Develop Reference

How to replace the Pixel Data of DICOM file using fo-DICOM?

I want to replace the pixel data of a DICOM file with another one. I used this code:
public bool ImportImage(string imageFile, string newFilePah, string oldDicomFile)
{
try
{
Bitmap bitmap = new Bitmap(imageFile);
bitmap = GetValidImage(bitmap);
int rows, columns;
byte[] pixels = GetPixels(bitmap, out rows, out columns);
MemoryByteBuffer buffer = new MemoryByteBuffer(pixels);
DicomDataset dataset = new DicomDataset();
var df = DicomFile.Open(oldDicomFile);
FillDataset(ref dataset, df);
DicomTransferSyntax dicomTransfer = df.Dataset.Get<DicomTransferSyntax>(DicomTag.TransferSyntaxUID, DicomTransferSyntax.JPEGProcess14);
dataset.AddOrUpdate(DicomTag.PhotometricInterpretation, PhotometricInterpretation.Rgb.Value);
dataset.AddOrUpdate(DicomTag.Rows, (ushort)rows);
dataset.AddOrUpdate(DicomTag.Columns, (ushort)columns);
dataset.AddOrUpdate(DicomTag.BitsAllocated, (ushort)8);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
pixelData.BitsStored = 8;
pixelData.SamplesPerPixel = 3;
pixelData.HighBit = 7;
pixelData.PixelRepresentation = 0;
pixelData.PlanarConfiguration = 0;
pixelData.AddFrame(buffer);
DicomFile dicomfile = new DicomFile(dataset.Clone(dicomTransfer));
dicomfile.Save(newFilePah);
return true;
}
catch(Exception ddd) { return false; }
}
private void FillDataset(ref DicomDataset dataset, DicomFile df)
{
foreach(var item in df.Dataset)
{
if(!item.Tag.Group.ToString().Equals("7FE0") && !item.Tag.Group.ToString().Equals("40"))
dataset.Add(item);
}
}
The output DICOM file loses many tags which affect image display.
I referred to this answer. But the AddOrUpdatePixelData method used in that answer is deprecated in version v4.0.0-rc1 that I am using. So that answer does not help me.
Is there any other way to change the pixel data of a DICOM file using fo-DICOM?

Following code does replace the pixel data correctly.
public static bool ImportImage(string imageFile, string newFilePah, string oldDicomFile)
{
Bitmap bitmap = new Bitmap(imageFile);
int rows, columns;
byte[] pixels = GetPixels(bitmap, out rows, out columns);
MemoryByteBuffer buffer = new MemoryByteBuffer(pixels);
DicomDataset dataset = new DicomDataset();
var dicomfile = DicomFile.Open(oldDicomFile);
dataset = dicomfile.Dataset.Clone();
dataset.AddOrUpdate(DicomTag.PhotometricInterpretation, PhotometricInterpretation.Rgb.Value);
dataset.AddOrUpdate(DicomTag.Rows, (ushort)rows);
dataset.AddOrUpdate(DicomTag.Columns, (ushort)columns);
dataset.AddOrUpdate(DicomTag.BitsAllocated, (ushort)8);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
pixelData.BitsStored = 8;
pixelData.SamplesPerPixel = 3;
pixelData.HighBit = 7;
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
pixelData.PixelRepresentation = 0;
pixelData.PlanarConfiguration = 0;
pixelData.Height = (ushort)rows;
pixelData.Width = (ushort)columns;
pixelData.AddFrame(buffer);
dicomfile = new DicomFile(dataset);
dicomfile.Save(newFilePah);
return true;
}
private static byte[] GetPixels(Bitmap bitmap, out int rows, out int columns)
{
using(var stream = new MemoryStream())
{
bitmap.Save(stream, System.Drawing.Imaging.ImageFormat.Bmp);
rows = bitmap.Height;
columns = bitmap.Width;
return stream.ToArray();
}
}
You can see I have cleaned up your code much.
But the major change is using System.Drawing.Imaging.ImageFormat.Bmp instead of other formats. This depends on actual input image format. Use the format as that of input image.
For detailed insight, please refer to this source code on github.

