private void TraverseDirectoryTree(string root)
{
StreamWriter MetadataTable = null;
StreamWriter CountsTable = null;
int errorCount = 0, copyCount = 0, deleteCount = 0, extractCount = 0, tableCount = 0;
lostTagCount = 0;
Stack <string> dirs = new Stack <string>(100);
List <string> files = new List <string>();
//Acquisition
if (!Directory.Exists(root))
{
throw new ArgumentException("Specified root directory doesn't exist: " + root);
}
dirs.Push(root);
while (dirs.Count > 0)
{
string currentDir = dirs.Pop();
string[] subDirs;
try { subDirs = Directory.GetDirectories(currentDir); }
catch (UnauthorizedAccessException) { continue; }
catch (DirectoryNotFoundException) { continue; }
foreach (string str in subDirs)
{
dirs.Push(str);
} // Push subdirectories on stack for traversal.
string[] DICOMFiles = null;
try { DICOMFiles = Directory.GetFiles(currentDir, "*.dcm"); }
catch (UnauthorizedAccessException) { continue; }
catch (DirectoryNotFoundException) { continue; }
foreach (string file in DICOMFiles)
{
files.Add(file);
}
} // while dirs.Count > 0
//Processing; could technically be split off into a separate fuuuuunctionnnnnn
//but i don't give a shit
bool DoSimpleParse = !(checkBoxCreateMetadataTable.Checked || checkBoxExtractMetadata.Checked);
List <StudyObject> StudyFiles = new List <StudyObject>();
int maxFiles = files.Count;
for (int i = 0; i < maxFiles; i++)
{
float progress = ((float)(i + 1) / maxFiles);
labelProgressBar.Text = string.Format("Processing file {0} of {1} ({2:p0})", i + 1, maxFiles, progress);
progressBarDICOMFiles.Value = (int)Math.Floor(progress * 100);
Application.DoEvents(); //keeps GUI alive by returning control to OS thread
string DICOMFile = files[i];
string NewFolderName, NewFileName, StudyTime, PatientName, StudyDate, PatientID;
int nFrames;
DICOM.File dcf = null;
try
{ //Take and open file, extract metadata
dcf = new DICOM.File(DICOMFile, DoSimpleParse);
PatientName = TagValueOrDefault(0x00100010, dcf.Tags);
PatientID = TagValueOrDefault(0x00100020, dcf.Tags);
StudyDate = TagValueOrDefault(0x00080023, dcf.Tags);
StudyTime = TagValueOrDefault(0x00080033, dcf.Tags);
if (!DoSimpleParse)
{
nFrames = int.Parse(TagValueOrDefault(0x00280008, dcf.Tags, "1"));
}
else
{
nFrames = ((new FileInfo(DICOMFile).Length / 1024) > 811) ? 125 : 1;
} //single-image files are always 811KB big, so 811 * 1024 bytes; 125 frames is max and an assumption...
switch (comboBoxCopyMode.SelectedIndex)
{
case 0: //Both
break;
case 1: //Images only
if (nFrames > 1)
{
continue;
}
break;
case 2: //Videos only
if (nFrames < 2)
{
continue;
}
break;
}
NewFolderName = string.Format("{0}_{1}_{2}", StudyDate, PatientID, PatientName);
foreach (char c in InvalidPathChars)
{
NewFolderName = NewFolderName.Replace(c.ToString(), "");
} //sanitize path input
foreach (char c in new char[] { '/', '\\', '?' })
{
NewFolderName = NewFolderName.Replace(c.ToString(), "-");
} //these aren't in InvalidPathChars since they're allowed in (full) paths
if (comboBoxExportMode.SelectedIndex == 1)
{
NewFolderName = PatientID.ToLowerInvariant() + Path.DirectorySeparatorChar + NewFolderName;
}
if (comboBoxExportMode.SelectedIndex == 2)
{
NewFolderName = "";
} //no subfolders
} // try
catch (FileNotFoundException) { errorCount++; continue; }
if (checkBoxExportPerStudyCounts.Checked || checkBoxCreateMetadataTable.Checked)
{
StudyObject obj = new StudyObject();
string[] FolderSplit = DICOMFile.Split(Path.DirectorySeparatorChar);
