use mat73 if .mat is v7.3, otherwise load the data by scipy.io

PINNICLE/modeldata/general_mat_data.py

@@ -1,8 +1,7 @@
 from . import DataBase
 from ..parameter import SingleDataParameter
 from ..physics import Constants
-from ..utils import plot_dict_data
-import mat73
+from ..utils import plot_dict_data, load_mat
 import numpy as np
 
 
@@ -28,7 +27,7 @@ def load_data(self):
         """ load scatter data from a `.mat` file, return a dict with the required data
         """
         # Reading matlab data
-        data = mat73.loadmat(self.parameters.data_path)
+        data = load_mat(self.parameters.data_path)
 
         # x,y coordinates
         self.X_dict['x'] = data['x']

PINNICLE/modeldata/issm_data.py

@@ -1,8 +1,7 @@
 from . import DataBase
 from ..parameter import SingleDataParameter
 from ..physics import Constants
-from ..utils import plot_dict_data
-import mat73
+from ..utils import plot_dict_data, load_mat
 import numpy as np
 
 
@@ -41,7 +40,7 @@ def load_data(self):
         """ load ISSM model from a `.mat` file
         """
         # Reading matlab data
-        data = mat73.loadmat(self.parameters.data_path)
+        data = load_mat(self.parameters.data_path)
         # get the model
         md = data['md']
         # create the output dict

PINNICLE/utils/helper.py

@@ -1,6 +1,7 @@
 import json
 import os
-
+import mat73
+import scipy.io
 
 def is_file_ext(path, ext):
     """ check if a given path is ended by ext
@@ -39,3 +40,12 @@ def load_dict_from_json(path, filename):
     else:
         data = {}
     return data
+
+def load_mat(file):
+    """ load .mat file, if the file is in MATLAB 7.3 format use mat73.loadmat, otherwise use scipy.io.loadmat()
+    """
+    try:
+        data = mat73.loadmat(file)
+    except TypeError:
+        data = scipy.io.loadmat(file)
+    return data

tests/test_utils.py

@@ -1,27 +1,41 @@
-import PINNICLE as pinn
 import pytest
 import tensorflow as tf
+import os
+from PINNICLE.utils import save_dict_to_json, load_dict_from_json, data_misfit, load_mat
 
 data = {"s":1, "v":[1, 2, 3]}
 
 
 def test_save_and_load_dict(tmp_path):
-    pinn.utils.save_dict_to_json(data, tmp_path, "temp.json")
-    pinn.utils.save_dict_to_json(data, tmp_path, "noextension")
-    assert data == pinn.utils.load_dict_from_json(tmp_path, "temp.json")
-    assert data == pinn.utils.load_dict_from_json(tmp_path, "temp")
-    assert data == pinn.utils.load_dict_from_json(tmp_path, "noextension.json")
+    save_dict_to_json(data, tmp_path, "temp.json")
+    save_dict_to_json(data, tmp_path, "noextension")
+    assert data == load_dict_from_json(tmp_path, "temp.json")
+    assert data == load_dict_from_json(tmp_path, "temp")
+    assert data == load_dict_from_json(tmp_path, "noextension.json")
 
 def test_data_misfit():
     with pytest.raises(Exception):
-        pinn.utils.data_misfit.get("not defined")
-    assert pinn.utils.data_misfit.get("MSE") != None
-    assert pinn.utils.data_misfit.get("VEL_LOG") != None
-    assert pinn.utils.data_misfit.get("MEAN_SQUARE_LOG") != None
-    assert pinn.utils.data_misfit.get("MAPE") != None
+        data_misfit.get("not defined")
+    assert data_misfit.get("MSE") != None
+    assert data_misfit.get("VEL_LOG") != None
+    assert data_misfit.get("MEAN_SQUARE_LOG") != None
+    assert data_misfit.get("MAPE") != None
 
 def test_data_misfit_functions():
-    assert  pinn.utils.data_misfit.get("MSE")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
-    assert  pinn.utils.data_misfit.get("VEL_LOG")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
-    assert  pinn.utils.data_misfit.get("MEAN_SQUARE_LOG")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
-    assert  pinn.utils.data_misfit.get("MAPE")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
+    assert  data_misfit.get("MSE")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
+    assert  data_misfit.get("VEL_LOG")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
+    assert  data_misfit.get("MEAN_SQUARE_LOG")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
+    assert  data_misfit.get("MAPE")(tf.convert_to_tensor([1.0]),tf.convert_to_tensor([1.0])) == 0.0
+
+def test_loadmat():
+    filename = "flightTracks.mat"
+    repoPath = os.path.dirname(__file__) + "/../examples/"
+    appDataPath = os.path.join(repoPath, "dataset")
+    path = os.path.join(appDataPath, filename)
+    assert load_mat(path)
+
+    filename = "flightTracks73.mat"
+    repoPath = os.path.dirname(__file__) + "/../examples/"
+    appDataPath = os.path.join(repoPath, "dataset")
+    path = os.path.join(appDataPath, filename)
+    assert load_mat(path)