Saving raw detph-data

I am trying to save my kinect raw depth-data and i dont want to use the Kinect Studio, because i need the raw-data for further calculations. I am using the kinectv2 and kinect sdk!
My problem is that i just get low FPS for the saved data. Its about 15-17FPS.
Here my Framereader ( in further steps i want to save colorstream also):
frameReader = kinectSensor.OpenMultiSourceFrameReader(FrameSourceTypes.Depth);
frameReader.MultiSourceFrameArrived += Reader_MultiSourceFrameArrived;
Here the Event:
void Reader_MultiSourceFrameArrived(object sender, MultiSourceFrameArrivedEventArgs e)
{
var reference = e.FrameReference.AcquireFrame();
saveFrameTest(reference);
frame_num++;
}
Here the saving-function:
private unsafe void saveFrameTest(Object reference)
{
MultiSourceFrame mSF = (MultiSourceFrame)reference;
using (var frame = mSF.DepthFrameReference.AcquireFrame())
{
if (frame != null)
{
using (Microsoft.Kinect.KinectBuffer depthBuffer = frame.LockImageBuffer())
{
if ((frame.FrameDescription.Width * frame.FrameDescription.Height) == (depthBuffer.Size / frame.FrameDescription.BytesPerPixel))
{
ushort* frameData = (ushort*)depthBuffer.UnderlyingBuffer;
byte[] rawDataConverted = new byte[(int)(depthBuffer.Size / 2)];
for (int i = 0; i < (int)(depthBuffer.Size / 2); ++i)
{
ushort depth = frameData[i];
rawDataConverted[i] = (byte)(depth >= frame.DepthMinReliableDistance && depth <= frame.DepthMaxReliableDistance ? (depth) : 0);
}
String date = string.Format("{0:hh-mm-ss}", DateTime.Now);
String filePath = System.IO.Directory.GetCurrentDirectory() + "/test/" +date+".raw";
File.WriteAllBytes(filePath, rawDataConverted);
rawDataConverted = null;
}
}
}
}
}
Further Infomration:
I included my code in a simple Console-Application on a Intel® Xeon® Processor E5-1620 3,7GHz with 16 GB RAM.
i think the for-loop is taking to much time:
for (int i = 0; i < (int)(depthBuffer.Size / 2); ++i)
{
ushort depth = frameData[i];
rawDataConverted[i] = (byte)(depth >= frame.DepthMinReliableDistance && depth <= frame.DepthMaxReliableDistance ? (depth) : 0);
}
I could improved my framerate. Now, i am accessing the kinectbuffer directly and resign the for-loop.
Microsoft.Kinect.KinectBuffer depthBuffer = frame.LockImageBuffer();
Marshal.Copy(depthBuffer.UnderlyingBuffer, rawData_depth, 0, (depthImageSize));
depthBuffer.Dispose();
frame.Dispose();
However i couldnt get the 30FPS-rate. Now it is about 25 FPS.

You could try something like this to get your array.
It's what I normally use.
var frame = frameReference.AcquireFrame();
var frameDescription = frame.FrameDescription;
ushort[] frameData = new ushort[frameDescription.Width * frameDescription.Height];
frame.CopyFrameDataToArray(frameData);

getting mulitple images from a single stream piped from ffmpeg stdout

I start a process to retrieve a few frames from a video file with ffmpeg,
ffmpeg -i "<videofile>.mp4" -frames:v 10 -f image2pipe pipe:1
and pipe the images to stdout -
var cmd = Process.Start(p);
var stream = cmd.StandardOutput.BaseStream;
var img = Image.FromStream(stream);
Getting the first image this way works, but how do I get all of them?

