C++ Reading back "incorrect" values from binary file? - c++

Question

The project I'm working on, as a custom file format consisting of the header of a few different variables, followed by the pixel data. My colleagues have developed a GUI, where processing, writing reading and displaying this type of file format works fine.
But my problem is, while I have assisted in writing the code for writing data to disk, I cannot myself read this kind of file and get satisfactorily values back. I am able to read the first variable back (char array) but not the following value(s).
So the file format matches the following structure:
typedef struct {
char hxtLabel[8];
u64 hxtVersion;
int motorPositions[9];
int filePrefixLength;
char filePrefix[100];
..
} HxtBuffer;
In the code, I create an object of the above structure and then set these example values:
setLabel("MY_LABEL");
setFormatVersion(3);
setMotorPosition( 2109, 5438, 8767, 1234, 1022, 1033, 1044, 1055, 1066);
setFilePrefixLength(7);
setFilePrefix( string("prefix_"));
setDataTimeStamp( string("000000_000000"));
My code for opening the file:
// Open data file, binary mode, reading
ifstream datFile(aFileName.c_str(), ios::in | ios::binary);
if (!datFile.is_open()) {
cout << "readFile() ERROR: Failed to open file " << aFileName << endl;
return false;
}
// How large is the file?
datFile.seekg(0, datFile.end);
int length = datFile.tellg();
datFile.seekg(0, datFile.beg);
cout << "readFile() file " << setw(70) << aFileName << " is: " << setw(15) << length << " long\n";
// Allocate memory for buffer:
char * buffer = new char[length];
// Read data as one block:
datFile.read(buffer, length);
datFile.close();
/// Looking at the start of the buffer, I should be seeing "MY_LABEL"?
cout << "buffer: " << buffer << " " << *(buffer) << endl;
int* mSSX = reinterpret_cast<int*>(*(buffer+8));
int* mSSY = reinterpret_cast<int*>(&buffer+9);
int* mSSZ = reinterpret_cast<int*>(&buffer+10);
int* mSSROT = reinterpret_cast<int*>(&buffer+11);
int* mTimer = reinterpret_cast<int*>(&buffer+12);
int* mGALX = reinterpret_cast<int*>(&buffer+13);
int* mGALY = reinterpret_cast<int*>(&buffer+14);
int* mGALZ = reinterpret_cast<int*>(&buffer+15);
int* mGALROT = reinterpret_cast<int*>(&buffer+16);
int* filePrefixLength = reinterpret_cast<int*>(&buffer+17);
std::string filePrefix; std::string dataTimeStamp;
// Read file prefix character by character into stringstream object
std::stringstream ss;
char* cPointer = (char *)(buffer+18);
int k;
for(k = 0; k < *filePrefixLength; k++)
{
//read string
char c;
c = *cPointer;
ss << c;
cPointer++;
}
filePrefix = ss.str();
// Read timestamp character by character into stringstream object
std::stringstream timeStampStream;
/// Need not increment cPointer, already pointing # 1st char of timeStamp
for (int l= 0; l < 13; l++)
{
char c;
c = * cPointer;
timeStampStream << c;
}
dataTimeStamp = timeStampStream.str();
cout << 25 << endl;
cout << " mSSX: " << mSSX << " mSSY: " << mSSY << " mSSZ: " << mSSZ;
cout << " mSSROT: " << mSSROT << " mTimer: " << mTimer << " mGALX: " << mGALX;
cout << " mGALY: " << mGALY << " mGALZ: " << mGALZ << " mGALROT: " << mGALROT;
Finally, what I see is here below. I added the 25 just to double check that not everything was coming out in hexadecimal. As you can see, I am able to see the label "MY_LABEL" as expected. But the 9 motorPositions all come out looking suspiciously like addresses are not values. The file prefix and the data timestamp (which should be strings, or at least characters), are just empty.
buffer: MY_LABEL M
25
mSSX: 0000000000000003 mSSY: 00000000001BF618 mSSZ: 00000000001BF620 mSSROT: 00000000001BF628 mTimer: 00000000001BF630 mGALX: 00000000001BF638 mGALY: 00000000001BF640 mGALZ: 00000000001BF648 mGALROT: 00000000001BF650filePrefix: dataTimeStamp:
I'm sure the solution can't be too complicated, but I reached a stage where I had this just spinning and I cannot make sense of things.
Many thanks for reading this somewhat long post.
-- Edit--
I might hit the maximum length allowed for a post, but just in case I thought I shall post the code that generates the data that I'm trying to read back:
bool writePixelOutput(string aOutputPixelFileName) {
// Write pixel histograms out to binary file
ofstream pixelFile;
pixelFile.open(aOutputPixelFileName.c_str(), ios::binary | ios::out | ios::trunc);
if (!pixelFile.is_open()) {
LOG(gLogConfig, logERROR) << "Failed to open output file " << aOutputPixelFileName;
return false;
}
// Write binary file header
string label("MY_LABEL");
pixelFile.write(label.c_str(), label.length());
pixelFile.write((const char*)&mFormatVersion, sizeof(u64));
// Include File Prefix/Motor Positions/Data Time Stamp - if format version > 1
if (mFormatVersion > 1)
{
pixelFile.write((const char*)&mSSX, sizeof(mSSX));
pixelFile.write((const char*)&mSSY, sizeof(mSSY));
pixelFile.write((const char*)&mSSZ, sizeof(mSSZ));
pixelFile.write((const char*)&mSSROT, sizeof(mSSROT));
pixelFile.write((const char*)&mTimer, sizeof(mTimer));
pixelFile.write((const char*)&mGALX, sizeof(mGALX));
pixelFile.write((const char*)&mGALY, sizeof(mGALY));
pixelFile.write((const char*)&mGALZ, sizeof(mGALZ));
pixelFile.write((const char*)&mGALROT, sizeof(mGALROT));
// Determine length of mFilePrefix string
int filePrefixSize = (int)mFilePrefix.size();
// Write prefix length, followed by prefix itself
pixelFile.write((const char*)&filePrefixSize, sizeof(filePrefixSize));
size_t prefixLen = 0;
if (mFormatVersion == 2) prefixLen = mFilePrefix.size();
else prefixLen = 100;
pixelFile.write(mFilePrefix.c_str(), prefixLen);
pixelFile.write(mDataTimeStamp.c_str(), mDataTimeStamp.size());
}
// Continue writing header information that is common to both format versions
pixelFile.write((const char*)&mRows, sizeof(mRows));
pixelFile.write((const char*)&mCols, sizeof(mCols));
pixelFile.write((const char*)&mHistoBins, sizeof(mHistoBins));
// Write the actual data - taken out for briefy sake
// ..
pixelFile.close();
LOG(gLogConfig, logINFO) << "Written output histogram binary file " << aOutputPixelFileName;
return true;
}
-- Edit 2 (11:32 09/12/2015) --
Thank you for all the help, I'm closer to solving the issue now. Going with the answer from muelleth, I try:
/// Read into char buffer
char * buffer = new char[length];
datFile.read(buffer, length);// length determined by ifstream.seekg()
/// Let's try HxtBuffer
HxtBuffer *input = new HxtBuffer;
cout << "sizeof HxtBuffer: " << sizeof *input << endl;
memcpy(input, buffer, length);
I can then display the different struct variables:
qDebug() << "Slice BUFFER label " << QString::fromStdString(input->hxtLabel);
qDebug() << "Slice BUFFER version " << QString::number(input->hxtVersion);
qDebug() << "Slice BUFFER hxtPrefixLength " << QString::number(input->filePrefixLength);
for (int i = 0; i < 9; i++)
{
qDebug() << i << QString::number(input->motorPositions[i]);
}
qDebug() << "Slice BUFFER filePrefix " << QString::fromStdString(input->filePrefix);
qDebug() << "Slice BUFFER dataTimeStamp " << QString::fromStdString(input->dataTimeStamp);
qDebug() << "Slice BUFFER nRows " << QString::number(input->nRows);
qDebug() << "Slice BUFFER nCols " << QString::number(input->nCols);
qDebug() << "Slice BUFFER nBins " << QString::number(input->nBins);
The output is then mostly as expected:
Slice BUFFER label "MY_LABEL"
Slice BUFFER version "3"
Slice BUFFER hxtPrefixLength "2"
0 "2109"
1 "5438"
...
7 "1055"
8 "1066"
Slice BUFFER filePrefix "-1"
Slice BUFFER dataTimeStamp "000000_000000P"
Slice BUFFER nRows "20480"
Slice BUFFER nCols "256000"
Slice BUFFER nBins "0"
EXCEPT, dataTimeStamp, which is 13 chars long, displays instead 14 chars. The 3 variables that follow: nRows, nCols and nBins are then incorrect. (Should be nRows=80, nCols=80, nBins=1000). My guess is that the bits belonging to the 14th char of dataTimeStamp should be read along with nRows, and so cascade on to produce the correct nCols and nBins.
I have separately verified (not shown here) using qDebug that what I'm writing into the file, really are the values I expect, and their individual sizes.

