Sometimes it is useful to reload isotope files from their original data files (e.g. after modifying raw data files in vendor software, or after upgrading to a newer version of the isoreader package that provides new functionality). The functions described below are intended to make this very easy. However, re-reading files from disc is only possible if file paths still point to the original raw data files. If they have moved, please use iso_set_file_root first to change the root directory of your iso_files.
iso_reread_files(iso_files, ...)
iso_reread_all_files(
iso_files,
...,
stop_if_missing = FALSE,
quiet = default(quiet)
)
iso_reread_changed_files(
iso_files,
...,
stop_if_missing = FALSE,
quiet = default(quiet)
)
iso_reread_outdated_files(
iso_files,
...,
stop_if_missing = FALSE,
quiet = default(quiet)
)
iso_reread_problem_files(
iso_files,
...,
stop_if_missing = FALSE,
reread_files_with_errors = TRUE,
reread_files_with_warnings = FALSE,
quiet = default(quiet)
)
iso_reread_storage(...)
iso_reread_archive(...)collection of iso_files
additional read parameters that should be used for re-reading the iso_files, see iso_read_dual_inlet, iso_read_continuous_flow and iso_read_scan for details (except read_cache which is always set to FALSE to force re-reads).
whether to stop re-reading if any of the original data files are missing (if FALSE, will warn about the missing files adding a warning to them, but also re-read those that do exist)
whether to display (quiet=FALSE) or silence (quiet = TRUE) information messages. Set parameter to overwrite global defaults for this function or set global defaults with calls to iso_turn_info_messages_on and iso_turn_info_messages_off
whether to re-read files that had read in with errors the last time (default TRUE)
whether to re-read files that had read in with warnings the last time (default TRUE)
To re-read files that have been modified on disc, please use iso_reread_changed_files(). To re-read files because of an isoreader version upgrade, please use iso_reread_outdated_files(). To try re-reading files that previously had warnings and/or errors, please use iso_reread_problem_files().
iso_reread_all_files re-reads all files in the collection.
iso_reread_changed_files re-reads all files that have been modified (e.g. in the vendor software) since they were last read by isoreader.
iso_reread_outdated_files re-reads all files that were read with an outdated version of isoreader.
iso_reread_problem_files re-reads all files that have had errors the last time they were read by isoreader (set reread_files_with_warnings = TRUE to also re-read those that have warnings).
iso_reread_storage is deprecated.
iso_reread_archive is deprecated.
# example for re-reading a saved isofile collection
iso_turn_reader_caching_off()
#> Info: caching turned off
saved_files_path <- "saved_isofile.scan.rds"
# create saved collection
iso_get_reader_examples_folder() |>
iso_read_scan() |>
iso_save(saved_files_path)
#> Info: preparing to read 4 data files...
#> Info: reading file 'background_scan_example.scn' with '.scn' reader...
#> Info: reading file 'full_scan_example.scn' with '.scn' reader...
#> Info: reading file 'peak_shape_scan_example.scn' with '.scn' reader...
#> Info: reading file 'time_scan_example.scn' with '.scn' reader...
#> Info: finished reading 4 files in 1.21 secs
#> Warning: file creation date could not be accessed for all files because this information is not available on some Linux systems, reporting last modified time for file_datetime instead. To turn these warnings off, call iso_turn_datetime_warnings_off() and reread these files with iso_reread_all_files().
#> Warning: encountered 4 problems.
#> # | FILE | PROBLEM | OCCURRED IN ...
#> 1 | background_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 2 | full_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 3 | peak_shape_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 4 | time_scan_example.scn | warning | extract_os_file_creation_datetime...
#> Use iso_get_problems(...) for more details.
#> Info: exporting data from 4 iso_files into R Data Storage 'saved_isofile.scan.rds'
# load collection
iso_read_scan(saved_files_path) |>
# reread outdated files (alternatively "_all_" or "_changed_")
iso_reread_outdated_files() |>
# re-save collection to its original location
iso_save(saved_files_path)
#> Info: preparing to read 1 data files...
#> Info: reading file 'saved_isofile.scan.rds' with '.scan.rds' reader...
#> Info: loaded 4 data files from R Data Storage
#> Info: finished reading 1 files in 0.09 secs
#> Warning: file creation date could not be accessed for all files because this information is not available on some Linux systems, reporting last modified time for file_datetime instead. To turn these warnings off, call iso_turn_datetime_warnings_off() and reread these files with iso_reread_all_files().
#> Warning: encountered 4 problems.
#> # | FILE | PROBLEM | OCCURRED IN ...
#> 1 | background_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 2 | full_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 3 | peak_shape_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 4 | time_scan_example.scn | warning | extract_os_file_creation_datetime...
#> Use iso_get_problems(...) for more details.
#> Info: found 0 outdated data file(s), re-reading 0/4.
#> Info: exporting data from 4 iso_files into R Data Storage 'saved_isofile.scan.rds'
# cleanup
unlink(saved_files_path)