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Commit 558e2873 authored by Christian Schulte zu Berge's avatar Christian Schulte zu Berge
Browse files

Cleaned up DevilImageReader to be working with all kinds of input images and... 

Cleaned up DevilImageReader to be working with all kinds of input images and being completely OpenGL free.
parent 3df868fd
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modules/devil/processors/devilimagereader.cpp
View file @ 558e2873
......@@ -50,20 +50,20 @@
namespace campvis {
const std::string DevilImageReader::loggerCat_ = "CAMPVis.modules.io.DevilImageReader";
GenericOption<std::string> importOptions[4] = {
GenericOption<std::string> importOptions[3] = {
GenericOption<std::string>("rt", "Render Target"),
GenericOption<std::string>("texture", "OpenGL Texture"),
GenericOption<std::string>("localIntensity", "Local Intensity Image"),
GenericOption<std::string>("localIntensity3", "Local Intensity Image RGB")
};
DevilImageReader::DevilImageReader()
: AbstractImageReader()
, p_importType("ImportType", "Import Type", importOptions, 4)
, p_importType("ImportType", "Import Type", importOptions, 3)
, p_importSimilar("ImportSimilar", "Import All Similar Files", false)
, _shader(nullptr)
, _devilTextureReader(nullptr)
{
this->_ext.push_back(".bmp");
this->_ext.push_back(".jpg");
this->_ext.push_back(".png");
this->_ext.push_back(".tif");
......@@ -75,8 +75,6 @@ namespace campvis {
addProperty(p_importSimilar);
_devilTextureReader = new tgt::TextureReaderDevil();
p_importType.selectById("localIntensity3");
}
DevilImageReader::~DevilImageReader() {
......@@ -96,96 +94,176 @@ namespace campvis {
}
void DevilImageReader::updateResult(DataContainer& data) {
std::string url = this->p_url.getValue();
std::string base = "", numstr = "", ext = "";
size_t _Pos = url.rfind('_');
size_t dotPos = url.rfind('.');
if (dotPos > _Pos && dotPos != std::string::npos && _Pos != std::string::npos ) {
numstr = url.substr(_Pos+1, dotPos);
base = url.substr(0, _Pos+1);
ext = url.substr(dotPos);
}
int suffix = StringUtils::fromString<int>(numstr);
std::cout << "\nfileName Suffix: "<<suffix <<" count: "<<dotPos-_Pos <<std::endl;
const std::string& url = p_url.getValue();
std::string directory = tgt::FileSystem::dirName(url);
std::string base = tgt::FileSystem::baseName(url);
std::string ext = tgt::FileSystem::fileExtension(url);
// FIXME: clean up this whole implementation mess and make it fully non-OpenGL!
OpenGLJobProcessor::ScopedSynchronousGlJobExecution glGuard;
tgt::Texture* tex = _devilTextureReader->loadTexture(p_url.getValue(), tgt::Texture::LINEAR, false, true, true, false);
// check whether we open an image series
size_t suffixPos = base.find_last_not_of("0123456789");
if (suffixPos != std::string::npos)
++suffixPos;
size_t suffixLength = (suffixPos == std::string::npos) ? 0 : base.length() - suffixPos;
if (tex != 0) {
if (p_importType.getOptionValue() == "rt") {
tgtAssert(false, "This type is no longer supported.");
}
else if (p_importType.getOptionValue() == "texture") {
ImageData* id = new ImageData(3, tex->getDimensions(), tex->getNumChannels());
ImageRepresentationGL::create(id, tex);
data.addData(p_targetImageID.getValue(), id);
// assemble the list of files to read
std::vector<std::string> files;
if (suffixLength == 0 || !p_importSimilar.getValue()) {
files.push_back(url);
}
else {
std::string prefix = base.substr(0, suffixPos);
int index = StringUtils::fromString<int>(base.substr(suffixPos));
while (tgt::FileSystem::fileExists(directory + "/" + prefix + StringUtils::toString(index, suffixLength, '0') + "." + ext)) {
files.push_back(directory + "/" + prefix + StringUtils::toString(index, suffixLength, '0') + "." + ext);
++index;
}
else if (p_importType.getOptionValue() == "localIntensity") {
// TODO: Clean up pre-MICCAI mess!
glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
tex->downloadTexture();
size_t numElements = tgt::hmul(tex->getDimensions());
ImageData* id = new ImageData(3, tex->getDimensions(), 1);
// TODO: use macro magic to switch through the different data types and number of channels
if (tex->getDataType() == GL_UNSIGNED_BYTE && tex->getNumChannels() == 3) {
tgt::Vector3<uint8_t>* data = reinterpret_cast<tgt::Vector3<uint8_t>*>(tex->getPixelData());
uint8_t* copy = new uint8_t[numElements];
for (size_t i = 0; i < numElements; ++i) {
copy[i] = data[i].x;
}
GenericImageRepresentationLocal<uint8_t, 1>::create(id, copy);
}
}
tgt::ivec3 imageSize(0, 0, static_cast<int>(files.size()));
uint8_t* buffer = nullptr;
ILint devilFormat = 0;
if (p_importType.getOptionValue() == "localIntensity")
devilFormat = IL_LUMINANCE;
else if (p_importType.getOptionValue() == "localIntensity3")
devilFormat = IL_RGB;
else if (p_importType.getOptionValue() == "rt")
devilFormat = IL_RGBA;
delete tex;
data.addData(p_targetImageID.getValue(), id);
ILint devilDataType = 0;
WeaklyTypedPointer::BaseType campvisDataType;
size_t numChannels = 1;
// start reading
for (size_t i = 0; i < files.size(); ++i) {
// prepare DevIL
ILuint img;
ilGenImages(1, &img);
ilBindImage(img);
// try load file
if (! ilLoadImage(files[i].c_str())) {
LERROR("Could not load image: " << files[i]);
delete [] buffer;
return;
}
else if (p_importType.getOptionValue() == "localIntensity3") {
glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
tex->downloadTexture();
size_t numElements = tgt::hmul(tex->getDimensions());
tgt::ivec3 temp = tex->getDimensions();
int zee = 0;
std::vector<tgt::Vector3<uint8_t> > vdata;
while (nullptr != tex) {
if (tex->getDataType() == GL_UNSIGNED_BYTE && tex->getNumChannels() == 3) {
tgt::Vector3<uint8_t>* data = reinterpret_cast<tgt::Vector3<uint8_t>*>(tex->getPixelData());
for (size_t i = 0; i < numElements*1; ++i) {
for(int k = 0; k < temp.z; k++){
vdata.push_back(data[i % numElements]);
}
}
zee+=1;
}
delete tex;
if (this->p_importSimilar.getValue() == true) {
numstr = StringUtils::toString(++suffix, dotPos-_Pos-1, '0');
std::cout << base+numstr+ext;
tex = _devilTextureReader->loadTexture(base+numstr+ext, tgt::Texture::LINEAR, false, true, true, false);
if(nullptr != tex)
tex->downloadTexture();
}
else {
// prepare buffer and perform dimensions check
if (i == 0) {
imageSize.x = ilGetInteger(IL_IMAGE_WIDTH);
imageSize.y = ilGetInteger(IL_IMAGE_HEIGHT);
if (devilFormat == 0)
devilFormat = ilGetInteger(IL_IMAGE_FORMAT);
switch (ilGetInteger(IL_IMAGE_TYPE)) {
case IL_UNSIGNED_BYTE:
devilDataType = IL_UNSIGNED_BYTE;
campvisDataType = WeaklyTypedPointer::UINT8;
break;
case IL_BYTE:
devilDataType = IL_BYTE;
campvisDataType = WeaklyTypedPointer::INT8;
break;
case IL_UNSIGNED_SHORT:
devilDataType = IL_UNSIGNED_SHORT;
campvisDataType = WeaklyTypedPointer::UINT16;
break;
case IL_SHORT:
devilDataType = IL_SHORT;
campvisDataType = WeaklyTypedPointer::INT16;
break;
case IL_UNSIGNED_INT:
devilDataType = IL_UNSIGNED_INT;
campvisDataType = WeaklyTypedPointer::UINT32;
break;
}
case IL_INT:
devilDataType = IL_INT;
campvisDataType = WeaklyTypedPointer::INT32;
break;
case IL_FLOAT:
devilDataType = IL_FLOAT;
campvisDataType = WeaklyTypedPointer::FLOAT;