obj.Folder = string.Join(Path.DirectorySeparatorChar.ToString(), FolderSplit.Take(FolderSplit.Length - 1));
obj.File = FolderSplit.Skip(FolderSplit.Length - 1).ToArray()[0];
obj.PatientID = PatientID;
obj.PatientName = PatientName;
obj.StudyDate = StudyDate;
obj.StudyTime = StudyTime;
obj.nFrames = (short)nFrames;
obj.NewFolder = NewFolderName;
StudyFiles.Add(obj);
}
DirectoryInfo OutputFolder = new DirectoryInfo(Path.Combine(textBoxOutputDirectory.Text, NewFolderName));
if (checkBoxCopyAndRename.Checked || checkBoxExtractMetadata.Checked)
{
//prepare receiving folder
if (!Directory.Exists(OutputFolder.FullName))
{
try { Directory.CreateDirectory(OutputFolder.FullName); }
catch (UnauthorizedAccessException)
{
MessageBox.Show("Cannot gain access to " + textBoxOutputDirectory.Text + ". Please select another directory or run as administrator.");
return;
}
} //if FolderName doesn't exist
}
if (checkBoxCopyAndRename.Checked)
{
//Ensure numbering is consistent and continuous
int nPictures = 1, nVideos = 1;
//HACK to ensure Image/Video numbers are study-specific even if no subfolders are being used - previous code searched *.dcm responding to ALL files from ALL studies
string searchStr = string.Format("{0}_*_{1}_*.dcm", StudyDate, PatientID, PatientName);
foreach (char c in new char[] { '/', '\\', '?' })
{
searchStr = searchStr.Replace(c.ToString(), "-");
} //these are invalid as f**k for files
foreach (char c in InvalidFileChars)
{
searchStr.Replace(c.ToString(), "");
}
FileInfo[] ExistingFiles = OutputFolder.GetFiles(searchStr);
nPictures += ExistingFiles.Where(n => n.Name.Contains("Image")).Count();
nVideos += ExistingFiles.Where(n => n.Name.Contains("Video")).Count();
NewFileName = string.Format("{0}_{1}_{2}_{3}_{4}.dcm", StudyDate, StudyTime, PatientID, PatientName, (nFrames > 1 ? ("Video" + nVideos) : ("Image" + nPictures)));
foreach (char c in new char[] { '/', '\\', '?' })
{
NewFileName = NewFileName.Replace(c.ToString(), "-");
} //these are invalid as f**k for files
foreach (char c in InvalidFileChars)
{
NewFileName.Replace(c.ToString(), "");
}
//Copy File, Test File, if there's a request, Delete File
string NewFilePath = Path.Combine(OutputFolder.FullName, NewFileName);
if (File.Exists(NewFilePath))
{ //Need to change name not to overwrite; safety first
int fileCount = OutputFolder.GetFiles(Path.GetFileNameWithoutExtension(NewFileName) + "*").Length + 1;
NewFileName = string.Format("{0}({1}){2}", Path.GetFileNameWithoutExtension(NewFileName), fileCount, Path.GetExtension(NewFileName));
NewFilePath = Path.Combine(OutputFolder.FullName, NewFileName);
} //File.Exists(NewFilePath)
try
{
File.Copy(DICOMFile, NewFilePath);
copyCount++;
}
catch (UnauthorizedAccessException) { MessageBox.Show("Access denied for export directory. Please select another directory or restart as administrator."); return; }
catch (IOException ioe) { MessageBox.Show("Unexpected IO Exception: " + ioe.Message); }
if (checkBoxCheckAndDeleteAfterCopy.Checked)
{
if (TestFileEquality(new FileInfo(DICOMFile), new FileInfo(NewFilePath)))
{
File.Delete(DICOMFile);
deleteCount++;
}
} //checkBoxCheckAndDeleteAfterCopy.Checked
} //if checkboxCopyAndRename.Checked
if (checkBoxExtractMetadata.Checked)
{
using (StreamWriter metadataFile = new StreamWriter(Path.Combine(OutputFolder.FullName, "metadata.txt"), true))
{
metadataFile.WriteLine("Metadata extracted from " + DICOMFile + "\nTag\tValue");
foreach (DICOM.Tag tag in dcf.Tags)
{
metadataFile.WriteLine(tag.Name + "\t" + tag.Value);
} //TODO something fucky here.
