pyNIBS 0.2024.8__py3-none-any.whl → 0.2026.1__py3-none-any.whl

pynibs/expio/localite.py

@@ -20,6 +20,7 @@ def get_tms_elements(xml_paths, verbose=False):
     ----------
     xml_paths : list of str or str
         Paths to coil0-file and optionally coil1-file. If there is no coil1-file, use empty string.
+        Paths to coil0-file and optionally coil1-file. If there is no coil1-file, use empty string.
     verbose : bool, default: False
         Flag indicating verbosity.
 
@@ -99,8 +100,8 @@ def get_tms_elements(xml_paths, verbose=False):
         xml_rv = coil0_tm.find('ResponseValues')
         xml_va = xml_rv.findall('Value')
 
-        # if valueA is NaN, compute dI/dt with amplitudeA
-        if xml_va[0].get('response') == 'NaN':
+        # if valueA is nan, compute dI/dt with amplitudeA
+        if xml_va[0].get('response') == 'nan':
             current_lst.append(str(round(float(xml_va[2].get('response')) * 1.4461)))  # was 1.38
         else:
             current_lst.append(xml_va[0].get('response'))
@@ -179,7 +180,7 @@ def match_instrument_marker_string(xml_paths, condition_order):
     -------
     coil_cond_lst : list of str
         Strings containing the right conditions.
-     drop_idx : list of int
+    drop_idx : list of int
         Indices of trigger markers that were dropped.
     """
     drop_idx = []
@@ -568,7 +569,6 @@ def read_triggermarker(fn_xml):
                 m[im_index1, im_index2, 0] = (float(im_ma.get('data' + str(im_index1) + str(im_index2))))
 
         # check if coil position is untracked
-        np.eye(4)
         if (m[:, :, 0] == np.eye(4)).all():
             print(f"Untracked coil position found for idx {m_nnav.shape[2]}.")
             m[:3, :4, 0] = np.nan
@@ -640,7 +640,7 @@ def merge_exp_data_localite(subject, coil_outlier_corr_cond, remove_coil_skin_di
             im_lst.append(im_lst[0])
 
     # handle coil serial numbers
-    coil_sn_lst = pynibs.get_coil_sn_lst(fn_coil)
+    coil_sn_lst = pynibs.expio.get_coil_sn_lst(fn_coil)
 
     # get TMS pulse onset
     tms_pulse_time = subject.exp[exp_idx]['tms_pulse_time']
@@ -678,7 +678,7 @@ def merge_exp_data_localite(subject, coil_outlier_corr_cond, remove_coil_skin_di
             len_conds.append(len(dict_lst) - len_conds[-1])
 
     # convert list of dict to dict of list
-    results_dct = pynibs.list2dict(dict_lst)
+    results_dct = pynibs.util.utils.list2dict(dict_lst)
 
     # check if we have a single pulse TMS experiments where every pulse is one condition
     single_pulse_experiment = np.zeros(len(len_conds))
@@ -744,25 +744,25 @@ def merge_exp_data_localite(subject, coil_outlier_corr_cond, remove_coil_skin_di
     #######################################################
     if coil_outlier_corr_cond:
         print("Removing coil position outliers")
-        results_dct = pynibs.coil_outlier_correction_cond(exp=results_dct,
-                                                          outlier_angle=5.,
-                                                          outlier_loc=3.,
-                                                          fn_exp_out=fn_exp_hdf5)
+        results_dct = pynibs.expio.coil_outlier_correction_cond(exp=results_dct,
+                                                                outlier_angle=5.,
+                                                                outlier_loc=3.,
+                                                                fn_exp_out=fn_exp_hdf5)
 
     # perform coil <-> head distance correction
     ###########################################
     if coil_distance_corr:
         print("Performing coil <-> head distance correction")
-        results_dct = pynibs.coil_distance_correction(exp=results_dct,
-                                                      fn_geo_hdf5=fn_mesh_hdf5,
-                                                      remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier,
-                                                      fn_plot=os.path.split(fn_exp_hdf5)[0])
+        results_dct = pynibs.expio.coil_distance_correction(exp=results_dct,
+                                                            fn_geo_hdf5=fn_mesh_hdf5,
+                                                            remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier,
+                                                            fn_plot=os.path.split(fn_exp_hdf5)[0])
 
     # plot finally used mep data
     ############################
     if plot:
         print("Creating MEP plots ...")
-        sampling_rate = pynibs.get_mep_sampling_rate(cfs_paths[0])
+        sampling_rate = pynibs.expio.get_mep_sampling_rate(cfs_paths[0])
 
