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matmef_mapping.c
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/**
* @file
* MEF 3.0 Library Matlab Wrapper
* Functions to map MEF3 objects and structures to Matlab structures
*
* Copyright 2020, Max van den Boom (Multimodal Neuroimaging Lab, Mayo Clinic, Rochester MN)
* Adapted from PyMef (by Jan Cimbalnik, Matt Stead, Ben Brinkmann, and Dan Crepeau)
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
* warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
* You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
#include "matmef_mapping.h"
#include "mex.h"
#include "matmef_dataconverter.h"
#include "meflib/meflib/meflib.h"
///
// Fields definitions for MEF3 matlab structs
///
// Universal Header Structures
const int UNIVERSAL_HEADER_NUMFIELDS = 20;
const char *UNIVERSAL_HEADER_FIELDNAMES[] = {
"header_CRC",
"body_CRC",
"file_type_string",
"mef_version_major",
"mef_version_minor",
"byte_order_code",
"start_time",
"end_time",
"number_of_entries",
"maximum_entry_size",
"segment_number",
"channel_name", // utf8[63], base name only, no extension
"session_name", // utf8[63], base name only, no extension
"anonymized_name", // utf8[63]
"level_UUID",
"file_UUID",
"provenance_UUID",
"level_1_password_validation_field",
"level_2_password_validation_field",
//"protected_region", // (not mapped, reserved, should not be used by end users)
"discretionary_region"
};
// Session, Channel, Segment Processing Structures
const int SEGMENT_NUMFIELDS = 12;
const char *SEGMENT_FIELDNAMES[] = {
"channel_type",
//"metadata_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the data held within is mapped to the 'metadata_uh' field
//"time_series_data_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the data held within is mapped to the 'time_series_data_uh' field
//"time_series_indices_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the (number of) time-series indices are mapped to the 'time_series_indices' field
//"video_indices_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the (number of) video indices are mapped to the 'video_indices' field
//"record_data_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the (number of) data-records are mapped to the 'records' field
//"record_indices_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the (number of) records-indices held within are mapped to the 'records' field
"name", // just base name, no extension
"path", // full path to enclosing directory (channel directory)
"channel_name", // just base name, no extension
"session_name", // just base name, no extension
"level_UUID",
// non-meflib fields, added for mapping (contains data normally held within the _fps structs)
"metadata",
"time_series_indices",
"video_indices",
"records",
"metadata_uh",
"time_series_data_uh"
};
const int CHANNEL_NUMFIELDS = 15;
const char *CHANNEL_FIELDNAMES[] = {
"channel_type",
"metadata",
//"record_data_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the records-data held within is mapped to the 'records' field
//"record_indices_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the records-indices held within are mapped to the 'records' field
"number_of_segments",
"segments",
"path", // full path to enclosing directory (session directory)
"name", // just base name, no extension
"extension", // channel directory extension
"session_name", // just base name, no extension
"level_UUID",
"anonymized_name",
// variables below refer to segments
"maximum_number_of_records",
"maximum_record_bytes",
"earliest_start_time",
"latest_end_time",
// non-meflib fields, added for mapping (contains data normally held within the _fps structs)
"records"
};
const int SESSION_NUMFIELDS = 15;
const char *SESSION_FIELDNAMES[] = {
"time_series_metadata",
"number_of_time_series_channels",
"time_series_channels",
"video_metadata",
"number_of_video_channels",
"video_channels",
//"record_data_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the record-data held within is mapped to the 'records' field
//"record_indices_fps", // instead of mapping the FILE_PROCESSING_STRUCT object, the record-indices held within are mapped to the 'records' field
"name",
"path",
"anonymized_name",
"level_UUID",
// below variables refer to channels
"maximum_number_of_records",
"maximum_record_bytes",
"earliest_start_time",
"latest_end_time",
// non-meflib fields, added for mapping (contains data normally held within the _fps structs)
"records"
};
// Metadata Structures
const int METADATA_SECTION_1_NUMFIELDS = 3;
const char *METADATA_SECTION_1_FIELDNAMES[] = {
"section_2_encryption",
"section_3_encryption",
//"protected_region", // (not mapped, reserved, should not be used by end users)
"discretionary_region"
};
const int TIME_SERIES_METADATA_SECTION_2_NUMFIELDS = 26;
const char *TIME_SERIES_METADATA_SECTION_2_FIELDNAMES[] = {
// type-independent fields