OK this was gobspackingly easy, kind of embarrassed I asked here. I'll post the answer in case it will help anyone else.
The first few bytes in the stream will be repeated every time there is a new image. I guessed the first 8 would do and voila.
static IEnumerable<Image> GetThumbnails(Stream stream)
{
byte[] allImages;
using (var ms = new MemoryStream())
{
stream.CopyTo(ms);
allImages = ms.ToArray();
}
var bof = allImages.Take(8).ToArray(); //??
var prevOffset = -1;
foreach (var offset in GetBytePatternPositions(allImages, bof))
{
if (prevOffset > -1)
yield return GetImageAt(allImages, prevOffset, offset);
prevOffset = offset;
}
if (prevOffset > -1)
yield return GetImageAt(allImages, prevOffset, allImages.Length);
}
static Image GetImageAt(byte[] data, int start, int end)
{
using (var ms = new MemoryStream(end - start))
{
ms.Write(data, start, end - start);
return Image.FromStream(ms);
}
}
static IEnumerable<int> GetBytePatternPositions(byte[] data, byte[] pattern)
{
var dataLen = data.Length;
var patternLen = pattern.Length - 1;
int scanData = 0;
int scanPattern = 0;
while (scanData < dataLen)
{
if (pattern[0] == data[scanData])
{
scanPattern = 1;
scanData++;
while (pattern[scanPattern] == data[scanData])
{
if (scanPattern == patternLen)
{
yield return scanData - patternLen;
break;
}
scanPattern++;
scanData++;
}
}
scanData++;
}
}

