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Component support for datasets #11

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Component support for datasets #11

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097fcc1
added support for components when not mem-mapping
ahota Feb 23, 2018
2a2f1cb
components support for mem-mapped files
ahota Feb 23, 2018
51a8113
added components as configuration parameter
ahota Feb 23, 2018
f0c6fab
added components to named variable volumes
ahota Feb 23, 2018
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1 change: 1 addition & 0 deletions include/Configuration.h
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ namespace pbnj {
int dataXDim;
int dataYDim;
int dataZDim;
unsigned int dataNumComponents;

int imageWidth;
int imageHeight;
Expand Down
3 changes: 2 additions & 1 deletion include/DataFile.h
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Expand Up @@ -12,7 +12,7 @@ namespace pbnj {
class DataFile {

public:
DataFile(int x, int y, int z);
DataFile(int x, int y, int z, unsigned int components=1);
~DataFile();

void loadFromFile(std::string filename, std::string variable="",
Expand All @@ -30,6 +30,7 @@ namespace pbnj {
unsigned long int yDim;
unsigned long int zDim;
unsigned long int numValues;
unsigned int numComponents;

float minVal; // these should
float maxVal; //
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5 changes: 3 additions & 2 deletions include/TimeSeries.h
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Expand Up @@ -13,9 +13,9 @@ namespace pbnj {
class TimeSeries {

public:
TimeSeries(std::vector<std::string> filenames, int x, int y, int z);
TimeSeries(std::vector<std::string> filenames, int x, int y, int z, unsigned int components=1);
TimeSeries(std::vector<std::string> filenames, std::string varname,
int x, int y, int z);
int x, int y, int z, unsigned int components=1);
~TimeSeries();

Volume *getVolume(unsigned int index);
Expand All @@ -38,6 +38,7 @@ namespace pbnj {
int xDim;
int yDim;
int zDim;
unsigned int numComponents;
unsigned int dataSize;
unsigned int maxVolumes;
unsigned int currentVolumes;
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4 changes: 2 additions & 2 deletions include/Volume.h
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Expand Up @@ -16,9 +16,9 @@ namespace pbnj {
public:
//Volume(DataFile *df);
Volume(std::string filename, int x, int y, int z,
bool memmap=false);
bool memmap=false, unsigned int components=1);
Volume(std::string filename, std::string var_name, int x, int y,
int z, bool memmap=false);
int z, bool memmap=false, unsigned int components=1);
~Volume();

void attenuateOpacity(float amount);
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9 changes: 9 additions & 0 deletions src/Configuration.cpp
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Expand Up @@ -188,6 +188,15 @@ Configuration::Configuration(rapidjson::Document& json)
else {
this->specularity = 0.1;
}

// number of data components
// defaults to 1 in DataFile if not used
if(json.HasMember("components")) {
this->dataNumComponents = json["components"].GetUint();
}
else {
this->dataNumComponents = 1;
}
}

void Configuration::selectColorMap(std::string userInput)
Expand Down
45 changes: 38 additions & 7 deletions src/DataFile.cpp
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Expand Up @@ -19,8 +19,9 @@

namespace pbnj {

DataFile::DataFile(int x, int y, int z) :
xDim(x), yDim(y), zDim(z), numValues(x*y*z), statsCalculated(false)
DataFile::DataFile(int x, int y, int z, unsigned int components) :
xDim(x), yDim(y), zDim(z), numValues(x*y*z), statsCalculated(false),
numComponents(components)
{
this->numValues = xDim * yDim * zDim;
}
Expand Down Expand Up @@ -86,9 +87,28 @@ void DataFile::loadFromFile(std::string filename, std::string var_name,
}
else {
if(memmap) {
int fd = fileno(dataFile);
this->data = (float *)mmap(NULL, this->numValues*sizeof(float),
PROT_READ, MAP_SHARED, fd, 0);
if(this->numComponents == 1) {
int fd = fileno(dataFile);
this->data = (float *)mmap(NULL, this->numValues*sizeof(float),
PROT_READ, MAP_SHARED, fd, 0);
}
else {
this->data = (float *)malloc(this->numValues * sizeof(float));
if(this->data == MAP_FAILED) {
switch(errno) {
case ENOMEM:
std::cerr << "ENOMEM out of memory" << std::endl;
break;
}
}
float *chunk = (float *)malloc(this->numComponents*sizeof(float));
for(int i = 0; i < this->numValues; i++) {
size_t numbytes = fread(chunk, sizeof(float),
this->numComponents, dataFile);
this->data[i] = std::sqrt(chunk[0]*chunk[0] +
chunk[1]*chunk[1] + chunk[2]*chunk[2]);
}
}
}
else {
this->data = (float *)malloc(this->numValues * sizeof(float));
Expand All @@ -99,8 +119,19 @@ void DataFile::loadFromFile(std::string filename, std::string var_name,
break;
}
}
size_t bytes = fread(this->data, sizeof(float), this->numValues,
dataFile);
if(this->numComponents == 1) {
size_t bytes = fread(this->data, sizeof(float),
this->numValues, dataFile);
}
else {
float *chunk = (float *)malloc(this->numComponents*sizeof(float));
for(int i = 0; i < this->numValues; i++) {
size_t numbytes = fread(chunk, sizeof(float),
this->numComponents, dataFile);
this->data[i] = std::sqrt(chunk[0]*chunk[0] +
chunk[1]*chunk[1] + chunk[2]*chunk[2]);
}
}
}
fclose(dataFile);
}
Expand Down
13 changes: 7 additions & 6 deletions src/TimeSeries.cpp
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Expand Up @@ -8,9 +8,9 @@
namespace pbnj {