"channel_description", // utf8[511];
"session_description", // utf8[511];
"recording_duration",
// type-specific fields
"reference_description", // utf8[511];
"acquisition_channel_number",
"sampling_frequency",
"low_frequency_filter_setting",
"high_frequency_filter_setting",
"notch_filter_frequency_setting",
"AC_line_frequency",
"units_conversion_factor",
"units_description", // utf8[31]
"maximum_native_sample_value",
"minimum_native_sample_value",
"start_sample",
"number_of_samples",
"number_of_blocks",
"maximum_block_bytes",
"maximum_block_samples",
"maximum_difference_bytes",
"block_interval",
"number_of_discontinuities",
"maximum_contiguous_blocks",
"maximum_contiguous_block_bytes",
"maximum_contiguous_samples",
//"protected_region", // (not mapped, reserved, should not be used by end users)
"discretionary_region"
};
const int VIDEO_METADATA_SECTION_2_NUMFIELDS = 11;
const char *VIDEO_METADATA_SECTION_2_FIELDNAMES[] = {
// type-independent fields
"channel_description", // utf8[511]
"session_description",
"recording_duration",
// type-specific fields
"horizontal_resolution",
"vertical_resolution",
"frame_rate",
"number_of_clips",
"maximum_clip_bytes",
"video_format",
"video_file_CRC",
//"protected_region", // (not mapped, reserved, should not be used by end users)
"discretionary_region"
};
const int METADATA_SECTION_3_NUMFIELDS = 9;
const char *METADATA_SECTION_3_FIELDNAMES[] = {
"recording_time_offset",
"DST_start_time",
"DST_end_time",
"GMT_offset",
"subject_name_1", // utf8[31]
"subject_name_2", // utf8[31]
"subject_ID", // utf8[31]
"recording_location", // utf8[127]
//"protected_region", // (not mapped, reserved, should not be used by end users)
"discretionary_region"
};
const int METADATA_NUMFIELDS = 3;
const char *METADATA_FIELDNAMES[] = {
"section_1",
"section_2", // non-meflib field, added for mapping 'time_series_section_2' or 'video_section_2' (since it is always one or the other)
//"time_series_section_2", // instead of mapping the time_series_section_2 object, the data is mapped to the 'section_2' field for time-series
//"video_section_2", // instead of mapping the video_section_2 object, the data is mapped to the 'section_2' field for video
"section_3"
};
// Record Structures
const int RECORD_HEADER_NUMFIELDS = 7;
const char *RECORD_HEADER_FIELDNAMES[] = {
"record_CRC",
"type_string",
"version_major",
"version_minor",
"encryption",
"bytes",
"time"
};
const int RECORD_INDEX_NUMFIELDS = 6;
const char *RECORD_INDEX_FIELDNAMES[] = {
"type_string",
"version_major",
"version_minor",
"encryption",
"file_offset",
"time"
};
// Block Indices Structures
const int TIME_SERIES_INDEX_NUMFIELDS = 9;
const char *TIME_SERIES_INDEX_FIELDNAMES[] = {
"file_offset",
"start_time",
"start_sample",
"number_of_samples",
"block_bytes",
"maximum_sample_value",
"minimum_sample_value",
//"protected_region", // (not mapped, reserved, should not be used by end users)
"RED_block_flags",
//"RED_block_protected_region", // (not mapped, reserved, should not be used by end users)
"RED_block_discretionary_region"
};
// Frame Indices Structures
const int VIDEO_INDEX_NUMFIELDS = 9;
const char *VIDEO_INDEX_FIELDNAMES[] = {
"start_time",
"end_time",
"start_frame",
"end_frame",
"file_offset",
"clip_bytes",
//"protected_region", // (not mapped, reserved, should not be used by end users)
"discretionary_region"
};
// File Processing Structures
const int FILE_PROCESSINGFILE_PROCESSING_NUMFIELDS = 16;
const char *FILE_PROCESSING_FIELDNAMES[] = {
"full_file_name", // full path including extension
"fp", // runtime file pointer (not mapped)
"fd", // runtime file descriptor (not mapped)
"file_length",
"file_type_code",
"universal_header",
"directives", // runtime struct (not mapped)
"password_data", // this will often be the same for all files
"metadata",
"time_series_indices",
"video_indices",
"records",
"record_indices",
"RED_blocks", // only used when type = TIME_SERIES_DATA_FILE_TYPE_CODE; (not mapped)
"raw_data_bytes",
"raw_data" // (not mapped)
};
// Record Type Structures
const int MEFREC_EDFA_1_0_NUMFIELDS = 1;
const char *MEFREC_EDFA_1_0_FIELDNAMES[] = {
"duration"
};
const int MEFREC_LNTP_1_0_NUMFIELDS = 1;
const char *MEFREC_LNTP_1_0_FIELDNAMES[] = {
"length"
};
const int MEFREC_SEIZ_1_0_NUMFIELDS = 8;
const char *MEFREC_SEIZ_1_0_FIELDNAMES[] = {
"earliest_onset",
"latest_offset",
"duration",
"number_of_channels",
"onset_code",
"marker_name_1",
"marker_name_2",
"annotation"
};
const int MEFREC_CSTI_1_0_NUMFIELDS = 4;
const char *MEFREC_CSTI_1_0_FIELDNAMES[] = {
"task_type",
"stimulus_duration",
"stimulus_type",
"patient_response"
};
const int MEFREC_ESTI_1_0_NUMFIELDS = 8;
const char *MEFREC_ESTI_1_0_FIELDNAMES[] = {
"amplitude",
"frequency",
"pulse_width",
"ampunit_code",
"mode_code",
"waveform",
"anode",
"catode"
};
const int MEFREC_CURS_1_0_NUMFIELDS = 5;
const char *MEFREC_CURS_1_0_FIELDNAMES[] = {
"id_number",
"trace_timestamp",
