mat73-reader 0.1.0__tar.gz

mat73_reader-0.1.0/.gitignore

@@ -0,0 +1,19 @@
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+.pytest_cache/
+.coverage
+htmlcov/
+.venv/
+venv/
+.env
+*.mat
+!tests/fixtures/*.mat
+.DS_Store
+.idea/
+.vscode/

mat73_reader-0.1.0/LICENSE

@@ -0,0 +1,190 @@
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mat73_reader-0.1.0/PKG-INFO

@@ -0,0 +1,213 @@
+Metadata-Version: 2.4
+Name: mat73-reader
+Version: 0.1.0
+Summary: Read MATLAB v7.3 HDF5 .mat files that scipy.io.loadmat cannot handle.
+Author-email: William Garrow <williamgarrow@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: hdf5,mat73,matlab,scientific-data,scipy
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Requires-Dist: h5py>=3.0
+Requires-Dist: numpy>=1.20
+Requires-Dist: pandas>=1.3
+Provides-Extra: dev
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# mat73-reader
+
+Read MATLAB v7.3 HDF5 `.mat` files in Python. **including MATLAB table objects** that other tools cannot decode.
+
+## The MATLAB Table Problem
+
+MATLAB v7.3 stores table objects using an undocumented internal system called MCOS (MATLAB Class Object System). Every existing Python tool (`scipy.io.loadmat()`, `mat73`, `hdf5storage`) fails on them:
+
+```python
+# scipy can't even open v7.3 files
+>>> scipy.io.loadmat("experiment.mat")
+NotImplementedError: Please use HDF reader for matlab v7.3 files
+
+# mat73 opens the file but returns None for every table
+>>> import mat73
+>>> data = mat73.loadmat("experiment.mat")
+ERROR: MATLAB type not supported: table, (uint32)   # x 800
+>>> data["task"]["gaze"][0]
+None
+```
+
+Tables are used extensively in neuroscience, signal processing, cognitive science, biomechanics, and clinical research datasets. If your `.mat` file contains tables, **mat73-reader is currently the only Python tool that can read them.**
+
+```python
+>>> from mat73_reader import load
+>>> data = load("experiment.mat")
+>>> data["task"]["gaze"][0]
+      gaze_timestamp  world_index  confidence  norm_pos_x  norm_pos_y  ...
+0        5410.551714          0.0    0.999499    0.446264    0.846886  ...
+1        5410.555834          0.0    0.999653    0.446534    0.847007  ...
+2        5410.559773          0.0    0.999648    0.446660    0.846410  ...
+...
+[8205 rows x 21 columns]
+```
+
+## How It Works
+
+When other tools encounter a MATLAB table, they see a `(1,6) uint32` header and stop. mat73-reader decodes the MCOS block structure to follow the reference chain to the actual data:
+
+```mermaid
+graph TD
+    subgraph "What other tools see"
+        A["Table Header<br/>(1,6) uint32<br/>0xDD000000 ..."] -->|"???"| B["None"]
+    end
+
+    subgraph "What mat73-reader decodes"
+        H["Table Header<br/>(1,6) uint32"] -->|"instance index"| M["MCOS Reference Array<br/>#subsystem#/MCOS"]
+        M -->|"block offset + 0"| D["Column Data Refs<br/>(ncols, 1) object"]
+        M -->|"block offset + 5"| N["Column Name Refs<br/>(ncols, 1) object"]
+        D -->|"dereference"| D1["timestamp<br/>float64 (1, N)"]
+        D -->|"dereference"| D2["confidence<br/>float64 (1, N)"]
+        D -->|"dereference"| D3["...<br/>float64 (1, N)"]
+        N -->|"dereference"| N1["'gaze_timestamp'<br/>uint16 chars"]
+        N -->|"dereference"| N2["'confidence'<br/>uint16 chars"]
+        N -->|"dereference"| N3["'...'<br/>uint16 chars"]
+        D1 & D2 & D3 & N1 & N2 & N3 -->|"assemble"| DF["pandas DataFrame"]
+    end
+
+    style B fill:#ff6b6b,color:#fff
+    style DF fill:#51cf66,color:#fff
+```
+
+Each table instance occupies a fixed block of 7 consecutive entries in the MCOS reference array:
+
+```
+Block layout (7 slots per table):
+  +0  (ncols, 1) object refs   --> column data arrays (float64, int, etc.)
+  +1  (1, 1) float64           --> ndims