TimeSeries::TimeSeries(std::vector<std::string> filenames,
int x, int y, int z) :
int x, int y, int z, unsigned int components) :
dataFilenames(filenames), length(filenames.size()), xDim(x), yDim(y),
zDim(z), dataSize(x*y*z*4)
zDim(z), dataSize(x*y*z*4), numComponents(components)
{
this->volumes = new Volume*[this->length];
for(int i = 0; i < this->length; i++)
Expand All @@ -22,9 +22,9 @@ TimeSeries::TimeSeries(std::vector<std::string> filenames,
}

TimeSeries::TimeSeries(std::vector<std::string> filenames,
std::string varname, int x, int y, int z) :
std::string varname, int x, int y, int z, unsigned int components) :
dataFilenames(filenames), length(filenames.size()), dataVariable(varname),
xDim(x), yDim(y), zDim(z), dataSize(x*y*z*4)
xDim(x), yDim(y), zDim(z), dataSize(x*y*z*4), numComponents(components)
{
this->volumes = new Volume*[this->length];
for(int i = 0; i < this->length; i++)
Expand Down Expand Up @@ -110,11 +110,12 @@ Volume *TimeSeries::getVolume(unsigned int index)
// load the volume
if(this->dataVariable.empty())
this->volumes[index] = new Volume(this->dataFilenames[index],
this->xDim, this->yDim, this->zDim, this->doMemoryMap);
this->xDim, this->yDim, this->zDim, this->doMemoryMap,
this->numComponents);
else
this->volumes[index] = new Volume(this->dataFilenames[index],
this->dataVariable, this->xDim, this->yDim, this->zDim,
this->doMemoryMap);
this->doMemoryMap, this->numComponents);

// set any given attributes
if(!this->colorMap.empty())
Expand Down
9 changes: 5 additions & 4 deletions src/Volume.cpp
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Expand Up @@ -8,24 +8,25 @@

namespace pbnj {

Volume::Volume(std::string filename, int x, int y, int z, bool memmap)
Volume::Volume(std::string filename, int x, int y, int z, bool memmap,
unsigned int components)
{
this->ID = createID();
//volumes contain a datafile
//one datafile per volume, one volume per renderer/camera
this->dataFile = new DataFile(x, y, z);
this->dataFile = new DataFile(x, y, z, components);
this->loadFromFile(filename, "", memmap);

this->init();
}

Volume::Volume(std::string filename, std::string var_name, int x, int y, int z,
bool memmap)
bool memmap, unsigned int components)
{
this->ID = createID();
//volumes contain a datafile
//one datafile per volume, one volume per renderer/camera
this->dataFile = new DataFile(x, y, z);
this->dataFile = new DataFile(x, y, z, components);
this->loadFromFile(filename, var_name, memmap);

this->init();
Expand Down
9 changes: 5 additions & 4 deletions src/test/simpleVolumeRender.cpp
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Expand Up @@ -59,18 +59,19 @@ int main(int argc, const char **argv)
case pbnj::SINGLE_NOVAR:
std::cout << "Single volume, no variable" << std::endl;
volume = new pbnj::Volume(config->dataFilename, config->dataXDim,
config->dataYDim, config->dataZDim, true);
config->dataYDim, config->dataZDim, true, config->dataNumComponents);
break;
case pbnj::SINGLE_VAR:
std::cout << "Single volume, variable" << std::endl;
volume = new pbnj::Volume(config->dataFilename,
config->dataVariable, config->dataXDim, config->dataYDim,
config->dataZDim);
config->dataZDim, config->dataNumComponents);
break;
case pbnj::MULTI_NOVAR:
std::cout << "Multiple volumes, no variable" << std::endl;
timeSeries = new pbnj::TimeSeries(config->globbedFilenames,
config->dataXDim, config->dataYDim, config->dataZDim);
config->dataXDim, config->dataYDim, config->dataZDim,
config->dataNumComponents);
timeSeries->setColorMap(config->colorMap);
timeSeries->setOpacityMap(config->opacityMap);
timeSeries->setOpacityAttenuation(config->opacityAttenuation);
Expand All @@ -81,7 +82,7 @@ int main(int argc, const char **argv)
std::cout << "Multiple volumes, variable" << std::endl;
timeSeries = new pbnj::TimeSeries(config->globbedFilenames,
config->dataVariable, config->dataXDim, config->dataYDim,
config->dataZDim);
config->dataZDim, config->dataNumComponents);
timeSeries->setColorMap(config->colorMap);
timeSeries->setOpacityMap(config->opacityMap);
timeSeries->setOpacityAttenuation(config->opacityAttenuation);
Expand Down