"latency",
"value",
"name"
};
const int MEFREC_EPOC_1_0_NUMFIELDS = 6;
const char *MEFREC_EPOC_1_0_FIELDNAMES[] = {
"id_number",
"timestamp",
"end_timestamp",
"duration",
"type",
"text"
};
///
// Functions to create new and initialized matlab-structs
///
/**
* Create and initialize a new MEF universal-header matlab-struct
*
* @return A pointer to the new matlab-struct
*/
mxArray *create_init_matlab_uh() {
mxArray *mat_uh = mxCreateStructMatrix(1, 1, UNIVERSAL_HEADER_NUMFIELDS, UNIVERSAL_HEADER_FIELDNAMES);
mxSetField(mat_uh, 0, "header_CRC", mxUint32ByValue(UNIVERSAL_HEADER_HEADER_CRC_NO_ENTRY));
mxSetField(mat_uh, 0, "body_CRC", mxUint32ByValue(UNIVERSAL_HEADER_BODY_CRC_NO_ENTRY));
mxSetField(mat_uh, 0, "file_type_string", mxCreateString(""));
mxSetField(mat_uh, 0, "mef_version_major", mxUint8ByValue(UNIVERSAL_HEADER_MEF_VERSION_MAJOR_NO_ENTRY));
mxSetField(mat_uh, 0, "mef_version_minor", mxUint8ByValue(UNIVERSAL_HEADER_MEF_VERSION_MINOR_NO_ENTRY));
mxSetField(mat_uh, 0, "byte_order_code", mxUint8ByValue(UNIVERSAL_HEADER_BYTE_ORDER_CODE_NO_ENTRY));
mxSetField(mat_uh, 0, "start_time", mxInt64ByValue(UNIVERSAL_HEADER_START_TIME_NO_ENTRY));
mxSetField(mat_uh, 0, "end_time", mxInt64ByValue(UNIVERSAL_HEADER_END_TIME_NO_ENTRY));
mxSetField(mat_uh, 0, "number_of_entries", mxInt64ByValue(UNIVERSAL_HEADER_NUMBER_OF_ENTRIES_NO_ENTRY));
mxSetField(mat_uh, 0, "maximum_entry_size", mxInt64ByValue(UNIVERSAL_HEADER_MAXIMUM_ENTRY_SIZE_NO_ENTRY));
mxSetField(mat_uh, 0, "segment_number", mxInt32ByValue(UNIVERSAL_HEADER_SEGMENT_NUMBER_NO_ENTRY));
mxSetField(mat_uh, 0, "channel_name", mxCreateString(""));
mxSetField(mat_uh, 0, "session_name", mxCreateString(""));
mxSetField(mat_uh, 0, "anonymized_name", mxCreateString(""));
mxSetField(mat_uh, 0, "level_UUID", mxCreateNumericMatrix(1, UUID_BYTES, mxUINT8_CLASS, mxREAL));
mxSetField(mat_uh, 0, "file_UUID", mxCreateNumericMatrix(1, UUID_BYTES, mxUINT8_CLASS, mxREAL));
mxSetField(mat_uh, 0, "provenance_UUID", mxCreateNumericMatrix(1, UUID_BYTES, mxUINT8_CLASS, mxREAL));
mxSetField(mat_uh, 0, "level_1_password_validation_field", mxCreateNumericMatrix(1, PASSWORD_VALIDATION_FIELD_BYTES, mxUINT8_CLASS, mxREAL));
mxSetField(mat_uh, 0, "level_2_password_validation_field", mxCreateNumericMatrix(1, PASSWORD_VALIDATION_FIELD_BYTES, mxUINT8_CLASS, mxREAL));
mxSetField(mat_uh, 0, "discretionary_region", mxCreateNumericMatrix(1, UNIVERSAL_HEADER_DISCRETIONARY_REGION_BYTES, mxUINT8_CLASS, mxREAL));
// return the struct
return mat_uh;
}
/**
* Create and initialize a new MEF time-series section 2 metadata matlab-struct
*
* @return A pointer to the new matlab-struct
*/
mxArray *create_init_matlab_tmd2() {
mxArray *mat_md = mxCreateStructMatrix(1, 1, TIME_SERIES_METADATA_SECTION_2_NUMFIELDS, TIME_SERIES_METADATA_SECTION_2_FIELDNAMES);
// type-independent fields
mxSetField(mat_md, 0, "channel_description", mxCreateString(""));
mxSetField(mat_md, 0, "session_description", mxCreateString(""));
mxSetField(mat_md, 0, "recording_duration", mxInt64ByValue(METADATA_RECORDING_DURATION_NO_ENTRY));
// type-specific fields
mxSetField(mat_md, 0, "reference_description", mxCreateString(""));
mxSetField(mat_md, 0, "acquisition_channel_number", mxInt64ByValue(TIME_SERIES_METADATA_ACQUISITION_CHANNEL_NUMBER_NO_ENTRY));
mxSetField(mat_md, 0, "sampling_frequency", mxDoubleByValue(TIME_SERIES_METADATA_SAMPLING_FREQUENCY_NO_ENTRY));
mxSetField(mat_md, 0, "low_frequency_filter_setting", mxDoubleByValue(TIME_SERIES_METADATA_LOW_FREQUENCY_FILTER_SETTING_NO_ENTRY));
mxSetField(mat_md, 0, "high_frequency_filter_setting", mxDoubleByValue(TIME_SERIES_METADATA_HIGH_FREQUENCY_FILTER_SETTING_NO_ENTRY));
mxSetField(mat_md, 0, "notch_filter_frequency_setting", mxDoubleByValue(TIME_SERIES_METADATA_NOTCH_FILTER_FREQUENCY_SETTING_NO_ENTRY));
mxSetField(mat_md, 0, "AC_line_frequency", mxDoubleByValue(TIME_SERIES_METADATA_AC_LINE_FREQUENCY_NO_ENTRY));
mxSetField(mat_md, 0, "units_conversion_factor", mxDoubleByValue(TIME_SERIES_METADATA_UNITS_CONVERSION_FACTOR_NO_ENTRY));
mxSetField(mat_md, 0, "units_description", mxCreateString(""));
mxSetField(mat_md, 0, "maximum_native_sample_value", mxDoubleByValue(TIME_SERIES_METADATA_MAXIMUM_NATIVE_SAMPLE_VALUE_NO_ENTRY));
mxSetField(mat_md, 0, "minimum_native_sample_value", mxDoubleByValue(TIME_SERIES_METADATA_MINIMUM_NATIVE_SAMPLE_VALUE_NO_ENTRY));
mxSetField(mat_md, 0, "start_sample", mxInt64ByValue(TIME_SERIES_METADATA_START_SAMPLE_NO_ENTRY));
mxSetField(mat_md, 0, "number_of_samples", mxInt64ByValue(TIME_SERIES_METADATA_NUMBER_OF_SAMPLES_NO_ENTRY));
mxSetField(mat_md, 0, "number_of_blocks", mxInt64ByValue(TIME_SERIES_METADATA_NUMBER_OF_BLOCKS_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_block_bytes", mxInt64ByValue(TIME_SERIES_METADATA_MAXIMUM_BLOCK_BYTES_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_block_samples", mxUint32ByValue(TIME_SERIES_METADATA_MAXIMUM_BLOCK_SAMPLES_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_difference_bytes", mxUint32ByValue(TIME_SERIES_METADATA_MAXIMUM_DIFFERENCE_BYTES_NO_ENTRY));
