Can't read fit files
muschellij2 opened this issue · comments
Can't read fit files
2019-08-05.zip
Reproducible example:
library(fitFileR)
destfile = tempfile(fileext = ".zip")
url = "https://github.com/grimbough/fitFileR/files/3473420/2019-08-05.zip"
dl = download.file(url = url, destfile = destfile)
tdir = tempfile()
dir.create(tdir)
files = unzip(destfile, exdir = tdir)
fileName = files[1]
readFitFile(fileName)
#> Error in .readRecordHeader(con): Compressed time stamp header not currently supported
sapply(files, readFitFile)
#> Error in .readRecordHeader(con): Compressed time stamp header not currently supportedCreated on 2019-08-06 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#> setting value
#> version R version 3.6.0 (2019-04-26)
#> os macOS Mojave 10.14.6
#> system x86_64, darwin15.6.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2019-08-06
#>
#> ─ Packages ──────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
#> backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
#> callr 3.3.0 2019-07-04 [1] CRAN (R 3.6.0)
#> cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
#> desc 1.2.0 2019-07-10 [1] Github (muschellij2/desc@b0c374f)
#> devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
#> digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0)
#> dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.0)
#> fitFileR * 0.0.3 2019-08-06 [1] Github (grimbough/fitFileR@1bebfda)
#> fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
#> glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
#> highr 0.8 2019-03-20 [1] CRAN (R 3.6.0)
#> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.0)
#> knitr 1.23 2019-05-18 [1] CRAN (R 3.6.0)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
#> pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
#> pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.0)
#> pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0)
#> pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
#> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
#> processx 3.4.0 2019-07-03 [1] CRAN (R 3.6.0)
#> ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
#> purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.0)
#> R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
#> Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
#> remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
#> rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
#> rmarkdown 1.13 2019-05-22 [1] CRAN (R 3.6.0)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
#> stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
#> testthat 2.1.1 2019-04-23 [1] CRAN (R 3.6.0)
#> tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
#> tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
#> usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
#> withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
#> xfun 0.8 2019-06-25 [1] CRAN (R 3.6.0)
#> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/librarySeems to be the 23rd record, which I'm not sure is relevant, but looks like developer_data = TRUE:
library(fitFileR)
destfile = tempfile(fileext = ".zip")
url = "https://github.com/grimbough/fitFileR/files/3473420/2019-08-05.zip"
dl = download.file(url = url, destfile = destfile)
tdir = tempfile()
dir.create(tdir)
files = unzip(destfile, exdir = tdir)
fileName = files[1]
con = file(fileName, "rb")
data("data_type_lookup", package = "fitFileR")
file_header <- fitFileR:::.readFileHeader(con)
plmt <- "-1";
pseudoMessageTab <- NULL
prev_lmt <- "0"
defs <- list()
defs_count <- list()
for (i in 1:23) {
print(paste0("index is ", seek(con, where = NA)))
if (seek(con, where = NA) < (file_header$data_size + 14)) {
print(i)
} else {
break
}
record_header <- fitFileR:::.readRecordHeader(con)
lmt <- as.character(record_header$local_message_type)
if(record_header$message_type == "definition") {
print('definition')
if(lmt == prev_lmt) {
plmt <- as.character(as.integer(plmt) + 1)
} else {
plmt <- lmt
}
pseudoMessageTab <- rbind(pseudoMessageTab, c(lmt, plmt))
prev_lmt <- lmt
message <- fitFileR:::.readMessage.definition(con, devFields = record_header$developer_data)
# print(message)
defs[[ plmt ]] <- message$message
defs_count[[ plmt ]] <- 0
} else if(record_header$message_type == "data") {
print('data')
defIdx <- pseudoMessageTab[ max(which(pseudoMessageTab[,1] == lmt)), 2]
message <- fitFileR:::.scanMessage.data(con, defs[[ defIdx ]])
# print(message)
defs_count[[ defIdx ]] <- defs_count[[ defIdx ]] + 1
} else {
stop("unknown message type")
}
}
#> [1] "index is 14"
#> [1] 1
#> [1] "definition"
#> [1] "index is 41"
#> [1] 2
#> [1] "data"
#> [1] "index is 59"
#> [1] 3
#> [1] "definition"
#> [1] "index is 80"
