableThreshold int `json:"loadings_variable_threshold"`

	// Maximum variables to display in biplot
	BiplotMaxVariables int `json:"biplot_max_variables"`

	// Maximum variables to display in circle of correlations
	CircleMaxVariables int `json:"circle_max_variables"`

	// Threshold for correlation circle
	CorrelationThreshold float64 `json:"correlation_threshold"`

	// Elbow threshold for scree plot
	ElbowThreshold float64 `json:"elbow_threshold"`

	// Diagnostic plot thresholds
	MahalanobisThreshold float64 `json:"mahalanobis_threshold"`
	RSSThreshold         float64 `json:"rss_threshold"`

	// Default confidence level for ellipses
	DefaultConfidenceLevel float64 `json:"default_confidence_level"`

	// Maximum samples for kernel matrix visualization
	MaxKernelMatrixSamples int `json:"max_kernel_matrix_samples"`
}