C# task async await smart card - UI thread blocked

I'm new to C#, and I'm trying to use task async await for a WinsForm GUI. I've read so many tutorials about it, but all of them implement tasks differently. Some tasks use functions, and others just put the code in to execute. Some use Task.Run() or just await. Furthermore, all the examples I've seen are of functions that are included in the UI class. I'm trying to run functions that are in classes that are within my UI. I'm just really confused now, and don't know what's right/wrong.
What I'm trying to do is write a file to an EEPROM, using the SpringCard API/ PC/SC library. I parse the file into packets and write it to the smart card. I also want to update a status label and progress bar. A lot of things can go wrong. I have flags set in the smart card, and right now I just a while loop running until it reads a certain flag, which will obviously stall the program if it's forever waiting for a flag.
I guess I'm just confused about how to set it up. Help. I've tried using Tasks. Here is my code so far.
/* Initialize open file dialog */
OpenFileDialog ofd = new OpenFileDialog();
ofd.Multiselect = false;
ofd.Filter = "BIN Files (.bin)|*.bin|HEX Files (.hex)|*.hex";
ofd.InitialDirectory = "C:";
ofd.Title = "Select File";
//Check open file dialog result
if (ofd.ShowDialog() != DialogResult.OK)
{
if (shade != null)
{
shade.Dispose();
shade = null;
}
return;
}
//progform.Show();
Progress<string> progress = new Progress<string>();
file = new ATAC_File(ofd.FileName);
try
{
cardchannel.DisconnectReset();
Task upgrade = upgradeASYNC();
if(cardchannel.Connect())
{
await upgrade;
}
else
{
add_log_text("Connection to the card failed");
MessageBox.Show("Failed to connect to the card in the reader : please check that you don't have another application running in background that tries to work with the smartcards in the same time");
if (shade != null)
{
shade.Dispose();
shade = null;
}
cardchannel = null;
}
}
private async Task upgradeASYNC()
{
int i = 0;
int totalpackets = 0;
add_log_text("Parsing file into packets.");
totalpackets = file.parseFile();
/*progress.Report(new MyTaskProgressReport
{
CurrentProgressAmount = i,
TotalProgressAmount = totalpackets,
CurrentProgressMessage = "Sending upgrade file..."
});*/
ST_EEPROMM24LR64ER chip = new ST_EEPROMM24LR64ER(this, cardchannel, file, EEPROM.DONOTHING);
bool writefile = chip.WriteFileASYNC();
if(writefile)
{
add_log_text("WRITE FILE OK.");
}
else
{
add_log_text("WRITE FILE BAD.");
}
}
In the file class:
public int parseFile()
{
FileStream fs = new FileStream(filename, FileMode.Open, FileAccess.Read);
BinaryReader br = new BinaryReader(fs);
FileInfo finfo = new FileInfo(filename);
int readbytecount = 0;
int packetcount = 0;
int numofbytesleft = 0;
byte[] hash = new byte[4];
byte[] packetinfo = new byte[4];
byte[] filechunk = null;
/* Read file until all file bytes read */
while (size_int > readbytecount)
{
//Initialize packet array
filechunk = new byte[MAXDATASIZE];
//read into byte array of max write size
if (packetcount < numoffullpackets)
{
//Initialize packet info array
packetinfo[0] = (byte)((size_int + 1) % 0x0100); //packetcountlo
packetinfo[1] = (byte)((size_int + 1) / 0x0100); //packetcounthi
packetinfo[2] = (byte)((packetcount + 1) / 0x0100); //packetcounthi
packetinfo[3] = (byte)((packetcount + 1) % 0x0100); //packetcountlo
//read bytes from file into packet array
bytesread = br.Read(filechunk, 0, MAXDATASIZE);
//add number of bytes read to readbytecount
readbytecount += bytesread;
}
//read EOF into byte array of size smaller than max write size
else if (packetcount == numoffullpackets)
{
//find out how many bytes left to read
numofbytesleft = size_int - (MAXDATASIZE * numoffullpackets);
//Initialize packet info array
packetinfo[0] = (byte)((size_int + 1) / 0x0100); //packetcounthi
packetinfo[1] = (byte)((size_int + 1) % 0x0100); //packetcountlo
packetinfo[2] = (byte)((packetcount + 1) / 0x0100); //packetcounthi
packetinfo[3] = (byte)((packetcount + 1) % 0x0100); //packetcountlo
//Initialize array and add byte padding, MAXWRITESIZE-4 because the other 4 bytes will be added when we append the CRC
//filechunk = new byte[numofbytesleft];
for (int j = 0; j < numofbytesleft; j++)
{
//read byte from file
filechunk[j] = br.ReadByte();
//add number of bytes read to readbytecount
readbytecount++;
}
for (int j = numofbytesleft; j < MAXDATASIZE; j++)
{
filechunk[j] = 0xFF;
}
}
else
{
MessageBox.Show("ERROR");
}
//calculate crc32 on byte array
int i = 0;
foreach (byte b in crc32.ComputeHash(filechunk))
{
hash[i++] = b;
}
//Append hash to filechunk to create new byte array named chunk
byte[] chunk = new byte[MAXWRITESIZE];
Buffer.BlockCopy(packetinfo, 0, chunk, 0, packetinfo.Length);
Buffer.BlockCopy(filechunk, 0, chunk, packetinfo.Length, filechunk.Length);
Buffer.BlockCopy(hash, 0, chunk, (packetinfo.Length + filechunk.Length), hash.Length);
//Add chunk to byte array list
packetcount++;
PacketBYTE.Add(chunk);
}
parseCMD();
return PacketBYTE.Count;
}
In the EEPROM class:
public bool WriteFileASYNC()
{
int blocknum = ATAC_CONSTANTS.RFBN_RFstartwrite;
byte[] response = null;
CAPDU[] EEPROMcmd = null;
int packetCount = 0;
log("ATTEMPT: Read response funct flag.");
do
{
StopRF();
Thread.SpinWait(100);
StartRF();
log("ATTEMPT: Write function flag.");
while (!WriteFlag(ATAC_CONSTANTS.RFBN_functflag, EEPROM.UPLOADAPP)) ;
} while (ReadFunctFlag(ATAC_CONSTANTS.RFBN_responseflag, 0) != EEPROM.UPLOADAPP);
for (int EEPROMcount = 0; EEPROMcount < file.CmdBYTE.Count; EEPROMcount++)
{
string temp = "ATTEMPT: Write EEPROM #" + EEPROMcount.ToString();
log(temp);
EEPROMcmd = file.CmdBYTE[EEPROMcount];
while (EEPROMcmd[blocknum] != null)
{
if (blocknum % 32 == 0)
{
string tempp = "ATTEMPT: Write packet #" + packetCount.ToString();
log("ATTEMPT: Write packet #");
packetCount++;
}
do
{
response = WriteBinaryASYNC(EEPROMcmd[blocknum]);
} while (response == null);
blocknum++;
}
log("ATTEMPT: Write packet flag.");
while (!WriteFlag(ATAC_CONSTANTS.RFBN_packetflag, ATAC_CONSTANTS.RFflag)) ;
log("ATTEMPT: Write packet flag.");
do
{
StopRF();
Thread.SpinWait(300);
StartRF();
} while (!ReadFlag(ATAC_CONSTANTS.RFBN_packetresponseflag, ((blocknum/32) - 1)*(EEPROMcount+1)));
blocknum = ATAC_CONSTANTS.RFBN_RFstartwrite;
}
return true;
}

