private static IndirectCalorimetry ParseRow(string filepath, string line)
{
IndirectCalorimetry exp = new IndirectCalorimetry(filepath);
// The lines in experiment file is separated by TABs. Split the line into tokens
string[] values = line.Split(',');
for (int i = 0; i < values.Length; i++)
{
string value = values[i].Trim();
if (value.StartsWith("\""))
{
value = value.Substring(1);
}
if (value.EndsWith("\""))
{
value = value.Substring(0, value.Length - 1);
}
exp.Add(i, value);
}
return(exp);
}
/// <summary>
/// A static method that parses the specified file and returns a list of IndirectCalorimetry instances
/// </summary>
/// <param name="args">
/// The experiment file path.
/// </param>
/// <returns>
/// Returns list of experiments that are contained in the specified file.
/// </returns>
public static List <IndirectCalorimetry> Parse(string filepath)
{
bool parsingHeaderCompleted = false;
// Initialize an empty list
List <IndirectCalorimetry> list = new List <IndirectCalorimetry>();
// Open and read the file line by line until we reach the end of the file.
using (StreamReader reader = File.OpenText(filepath))
{
while (!reader.EndOfStream)
{
string line = reader.ReadLine();
// If the line starts with "DateTime", we know that we have reached the header line
if (
line.StartsWith($"\"{IndirectCalorimetry.DateTime}\"") ||
line.StartsWith(IndirectCalorimetry.DateTime))
{
ParseHeader(filepath, line);
parsingHeaderCompleted = true;
continue;
}
// Only after the header is processed, we know that the rest of the file
// contains the experiment records. Ignore the line if we have not yet
// processed the header.
if (parsingHeaderCompleted)
{
IndirectCalorimetry exp = ParseRow(filepath, line);
list.Add(exp);
}
}
}
return(list);
}
private static string[] ParseHeader(string filepath, string line)
{
// The lines in experiment file is separated by Comma. Split the line into tokens
string[] columns = line.Split(',');
for (int i = 0; i < columns.Length; i++)
{
string column = columns[i].Trim();
if (column.StartsWith("\""))
{
column = column.Substring(1);
}
if (column.EndsWith("\""))
{
column = column.Substring(0, column.Length - 1);
}
// Ensure that the column name is valid for this index
IndirectCalorimetry.EnsurePropertyNameIsValid(i, column);
}
return(columns);
}
// Main driver method
static void Main(string[] args)
{
int lightsOnTime = 6; // Read the lights on time from the args later.
int lightsOffTime = 14;
string filepath = "/Users/rahul/Desktop/Schwartz_Project/2020.11.13_HFHS_Final-Calorimetry-1hbin_formatted.csv";
// Create a FileInfo object using the filepath
FileInfo fileInfo = new FileInfo(filepath);
//Parse the file and get list of IndirectCalorimetry ojects
List <IndirectCalorimetry> list = IndirectCalorimetryParser.Parse(fileInfo.FullName);
List <IndirectCalorimetry> updatedList = new List <IndirectCalorimetry>();
foreach (IndirectCalorimetry item in list)
{
string animalName = item.Get(IndirectCalorimetry.Animal);
if (string.IsNullOrWhiteSpace(animalName) || animalName.Equals("NA", StringComparison.OrdinalIgnoreCase))
{
// Invalid animal. Ignore this item.
