import live www.sillylaird.ca webrootHEADmain

5 files changed, 704 insertions, 0 deletions

diff --git a/.agents/skills/architecture-design/examples/augmentation_example.py b/.agents/skills/architecture-design/examples/augmentation_example.py
new file mode 100644
index 0000000..949b033
--- /dev/null
+++ b/.agents/skills/architecture-design/examples/augmentation_example.py
@@ -0,0 +1,117 @@
+"""
+Data Augmentation Example
+
+Demonstrates how to create a custom data augmentation function
+following the architecture design pattern.
+"""
+
+import torch
+from typing import Dict
+from src.data_module.augmentation import register_augmentation
+
+
+@register_augmentation("time_shift")
+def time_shift(signal: torch.Tensor, max_shift: int = 10) -> torch.Tensor:
+    """Randomly shift signal in time.
+
+    Args:
+        signal: Input signal tensor of shape (channels, time_steps)
+        max_shift: Maximum number of steps to shift
+
+    Returns:
+        Shifted signal tensor
+    """
+    shift = torch.randint(-max_shift, max_shift + 1, (1,)).item()
+    return torch.roll(signal, shifts=shift, dims=-1)
+
+
+@register_augmentation("amplitude_scale")
+def amplitude_scale(
+    signal: torch.Tensor,
+    min_scale: float = 0.8,
+    max_scale: float = 1.2
+) -> torch.Tensor:
+    """Randomly scale signal amplitude.
+
+    Args:
+        signal: Input signal tensor of shape (channels, time_steps)
+        min_scale: Minimum scaling factor
+        max_scale: Maximum scaling factor
+
+    Returns:
+        Scaled signal tensor
+    """
+    scale = torch.empty(1).uniform_(min_scale, max_scale).item()
+    return signal * scale
+
+
+@register_augmentation("gaussian_noise")
+def add_gaussian_noise(
+    signal: torch.Tensor,
+    mean: float = 0.0,
+    std: float = 0.1
+) -> torch.Tensor:
+    """Add Gaussian noise to signal.
+
+    Args:
+        signal: Input signal tensor of shape (channels, time_steps)
+        mean: Mean of Gaussian noise
+        std: Standard deviation of Gaussian noise
+
+    Returns:
+        Signal with added noise
+    """
+    noise = torch.randn_like(signal) * std + mean
+    return signal + noise
+
+
+# Example: Composed augmentation
+@register_augmentation("composed")
+def composed_augmentation(signal: torch.Tensor, cfg) -> torch.Tensor:
+    """Apply multiple augmentations in sequence.
+
+    Args:
+        signal: Input signal tensor
+        cfg: Configuration object with augmentation parameters
+
+    Returns:
+        Augmented signal tensor
+    """
+    # Apply each augmentation based on config
+    if cfg.augmentation.time_shift:
+        signal = time_shift(signal, cfg.augmentation.max_shift)
+
+    if cfg.augmentation.amplitude_scale:
+        signal = amplitude_scale(
+            signal,
+            cfg.augmentation.min_scale,
+            cfg.augmentation.max_scale
+        )
+
+    if cfg.augmentation.gaussian_noise:
+        signal = add_gaussian_noise(
+            signal,
+            cfg.augmentation.noise_mean,
+            cfg.augmentation.noise_std
+        )
+
+    return signal
+
+
+# Usage in dataset class
+class AugmentedDataset:
+    """Example dataset with augmentation support."""
