private static TimePoint AnnotateToTimePoint(string str)
{
if (str == "" || str == "YMDHMS")
{
return(null);
}
Regex pointRegex = new Regex(@"(?<year>[0-9]*)Y(?<month>[0-9]*)M(?<day>[0-9]*)D(?<hour>[0-9]*)H(?<minute>[0-9]*)M(?<second>[0-9]*)S");
Match match = pointRegex.Match(str);
if (match == null)
{
return(null);
}
TimePoint ret = new TimePoint();
string[] names = { "year", "month", "day", "hour", "minute", "second" };
for (int i = 0; i < names.Length; i++)
{
string val = match.Groups[names[i]].Value;
if (val != "")
{
switch (i)
{
case 0: ret.setYear(Convert.ToInt32(val)); break;
case 1: ret.setMonth(Convert.ToInt32(val)); break;
case 2: ret.setDay(Convert.ToInt32(val)); break;
case 3: ret.setHour(Convert.ToInt32(val)); break;
case 4: ret.setMinute(Convert.ToInt32(val)); break;
case 5: ret.setSecond(Convert.ToInt32(val)); break;
}
}
}
return(ret);
}
public virtual void Load()
{
string[] lines;
Console.WriteLine("Loading " + Filename + " ...");
string[] wikifile = File.ReadAllLines(@".\" + Filename + ".wiki");
//Load words
lines = File.ReadAllLines(filename + raw_suffix);
words = new List <List <Word> >();
texts = new List <string>();
for (int i = 0; i < lines.Length; i++)
{
texts.Add(lines[i]);
string[] terms = lines[i].Split(new char[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
List <Word> lst = new List <Word>();
for (int j = 0; j < terms.Length; j++)
{
if (terms[j] != ";" && terms[j].Contains(";"))
{
terms[j].Replace(";", "");
}
if (terms[j] != ":" && terms[j].Contains(":"))
{
terms[j].Replace(":", "");
}
Word word = new Word(terms[j], new TimeExtractor.units.TextIdentifier(Filename, i + 1, j));
word.Pos = j;
for (int c = 0; c < wikifile.Count(); c++)
{
if (wikifile[c].Substring(0, wikifile[c].IndexOf("|")).Contains(terms[j].ToLower()) && wikifile[c].Length > (wikifile[c].LastIndexOf('|') + 1))
{
word.Wiki = (wikifile[c].Substring(wikifile[c].LastIndexOf('|') + 1)).Split(new char[] { ' ', '_' }, StringSplitOptions.RemoveEmptyEntries);
}
}
lst.Add(word);
}
words.Add(lst);
}
//Load time entities (including normalization)
entities = new List <Entity>();
if (File.Exists(filename + time_con_suffix))
{
lines = File.ReadAllLines(filename + time_con_suffix);
foreach (string line in lines)
{
Entity entity = EntityUtil.I2b2formToEntity(line, filename);
entity.Fr = this;
entities.Add(entity);
}
}
//Load PMT entities
if (File.Exists(filename + event_con_suffix))
{
lines = File.ReadAllLines(filename + event_con_suffix);
List <Entity> e = new List <Entity>();
foreach (string line in lines)
{
Entity entity = EntityUtil.I2b2formToEntity(line, filename);
entity.Fr = this;
entities.Add(entity);
}
}
//remove duplicate entities
RemoveDuplicateEntities();
//Load TLinks
if (File.Exists(filename + tlink_suffix))
{
lines = File.ReadAllLines(filename + tlink_suffix);
links = new List <EntityLink>();
foreach (string line in lines)
{
EntityLink link = EntityUtil.I2b2formToTLink(line, filename, this);
if (link != null)
{
links.Add(link);
}
}
}
//Load Section entities
if (File.Exists(filename + section_entity_suffix))
{
ad_tp = new TimePoint();
dc_tp = new TimePoint();
lines = File.ReadAllLines(filename + section_entity_suffix);
List <Entity> e = new List <Entity>();
int i = 0;
foreach (string line in lines)
{
Entity entity = EntityUtil.I2b2formToEntity(line, filename);
entity.Fr = this;
entity.is_section = true;
entities.Add(entity);
if (i == 0)
{
ad_tp = entity.getFirstTimePoint();
}
if (i == 1)
{
dc_tp = entity.getFirstTimePoint();
}
i++;
}
}
else
{
//very naive way to extract the admission date and discharge date
ad_tp = new TimePoint();
dc_tp = new TimePoint();
int adline = -1;
int dcline = -1;