continue;
}
string vo2_m = item.Get(IndirectCalorimetry.VO2_M);
if (string.IsNullOrWhiteSpace(vo2_m) || vo2_m.Equals("NA", StringComparison.OrdinalIgnoreCase))
{
continue;
}
item.AnimalName = animalName;
if (DateTime.TryParseExact(item.Get(IndirectCalorimetry.DateTime),
"dd/MM/yyyy HH:mm", CultureInfo.InvariantCulture, DateTimeStyles.None, out DateTime dt))
{
DateTime newDt = dt.Subtract(TimeSpan.FromHours(lightsOnTime));
item.ZTTime = newDt;
updatedList.Add(item);
}
}
Dictionary <string, List <IndirectCalorimetry> > itemsGroupedByAnimal = updatedList
.GroupBy(o => o.AnimalName)
.ToDictionary(g => g.Key, g => g.ToList());
Dictionary <string, List <Result> > results = new Dictionary <string, List <Result> >();
foreach (var animal in itemsGroupedByAnimal.Keys)
{
List <IndirectCalorimetry> items = itemsGroupedByAnimal[animal];
int day = 0;
DateTime?previousMaxDateTime = null;
while (true)
{
Result result = new Result()
{
Animal = animal
};
int i = 0;
for (; i < 24; i++)
{
int index = i + day * 24;
if (index >= items.Count)
{
break;
}
IndirectCalorimetry item = items[index];
float v02_m = float.Parse(item.Get(IndirectCalorimetry.VO2_M));
if (i == 0)
{
result.StartTime = item.ZTTime;
result.MaxVO2_M = v02_m;
result.MaxOccurredAtTime = item.ZTTime;
result.MinVO2_M = v02_m;
result.MinOccurredAtTime = item.ZTTime;
}
else
{
result.EndTime = item.ZTTime;
if (result.MaxVO2_M < v02_m)
{
result.MaxVO2_M = v02_m;
result.MaxOccurredAtTime = item.ZTTime;
}
if (result.MinVO2_M > v02_m)
{
result.MinVO2_M = v02_m;
result.MinOccurredAtTime = item.ZTTime;
}
}
}
DateTime tempDate = new DateTime(
result.MaxOccurredAtTime.Year,
result.MaxOccurredAtTime.Month,
result.MaxOccurredAtTime.Day,
lightsOffTime,
0,
0);
TimeSpan timeDiff = result.MaxOccurredAtTime - tempDate;
result.LatencyToPeakInMin = timeDiff.TotalMinutes;
result.PeakToPeakAmplitude = result.MaxVO2_M - result.MinVO2_M;
if (day == 0)
{
previousMaxDateTime = result.MaxOccurredAtTime;
}
else
{
result.PeriodInMin = (result.MaxOccurredAtTime - previousMaxDateTime.Value).TotalMinutes;
previousMaxDateTime = result.MaxOccurredAtTime;
}
List <Result> r;
if (!results.TryGetValue(animal, out r))
{
r = new List <Result>();
results.Add(animal, r);
}
r.Add(result);
if (i < 24)
{
break;
}
day++;
}
}
string resultsFileName = $"{fileInfo.Directory.FullName}/{Path.GetFileNameWithoutExtension(fileInfo.FullName)}_Results.csv";
using (var stream = new StreamWriter(
File.Open(resultsFileName,
FileMode.Create,
FileAccess.ReadWrite,
FileShare.ReadWrite)))
{
stream.Write("Animal");
stream.Write(",");
stream.Write("StartTime");
stream.Write(",");
stream.Write("EndTime");
stream.Write(",");
stream.Write("MaxOccurredAtTime");
stream.Write(",");
stream.Write("MaxVO2_M");
stream.Write(",");
stream.Write("MinOccurredAtTime");
stream.Write(",");
stream.Write("MinVO2_M");
stream.Write(",");
stream.Write("LatencyToPeakInMin");
stream.Write(",");
stream.Write("PeakToPeakAmplitude");
stream.Write(",");
stream.Write("PeriodInMin");
stream.WriteLine();
var animalNames = results.Keys.ToList();
animalNames.Sort();
foreach (var animalName in animalNames)
{
var resultItems = results[animalName];
foreach (var item in resultItems)
{
stream.Write(item.Animal);
stream.Write(",");
stream.Write(item.StartTime);
stream.Write(",");
stream.Write(item.EndTime);
stream.Write(",");
stream.Write(item.MaxOccurredAtTime.ToString("G"));
stream.Write(",");
stream.Write(item.MaxVO2_M);
stream.Write(",");
stream.Write(item.MinOccurredAtTime.ToString("G"));
stream.Write(",");
stream.Write(item.MinVO2_M);
stream.Write(",");
stream.Write(item.LatencyToPeakInMin);
stream.Write(",");
stream.Write(item.PeakToPeakAmplitude);
stream.Write(",");
stream.Write(item.PeriodInMin);
stream.WriteLine();
}
}
}
Console.WriteLine();
}