#> [1] 4
#> [1] "data"
#> [1] "index is 95"
#> [1] 5
#> [1] "definition"
#> [1] "index is 113"
#> [1] 6
#> [1] "data"
#> [1] "index is 125"
#> [1] 7
#> [1] "definition"
#> [1] "index is 137"
#> [1] 8
#> [1] "data"
#> [1] "index is 143"
#> [1] 9
#> [1] "data"
#> [1] "index is 149"
#> [1] 10
#> [1] "data"
#> [1] "index is 155"
#> [1] 11
#> [1] "data"
#> [1] "index is 161"
#> [1] 12
#> [1] "data"
#> [1] "index is 167"
#> [1] 13
#> [1] "data"
#> [1] "index is 173"
#> [1] 14
#> [1] "data"
#> [1] "index is 179"
#> [1] 15
#> [1] "data"
#> [1] "index is 185"
#> [1] 16
#> [1] "data"
#> [1] "index is 191"
#> [1] 17
#> [1] "data"
#> [1] "index is 197"
#> [1] 18
#> [1] "data"
#> [1] "index is 203"
#> [1] 19
#> [1] "data"
#> [1] "index is 209"
#> [1] 20
#> [1] "data"
#> [1] "index is 215"
#> [1] 21
#> [1] "definition"
#> [1] "index is 224"
#> [1] 22
#> [1] "data"
#> [1] "index is 225"
#> [1] 23
#> Error in fitFileR:::.readRecordHeader(con): Compressed time stamp header not currently supported
close(con)Created on 2019-08-06 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#> setting value
#> version R version 3.6.0 (2019-04-26)
#> os macOS Mojave 10.14.6
#> system x86_64, darwin15.6.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2019-08-06
#>
#> ─ Packages ──────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
#> backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
#> callr 3.3.0 2019-07-04 [1] CRAN (R 3.6.0)
#> cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
#> desc 1.2.0 2019-07-10 [1] Github (muschellij2/desc@b0c374f)
#> devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
#> digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0)
#> dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.0)
#> fitFileR * 0.0.3 2019-08-06 [1] Github (grimbough/fitFileR@1bebfda)
#> fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
#> glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
#> highr 0.8 2019-03-20 [1] CRAN (R 3.6.0)
#> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.0)
#> knitr 1.23 2019-05-18 [1] CRAN (R 3.6.0)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
#> pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
#> pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.0)
#> pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0)
#> pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
#> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
#> processx 3.4.0 2019-07-03 [1] CRAN (R 3.6.0)
#> ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
#> purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.0)
#> R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
#> Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
#> remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
#> rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
#> rmarkdown 1.13 2019-05-22 [1] CRAN (R 3.6.0)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
#> stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
#> testthat 2.1.1 2019-04-23 [1] CRAN (R 3.6.0)
#> tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
#> tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
#> usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
#> withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
#> xfun 0.8 2019-06-25 [1] CRAN (R 3.6.0)
#> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
This was patched a while ago and you should be able to read those files now e.g.
library(fitFileR)
destfile = tempfile(fileext = ".zip")
url = "https://github.com/grimbough/fitFileR/files/3473420/2019-08-05.zip"
dl = download.file(url = url, destfile = destfile)
tdir = tempfile()
dir.create(tdir)
files = unzip(destfile, exdir = tdir)
fit_list <- lapply(files, readFitFile)
lapply(fit_list, names)
#> [[1]]
#> [1] "file_id" "device_info"
#>
#> [[2]]
#> [1] "file_id" "device_info"
#>
#> [[3]]
#> [1] "file_id" "file_creator" "device_info"
#>
#> [[4]]
#> [1] "file_id" "device_info" "software" "monitoring_info"
#> [5] "monitoring" "ohr_settings" "stress_level" "event"
#>
#> [[5]]
#> [1] "file_id" "device_info" "software" "monitoring_info"
#> [5] "monitoring" "ohr_settings" "stress_level" "event"
fit_list[[5]][['event']]
#> # A tibble: 150 x 4
#> timestamp data16 event event_type
#> <dttm> <int> <chr> <chr>
#> 1 2019-08-05 06:29:00 80 <NA> marker
#> 2 2019-08-05 06:30:00 1 <NA> marker
#> 3 2019-08-05 11:07:00 277 <NA> marker
#> 4 2019-08-05 11:10:00 3 <NA> marker
#> 5 2019-08-05 11:56:00 46 <NA> marker
#> 6 2019-08-05 11:57:00 1 <NA> marker
#> 7 2019-08-05 15:23:00 206 <NA> marker
#> 8 2019-08-05 15:28:00 5 <NA> marker
#> 9 2019-08-05 15:29:00 1 <NA> marker
#> 10 2019-08-05 15:30:00 1 <NA> marker
#> # … with 140 more rows