/*
* R_GatingSet.cpp
*
*these are R APIs
*
* Created on: Mar 30, 2012
* Author: wjiang2
*/
#include <cpp11.hpp>
#include "CytoML/openWorkspace.hpp"
#include "flowWorkspace.h"
using namespace cytolib;
using namespace CytoML;
WS_INIT()
//only needed for win
[[cpp11::register]]
void setLogLevel(int short loglevel) {
g_loglevel = loglevel;
}
GatingSet * getGsPtr(SEXP _gsPtr){
if(R_ExternalPtrAddr(_gsPtr)==0)
throw(domain_error("Null GatingSet pointer!"));
cpp11::external_pointer<GatingSet>gs(_gsPtr);
return gs.get();
}
/*
* can't use module for exposing overloaded methods
*/
[[cpp11::register]]
cpp11::external_pointer<flowJoWorkspace> open_workspace(std::string filename, int sample_name_location, int xmlParserOption)
{
unique_ptr<flowJoWorkspace> ws = openWorkspace(filename, static_cast<SAMPLE_NAME_LOCATION>(sample_name_location),xmlParserOption);
return cpp11::external_pointer<flowJoWorkspace>(ws.release());
}
[[cpp11::register]]
cpp11::external_pointer<GatingSet> parse_workspace(cpp11::external_pointer<flowJoWorkspace> ws
, int group_id
, cpp11::list subset
, bool execute
, std::string path
, cpp11::external_pointer<GatingSet> cytoset
, std::string backend_dir
, std::string backend
, bool includeGates
, vector<std::string> additional_keys
, bool additional_sampleID
, vector<std::string> keywords
, bool is_pheno_data_from_FCS
, bool keyword_ignore_case
, float extend_val
, float extend_to
, bool channel_ignore_case
, bool leaf_bool
, bool include_empty_tree
, bool skip_faulty_gate
, cpp11::list comps
, bool transform
, std::string fcs_file_extension
, bool greedy_match
, SEXP fcs_parse_arg
, int num_threads = 1
)
{
ParseWorkspaceParameters config;
//ws parser config
config.data_dir = path;
config.cf_dir = backend_dir;
config.fmt = FileFormat::H5;
config.is_gating = execute;
config.is_parse_gate = includeGates;
config.is_pheno_data_from_FCS = is_pheno_data_from_FCS;
config.keyword_ignore_case = keyword_ignore_case;
config.keywords_for_pheno_data = keywords;
config.keywords_for_uid = additional_keys;
config.keywords_for_uid_sampleID = additional_sampleID;
config.gate_extend_trigger_value = extend_val;
config.gate_extend_to = extend_to;
config.channel_ignore_case = channel_ignore_case;
config.compute_leaf_bool_node = leaf_bool;
config.include_empty_tree = include_empty_tree;
config.skip_faulty_node = skip_faulty_gate;
config.fcs_file_extension = fcs_file_extension;
config.greedy_match = greedy_match;
config.transform = transform;
SEXP nm = subset.names();
if(!Rf_isNull(nm))//without NULL checking, the following line will fail
{
vector<std::string> filter_names = cpp11::as_cpp<vector<std::string> >(nm);
for(int i = 0; i < filter_names.size(); i++)
{
std::string filter_name = filter_names[i];
config.sample_filters[filter_name] = cpp11::as_cpp<vector<std::string>>(subset[filter_name]);
}
}
//fcs parser config
config.fcs_read_param = sexp_to_fcs_read_param(fcs_parse_arg);
// config.fcs_read_param.data.num_threads = num_threads;
config.num_threads = num_threads;
if(comps.size()==1&&Rf_isNull(comps.names()))
{
if(!Rf_isMatrix(comps[0]))
cpp11::stop("compensation must be of the type of cpp11::doubles_matrix<>, ");
config.global_comp = mat_to_comp(cpp11::as_cpp<cpp11::doubles_matrix<>>(comps[0]));
}
else
config.compensation_map = list_to_comps(comps);
unique_ptr<GatingSet> gs = ws->to_GatingSet(group_id, config, *cytoset);
return cpp11::external_pointer<GatingSet>(gs.release());
}
[[cpp11::register]]
SEXP get_keywords_by_id(cpp11::external_pointer<flowJoWorkspace> ws, int sample_id)
{
return kw_to_sexp(ws->get_keywords(sample_id).getPairs());
}
[[cpp11::register]]
SEXP get_keywords_by_name(cpp11::external_pointer<flowJoWorkspace> ws, std::string sample_name)
{
wsSampleNode node = ws->get_sample_node(sample_name);
return kw_to_sexp(ws->get_keywords(node).getPairs());
}
[[cpp11::register]]
cpp11::list get_sample_groups(cpp11::external_pointer<flowJoWorkspace> ws)
{
vector<SampleGroup> groups = ws->get_sample_groups();
int nGroup = groups.size();
cpp11::writable::integers group_ids(nGroup);
cpp11::writable::strings group_names(nGroup);
cpp11::writable::list sample_ids(nGroup);
for(int i = 0; i < nGroup; i++)
{
group_ids[i] = i;
group_names[i] = groups[i].group_name;
int nSample = groups[i].sample_ids.size();
cpp11::writable::integers sample_id_vec(nSample);
for(int j = 0; j < nSample; j++)
sample_id_vec[j] = groups[i].sample_ids[j];
sample_ids[i] = sample_id_vec;
}
return cpp11::list({cpp11::named_arg("groupID") = group_ids
, cpp11::named_arg("groupName") = group_names
, cpp11::named_arg("sampleID") = sample_ids
});
}
[[cpp11::register]]
cpp11::list get_samples(cpp11::external_pointer<flowJoWorkspace> ws)
{
vector<SampleGroup> groups = ws->get_sample_groups();
int nGroup = groups.size();
cpp11::writable::list grouplist(nGroup);
ParseWorkspaceParameters config;
config.include_empty_tree = true;
for(int i = 0; i < nGroup; i++)
{
const vector<SampleInfo> & sample_info_vec = ws->get_sample_info(groups[i].sample_ids, config);
int nSample = sample_info_vec.size();
cpp11::writable::list samples(nSample);
for(int j = 0; j < nSample; j++)
{
const SampleInfo & sample_info = sample_info_vec[j];
samples[j] = cpp11::list({cpp11::named_arg("sampleID") = sample_info.sample_id
, cpp11::named_arg("name") = sample_info.sample_name
, cpp11::named_arg("count") = sample_info.total_event_count
, cpp11::named_arg("pop.counts") = sample_info.population_count
});
}
grouplist[i] = samples;
}
return grouplist;
}
[[cpp11::register]]
std::string get_xml_file_path(cpp11::external_pointer<flowJoWorkspace> ws)
{
return ws->get_xml_file_path();
}
