public static void csvWritePhase(DataStruc Result, StreamWriter myWriterPhase, string filename)
{
for (int i = 0; i < Result.key.Count(); i++)
{
myWriterPhase.Write(
Result.ID + "," +
Result.course + "," +
Result.plan + "," +
Result.protocol + "," +
Result.PD + "," +
Result.plannedOn + "," +
Result.SSiD + "," +
Result.fourD + "," +
Result.phase[i] + "," +
Result.GTVPhVol[i] + "," +
Result.xGTVph[i] / 10 + "," +
Result.yGTVph[i] / 10 + "," +
Result.zGTVph[i] / 10 + "," +
Result.xGTVph2Lung[i] / 10 + "," +
Result.yGTVph2Lung[i] / 10 + "," +
Result.zGTVph2Lung[i] / 10 + "," +
Result.xGTVph2PTV[i] / 10 + "," +
Result.yGTVph2PTV[i] / 10 + "," +
Result.zGTVph2PTV[i] / 10 + "," +
Result.PTVVol + "," +
Result.LungVol + "," +
Result.key[i]);
myWriterPhase.Write("\n");
}
}
public static void csvWritePlan(DataStruc Result, StreamWriter myWriterPlan, string filename)
{
//Summarises the 4D information per plan into 1 line.
string output =
Result.planKey + "," +
Result.ID + "," +
Result.course + "," +
Result.Site + "," +
Result.plan + "," +
Result.protocol + "," +
Result.PD + "," +
Result.plannedOn + "," +
Result.SSiD + "," +
Result.PTVVol + "," +
Result.LungVol + "," +
Result.fourD;
//Only includes 4D data if it was found.
if (Result.GTVPhVol.Count() != 0)
{
//Determines laterality from tumour co-ordinates.
string Laterality = "Unknown";
if (Result.xGTVph2Lung.Average() < -20 && Result.zGTVph2Lung.Average() < 0)
{
Laterality = "Left Upper";
}
else if (Result.xGTVph2Lung.Average() < -20 && Result.zGTVph2Lung.Average() >= 0)
{
Laterality = "Left Lower";
}
else if (Result.xGTVph2Lung.Average() > 20 && Result.zGTVph2Lung.Average() < 0)
{
Laterality = "Right Upper";
}
else if (Result.xGTVph2Lung.Average() > 20 && Result.zGTVph2Lung.Average() >= 0)
{
Laterality = "Right Lower";
}
else
{
if (Result.zGTVph2Lung.Average() < 0)
{
Laterality = "Central Upper";
}
else if (Result.zGTVph2Lung.Average() > 0)
{
Laterality = "Central Lower";
}
}
output = output + "," +
Result.GTVPhVol.Average() + "," +
Result.xGTVph.Max() / 10 + "," +
Result.yGTVph.Max() / 10 + "," +
Result.zGTVph.Max() / 10 + "," +
Result.xGTVph2Lung.Average() / 10 + "," +
Result.yGTVph2Lung.Average() / 10 + "," +
Result.zGTVph2Lung.Average() / 10 + "," +
Result.xGTVph2PTV.Average() / 10 + "," +
Result.yGTVph2PTV.Average() / 10 + "," +
Result.zGTVph2PTV.Average() / 10 + "," +
Laterality;
}
//Outputs string.
myWriterPlan.Write(output);
myWriterPlan.Write("\n");
}
static void Execute(Application app)
{
//Intro
Console.WriteLine("Standalone script to pull imaging data from 4DCT planning scan structure sets");
//Open input text file for list of ID numbers.
StreamReader myReader = new StreamReader(getFilePath(@"\\oncology-is\VA_DATA$\physicists\ESAPI Scripting\Patient lists"));
System.Collections.ArrayList IDList = new System.Collections.ArrayList(); //empty array
//Reads in ID number and assigns to array.
string IDNo = myReader.ReadLine();
while (IDNo != null)
{
IDList.Add(IDNo);
IDNo = myReader.ReadLine();
}
//set output file location
string outputDir = @"\\oncology-is\VA_DATA$\physicists\ESAPI Scripting\Reports";
string filename = string.Format(@"{0}\LungMotionPhase_{1}.csv",
outputDir, DateTime.Now.ToString("dd_MM_yyyy"));
Console.WriteLine("Output location for Phase info:");
Console.WriteLine(filename);
string filename2 = string.Format(@"{0}\LungMotionPlan_{1}.csv",
outputDir, DateTime.Now.ToString("dd_MM_yyyy"));
Console.WriteLine("Output location for Plan info:");
Console.WriteLine(filename2);
//Creates file for phase information
System.IO.StreamWriter myWriterPhase = new StreamWriter(filename); //creates empty .csv
myWriterPhase.AutoFlush = true;
//Writes header for csv for phases
myWriterPhase.Write("ID, Course, Plan, Protocol, Dose, Plan creation, Structure Set, 4D?, Phase, GTVvolume (cc)," +
"x-lat (cm),y-vrt (cm),z-lng (cm), " +
"x-lat2Lung (cm),y-vrt2Lung (cm),z-lng2Lung (cm), " +
"x-lat2PTV (cm),y-vrt2PTV (cm),z-lng2PTV (cm), " +
"PTV Vol(cc), lungVol(cc), key");
myWriterPhase.Write("\n");
//Creates file for summary information for each plan.