         # Compute start and stop idx according to sampling rate
         start_mep = int((20 / 1000.) * sampling_rate)
@@ -848,12 +848,9 @@ def merge_exp_data_localite(subject, coil_outlier_corr_cond, remove_coil_skin_di
     df_phys_data_postproc_emg = pd.DataFrame.from_dict(phys_data_postproc_emg)
 
     # save in .hdf5 file
-    df_stim_data.to_hdf(fn_exp_hdf5, "stim_data")
-    # df_stim_data[['coil_mean']].to_hdf(fn_exp_hdf5, "stim_data")
-    # [print(type(df_stim_data[['coil_mean']].iloc[0].values)) for i in range(df_stim_data.shape[0])]
-    # df_stim_data.columns
-    df_phys_data_postproc_emg.to_hdf(fn_exp_hdf5, "phys_data/postproc/EMG")
-    df_phys_data_raw_emg.to_hdf(fn_exp_hdf5, "phys_data/raw/EMG")
+    df_stim_data.to_hdf(fn_exp_hdf5, key="stim_data")
+    df_phys_data_postproc_emg.to_hdf(fn_exp_hdf5, key="phys_data/postproc/EMG")
+    df_phys_data_raw_emg.to_hdf(fn_exp_hdf5, key="phys_data/raw/EMG")
 
     with h5py.File(fn_exp_hdf5, "a") as f:
         f.create_dataset(name="stim_data/info/channels", data=np.array(channels).astype("|S"))
@@ -909,7 +906,7 @@ def merge_exp_data_rt(subject, coil_outlier_corr_cond, remove_coil_skin_distance
             im_lst.append(im_lst[0])
 
     # handle coil serial numbers
-    coil_sn_lst = pynibs.get_coil_sn_lst(fn_coil)
+    coil_sn_lst = pynibs.expio.get_coil_sn_lst(fn_coil)
 
     # get TMS pulse onset
     tms_pulse_time = subject.exp[exp_idx]['tms_pulse_time']
@@ -938,7 +935,7 @@ def merge_exp_data_rt(subject, coil_outlier_corr_cond, remove_coil_skin_distance
             len_conds.append(len(dict_lst) - len_conds[-1])
 
     # convert list of dict to dict of list
-    results_dct = pynibs.list2dict(dict_lst)
+    results_dct = pynibs.util.utils.list2dict(dict_lst)
 
     # check if we have a single pulse TMS experiments where every pulse is one condition
     single_pulse_experiment = np.zeros(len(len_conds))
@@ -992,19 +989,19 @@ def merge_exp_data_rt(subject, coil_outlier_corr_cond, remove_coil_skin_distance
     #######################################################
     if coil_outlier_corr_cond:
         print("Removing coil position outliers")
-        results_dct = pynibs.coil_outlier_correction_cond(exp=results_dct,
-                                                          outlier_angle=5.,
-                                                          outlier_loc=3.,
-                                                          fn_exp_out=fn_exp_hdf5)
+        results_dct = pynibs.expio.coil_outlier_correction_cond(exp=results_dct,
+                                                                outlier_angle=5.,
+                                                                outlier_loc=3.,
+                                                                fn_exp_out=fn_exp_hdf5)
 
     # perform coil <-> head distance correction
     ###########################################
     if coil_distance_corr:
         print("Performing coil <-> head distance correction")
-        results_dct = pynibs.coil_distance_correction(exp=results_dct,
-                                                      fn_geo_hdf5=fn_mesh_hdf5,
-                                                      remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier,
-                                                      fn_plot=os.path.split(fn_exp_hdf5)[0])
+        results_dct = pynibs.expio.coil_distance_correction(exp=results_dct,
+                                                            fn_geo_hdf5=fn_mesh_hdf5,
+                                                            remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier,
+                                                            fn_plot=os.path.split(fn_exp_hdf5)[0])
 
     # plot finally used rt data
     ############################
@@ -1018,7 +1015,7 @@ def merge_exp_data_rt(subject, coil_outlier_corr_cond, remove_coil_skin_distance
         average_y = []
         for ind in range(len(y) - avg_window + 1):
             average_y.append(np.mean(y[ind:ind + avg_window]))
-        # insert NaNs to match lengths
+        # insert nan to match lengths
         for ind in range(avg_window - 1):
             average_y.insert(0, np.nan)
 