Answer 1

I personally would try to read exactly the number of bytes your struct is from the file, i.e. something like
int length = sizeof(HxtBuffer);
and then simply use memcpy to assign a local structure from the read buffer:
HxtBuffer input;
memcpy(&input, buffer, length);
You can then access your data e.g. like:
std::cout << "Data: " << input.hxtLabel << std::endl;

Answer 2

Why do you read to buffer, instead of using the structure for reading?
HxtBuffer data;
datFile.read(reinterpret_cast<char *>(&data), sizeof data);
if(datFile && datFile.gcount()!=sizeof data)
throw io_exception();
// Can use data.
If you want to read to a chracter buffer, than your way of getting the data is just wrong. You probably want to do something like this.
char *buf_offset=buffer+8+sizeof(u64); // Skip label (8 chars) and version (int64)
int mSSX = *reinterpret_cast<int*>(buf_offset);
buf_offset+=sizeof(int);
int mSSY = *reinterpret_cast<int*>(buf_offset);
buf_offset+=sizeof(int);
int mSSZ = *reinterpret_cast<int*>(buf_offset);
/* etc. */
Or, a little better (provided you don't change the contents of the buffer).
int *ptr_motors=reinterpret_cast<int *>(buffer+8+sizeof(u64));
int &mSSX = ptr_motors[0];
int &mSSY = ptr_motors[1];
int &mSSZ = ptr_motors[2];
/* etc. */
Notice that I don't declare mSSX, mSSY etc. as pointers. Your code was printing them as addresses because you told the compiler that they were addresses (pointers).