System.IO.StreamWriter myWriterPlan = new StreamWriter(filename2); //creates empty .csv
myWriterPhase.AutoFlush = true;
//Writes header for csv for plan.
myWriterPlan.Write("Key, ID, Course, Site, Plan, Protocol, Dose, Plan creation, Structure Set, " +
"PTV Vol (cc), lungVol (cc), 4D?, GTV mean vol (cc), " +
"x-lat range (cm),y-vrt range (cm), z-lng range (cm), " +
"x-lat2Lung (cm), y-vrt2Lung (cm), z-lng2Lung (cm), " +
"x-lat2PTV (cm), y-vrt2PTV (cm), z-lng2PTV (cm), Laterality,");
myWriterPlan.Write("\n");
double Count = 0; //counts patients.
foreach (string id in IDList) //runs through list of IDs
{
Count++;
Console.WriteLine("Processing patient {0} of {1}, id: {2}", Count, IDList.Count, id);
Patient pat = app.OpenPatientById(id);
foreach (var course in pat.Courses) //Runs through all courses
{
//filters for relevant course
if (course.Id.ToUpper().Contains("QA") ||
course.Id.ToUpper().Contains("QC") ||
course.Id.ToUpper().Contains("XIO") ||
!course.Id.ToUpper().Contains("LUNG"))
{
//skips irrelevant courses for loop
continue;
}
foreach (var ps in course.PlanSetups) //Runs through all plans
{
// Checks for arcs.
int arcs = 0;
for (int Beams = 0; Beams < ps.Beams.Count(); Beams++)
{
if ((ps.Beams.ElementAt(Beams).IsSetupField))
{
continue;
}
if (ps.Beams.ElementAt(Beams).Technique.Id.ToUpper().Contains("ARC"))
{
arcs++;
} //adds to index if criteria are met.
}
string Approval = ps.ApprovalStatus.ToString();
//Filters plans
if (!(ps.IsDoseValid) // skip plans with no dose
// || Approval.Contains("Retired") // skips retired
|| Approval.Contains("Rejected") // skips rejected
// || !(Approval.Contains("TreatmentApproved")) // only includes treatment approved plans
|| ps.Id.ToUpper().Contains("QA") || // skip QA plans
ps.Id.ToUpper().Contains("SCRIPT") || // skip plans with script in ID
ps.Id.ToUpper().Contains("#")
//|| !ps.Id.ToUpper().Contains("SABR")
|| ps.StructureSet == null || // no structure set
arcs == 0 // no arcs
)
{
continue;
}
if (ps.IsTreated)
{
//placed in a try catch loop to catch errors but not end code.
try
{
//Passes data to method to work out results.
DataStruc tempData = processPlan(pat, ps);
//Writes phases information to csv
csvWritePhase(tempData, myWriterPhase, filename);
//Writes plan information to csv
csvWritePlan(tempData, myWriterPlan, filename2);
}
catch (Exception e)
{
//outputs error to console.
Console.Error.WriteLine(e.ToString());
}
}
}
}
app.ClosePatient();
}
myWriterPhase.Close();
myWriterPlan.Close();
Console.WriteLine("All patients processed. Hit Return to open results and exit console");
Console.ReadLine();
System.Diagnostics.Process.Start(filename); //opens results spreadsheet
System.Diagnostics.Process.Start(filename2); //opens results spreadsheet
}
public static DataStruc processPlan(Patient pat, PlanSetup ps)
{
//Sets the image FOR which is unique to images acquired at the same time.
string FOR = ps.StructureSet.Image.FOR;
StructureSet mainSS = ps.StructureSet;
//Makes place holder for results.
DataStruc Result = new DataStruc();
//Produces generic plan results.
Result.ID = pat.Id;
Result.SSiD = mainSS.Id;
Result.PD = ps.TotalDose.Dose;
Result.protocol = ps.ProtocolID;
Result.plan = ps.Id;
Result.plannedOn = ps.HistoryDateTime;
Result.Site = SiteFind(ps.ProtocolID, ps.Course.Id);
Result.course = ps.Course.Id;
Result.planKey = ps.UID + ps.Id;
Result.fourD = "No";
//Pre-creates list to assign phase data to.