mxSetField(mat_md, 0, "block_interval", mxInt64ByValue(TIME_SERIES_METADATA_BLOCK_INTERVAL_NO_ENTRY));
mxSetField(mat_md, 0, "number_of_discontinuities", mxInt64ByValue(TIME_SERIES_METADATA_NUMBER_OF_DISCONTINUITIES_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_contiguous_blocks", mxInt64ByValue(TIME_SERIES_METADATA_MAXIMUM_CONTIGUOUS_BLOCKS_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_contiguous_block_bytes", mxInt64ByValue(TIME_SERIES_METADATA_MAXIMUM_CONTIGUOUS_BLOCK_BYTES_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_contiguous_samples", mxInt64ByValue(TIME_SERIES_METADATA_MAXIMUM_CONTIGUOUS_SAMPLES_NO_ENTRY));
mxSetField(mat_md, 0, "discretionary_region", mxCreateNumericMatrix(1, TIME_SERIES_METADATA_SECTION_2_DISCRETIONARY_REGION_BYTES, mxUINT8_CLASS, mxREAL));
// return the struct
return mat_md;
}
/**
* Create and initialize a new MEF video section 2 metadata matlab-struct
*
* @return A pointer to the new matlab-struct
*/
mxArray *create_init_matlab_vmd2() {
mxArray *mat_md = mxCreateStructMatrix(1, 1, VIDEO_METADATA_SECTION_2_NUMFIELDS, VIDEO_METADATA_SECTION_2_FIELDNAMES);
// type-independent fields
mxSetField(mat_md, 0, "channel_description", mxCreateString(""));
mxSetField(mat_md, 0, "session_description", mxCreateString(""));
mxSetField(mat_md, 0, "recording_duration", mxInt64ByValue(METADATA_RECORDING_DURATION_NO_ENTRY));
// type-specific fields
mxSetField(mat_md, 0, "horizontal_resolution", mxInt64ByValue(VIDEO_METADATA_HORIZONTAL_RESOLUTION_NO_ENTRY));
mxSetField(mat_md, 0, "vertical_resolution", mxInt64ByValue(VIDEO_METADATA_VERTICAL_RESOLUTION_NO_ENTRY));
mxSetField(mat_md, 0, "frame_rate", mxDoubleByValue(VIDEO_METADATA_FRAME_RATE_NO_ENTRY));
mxSetField(mat_md, 0, "number_of_clips", mxInt64ByValue(VIDEO_METADATA_NUMBER_OF_CLIPS_NO_ENTRY));
mxSetField(mat_md, 0, "maximum_clip_bytes", mxInt64ByValue(VIDEO_METADATA_MAXIMUM_CLIP_BYTES_NO_ENTRY));
mxSetField(mat_md, 0, "video_format", mxCreateString(""));
mxSetField(mat_md, 0, "video_file_CRC", mxUint32ByValue(VIDEO_METADATA_VIDEO_FILE_CRC_NO_ENTRY));
mxSetField(mat_md, 0, "discretionary_region", mxCreateNumericMatrix(1, VIDEO_METADATA_SECTION_2_DISCRETIONARY_REGION_BYTES, mxUINT8_CLASS, mxREAL));
// return the struct
return mat_md;
}
/**
* Create and initialize a new MEF section 3 metadata matlab-struct
*
* @return A pointer to the new matlab-struct
*/
mxArray *create_init_matlab_md3() {
mxArray *mat_md = mxCreateStructMatrix(1, 1, METADATA_SECTION_3_NUMFIELDS, METADATA_SECTION_3_FIELDNAMES);
mxSetField(mat_md, 0, "recording_time_offset", mxInt64ByValue(METADATA_RECORDING_TIME_OFFSET_NO_ENTRY));
mxSetField(mat_md, 0, "DST_start_time", mxInt64ByValue(METADATA_DST_START_TIME_NO_ENTRY));
mxSetField(mat_md, 0, "DST_end_time", mxInt64ByValue(METADATA_DST_END_TIME_NO_ENTRY));
mxSetField(mat_md, 0, "GMT_offset", mxInt32ByValue(GMT_OFFSET_NO_ENTRY));
mxSetField(mat_md, 0, "subject_name_1", mxCreateString(""));
mxSetField(mat_md, 0, "subject_name_2", mxCreateString(""));
mxSetField(mat_md, 0, "subject_ID", mxCreateString(""));
mxSetField(mat_md, 0, "recording_location", mxCreateString(""));
mxSetField(mat_md, 0, "discretionary_region", mxCreateNumericMatrix(1, METADATA_SECTION_3_DISCRETIONARY_REGION_BYTES, mxUINT8_CLASS, mxREAL));
// return the struct
return mat_md;
}
///
// Functions to map c-objects to matlab-structs
///
/**
* Map a MEF segment c-struct to an exising matlab-struct
*
* The given matlab-struct have multiple entries, the MEF
* struct will be mapped on the given index
*
* @param segment Pointer to the MEF segment c-struct
* @param map_indices_flag Whether to map the time-series and video indices
* @param mat_segment Pointer to the existing matlab-struct
* @param mat_index The index in the existing matlab-struct at which to map the data
*/
void map_mef3_segment_tostruct(SEGMENT *segment, si1 map_indices_flag, mxArray *mat_segment, int mat_index) {
// set segment properties
mxSetField(mat_segment, mat_index, "channel_type", mxInt32ByValue(segment->channel_type));
mxSetField(mat_segment, mat_index, "name", mxCreateString(segment->name));
mxSetField(mat_segment, mat_index, "path", mxCreateString(segment->path));
mxSetField(mat_segment, mat_index, "channel_name", mxCreateString(segment->channel_name));
mxSetField(mat_segment, mat_index, "session_name", mxCreateString(segment->session_name));
mxSetField(mat_segment, mat_index, "level_UUID", mxUint8ArrayByValue(segment->level_UUID, UUID_BYTES));
//
// universal headers (from file processing struct)
//
mxSetField(mat_segment, mat_index, "metadata_uh", map_mef3_uh(segment->metadata_fps->universal_header));
if (segment->channel_type == TIME_SERIES_CHANNEL_TYPE)
mxSetField(mat_segment, mat_index, "time_series_data_uh", map_mef3_uh(segment->time_series_data_fps->universal_header));
