From 2e23ba9bf019731f2aac15e586da49dd501e913c Mon Sep 17 00:00:00 2001
From: Adam Li <adam2392@gmail.com>
Date: Fri, 9 Jul 2021 17:37:54 -0400
Subject: [PATCH] PUshing for gotman.

---
 docs/tutorials/convert_gotman_bids.py | 108 ++++++++++++++++++++++++++
 mne_hfo/io.py                         |   2 +-
 2 files changed, 109 insertions(+), 1 deletion(-)
 create mode 100644 docs/tutorials/convert_gotman_bids.py

diff --git a/docs/tutorials/convert_gotman_bids.py b/docs/tutorials/convert_gotman_bids.py
new file mode 100644
index 0000000..5b9382d
--- /dev/null
+++ b/docs/tutorials/convert_gotman_bids.py
@@ -0,0 +1,108 @@
+from mne.io import RawArray
+from mne import create_info
+from  mne_bids import read_raw_bids, write_raw_bids, BIDSPath, get_entities_from_fname
+from pathlib import Path
+
+
+import scipy.io
+
+
+class MatReader:
+    """
+    Object to read mat files into a nested dictionary if need be.
+    Helps keep structure from matlab similar to what is used in python.
+    """
+
+    def __init__(self, filename=None):
+        self.filename = filename
+
+    def loadmat(self, filename):
+        """
+        this function should be called instead of direct spio.loadmat
+        as it cures the problem of not properly recovering python dictionaries
+        from mat files. It calls the function check keys to cure all entries
+        which are still mat-objects
+        """
+        try:
+            data = scipy.io.loadmat(
+                filename, struct_as_record=False, squeeze_me=True, chars_as_strings=True
+            )
+        except NotImplementedError as e:
+            print(e)
+            data = hdf5storage.loadmat(filename)
+        return self._check_keys(data)
+
+    def _check_keys(self, dict):
+        """
+        checks if entries in dictionary are mat-objects. If yes
+        todict is called to change them to nested dictionaries
+        """
+        print(f"Found these keys {dict.keys()}")
+        for key in dict:
+            if isinstance(dict[key], scipy.io.matlab.mio5_params.mat_struct):
+                dict[key] = self._todict(dict[key])
+        return dict
+
+    def _todict(self, matobj):
+        """
+        A recursive function which constructs from matobjects nested dictionaries
+        """
+        dict = {}
+        for strg in matobj._fieldnames:
+            elem = matobj.__dict__[strg]
+            if isinstance(elem, scipy.io.matlab.mio5_params.mat_struct):
+                dict[strg] = self._todict(elem)
+            elif isinstance(elem, np.ndarray):
+                dict[strg] = self._tolist(elem)
+            else:
+                dict[strg] = elem
+        return dict
+
+    def _tolist(self, ndarray):
+        """
+        A recursive function which constructs lists from cellarrays
+        (which are loaded as numpy ndarrays), recursing into the elements
+        if they contain matobjects.
+        """
+        elem_list = []
+        for sub_elem in ndarray:
+            if isinstance(sub_elem, scipy.io.matlab.mio5_params.mat_struct):
+                elem_list.append(self._todict(sub_elem))
+            elif isinstance(sub_elem, np.ndarray):
+                elem_list.append(self._tolist(sub_elem))
+            else:
+                elem_list.append(sub_elem)
+        return elem_list
+
+def _load_mat_file(mat_fname):
+    mat_dict = MatReader().loadmat(mat_fname)['data']
+
+    info = create_info(sfreq, ch_names, ch_type=)
+    raw = RawArray()
+
+def convert_gotman_bids(source_path, root):
+    recording_path = source_path / 'Recordings'
+
+    suffix = 'ieeg'
+    datatype = 'ieeg'
+
+    raw_files = recording_path.glob('*.mat')
+    for fname in raw_files:
+        _, subject, num, _ = fname.name.split('_')
+
+        # create BIDS Path
+        bids_path = BIDSPath(subject=subject, task='interictal',
+                             suffix=suffix, datatype=datatype,
+                             extension='.vhdr')
+
+        # read in the matlab data as a raw data
+        raw = _load_mat_file(fname)
+
+        # write output to BIDS
+        write_raw_bids(raw, bids_path)
+
+if __name__ == '__main__':
+    root = Path('/Users/adam2392/OneDrive - Johns Hopkins/Gotman Zelman HFO dataset')
+    source_path = root / 'sourcedata'
+
+    convert_gotman_bids(source_path, root)
\ No newline at end of file
diff --git a/mne_hfo/io.py b/mne_hfo/io.py
index 98be59e..4022117 100644
--- a/mne_hfo/io.py
+++ b/mne_hfo/io.py
@@ -361,7 +361,7 @@ def read_annotations(fname: Union[str, Path], root: Path = None) \
         )
 
     # read data
-    raw = read_raw_bids(raw_fpath)
+    raw = read_raw_bids(raw_fpath, verbose=False)
     sfreq = raw.info['sfreq']
 
     # create sample column