Feat/eit parser complete

README.md

@@ -36,6 +36,12 @@ print(data.n_frames, data.fs)       # e.g. 11500, 50.0
 print(data.pixels.shape)            # (11500, 32, 32)
 print(data.global_signal[:10])      # first 10 frames global EIT signal
 
+# Dräger .eit — raw transimpedances for pyEIT reconstruction
+data = load_data("patient01.eit")
+print(data.n_frames, data.fs)          # e.g. 11500, 50.0
+print(data.measurements.shape)        # (11500, 208) — 208 = 16 inj × 13 meas
+print(list(data.aux_signals.keys()))   # timestamp, I_real, V_diff, medibus, ...
+
 # Dräger .asc — continuous frame-by-frame signal export
 data = load_data("patient01.asc")
 print(data.n_frames, data.fs)       # e.g. 11500, 50.0
@@ -57,24 +63,36 @@ Pre-alpha. Data model and parsing layer implemented.
 |-------|---------|-------------|
 | `ReconstructedFrameData` | 32×32 pixel matrices + synchronized signals | `.bin`, `.txt` |
 | `ContinuousSignalData` | Signal table, one row per frame | `.asc` |
-| `RawImpedanceData` | Raw transimpedances for pyEIT | `.eit` (scaffold) |
+| `RawImpedanceData` | Calibrated transimpedances + aux signals for pyEIT | `.eit` |
 
 **Parsers** (`parsers/`):
 
 | Parser | Status | Formats |
 |--------|--------|---------|
 | `DragerBinParser` | Implemented | `.bin` — base frame (4358 b) and PressurePod frame (4382 b); registry-driven, new frame sizes require only a dtype + one entry |
 | `DragerAscParser` | Implemented | `.asc`, `.txt`, `.csv` — continuous waveform export |
-| `DragerEitParser` | Scaffold | `.eit` (Fase 2) |
+| `DragerEitParser` | Implemented | `.eit` — ASCII header + binary frames (5495 b/frame); 208 calibrated transimpedances + Medibus aux signals |
 | `TimpelTabularParser` | Implemented | `.csv`, `.txt` — reconstructed frame export |
 
 All parsers are accessible via the single entry point `load_data(path)`, which
 auto-detects vendor and format.
 
+`RawImpedanceData` from `.eit` files can be reconstructed to 32×32 pixel images via
+which is an example of pyEIT wrapping `reconstruct_greit()` (optional dependency: `pip install fasteit[pyeit]`; implements
+GREIT — Adler et al., *Physiol. Meas.* 2009, DOI: 10.1088/0967-3334/30/6/S03):
+
+```python
+from fasteit.parsers.draeger.eit.eit_pyeit_bridge import reconstruct_greit
+
+data = load_data("patient01.eit")
+images = reconstruct_greit(data.measurements)  # (N_frames, 32, 32)
+```
+
 ## Documentation
 
-- [`docs/data_model.md`](docs/data_model.md) — data containers and parsing flow per file type
-- [`docs/parsing_layer.md`](docs/parsing_layer.md) — how to extend: new frame sizes, new vendors, new formats
+- [`docs/data_model.md`](docs/data_model.md) — data container field specifications
+- [`docs/parsers.md`](docs/parsers.md) — parser reference: formats, calibration, GREIT bridge, loader utilities
+- [`docs/parsing_layer.md`](docs/parsing_layer.md) — architecture and extension recipes
 
 ## Contributing
 

docs/data_model.md

@@ -1,25 +1,14 @@
 # fastEIT — Data Model
 
-Specifications for all data containers. For parsing flow, detection logic, and
-extension recipes see [`parsing_layer.md`](parsing_layer.md).
-
----
-
-## 1. Overview
-
-| File | Vendor | Container | Content |
-|------|--------|-----------|---------|
-| `.bin` | Dräger | `ReconstructedFrameData` | 32×32 pixel matrices + Medibus signals |
-| `.csv` / `.txt` / `.asc` | Timpel | `ReconstructedFrameData` | 32×32 pixel matrices + 6 device signals |
-| `.asc` | Dräger | `ContinuousSignalData` | Frame-by-frame signal table, no matrices |
-| `.eit` | Dräger | `RawImpedanceData` | 208 raw transimpedances per frame |
-| `.x`   | Timpel | `RawImpedanceData` | 208 raw transimpedances per frame |
+Specifications for all data containers. For parser details, calibration
+constants, and loader utilities see [`parsers.md`](parsers.md). For architecture
+and extension recipes see [`parsing_layer.md`](parsing_layer.md).
 
 All containers inherit from `BaseData` (`models/base_data.py`).
 
 ---
 
-## 2. `BaseData` — common base
+## 1. `BaseData` — common base
 
 ```
 filename    str          Source file path
@@ -33,7 +22,7 @@ duration    float        n_frames / fs  (0.0 if fs is None)
 
 ---
 
-## 3. `ReconstructedFrameData`
+## 2. `ReconstructedFrameData`
 
 **File:** `models/reconstructed_data.py`
 **Produced by:** `DragerBinParser` (`.bin`), `TimpelTabularParser` (`.csv/.txt/.asc`)
@@ -80,7 +69,7 @@ is applied in the preprocessing layer.
 
 ---
 
-## 4. `ContinuousSignalData`
+## 3. `ContinuousSignalData`
 
 **File:** `models/continuous_data.py`
 **Produced by:** `DragerAscParser` (`.asc`)
@@ -97,16 +86,34 @@ table   pd.DataFrame   One row per EIT frame. Snake_case column names.
 
 ---
 
-## 5. `RawImpedanceData`
+## 4. `RawImpedanceData`
 
 **File:** `models/raw_impedance_data.py`
-**Produced by:** `DragerEitParser` (`.eit`), `TimpelRawParser` (`.x`) — both scaffold
+**Produced by:** `DragerEitParser` (`.eit`); `TimpelRawParser` (`.x`) — scaffold
 
 ```
 measurements   np.ndarray   shape (N_frames, 208)
+                            Calibrated transimpedances (not raw ADC counts, not
+                            yet image-reconstructed). For Dräger:
+                            vv = FT_A*trans_A - FT_B*trans_B (EIDORS, Adler 2016)
                             208 = 16 electrodes × 13 measurement pairs
-                            Adjacent drive pattern (Dräger and Timpel)
+                            (adjacent drive, standard Dräger pattern)
+
+aux_signals    dict|None    Named per-frame arrays. Populated by DragerEitParser:
+                              "timestamp"          float64 (N,)    fraction of day
+                              "trans_A"            float64 (N,208) raw ADC — primary
+                              "trans_B"            float64 (N,208) raw ADC — reference
+                              "injection_current"  float64 (N,16)  raw ADC counts
+                              "I_real"             float64 (N,16)  injected current [A]
+                              "voltage_A"          float64 (N,16)  raw ADC counts
+                              "voltage_B"          float64 (N,16)  raw ADC counts
+                              "V_diff"             float64 (N,16)  differential voltage [V]
+                              "frame_counter"      uint16  (N,)
+                              "medibus"            float32 (N,67)  ventilator channels
+                            None if the source file carries no auxiliary signals.
 ```
 
-Intended consumer: **pyEIT** or any reconstruction library.
-fastEIT does not perform image reconstruction — it ingests vendor-reconstructed files.
+Intended consumer: `reconstruct_greit()` (in `fasteit.parsers.draeger.eit.eit_pyeit_bridge`,
+requires optional `pyeit` dependency) or any external reconstruction library.
+For `.bin` and Timpel `.csv` files, fastEIT ingests vendor-reconstructed images
+and does not re-reconstruct them.