// output from this are a functioning wells file and a beadfind mask
// images are only known internally to this.
void RealImagesToWells (
OptArgs &opts,
CommandLineOpts& inception_state,
SeqListClass& my_keys,
TrackProgress& my_progress,
ImageSpecClass& my_image_spec,
SlicedPrequel& my_prequel_setup )
{
Region wholeChip(0, 0, my_image_spec.cols, my_image_spec.rows);
ComplexMask* complex_mask = 0;
BkgFitterTracker* bkg_fitter_tracker = 0;
if(inception_state.bkg_control.signal_chunks.restart_from.empty())
{
// do separator if necessary: generate mask
IsolatedBeadFind ( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.GetResultsFolder(), inception_state.sys_context.analysisLocation, my_keys, my_progress );
}
else
{
// restarting execution from known state, restore my_prequel_setup
// no matter what I do seems like all restoration has to happen in this scope
string filePath = inception_state.sys_context.analysisLocation + inception_state.bkg_control.signal_chunks.restart_from;
time_t begin_load_time;
time ( &begin_load_time );
ifstream ifs(filePath.c_str(), ifstream::in);
assert(ifs.good());
// boost::archive::text_iarchive in_archive(ifs);
boost::archive::binary_iarchive in_archive(ifs);
string saved_git_hash;
in_archive >> saved_git_hash
>> my_prequel_setup
>> complex_mask
>> bkg_fitter_tracker;
ifs.close();
time_t finish_load_time;
time ( &finish_load_time );
fprintf ( stdout, "Loading restart state from archive %s took %0.1f sec\n",
filePath.c_str(), difftime ( finish_load_time, begin_load_time ));
if ( inception_state.bkg_control.signal_chunks.restart_check ){
string git_hash = IonVersion::GetGitHash();
ION_ASSERT( (saved_git_hash.compare(git_hash) == 0),
"This GIT hash " + git_hash + " of Analysis does not match the GIT hash " + saved_git_hash + " where " + filePath + " was saved; disable this check by using --no-restart-check");
}
// set file locations
my_prequel_setup.FileLocations ( inception_state.sys_context.analysisLocation );
}
// Check if we have enoguh flows to perform signal processing.
// If we are starting from flow 0 we should have at least number of flows
// equalling flow block size (currently 20) to perform regional paramter
// fitting in background model and derive any actional information for the
// next set of flows. If we dont have thes minimum number of flows then give
// an appropriate message and error out
if (!CheckForMinimumNumberOfFlows(inception_state)) {
std::cout << "ERROR: Insufficient number of flows to start signal processing. "
<< "Minimum number of flows required is 20." << std::endl;
exit(EXIT_FAILURE);
}
// do signal processing generate wells conditional on a separator
IsolatedSignalProcessing ( my_prequel_setup, my_image_spec, wholeChip, opts, inception_state,
inception_state.sys_context.analysisLocation, my_keys, my_progress, complex_mask, bkg_fitter_tracker );
// @TODO cleanup causes crash when restarted, why?