@@ -1058,8 +1055,8 @@ def merge_exp_data_rt(subject, coil_outlier_corr_cond, remove_coil_skin_distance
     df_behave_data = pd.DataFrame.from_dict(behave_dict)
 
     # save in .hdf5 file
-    df_stim_data.to_hdf(fn_exp_hdf5, "stim_data")
-    df_behave_data.to_hdf(fn_exp_hdf5, "behavioral_data")
+    df_stim_data.to_hdf(fn_exp_hdf5, key="stim_data")
+    df_behave_data.to_hdf(fn_exp_hdf5, key="behavioral_data")
 
 
 def merge_exp_data_ft(subject, coil_outlier_corr_cond, remove_coil_skin_distance_outlier, coil_distance_corr,
@@ -1112,7 +1109,7 @@ def merge_exp_data_ft(subject, coil_outlier_corr_cond, remove_coil_skin_distance
             im_lst.append(im_lst[0])
 
     # handle coil serial numbers
-    coil_sn_lst = pynibs.get_coil_sn_lst(fn_coil)
+    coil_sn_lst = pynibs.util.utlis.get_coil_sn_lst(fn_coil)
 
     # get TMS pulse onset
     tms_pulse_time = subject.exp[exp_idx]['tms_pulse_time']
@@ -1141,7 +1138,7 @@ def merge_exp_data_ft(subject, coil_outlier_corr_cond, remove_coil_skin_distance
             len_conds.append(len(dict_lst) - len_conds[-1])
 
     # convert list of dict to dict of list
-    results_dct = pynibs.list2dict(dict_lst)
+    results_dct = pynibs.util.utils.list2dict(dict_lst)
 
     # check if we have a single pulse TMS experiments where every pulse is one condition
     single_pulse_experiment = np.zeros(len(len_conds))
@@ -1201,19 +1198,19 @@ def merge_exp_data_ft(subject, coil_outlier_corr_cond, remove_coil_skin_distance
     #######################################################
     if coil_outlier_corr_cond:
         print("Removing coil position outliers")
-        results_dct = pynibs.coil_outlier_correction_cond(exp=results_dct,
-                                                          outlier_angle=5.,
-                                                          outlier_loc=3.,
-                                                          fn_exp_out=fn_exp_hdf5)
+        results_dct = pynibs.expio.coil_outlier_correction_cond(exp=results_dct,
+                                                                outlier_angle=5.,
+                                                                outlier_loc=3.,
+                                                                fn_exp_out=fn_exp_hdf5)
 
     # perform coil <-> head distance correction
     ###########################################
     if coil_distance_corr:
         print("Performing coil <-> head distance correction")
-        results_dct = pynibs.coil_distance_correction(exp=results_dct,
-                                                      fn_geo_hdf5=fn_mesh_hdf5,
-                                                      remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier,
-                                                      fn_plot=os.path.split(fn_exp_hdf5)[0])
+        results_dct = pynibs.expio.coil_distance_correction(exp=results_dct,
+                                                            fn_geo_hdf5=fn_mesh_hdf5,
+                                                            remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier,
+                                                            fn_plot=os.path.split(fn_exp_hdf5)[0])
 
     # plot finally used ft data
     ############################
@@ -1227,7 +1224,7 @@ def merge_exp_data_ft(subject, coil_outlier_corr_cond, remove_coil_skin_distance
         average_y = []
         for ind in range(len(y) - avg_window + 1):
             average_y.append(np.mean(y[ind:ind + avg_window]))
-        # insert NaNs to match lengths
+        # insert nan to match lengths
         for ind in range(avg_window - 1):
             average_y.insert(0, np.nan)
 
@@ -1267,8 +1264,8 @@ def merge_exp_data_ft(subject, coil_outlier_corr_cond, remove_coil_skin_distance
     df_behave_data = pd.DataFrame.from_dict(behave_dict)
 
     # save in .hdf5 file
-    df_stim_data.to_hdf(fn_exp_hdf5, "stim_data")
-    df_behave_data.to_hdf(fn_exp_hdf5, "behavioral_data")
+    df_stim_data.to_hdf(fn_exp_hdf5, key="stim_data")
+    df_behave_data.to_hdf(fn_exp_hdf5, key="behavioral_data")
 
 
 def match_behave_and_triggermarker(mep_time_lst, xml_paths, bnd_factor=0.99 / 2, isi=None):
@@ -1301,7 +1298,7 @@ def match_behave_and_triggermarker(mep_time_lst, xml_paths, bnd_factor=0.99 / 2,
     #     _, mep_time_lst_tmp = get_mep_elements(cfs_path, tms_pulse_time)
     #     mep_time_lst.extend(mep_time_lst_tmp)
 
