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Merged
transfix merged 7 commits into from
May 2, 2026
Merged

Remove cvcapp singleton: thread cvc::app& through libcvc (Phase A, part 1) #11

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dac67ed
cvc-mesher: thread cvc::app through Mesher main()
transfix May 1, 2026
fab6789
rawv_io: pass app& through thread_info ctor
transfix May 1, 2026
fe32a76
libcvc CLI: thread cvc::app& through dispatch table
transfix May 1, 2026
4c0c026
volume_file_io/utility: delete ctx-less free-function bridges
transfix May 1, 2026
f325f71
volume_file_io subclasses: thread cvc::app& through virtual method bo…
transfix May 1, 2026
5f65657
hdf5_utils: delete ctx-less inline overloads
transfix May 1, 2026
dcf64c5
clang-format: reformat changed lines per CI
transfix May 1, 2026
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102 changes: 1 addition & 101 deletions inc/cvc/hdf5_utils.h
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Expand Up @@ -1334,107 +1334,7 @@ inline void setAttribute(app &ctx, const std::string &hdf5_filename,
setAttribute(ctx, hdf5_filename, hdf5_objname, attribname, std::string(value));
}

// ============================================================
// Context-less convenience overloads (inject cvc::app::instance())
// ============================================================
inline bool isGroup(const std::string &hdf5_filename, const std::string &hdf5_objname) {
return isGroup(app::instance(), hdf5_filename, hdf5_objname);
}

inline bool isDataSet(const std::string &hdf5_filename, const std::string &hdf5_objname) {
return isDataSet(app::instance(), hdf5_filename, hdf5_objname);
}

inline bool objectExists(const std::string &hdf5_filename, const std::string &hdf5_objname) {
return objectExists(app::instance(), hdf5_filename, hdf5_objname);
}

inline void removeObject(const std::string &hdf5_filename, const std::string &hdf5_objname) {
removeObject(app::instance(), hdf5_filename, hdf5_objname);
}

inline void createHDF5File(const std::string &hdf5_filename) {
createHDF5File(app::instance(), hdf5_filename);
}

inline void createGroup(const std::string &hdf5_filename, const std::string &hdf5_objname,
bool replace = false) {
createGroup(app::instance(), hdf5_filename, hdf5_objname, replace);
}

inline void createDataSet(const std::string &hdf5_filename, const std::string &hdf5_objname,
const bounding_box &boundingBox, const dimension &dimension,
data_type dataType, const bool replace = false,
const bool createGroups = true) {
createDataSet(app::instance(), hdf5_filename, hdf5_objname, boundingBox, dimension, dataType,
replace, createGroups);
}

inline void createDataSet(const std::string &hdf5_filename, const std::string &hdf5_objname,
const dimension &dimension, data_type dataType,
const bool createGroups = true) {
createDataSet(app::instance(), hdf5_filename, hdf5_objname, dimension, dataType, createGroups);
}

inline void createDataSet(const std::string &hdf5_filename, const std::string &hdf5_objname,
const std::string &value, bool createGroups = true) {
createDataSet(app::instance(), hdf5_filename, hdf5_objname, value, createGroups);
}

inline dimension getObjectDimension(const std::string &hdf5_filename,
const std::string &hdf5_objname) {
return getObjectDimension(app::instance(), hdf5_filename, hdf5_objname);
}

inline void setObjectDimension(const std::string &hdf5_filename, const std::string &hdf5_objname,
const dimension &dim) {
setObjectDimension(app::instance(), hdf5_filename, hdf5_objname, dim);
}

inline dimension getDataSetDimensionForBoundingBox(const std::string &hdf5_filename,
const std::string &hdf5_objname,
const bounding_box &subvolbox) {
return getDataSetDimensionForBoundingBox(app::instance(), hdf5_filename, hdf5_objname, subvolbox);
}

inline dimension getDataSetDimension(const std::string &hdf5_filename,
const std::string &hdf5_objname, const bounding_box &subvolbox,
const dimension &maxdim = dimension(256, 256, 256)) {
return getDataSetDimension(app::instance(), hdf5_filename, hdf5_objname, subvolbox, maxdim);
}

inline bounding_box getObjectBoundingBox(const std::string &hdf5_filename,
const std::string &hdf5_objname) {
return getObjectBoundingBox(app::instance(), hdf5_filename, hdf5_objname);
}

inline void setObjectBoundingBox(const std::string &hdf5_filename, const std::string &hdf5_objname,
const bounding_box &boundingBox) {
setObjectBoundingBox(app::instance(), hdf5_filename, hdf5_objname, boundingBox);
}

