Refactoring: Project structure improvements and documentation updates (#3)

* some refactor + improved readme

* Refactored project structure + removed unused stuff

* s'more refactorin'

* removed some plots. improved readme

* Added disclaimer

* Added plots to README.md

Author: DeDuckProject

README.md

@@ -1,15 +1,91 @@
-# Tesseract Code
+# Stim implementation of the [[16,4,4]] Tesseract Code
 
-This repository contains implementations and simulations of the Tesseract quantum error correction code using Stim and PyMatching.
+This repository contains implementations and simulations of the Tesseract quantum error correction code [[1]](#references) using Stim [[3]](#references).
 
-## Features
+## Overview
+### Motivation
+The 16-qubit tesseract subsystem color code offers a useful comprosmise between protection against errors and overhead. It encodes 4 logical qubits with a code rate of 1/4. By reducing 2 logical qubit from the original [[16,6,4]] code, this code achieves single-shot error correction, with only 2 ancilla qubits. This makes this code practical for current trapped-ion platforms. Recent experiments on Quantinuum hardware[[1]](#references) demonstrated preparing high-fidelity encoded graph states of up to 12 logical qubits, as well as protecting encoded states through 5 rounds of error correction. This repository reproduces these results in simulation, providing modular Stim circuits, noise modelling, and verification tests to support further research on low-overhead fault tolerance.
 
-- Circuit implementation of the Tesseract code
-- Error simulation and correction
-- Jupyter notebooks with various experiments and visualizations
-- Utility functions for circuit manipulation and analysis
+![Figure 1: Tesseract code structure (from [1])](docs/images/fig1_tesseract_code.png)
 
-## Installation
+### Project status
+This codebase is an active work-in-progress.  
+• All building blocks (encoding, noise, measurement, decoder) are implemented.  
+• The end-to-end error-correction success rate is **not yet at the target level**.
+Community testing, bug-fixes, and feature PRs are highly appreciated!
+
+**Disclaimer:** This repository is an independent, community-driven implementation.  
+It is **not** affiliated with Microsoft, Quantinuum, nor the authors of the original tesseract-code paper.
+
+### Features
+
+- Circuit implementation of the [[16,4,4]] Tesseract subsystem color code [[2]](#references) in Stim, including encoding, error correction rounds and final measurements.
+- Simulation of an error correction experiment with configurable noise setting, rounds, shot and more.
+- Plotting: sweeping of different parameters and obtaining acceptance rate and logical success rate.
+
+### Implementation details
+
+In order to mimic the original paper's error correction, the different parts of the experiment are implemented in the gate level, and not using Stim's `MPP` stabilizer measurements, or detectors, for example.
+The experiment implemented here is an error correction experiment based on Microsoft's paper[[1]](#references), and resembles the experimental setup shown in Figure 8 below.
+
+![Figure 8: Error correction experiment (from [1])](docs/images/fig8_error_correction_experiment.png)
+
+The experiment goes as follows:
+
+1. **Encoding** - The initial state is encoded using the circuits in Fig. 9a or 9b. This part is noiseless for simplicity.
+2. **Channel Noise** - Optional noise is applied on all qubits.
+3. **Error correction rounds** - Each round is composed of measureing rows/columns and X/Z stabilizers. Measurements results are saved.
+4. **Logical measurements** - Qubits are measured by breaking apart the code into two smaller codes. Each code is the [[8,3,2]] color code [[4]](#references). See [measure_logical_operators_tesseract](tesseract_sim/error_correction/measurement_rounds.py) and [verify_final_state](tesseract_sim/error_correction/decoder_manual.py) for more details.
+5. **Post processing** - Each shot is accepted or not (based on the error correction rounds); For accepted rounds, the qubits are corrected based on Pauli frame (if enabled in simulation). Next, logical qubits are measured and validated to determine the logical error rate.
+
+### Code
+#### Structure
+
+```
+tesseract-code-stim/
+├── tesseract_sim/           # Main simulation package
+│   ├── common/              # Shared utilities and base components
+│   │   ├── circuit_base.py  # Basic circuit operations and initialization
+│   │   └── code_commons.py  # Tesseract code definitions (stabilizers, operators)
+│   ├── encoding/            # State encoding implementations
+│   │   ├── encoding_manual_9a.py  # |++0000⟩ encoding (Fig 9a)
+│   │   └── encoding_manual_9b.py  # |+0+0+0⟩ encoding (Fig 9b)
+│   ├── error_correction/    # Error correction and measurement
+│   │   ├── correction_rules.py     # Correction logic for different error types
+│   │   ├── decoder_manual.py       # Manual decoder implementation
+│   │   └── measurement_rounds.py   # Stabilizer measurements and rounds
+│   ├── noise/               # Noise modeling and injection
+│   │   ├── noise_cfg.py     # Noise configuration dataclass
+│   │   └── noise_utils.py   # Noise injection utilities
+│   ├── plotting/            # Visualization and analysis
+│   │   └── plot_acceptance_rates.py  # Generate acceptance/success rate plots
+│   └── run.py               # Main simulation entry point
+├── notebooks/               # Jupyter notebooks for experiments
+│   ├── encoding_circuits_visualization.ipynb    # Circuit visualization
+│   ├── entire_experiment_circuit.ipynb          # Complete experiment demo
+│   └── tesseract_stim_simulation_real_decoder.ipynb  # Full simulation
+├── tests/                   # Test suite
+│   ├── encoding/            # Encoding tests
+│   ├── noise/               # Noise injection tests
+│   └── test_*.py            # Various experiment and functionality tests
+├── plots/                   # Generated plot outputs
+├── requirements.txt         # Python dependencies
+└── setup.py                 # Package configuration
+```
+
+#### Key Components
+
+- **`tesseract_sim/run.py`**: Main entry point for running simulations with configurable noise parameters
+- **`tesseract_sim/encoding/`**: Two encoding modes based on paper figures 9a and 9b
+- **`tesseract_sim/error_correction/`**: Manual decoder with correction rules and measurement rounds
+- **`tesseract_sim/noise/`**: Configurable noise injection for encoding and error correction phases
+- **`tesseract_sim/plotting/`**: Analysis and visualization tools for acceptance rates and logical success rates
+- **`notebooks/`**: Interactive Jupyter notebooks for experiments and visualization
+- **`tests/`**: Comprehensive test suite covering all major functionality
+
+## Quick Start
+
+### Installation
 
 ```bash
 # Clone the repository
@@ -24,19 +100,6 @@ source venv/bin/activate  # On Windows: venv\Scripts\activate
 pip install -r requirements.txt
 ```
 
