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

pynibs/expio/brainsight.py

@@ -32,7 +32,6 @@ class BrainsightCSVParser:
     parse_line(line)
         Parses a line and updates the corresponding attributes.
     """
-
     class State:
         FILE_HEADER = 0
         SKIPPING = 1
@@ -116,7 +115,6 @@ def write_targets_brainsight(targets, fn_out, names=None, overwrite=True):
     -------
     <file> .txt file containing the targets for import into Brainsight
     """
-
     targets = np.atleast_3d(targets)
 
     if names is None:
@@ -228,7 +226,7 @@ def create_merged_nnav_emg_file_brainsight(fn_brainsight_nnav_info, fn_emg_info,
 
                 num_stim = emg_data.shape[0]
                 num_channels = emg_data.shape[1]
-                num_emg_samples = emg_data.shape[2]
+                # num_emg_samples = emg_data.shape[2]
 
                 emg_timestamps_h5_ref = data_h5[f"/{keys[0]}/frameinfo/start"][:]
                 emg_timestamps = []
@@ -241,7 +239,8 @@ def create_merged_nnav_emg_file_brainsight(fn_brainsight_nnav_info, fn_emg_info,
 
     elif ext == ".cfs":
         emg_data, emg_timestamps, num_stim, num_channels, num_emg_samples, sampling_rate = \
-            pynibs.read_biosig_emg_data(fn_data=fn_emg_info, include_first_trigger=True, type="cfs")
+            pynibs.expio.signal_ced.read_biosig_emg_data(fn_data=fn_emg_info, include_first_trigger=True,
+                                                         filetype="cfs")
         emg_res = 1000 / sampling_rate  # [ms]
         emg_start = 0  # EMG start time not included in CSF file / always 0 for CED Signal (?)
     else:
@@ -259,7 +258,7 @@ def create_merged_nnav_emg_file_brainsight(fn_brainsight_nnav_info, fn_emg_info,
             csv_parser.parse_line(line)
 
         nnav_timestamps = []
-        start_time_string = current_time_string = csv_parser.data[0][24]  # 25. column of CSv data = time stamp
+        start_time_string = csv_parser.data[0][24]  # 25. column of CSv data = time stamp
         start_time = datetime.datetime.strptime(start_time_string, '%H:%M:%S.%f')
         for c_idx in range(0, num_stim):
             current_time_string = csv_parser.data[c_idx][24]  # 25. column of CSv data = time stamp
@@ -421,18 +420,18 @@ def merge_exp_data_brainsight(subject, exp_idx, mesh_idx, coil_outlier_corr_cond
         print(f"Transforming coil positions from Brainsight to SimNIBS space")
     print(nii_conform_path)
 
-    m_simnibs = pynibs.nnav2simnibs(fn_exp_nii=nii_exp_path_lst[0][0],
-                                    fn_conform_nii=nii_conform_path,
-                                    m_nnav=m_nnav,
-                                    nnav_system="brainsight",
-                                    mesh_approach="headreco",
-                                    fiducials=None,
-                                    orientation='RAS',
-                                    fsl_cmd=None,
-                                    target='simnibs',
-                                    temp_dir=temp_dir,
-                                    rem_tmp=True,
-                                    verbose=verbose)
+    m_simnibs = pynibs.expio.nnav2simnibs(fn_exp_nii=nii_exp_path_lst[0][0],
+                                          fn_conform_nii=nii_conform_path,
+                                          m_nnav=m_nnav,
+                                          nnav_system="brainsight",
+                                          mesh_approach="headreco",
+                                          fiducials=None,
+                                          orientation='RAS',
+                                          fsl_cmd=None,
+                                          target='simnibs',
+                                          temp_dir=temp_dir,
+                                          rem_tmp=True,
+                                          verbose=verbose)
 
     # create dictionary containing stimulation and physiological data
     if verbose:
@@ -456,7 +455,7 @@ def merge_exp_data_brainsight(subject, exp_idx, mesh_idx, coil_outlier_corr_cond
 
     for i in range(n_stims):
         d['coil_0'].append(m_simnibs[:, :, i])
-        d['coil_1'].append(np.zeros((4, 4)) * np.NaN)
+        d['coil_1'].append(np.zeros((4, 4)) * np.nan)
         d['coil_mean'].append(np.nanmean(np.stack((d['coil_0'][-1],
                                                    d['coil_1'][-1]), axis=2), axis=2))
         d['number'].append(d_bs['Index'][i])
@@ -519,12 +518,12 @@ def merge_exp_data_brainsight(subject, exp_idx, mesh_idx, coil_outlier_corr_cond
                 os.makedirs(fn_channel, exist_ok=True)
 