+
+    def __init__(self, cfg):
+        self.cfg = cfg
+        self.augmentation_fn = AugmentationFactory(cfg.augmentation.name)
+
+    def __getitem__(self, idx: int) -> Dict[str, torch.Tensor]:
+        # Load signal
+        signal = self.load_signal(idx)
+
+        # Apply augmentation (training mode only)
+        if self.training and self.augmentation_fn:
+            signal = self.augmentation_fn(signal, self.cfg)
+
+        return {"signal": signal, "label": self.labels[idx]}
diff --git a/.agents/skills/architecture-design/examples/config_example.yaml b/.agents/skills/architecture-design/examples/config_example.yaml
new file mode 100644
index 0000000..8b61442
--- /dev/null
+++ b/.agents/skills/architecture-design/examples/config_example.yaml
@@ -0,0 +1,131 @@
+# Hydra Configuration Example
+# This demonstrates the config structure for training pipeline
+
+# Run with: python train.py --config-name=config_example
+
+defaults:
+  - training: default
+  - dataset: brain_decoder
+  - model: transformer
+  - override hydra/launcher: submitit_local
+
+# Project settings
+project_name: brain_decoder
+experiment_name: transformer_baseline
+
+# Random seed
+seed: 42
+
+# Device settings
+device: cuda
+num_workers: 4
+pin_memory: true
+
+# Training configuration
+training:
+  epochs: 100
+  batch_size: 32
+  learning_rate: 0.001
+  weight_decay: 0.0001
+  gradient_clip: 1.0
+  early_stopping:
+    patience: 10
+    min_delta: 0.001
+
+  # Optimizer settings
+  optimizer: adamw
+  optimizer_params:
+    betas: [0.9, 0.999]
+    eps: 1.0e-08
+
+  # Scheduler settings
+  scheduler: cosine
+  scheduler_params:
+    warmup_epochs: 10
+    min_lr: 1.0e-06
+
+  # Checkpoint settings
+  checkpoint:
+    save_every: 5
+    save_best: true
+    monitor: val_loss
+    mode: min
+
+# Dataset configuration
+dataset:
+  name: brain_decoder
+  task: movement_classification
+  target_size:
+    movement_classification: 5
+    reconstruction: [64, 64]
+
+  # Data paths
+  data_dir: ${dir.data_dir}/processed
+  train_split: train
+  val_split: val
+  test_split: test
+
+  # Data loading
+  num_channels: 64
+  sampling_rate: 1000
+  sequence_length: 1000
+
+  # Augmentation
+  augmentation:
+    name: composed
+    time_shift: true
+    amplitude_scale: true
+    gaussian_noise: true
+    max_shift: 10
+    min_scale: 0.8
+    max_scale: 1.2
+    noise_mean: 0.0
+    noise_std: 0.1
+
+# Model configuration
+model:
+  name: Transformer
+  hidden_dim: 256
+  num_heads: 8
+  num_layers: 6
+  dropout: 0.1
+  activation: gelu
+
+  # Architecture specific
+  encoder:
+    input_dim: 64
+    embedding_dim: 256
+    positional_encoding: true
+
+  decoder:
+    output_dim: ${dataset.target_size.${dataset.task}}
+    pooling: avg
+
+# Logging configuration
+logging:
+  logger: wandb
+  log_every: 10
+  log_grads: false
+
+  # TensorBoard
+  tensorboard: true
+  histogram: true
+
+  # W&B
+  wandb:
+    project: ${project_name}
+    entity: null
+    tags: ["baseline", "transformer"]
+
+# Output directories
+dir:
+  data_dir: ./data
+  output_dir: ./outputs
+  log_dir: ${dir.output_dir}/logs
+  checkpoint_dir: ${dir.output_dir}/checkpoints
+  figure_dir: ${dir.output_dir}/figures
+  table_dir: ${dir.output_dir}/tables
+
+# Debug settings
+debug: false
+fast_dev_run: false
diff --git a/.agents/skills/architecture-design/examples/custom_dataset.py b/.agents/skills/architecture-design/examples/custom_dataset.py
new file mode 100644
index 0000000..c9fe002
--- /dev/null
+++ b/.agents/skills/architecture-design/examples/custom_dataset.py
@@ -0,0 +1,50 @@
+"""
+Example: Creating a Custom Dataset
+
+This example shows how to add a new dataset following the project architecture.
+"""
+
+from torch.utils.data import Dataset
+from typing import Dict
+import torch
+from src.data_module.dataset import register_dataset
+
+
+@register_dataset("time_series")
+class TimeSeriesDataset(Dataset):
+    """
+    Time series dataset for sequence modeling.
+
+    Args:
+        sequences: List of time series sequences
+        seq_length: Fixed sequence length (pad or truncate if needed)
+    """
+
+    def __init__(self, sequences: list, seq_length: int = 100):
+        self.sequences = sequences
+        self.seq_length = seq_length
+
+    def __len__(self) -> int:
+        return len(self.sequences)
+
+    def __getitem__(self, i: int) -> Dict[str, torch.Tensor]:
+        sequence = self.sequences[i]
+
+        # Pad or truncate to fixed length
+        if len(sequence) < self.seq_length:
+            padding = torch.zeros(self.seq_length - len(sequence))
+            sequence = torch.cat([sequence, padding])
+        else:
+            sequence = sequence[:self.seq_length]
+
+        return {
+            "input": sequence,
+            "label": sequence,  # For autoencoder, etc.