//
// records
//
// check segment records and (if existent) add
if ((segment->record_indices_fps != NULL) & (segment->record_data_fps != NULL))
mxSetField(mat_segment, mat_index, "records", map_mef3_records(segment->record_indices_fps, segment->record_data_fps));
//
// metadata
//
// create a metadata struct (for the segment) and assign it to the 'metadata' field
mxArray *segment_metadata_struct = mxCreateStructMatrix(1, 1, METADATA_NUMFIELDS, METADATA_FIELDNAMES);
mxSetField(mat_segment, mat_index, "metadata", segment_metadata_struct);
// map segment metadata sections
mxSetField(segment_metadata_struct, 0, "section_1", map_mef3_md1(segment->metadata_fps->metadata.section_1));
switch (segment->channel_type){
case TIME_SERIES_CHANNEL_TYPE:
mxSetField(segment_metadata_struct, 0, "section_2", map_mef3_tmd2(segment->metadata_fps->metadata.time_series_section_2));
break;
case VIDEO_CHANNEL_TYPE:
mxSetField(segment_metadata_struct, 0, "section_2", map_mef3_vmd2(segment->metadata_fps->metadata.video_section_2));
break;
default:
mexErrMsgTxt("Unrecognized channel type, exiting...");
}
mxSetField(segment_metadata_struct, 0, "section_3", map_mef3_md3(segment->metadata_fps->metadata.section_3));
//
// map indices
//
// check if indices should be mapped
if (map_indices_flag) {
switch (segment->channel_type){
case TIME_SERIES_CHANNEL_TYPE:
// check if the time-series indices are available
if (segment->time_series_indices_fps != NULL) {
// create a time-series indices struct (for the segment) and assign it to the 'time_series_indices' field
mxSetField( mat_segment,
mat_index,
"time_series_indices",
map_mef3_ti( segment->time_series_indices_fps->time_series_indices,
segment->time_series_indices_fps->universal_header->number_of_entries));
}
break;
case VIDEO_CHANNEL_TYPE:
// check if the video indices are available
if (segment->video_indices_fps != NULL) {
// create a video indices struct (for the segment) and assign it to the 'video_indices' field
mxSetField( mat_segment,
mat_index,
"video_indices",
map_mef3_vi( segment->video_indices_fps->video_indices,
segment->video_indices_fps->universal_header->number_of_entries));
}
break;
default:
mexErrMsgTxt("Unrecognized channel type, exiting...");
}
}
}
/**
* Map a MEF segment c-struct to a newly created matlab-struct
*
* @param segment Pointer to the MEF segment c-struct
* @param map_indices_flag Whether to map the time-series and video indices
* @return Pointer to the new matlab-struct
*/
mxArray *map_mef3_segment(SEGMENT *segment, si1 map_indices_flag) {
mxArray *mat_segment = mxCreateStructMatrix(1, 1, SEGMENT_NUMFIELDS, SEGMENT_FIELDNAMES);
map_mef3_segment_tostruct(segment, map_indices_flag, mat_segment, 0);
return mat_segment;
}
/**
* Map a MEF channel c-struct to an exising matlab-struct
*
* The given matlab-struct have multiple entries, the MEF
* struct will be mapped on the given index
*
*
* note: this funtion also loops through segments
*
* @param channel A pointer to the MEF channel c-struct
* @param map_indices_flag Whether to map the time-series and video indices
* @param mat_channel A pointer to the existing matlab-struct
* @param mat_index The index in the existing matlab-struct at which to map the data
*/
void map_mef3_channel_tostruct(CHANNEL *channel, si1 map_indices_flag, mxArray *mat_channel, int mat_index) {
si4 i;
SEGMENT *segment;
// set channel specific properties
mxSetField(mat_channel, mat_index, "channel_type", mxInt32ByValue(channel->channel_type));
mxSetField(mat_channel, mat_index, "number_of_segments", mxInt64ByValue(channel->number_of_segments));
mxSetField(mat_channel, mat_index, "path", mxCreateString(channel->path));
mxSetField(mat_channel, mat_index, "name", mxCreateString(channel->name));
mxSetField(mat_channel, mat_index, "extension", mxCreateString(channel->extension));
mxSetField(mat_channel, mat_index, "session_name", mxCreateString(channel->session_name));
mxSetField(mat_channel, mat_index, "level_UUID", mxUint8ArrayByValue(channel->level_UUID, UUID_BYTES));
mxSetField(mat_channel, mat_index, "anonymized_name", mxCreateString(channel->anonymized_name));
mxSetField(mat_channel, mat_index, "maximum_number_of_records", mxInt64ByValue(channel->maximum_number_of_records));
mxSetField(mat_channel, mat_index, "maximum_record_bytes", mxInt64ByValue(channel->maximum_record_bytes));
mxSetField(mat_channel, mat_index, "earliest_start_time", mxInt64ByValue(channel->earliest_start_time));
mxSetField(mat_channel, mat_index, "latest_end_time", mxInt64ByValue(channel->latest_end_time));
//
// records
//
// check channel records and (if existent) add
if ((channel->record_indices_fps != NULL) & (channel->record_data_fps != NULL)) {
mxSetField(mat_channel, mat_index, "records", map_mef3_records(channel->record_indices_fps, channel->record_data_fps));
}
//
// metadata
//