metadataFile.WriteLine("\n");
extractCount++;
}
} //if checkboxExtractMetadata.Checked
} //foreach DICOMFile
if (checkBoxCreateMetadataTable.Checked)
{
MetadataTable = new StreamWriter(Path.Combine(textBoxOutputDirectory.Text, DateTime.Now.ToString("yyyy-MM-dd_HH-mm") + "_DICOMFilesMetadata-Table.txt"), false);
MetadataTable.WriteLine("Filename\tPatient ID\tPatient Name\tStudy Date\tStudy Time\tData Type\tFrames");
foreach (var obj in StudyFiles)
{
MetadataTable.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", Path.Combine(obj.Folder, obj.File), obj.PatientID, obj.PatientName, obj.StudyDate, obj.StudyTime, (obj.nFrames > 1 ? "Movie" : "Image"), obj.nFrames));
tableCount++;
}
MetadataTable.Flush();
MetadataTable.Close();
}
if (checkBoxExportPerStudyCounts.Checked)
{
HashSet <string> DataFolders = new HashSet <string>(StudyFiles.Select(x => x.Folder));
CountsTable = new StreamWriter(Path.Combine(textBoxOutputDirectory.Text, DateTime.Now.ToString("yyyy-MM-dd_HH-mm") + "_DICOMFiles-DataPerStudyTable.txt"), false);
CountsTable.WriteLine("Full Path\tStudy\tImages\tVideos");
foreach (var DataFolder in DataFolders)
{
HashSet <string> Studies = new HashSet <string>(StudyFiles.Where(x => x.Folder == DataFolder).Select(x => x.NewFolder));
foreach (var Study in Studies)
{
IEnumerable <StudyObject> Members = StudyFiles.Where(x => (x.NewFolder == Study && x.Folder == DataFolder));
CountsTable.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}", DataFolder, Study, Members.Count(y => y.nFrames <= 1), Members.Count(y => y.nFrames > 1)));
}
}
CountsTable.Flush();
CountsTable.Close();
}
//Generating success message to user
string Report = "Operation(s) completed successfully\n";
string LostTagReport = lostTagCount > 0 ? lostTagCount + " values could not found and defaulted to 'undefined'.\n" : "";
if (checkBoxCopyAndRename.Checked)
{
Report += copyCount + " files copied and renamed. " + LostTagReport;
}
if (checkBoxCheckAndDeleteAfterCopy.Checked)
{
Report += deleteCount + " files deleted.\n";
}
if (checkBoxExtractMetadata.Checked)
{
Report += "Metadata extracted for " + extractCount + " files. " + LostTagReport;
}
if (checkBoxCreateMetadataTable.Checked)
{
Report += tableCount + " files processed for metadata table. " + LostTagReport;
}
progressBarDICOMFiles.Value = 100;
Application.DoEvents();
MessageBox.Show(Report, "DICOM processing complete.");
} // TraverseDirectoryTree
//default constructor
public Tag(DICOM.File Dicomfile)
{
GroupElement = (uint)((Dicomfile.EASR.GetUShort() << 16) | Dicomfile.EASR.GetUShort()); //grab two Ushorts, mash together into GroupElement
Console.WriteLine("* Reading element 0x{0:x8}", GroupElement);
if (DICOMSpec.Tags.ContainsKey(GroupElement))
{
Name = DICOMSpec.Tags[GroupElement];
Console.WriteLine("* Element identified as \"{0}\"", Name);
}
if (Dicomfile.TransferSyntax == TransferSyntax.ExplicitVR)
{
//If VR is explicit (according to transfer syntax agreed upon in file header), there's two different types of possible encoding (Table 7.1-1 and 7.1-2)
VR = Dicomfile.EASR.GetString(2);
if (TwoByteVRCodes.Contains(VR)) //some VR types encode themselves differently and need two bytes of spacing after the actual value, for SOME reason.
{
Dicomfile.EASR.GetUShort(); //Advance by two bytes (those two bytes are padding set to 0x000, thus they're discarded)
//Those bytes have to be discarded; if you just did a ReadInt32() you'd get a wrong number... right?
ValueLength = Dicomfile.EASR.GetInt(); //Value length field is 4 bytes long for these VR codes
}
else
{
ValueLength = Dicomfile.EASR.GetUShort();
} //Value length is a simple 2 byte integer for all other VR codes
} //if TransferSyntax == TransferSyntax.ExplicitVR
if (Dicomfile.TransferSyntax == TransferSyntax.ImplicitVR)
{
//If VR is implicit (according to transfer syntax agreed upon in file header), there's just one possible encoding (Table 7.1-3)
VR = "IMPLICIT";
ValueLength = Dicomfile.EASR.GetInt(); //Value length field is 4 bytes long for these VR codes
}
if (GroupElement == 0xFFFEE0DD && ValueLength == 0) //Sequence Delimination tag (not item delimination!) found, e.g. a sequence has ended
{
Dicomfile.Tags.Add(new Tag(GroupElement, -1, "Sequence End", new byte[0]));
return;
} //if (SubTag is Sequence End Tag)
if (Dicomfile.TransferSyntax == TransferSyntax.ExplicitVR && VR == "SQ") //|| (Dicomfile.TransferSyntax == TransferSyntax.ImplicitVR && DICOMDataDictionary.SequenceItems.Keys.Contains(GroupElement))
{
Dicomfile.Tags.Add(new Tag(this.GroupElement, this.ValueLength, "Sequence Start", new byte[0]));
if (this.ValueLength > 0)
{
Dicomfile.EASR.BaseStream.Seek(this.ValueLength, SeekOrigin.Current);
Dicomfile.Tags.Add(new Tag(this.GroupElement, 0, "Sequence End", new byte[0]));
return;
} //skip this data. TODO: Do proper implementation, see Table 7.5-1
else
{
//this is very hack-y and I apologise
ushort LastUS2 = 0;
while (true)
{
ushort us1 = Dicomfile.EASR.GetUShort();
ushort us2 = Dicomfile.EASR.GetUShort();
uint GE1 = (uint)((us1 << 16) | us2);
uint GE2 = (uint)((LastUS2 << 16) | us1);
if (GE1 == 0xFFFEE0DD || GE2 == 0xFFFEE0DD)
{
Dicomfile.EASR.GetInt();
return;
} //0xFFFEE0DD is the Sequence Delimiter, followed by 0x00000000 (thus the GetInt())
else
{
LastUS2 = us2;
}
}
}
} // if VR == SQ and transfer syntax == Explicit
if (Name == "Pixel Data")
{
return;
} //again, stop reading in a bajillion pixels.