inline double getDataSetMinimum(const std::string &hdf5_filename, const std::string &hdf5_objname) {
return getDataSetMinimum(app::instance(), hdf5_filename, hdf5_objname);
}

inline double getDataSetMaximum(const std::string &hdf5_filename, const std::string &hdf5_objname) {
return getDataSetMaximum(app::instance(), hdf5_filename, hdf5_objname);
}

inline std::string getDataSetInfo(const std::string &hdf5_filename,
const std::string &hdf5_objname) {
return getDataSetInfo(app::instance(), hdf5_filename, hdf5_objname);
}

inline data_type getDataSetType(const std::string &hdf5_filename, const std::string &hdf5_objname) {
return getDataSetType(app::instance(), hdf5_filename, hdf5_objname);
}

inline std::vector<std::string> getChildObjects(const std::string &hdf5_filename,
const std::string &hdf5_objname = "/",
const std::string &filter = std::string()) {
return getChildObjects(app::instance(), hdf5_filename, hdf5_objname, filter);
}
// All hdf5_utils free functions require an explicit cvc::app context.
} // namespace hdf5_utils
} // namespace CVC_NAMESPACE

Expand Down
30 changes: 3 additions & 27 deletions inc/cvc/utility.h
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Original file line number Diff line number Diff line change
Expand Up @@ -103,14 +103,9 @@ static inline double getTriVal(double val[8], double x, double y, double z, doub
}

/*
Shortcut for creating a volume file based on a volume file info object
Shortcut for creating a volume file based on a volume file info object.
All overloads require an explicit cvc::app context.
*/
static inline void createVolumeFile(const std::string &filename, const volume_file_info &volinfo) {
createVolumeFile(filename, volinfo.boundingBox(), volinfo.voxel_dimensions(),
volinfo.voxelTypes(), volinfo.numVariables(), volinfo.numTimesteps(),
volinfo.TMin(), volinfo.TMax());
}

static inline void createVolumeFile(app &ctx, const std::string &filename,
const volume_file_info &volinfo) {
createVolumeFile(ctx, filename, volinfo.boundingBox(), volinfo.voxel_dimensions(),
Expand All @@ -126,12 +121,6 @@ static inline void createVolumeFile(app &ctx, const std::string &filename,
// writes the volume data in the object to the specified file.
// ---- Change History ----
// 01/04/2010 -- Joe R. -- Creation.
static inline void createVolumeFile(const volume &vol, const std::string &filename) {
createVolumeFile(filename, vol.boundingBox(), vol.voxel_dimensions(),
std::vector<data_type>(1, vol.voxelType()));
writeVolumeFile(vol, filename);
}

static inline void createVolumeFile(app &ctx, const volume &vol, const std::string &filename) {
createVolumeFile(ctx, filename, vol.boundingBox(), vol.voxel_dimensions(),
std::vector<data_type>(1, vol.voxelType()));
Expand All @@ -146,10 +135,6 @@ static inline void createVolumeFile(app &ctx, const volume &vol, const std::stri
// createVolumeFile call
// ---- Change History ----
// 01/04/2010 -- Joe R. -- Creation.
static inline void createVolumeFile(const std::string &filename, const volume &vol) {
createVolumeFile(vol, filename);
}

static inline void createVolumeFile(app &ctx, const std::string &filename, const volume &vol) {
createVolumeFile(ctx, vol, filename);
}
Expand All @@ -160,14 +145,7 @@ static inline void createVolumeFile(app &ctx, const std::string &filename, const
(UChar, UShort, UInt), the first half of the set of integers maps to [-1.0,0) and the last half
maps to (0,1.0].
*/
void calcGradient(std::vector<volume> &grad, const volume &vol, data_type vt = Float);

void sub(volume &dest, const volume &vol, uint64 off_x, uint64 off_y, uint64 off_z,
const dimension &subvoldim);

void volconvert(const std::string &input_volume_file, const std::string &output_volume_file);

// ---- Overloads accepting explicit app& context ----
// ---- All free functions take an explicit cvc::app context. ----
void calcGradient(app &ctx, std::vector<volume> &grad, const volume &vol, data_type vt = Float);

void sub(app &ctx, volume &dest, const volume &vol, uint64 off_x, uint64 off_y, uint64 off_z,
Expand Down Expand Up @@ -241,7 +219,5 @@ bool is_volume(const boost::any &data);
bool is_volume_file_info(const boost::any &data);
bool is_geometry_filename(const std::string &filename);
bool is_volume_filename(const std::string &filename);
boost::any load(const std::string &filename);
void save(const boost::any &data, const std::string &filename);
} // namespace CVC_NAMESPACE
#endif
65 changes: 5 additions & 60 deletions inc/cvc/volume_file_io.h
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Original file line number Diff line number Diff line change
Expand Up @@ -244,66 +244,11 @@ struct volume_file_io {
};