+            "length": torch.tensor(min(len(self.sequences[i]), self.seq_length))
+        }
+
+
+# Usage in training:
+# from src.data_module.dataset import DatasetFactory
+# dataset = DatasetFactory("time_series")(sequences=training_data, seq_length=128)
+# dataloader = DataLoader(dataset, batch_size=32, shuffle=True)
diff --git a/.agents/skills/architecture-design/examples/custom_model.py b/.agents/skills/architecture-design/examples/custom_model.py
new file mode 100644
index 0000000..0e00752
--- /dev/null
+++ b/.agents/skills/architecture-design/examples/custom_model.py
@@ -0,0 +1,217 @@
+"""
+Example: Creating a Custom Model
+
+This example shows how to add a new model following the project architecture.
+IMPORTANT: Models use a config-driven pattern where __init__ only accepts cfg.
+
+Key Requirements:
+- Use @register_model('ModelName') decorator
+- __init__ accepts ONLY cfg parameter
+- All hyperparameters come from cfg (cfg.model.*, cfg.dataset.*, etc.)
+- forward() returns dict: {"loss": loss, "labels": labels, "logits": logits}
+"""
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+from typing import Dict, Optional
+
+# Import the register_model decorator
+# Location may vary: src.model_module.brain_decoder or src.model_module.model
+from src.model_module.brain_decoder import register_model
+
+
+@register_model('SimpleMLP')
+class SimpleMLP(nn.Module):
+    """
+    Simple Multi-Layer Perceptron for classification tasks.
+
+    Config structure ( Hydra YAML ):
+        model:
+            input_dim: 100
+            hidden_dim: 256
+            output_dim: 10
+            num_layers: 3
+            dropout: 0.1
+        dataset:
+            task: classification  # Used to get target_size
+            target_size:
+                classification: 10
+    """
+
+    def __init__(self, cfg):
+        super().__init__()
+
+        # Store config
+        self.cfg = cfg
+
+        # Get task info from config
+        self.task = cfg.dataset.task
+
+        # Build model - ALL parameters from cfg
+        self.input_dim = cfg.model.input_dim
+        self.hidden_dim = cfg.model.get('hidden_dim', 256)
+        self.output_dim = cfg.dataset.target_size[cfg.dataset.task]
+        self.num_layers = cfg.model.get('num_layers', 3)
+        self.dropout = cfg.model.get('dropout', 0.1)
+
+        # Build layers
+        layers = []
+        in_dim = self.input_dim
+
+        for i in range(self.num_layers):
+            layers.extend([
+                nn.Linear(in_dim, self.hidden_dim),
+                nn.ReLU(),
+                nn.Dropout(self.dropout)
+            ])
+            in_dim = self.hidden_dim
+
+        # Output layer
+        layers.append(nn.Linear(self.hidden_dim, self.output_dim))
+        self.network = nn.Sequential(*layers)
+
+        # Loss function
+        self.loss_fn = nn.CrossEntropyLoss()
+
+    def forward(
+        self,
+        x: torch.Tensor,
+        labels: Optional[torch.Tensor] = None,
+        **kwargs
+    ) -> Dict[str, Optional[torch.Tensor]]:
+        """
+        Forward pass.
+
+        Args:
+            x: Input tensor of shape (batch_size, input_dim)
+            labels: Ground truth labels (optional, for training)
+
+        Returns:
+            Dictionary with:
+                - loss: Computed loss (None if labels not provided)
+                - labels: Ground truth labels
+                - logits: Model predictions
+        """
+        logits = self.network(x)
+
+        loss = None
+        if labels is not None:
+            # Convert labels to long type if needed
+            if labels.dtype != torch.long:
+                labels = labels.long()
+            loss = self.loss_fn(logits, labels)
+
+        return {
+            "loss": loss,
+            "labels": labels,
+            "logits": logits
+        }
+
+
+# ============================================
+# Example with Training/Inference Modes
+# ============================================
+
+@register_model('SimpleMLPWithModes')
+class SimpleMLPWithModes(nn.Module):
+    """
+    MLP with separate training and inference logic.