// create a metadata struct and assign it to the 'metadata' field
mxArray *channel_metadata_struct = mxCreateStructMatrix(1, 1, METADATA_NUMFIELDS, METADATA_FIELDNAMES);
mxSetField(mat_channel, mat_index, "metadata", channel_metadata_struct);
// map channel metadata sections
mxSetField(channel_metadata_struct, 0, "section_1", map_mef3_md1(channel->metadata.section_1));
switch (channel->channel_type){
case TIME_SERIES_CHANNEL_TYPE:
mxSetField(channel_metadata_struct, 0, "section_2", map_mef3_tmd2(channel->metadata.time_series_section_2));
break;
case VIDEO_CHANNEL_TYPE:
mxSetField(channel_metadata_struct, 0, "section_2", map_mef3_vmd2(channel->metadata.video_section_2));
break;
default:
mexErrMsgTxt("Unrecognized channel type, exiting...");
}
mxSetField(channel_metadata_struct, 0, "section_3", map_mef3_md3(channel->metadata.section_3));
// check if there are segments for this channel
if (channel->number_of_segments > 0) {
// create a segments struct
mxArray *segmentsStruct = mxCreateStructMatrix(1, channel->number_of_segments, SEGMENT_NUMFIELDS, SEGMENT_FIELDNAMES);
// map the segments
for (i = 0; i < channel->number_of_segments; ++i) {
segment = channel->segments + i;
map_mef3_segment_tostruct(segment, map_indices_flag, segmentsStruct, i);
}
// assign the channels matlab-struct to the 'segments' field
mxSetField(mat_channel, mat_index, "segments", segmentsStruct);
}
}
/**
* Map a MEF channel c-struct to a newly created matlab-struct
*
* note: this funtion also loops through segments
*
* @param channel A pointer to the MEF channel c-struct
* @param map_indices_flag Whether to map the time-series and video indices
* @return A pointer to the new matlab-struct
*/
mxArray *map_mef3_channel(CHANNEL *channel, si1 map_indices_flag) {
mxArray *mat_channel = mxCreateStructMatrix(1, 1, CHANNEL_NUMFIELDS, CHANNEL_FIELDNAMES);
map_mef3_channel_tostruct(channel, map_indices_flag, mat_channel, 0);
return mat_channel;
}
/**
* Map a MEF session c-struct to a newly created matlab-struct
*
* @param session A pointer to the MEF session c-struct
* @param map_indices_flag Whether to map the time-series and video indices
* @return A pointer to the new matlab-struct
*/
mxArray *map_mef3_session(SESSION *session, si1 map_indices_flag) {
si4 i;
CHANNEL *channel;
// create the a matlab 'session' struct
mxArray *mat_session = mxCreateStructMatrix(1, 1, SESSION_NUMFIELDS, SESSION_FIELDNAMES);
// set session-specific properties
mxSetField(mat_session, 0, "number_of_time_series_channels", mxInt32ByValue(session->number_of_time_series_channels));
mxSetField(mat_session, 0, "number_of_video_channels", mxInt32ByValue(session->number_of_video_channels));
mxSetField(mat_session, 0, "name", mxCreateString(session->name));
mxSetField(mat_session, 0, "path", mxCreateString(session->path));
mxSetField(mat_session, 0, "anonymized_name", mxCreateString(session->anonymized_name));
mxSetField(mat_session, 0, "level_UUID", mxUint8ArrayByValue(session->level_UUID, UUID_BYTES));
mxSetField(mat_session, 0, "maximum_number_of_records", mxInt64ByValue(session->maximum_number_of_records));
mxSetField(mat_session, 0, "maximum_record_bytes", mxInt64ByValue(session->maximum_record_bytes));
mxSetField(mat_session, 0, "earliest_start_time", mxInt64ByValue(session->earliest_start_time));
mxSetField(mat_session, 0, "latest_end_time", mxInt64ByValue(session->latest_end_time));
//
// records
//
// check session records and (if existent) add
if ((session->record_indices_fps != NULL) & (session->record_data_fps != NULL)) {
mxSetField(mat_session, 0, "records", map_mef3_records(session->record_indices_fps, session->record_data_fps));
}
//
// time_series
//
// check if there are time series channels
if (session->number_of_time_series_channels > 0) {
//
// time_series_metadata
//
// create a metadata struct and assign it to the 'time_series_metadata' field
mxArray *time_series_metadata_struct = mxCreateStructMatrix(1, 1, METADATA_NUMFIELDS, METADATA_FIELDNAMES);
mxSetField(mat_session, 0, "time_series_metadata", time_series_metadata_struct);
// map metadata sections
mxSetField(time_series_metadata_struct, 0, "section_1", map_mef3_md1(session->time_series_metadata.section_1));
mxSetField(time_series_metadata_struct, 0, "section_2", map_mef3_tmd2(session->time_series_metadata.time_series_section_2));
mxSetField(time_series_metadata_struct, 0, "section_3", map_mef3_md3(session->time_series_metadata.section_3));
//
// time_series_channels
//
// create a channels struct
mxArray *channels_struct = mxCreateStructMatrix(1, session->number_of_time_series_channels, CHANNEL_NUMFIELDS, CHANNEL_FIELDNAMES);
// map the time-serie channels
for (i = 0; i < session->number_of_time_series_channels; ++i) {
channel = session->time_series_channels + i;
map_mef3_channel_tostruct(channel, map_indices_flag, channels_struct, i);
}
// assign the channels matlab-struct to the 'time_series_channels' field
