public string DicomToGraphicalJSON(string filePathToDir)
{
string[] allFilePaths = System.IO.Directory.GetFiles(filePathToDir);
// store all of the dicoms as a list of dicom files
List <DicomFile> dicoms = new List <DicomFile>();
// get the amount of data
DicomFileData dicomFile = null;
ArrayList data = new ArrayList();
// loop though all of the files and open them
foreach (string filePath in allFilePaths)
{
try
{
dicoms.Add(DicomFile.Open(filePath));
}
catch (Exception)
{
Console.WriteLine("file at \"" + filePath + "\" readable as a dicom file");
}
}
// sort the order of all the dicom objects so they work in the correct order
dicoms.Sort((d1, d2) => d1.Dataset.GetSingleValue <int>(DicomTag.InstanceNumber).CompareTo(d2.Dataset.GetSingleValue <int>(DicomTag.InstanceNumber)));
// sort out the intial values based on the first dicom in the list
// get the pixel data out as much as possible
DicomPixelData header = DicomPixelData.Create(dicoms[0].Dataset);
IPixelData pixelData = PixelDataFactory.Create(header, 0);
// Build the correct file for this data depending on what is stored in the dicom files
if (pixelData is GrayscalePixelDataU16)
{
data.AddRange(((GrayscalePixelDataU16)pixelData).Data);
dicomFile = new U16DicomFileData();
}
else if (pixelData is GrayscalePixelDataS16)
{
data.AddRange(((GrayscalePixelDataS16)pixelData).Data);
dicomFile = new S16DicomFileData();
}
else if (pixelData is GrayscalePixelDataU8)
{
data.AddRange(((GrayscalePixelDataU8)pixelData).Data);
dicomFile = new U8bitDicomFileData();
}
else if (pixelData is GrayscalePixelDataS32)
{
data.AddRange(((GrayscalePixelDataS32)pixelData).Data);
dicomFile = new S32DicomDataFile();
}
else if (pixelData is GrayscalePixelDataU32)
{
data.AddRange(((GrayscalePixelDataU32)pixelData).Data);
dicomFile = new U32DicomDataFile();
}
else if (pixelData is ColorPixelData24)
{
// note that this one will take some work
// 0 == red, 1 == Green, 2 == Blue and so on
data.AddRange(((ColorPixelData24)pixelData).Data);
dicomFile = new RGBColourDicomFileData();
}
else if (pixelData is SingleBitPixelData)
{
data.AddRange(((SingleBitPixelData)pixelData).Data);
dicomFile = new U8bitDicomFileData();
}
// get the amount of rows the image data set has out of the dicom file.
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.Rows, out dicomFile.width))
{
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.NumberOfVerticalPixels, out dicomFile.width))
{
// if the value for rows dosn't exist mark the entry as -1
dicomFile.width = -1;
}
}
// get the amount of coloumns in the image
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.Columns, out dicomFile.height))
{
// try getting this data another way then
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.NumberOfHorizontalPixels, out dicomFile.height))
{
// if the value for rows dosn't exist mark the entry as -1
dicomFile.height = -1;
}
}
// Datastucture that will hold the final DS
float[] aspectOfPixel = new float[2];
// get the amount of coloumns in the image
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.PixelSpacing, out aspectOfPixel))
{
// all these methods will try to do it until one works or this feild will be made invalid
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.ImagerPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.NominalScannedPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.CompensatorPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.DetectorElementSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.PresentationPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.PrinterPixelSpacing, out aspectOfPixel))
{
if (!dicoms[0].Dataset.TryGetValues <float>(DicomTag.ObjectPixelSpacingInCenterOfBeam, out aspectOfPixel))
{
// if none of the above methods work mark the objects as invalid
aspectOfPixel[0] = -1;
aspectOfPixel[1] = -1;
// This could be valid in a case were only one row of data was colected
}
}
}
}
}
}
}
}
// TODO this dosn't take into account what will happen if the user only recorded one line of pixels since my work dosn't focus on it
// Save the data from pixel spacing
dicomFile.pixelSpacingX = aspectOfPixel[0];
dicomFile.pixelSpacingY = aspectOfPixel[1];
// try to get the thickness of the the slice or else set it to an invalid number
if (dicoms[0].Dataset.TryGetSingleValue(DicomTag.SliceThickness, out dicomFile.sliceThickness))
{
dicomFile.sliceThickness = -1;
}
// try to get how much room is between each slice
if (!dicoms[0].Dataset.TryGetSingleValue(DicomTag.SpacingBetweenSlices, out dicomFile.spacingBetweenSlices))
{
dicomFile.spacingBetweenSlices = -1;
}
dicomFile.breath = dicoms.Count;
// loop though all of the dicoms in order now
for (int index = 1; index < dicoms.Count; index++)
{
// get the pixel data out as much as possible
header = DicomPixelData.Create(dicoms[index].Dataset);
pixelData = PixelDataFactory.Create(header, 0);
// Build the correct file for this data depending on what is stored in the dicom files
if (pixelData is GrayscalePixelDataU16)
{
data.AddRange(((GrayscalePixelDataU16)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataS16)
{
data.AddRange(((GrayscalePixelDataS16)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataU8)
{
data.AddRange(((GrayscalePixelDataU8)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataS32)
{
data.AddRange(((GrayscalePixelDataS32)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataU32)
{
data.AddRange(((GrayscalePixelDataU32)pixelData).Data);
}
else if (pixelData is ColorPixelData24)
{
// note that this one will take some work
// 0 == red, 1 == Green, 2 == Blue and so on
data.AddRange(((ColorPixelData24)pixelData).Data);
}
else if (pixelData is SingleBitPixelData)
{
data.AddRange(((SingleBitPixelData)pixelData).Data);
}
int tempDicomRows = -1;
// get the amount of rows the image data set has out of the dicom file.