Regex regex = new Regex(@"^(?<d1>[0-9]+)(\\|\/|\-)(?<d2>[0-9]+)(\\|\/|\-)(?<d3>[0-9]+)$");
Regex regex2 = new Regex(@"^(?<d1>[0-9]{4})(?<d2>[0-9]{2})(?<d3>[0-9]{2})$");
for (int i = 0; i < words.Count; i++)
{
if (i > 0 && (texts[i - 1].ToLower().Replace(" ", "") == "admissiondate:" ||
texts[i - 1].ToLower().Replace(" ", "") == "registrationdate:" ||
texts[i - 1].ToLower().Replace(" ", "") == "dischargedate:"))
{
for (int j = 0; j < words[i].Count; j++)
{
if (j > 0)
{
break;
}
string s = words[i][j].WordText;
if (regex.IsMatch(s))
{
Match match = regex.Match(s);
int d1 = Convert.ToInt32(match.Groups["d1"].Value);
int d2 = Convert.ToInt32(match.Groups["d2"].Value);
int d3 = Convert.ToInt32(match.Groups["d3"].Value);
if (texts[i - 1].ToLower().Replace(" ", "") == "admissiondate:" ||
texts[i - 1].ToLower().Replace(" ", "") == "registrationdate:")
{
ad_tp = get_tp_from_3digit(d1, d2, d3);
adline = i;
}
else
{
dc_tp = get_tp_from_3digit(d1, d2, d3);
dcline = i;
}
}
if (regex2.IsMatch(s))
{
Match match = regex2.Match(s);
int d1 = Convert.ToInt32(match.Groups["d1"].Value);
int d2 = Convert.ToInt32(match.Groups["d2"].Value);
int d3 = Convert.ToInt32(match.Groups["d3"].Value);
if (texts[i - 1].ToLower().Replace(" ", "") == "admissiondate:" ||
texts[i - 1].ToLower().Replace(" ", "") == "registrationdate:")
{
ad_tp = get_tp_from_3digit(d1, d2, d3);
adline = i;
}
else
{
dc_tp = get_tp_from_3digit(d1, d2, d3);
dcline = i;
}
}
}
}
}
//Store the section time into the section time file
List <string> seccons = new List <string>();
if (adline != -1)
{
seccons.Add("SECTIME=\"" + words[adline][0].WordText + "\" " + (adline + 1) + ":0 " + (adline + 1) + ":0||type=\"ADMISSION\"||dvalue=\"" + append_zero(ad_tp.getYear(), 4) + "-" + append_zero(ad_tp.getMonth(), 2) + "-" + append_zero(ad_tp.getDay(), 2) + "\"");
}
if (dcline != -1)
{
seccons.Add("SECTIME=\"" + words[dcline][0].WordText + "\" " + (dcline + 1) + ":0 " + (dcline + 1) + ":0||type=\"DISCHARGE\"||dvalue=\"" + append_zero(dc_tp.getYear(), 4) + "-" + append_zero(dc_tp.getMonth(), 2) + "-" + append_zero(dc_tp.getDay(), 2) + "\"");
}
File.WriteAllLines(filename + section_entity_suffix, seccons.ToArray());
}
//Load Sections
sections = new List <string>();
if (File.Exists(filename + section_suffix))
{
lines = File.ReadAllLines(filename + section_suffix);
foreach (string line in lines)
{
int t = line.LastIndexOf("\t");
sections.Add(line.Substring(t + 1));
}
}
else
{
for (int i = 0; i < texts.Count; i++)
{
sections.Add(texts[i]);
}
}
//Load and generate "virtual" entities (special entities)
OpEntity = new TimeEntity();
AdEntity = new TimeEntity();
DcEntity = new TimeEntity();
TrEntity = new TimeEntity();
TimePoint admissionTP = new TimePoint();
TimePoint dischargeTP = new TimePoint();
if (File.Exists(Filename + keytp_suffix))
{
string text = File.ReadAllText(Filename + keytp_suffix);
//text = text.Replace(" ", "");
//text = text.Replace("\t", "");
Regex adRegex = new Regex(@"admission=(?<year>[0-9]+)\s(?<month>[0-9]+)\s(?<day>[0-9]+)");
if (adRegex.IsMatch(text))
{
Match match = adRegex.Match(text);
admissionTP.setYear(Convert.ToInt32(match.Groups["year"].Value));
admissionTP.setMonth(Convert.ToInt32(match.Groups["month"].Value));
admissionTP.setDay(Convert.ToInt32(match.Groups["day"].Value));
}
Regex dcRegex = new Regex(@"discharge=(?<year>[0-9]+)\s(?<month>[0-9]+)\s(?<day>[0-9]+)");
if (dcRegex.IsMatch(text))
{
Match match = dcRegex.Match(text);
dischargeTP.setYear(Convert.ToInt32(match.Groups["year"].Value));
dischargeTP.setMonth(Convert.ToInt32(match.Groups["month"].Value));
dischargeTP.setDay(Convert.ToInt32(match.Groups["day"].Value));
}
}
AdEntity.addTimePoint(admissionTP);
DcEntity.addTimePoint(dischargeTP);
}
