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Add debug capabilities for agcalibrate #38

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merged 4 commits into from
Jun 5, 2024
Merged

Add debug capabilities for agcalibrate #38

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923ee0f
removed : from verbose messages
muschellij2 May 24, 2024
12c5083
added docs
muschellij2 May 24, 2024
f8a6f0f
added more debugging
muschellij2 Jun 4, 2024
5f037cc
added more debugging
muschellij2 Jun 4, 2024
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4 changes: 2 additions & 2 deletions R/RcppExports.R
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

gcalibrateC <- function(pathname = NULL, dataset = NULL, sf = NA_integer_) {
.Call(`_agcounts_gcalibrateC`, pathname, dataset, sf)
gcalibrateC <- function(pathname = NULL, dataset = NULL, sf = NA_integer_, debug = FALSE) {
.Call(`_agcounts_gcalibrateC`, pathname, dataset, sf, debug)
}

#' Upsample data if frequency is 30, 60, or 90 Hertz
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7 changes: 5 additions & 2 deletions R/agread.R
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Expand Up @@ -86,6 +86,7 @@ agread <- function(path, parser = c("pygt3x", "GGIR", "read.gt3x"), tz = "UTC",
#' @param tz the desired timezone, Default: \code{UTC}
#' @param imputeTimeGaps Imputes gaps in the raw acceleration data, Default: FALSE
#' @param ... Additional arguments to pass into the agread function
#' @param debug print out diagnostic information for C++ code
#' @return Returns the calibrated raw acceleration data
#' @details This function uses a C++ implementation of the GGIR `g.calibrate` function to
#' return calibrated raw acceleration data.
Expand All @@ -101,10 +102,12 @@ agread <- function(path, parser = c("pygt3x", "GGIR", "read.gt3x"), tz = "UTC",
#' @importFrom data.table setDT setDF


agcalibrate <- function(raw, verbose = FALSE, tz = "UTC", imputeTimeGaps = FALSE, ...){
agcalibrate <- function(raw, verbose = FALSE, tz = "UTC", imputeTimeGaps = FALSE, ...,
debug = FALSE){
if(any(.get_sleep(raw))) stop("Calibration requires the data to be imported without imputed zeros.")
sf = .get_frequency(raw)
C <- gcalibrateC(dataset = as.matrix(raw[, c("X", "Y", "Z")]), sf = sf)
C <- gcalibrateC(dataset = as.matrix(raw[, c("X", "Y", "Z")]), sf = sf,
debug = as.logical(debug))

if(imputeTimeGaps){
if("last_sample_time" %in% names(attributes(raw))){
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11 changes: 10 additions & 1 deletion man/agcalibrate.Rd
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6 changes: 5 additions & 1 deletion man/agcounts-package.Rd
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9 changes: 5 additions & 4 deletions src/RcppExports.cpp
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Expand Up @@ -12,15 +12,16 @@ Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// gcalibrateC
Rcpp::List gcalibrateC(Rcpp::Nullable<Rcpp::String> pathname, Rcpp::Nullable<Rcpp::NumericMatrix> dataset, int sf);
RcppExport SEXP _agcounts_gcalibrateC(SEXP pathnameSEXP, SEXP datasetSEXP, SEXP sfSEXP) {
Rcpp::List gcalibrateC(Rcpp::Nullable<Rcpp::String> pathname, Rcpp::Nullable<Rcpp::NumericMatrix> dataset, int sf, const bool debug);
RcppExport SEXP _agcounts_gcalibrateC(SEXP pathnameSEXP, SEXP datasetSEXP, SEXP sfSEXP, SEXP debugSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< Rcpp::Nullable<Rcpp::String> >::type pathname(pathnameSEXP);
Rcpp::traits::input_parameter< Rcpp::Nullable<Rcpp::NumericMatrix> >::type dataset(datasetSEXP);
Rcpp::traits::input_parameter< int >::type sf(sfSEXP);
rcpp_result_gen = Rcpp::wrap(gcalibrateC(pathname, dataset, sf));
Rcpp::traits::input_parameter< const bool >::type debug(debugSEXP);
rcpp_result_gen = Rcpp::wrap(gcalibrateC(pathname, dataset, sf, debug));
return rcpp_result_gen;
END_RCPP
}
Expand All @@ -38,7 +39,7 @@ END_RCPP
}

static const R_CallMethodDef CallEntries[] = {
{"_agcounts_gcalibrateC", (DL_FUNC) &_agcounts_gcalibrateC, 3},
{"_agcounts_gcalibrateC", (DL_FUNC) &_agcounts_gcalibrateC, 4},
{"_agcounts_upsampleC", (DL_FUNC) &_agcounts_upsampleC, 2},
{NULL, NULL, 0}
};
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