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.Rows, out tempDicomRows))
{
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.NumberOfVerticalPixels, out tempDicomRows))
{
if (dicomFile.height != tempDicomRows)
{
throw new NonConsistantDicomDirectoryException("The number of rows at index" + index);
}
}
}
else if (dicomFile.width != tempDicomRows)
{
throw new NonConsistantDicomDirectoryException("The number of rows at index" + index);
}
// get the amount of coloumns in the image and ensure it stays the same
int tempDicomCols = -1;
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.Columns, out tempDicomCols))
{
// try getting this data another way then
if (dicoms[index].Dataset.TryGetSingleValue(DicomTag.NumberOfHorizontalPixels, out tempDicomCols))
{
if (dicomFile.height != tempDicomCols)
{
throw new NonConsistantDicomDirectoryException("The number of columns at index" + index);
}
}
}
else if (dicomFile.height != tempDicomCols)
{
throw new NonConsistantDicomDirectoryException("The number of columns at index" + index);
}
// TODO Maybe change how this works going forward
aspectOfPixel = new float[2];
// get the amount of coloumns in the image
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PixelSpacing, out aspectOfPixel))
{
// all these methods will try to do it until one works or this feild will be made invalid
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.ImagerPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.NominalScannedPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.CompensatorPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.DetectorElementSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PresentationPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PrinterPixelSpacing, out aspectOfPixel))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.ObjectPixelSpacingInCenterOfBeam, out aspectOfPixel))
{
// if none of the above methods work mark the objects as invalid
aspectOfPixel[0] = -1;
aspectOfPixel[1] = -1;
// This could be valid in a case were only one row of data was colected
}
}
}
}
}
}
}
}
// check input data against the old data and throw an exception if the file isn't exact
if (dicomFile.pixelSpacingX != aspectOfPixel[0] || dicomFile.pixelSpacingY != aspectOfPixel[1])
{
throw new NonConsistantDicomDirectoryException("Pixel Spacing Dicom Tag at index " + index);
}
// check the slice thickness is constisant
if (dicoms[index].Dataset.TryGetSingleValue(DicomTag.SliceThickness, out float tempSliceThickness))
{
if (dicomFile.sliceThickness == -1)
{
dicomFile.sliceThickness = tempSliceThickness;
}
else if (tempSliceThickness != dicomFile.sliceThickness)
{
throw new NonConsistantDicomDirectoryException("Slice Thickness at index" + index);
}
}
// try to get how much room is between each slice
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.SpacingBetweenSlices, out float tempSliceSpacing))
{
if (dicomFile.spacingBetweenSlices == -1)
{
dicomFile.spacingBetweenSlices = tempSliceSpacing;
}
else if (tempSliceThickness != dicomFile.sliceThickness)
{
throw new NonConsistantDicomDirectoryException("Spacing between slices at index" + index);
}
}
}
dicomFile.SetPixelBuffer(data);
// return the json strings here
return(Newtonsoft.Json.JsonConvert.SerializeObject(dicomFile));
}
/// <summary>
///
/// </summary>
/// <param name="filePathToDir"></param>
/// <returns></returns>
public string[] DicomToGraphicalJSONArray(string filePathToDir)
{
string[] allFilePaths = System.IO.Directory.GetFiles(filePathToDir);
// store all of the dicoms as a list of dicom files
List <DicomFile> dicoms = new List <DicomFile>();
// the output datastructure for this method
string[] jsonStrings = null;
// loop though all of the files and open them
foreach (string filePath in allFilePaths)
{
try
{
dicoms.Add(DicomFile.Open(filePath));
}
catch (Exception)
{
Console.WriteLine("file at \"" + filePath + "\" readable as a dicom file");
}
}
// set the amount of output files to the amount of Json Strings
jsonStrings = new string[dicoms.Count];
// sort the order of all the dicom objects so they work in the correct order
dicoms.Sort((d1, d2) => d1.Dataset.GetSingleValue <int>(DicomTag.InstanceNumber).CompareTo(d2.Dataset.GetSingleValue <int>(DicomTag.InstanceNumber)));
// loop though all of the dicoms in order now
for (int index = 0; index < jsonStrings.Length; index++)