// ------------------------- Volume I/O API

/*
read the specified subvolume from the specified file and copy it to the object
vol.
*/
void readVolumeFile(volume &vol, const std::string &filename, unsigned int var, unsigned int time,
uint64 off_x, uint64 off_y, uint64 off_z, const dimension &subvoldim);

/*
read the specified subvolume from the specified file and copy it to the object
vol.
*/
void readVolumeFile(volume &vol, const std::string &filename, unsigned int var, unsigned int time,
const bounding_box &subvolbox);

/*
read the entire volume from the specified file and copy it to the object vol.
*/
void readVolumeFile(volume &vol, const std::string &filename, unsigned int var = 0,
unsigned int time = 0);

/*
Read multi-volume file and add each volume to the vector vols.
*/
void readVolumeFile(std::vector<volume> &vols, const std::string &filename);

/*
write the specified volume to the specified offset in file 'filename'
*/
void writeVolumeFile(const volume &vol, const std::string &filename, unsigned int var = 0,
unsigned int time = 0, uint64 off_x = 0, uint64 off_y = 0, uint64 off_z = 0);

/*
write the specified volume to the specified subvolume bounding box in file 'filename'
*/
void writeVolumeFile(const volume &vol, const std::string &filename, unsigned int var,
unsigned int time, const bounding_box &subvolbox);

/*
Writes the vector 'vols' to the specified file. Make sure that the file extension
specified is for a volume file type that supports multi-volumes. Assumes 1 timestep.
*/
void writeVolumeFile(const std::vector<volume> &vols, const std::string &filename);

/*
Creates a volume file using the specified information.
*/
void createVolumeFile(const std::string &filename, const bounding_box &boundingBox,
const dimension &dimension,
const std::vector<data_type> &voxelTypes = std::vector<data_type>(1, UChar),
unsigned int numVariables = 1, unsigned int numTimesteps = 1,
double min_time = 0.0, double max_time = 0.0);

// Functions for reading and writing volume bounding boxes
bounding_box readBoundingBox(const std::string &filename);
void writeBoundingBox(const bounding_box &bbox, const std::string &filename);

// ---- Overloads accepting explicit app& context ----
// These avoid the app::instance() singleton. Legacy overloads above
// delegate to app::instance() internally.
//
// All free-function I/O takes an explicit cvc::app context so each
// caller controls thread/property/data scoping. (The earlier
// parameterless overloads that delegated to app::instance() have been
// removed.)

void readVolumeFile(app &ctx, volume &vol, const std::string &filename, unsigned int var = 0,
unsigned int time = 0);
Expand Down
4 changes: 3 additions & 1 deletion src/cvc/cvc-mesher/Mesher/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,14 @@
#include <string>
#include <cstdlib>
#include <VolMagickCompat.h>
#include <cvc/app.h>
#include <mesher.h>
#include <boost/program_options.hpp>
#include <stdexcept>

int main(int argc, char **argv)
{
CVC_NAMESPACE::app cvc_ctx;
using namespace std;
namespace po = boost::program_options;

Expand Down Expand Up @@ -79,7 +81,7 @@ int main(int argc, char **argv)
if(operation == "mesh")
{
VolMagick::Volume vol;
VolMagick::readVolumeFile(vol,input_file);
CVC_NAMESPACE::readVolumeFile(cvc_ctx, vol, input_file);

// Convert string arguments to enums
LBIE::Mesher::ExtractionMethod extraction_method_enum;
Expand Down
31 changes: 15 additions & 16 deletions src/cvc/hdf5_io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -311,12 +311,12 @@ struct hdf5_io : public volume_file_io {
// 09/02/2011 -- Joe R. -- Forgot to copy filename to data.
// 09/09/2011 -- Joe R. -- Adding support for ungrouped, lone datasets to make
// multi-res hierarchy thread code simpler.
virtual void getVolumeFileInfo(app & /*ctx*/, volume_file_info::data &d,
virtual void getVolumeFileInfo(app &ctx, volume_file_info::data &d,
const std::string &filename) const {
using namespace hdf5_utils;
using namespace boost;