+  +2  (1, 1) float64           --> nrows
+  +3  (2,) uint64              --> segment info
+  +4  (1, 1) float64           --> nvars (number of columns)
+  +5  (ncols, 1) object refs   --> column name strings (uint16-encoded)
+  +6  Group                    --> table properties (units, descriptions, etc.)
+```
+
+The instance index from the table header maps to a block offset:
+
+```
+block_start = 2 + (instance - 1) * 7
+```
+
+This structure is not documented by MathWorks. It was reverse-engineered by analyzing real-world scientific datasets.
+
+## Real-World Validation
+
+mat73-reader has been validated against the [COLET dataset](https://zenodo.org/records/7766785) (Cognitive workLoad Estimation via Eye-Tracking), a 3.8 GB MATLAB v7.3 file containing:
+
+- 47 subjects, 4 tasks per subject
+- 4 data fields per task (gaze, pupil, blinks, annotation)
+- **752 MATLAB table objects** total
+- Over 14,000 individual data arrays
+
+Every table was successfully decoded into a pandas DataFrame with correct column names and data types. Other Python tools return `None` for all 752 tables.
+
+## Installation
+
+```bash
+pip install mat73-reader
+```
+
+Or install from source:
+
+```bash
+git clone https://github.com/WilliamGarrow/mat73-reader.git
+cd mat73-reader
+pip install -e ".[dev]"
+```
+
+## Usage
+
+### Python API
+
+```python
+from mat73_reader import load, inspect
+
+# Inspect file contents without loading data
+variables = inspect("experiment.mat")
+for var in variables:
+    print(var)
+
+# Load everything
+data = load("experiment.mat")
+
+# Load a specific top-level variable
+results = load("experiment.mat", variable="results")
+
+# Force all compatible arrays to pandas DataFrames
+data = load("experiment.mat", as_dataframe=True)
+```
+
+MATLAB tables are always returned as DataFrames automatically, no flags needed.
+
+### Command Line
+
+```bash
+# List variables, types, and shapes
+mat73-reader inspect experiment.mat
+
+# Convert to CSV (one file per variable)
+mat73-reader convert experiment.mat --format csv --output ./csv_output/
+
+# Convert to JSON
+mat73-reader convert experiment.mat --format json --output experiment.json
+
+# Convert a single variable
+mat73-reader convert experiment.mat --variable gaze_data --format csv
+```
+
+## What It Handles
+
+| MATLAB Type | Python Type | Notes |
+|------------|-------------|-------|
+| **Table objects** | **`pandas.DataFrame`** | **Column names and data types preserved** |
+| Numeric arrays | `numpy.ndarray` | Transposed to row-major order |
+| Structs | `dict` | Nested to arbitrary depth |
+| Cell arrays | `list` | HDF5 object references resolved |
+| Char arrays | `str` | Decoded from uint16 |
+| Scalars | Python `int`/`float` | Single-element arrays squeezed |
+
+## When to Use This vs. Other Tools
+
+| Scenario | Tool |
+|----------|------|
+| `.mat` v5 or earlier (no tables) | `scipy.io.loadmat()` |
+| `.mat` v7.3 with arrays and structs only | `mat73` or **mat73-reader** |
+| `.mat` v7.3 with **table objects** | **mat73-reader** (only option in Python) |
+| Not sure what format you have | Try `mat73-reader` first; it will tell you if it's not v7.3 |
+
+## Development
+
+```bash
+git clone https://github.com/WilliamGarrow/mat73-reader.git
+cd mat73-reader
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+pytest
+```
+
+### Test Suite
+
+38 tests covering:
+- Standard v7.3 reading (arrays, structs, cell arrays, char arrays, scalars)
+- MCOS table header detection (positive and negative cases)
+- Single and multi-table decoding with synthetic fixtures
+- Column name extraction and data value verification
+- Edge cases (non-table uint32 arrays, missing variables, invalid files)
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE) for details.