-    _, tms_ts_lst, _, tms_idx_invalid = pynibs.localite.get_tms_elements(xml_paths, verbose=True)
+    _, tms_ts_lst, _, tms_idx_invalid = get_tms_elements(xml_paths, verbose=True)
 
     # get timestamp difference of mep measurements
     if isi is None:
@@ -1474,7 +1471,7 @@ def combine_nnav_mep(xml_paths, cfs_paths, im, coil_sn,
           'patient_id'
     """
     # get arrays and lists
-    coil_array, ts_tms_lst, current_lst, tms_idx_invalid = pynibs.get_tms_elements(xml_paths, verbose=False)
+    coil_array, ts_tms_lst, current_lst, tms_idx_invalid = get_tms_elements(xml_paths, verbose=False)
 
     # get MEP amplitudes from .cfs files
     time_mep_lst, mep_latencies = [], []
@@ -1489,14 +1486,14 @@ def combine_nnav_mep(xml_paths, cfs_paths, im, coil_sn,
         # calc MEP amplitudes and MEP onset times from .cfs file
         p2p_array_tmp, time_mep_lst_tmp, \
             mep_raw_data_tmp, mep_filt_data_tmp, \
-            mep_raw_data_time, mep_latency = pynibs.get_mep_elements(mep_fn=cfs_path,
-                                                                     tms_pulse_time=tms_pulse_time,
-                                                                     drop_mep_idx=drop_mep_idx,
-                                                                     cfs_data_column=cfs_data_column,
-                                                                     channels=channels,
-                                                                     plot=plot,
-                                                                     start_mep=start_mep,
-                                                                     end_mep=end_mep)
+            mep_raw_data_time, mep_latency = pynibs.expio.signal_ced.get_mep_elements(mep_fn=cfs_path,
+                                                                                      tms_pulse_time=tms_pulse_time,
+                                                                                      drop_mep_idx=drop_mep_idx,
+                                                                                      cfs_data_column=cfs_data_column,
+                                                                                      channels=channels,
+                                                                                      plot=plot,
+                                                                                      start_mep=start_mep,
+                                                                                      end_mep=end_mep)
 
         # add .cfs onsets from subject object and add onset of last mep from last .cfs file
         if mep_onsets is not None:
@@ -1525,7 +1522,7 @@ def combine_nnav_mep(xml_paths, cfs_paths, im, coil_sn,
                                                                                 bnd_factor=0.99 / 2)  # 0.99/2
 
     if cfs_paths[0].endswith("cfs"):
-        experiment_date_time = pynibs.get_time_date(cfs_paths)
+        experiment_date_time = pynibs.expio.get_time_date(cfs_paths)
     else:
         experiment_date_time = "N/A"
 
@@ -1543,20 +1540,20 @@ def combine_nnav_mep(xml_paths, cfs_paths, im, coil_sn,
     else:
         # get conditions from instrument markers
         if os.path.isfile(im[0]):
-            coil_cond_lst, drop_idx = pynibs.match_instrument_marker_file(xml_paths, im[0])
+            coil_cond_lst, drop_idx = match_instrument_marker_file(xml_paths, im[0])
         else:
-            coil_cond_lst, drop_idx = pynibs.match_instrument_marker_string(xml_paths, im)
+            coil_cond_lst, drop_idx = match_instrument_marker_string(xml_paths, im)
 
     # coordinate transform (for coil_0, coil_1, coil_mean)
     for idx in range(coil_array.shape[0]):
         # move axis, calculate and move back
         m_simnibs = np.moveaxis(coil_array[idx, :, :, :], 0, 2)
-        m_simnibs = pynibs.nnav2simnibs(fn_exp_nii=nii_exp_path[0],
-                                        fn_conform_nii=nii_conform_path,
-                                        m_nnav=m_simnibs,
-                                        nnav_system=nnav_system,
-                                        mesh_approach=mesh_approach,
-                                        temp_dir=temp_dir)
+        m_simnibs = pynibs.expio.nnav2simnibs(fn_exp_nii=nii_exp_path[0],
+                                              fn_conform_nii=nii_conform_path,
+                                              m_nnav=m_simnibs,
+                                              nnav_system=nnav_system,
+                                              mesh_approach=mesh_approach,
+                                              temp_dir=temp_dir)
 
         coil_array[idx, :, :, :] = np.moveaxis(m_simnibs, 2, 0)
 