+    Shows how to handle different modes using self.training.
+    """
+
+    def __init__(self, cfg):
+        super().__init__()
+        self.cfg = cfg
+        self.task = cfg.dataset.task
+
+        self.input_dim = cfg.model.input_dim
+        self.hidden_dim = cfg.model.get('hidden_dim', 256)
+        self.output_dim = cfg.dataset.target_size[cfg.dataset.task]
+
+        self.fc_in = nn.Linear(self.input_dim, self.hidden_dim)
+        self.ln = nn.LayerNorm(self.hidden_dim)
+        self.fc_out = nn.Linear(self.hidden_dim, self.output_dim)
+        self.loss_fn = nn.CrossEntropyLoss()
+
+        # Test-time augmentation config
+        self.tta_times = cfg.model.get('tta_times', 1)
+
+    def forward(
+        self,
+        x: torch.Tensor,
+        labels: Optional[torch.Tensor] = None,
+        **kwargs
+    ) -> Dict[str, Optional[torch.Tensor]]:
+        """
+        Forward pass with training/inference modes.
+        """
+        if self.training:
+            # Training mode
+            x = x.float()
+            x = self.fc_in(x)
+            x = self.ln(x)
+            x = F.relu(x)
+            logits = self.fc_out(x)
+
+            loss = None
+            if labels is not None:
+                if labels.dtype != torch.long:
+                    labels = labels.long()
+                loss = self.loss_fn(logits, labels)
+
+            return {
+                "loss": loss,
+                "labels": labels,
+                "logits": logits
+            }
+        else:
+            # Inference mode with TTA
+            all_logits = []
+            with torch.no_grad():
+                x = x.float()
+                for _ in range(self.tta_times):
+                    x_aug = x.clone()
+                    # Apply TTA transformations here if needed
+
+                    x_aug = self.fc_in(x_aug)
+                    x_aug = self.ln(x_aug)
+                    x_aug = F.relu(x_aug)
+                    logits = self.fc_out(x_aug)
+                    all_logits.append(logits)
+
+            # Average predictions
+            avg_logits = torch.mean(torch.stack(all_logits), dim=0)
+
+            loss = None
+            if labels is not None:
+                if labels.dtype != torch.long:
+                    labels = labels.long()
+                loss = self.loss_fn(avg_logits, labels)
+
+            return {
+                "loss": loss,
+                "labels": labels,
+                "logits": avg_logits
+            }
+
+
+# ============================================
+# Config Example (Hydra YAML)
+# ============================================
+"""
+# run/conf/model/simple_mlp.yaml
+
+model:
+  name: SimpleMLP
+  input_dim: 100
+  hidden_dim: 256
+  output_dim: 10
+  num_layers: 3
+  dropout: 0.1
+  tta_times: 1
+
+# Then in training pipeline:
+# from src.model_module.brain_decoder import ModelFactory
+# model = ModelFactory(cfg.model.name)(cfg)
+"""
diff --git a/.agents/skills/architecture-design/examples/pipeline_example.sh b/.agents/skills/architecture-design/examples/pipeline_example.sh
new file mode 100755
index 0000000..abd7b46
--- /dev/null
+++ b/.agents/skills/architecture-design/examples/pipeline_example.sh
@@ -0,0 +1,189 @@
+#!/bin/bash
+###############################################################################
+# Training Pipeline Script
+#
+# This script demonstrates the standard training pipeline execution pattern.
+# It handles environment setup, configuration, and execution with proper
+# error handling and logging.
+#
+# Usage:
+#   ./run/pipeline/training/train.sh --config-name=config_example
+###############################################################################
+
+set -e  # Exit on error
+set -o pipefail  # Exit on pipe failure
+
+# Script configuration
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+PROJECT_ROOT="$(cd "${SCRIPT_DIR}/../.." && pwd)"
+EXPERIMENT_NAME="baseline_experiment"
+TIMESTAMP=$(date +"%Y%m%d_%H%M%S")
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+###############################################################################
+# Helper Functions
+###############################################################################
+
+log_info() {
+    echo -e "${GREEN}[INFO]${NC} $1"
+}
+
+log_warn() {
+    echo -e "${YELLOW}[WARN]${NC} $1"
+}
+
+log_error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+cleanup() {
+    log_info "Cleaning up..."