mat73_reader-0.1.0/README.md

@@ -0,0 +1,191 @@
+# mat73-reader
+
+Read MATLAB v7.3 HDF5 `.mat` files in Python. **including MATLAB table objects** that other tools cannot decode.
+
+## The MATLAB Table Problem
+
+MATLAB v7.3 stores table objects using an undocumented internal system called MCOS (MATLAB Class Object System). Every existing Python tool (`scipy.io.loadmat()`, `mat73`, `hdf5storage`) fails on them:
+
+```python
+# scipy can't even open v7.3 files
+>>> scipy.io.loadmat("experiment.mat")
+NotImplementedError: Please use HDF reader for matlab v7.3 files
+
+# mat73 opens the file but returns None for every table
+>>> import mat73
+>>> data = mat73.loadmat("experiment.mat")
+ERROR: MATLAB type not supported: table, (uint32)   # x 800
+>>> data["task"]["gaze"][0]
+None
+```
+
+Tables are used extensively in neuroscience, signal processing, cognitive science, biomechanics, and clinical research datasets. If your `.mat` file contains tables, **mat73-reader is currently the only Python tool that can read them.**
+
+```python
+>>> from mat73_reader import load
+>>> data = load("experiment.mat")
+>>> data["task"]["gaze"][0]
+      gaze_timestamp  world_index  confidence  norm_pos_x  norm_pos_y  ...
+0        5410.551714          0.0    0.999499    0.446264    0.846886  ...
+1        5410.555834          0.0    0.999653    0.446534    0.847007  ...
+2        5410.559773          0.0    0.999648    0.446660    0.846410  ...
+...
+[8205 rows x 21 columns]
+```
+
+## How It Works
+
+When other tools encounter a MATLAB table, they see a `(1,6) uint32` header and stop. mat73-reader decodes the MCOS block structure to follow the reference chain to the actual data:
+
+```mermaid
+graph TD
+    subgraph "What other tools see"
+        A["Table Header<br/>(1,6) uint32<br/>0xDD000000 ..."] -->|"???"| B["None"]
+    end
+
+    subgraph "What mat73-reader decodes"
+        H["Table Header<br/>(1,6) uint32"] -->|"instance index"| M["MCOS Reference Array<br/>#subsystem#/MCOS"]
+        M -->|"block offset + 0"| D["Column Data Refs<br/>(ncols, 1) object"]
+        M -->|"block offset + 5"| N["Column Name Refs<br/>(ncols, 1) object"]
+        D -->|"dereference"| D1["timestamp<br/>float64 (1, N)"]
+        D -->|"dereference"| D2["confidence<br/>float64 (1, N)"]
+        D -->|"dereference"| D3["...<br/>float64 (1, N)"]
+        N -->|"dereference"| N1["'gaze_timestamp'<br/>uint16 chars"]
+        N -->|"dereference"| N2["'confidence'<br/>uint16 chars"]
+        N -->|"dereference"| N3["'...'<br/>uint16 chars"]
+        D1 & D2 & D3 & N1 & N2 & N3 -->|"assemble"| DF["pandas DataFrame"]
+    end
+
+    style B fill:#ff6b6b,color:#fff
+    style DF fill:#51cf66,color:#fff
+```
+
+Each table instance occupies a fixed block of 7 consecutive entries in the MCOS reference array:
+
+```
+Block layout (7 slots per table):
+  +0  (ncols, 1) object refs   --> column data arrays (float64, int, etc.)
+  +1  (1, 1) float64           --> ndims
+  +2  (1, 1) float64           --> nrows
+  +3  (2,) uint64              --> segment info
+  +4  (1, 1) float64           --> nvars (number of columns)
+  +5  (ncols, 1) object refs   --> column name strings (uint16-encoded)
+  +6  Group                    --> table properties (units, descriptions, etc.)
+```
+
+The instance index from the table header maps to a block offset:
+
+```
+block_start = 2 + (instance - 1) * 7
+```
+
+This structure is not documented by MathWorks. It was reverse-engineered by analyzing real-world scientific datasets.
+
+## Real-World Validation
+
+mat73-reader has been validated against the [COLET dataset](https://zenodo.org/records/7766785) (Cognitive workLoad Estimation via Eye-Tracking), a 3.8 GB MATLAB v7.3 file containing:
+
+- 47 subjects, 4 tasks per subject
+- 4 data fields per task (gaze, pupil, blinks, annotation)
+- **752 MATLAB table objects** total
+- Over 14,000 individual data arrays
+
+Every table was successfully decoded into a pandas DataFrame with correct column names and data types. Other Python tools return `None` for all 752 tables.
+
+## Installation
+
+```bash
+pip install mat73-reader
+```
+
+Or install from source:
+
+```bash
+git clone https://github.com/WilliamGarrow/mat73-reader.git
+cd mat73-reader
+pip install -e ".[dev]"
+```
+
+## Usage
+
+### Python API
+
+```python
+from mat73_reader import load, inspect
+
+# Inspect file contents without loading data
+variables = inspect("experiment.mat")
+for var in variables:
+    print(var)
+
+# Load everything
+data = load("experiment.mat")
+
+# Load a specific top-level variable
+results = load("experiment.mat", variable="results")
+
+# Force all compatible arrays to pandas DataFrames
+data = load("experiment.mat", as_dataframe=True)
+```
+
+MATLAB tables are always returned as DataFrames automatically, no flags needed.
+
+### Command Line
+
+```bash
+# List variables, types, and shapes
+mat73-reader inspect experiment.mat
+
+# Convert to CSV (one file per variable)
+mat73-reader convert experiment.mat --format csv --output ./csv_output/
+
+# Convert to JSON
+mat73-reader convert experiment.mat --format json --output experiment.json
+
+# Convert a single variable
+mat73-reader convert experiment.mat --variable gaze_data --format csv
+```
+
+## What It Handles
+
+| MATLAB Type | Python Type | Notes |
+|------------|-------------|-------|
+| **Table objects** | **`pandas.DataFrame`** | **Column names and data types preserved** |
+| Numeric arrays | `numpy.ndarray` | Transposed to row-major order |
+| Structs | `dict` | Nested to arbitrary depth |
+| Cell arrays | `list` | HDF5 object references resolved |
+| Char arrays | `str` | Decoded from uint16 |
+| Scalars | Python `int`/`float` | Single-element arrays squeezed |
+
+## When to Use This vs. Other Tools
+
+| Scenario | Tool |
+|----------|------|
+| `.mat` v5 or earlier (no tables) | `scipy.io.loadmat()` |
+| `.mat` v7.3 with arrays and structs only | `mat73` or **mat73-reader** |
+| `.mat` v7.3 with **table objects** | **mat73-reader** (only option in Python) |
+| Not sure what format you have | Try `mat73-reader` first; it will tell you if it's not v7.3 |
+
+## Development
+
+```bash
+git clone https://github.com/WilliamGarrow/mat73-reader.git
+cd mat73-reader
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+pytest
+```
+
+### Test Suite
+
+38 tests covering:
+- Standard v7.3 reading (arrays, structs, cell arrays, char arrays, scalars)
+- MCOS table header detection (positive and negative cases)
+- Single and multi-table decoding with synthetic fixtures
+- Column name extraction and data value verification
+- Edge cases (non-table uint32 arrays, missing variables, invalid files)
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE) for details.