@@ -1680,7 +1677,7 @@ def combine_nnav_rt(xml_paths, behavior_paths, im, coil_sn,
     """
 
     # get arrays and lists
-    coil_array, ts_tms_lst, current_lst, tms_idx_invalid = pynibs.get_tms_elements(xml_paths, verbose=False)
+    coil_array, ts_tms_lst, current_lst, tms_idx_invalid = get_tms_elements(xml_paths, verbose=False)
 
     # get RT from .csv files
     time_mep_lst = []
@@ -1692,10 +1689,10 @@ def combine_nnav_rt(xml_paths, behavior_paths, im, coil_sn,
 
     for idx, behavior_path in enumerate(behavior_paths):
         # get RT and trial onsets from .csv file
-        rt_array_tmp, trial_onset_lst_tmp, mean_isi = pynibs.get_trial_data_from_csv(behavior_fn=behavior_path,
-                                                                                     drop_trial_idx=drop_trial_idx,
-                                                                                     cond=cond,
-                                                                                     only_corr=True)
+        rt_array_tmp, trial_onset_lst_tmp, mean_isi = pynibs.expio.get_trial_data_from_csv(behavior_fn=behavior_path,
+                                                                                           drop_trial_idx=drop_trial_idx,
+                                                                                           cond=cond,
+                                                                                           only_corr=True)
 
         time_mep_lst.extend(trial_onset_lst_tmp)
 
@@ -1729,20 +1726,20 @@ def combine_nnav_rt(xml_paths, behavior_paths, im, coil_sn,
     else:
         # get conditions from instrument markers
         if os.path.isfile(im[0]):
-            coil_cond_lst, drop_idx = pynibs.match_instrument_marker_file(xml_paths, im[0])
+            coil_cond_lst, drop_idx = match_instrument_marker_file(xml_paths, im[0])
         else:
-            coil_cond_lst, drop_idx = pynibs.match_instrument_marker_string(xml_paths, im)
+            coil_cond_lst, drop_idx = match_instrument_marker_string(xml_paths, im)
 
     # coordinate transform (for coil_0, coil_1, coil_mean)
     for idx in range(coil_array.shape[0]):
         # move axis, calculate and move back
         m_simnibs = np.moveaxis(coil_array[idx, :, :, :], 0, 2)
-        m_simnibs = pynibs.nnav2simnibs(fn_exp_nii=nii_exp_path[0],
-                                        fn_conform_nii=nii_conform_path,
-                                        m_nnav=m_simnibs,
-                                        nnav_system=nnav_system,
-                                        mesh_approach=mesh_approach,
-                                        temp_dir=temp_dir)
+        m_simnibs = pynibs.expio.nnav2simnibs(fn_exp_nii=nii_exp_path[0],
+                                              fn_conform_nii=nii_conform_path,
+                                              m_nnav=m_simnibs,
+                                              nnav_system=nnav_system,
+                                              mesh_approach=mesh_approach,
+                                              temp_dir=temp_dir)
 
         coil_array[idx, :, :, :] = np.moveaxis(m_simnibs, 2, 0)
 
@@ -1862,7 +1859,7 @@ def combine_nnav_ft(xml_paths, behavior_paths, im, coil_sn,
     """
 
     # get arrays and lists
-    coil_array, ts_tms_lst, current_lst, tms_idx = pynibs.get_tms_elements(xml_paths, verbose=False)
+    coil_array, ts_tms_lst, current_lst, tms_idx = get_tms_elements(xml_paths, verbose=False)
 
     # get finger tapping data from .csv files
     time_ft_lst = []
@@ -1874,9 +1871,9 @@ def combine_nnav_ft(xml_paths, behavior_paths, im, coil_sn,
 
     for idx, behavior_path in enumerate(behavior_paths):
         # get finger tapping data and trial onsets from .csv file
-        ft_array_tmp, trial_onset_lst_tmp, mean_isi = pynibs.get_ft_data_from_csv(behavior_fn=behavior_path,
-                                                                                  drop_trial_idx=drop_trial_idx,
-                                                                                  cond=cond)
+        ft_array_tmp, trial_onset_lst_tmp, mean_isi = get_ft_data_from_csv(behavior_fn=behavior_path,
+                                                                           drop_trial_idx=drop_trial_idx,
+                                                                           cond=cond)
 
         time_ft_lst.extend(trial_onset_lst_tmp)
 