+    # Add cleanup logic here (e.g., kill background processes)
+}
+
+trap cleanup EXIT
+
+###############################################################################
+# Environment Setup
+###############################################################################
+
+setup_environment() {
+    log_info "Setting up environment..."
+
+    # Activate virtual environment if it exists
+    if [ -f "${PROJECT_ROOT}/.venv/bin/activate" ]; then
+        source "${PROJECT_ROOT}/.venv/bin/activate"
+        log_info "Activated virtual environment"
+    fi
+
+    # Check required commands
+    command -v python >/dev/null 2>&1 || { log_error "Python not found"; exit 1; }
+
+    # Set Python path
+    export PYTHONPATH="${PROJECT_ROOT}/src:${PYTHONPATH}"
+    log_info "PYTHONPATH set to: ${PYTHONPATH}"
+}
+
+###############################################################################
+# Configuration
+###############################################################################
+
+parse_arguments() {
+    # Default values
+    CONFIG="default"
+    GPUS=0
+    SEED=42
+
+    # Parse arguments
+    while [[ $# -gt 0 ]]; do
+        case $1 in
+            --config-name|-c)
+                CONFIG="$2"
+                shift 2
+                ;;
+            --gpus|-g)
+                GPUS="$2"
+                shift 2
+                ;;
+            --seed|-s)
+                SEED="$2"
+                shift 2
+                ;;
+            *)
+                log_warn "Unknown argument: $1"
+                shift
+                ;;
+        esac
+    done
+
+    log_info "Configuration: ${CONFIG}"
+    log_info "GPUs: ${GPUS}"
+    log_info "Seed: ${SEED}"
+}
+
+###############################################################################
+# Main Training Function
+###############################################################################
+
+run_training() {
+    log_info "Starting training..."
+
+    # Output directory for this run
+    OUTPUT_DIR="${PROJECT_ROOT}/outputs/${EXPERIMENT_NAME}/${TIMESTAMP}"
+    mkdir -p "${OUTPUT_DIR}"
+
+    log_info "Output directory: ${OUTPUT_DIR}"
+
+    # Training command with Hydra
+    python "${PROJECT_ROOT}/train.py" \
+        --config-name="${CONFIG}" \
+        seed=${SEED} \
+        dir.output_dir="${OUTPUT_DIR}" \
+        training.device=cuda \
+        hydra.output_dir="${OUTPUT_DIR}/hydra" \
+        hydra.run.dir="${OUTPUT_DIR}/hydra" || {
+        log_error "Training failed!"
+        exit 1
+    }
+
+    log_info "Training completed successfully!"
+}
+
+###############################################################################
+# Post-Processing
+###############################################################################
+
+post_process() {
+    log_info "Post-processing results..."
+
+    # Copy logs to output directory
+    if [ -f "${OUTPUT_DIR}/hydra/*.log" ]; then
+        cp "${OUTPUT_DIR}/hydra/"*.log "${OUTPUT_DIR}/"
+    fi
+
+    # Generate summary
+    log_info "Run summary:"
+    log_info "  Config: ${CONFIG}"
+    log_info "  Seed: ${SEED}"
+    log_info "  Output: ${OUTPUT_DIR}"
+
+    # Print path to best checkpoint
+    BEST_CHECKPOINT=$(find "${OUTPUT_DIR}" -name "best*.pt" | head -n 1)
+    if [ -n "${BEST_CHECKPOINT}" ]; then
+        log_info "  Best checkpoint: ${BEST_CHECKPOINT}"
+    fi
+}
+
+###############################################################################
+# Main Execution
+###############################################################################
+
+main() {
+    log_info "=========================================="
+    log_info "Training Pipeline"
+    log_info "=========================================="
+
+    # Setup
+    setup_environment
+
+    # Parse arguments
+    parse_arguments "$@"
+
+    # Run training
+    run_training
+
+    # Post-process
+    post_process
+
+    log_info "=========================================="
+    log_info "Pipeline completed successfully!"
+    log_info "=========================================="
+}
+
+# Run main function
+main "$@"