             # filter data and calculate p2p values
-            p2p, mep_filt_data, latency = pynibs.calc_p2p(sweep=d_bs[f"EMG Data {c_idx}"][i],
-                                                          tms_pulse_time=d_bs[f"Offset"][i],
-                                                          sampling_rate=1000 / d_bs["EMG Res."][i],
-                                                          start_mep=start_mep, end_mep=end_mep,
-                                                          measurement_start_time=float(d["EMG Start"][i]),
-                                                          fn_plot=fn_plot)
+            p2p, mep_filt_data, latency = pynibs.expio.calc_p2p(sweep=d_bs[f"EMG Data {c_idx}"][i],
+                                                                tms_pulse_time=d_bs[f"Offset"][i],
+                                                                sampling_rate=1000 / d_bs["EMG Res."][i],
+                                                                start_mep=start_mep, end_mep=end_mep,
+                                                                measurement_start_time=float(d["EMG Start"][i]),
+                                                                fn_plot=fn_plot)
 
             d[f"mep_raw_data_time_{chan_name}"].append(np.arange(d_bs["EMG Start"][i],
                                                                  d_bs["EMG End"][i], d_bs["EMG Res."][i]))
@@ -551,16 +550,16 @@ def merge_exp_data_brainsight(subject, exp_idx, mesh_idx, coil_outlier_corr_cond
     if coil_outlier_corr_cond:
         if verbose:
             print("Removing coil position outliers")
-        d = pynibs.coil_outlier_correction_cond(exp=d, outlier_angle=5., outlier_loc=3., fn_exp_out=fn_exp_hdf5)
+        d = pynibs.expio.coil_outlier_correction_cond(exp=d, outlier_angle=5., outlier_loc=3., fn_exp_out=fn_exp_hdf5)
 
     # perform coil <-> head distance correction
     if coil_distance_corr:
         if verbose:
             print("Performing coil <-> head distance correction")
-        d = pynibs.coil_distance_correction(exp=d,
-                                            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])
+        d = pynibs.expio.coil_distance_correction(exp=d,
+                                                  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])
 
     d_avg = dict()
     for key in d.keys():
@@ -753,15 +752,13 @@ def transform_brainsight(data, col_names):
     data: list of lists with positions
     col_names: list of str
 
-    Returns:
-    --------
+    Returns
+    -------
     names : list of str
         Samples/target names. len(names) = n_pos
     matsimnibs: np.ndarray
         Coil position/orientation in matsimnibs style with Brainsight coil axes definition
         shape: (n_pos, 4, 4)
-
-    Written by Ole Numssen, numssen@cbs.mpg.de, 2022.
     """
     matsimnibs = np.zeros((len(data), 4, 4))
     pos_names = []
@@ -899,11 +896,11 @@ def read_triggermarker(fn):
     Read instrument-marker and conditions from Brainsight session.
 
     BrainSight stores recorded coil placements as 'Samples' and predefined coil placements
-     as 'Targets'.
+    as 'Targets'.
 
     Coil axes definitions as defined by Brainsight.
     dI/dt is returned as list of [-1] to keep consistent with read_triggermarker functions for other neuronavigation
-     systems.
+    systems.
 
     Parameters
     ----------
@@ -913,7 +910,7 @@ def read_triggermarker(fn):
     Returns
     -------
     matsimnibs : np.ndarray of float
-        (4, 4, N) Instrument marker matrices
+        (4, 4, N) Instrument marker matrices.
     didt : np.ndarray of float
         (N) Rate of change of coil current in (A/us).
     stim_int : np.ndarray of float
@@ -963,7 +960,7 @@ def read_triggermarker(fn):
         else:
             names_samples, matsimnibs_samples = [], None
 
-        if (matsimnibs_samples is None or matsimnibs_samples.size == 0):
+        if matsimnibs_samples is None or matsimnibs_samples.size == 0:
             raise ValueError(f"Could not find any targets in {fn}.")
 
