public static void WriteConfig(CapiConfig config)
{
var configFilePath = Path.GetFullPath(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, $@"..{Path.DirectorySeparatorChar}cfg{Path.DirectorySeparatorChar}config.json"));
FileSystem.DirectoryExistsIfNotCreate(Path.GetFullPath(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, $@"..{Path.DirectorySeparatorChar}cfg{Path.DirectorySeparatorChar}")));
File.WriteAllText(configFilePath, JsonConvert.SerializeObject(config, new CapiConfigJsonConverter()));
}
private void HandleDicomConf(CapiConfig conf, JToken jtoken)
{
// This needs extra attention because we're using a list of abstracts.
conf.DicomConfig.LocalNode = JsonConvert.DeserializeObject <DicomConfig.DicomConfigNode>(jtoken["LocalNode"].ToString());
var remoteNodes = JsonConvert.DeserializeObject <List <DicomConfig.DicomConfigNode> >(jtoken["RemoteNodes"].ToString());
conf.DicomConfig.RemoteNodes = new List <IDicomNode>();
foreach (var remoteNode in remoteNodes)
{
conf.DicomConfig.RemoteNodes.Add(remoteNode);
}
}
public override object ReadJson(JsonReader reader, Type objectType, object existingValue, JsonSerializer serializer)
{
var jsonToken = JToken.Load(reader);
var conf = CapiConfig.GenerateDefault();
if (jsonToken["AgentDbConnectionString"] != null)
{
conf.AgentDbConnectionString = jsonToken["AgentDbConnectionString"].ToString();
}
if (jsonToken["Binaries"] != null)
{
conf.Binaries = jsonToken["Binaries"].ToObject <Binaries>();
}
if (jsonToken["DefaultRecipePath"] != null)
{
conf.DefaultRecipePath = jsonToken["DefaultRecipePath"].ToString();
}
if (jsonToken["DicomConfig"] != null)
{
HandleDicomConf(conf, jsonToken["DicomConfig"]);
}
if (jsonToken["Hl7ProcessPath"] != null)
{
conf.Hl7ProcessPath = jsonToken["Hl7ProcessPath"].ToString();
}
if (jsonToken["ProcessCasesAddedByHL7"] != null)
{
conf.ProcessCasesAddedByHL7 = jsonToken["ProcessCasesAddedByHL7"].ToObject <bool>();
}
if (jsonToken["ManualProcessPath"] != null)
{
conf.ManualProcessPath = jsonToken["ManualProcessPath"].ToString();
}
if (jsonToken["ProcessCasesAddedManually"] != null)
{
conf.ProcessCasesAddedManually = jsonToken["ProcessCasesAddedManually"].ToObject <bool>();
}
if (jsonToken["RunInterval"] != null)
{
conf.RunInterval = jsonToken["RunInterval"].ToString();
}
if (jsonToken["ImagePaths"] != null)
{
conf.ImagePaths = jsonToken["ImagePaths"].ToObject <ImagePaths>();
}
return(conf);
}
public static Recipe Default()
{
CapiConfig conf = CapiConfig.GetConfig();
string sourceAet = "";
string destAet = "";
if (conf.DicomConfig?.RemoteNodes != null && conf.DicomConfig.RemoteNodes.Count > 0)
{
sourceAet = conf.DicomConfig.RemoteNodes[0].AeTitle;
if (conf.DicomConfig.RemoteNodes.Count > 1)
{
destAet = conf.DicomConfig.RemoteNodes[1].AeTitle;
}
else
{
destAet = sourceAet;
}
}
// By default we will match any of the following series.
const string SERIES_DESC = "flair sag;flair sag 3d;t2 sag flair;flair sag fs;flair sag 3d - t2 space da-fl;3d sag flair fs;t2 sag flair 3d;flair 3d t2_spc_irprep_ns_sag_p2_da-fl_iso;3d flair_sag_p3_iso;3d t2 flair sag;t2_spc_irprep_ns_sag_p2_da-fl_iso;flair 3d;t2_3d_sag flair iso;sag 3d flair;t2 sag flair 3d;sag 3d flair";
return(new Recipe()
{
SourceAet = sourceAet,
PatientId = "",
PatientFullName = "",
PatientBirthDate = "",
CurrentAccession = "",
PriorAccession = "",
ExtractBrain = true,
RegisterTo = RegisterToOption.CURRENT,
BiasFieldCorrection = true,
CurrentSeriesCriteria = new List <SeriesSelectionCriteria>(new[] { new SeriesSelectionCriteria()
{
PriorStudyIndex = 0, // 0-based index i.e. 0=most recent, 1=second most recent
MostRecentPriorStudy = false, // overrides PriorStudyIndex if true; true equals PriorStudyIndex of 0
OldestPriorStudy = false, // overrides PriorStudyIndex if true
CutOffPeriodValueInMonths = "", // leave blank to include all dates
StudyDescription = "demyelin",
StudyDescriptionOperand = Common.StringOperand.Contains,
StudyDate = "",
StudyDateOperand = Common.DateOperand.Before,
SeriesDescription = SERIES_DESC,
SeriesDescriptionOperand = Common.StringOperand.OccursIn,
SeriesDescriptionDelimiter = ";"
} }),
PriorSeriesCriteria = new List <SeriesSelectionCriteria>(new[] { new SeriesSelectionCriteria()
{
PriorStudyIndex = 0, // 0-based index i.e. 0=most recent, 1=second most recent
MostRecentPriorStudy = false, // overrides PriorStudyIndex if true; true equals PriorStudyIndex of 0
OldestPriorStudy = false, // overrides PriorStudyIndex if true
CutOffPeriodValueInMonths = "", // leave blank to include all dates
StudyDescription = "",
StudyDescriptionOperand = Common.StringOperand.Contains,
StudyDate = "",
StudyDateOperand = Common.DateOperand.Before,
SeriesDescription = SERIES_DESC,
SeriesDescriptionOperand = Common.StringOperand.OccursIn,
SeriesDescriptionDelimiter = ";"
} }),
CompareSettings = new CompareSettings()
{
CompareIncrease = true,
CompareDecrease = true,
BackgroundThreshold = 10,
MinRelevantStd = -1,
MaxRelevantStd = 5,
MinChange = 0.8f,
MaxChange = 5,
GenerateHistogram = true
},
OutputSettings = new OutputSettings()
{
ResultsDicomSeriesDescription = "VisTarsier Results",
ReslicedDicomSeriesDescription = "VisTarsier Resliced",
FilesystemDestinations = new List <string>(),
OnlyCopyResults = false,
DicomDestinations = new List <string> (new[] { destAet })
}
});
}
