How to use the mne.io.write.write_int function in mne

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github mne-tools / mne-python / mne / io / meas_info.py View on Github external
end_block(fid, FIFF.FIFFB_MNE_BAD_CHANNELS)

    #   General
    if info.get('experimenter') is not None:
        write_string(fid, FIFF.FIFF_EXPERIMENTER, info['experimenter'])
    if info.get('description') is not None:
        write_string(fid, FIFF.FIFF_DESCRIPTION, info['description'])
    if info.get('proj_id') is not None:
        write_int(fid, FIFF.FIFF_PROJ_ID, info['proj_id'])
    if info.get('proj_name') is not None:
        write_string(fid, FIFF.FIFF_PROJ_NAME, info['proj_name'])
    if info.get('meas_date') is not None:
        write_int(fid, FIFF.FIFF_MEAS_DATE, _dt_to_stamp(info['meas_date']))
    if info.get('utc_offset') is not None:
        write_string(fid, FIFF.FIFF_UTC_OFFSET, info['utc_offset'])
    write_int(fid, FIFF.FIFF_NCHAN, info['nchan'])
    write_float(fid, FIFF.FIFF_SFREQ, info['sfreq'])
    if info['lowpass'] is not None:
        write_float(fid, FIFF.FIFF_LOWPASS, info['lowpass'])
    if info['highpass'] is not None:
        write_float(fid, FIFF.FIFF_HIGHPASS, info['highpass'])
    if info.get('line_freq') is not None:
        write_float(fid, FIFF.FIFF_LINE_FREQ, info['line_freq'])
    if info.get('gantry_angle') is not None:
        write_float(fid, FIFF.FIFF_GANTRY_ANGLE, info['gantry_angle'])
    if data_type is not None:
        write_int(fid, FIFF.FIFF_DATA_PACK, data_type)
    if info.get('custom_ref_applied'):
        write_int(fid, FIFF.FIFF_MNE_CUSTOM_REF, info['custom_ref_applied'])
    if info.get('xplotter_layout'):
        write_string(fid, FIFF.FIFF_XPLOTTER_LAYOUT, info['xplotter_layout'])
github mne-tools / mne-python / mne / epochs.py View on Github external
data *= decal[np.newaxis, :, np.newaxis]

    write_function(fid, FIFF.FIFF_EPOCH, data)

    # undo modifications to data
    data /= decal[np.newaxis, :, np.newaxis]

    write_string(fid, FIFF.FIFF_MNE_EPOCHS_DROP_LOG,
                 json.dumps(epochs.drop_log))

    reject_params = _pack_reject_params(epochs)
    if reject_params:
        write_string(fid, FIFF.FIFF_MNE_EPOCHS_REJECT_FLAT,
                     json.dumps(reject_params))

    write_int(fid, FIFF.FIFF_MNE_EPOCHS_SELECTION,
              epochs.selection)

    # And now write the next file info in case epochs are split on disk
    if next_fname is not None and n_parts > 1:
        start_block(fid, FIFF.FIFFB_REF)
        write_int(fid, FIFF.FIFF_REF_ROLE, FIFF.FIFFV_ROLE_NEXT_FILE)
        write_string(fid, FIFF.FIFF_REF_FILE_NAME, op.basename(next_fname))
        if meas_id is not None:
            write_id(fid, FIFF.FIFF_REF_FILE_ID, meas_id)
        write_int(fid, FIFF.FIFF_REF_FILE_NUM, next_idx)
        end_block(fid, FIFF.FIFFB_REF)