         # get timings for samples

pynibs/expio/cobot.py

@@ -80,7 +80,7 @@ def merge_exp_data_cobot(subject, exp_idx, mesh_idx, coil_outlier_corr_cond=Fals
         # compute indices in data block corresponding to the events
         if event["TYP"] == "0x7ffe":
             trigger_event_idcs.append(
-                    round(event["POS"] * cfs_header["Samplingrate"])
+                round(event["POS"] * cfs_header["Samplingrate"])
             )
 
     num_sweeps = min(num_sweeps, len(trigger_event_idcs))
@@ -95,8 +95,8 @@ def merge_exp_data_cobot(subject, exp_idx, mesh_idx, coil_outlier_corr_cond=Fals
         #   beginning) we would need to adhere to the entire trigger_event_indices
         #   list.
         channel_emg = np.reshape(
-                cfs_emg[trigger_event_idcs[0]:, c_idx],
-                (num_sweeps, samples_per_sweep)
+            cfs_emg[trigger_event_idcs[0]:, c_idx],
+            (num_sweeps, samples_per_sweep)
         )
 
         d[f"mep_raw_data_time_{c_idx}"] = []
@@ -113,14 +113,14 @@ def merge_exp_data_cobot(subject, exp_idx, mesh_idx, coil_outlier_corr_cond=Fals
                 os.makedirs(fn_channel, exist_ok=True)
 
             # filter data and calculate p2p values
-            p2p, mep_filt_data, latency = pynibs.calc_p2p(
-                    sweep=channel_emg[s_idx],
-                    tms_pulse_time=tms_pulse_time,
-                    sampling_rate=sampling_rate,
-                    start_mep=start_mep_ms,
-                    end_mep=end_mep_ms,
-                    measurement_start_time=0,
-                    fn_plot=fn_plot
+            p2p, mep_filt_data, latency = pynibs.expio.calc_p2p(
+                sweep=channel_emg[s_idx],
+                tms_pulse_time=tms_pulse_time,
+                sampling_rate=sampling_rate,
+                start_mep=start_mep_ms,
+                end_mep=end_mep_ms,
+                measurement_start_time=0,
+                fn_plot=fn_plot
             )
 
             d[f"mep_raw_data_time_{c_idx}"].append(time)
@@ -169,10 +169,10 @@ def merge_exp_data_cobot(subject, exp_idx, mesh_idx, coil_outlier_corr_cond=Fals
     if coil_distance_corr:
         if verbose:
             print("Performing coil <-> head distance correction")
-        matsimnibs_t = pynibs.coil_distance_correction_matsimnibs(matsimnibs=matsimnibs_t,
-                                                           fn_mesh_hdf5=fn_mesh_hdf5,
-                                                           distance=1,
-                                                           remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier)
+        matsimnibs_t = pynibs.expio.coil_distance_correction_matsimnibs(matsimnibs=matsimnibs_t,
+                                                                        fn_mesh_hdf5=fn_mesh_hdf5,
+                                                                        distance=1,
+                                                                        remove_coil_skin_distance_outlier=remove_coil_skin_distance_outlier)
 
     d["coil_0"] = []
     for i in range(centers.shape[0]):
@@ -182,13 +182,13 @@ def merge_exp_data_cobot(subject, exp_idx, mesh_idx, coil_outlier_corr_cond=Fals
 
     # 3) save in "experiment.hdf5"
     coil_0_np = np.array(d['coil_0'])
-    pynibs.write_coil_pos_hdf5(
-            fn_hdf=out_coil_pos_fn,
-            centers=coil_0_np[:, :3, 3],  # np.array(centers),
-            m0=coil_0_np[:, :3, 0],  # np.array(m0),
-            m1=coil_0_np[:, :3, 1],  # np.array(m1),
-            m2=coil_0_np[:, :3, 2],  # np.array(m2),
-            overwrite=True
+    pynibs.coil.write_coil_pos_hdf5(
+        fn_hdf=out_coil_pos_fn,
+        centers=coil_0_np[:, :3, 3],  # np.array(centers),
+        m0=coil_0_np[:, :3, 0],  # np.array(m0),
+        m1=coil_0_np[:, :3, 1],  # np.array(m1),
+        m2=coil_0_np[:, :3, 2],  # np.array(m2),
+        overwrite=True
     )
 