Result.GTVPhVol = new List <double>();
Result.phase = new List <string>();
Result.xGTVph = new List <double>();
Result.yGTVph = new List <double>();
Result.zGTVph = new List <double>();
Result.xGTVph2Lung = new List <double>();
Result.yGTVph2Lung = new List <double>();
Result.zGTVph2Lung = new List <double>();
Result.xGTVph2PTV = new List <double>();
Result.yGTVph2PTV = new List <double>();
Result.zGTVph2PTV = new List <double>();
Result.key = new List <string>();
//Creates relevant structures using linq.
Structure Lungs = null;
Lungs = mainSS.Structures.Where(x => x.Id.ToUpper() == "LUNGS").FirstOrDefault();
if (Lungs == null)
{
Lungs = mainSS.Structures.Where(x => x.Id.ToUpper() == "WHOLE LUNG").FirstOrDefault();
}
if (Lungs == null)
{
Lungs = mainSS.Structures.Where(x => x.Id.ToUpper() == "LUNGS-GTV").FirstOrDefault();
}
if (Lungs != null)
{
Result.LungVol = Lungs.Volume;
}
else
{
Result.LungVol = 0;
}
Structure PTV = null;
PTV = mainSS.Structures.Where(x => x.Id.ToUpper() == "PTV").FirstOrDefault();
if (PTV == null)
{
PTV = mainSS.Structures.Where(x => x.Id.ToUpper().Contains("PTV")).FirstOrDefault();
}
Result.PTVVol = PTV.Volume;
//Makes a collection of 4DCT phases, not including CBCT.
var SSColl = pat.StructureSets.Where(x => x.Image.FOR == FOR &&
!x.Id.ToUpper().Contains("CBCT") &&
!x.Id.ToUpper().Contains("INTERPLAY") &&
x.Id.ToUpper().Contains("CT"));
if (SSColl != null)
{
//Cycle through phases to find CoM and volumes.
foreach (var SS in SSColl)
{
//Cycles through structures in structureset.
foreach (var S in SS.Structures)
{
if (S.Id.ToUpper().Equals("GTV PH") && S.IsEmpty != true) // finds the centre of the GTV
{
//Commit phase ranges to list.
Result.xGTVph.Add(S.CenterPoint.x);
Result.yGTVph.Add(S.CenterPoint.y);
Result.zGTVph.Add(S.CenterPoint.z);
Result.GTVPhVol.Add(S.Volume);
Result.phase.Add(SS.Id);
//Adds to primary key if phases are present.
Result.key.Add(ps.UID + SS.Id);
//Determines offset between PTV and phase. +1000 removes the impact of sign changes.
Result.xGTVph2PTV.Add((1000 + PTV.CenterPoint.x) - (1000 + S.CenterPoint.x));
Result.yGTVph2PTV.Add((1000 + PTV.CenterPoint.y) - (1000 + S.CenterPoint.y));
Result.zGTVph2PTV.Add((1000 + PTV.CenterPoint.z) - (1000 + S.CenterPoint.z));
if (Lungs != null)
{
Result.xGTVph2Lung.Add((1000 + Lungs.CenterPoint.x) - (1000 + S.CenterPoint.x));
Result.yGTVph2Lung.Add((1000 + Lungs.CenterPoint.y) - (1000 + S.CenterPoint.y));
Result.zGTVph2Lung.Add((1000 + Lungs.CenterPoint.z) - (1000 + S.CenterPoint.z));
}
else
{
Result.xGTVph2Lung.Add(0);
Result.yGTVph2Lung.Add(0);
Result.zGTVph2Lung.Add(0);
}
}
}
}
//Reduces the GTV phase co-ordinate to be relative to zero.
if (Result.xGTVph.Count >= 1)
{
Result.fourD = "Yes";
double minX = Result.xGTVph.Min();
double minY = Result.yGTVph.Min();
double minZ = Result.zGTVph.Min();
for (int i = 0; i < Result.key.Count(); i++)
{
Result.xGTVph[i] = (1000 + Result.xGTVph[i]) - (1000 + minX); //1000 + removes problem of going over the axis, result is relative anyway.
Result.yGTVph[i] = (1000 + Result.yGTVph[i]) - (1000 + minY);
Result.zGTVph[i] = (1000 + Result.zGTVph[i]) - (1000 + minZ);
}
}
}
else
{
Result.key.Add(ps.UID + ps.Id);
}
return(Result); //returns result.
}