@@ -1910,20 +1907,20 @@ def combine_nnav_ft(xml_paths, behavior_paths, im, coil_sn,
     else:
         # get conditions from instrument markers
         if os.path.isfile(im[0]):
-            coil_cond_lst, drop_idx = pynibs.match_instrument_marker_file(xml_paths, im[0])
+            coil_cond_lst, drop_idx = match_instrument_marker_file(xml_paths, im[0])
         else:
-            coil_cond_lst, drop_idx = pynibs.match_instrument_marker_string(xml_paths, im)
+            coil_cond_lst, drop_idx = match_instrument_marker_string(xml_paths, im)
 
     # coordinate transform (for coil_0, coil_1, coil_mean)
     for idx in range(coil_array.shape[0]):
         # move axis, calculate and move back
         m_simnibs = np.moveaxis(coil_array[idx, :, :, :], 0, 2)
-        m_simnibs = pynibs.nnav2simnibs(fn_exp_nii=nii_exp_path[0],
-                                        fn_conform_nii=nii_conform_path,
-                                        m_nnav=m_simnibs,
-                                        nnav_system=nnav_system,
-                                        mesh_approach=mesh_approach,
-                                        temp_dir=temp_dir)
+        m_simnibs = pynibs.expio.nnav2simnibs(fn_exp_nii=nii_exp_path[0],
+                                              fn_conform_nii=nii_conform_path,
+                                              m_nnav=m_simnibs,
+                                              nnav_system=nnav_system,
+                                              mesh_approach=mesh_approach,
+                                              temp_dir=temp_dir)
 
         coil_array[idx, :, :, :] = np.moveaxis(m_simnibs, 2, 0)
 
@@ -1985,3 +1982,105 @@ def combine_nnav_ft(xml_paths, behavior_paths, im, coil_sn,
             idx += 1
 