mxSetField(mat_session, 0, "time_series_channels", channels_struct);
}
//
// video
//
// check if there are video channels
if (session->number_of_video_channels > 0) {
//
// video_metadata
//
// create a metadata struct and assign it to the 'video_metadata' field
mxArray *video_metadata_struct = mxCreateStructMatrix(1, 1, METADATA_NUMFIELDS, METADATA_FIELDNAMES);
mxSetField(mat_session, 0, "video_metadata", video_metadata_struct);
// map metadata sections
mxSetField(video_metadata_struct, 0, "section_1", map_mef3_md1(session->video_metadata.section_1));
mxSetField(video_metadata_struct, 0, "section_2", map_mef3_vmd2(session->video_metadata.video_section_2));
mxSetField(video_metadata_struct, 0, "section_3", map_mef3_md3(session->video_metadata.section_3));
//
// video_channels
//
// create a channels struct
mxArray *channels_struct = mxCreateStructMatrix(1, session->number_of_video_channels, CHANNEL_NUMFIELDS, CHANNEL_FIELDNAMES);
// map the video channels
for (i = 0; i < session->number_of_video_channels; ++i) {
channel = session->video_channels + i;
map_mef3_channel_tostruct(channel, map_indices_flag, channels_struct, i);
}
// assign the channels matlab-struct to the 'video_channels' field
mxSetField(mat_session, 0, "video_channels", channels_struct);
}
// return the output-struct
return mat_session;
}
/**
* Map a MEF section 1 metadata c-struct to a newly created matlab-struct
*
* @param md1 A pointer to the MEF section 1 metadata c-struct
* @return A pointer to the new matlab-struct
*/
mxArray *map_mef3_md1(METADATA_SECTION_1 *md1) {
mxArray *mat_md = mxCreateStructMatrix(1, 1, METADATA_SECTION_1_NUMFIELDS, METADATA_SECTION_1_FIELDNAMES);
mxSetField(mat_md, 0, "section_2_encryption", mxInt8ByValue(md1->section_2_encryption));
mxSetField(mat_md, 0, "section_3_encryption", mxInt8ByValue(md1->section_3_encryption));
mxSetField(mat_md, 0, "discretionary_region", mxUint8ArrayByValue(md1->discretionary_region, METADATA_SECTION_1_DISCRETIONARY_REGION_BYTES));
// return the struct
return mat_md;
}
/**
* Map a MEF section 2 time-series metadata c-struct to a newly created matlab-struct
*
* @param tmd2 A pointer to the MEF section 2 time-series metadata c-struct
* @return A pointer to the new matlab-struct
*/
mxArray *map_mef3_tmd2(TIME_SERIES_METADATA_SECTION_2 *tmd2) {
mxArray *mat_md = mxCreateStructMatrix(1, 1, TIME_SERIES_METADATA_SECTION_2_NUMFIELDS, TIME_SERIES_METADATA_SECTION_2_FIELDNAMES);
mxSetField(mat_md, 0, "channel_description", mxCreateString(tmd2->channel_description));
mxSetField(mat_md, 0, "session_description", mxCreateString(tmd2->session_description));
mxSetField(mat_md, 0, "recording_duration", mxInt64ByValue(tmd2->recording_duration));
mxSetField(mat_md, 0, "reference_description", mxCreateString(tmd2->reference_description));
mxSetField(mat_md, 0, "acquisition_channel_number", mxInt64ByValue(tmd2->acquisition_channel_number));
mxSetField(mat_md, 0, "sampling_frequency", mxDoubleByValue(tmd2->sampling_frequency));
mxSetField(mat_md, 0, "low_frequency_filter_setting", mxDoubleByValue(tmd2->low_frequency_filter_setting));
mxSetField(mat_md, 0, "high_frequency_filter_setting", mxDoubleByValue(tmd2->high_frequency_filter_setting));
mxSetField(mat_md, 0, "notch_filter_frequency_setting", mxDoubleByValue(tmd2->notch_filter_frequency_setting));
mxSetField(mat_md, 0, "AC_line_frequency", mxDoubleByValue(tmd2->AC_line_frequency));
mxSetField(mat_md, 0, "units_conversion_factor", mxDoubleByValue(tmd2->units_conversion_factor));
mxSetField(mat_md, 0, "units_description", mxCreateString(tmd2->units_description));
mxSetField(mat_md, 0, "maximum_native_sample_value", mxDoubleByValue(tmd2->maximum_native_sample_value));
mxSetField(mat_md, 0, "minimum_native_sample_value", mxDoubleByValue(tmd2->minimum_native_sample_value));
mxSetField(mat_md, 0, "start_sample", mxInt64ByValue(tmd2->start_sample));
mxSetField(mat_md, 0, "number_of_samples", mxInt64ByValue(tmd2->number_of_samples));
mxSetField(mat_md, 0, "number_of_blocks", mxInt64ByValue(tmd2->number_of_blocks));
mxSetField(mat_md, 0, "maximum_block_bytes", mxInt64ByValue(tmd2->maximum_block_bytes));
mxSetField(mat_md, 0, "maximum_block_samples", mxUint32ByValue(tmd2->maximum_block_samples));
mxSetField(mat_md, 0, "maximum_difference_bytes", mxUint32ByValue(tmd2->maximum_difference_bytes));
mxSetField(mat_md, 0, "block_interval", mxInt64ByValue(tmd2->block_interval));
mxSetField(mat_md, 0, "number_of_discontinuities", mxInt64ByValue(tmd2->number_of_discontinuities));
mxSetField(mat_md, 0, "maximum_contiguous_blocks", mxInt64ByValue(tmd2->maximum_contiguous_blocks));
mxSetField(mat_md, 0, "maximum_contiguous_block_bytes", mxInt64ByValue(tmd2->maximum_contiguous_block_bytes));
mxSetField(mat_md, 0, "maximum_contiguous_samples", mxInt64ByValue(tmd2->maximum_contiguous_samples));
mxSetField(mat_md, 0, "discretionary_region", mxUint8ArrayByValue(tmd2->discretionary_region, TIME_SERIES_METADATA_SECTION_2_DISCRETIONARY_REGION_BYTES));