     # create dictionary of stimulation data
@@ -232,8 +232,8 @@ def merge_exp_data_cobot(subject, exp_idx, mesh_idx, coil_outlier_corr_cond=Fals
     df_phys_data_postproc = pd.DataFrame.from_dict(d_phys_data_postproc)
 
     # save in .hdf5 file
-    df_stim_data.to_hdf(fn_exp_hdf5, "stim_data")
-    df_phys_data_raw.to_hdf(fn_exp_hdf5, "phys_data/raw/EMG")
-    df_phys_data_postproc.to_hdf(fn_exp_hdf5, "phys_data/postproc/EMG")
+    df_stim_data.to_hdf(fn_exp_hdf5, key="stim_data")
+    df_phys_data_raw.to_hdf(fn_exp_hdf5, key="phys_data/raw/EMG")
+    df_phys_data_postproc.to_hdf(fn_exp_hdf5, key="phys_data/postproc/EMG")
 
     print("Done.")

pynibs/expio/exp.py

@@ -409,7 +409,7 @@ def nnav2simnibs(fn_exp_nii, fn_conform_nii, m_nnav, nnav_system, mesh_approach=
     fn_exp_nii : str
         Filename of .nii file the experiments were conducted with.
     fn_conform_nii : str
-        Filename of .nii file from SimNIBS mri2msh function, e.g. ´´".../fs_subjectID/subjectID_T1fs_conform.nii.gz"´´.
+        Filename of .nii file from SimNIBS mri2msh function, e.g. ``".../fs_subjectID/subjectID_T1fs_conform.nii.gz"``.
     m_nnav : np.ndarray
         (4, 4, N) Position matrices from neuronavigation.
     nnav_system : str
@@ -422,16 +422,19 @@ def nnav2simnibs(fn_exp_nii, fn_conform_nii, m_nnav, nnav_system, mesh_approach=
         Approach the mesh is generated with (``"headreco"`` or ``"mri2mesh"``).
     fiducials : np.ndarray of float, optional
         (3, 3) Fiducial points in ANT nifti space from file,
-        e.g.: ´´"/data/pt_01756/probands/33791.b8/exp/1/33791.b8_recording/MRI/33791.b8_recording.mri"´´
+        e.g.: ``"/data/pt_01756/probands/33791.b8/exp/1/33791.b8_recording/MRI/33791.b8_recording.mri"``
         (x frontal-occipital, y right-left, z inferior-superior).
 
         .. code-block:: sh
+
             VoxelOnPositiveXAxis (Nasion, first row)
             221	131	127
             VoxelOnPositiveYAxis (left ear, second row)
             121	203	105
             VoxelOnNegativeYAxis (right ear, third row)
             121	57	105
+
+
     orientation : str, default: 'RAS'
         Orientation convention (``'RAS'`` or ``'LPS'``), can be read from neuronavigation .xml
         file under ``coordinateSpace="RAS"``.
@@ -1097,7 +1100,7 @@ def coil_outlier_correction_cond(exp=None, fn_exp=None, fn_exp_out=None, outlier
     """
     if exp is not None:
         if type(exp) is list:
-            exp = pynibs.list2dict(exp)
+            exp = pynibs.util.utils.list2dict(exp)
     elif fn_exp is not None:
         exp = read_csv(fn_exp)
     else:
@@ -1519,7 +1522,7 @@ def coil_distance_correction(exp=None, fn_exp=None, fn_exp_out=None, fn_geo_hdf5
 
     if exp is not None:
         if type(exp) is list:
-            exp = pynibs.list2dict(exp)
+            exp = pynibs.util.utils.list2dict(exp)
     elif fn_exp is not None:
         exp = read_csv(fn_exp)
     else:
@@ -1534,7 +1537,7 @@ def coil_distance_correction(exp=None, fn_exp=None, fn_exp_out=None, fn_geo_hdf5
     n_conditions = len(exp_cond)
 
     # read head mesh and extract skin surface
-    msh = pynibs.load_mesh_hdf5(fn_geo_hdf5)
+    msh = pynibs.hdf5_io.load_mesh_hdf5(fn_geo_hdf5)
     triangles = msh.triangles[msh.triangles_regions == 1005]
     point_idx_unique = np.unique(triangles)
     points = msh.points[point_idx_unique, :]
@@ -1563,7 +1566,7 @@ def coil_distance_correction(exp=None, fn_exp=None, fn_exp_out=None, fn_geo_hdf5
     if remove_coil_skin_distance_outlier:
         distance_mean = np.median(distance)
         distance_zm = distance - distance_mean
-        coil_pos_selected = np.logical_and(min_dist < distance_zm, distance_zm < max_dist)  # TODO: remove hardcoded dists
+        coil_pos_selected = np.logical_and(min_dist < distance_zm, distance_zm < max_dist)
 