     return dict_lst
+
+
+def hdf5_from_xml(fn_xml):
+    """
+    Convert a Localite XML TriggerMarker file to HDF5 and XDMF format.
+
+    Parameters
+    ----------
+    fn_xml : str
+        Path to the XML file.
+
+    Returns
+    -------
+    <file> .xdmf/.hdf5 tuple
+    """
+    assert fn_xml.endswith('.xml'), "File must be an XML file"
+    fn_hdf5 = fn_xml.replace('.xml', '.hdf5')
+    fn_xdmf = fn_xml.replace('.xml', '.xdmf')
+
+    for markertype in ['TriggerMarker', 'InstrumentMarker']:
+        m_nnav = get_marker(fn_xml, markertype=markertype)[0]
+        if len(m_nnav):
+            break
+    assert len(m_nnav), f"Could not find any markers in {fn_xml}"
+    # m_nnav, didt, stim_int, descr, rec_time = read_triggermarker(fn_xml)
+    centers = m_nnav[:,:3, 3]
+    n_coils = centers.shape[0]
+
+    m0 = np.squeeze(m_nnav[:, :3, 0]).T
+    m1 = np.squeeze(m_nnav[:, :3, 1]).T
+    m2 = np.squeeze(m_nnav[:, :3, 2]).T
+
+    with h5py.File(fn_hdf5, 'w') as f_hdf5:
+        f_hdf5.create_dataset('centers', data=centers.astype(np.float64))
+        f_hdf5.create_dataset('m0', data=m0.astype(np.float64))
+        f_hdf5.create_dataset('m1', data=m1.astype(np.float64))
+        f_hdf5.create_dataset('m2', data=m2.astype(np.float64))
+    fn_hdf5 = os.path.split(fn_hdf5)[1]
+    with open(fn_xdmf, 'w') as f_xdmf:
+        f_xdmf.write('<?xml version="1.0"?>\n')
+        f_xdmf.write('<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>\n')
+        f_xdmf.write('<Xdmf Version="2.0" xmlns:xi="http://www.w3.org/2001/XInclude">\n')
+        f_xdmf.write('<Domain>\n')
+        f_xdmf.write('<Grid\nCollectionType="Spatial"\nGridType="Collection"\nName="Collection">\n')
+
+        # one grid for coil dipole nodes...store data hdf5.
+        #######################################################
+        f_xdmf.write('<Grid Name="stimsites" GridType="Uniform">\n')
+        f_xdmf.write(f'<Topology NumberOfElements="{n_coils}" TopologyType="Polyvertex" Name="Tri">\n')
+        f_xdmf.write(f'<DataItem Format="XML" Dimensions="{n_coils} 1">\n')
+        # f.write(hdf5_fn + ':' + path + '/triangle_number_list\n')
+        np.savetxt(f_xdmf, list(range(centers.shape[0])), fmt='%d', delimiter=' ')  # 1 2 3 4 ... N_Points
+        f_xdmf.write('</DataItem>\n')
+        f_xdmf.write('</Topology>\n')
+
+        # nodes
+        f_xdmf.write('<Geometry GeometryType="XYZ">\n')
+        f_xdmf.write(f'<DataItem Format="HDF" Dimensions="{n_coils} 3">\n')
+        f_xdmf.write(f'{fn_hdf5}:/centers\n')
+        f_xdmf.write('</DataItem>\n')
+        f_xdmf.write('</Geometry>\n')
+
+        # data
+        # dipole magnitude
+        # the 4 vectors
+        for i in range(3):
+            f_xdmf.write(f'<Attribute Name="dir_{i}" AttributeType="Vector" Center="Cell">\n')
+            f_xdmf.write(f'<DataItem Format="HDF" Dimensions="{n_coils} 3">\n')
+            f_xdmf.write(f"{fn_hdf5}:/m{i}\n")
+            f_xdmf.write('</DataItem>\n')
+            f_xdmf.write('</Attribute>\n\n')
+
+        #  angles
+        # f_xdmf.write('<Attribute Name="angles" AttributeType="Scalar" Center="Cell">\n')
+        # f_xdmf.write(f'<DataItem Format="HDF" Dimensions="{centers.shape[0]} 1">\n')
+        # f_xdmf.write(f'{fn_hdf5}:/angles\n')
+        # f_xdmf.write('</DataItem>\n')
+        # f_xdmf.write('</Attribute>\n\n')
+
+        #  data
+        # if data_dict is not None:
+        #     f_xdmf.write('<Attribute Name="data" AttributeType="Scalar" Center="Cell">\n')
+        #     f_xdmf.write('<DataItem Format="HDF" Dimensions="' + str(data.shape[0]) + ' 1">\n')
+        #     f_xdmf.write(f'{fn_hdf5}:/data\n')
+        #     f_xdmf.write('</DataItem>\n')
+        #     f_xdmf.write('</Attribute>\n\n')
+
+        # site idx
+        # f_xdmf.write('<Attribute Name="sites_idx" AttributeType="Scalar" Center="Cell">\n')
+        # f_xdmf.write(f'<DataItem Format="HDF" Dimensions="{centers.shape[0]} 1">\n')
+        # f_xdmf.write(f'{fn_hdf5}:/sites_idx\n')
+        # f_xdmf.write('</DataItem>\n')
+        # f_xdmf.write('</Attribute>\n\n')
+
+        f_xdmf.write('</Grid>\n')
+        # end coil dipole data
+
+        # footer
+        f_xdmf.write('</Grid>\n')
+        f_xdmf.write('</Domain>\n')
+        f_xdmf.write('</Xdmf>\n')
+        f_xdmf.close()