thread_info ti(BOOST_CURRENT_FUNCTION);
thread_info ti(ctx, BOOST_CURRENT_FUNCTION);

std::string actualFileName;
std::string objectName;
Expand Down Expand Up @@ -456,14 +456,14 @@ struct hdf5_io : public volume_file_io {
// 08/05/2011 -- Joe R. -- Using HDF5 Utilities now.
// 09/09/2011 -- Joe R. -- Adding support for ungrouped, lone datasets to make
// multi-res hierarchy thread code simpler.
virtual void readVolumeFile(app & /*ctx*/, volume &vol, const std::string &filename,
unsigned int var, unsigned int time, uint64 off_x, uint64 off_y,
uint64 off_z, const dimension &subvoldim) const {
virtual void readVolumeFile(app &ctx, volume &vol, const std::string &filename, unsigned int var,
unsigned int time, uint64 off_x, uint64 off_y, uint64 off_z,
const dimension &subvoldim) const {
using namespace H5;
using namespace hdf5_utils;
using namespace boost;

thread_info ti(BOOST_CURRENT_FUNCTION);
thread_info ti(ctx, BOOST_CURRENT_FUNCTION);

std::string actualFileName;
std::string objectName;
Expand Down Expand Up @@ -542,13 +542,12 @@ struct hdf5_io : public volume_file_io {
// multi-res hierarchy thread code simpler.
// 09/17/2011 -- Joe R. -- Picking out the closest dimension to the maxdim in
// the hierarchy.
virtual void readVolumeFile(app & /*ctx*/, volume &vol, const std::string &filename,
unsigned int var, unsigned int time,
const bounding_box &subvolbox) const {
virtual void readVolumeFile(app &ctx, volume &vol, const std::string &filename, unsigned int var,
unsigned int time, const bounding_box &subvolbox) const {
using namespace hdf5_utils;
using namespace boost;

thread_info ti(BOOST_CURRENT_FUNCTION);
thread_info ti(ctx, BOOST_CURRENT_FUNCTION);

std::string actualFileName;
std::string objectName;
Expand Down Expand Up @@ -666,15 +665,15 @@ struct hdf5_io : public volume_file_io {
// 09/02/2011 -- Joe R. -- Calling new createHDF5File function.
// 09/08/2011 -- Joe R. -- Only creating a file if none exists, else just re-using it.
// 09/30/2011 -- Joe R. -- Added objectType attribute.
virtual void createVolumeFile(app & /*ctx*/, const std::string &filename,
virtual void createVolumeFile(app &ctx, const std::string &filename,
const bounding_box &boundingBox, const dimension &dimension,
const std::vector<data_type> &voxelTypes, unsigned int numVariables,
unsigned int numTimesteps, double min_time, double max_time) const {
using namespace hdf5_utils;
namespace fs = boost::filesystem;
using boost::filesystem::path;

thread_info ti(BOOST_CURRENT_FUNCTION);
thread_info ti(ctx, BOOST_CURRENT_FUNCTION);

std::string actualFileName;
std::string objectName;
Expand Down Expand Up @@ -738,13 +737,13 @@ struct hdf5_io : public volume_file_io {
// 08/28/2011 -- Joe R. -- Using HDF5 Utilities now.
// 09/09/2011 -- Joe R. -- Adding support for ungrouped, lone datasets to make
// multi-res hierarchy thread code simpler.
virtual void writeVolumeFile(app & /*ctx*/, const volume &wvol, const std::string &filename,
virtual void writeVolumeFile(app &ctx, const volume &wvol, const std::string &filename,
unsigned int var, unsigned int time, uint64 off_x, uint64 off_y,
uint64 off_z) const {
using namespace hdf5_utils;
using namespace boost;

thread_info ti(BOOST_CURRENT_FUNCTION);
thread_info ti(ctx, BOOST_CURRENT_FUNCTION);

std::string actualFileName;
std::string objectName;
Expand Down Expand Up @@ -825,12 +824,12 @@ struct hdf5_io : public volume_file_io {
// Writes the specified bounding box to the file.
// ---- Change History ----
// 04/06/2012 -- Joe R. -- Creation.
virtual void writeBoundingBox(app & /*ctx*/, const bounding_box &bbox,
virtual void writeBoundingBox(app &ctx, const bounding_box &bbox,
const std::string &filename) const {
using namespace hdf5_utils;
using namespace boost;

thread_info ti(BOOST_CURRENT_FUNCTION);
thread_info ti(ctx, BOOST_CURRENT_FUNCTION);

std::string actualFileName;
std::string objectName;
Expand Down
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