         # distance distribution (original)
         plt.hist(distance, bins=50, density=True)
@@ -1686,7 +1689,7 @@ def coil_distance_correction_matsimnibs(matsimnibs, fn_mesh_hdf5, distance=0, re
     matsimnibs_corrected = copy.deepcopy(matsimnibs)
 
     # read head mesh and extract skin surface
-    msh = pynibs.load_mesh_hdf5(fn_mesh_hdf5)
+    msh = pynibs.hdf5_io.load_mesh_hdf5(fn_mesh_hdf5)
     triangles = msh.triangles[msh.triangles_regions == 1005]  # this is skin
     point_idx_unique = np.unique(triangles)
     points = msh.points[point_idx_unique, :]

pynibs/expio/fit_funs.py

@@ -183,6 +183,9 @@ def linear_log(x, m, n):
     return y
 
 
+def step(x, a): return (x > a).astype(int)
+
+
 def exp(x, x0, r, y0):
     """
     Parametrized exponential function.

pynibs/expio/invesalius.py

@@ -0,0 +1,70 @@
+""" Functions to import data from Invesalius """
+
+import transformations as tr
+import pandas as pd
+import numpy as np
+import datetime
+
+
+def read_triggermarker(fn_mkss):
+    """
+    Read instrument-marker and conditions from neuronavigator .xml-file.
+
+    Parameters
+    ----------
+    fn_mkss : str
+        Path to TriggerMarker.fn_mkss file
+
+    Returns
+    -------
+    m_nnav : np.ndarray of float
+        (4, 4, N) Neuronavigation coordinates of N stimuli (4x4 matsimnibs matrices).
+    didt : np.ndarray of float
+        (N) Rate of change of coil current in (A/us). At the moment: NAN.
+    stim_int : np.ndarray of float
+        (N) Stimulator intensity in (% MSO). At the moment: NAN.
+    descr : list of str
+        (N) Labels of the instrument-marker-conditions.
+    rec_time : list of str
+        (N) Recording time in ms.
+    """
+    data = pd.read_csv(fn_mkss, skiprows=1, sep="\t")
+    data = data[data['marker_type'] == 4]
+    if 'is_tracked' not in data.columns:
+        print("is_tracked column not found, assuming all markers are tracked")
+        tracking_missing = True
+    else:
+        tracking_missing = False
+        print(f"{data[data['is_tracked'] == 0].shape[0]} untracked markers found.")
+        # data = data[data['is_tracked'] == 1]
+    print(f"{data.shape[0]} coil placements found in {fn_mkss}")
+
+    # build matsimnibs from data
+    matsimnibs = []
+    desc = []
+    rec_time = []
+    start_time = data['timestamp'].iloc[0]
+    dt_format = "%Y-%m-%d %H:%M:%S.%f"
+    start_time = datetime.datetime.strptime(start_time, dt_format)
+    for idx, row in data.iterrows():
+        if not tracking_missing and row[data['is_tracked'] == 0]:
+            print(f"Skipping untracked marker {idx}")
+            r = np.eye(4)
+            r[:3, :4] = np.nan
+        r = tr.euler_matrix(row["alpha_world"], row["beta_world"], row["gamma_world"], "sxyz")
+        r[:3,3] = row[["x_world", "y_world", "z_world"]].values
+        matsimnibs.append(r)
+
+        desc.append(row["marker_id"])
+        rec_time.append((datetime.datetime.strptime(row["timestamp"], dt_format) - start_time).total_seconds() * 1000)
+    matsimnibs = np.array(matsimnibs)
+    matsimnibs = np.moveaxis(matsimnibs, 0, -1)
+
+    didt, stim_int, descr = (np.zeros(matsimnibs.shape[-1]),
+                             np.zeros(matsimnibs.shape[-1]),
+                             np.zeros(matsimnibs.shape[-1]))
+
+    # currently not storted by Invesalius
+    didt[:] = np.nan
+    stim_int[:] = np.nan
+    return matsimnibs, didt, stim_int, desc, rec_time