-## Structure
-
-- `circuit_commons.py`: Core circuit components and helper functions
-- `stim_simulation_utils.py`: Simulation and plotting utilities
-- `stim_utils.py`: Stim-specific helper functions
-- Notebooks:
-  - `01_stim_playground.ipynb`: Initial Stim experiments
-  - `03_tesseract_stim_simulation_pymatching.ipynb`: Main simulation with PyMatching
-  - `04_stim_example_5_qubit_code.ipynb`: Five-qubit code reference
-  - And more...
-
-## Usage
-
 The main workflow is through Jupyter notebooks. After installation:
 
 ```bash
@@ -45,9 +108,9 @@ jupyter notebook
 
 Then navigate to one of the notebooks to run experiments and simulations.
 
-### Running Simulations with Noise
+### Running Simulations
 
-The `tesseract_sim/run.py` script now supports configurable noise injection during encoding and error correction phases. You can control whether noise is active and set independent 1-qubit and 2-qubit error rates for each phase.
+The `tesseract_sim/run.py` script supports configurable noise injection during encoding and error correction phases. You can control whether noise is active and set independent 1-qubit and 2-qubit error rates for each phase.
 
 ```bash
 python -m tesseract_sim.run --help
@@ -88,33 +151,47 @@ The `plotting/plot_acceptance_rates.py` script generates acceptance and logical
 
 *   **Generate plots with Pauli frame correction enabled and 9a encoding:**
     ```bash
-    python plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9a
+    python tesseract_sim/plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9a
     ```
 
 *   **Generate plots with Pauli frame correction disabled and 9a encoding:**
     ```bash
-    python plotting/plot_acceptance_rates.py --apply_pauli_frame false --encoding-mode 9a
+    python tesseract_sim/plotting/plot_acceptance_rates.py --apply_pauli_frame false --encoding-mode 9a
     ```
 
 *   **Generate plots with 9b encoding and custom shot count:**
     ```bash
-    python plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9b --shots 5000
+    python tesseract_sim/plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9b --shots 5000
     ```
 