mat73_reader-0.1.0/examples/basic_usage.py

@@ -0,0 +1,47 @@
+"""Basic usage examples for mat73-reader."""
+
+from mat73_reader import load, inspect
+
+# Replace with the path to your .mat v7.3 file
+MAT_FILE = "your_file.mat"
+
+
+def example_inspect():
+    """See what variables are in a file before loading."""
+    variables = inspect(MAT_FILE)
+    for var in variables:
+        print(f"  {var['name']}: {var['type']}", end="")
+        if var["type"] == "dataset":
+            print(f" shape={var['shape']} dtype={var['dtype']}")
+        elif var["type"] == "group":
+            print(f" children={var['children']}")
+        else:
+            print()
+
+
+def example_load_all():
+    """Load every variable from the file."""
+    data = load(MAT_FILE)
+    for name, value in data.items():
+        print(f"  {name}: {type(value).__name__}")
+
+
+def example_load_one():
+    """Load a single variable by name."""
+    result = load(MAT_FILE, variable="x")
+    print(f"  shape: {result.shape}, dtype: {result.dtype}")
+
+
+def example_load_as_dataframe():
+    """Load and convert 2D arrays to pandas DataFrames."""
+    data = load(MAT_FILE, as_dataframe=True)
+    for name, value in data.items():
+        print(f"  {name}: {type(value).__name__}")
+
+
+if __name__ == "__main__":
+    print("Inspecting file:")
+    example_inspect()
+
+    print("\nLoading all variables:")
+    example_load_all()