{
int bytesUsed = -1;
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.BitsAllocated, out bytesUsed))
{
// this is required for all dicom images so if this code has been reached the code is invalid
Console.WriteLine("A invalid file was found at index " + index);
continue;
}
Console.WriteLine("Amount of Bytes Required: " + bytesUsed);
// get the amount of data
DicomFileData dicomFile = null;
// get the pixel data out as much as possible
DicomPixelData header = DicomPixelData.Create(dicoms[index].Dataset);
var pixelData = PixelDataFactory.Create(header, 0);
// Build the correct file for this data depending on what is stored in the dicom files
if (pixelData is GrayscalePixelDataU16)
{
dicomFile = new U16DicomFileData(((GrayscalePixelDataU16)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataS16)
{
dicomFile = new S16DicomFileData(((GrayscalePixelDataS16)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataU8)
{
dicomFile = new U8bitDicomFileData(((GrayscalePixelDataU8)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataS32)
{
dicomFile = new S32DicomDataFile(((GrayscalePixelDataS32)pixelData).Data);
}
else if (pixelData is GrayscalePixelDataU32)
{
dicomFile = new U32DicomDataFile(((GrayscalePixelDataU32)pixelData).Data);
}
else if (pixelData is ColorPixelData24)
{
// note that this one will take some work
// 0 == red, 1 == Green, 2 == Blue and so on
dicomFile = new RGBColourDicomFileData(((ColorPixelData24)pixelData).Data);
}
else if (pixelData is SingleBitPixelData)
{
dicomFile = new RGBColourDicomFileData(((SingleBitPixelData)pixelData).Data);
}
// get the amount of rows the image data set has out of the dicom file.
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.Rows, out dicomFile.width))
{
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.NumberOfVerticalPixels, out dicomFile.width))
{
// if the value for rows dosn't exist mark the entry as -1
dicomFile.width = -1;
}
}
// get the amount of coloumns in the image
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.Columns, out dicomFile.height))
{
// try getting this data another way then
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.NumberOfHorizontalPixels, out dicomFile.height))
{
// if the value for rows dosn't exist mark the entry as -1
dicomFile.height = -1;
}
}
float[] temp = new float[2];
// get the amount of coloumns in the image
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PixelSpacing, out temp))
{
// all these methods will try to do it until one works or this feild will be made invalid
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.ImagerPixelSpacing, out temp))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.NominalScannedPixelSpacing, out temp))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.CompensatorPixelSpacing, out temp))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.DetectorElementSpacing, out temp))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PresentationPixelSpacing, out temp))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.PrinterPixelSpacing, out temp))
{
if (!dicoms[index].Dataset.TryGetValues <float>(DicomTag.ObjectPixelSpacingInCenterOfBeam, out temp))
{
// if none of the above methods work mark the objects as invalid
temp[0] = -1;
temp[1] = -1;
// This could be valid in a case were only one row of data was colected
}
}
}
}
}
}
}
}
// TODO this dosn't take into account what will happen if the user only recorded one line of pixels since my work dosn't focus on it
// This should always return a value that is has a length of two
// This will be the value for each row which should always be the first value found
dicomFile.pixelSpacingX = temp[0];
dicomFile.pixelSpacingY = temp[1];
// try to get the thickness of the the slice or else set it to an invalid number
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.SliceThickness, out dicomFile.sliceThickness))
{
dicomFile.sliceThickness = -1;
}
// try to get how much room is between each slice
if (!dicoms[index].Dataset.TryGetSingleValue(DicomTag.SpacingBetweenSlices, out dicomFile.spacingBetweenSlices))
{
dicomFile.spacingBetweenSlices = -1;
}
// get the JSON output as a string and place it to the correct place in the array
jsonStrings[index] = Newtonsoft.Json.JsonConvert.SerializeObject(dicomFile);
}
// return the json strings here
return(jsonStrings);
}