// if (complex_mask != NULL) delete complex_mask;
// if (bkg_fitter_tracker != NULL) delete bkg_fitter_tracker;
}
void SetUpOrLoadInitialState(CommandLineOpts &inception_state, SeqListClass &my_keys, TrackProgress &my_progress, ImageSpecClass &my_image_spec, SlicedPrequel& my_prequel_setup)
{
if ( !inception_state.bkg_control.signal_chunks.restart_from.empty() )
{
// restarting from saved computational state
// beadfind, bfmask.bin and beadfind.h5 will be ignored
// note that if we are here we will never load the separator data
inception_state.sys_context.GenerateContext (); // find our directories
inception_state.sys_context.SetUpAnalysisLocation();
LoadBeadFindState(inception_state, my_keys, my_image_spec);
}
else if (inception_state.mod_control.reusePriorBeadfind && inception_state.bkg_control.signal_chunks.restart_from.empty())
{
// starting execution fresh, justBeadFind already run
// get any state from beadFind
LoadBeadFindState(inception_state, my_keys, my_image_spec);
// save current command line options to state file
std::string stateFile = inception_state.sys_context.analysisLocation + "/analysisState.json";
if (rename(stateFile.c_str(),(inception_state.sys_context.analysisLocation+"/analysisState_beadfind.json").c_str()) )
{
fprintf(stdout, "Unable to copy beadfind analysisState.json");
}
SetUpKeys(my_keys, inception_state.key_context, inception_state.flow_context);
ProgramState state ( stateFile );
state.Save ( inception_state,my_keys,my_image_spec );
state.WriteState();
// region layout saved in inception_state.loc_context
// region definitions in background model via my_prequel_setup
my_prequel_setup.SetRegions ( inception_state.loc_context.numRegions,
my_image_spec.rows,my_image_spec.cols,
inception_state.loc_context.regionXSize,
inception_state.loc_context.regionYSize );
my_prequel_setup.FileLocations ( inception_state.sys_context.analysisLocation );
}
else
{
// starting execution fresh, justBeadFind not run
inception_state.SetUpProcessing();
CreateResultsFolder (inception_state.sys_context.GetResultsFolder());
inception_state.sys_context.SetUpAnalysisLocation();
// convert from old key representatino to more useful modern style
SetUpKeys(my_keys, inception_state.key_context, inception_state.flow_context);
//@TODO: side effects here on the entire image class
// after this point, Images will behave differently when read in
SetUpToProcessImages ( my_image_spec, inception_state );
// region layout saved into inception_state.loc_context
SetUpRegionsForAnalysis ( my_image_spec.rows, my_image_spec.cols, inception_state.loc_context );
// region layout shared in background model and beadfind via my_prequel_setup
my_prequel_setup.SetRegions ( inception_state.loc_context.numRegions,
my_image_spec.rows,my_image_spec.cols,
inception_state.loc_context.regionXSize,
inception_state.loc_context.regionYSize );
my_prequel_setup.FileLocations ( inception_state.sys_context.analysisLocation );
}
strncpy(ImageTransformer::PCATest,inception_state.img_control.PCATest,sizeof(ImageTransformer::PCATest)-1);
fprintf(stdout, "Analysis region size is width %d, height %d\n", inception_state.loc_context.regionXSize, inception_state.loc_context.regionYSize);
}
void IsolatedSignalProcessing (
SlicedPrequel &my_prequel_setup,
ImageSpecClass &my_image_spec,
Region &wholeChip,
OptArgs &opts,
CommandLineOpts &inception_state,
string &analysisLocation,
SeqListClass &my_keys,
TrackProgress &my_progress,
ComplexMask *complex_mask,
BkgFitterTracker *bkg_fitter_tracker)
{
//@TODO: split function here as we immediately pick up the files
ComplexMask from_beadfind_mask; //Todo: check if we can move this one level up so it is at the same level as the read in from the archive.
if(!(inception_state.bkg_control.signal_chunks.restart_from.empty()))
{
from_beadfind_mask = *complex_mask;
}
else
{
// starting execution fresh
from_beadfind_mask.InitMask();
my_prequel_setup.LoadBeadFindForSignalProcessing ( true );
Json::Value json1;
vector<int> region_list;
RetrieveParameterVectorInt(opts, json1, '-', "region-list", "", region_list);
if(!region_list.empty())
{
my_prequel_setup.RestrictRegions(region_list);
}
if ( inception_state.bfd_control.beadMaskFile != NULL )
{
fprintf ( stdout, "overriding beadfind mask with %s\n", inception_state.bfd_control.beadMaskFile );
from_beadfind_mask.my_mask->LoadMaskAndAbortOnFailure ( inception_state.bfd_control.beadMaskFile );
}
else
{
from_beadfind_mask.my_mask->LoadMaskAndAbortOnFailure ( my_prequel_setup.bfMaskFile.c_str() );
}
from_beadfind_mask.InitPinnedInFlow ( inception_state.flow_context.GetNumFlows() );
}
/********************************************************************
*
* Background Modelling Process
*
*******************************************************************/
// set up the directory for a new temporary wells file
// clear out previous ones (can be bad with re-entrant processing!)