// return the struct
return mat_md;
}
/**
* Map a MEF section 2 video metadata c-struct to a newly created matlab-struct
*
* @param vmd2 A pointer to the MEF section 2 video metadata c-struct
* @return A pointer to the new matlab-struct
*/
mxArray *map_mef3_vmd2(VIDEO_METADATA_SECTION_2 *vmd2) {
mxArray *mat_md = mxCreateStructMatrix(1, 1, VIDEO_METADATA_SECTION_2_NUMFIELDS, VIDEO_METADATA_SECTION_2_FIELDNAMES);
mxSetField(mat_md, 0, "channel_description", mxCreateString(vmd2->channel_description));
mxSetField(mat_md, 0, "session_description", mxCreateString(vmd2->session_description));
mxSetField(mat_md, 0, "recording_duration", mxInt64ByValue(vmd2->recording_duration));
mxSetField(mat_md, 0, "horizontal_resolution", mxInt64ByValue(vmd2->horizontal_resolution));
mxSetField(mat_md, 0, "vertical_resolution", mxInt64ByValue(vmd2->vertical_resolution));
mxSetField(mat_md, 0, "frame_rate", mxDoubleByValue(vmd2->frame_rate));
mxSetField(mat_md, 0, "number_of_clips", mxInt64ByValue(vmd2->number_of_clips));
mxSetField(mat_md, 0, "maximum_clip_bytes", mxInt64ByValue(vmd2->maximum_clip_bytes));
mxSetField(mat_md, 0, "video_format", mxCreateString(vmd2->video_format));
mxSetField(mat_md, 0, "video_file_CRC", mxUint32ByValue(vmd2->video_file_CRC));
mxSetField(mat_md, 0, "discretionary_region", mxUint8ArrayByValue(vmd2->discretionary_region, VIDEO_METADATA_SECTION_2_DISCRETIONARY_REGION_BYTES));
// return the struct
return mat_md;
}
/**
* Map a MEF section 3 metadata c-struct to a newly created matlab-struct
*
* @param md3 A pointer to the MEF section 3 metadata c-struct
* @return A pointer to the new matlab-struct
*/
mxArray *map_mef3_md3(METADATA_SECTION_3 *md3) {
mxArray *mat_md = mxCreateStructMatrix(1, 1, METADATA_SECTION_3_NUMFIELDS, METADATA_SECTION_3_FIELDNAMES);
mxSetField(mat_md, 0, "recording_time_offset", mxInt64ByValue(md3->recording_time_offset));
mxSetField(mat_md, 0, "DST_start_time", mxInt64ByValue(md3->DST_start_time));
mxSetField(mat_md, 0, "DST_end_time", mxInt64ByValue(md3->DST_end_time));
mxSetField(mat_md, 0, "GMT_offset", mxInt32ByValue(md3->GMT_offset));
mxSetField(mat_md, 0, "subject_name_1", mxCreateString(md3->subject_name_1));
mxSetField(mat_md, 0, "subject_name_2", mxCreateString(md3->subject_name_2));
mxSetField(mat_md, 0, "subject_ID", mxCreateString(md3->subject_ID));
mxSetField(mat_md, 0, "recording_location", mxCreateString(md3->recording_location));
mxSetField(mat_md, 0, "discretionary_region", mxUint8ArrayByValue(md3->discretionary_region, METADATA_SECTION_3_DISCRETIONARY_REGION_BYTES));
// return the struct
return mat_md;
}
mxArray *map_mef3_ti(TIME_SERIES_INDEX *ti, si8 number_of_entries) {
// create the a matlab 'time_series_index' struct
mxArray *mat_ti = mxCreateStructMatrix(1, number_of_entries, TIME_SERIES_INDEX_NUMFIELDS, TIME_SERIES_INDEX_FIELDNAMES);
// loop through the time-series indices
si8 i;
for (i = 0; i < number_of_entries; ++i) {
TIME_SERIES_INDEX *cur_ti = ti + i;
mxSetField(mat_ti, i, "file_offset", mxInt64ByValue(cur_ti->file_offset));
mxSetField(mat_ti, i, "start_time", mxInt64ByValue(cur_ti->start_time));
mxSetField(mat_ti, i, "start_sample", mxInt64ByValue(cur_ti->start_sample));
mxSetField(mat_ti, i, "number_of_samples", mxUint32ByValue(cur_ti->number_of_samples));
mxSetField(mat_ti, i, "block_bytes", mxUint32ByValue(cur_ti->block_bytes));
mxSetField(mat_ti, i, "maximum_sample_value", mxInt32ByValue(cur_ti->maximum_sample_value));
mxSetField(mat_ti, i, "minimum_sample_value", mxInt32ByValue(cur_ti->minimum_sample_value));
mxSetField(mat_ti, i, "RED_block_flags", mxUint8ByValue(cur_ti->RED_block_flags));
mxSetField(mat_ti, i, "RED_block_discretionary_region", mxUint8ArrayByValue(cur_ti->RED_block_discretionary_region, RED_BLOCK_DISCRETIONARY_REGION_BYTES));
}
// return the struct
return mat_ti;
}
mxArray *map_mef3_vi(VIDEO_INDEX *vi, si8 number_of_entries) {
// create the a matlab 'video_index' struct
mxArray *mat_vi = mxCreateStructMatrix(1, number_of_entries, VIDEO_INDEX_NUMFIELDS, VIDEO_INDEX_FIELDNAMES);
// loop through the video indices
si8 i;
for (i = 0; i < number_of_entries; ++i) {
VIDEO_INDEX *cur_vi = vi + i;
mxSetField(mat_vi, i, "start_time", mxInt64ByValue(cur_vi->start_time));
mxSetField(mat_vi, i, "end_time", mxInt64ByValue(cur_vi->end_time));
mxSetField(mat_vi, i, "start_frame", mxUint32ByValue(cur_vi->start_frame));
mxSetField(mat_vi, i, "end_frame", mxUint32ByValue(cur_vi->end_frame));
mxSetField(mat_vi, i, "file_offset", mxInt64ByValue(cur_vi->file_offset));
mxSetField(mat_vi, i, "clip_bytes", mxInt64ByValue(cur_vi->clip_bytes));
mxSetField(mat_vi, i, "discretionary_region", mxUint8ArrayByValue(cur_vi->discretionary_region, VIDEO_INDEX_DISCRETIONARY_REGION_BYTES));
}
// return the struct
return mat_vi;
}
/**
* Map the MEF records to a matlab-struct
*
* @param ri_fps
* @param rd_fps