    end_block(fid, FIFF.FIFFB_MNE_EPOCHS)
    end_block(fid, FIFF.FIFFB_PROCESSED_DATA)
    end_block(fid, FIFF.FIFFB_MEAS)
    end_file(fid)
github mne-tools / mne-python / mne / io / meas_info.py View on Github external
for hpi_meas in info['hpi_meas']:
        start_block(fid, FIFF.FIFFB_HPI_MEAS)
        if hpi_meas.get('creator') is not None:
            write_string(fid, FIFF.FIFF_CREATOR, hpi_meas['creator'])
        if hpi_meas.get('sfreq') is not None:
            write_float(fid, FIFF.FIFF_SFREQ, hpi_meas['sfreq'])
        if hpi_meas.get('nchan') is not None:
            write_int(fid, FIFF.FIFF_NCHAN, hpi_meas['nchan'])
        if hpi_meas.get('nave') is not None:
            write_int(fid, FIFF.FIFF_NAVE, hpi_meas['nave'])
        if hpi_meas.get('ncoil') is not None:
            write_int(fid, FIFF.FIFF_HPI_NCOIL, hpi_meas['ncoil'])
        if hpi_meas.get('first_samp') is not None:
            write_int(fid, FIFF.FIFF_FIRST_SAMPLE, hpi_meas['first_samp'])
        if hpi_meas.get('last_samp') is not None:
            write_int(fid, FIFF.FIFF_LAST_SAMPLE, hpi_meas['last_samp'])
        for hpi_coil in hpi_meas['hpi_coils']:
            start_block(fid, FIFF.FIFFB_HPI_COIL)
            if hpi_coil.get('number') is not None:
                write_int(fid, FIFF.FIFF_HPI_COIL_NO, hpi_coil['number'])
            if hpi_coil.get('epoch') is not None:
                write_float_matrix(fid, FIFF.FIFF_EPOCH, hpi_coil['epoch'])
            if hpi_coil.get('slopes') is not None:
                write_float(fid, FIFF.FIFF_HPI_SLOPES, hpi_coil['slopes'])
            if hpi_coil.get('corr_coeff') is not None:
                write_float(fid, FIFF.FIFF_HPI_CORR_COEFF,
                            hpi_coil['corr_coeff'])
            if hpi_coil.get('coil_freq') is not None:
                write_float(fid, FIFF.FIFF_HPI_COIL_FREQ,
                            hpi_coil['coil_freq'])
            end_block(fid, FIFF.FIFFB_HPI_COIL)
        end_block(fid, FIFF.FIFFB_HPI_MEAS)
github mne-tools / mne-python / mne / io / proj.py View on Github external
"""Write a projection operator to a file.

    Parameters
    ----------
    fid : file
        The file descriptor of the open file.
    projs : dict
        The projection operator.
    """
    if len(projs) == 0:
        return
    start_block(fid, FIFF.FIFFB_PROJ)

    for proj in projs:
        start_block(fid, FIFF.FIFFB_PROJ_ITEM)
        write_int(fid, FIFF.FIFF_NCHAN, proj['data']['ncol'])
        write_name_list(fid, FIFF.FIFF_PROJ_ITEM_CH_NAME_LIST,
                        proj['data']['col_names'])
        write_string(fid, FIFF.FIFF_NAME, proj['desc'])
        write_int(fid, FIFF.FIFF_PROJ_ITEM_KIND, proj['kind'])
        if proj['kind'] == FIFF.FIFFV_PROJ_ITEM_FIELD:
            write_float(fid, FIFF.FIFF_PROJ_ITEM_TIME, 0.0)

        write_int(fid, FIFF.FIFF_PROJ_ITEM_NVEC, proj['data']['nrow'])
        write_int(fid, FIFF.FIFF_MNE_PROJ_ITEM_ACTIVE, proj['active'])
        write_float_matrix(fid, FIFF.FIFF_PROJ_ITEM_VECTORS,
                           proj['data']['data'])
        if proj['explained_var'] is not None:
            write_float(fid, FIFF.FIFF_MNE_ICA_PCA_EXPLAINED_VAR,
                        proj['explained_var'])
        end_block(fid, FIFF.FIFFB_PROJ_ITEM)
github mne-tools / mne-python / mne / source_space.py View on Github external
data = this.get('subject_his_id', None)
    if data:
        write_string(fid, FIFF.FIFF_SUBJ_HIS_ID, data)
    write_int(fid, FIFF.FIFF_MNE_COORD_FRAME, this['coord_frame'])

    write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS, this['np'])
    write_float_matrix(fid, FIFF.FIFF_MNE_SOURCE_SPACE_POINTS, this['rr'])
    write_float_matrix(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NORMALS, this['nn'])

