void lsFunction(int fd, char * dirName){
printf("LS -> LOG Header %s \n", dirName);
static char buffer[BUFSIZE + 1];
sprintf(buffer, "%s", listFilesDir(dirName));
write(fd,buffer,BUFSIZE);
}
void mgetFunction(int fd, char *dirName)
{
FILE *fp;
char path[255];
static char buffer[BUFSIZE + 1];
printf("MGET COUNT -> LOG Header %s \n", dirName);
sprintf(buffer, "%s", listFilesDir(dirName));
write(fd,buffer,BUFSIZE);
}
int main(int argc, char *argv[])
{
//Check for minimum number of required arguments
if(argc < 2)
{
std::cerr << "Usage: Executable Input-File Optional-Command" << std::endl;
return -1;
}
//If command argument is given, set it
std::string argCommand;
if(argc == 3)
{
argCommand = argv[2];
}
int counter = 0;
std::vector<vtkSmartPointer<vtkPolyData> > polyVect;
float scale[3];
std::vector<std::string> fileNames;
std::vector<std::string> plyFiles;
std::string fileName;
std::string colorFile;
std::string outputFile;
std::string fileExt;
std::string plyFile;
//Open parameters file
ifstream segParam(argv[1]);
if(!segParam)
{
std::cerr << "Error opening segmentation parameter file" << std::endl;
return -1;
}
//Read in image scale
segParam >> scale[0] >> scale[1] >> scale[2];
//Read in label image file name
segParam >> fileName;
segParam.close();
//Check the image file extension
if(fileName != " " && fileName != "")
{
//Get file extension and output file base (file name without extension)
fileExt = getFileExt(fileName);
outputFile = getOrigFileName(fileName);
//If tif, process
if(fileExt == "tif" || fileExt == "tiff" || fileExt == "TIF" || fileExt == "TIFF")
{
//If running from cache
if(argCommand == "-c")
{
std::cout << "Running from cache..." << std::endl;
std::vector<std::string> *dirFiles = listFilesDir("cache");
if(dirFiles->size() <= 2)
{
std::cout << "Cache doesn't exist/nothing in cache" << std::endl;
return -1;
}
std::string cacheFileExt;
//Iterate through vector of strings containing file names in the cache directory
for(std::vector<std::string>::iterator it = dirFiles->begin(); it != dirFiles->end(); ++it)
{
//If the proper file name base is found
if((*it).find(outputFile) == 0)
{
//Get cache file extension
cacheFileExt = getFileExt((*it));
//If the file is a poly data file
if (cacheFileExt == "ply")
{
//Add it to the poly data file list
std::string output = "cache/";
counter++;
output.append((*it));
plyFiles.push_back(output);
}
}
}
//Render poly data
if(counter == 0)
{
std::cout << "No cached files for this image" << std::endl;
return -1;
}
renderPolyData(counter, scale, plyFiles);
}
else
{
//Make a cache directory if one isn't already there
MKDIR("cache");
//Append ouput string to original file name for colored images
outputFile.append("_out.tif");
//Create relative address string for the colored images to be cached
std::string output = "cache/";
output.append(outputFile);
std::cout << "here" << std::endl;
//Run graph coloring on the original image, to divide it into colored images
ftk::NuclearSegmentation *segmentation = new ftk::NuclearSegmentation();
std::vector<std::string> colorFiles = segmentation->RunGraphColoring(fileName, output);
//Set counter variable to number of outputted color images
counter = (int)colorFiles.size();
//Cycle through the colored images
for(int i = 0; i < counter; i++)
{
//Create string for .ply file name
colorFile = colorFiles[i];
plyFile = colorFiles[i].append(".ply");
//Add this .ply file to the vector of poly data files to be rendered later
plyFiles.push_back(plyFile);
//If this .ply file doesn't already exist, generate the poly data and write the
//.ply file from the colored image files
generatePolyData(colorFile, plyFiles[i], polyVect);
}
delete segmentation;
renderPolyData(counter, scale, plyFiles);
//renderPolyData(counter, scale, polyVect, plyFiles);
}
}
//If file not of the proper type, print error
else
{
std::cerr << "Invalid file type for segmentation output" << std::endl;
return -1;
}
}
//If parameter file can't be opened, print error
else
{
std::cerr << "Invalid filename in parameters, load valid parameter file" << std::endl;
return -1;
}
return 0;
}
