Ascii file in R as.numeric integers are incorrect - r

Question

I have read an ascii (.spe) file into R. This file contains one column of, mostly, integers. However R is interpreting these integers incorrectly, probably because I am not specifying the correct format or something like that. The file was generated in Ortec Maestro software. Here is the code:
library(SDMTools)
strontium<-read.table("C:/Users/Hal 2/Desktop/beta_spec/strontium 90 spectrum.spe",header=F,skip=2)
str_spc<-vector(mode="numeric")
for (i in 1:2037)
{
str_spc[i]<-as.numeric(strontium$V1[i+13])
}
Here, for example, strontium$V1[14] has the value 0, but R is interpreting it as a 10. I think I may have to convert the data to some other format, or something like that, but I'm not sure and I'm probably googling the wrong search terms.
Here are the first few lines from the file:
$SPEC_ID:
No sample description was entered.
$SPEC_REM:
DET# 1
DETDESC# MCB 129
AP# Maestro Version 6.08
$DATE_MEA:
10/14/2014 15:13:16
$MEAS_TIM:
1516 1540
$DATA:
0 2047
Here is a link to the file: https://www.dropbox.com/sh/y5x68jen487qnmt/AABBZyC6iXBY3e6XH0XZzc5ba?dl=0
Any help appreciated.

Answer 1

I saw someone had made a parser for SPE Spectra files in python and I can't let that stand without there being at least a minimally functioning R version, so here's one that parses some of the fields, but gets you your data:
library(stringr)
library(gdata)
library(lubridate)
read.spe <- function(file) {
tmp <- readLines(file)
tmp <- paste(tmp, collapse="\n")
records <- strsplit(tmp, "\\$")[[1]]
records <- records[records!=""]
spe <- list()
spe[["SPEC_ID"]] <- str_match(records[which(startsWith(records, "SPEC_ID"))],
"^SPEC_ID:[[:space:]]*([[:print:]]+)[[:space:]]+")[2]
spe[["SPEC_REM"]] <- strsplit(str_match(records[which(startsWith(records, "SPEC_REM"))],
"^SPEC_REM:[[:space:]]*(.*)")[2], "\n")
spe[["DATE_MEA"]] <- mdy_hms(str_match(records[which(startsWith(records, "DATE_MEA"))],
"^DATE_MEA:[[:space:]]*(.*)[[:space:]]$")[2])
spe[["MEAS_TIM"]] <- strsplit(str_match(records[which(startsWith(records, "MEAS_TIM"))],
"^MEAS_TIM:[[:space:]]*(.*)[[:space:]]$")[2], "\n")[[1]]
spe[["ROI"]] <- str_match(records[which(startsWith(records, "ROI"))],
"^ROI:[[:space:]]*(.*)[[:space:]]$")[2]
spe[["PRESETS"]] <- strsplit(str_match(records[which(startsWith(records, "PRESETS"))],
"^PRESETS:[[:space:]]*(.*)[[:space:]]$")[2], "\n")[[1]]
spe[["ENER_FIT"]] <- strsplit(str_match(records[which(startsWith(records, "ENER_FIT"))],
"^ENER_FIT:[[:space:]]*(.*)[[:space:]]$")[2], "\n")[[1]]
spe[["MCA_CAL"]] <- strsplit(str_match(records[which(startsWith(records, "MCA_CAL"))],
"^MCA_CAL:[[:space:]]*(.*)[[:space:]]$")[2], "\n")[[1]]
spe[["SHAPE_CAL"]] <- str_match(records[which(startsWith(records, "SHAPE_CAL"))],
"^SHAPE_CAL:[[:space:]]*(.*)[[:space:]]*$")[2]
spe_dat <- strsplit(str_match(records[which(startsWith(records, "DATA"))],
"^DATA:[[:space:]]*(.*)[[:space:]]$")[2], "\n")[[1]]
spe[["SPE_DAT"]] <- as.numeric(gsub("[[:space:]]", "", spe_dat)[-1])
return(spe)
}
dat <- read.spe("strontium 90 spectrum.Spe")
str(dat)
## List of 10
## $ SPEC_ID : chr "No sample description was entered."
## $ SPEC_REM :List of 1
## ..$ : chr [1:3] "DET# 1" "DETDESC# MCB 129" "AP# Maestro Version 6.08"
## $ DATE_MEA : POSIXct[1:1], format: "2014-10-14 15:13:16"
## $ MEAS_TIM : chr "1516 1540"
## $ ROI : chr "0"
## $ PRESETS : chr [1:3] "None" "0" "0"
## $ ENER_FIT : chr "0.000000 0.002529"
## $ MCA_CAL : chr [1:2] "3" "0.000000E+000 2.529013E-003 0.000000E+000 keV"
## $ SHAPE_CAL: chr "3\n3.100262E+001 0.000000E+000 0.000000E+000"
## $ SPE_DAT : num [1:2048] 0 0 0 0 0 0 0 0 0 0 ...
head(dat$SPE_DAT)
## [1] 0 0 0 0 0 0
It needs some polish and there's absolutely no error checking (i.e. for missing fields), but no time today to deal with that. I'll finish the parsing and make a minimal package wrapper for it over the next couple days.