    #   Which vertices are active
    write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_SELECTION, this['inuse'])
    write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NUSE, this['nuse'])

    if this['ntri'] > 0:
        write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NTRI, this['ntri'])
        write_int_matrix(fid, FIFF.FIFF_MNE_SOURCE_SPACE_TRIANGLES,
                         this['tris'] + 1)

    if this['type'] != 'vol' and this['use_tris'] is not None:
        #   Use triangulation
        write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NUSE_TRI, this['nuse_tri'])
        write_int_matrix(fid, FIFF.FIFF_MNE_SOURCE_SPACE_USE_TRIANGLES,
                         this['use_tris'] + 1)

    if this['type'] == 'vol':
        neighbor_vert = this.get('neighbor_vert', None)
        if neighbor_vert is not None:
            nneighbors = np.array([len(n) for n in neighbor_vert])
            neighbors = np.concatenate(neighbor_vert)
            write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NNEIGHBORS, nneighbors)
            write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NEIGHBORS, neighbors)
github mne-tools / mne-python / mne / evoked.py View on Github external
write_string(fid, FIFF.FIFF_COMMENT, e.comment)

            # First time, num. samples, first and last sample
            write_float(fid, FIFF.FIFF_FIRST_TIME, e.times[0])
            write_int(fid, FIFF.FIFF_NO_SAMPLES, len(e.times))
            write_int(fid, FIFF.FIFF_FIRST_SAMPLE, e.first)
            write_int(fid, FIFF.FIFF_LAST_SAMPLE, e.last)

            # The epoch itself
            if e.info.get('maxshield'):
                aspect = FIFF.FIFFB_IAS_ASPECT
            else:
                aspect = FIFF.FIFFB_ASPECT
            start_block(fid, aspect)

            write_int(fid, FIFF.FIFF_ASPECT_KIND, e._aspect_kind)
            # convert nave to integer to comply with FIFF spec
            nave_int = int(round(e.nave))
            if nave_int != e.nave and not warned:
                warn('converting "nave" to integer before saving evoked; this '
                     'can have a minor effect on the scale of source '
                     'estimates that are computed using "nave".')
                warned = True
            write_int(fid, FIFF.FIFF_NAVE, nave_int)
            del nave_int

            decal = np.zeros((e.info['nchan'], 1))
            for k in range(e.info['nchan']):
                decal[k] = 1.0 / (e.info['chs'][k]['cal'] *
                                  e.info['chs'][k].get('scale', 1.0))

            write_float_matrix(fid, FIFF.FIFF_EPOCH, decal * e.data)
github mne-tools / mne-python / mne / io / meas_info.py View on Github external
start_block(fid, FIFF.FIFFB_EVENTS)
        if event.get('channels') is not None:
            write_int(fid, FIFF.FIFF_EVENT_CHANNELS, event['channels'])
        if event.get('list') is not None:
            write_int(fid, FIFF.FIFF_EVENT_LIST, event['list'])
        end_block(fid, FIFF.FIFFB_EVENTS)

    #   HPI Result
    for hpi_result in info['hpi_results']:
        start_block(fid, FIFF.FIFFB_HPI_RESULT)
        write_dig_points(fid, hpi_result['dig_points'])
        if 'order' in hpi_result:
            write_int(fid, FIFF.FIFF_HPI_DIGITIZATION_ORDER,
                      hpi_result['order'])
        if 'used' in hpi_result:
            write_int(fid, FIFF.FIFF_HPI_COILS_USED, hpi_result['used'])
        if 'moments' in hpi_result:
            write_float_matrix(fid, FIFF.FIFF_HPI_COIL_MOMENTS,
                               hpi_result['moments'])
        if 'goodness' in hpi_result:
            write_float(fid, FIFF.FIFF_HPI_FIT_GOODNESS,
                        hpi_result['goodness'])
        if 'good_limit' in hpi_result:
            write_float(fid, FIFF.FIFF_HPI_FIT_GOOD_LIMIT,
                        hpi_result['good_limit'])
        if 'dist_limit' in hpi_result:
            write_float(fid, FIFF.FIFF_HPI_FIT_DIST_LIMIT,
                        hpi_result['dist_limit'])
        if 'accept' in hpi_result:
            write_int(fid, FIFF.FIFF_HPI_FIT_ACCEPT, hpi_result['accept'])
        if 'coord_trans' in hpi_result:
            write_coord_trans(fid, hpi_result['coord_trans'])
github mne-tools / mne-python / mne / epochs.py View on Github external
_check_option('fmt', fmt, ['single', 'double'])