ClearStaleWellsFile();
inception_state.sys_context.MakeNewTmpWellsFile ( inception_state.sys_context.GetResultsFolder() );
// feenableexcept(FE_DIVBYZERO | FE_INVALID); // | FE_OVERFLOW);
// we might use some other model here
if ( true )
{
DoThreadedSignalProcessing ( opts, inception_state, from_beadfind_mask, ChipIdDecoder::GetChipType(), my_image_spec,
my_prequel_setup,my_keys, inception_state.mod_control.passTau, bkg_fitter_tracker);
} // end BKG_MODL
// whatever model we run, copy the signals to permanent location
inception_state.sys_context.CopyTmpWellFileToPermanent ( inception_state.sys_context.GetResultsFolder() );
inception_state.sys_context.CleanupTmpWellsFile (); // remove local file(!) how will this work with re-entrant processing????
// mask file may be updated by model processing
// analysis.bfmask.bin is what BaseCaller expects
string analysisMaskFile = analysisLocation + "analysis.bfmask.bin";
string analysisStatFile = analysisLocation + "analysis.bfmask.stats";
from_beadfind_mask.my_mask->UpdateBeadFindOutcomes ( wholeChip, analysisMaskFile.c_str(), !inception_state.bfd_control.SINGLEBF, 0, analysisStatFile.c_str() );
my_progress.ReportState ( "Raw flowgrams complete" );
}
// output from this are a functioning wells file and a beadfind mask
// images are only known internally to this.
void RealImagesToWells (
CommandLineOpts& inception_state,
SeqListClass& my_keys,
TrackProgress& my_progress,
ImageSpecClass& my_image_spec,
SlicedPrequel& my_prequel_setup )
{
Region wholeChip(0, 0, my_image_spec.cols, my_image_spec.rows);
ComplexMask* complex_mask = 0;
BkgFitterTracker* bkg_fitter_tracker = 0;
if(inception_state.bkg_control.restart_from.empty())
{
// do separator if necessary: generate mask
IsolatedBeadFind ( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.GetResultsFolder(), inception_state.sys_context.analysisLocation, my_keys, my_progress );
}
else
{
// restarting execution from known state, restore my_prequel_setup
// no matter what I do seems like all restoration has to happen in this scope
string filePath = inception_state.sys_context.analysisLocation + inception_state.bkg_control.restart_from;
time_t begin_load_time;
time ( &begin_load_time );
ifstream ifs(filePath.c_str(), ifstream::in);
assert(ifs.good());
//boost::archive::text_iarchive in_archive(ifs);
boost::archive::binary_iarchive in_archive(ifs);
string saved_svn_rev;
in_archive >> saved_svn_rev
>> my_prequel_setup
>> complex_mask
>> bkg_fitter_tracker;
ifs.close();
time_t finish_load_time;
time ( &finish_load_time );
fprintf ( stdout, "Loading restart state from archive %s took %0.1f sec\n",
filePath.c_str(), difftime ( finish_load_time, begin_load_time ));
if ( inception_state.bkg_control.restart_check ){
string svn_rev = IonVersion::GetSvnRev();
ION_ASSERT( (saved_svn_rev.compare(svn_rev) == 0),
"This SVN rev " + svn_rev + " of Analysis does not match the SV rev " + saved_svn_rev + " where " + filePath + " was saved; disable this check by using --no-restart-check");
}
// set file locations
my_prequel_setup.FileLocations ( inception_state.sys_context.analysisLocation );
}
// do signal processing generate wells conditional on a separator
IsolatedSignalProcessing ( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.analysisLocation, my_keys, my_progress, complex_mask, bkg_fitter_tracker );
// @TODO cleanup causes crash when restarted, why?
// if (complex_mask != NULL) delete complex_mask;
// if (bkg_fitter_tracker != NULL) delete bkg_fitter_tracker;
}