if (ValueLength == -1)
{
ValueLength = 0;
Dicomfile.Tags.Add(this);
return;
}
if (ValueLength % 2 != 0)
{
throw new ArgumentException("Value Length must be an even number?!");
}
_Value = Dicomfile.EASR.ReadBytes(ValueLength);
Value = System.Text.Encoding.UTF8.GetString(_Value);
DateTime ConversionDummy = new DateTime();
switch (VR)
{
//---Important ones:---
case "DA": //date, 8b fixed, YYYYMMDD
if (DateTime.TryParseExact(Value, "yyyyMMdd", CultureInfo.InvariantCulture, DateTimeStyles.None, out ConversionDummy))
{
Value = ConversionDummy.ToString("yyyy-MM-dd");
}
break;
case "DT": //DateTime 26b max, YYYYMMDDHHMMSS.FFFFFF&ZZXX
if (DateTime.TryParseExact(Value, "yyyyMMddHHmmss.ffffff", CultureInfo.InvariantCulture, DateTimeStyles.None, out ConversionDummy))
{
Value = ConversionDummy.ToString("yyyy-MM-dd_HH-mm");
}
break;
case "TM": //Time
string format = Value.Contains('.') ? "HHmmss.ffffff" : "HHmmss";
if (DateTime.TryParseExact(Value, format, CultureInfo.InvariantCulture, DateTimeStyles.None, out ConversionDummy))
{
Value = ConversionDummy.ToString("HH-mm-ss");
}
break;
case "FL":
if (ValueLength == 4)
{
Value = System.BitConverter.ToSingle(_Value, 0).ToString();
}
break;
case "FD":
if (ValueLength == 8)
{
Value = System.BitConverter.ToDouble(_Value, 0).ToString();
}
break;
case "SS":
if (ValueLength == 2)
{
Value = System.BitConverter.ToInt16(_Value, 0).ToString();
}
break;
case "US":
if (ValueLength == 2)
{
Value = System.BitConverter.ToUInt16(_Value, 0).ToString();
}
break;
case "SL":
if (ValueLength == 4)
{
Value = System.BitConverter.ToInt32(_Value, 0).ToString();
}
break;
case "UL":
if (ValueLength == 4)
{
Value = System.BitConverter.ToUInt32(_Value, 0).ToString();
}
break;
//---values no one cares about---
case "UI":
case "UN":
case "UR":
case "UT":
//Unique Identifier Unknown Universal Resource Locator Unlimited text
case "CS":
//Code string, 16b max, trim leading/trailing space [20]
case "UC":
case "SH":
case "LO":
//Unlimited Characters short string Long string
case "LT":
case "OB":
case "OD":
case "OF":
case "OL":
//Long Text Other Byte Other Double Other Float Other Long
case "OW":
case "AT":
case "DS":
//Other Word "Attribute Tag" decimal string
case "AE":
case "ST":
case "AS":
//Application Entity Short Text Age String, 4 bytes fixed
case "IS": //12b max, 0-9+-[space]
//int BufferInt;
//if (int.TryParse(Value, out BufferInt)) { }
case "PN": //Person Name 64char max times 5, = [3D] delimits groups
//Value = "PN Converted: " + System.Text.Encoding.UTF8.GetString(_Value);
case "SQ": //Sequence of Items
//TODO do multiplicity = n, loop until next SQ (get length, read length bytes, repeat)
default:
break;
} //switch VR
Dicomfile.Tags.Add(this);
} //public Tag