added config file

code/modules/filehandling.py

@@ -0,0 +1,54 @@
+import os
+
+import yaml
+import numpy as np
+from thunderfish.dataloader import DataLoader
+
+
+class ConfLoader:
+    """
+    Load configuration from yaml file as class attributes
+    """
+
+    def __init__(self, path: str) -> None:
+        with open(path) as file:
+            try:
+                conf = yaml.safe_load(file)
+                for key in conf:
+                    setattr(self, key, conf[key])
+            except yaml.YAMLError as error:
+                raise error
+
+
+class LoadData:
+    """
+    Attributes
+    ----------
+    data : DataLoader object containing raw data
+    samplerate : sampling rate of raw data
+    time : array of time for tracked fundamental frequency
+    freq : array of fundamental frequency
+    idx : array of indices to access time array
+    ident : array of identifiers for each tracked fundamental frequency
+    ids : array of unique identifiers exluding NaNs
+    """
+
+    def __init__(self, datapath: str) -> None:
+
+        # load raw data
+        self.file = os.path.join(datapath, "traces-grid1.raw")
+        self.data = DataLoader(self.file, 60.0, 0, channel=-1)
+        self.samplerate = self.data.samplerate
+
+        # load wavetracker files
+        self.time = np.load(datapath + "times.npy", allow_pickle=True)
+        self.freq = np.load(datapath + "fund_v.npy", allow_pickle=True)
+        self.idx = np.load(datapath + "idx_v.npy", allow_pickle=True)
+        self.ident = np.load(datapath + "ident_v.npy", allow_pickle=True)
+        self.ids = np.unique(self.ident[~np.isnan(self.ident)])
+
+    def __repr__(self) -> str:
+        return f"LoadData({self.file})"
+
+    def __str__(self) -> str:
+        return f"LoadData({self.file})"