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EDFparser.go
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package main
import (
"bytes"
"encoding/binary"
"encoding/csv"
"encoding/json"
"flag"
"log"
"os"
"strconv"
)
type HeaderRecord struct {
PatientID string
RecordID string
StartDate string
StartTime string
NumOfBytes int `json:"-"`
NumOfDR int `json:"Records"` // Number of data records
DurationOfDR int `json:"Duration"` // Duration of data record, in seconds
NumOfSignals int `json:"Signals"` // Number of signals in data record
NumOfSamples []int `json:"Samples"` // Number of samples in each data record
Label []string `json:"Labels"` // Label of each signal
TrType []string `json:"Transducer"` // Transducer type
PhDim []string // Physical dimension
PhMin []string // Physical minimum
PhMax []string // Physical maximum
DigMin []string // Digital minimum
DigMax []string // Digital maximum
Prefiltering []string
}
// Reads header record from source file and write it into the structure
func (header *HeaderRecord) ReadHeader(source *os.File) {
if !(bytes.Equal(bytes.TrimSpace(readBytes(source, 8, 0, 0)), []byte{48})) {
log.Fatal("File format is not valid.", readBytes(source, 8, 0, 0))
}
header.PatientID = string(bytes.TrimSpace(readBytes(source, 80, 8, 0)))
header.RecordID = string(bytes.TrimSpace(readBytes(source, 80, 0, 1)))
header.StartDate = string(bytes.TrimSpace(readBytes(source, 8, 0, 1)))
header.StartTime = string(bytes.TrimSpace(readBytes(source, 8, 0, 1)))
header.NumOfBytes, _ = strconv.Atoi(string(bytes.TrimSpace(readBytes(source, 8, 0, 1))))
header.NumOfDR, _ = strconv.Atoi(string(bytes.TrimSpace(readBytes(source, 8, 44, 1))))
header.DurationOfDR, _ = strconv.Atoi(string(bytes.TrimSpace(readBytes(source, 8, 0, 1))))
header.NumOfSignals, _ = strconv.Atoi(string(bytes.TrimSpace(readBytes(source, 4, 0, 1))))
for ns := 0; ns < header.NumOfSignals; ns++ {
header.Label = append(header.Label, string(bytes.TrimSpace(readBytes(source, 16, int64(256+ns*16), 0))))
header.TrType = append(header.TrType, string(bytes.TrimSpace(readBytes(source, 80, int64(256+header.NumOfSignals*16+ns*80), 0))))
header.PhDim = append(header.PhDim, string(bytes.TrimSpace(readBytes(source, 8, int64(256+header.NumOfSignals*96+ns*8), 0))))
header.PhMin = append(header.PhMin, string(bytes.TrimSpace(readBytes(source, 8, int64(256+header.NumOfSignals*104+ns*8), 0))))
header.PhMax = append(header.PhMax, string(bytes.TrimSpace(readBytes(source, 8, int64(256+header.NumOfSignals*112+ns*8), 0))))
header.DigMin = append(header.DigMin, string(bytes.TrimSpace(readBytes(source, 8, int64(256+header.NumOfSignals*120+ns*8), 0))))
header.DigMax = append(header.DigMax, string(bytes.TrimSpace(readBytes(source, 8, int64(256+header.NumOfSignals*128+ns*8), 0))))
header.Prefiltering = append(header.Prefiltering, string(bytes.TrimSpace(readBytes(source, 80, int64(256+header.NumOfSignals*136+ns*80), 0))))
tmp, _ := strconv.Atoi(string(bytes.TrimSpace(readBytes(source, 8, int64(256+header.NumOfSignals*216+ns*8), 0))))
header.NumOfSamples = append(header.NumOfSamples, tmp)
}
}
// Converts header structure to .json file
func (header *HeaderRecord) HeaderToJSON() {
jsonHeader, _ := json.MarshalIndent(header, "", " ")
result, err := os.Create("header_" + header.StartDate + "_" + header.StartTime + ".json")
if err != nil {
log.Fatal("Creating JSON file failed: ", err)
}
defer result.Close()
result.Write(jsonHeader)
}
// Converts record data from source file to .csv file
func (header *HeaderRecord) DataToCSV(source *os.File, showLabels *bool) {
if _, err := source.Seek(int64(header.NumOfBytes), 0); err != nil {
log.Fatal("Seeking failed: ", err)
}
// String array of samples. Row - signals, column - number of sample
record := make([][]string, header.NumOfSignals)
for row := range record {
if *showLabels == true {
record[row] = make([]string, header.NumOfDR*header.NumOfSamples[row]+1)
record[row][0] = header.Label[row]
} else {
record[row] = make([]string, header.NumOfDR*header.NumOfSamples[row])
}
}
// Filling array
var tmp int16
for DR := 0; DR < header.NumOfDR; DR++ {
for row := range record {
if *showLabels == true {
for col := header.NumOfSamples[row]*DR + 1; col < (DR+1)*header.NumOfSamples[row]; col++ {
if err := binary.Read(bytes.NewReader(readBytes(source, 2, 0, 1)), binary.LittleEndian, &tmp); err != nil {
log.Fatal("Converting bytes to int16 failed: ", err)
}
record[row][col] = strconv.Itoa(int(tmp))
}
} else {
for col := header.NumOfSamples[row] * DR; col < (DR+1)*header.NumOfSamples[row]; col++ {
if err := binary.Read(bytes.NewReader(readBytes(source, 2, 0, 1)), binary.LittleEndian, &tmp); err != nil {
log.Fatal("Converting bytes to int16 failed: ", err)
}
record[row][col] = strconv.Itoa(int(tmp))
}
}
}
}
result, err := os.Create("data_" + header.StartDate + "_" + header.StartTime + ".csv")
if err != nil {
log.Fatal("Creating CSV file failed: ", err)
}
defer result.Close()
w := csv.NewWriter(result)
if err = w.WriteAll(record); err != nil {
log.Fatal("Error writing records to csv:", err)
}
}
//Read numToRead bytes from source file with some offset (More about Seek func: https://golang.org/pkg/os/#File.Seek)
func readBytes(source *os.File, numToRead int, seekOffset int64, seekWhence int) []byte {
if _, err := source.Seek(seekOffset, seekWhence); err != nil {
log.Fatal("Seeking failed: ", err)
}
bytesSlice := make([]byte, numToRead)
if _, err := source.Read(bytesSlice); err != nil {
log.Fatal("Reading from file failed: ", err)
}
return bytesSlice
}
func main() {
fPath := flag.String("f", "source.edf", "Path to source edf/edf+ file")
whatToRecord := flag.Int("r", 2, "Save only header record - 0, only data record - 1, both - 2")
showLabels := flag.Bool("l", true, "Data record without labels - false")
flag.Parse()
source, err := os.Open(*fPath)
if err != nil {
log.Fatal("Opening file failed: ", err)
}
defer source.Close()
header := HeaderRecord{}
header.ReadHeader(source)
if *whatToRecord == 0 || *whatToRecord == 2 {
header.HeaderToJSON()
}
if *whatToRecord == 1 || *whatToRecord == 2 {
header.DataToCSV(source, showLabels)
}
}