break;
default:
LERROR("unsupported data type: " << ilGetInteger(IL_IMAGE_TYPE) << " (" << files[i] << ")");
return;
}
temp.z = zee;
ImageData* id = new ImageData(3, temp, 3);
switch (devilFormat) {
case IL_LUMINANCE:
numChannels = 1;
break;
case IL_LUMINANCE_ALPHA:
numChannels = 2;
break;
case IL_RGB:
numChannels = 3;
break;
case IL_RGBA:
numChannels = 4;
break;
default:
LERROR("unsupported image format: " << devilFormat << " (" << files[i] << ")");
return;
}
buffer = new uint8_t[tgt::hmul(imageSize) * WeaklyTypedPointer::numBytes(campvisDataType, numChannels)];
}
else {
if (imageSize.x != ilGetInteger(IL_IMAGE_WIDTH)) {
LERROR("Could not load images: widths do not match!");
delete [] buffer;
return;
}
if (imageSize.y != ilGetInteger(IL_IMAGE_HEIGHT)) {
LERROR("Could not load images: heights do not match!");
delete [] buffer;
return;
}
}
tgt::Vector3<uint8_t>* data3d = new tgt::Vector3<uint8_t>[temp.x * temp.y * temp.z];
memcpy(data3d, &vdata.front(), temp.x*temp.y*temp.z *3);
GenericImageRepresentationLocal<uint8_t, 3>::create(id, data3d);
// get data from image and transform to single intensity image:
ILubyte* data = ilGetData();
id->setMappingInformation(ImageMappingInformation(id->getSize(), id->getMappingInformation().getOffset(), id->getMappingInformation().getVoxelSize() * tgt::vec3(1, 1, 1) ));
data.addData(p_targetImageID.getValue(), id);
ilCopyPixels(0, 0, 0, imageSize.x, imageSize.y, 1, devilFormat, devilDataType, buffer + (WeaklyTypedPointer::numBytes(campvisDataType, numChannels) * i * imageSize.x * imageSize.y));
ILint err = ilGetError();
if (err != IL_NO_ERROR) {
LERROR("Error during conversion: " << iluErrorString(err));
delete [] buffer;
return;
}
ilDeleteImage(img);
}
size_t dimensionality = 3;
if (imageSize.z == 1)
dimensionality = 2;
if (imageSize.y == 1)
dimensionality = 1;
ImageData* id = new ImageData(dimensionality, imageSize, numChannels);
WeaklyTypedPointer wtp(campvisDataType, numChannels, buffer);
ImageRepresentationLocal::create(id, wtp);
//id->setMappingInformation(ImageMappingInformation(imageSize, p_imageOffset.getValue(), p_voxelSize.getValue()));
if (p_importType.getOptionValue() == "rt") {
RenderData* rd = new RenderData();
rd->addColorTexture(id);
// create fake depth image
ImageData* idDepth = new ImageData(dimensionality, imageSize, 1);
float* ptr = new float[tgt::hmul(imageSize)];
WeaklyTypedPointer wtpDepth(campvisDataType, 1, ptr);
ImageRepresentationLocal::create(idDepth, wtpDepth);
rd->setDepthTexture(idDepth);
data.addData(p_targetImageID.getValue(), rd);
}
else {
LDEBUG("Could not load image.");
data.addData(p_targetImageID.getValue(), id);
}
}
}
\ No newline at end of file
modules/microscopysegmentation/pipelines/microscopyimagesegmentationdemo.cpp
View file @ 558e2873
......@@ -64,6 +64,9 @@ namespace campvis {
tgtAssert(nullptr != bp, "This should not happen.");
bp->setValue(true);
if (GenericOptionProperty<std::string>* tester = dynamic_cast<GenericOptionProperty<std::string>*>(_imageReader.getNestedProperty("DevilImageReaderMetaProp::ImportType")))
tester->selectById("localIntensity3");
_imageReader.setTargetImageId("mscopy.output");
_imageReader.setTargetImageIdSharedProperty(&_ve.p_inputVolume);
......
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