Tasks are threads.
When you write this:
Task upgrade = upgradeASYNC();
you are simply executing upgradeASYNC in a new thread.
When you write this:
await upgrade;
You are only waiting for the new thread to finish (before going to the next instruction).
And this method
private async Task upgradeASYNC()
returns a Task object only because you add the async keyword. But in the body of this method there is no await. So it just runs synchronously, like any thread job.
I don't have time to rewrite your code, i let that to another stackoverflow user. You should learn and work harder ;)

How to create a gif image with C#

I want to create a gif file with several frames.
I want to use the Method which Microsoft support--Image.SaveAdd
But I don't know how to set the EncoderParameters Paramater to make up a gif file.
I can't find documents to refer. So how to create a gif file with Image.SaveAdd

Probably, too late to be useful for the original poster, but I managed to create a proper gif using just System.Drawing. The code below is based on jschroedl's answer, but also sets the frame delays and number of animation loops.
// Gdi+ constants absent from System.Drawing.
const int PropertyTagFrameDelay = 0x5100;
const int PropertyTagLoopCount = 0x5101;
const short PropertyTagTypeLong = 4;
const short PropertyTagTypeShort = 3;
const inr UintBytes = 4;
//...
var gifEncoder = GetEncoder(ImageFormat.Gif);
// Params of the first frame.
var encoderParams1 = new EncoderParameters(1);
encoderParams1.Param[0] = new EncoderParameter(Encoder.SaveFlag, (long)EncoderValue.MultiFrame);
// Params of other frames.
var encoderParamsN = new EncoderParameters(1);
encoderParamsN.Param[0] = new EncoderParameter(Encoder.SaveFlag, (long)EncoderValue.FrameDimensionTime);
// Params for the finalizing call.
var encoderParamsFlush = new EncoderParameters(1);
encoderParamsFlush.Param[0] = new EncoderParameter(Encoder.SaveFlag, (long)EncoderValue.Flush);
// PropertyItem for the frame delay (apparently, no other way to create a fresh instance).
var frameDelay = (PropertyItem)FormatterServices.GetUninitializedObject(typeof(PropertyItem));
frameDelay.Id = PropertyTagFrameDelay;
frameDelay.Type = PropertyTagTypeLong;
// Length of the value in bytes.
frameDelay.Len = Bitmaps.Count * UintBytes;
// The value is an array of 4-byte entries: one per frame.
// Every entry is the frame delay in 1/100-s of a second, in little endian.
frameDelay.Value = new byte[Bitmaps.Count * UintBytes];
// E.g., here, we're setting the delay of every frame to 1 second.
var frameDelayBytes = BitConverter.GetBytes((uint)100);
for (int j = 0; j < Bitmaps.Count; ++j)
Array.Copy(frameDelayBytes, 0, frameDelay.Value, j * UintBytes, UintBytes);
// PropertyItem for the number of animation loops.
var loopPropertyItem = (PropertyItem)FormatterServices.GetUninitializedObject(typeof(PropertyItem));
loopPropertyItem.Id = PropertyTagLoopCount;
loopPropertyItem.Type = PropertyTagTypeShort;
loopPropertyItem.Len = 1;
// 0 means to animate forever.
loopPropertyItem.Value = BitConverter.GetBytes((ushort)0);
using (var stream = new FileStream("animation.gif", FileMode.Create))
{
bool first = true;
Bitmap firstBitmap = null;
// Bitmaps is a collection of Bitmap instances that'll become gif frames.
foreach (var bitmap in Bitmaps)
{
if (first)
{
firstBitmap = bitmap;
firstBitmap.SetPropertyItem(frameDelay);
firstBitmap.SetPropertyItem(loopPropertyItem);
firstBitmap.Save(stream, gifEncoder, encoderParams1);
first = false;
}
else
{
firstBitmap.SaveAdd(bitmap, encoderParamsN);
}
}
firstBitmap.SaveAdd(encoderParamsFlush);
}
// ...
private ImageCodecInfo GetEncoder(ImageFormat format)
{
ImageCodecInfo[] codecs = ImageCodecInfo.GetImageDecoders();
foreach (ImageCodecInfo codec in codecs)
{
if (codec.FormatID == format.Guid)
{
return codec;
}
}
return null;
}