    if np.iscomplexobj(data):
        if fmt == 'single':
            write_function = write_complex_float_matrix
        elif fmt == 'double':
            write_function = write_complex_double_matrix
    else:
        if fmt == 'single':
            write_function = write_float_matrix
        elif fmt == 'double':
            write_function = write_double_matrix

    start_block(fid, FIFF.FIFFB_MNE_EVENTS)
    write_int(fid, FIFF.FIFF_MNE_EVENT_LIST, epochs.events.T)
    mapping_ = ';'.join([k + ':' + str(v) for k, v in
                         epochs.event_id.items()])

    write_string(fid, FIFF.FIFF_DESCRIPTION, mapping_)
    end_block(fid, FIFF.FIFFB_MNE_EVENTS)

    # Metadata
    if epochs.metadata is not None:
        start_block(fid, FIFF.FIFFB_MNE_METADATA)
        metadata = _prepare_write_metadata(epochs.metadata)
        write_string(fid, FIFF.FIFF_DESCRIPTION, metadata)
        end_block(fid, FIFF.FIFFB_MNE_METADATA)

    # First and last sample
    first = int(round(epochs.tmin * info['sfreq']))  # round just to be safe
    last = first + len(epochs.times) - 1
github mne-tools / mne-python / mne / io / meas_info.py View on Github external
if hs.get('hpi_coils') is not None:
            for coil in hs['hpi_coils']:
                start_block(fid, FIFF.FIFFB_HPI_COIL)
                if coil.get('event_bits') is not None:
                    write_int(fid, FIFF.FIFF_EVENT_BITS,
                              coil['event_bits'])
                end_block(fid, FIFF.FIFFB_HPI_COIL)
        end_block(fid, FIFF.FIFFB_HPI_SUBSYSTEM)
        del hs

    #   CTF compensation info
    write_ctf_comp(fid, info['comps'])

    #   KIT system ID
    if info.get('kit_system_id') is not None:
        write_int(fid, FIFF.FIFF_MNE_KIT_SYSTEM_ID, info['kit_system_id'])

    end_block(fid, FIFF.FIFFB_MEAS_INFO)

    #   Processing history
    _write_proc_history(fid, info)
github mne-tools / mne-python / mne / source_space.py View on Github external
write_coord_trans(fid, this['mri_ras_t'])
        write_coord_trans(fid, this['vox_mri_t'])

        mri_volume_name = this.get('mri_volume_name', None)
        if mri_volume_name is not None:
            write_string(fid, FIFF.FIFF_MNE_FILE_NAME, mri_volume_name)

        write_float_sparse_rcs(fid, FIFF.FIFF_MNE_SOURCE_SPACE_INTERPOLATOR,
                               this['interpolator'])

        if 'mri_file' in this and this['mri_file'] is not None:
            write_string(fid, FIFF.FIFF_MNE_SOURCE_SPACE_MRI_FILE,
                         this['mri_file'])

        write_int(fid, FIFF.FIFF_MRI_WIDTH, this['mri_width'])
        write_int(fid, FIFF.FIFF_MRI_HEIGHT, this['mri_height'])
        write_int(fid, FIFF.FIFF_MRI_DEPTH, this['mri_depth'])

        end_block(fid, FIFF.FIFFB_MNE_PARENT_MRI_FILE)

    #   Patch-related information
    if this['nearest'] is not None:
        write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST, this['nearest'])
        write_float_matrix(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST,
                           this['nearest_dist'])

    #   Distances
    if this['dist'] is not None:
        # Save only upper triangular portion of the matrix
        dists = this['dist'].copy()
        dists = sparse.triu(dists, format=dists.format)
        write_float_sparse_rcs(fid, FIFF.FIFF_MNE_SOURCE_SPACE_DIST, dists)