Dfp pclr zoo (#594)

* ENH: Add C3PO PCLR models

* ENH: edit get_model() and get_representations() to add the c3po pclr models

* STYLE: Update README

* FIX: Upload the correct c3po_pclr model

Author: daniellepace

model_zoo/PCLR/.gitattributes

@@ -0,0 +1 @@
+*.h5 filter=lfs diff=lfs merge=lfs -text

model_zoo/PCLR/README.md

@@ -22,7 +22,7 @@ python -i get_representations.py  # test the setup worked
 You can get ECG representations using [get_representations.py](./get_representations.py).
 `get_representations.get_representations` builds `N x 320` ECG representations from `N` ECGs.
 
-The model expects 10s 12-lead ECGs with a specific lead order and interpolated to be 4,096 samples long.
+The model expects 10s 12-lead ECGs meaured in milli-volts with a specific lead order and interpolated to be 4,096 samples long.
 [preprocess_ecg.py](./preprocess_ecg.py) shows how to do the pre-processing.
 
 ### Use git LFS to localize the model file
@@ -103,6 +103,24 @@ the model only takes lead I of the ECG as input.
 ## Lead II PCLR
 [Lead II PCLR](./PCLR_lead_II.h5) is like lead I PCLR except it was trained with all ECGs sampled to 250Hz.
 
+## C3PO PCLR and AUG C3PO PCLR
+We also provide PCLR models trained using subjects from the C3PO cohort, with and without augmentation.
+The model files are available via:
+
+`git lfs pull --include model_zoo/PCLR/c3po_pclr.h5`
+
+`git lfs pull --include model_zoo/PCLR/aug_c3po_pclr.h5`
+
+You can get ECG representations using for example [get_representations.py(ecgs, model_name='c3po_pclr')](./get_representations.py).
+`get_representations.get_representations` builds `N x 320` ECG representations from `N` ECGs.
+
+The model expects 10s 12-lead ECGs measured in milli-volts with a specific lead order and interpolated to be 2,500 samples long. Note that this interpolation is different from the standard PCLR model.
+[preprocess_ecg.py](./preprocess_ecg.py) shows how to do the pre-processing; when calling it remember to set `ecg_samples=2500`.
+
+The code snippet above showing example inference with UKB ECGs is also appropriate for these models. Remember to:
+1. Load `c3po_pclr.h5` or `aug_c3po_pclr.h5` instead of `PCLR.h5`.
+2. Interpolate to 2500 instead of 4096.
+
 ## Alternative save format
 The newer keras saved model format is available for the 12-lead and single lead models at [PCLR](./PCLR)
 and [PCLR_lead_I](./PCLR_lead_I) and [PCLR_lead_II](./PCLR_lead_II).

model_zoo/PCLR/aug_c3po_pclr.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:aea32327873194c38b000a1a0ba25e0b0d7ddbfcc4d68b18c34a423a8fff873d
+size 25688728

model_zoo/PCLR/c3po_pclr.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cef43254d129ea7741b670c868b9423cd140186ee46ba051bc1b9eea5cc7093e
+size 25688728

model_zoo/PCLR/get_representations.py

@@ -6,20 +6,27 @@
 from preprocess_ecg import process_ecg, LEADS
 
 
-def get_model() -> Model:
+def get_model(model_name = 'pclr') -> Model:
     """Get PCLR embedding model"""
-    return load_model("./PCLR.h5")
+    if model_name == 'pclr':
+        return load_model("./PCLR.h5")
+    elif model_name == 'c3po_pclr':
+        return load_model("./c3po_pclr.h5")
+    elif model_name == 'aug_c3po_pclr':
+        return load_model("./aug_c3po_pclr.h5")
 
 
-def get_representations(ecgs: List[Dict[str, np.ndarray]]) -> np.ndarray:
+def get_representations(ecgs: List[Dict[str, np.ndarray]], model_name:str = 'pclr') -> np.ndarray:
     """
     Uses PCLR trained model to build representations of ECGs
     :param ecgs: A list of dictionaries mapping lead name to lead values.
                  The lead values should be measured in milli-volts.
                  Each lead should represent 10s of samples.
+    :param model_name: Specifies the model to use: either 'pclr', 'c3po_pclr' or 'aug_c3po_pclr'.
+                 Default is 'pclr'
     :return:
     """
-    model = get_model()
+    model = get_model(model_name)
     ecgs = np.stack(list(map(process_ecg, ecgs)))
     return model.predict(ecgs)