I had success with these parameters. img1,2,3,4... are the images I want to combine.
ULONG parameterValue;
EncoderParameters encoderParameters;
encoderParameters.Count = 1;
encoderParameters.Parameter[0].Guid = EncoderSaveFlag;
encoderParameters.Parameter[0].Type = EncoderParameterValueTypeLong;
encoderParameters.Parameter[0].NumberOfValues = 1;
encoderParameters.Parameter[0].Value = &parameterValue;
// Save the first frame
parameterValue = EncoderValueMultiFrame;
rc = img1->Save(L"Output.gif", &encoderClsid, &encoderParameters);
assert(rc == Ok);
// Add the second frame
parameterValue = EncoderValueFrameDimensionTime;
rc = img1->SaveAdd(img2, &encoderParameters);
assert(rc == Ok);
// etc...adding frames img3,4,5...
// Done...
parameterValue = EncoderValueFlush;
rc = img1->SaveAdd(&encoderParameters);
assert(rc == Ok);
Edit: I just realized that you asked for C# and I have C++ code. Hopefully the parameters still apply.

If you want create gif with many picture you can use ngif. see this
//you should replace filepath
String [] imageFilePaths = new String[]{"c:\\01.png","c:\\02.png","c:\\03.png"};
String outputFilePath = "c:\\test.gif";
AnimatedGifEncoder e = new AnimatedGifEncoder();
e.Start( outputFilePath );
e.SetDelay(500);
//-1:no repeat,0:always repeat
e.SetRepeat(0);
for (int i = 0, count = imageFilePaths.Length; i < count; i++ )
{
e.AddFrame( Image.FromFile( imageFilePaths[i] ) );
}
e.Finish();
/* extract Gif */
string outputPath = "c:\\";
GifDecoder gifDecoder = new GifDecoder();
gifDecoder.Read( "c:\\test.gif" );
for ( int i = 0, count = gifDecoder.GetFrameCount(); i < count; i++ )
{
Image frame = gifDecoder.GetFrame( i ); // frame i
frame.Save( outputPath + Guid.NewGuid().ToString()
+ ".png", ImageFormat.Png );
}