pynibs/expio/neurone.py

@@ -0,0 +1,139 @@
+import glob
+import os
+import pynibs
+import datetime
+import numpy as np
+
+
+def get_mep_elements(session_path, chan_idx=None, recording_id=None,
+                     tms_port_id=2, mep_start_ms=16, mep_end_ms=40, plot_folder=None, verbose=False):
+    """
+    This function calculates the MEP elements for a given session and channel for Neurone Tesla EEG data.
+
+    Parameters
+    ----------
+    session_path : str
+        Path to the session folder.
+    mep_start_ms : int
+        Start time of the MEP in ms.
+    mep_end_ms : int
+        End time of the MEP in ms.
+    chan_idx : int, optional
+        Channel index. Default: All channels.
+    recording_id : int, optional
+        Recording ID. Default: All recordings
+    tms_port_id : int
+        TMS port ID for the pulse trigger.
+    verbose : bool
+        Print verbose output.
+    plot_folder : str, optional
+        Folder to store the plots.
+
+    Returns
+    -------
+    p2p_array : np.ndarray of float
+        (N_stim) Peak to peak values of N sweeps.
+    time_mep_lst : list of datetime.timedelta
+        MEP-timestamps
+    mep_raw_data : np.ndarray of float
+        (N_channel, N_stim, N_samples) Raw (unfiltered) MEP data.
+    mep_filt_data : np.ndarray of float
+        (N_channel, N_stim, N_samples) Filtered MEP data (Butterworth lowpass filter).
+    time : np.ndarray of float
+        (N_samples) Time axis corresponding to MEP data.
+    mep_onset_array : np.ndarray of float
+        (S_samples) MEP onset after TMS pulse.
+    """
+    from neurone_tools import neurone_tools
+    # read all recordings in the session
+    if recording_id is None:
+        subdirs = glob.glob(f"{session_path}/*")
+        n_subdirs = len([os.path.split(subdir)[1] for subdir in subdirs if os.path.isdir(subdir)])
+        if verbose:
+            print(f"Found {n_subdirs} recordings in session {session_path}")
+        recording_ids = list(range(1, n_subdirs+1))
+    else:
+        recording_ids = [recording_id]
+
+    # read all channels in the recording
+    nt = neurone_tools(session_path, recording_ids[0], channels='all')
+    if chan_idx is None:
+        chan_ids = range(len(nt.get_channel_info()))
+        if verbose:
+            print(f"Found {len(chan_ids)} channels in recording {recording_id}")
+    else:
+        chan_ids = [chan_idx]
+
+    p2p_arr = []
+    mep_raw_arr = []
+    mep_filt_arr = []
+    mep_onset_arr = []
+    time_tms_pulse_list_chan = []
+    time_axes_chan = []
+
+    for chan_idx in chan_ids:
+        p2p_arr_chan = []
+        time_tms_pulse_list_chan = []
+        mep_raw_arr_chan = []
+        mep_filt_arr_chan = []
+        time_axes_chan = []
+        mep_onset_arr_chan = []
+
+        for recording_id in recording_ids:
+            nt = neurone_tools(session_path, recording_id, channels='all')
+            fsample = nt.get_sampling_rate()
+
+            if nt.get_channel_info()[chan_idx]['Unit'] == 'µV':
+                fac = 1/1000
+            else:
+                raise ValueError(f"Unknown unit {nt.get_channel_info()[chan_idx]['Unit']}")
+
+            # mep_start_sample = int(fsample * mep_start_ms/1000)
+            mep_end_sample = int(fsample * mep_end_ms*2/1000)
+
+            events = nt.load_events()
+            tms_pulse_idx = events['start_sample_index'][events['source_port'] == tms_port_id].values
+            data, chan_names = nt.load_data()
+            if not len(tms_pulse_idx):
+                print(f"No TMS pulses found in session {recording_id}")
+                continue
+            timedelta = datetime.timedelta(milliseconds=0)
+            for pulse_id, pulse in enumerate(tms_pulse_idx):
+                sweep = data[pulse:int(mep_end_sample + pulse), chan_idx]
+                sweep *= fac
+                sweep -= sweep.mean()
+
+                if plot_folder is not None:
+                    fn_plot = f"{plot_folder}/ses{recording_id:0>2}_chan{chan_idx}_{pulse_id:0>3}_mep.png"
+                else:
+                    fn_plot = None
+                p2p, sweep_filt, onset = pynibs.expio.calc_p2p(sweep, tms_pulse_time=0,
+                                                               start_mep=mep_start_ms,
+                                                               end_mep=mep_end_ms,
+                                                               measurement_start_time=0,
+                                                               sampling_rate=fsample,
+                                                               cutoff_freq=500,
+                                                               fn_plot=fn_plot)
+                p2p_arr_chan.append(p2p)
+
+                time_tms_pulse_list_chan.append(timedelta)
+                timedelta += datetime.timedelta(milliseconds=1000 * (pulse / fsample))
+                mep_filt_arr_chan.append(sweep_filt)
+                mep_onset_arr_chan.append(onset)
+                mep_raw_arr_chan.append(sweep)
+                time_axes_chan.append(np.arange(sweep.shape[0]) / fsample)
+
+            print(f"channel {chan_idx} session {recording_id: >2}: {(events['source_port'] == tms_port_id).sum()}")
+        mep_raw_arr_chan = np.vstack(mep_raw_arr_chan)
+        mep_filt_arr_chan = np.vstack(mep_filt_arr_chan)
+
+        p2p_arr.append(p2p_arr_chan)
+        mep_filt_arr.append(mep_filt_arr_chan)
+        mep_onset_arr.append(mep_onset_arr_chan)
+        mep_raw_arr.append(mep_raw_arr_chan)
+    p2p_arr = np.vstack(p2p_arr)
+    mep_raw_arr = np.stack(mep_raw_arr, 0)
+    mep_filt_arr = np.stack(mep_filt_arr, 0)
+    mep_onset_arr = np.vstack(mep_onset_arr)
+
+    return p2p_arr, time_tms_pulse_list_chan, mep_raw_arr, mep_filt_arr, time_axes_chan, mep_onset_arr