 *   **Generate plots with channel noise sweep instead of EC noise:**
     ```bash
-    python plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9a --sweep-channel-noise
+    python tesseract_sim/plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9a --sweep-channel-noise
     ```
 
 *   **Specify custom output directory:**
     ```bash
-    python plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9a --out-dir ./custom_plots
+    python tesseract_sim/plotting/plot_acceptance_rates.py --apply_pauli_frame true --encoding-mode 9a --out-dir ./custom_plots
     ```
 
 The script generates two types of plots:
 - **Acceptance Rate Plots**: Show how well the error correction accepts states across different noise levels and rounds
 - **Logical Success Rate Plots**: Show the conditional probability of logical success given acceptance
 
+**Example Results:**
+
+![Acceptance Rates vs Error Correction Noise](plots/acceptance_rates_ec_noise_ec_experiment.png)
+
+## References
+
+[1] B. W. Reichardt et al., "Demonstration of quantum computation and error correction with a tesseract code", (2024) [arXiv:2409.04628](https://arxiv.org/abs/2409.04628)
+
+[2] "\([[16,6,4]]\) Tesseract color code", The Error Correction Zoo (V. V. Albert & P. Faist, eds.), 2024. https://errorcorrectionzoo.org/c/stab_16_6_4
+
+[3] C. Gidney, "Stim: a fast stabilizer circuit simulator", Quantum 5, 497 (2021). https://doi.org/10.22331/q-2021-07-06-497
+
+[4] E. Campbell, "The smallest interesting colour code", (2016). https://earltcampbell.com/2016/09/26/the-smallest-interesting-colour-code/
+
 ## License
 
 MIT License 

docs/images/fig1_tesseract_code.png

@@ -18,12 +18,12 @@
     }
    },
    "source": [
-    "import stim\n",
     "\n",
-    "from tesseract_sim.circuit_base import init_circuit\n",
-    "from tesseract_sim.encoding_manual_9a import encode_manual_fig9a\n",
-    "from tesseract_sim.encoding_manual_9b import encode_manual_fig9b\n",
-    "from tesseract_sim.noise_cfg import NO_NOISE\n"
+    "\n",
+    "from tesseract_sim.common.circuit_base import init_circuit\n",
+    "from tesseract_sim.encoding.encoding_manual_9a import encode_manual_fig9a\n",
+    "from tesseract_sim.encoding.encoding_manual_9b import encode_manual_fig9b\n",
+    "from tesseract_sim.noise.noise_cfg import NO_NOISE\n"
    ],
    "outputs": [],
    "execution_count": 2

docs/images/fig8_error_correction_experiment.png

@@ -99,7 +99,7 @@
    ],
    "source": [
     "from tesseract_sim.run import build_circuit_ec_experiment\n",
-    "from tesseract_sim.noise_cfg import NO_NOISE\n",
+    "from tesseract_sim.noise.noise_cfg import NO_NOISE\n",
     "\n",
     "# Initialize circuit with experiment 2 parameters\n",
     "circuit = build_circuit_ec_experiment(rounds=1, cfg=NO_NOISE, encoding_mode='9a')\n",

docs/images/fig9_encoding.png

@@ -12,7 +12,7 @@
     "%autoreload 2\n",
     "\n",
     "import stim\n",
-    "import numpy as np\n",
+    "\n",
     "print(stim.__version__)"
    ]
   },
@@ -74,7 +74,7 @@
     "SHOTS = 100000\n",
     "\n",
     "# Create noise configuration\n",
-    "from tesseract_sim.noise_cfg import NoiseCfg\n",
+    "from tesseract_sim.noise.noise_cfg import NoiseCfg\n",
     "noise_cfg = NoiseCfg(\n",
     "    ec_active=True,  # Enable noise during error correction\n",
     "    ec_rate_1q=0.001,  # 0.1% error rate for 1-qubit gates\n",
@@ -123,7 +123,7 @@
     "SHOTS = 100000\n",
     "\n",
     "# Create noise configuration\n",
-    "from tesseract_sim.noise_cfg import NoiseCfg\n",
+    "from tesseract_sim.noise.noise_cfg import NoiseCfg\n",
     "noise_cfg = NoiseCfg(\n",
     "    ec_active=True,  # Enable noise during error correction\n",
     "    ec_rate_1q=0.001,  # 0.1% error rate for 1-qubit gates\n",