emuR (development version)
emuR 2.5.2
add_signalVia...(): Minor iteration on the function
signatures
bug fixes
emuR 2.5.1
- Documentation: Include package anchors in links for CRAN’s new HTML
reference manuals
add_signalVia...(): Drafting a new family of functions
that allows users to use signal procissing from outside Wrassp; starting
with Matlab
bug fixes
emuR 2.5.0
- CRUD operations:
create_itemsInLevel() can now be used
in more ways than before
- CRUD operations: Improved documentation for
create/update/delete_itemsInLevel(); this is ongoing
work
bug fixes
- remove one instance of is.R() because it is no longer allowed on
CRAN
- CRUD operations:
delete_itemsInLevel() was heavily
flawed and is now usable
emuR 2.4.2
- experimental: signal tracks can be stored in Rda format as well as
SSFF
bug fixes
- passing a data frame or tibble as language option to BAS Web
Services calls was broken (closes #272, thanks to @johannacronenberg)
- fix error in create_itemsInLevel where end of last segment in a
level could be miscalculated
emuR 2.4.1
bug fixes
- worked around a problem in vroom_write_lines that could materialize
on Windows in rare cases
- fix loading databases with empty sessions (thanks to @FredrikKarlssonSpeech via
#268, #271)
emuR 2.4.0
- cache for onTheFly computations in
get_trackData()
(thanks to @samgregory via #254)
- improved a small number of error messages
bug fixes
add_files not correctly matching file extension (thanks
to @samgregory via
#254)- fixed level attribute mixup in generation of seglist (closes
#263)
- workaround for
wrassp::readDataObj() crashing R
session. Temporary fix for issue #261.
- generic functions Math2/round and Math2/signif did not accept digits
parameter for legacy trackdata objects
- adaptations to Tidyverse 2.0.0 and other adapations to make unit
tests and cran checks smooth again
emuR 2.3.0
- added explicit checks for all
dir.create() (closes
#49)
- checking dir parameter in
import_mediaFiles() (closes
#108)
add_files() now works with strings like
_annot.json as fileExtension (closes
#246)- now prechecking user defined options in
.onLoad()
(closes #240)
- added new
sessionPattern and bundlePattern
args to list_bundles() and list_sessions()
(closes #201)
- better output for warning in
get_trackdata() regarding
heterogeneous sampling rates (closes #189)
- using
cli package to improve output of
summary(emuDBhandle)
- slight performance increase in EQL by avoiding full table scans due
to REGEXP
- checking for repeating sequences in
normalize_length()
(closes #211)
- added explicit error message when bad column name is used in
DBconfig (closes #212)
- removing linkDefinition on error if it was added be4 (closes
#226)
bug fixes
- fixed bug in requery workflows like:
sl = query(ae, "[Phonetic== V]"); requery_hier(ae, sl[1:2,], level = "Text")
- added missing loading of DBconfig to
write_bundleList()
(fixes #248)
- fixed bad handeling of dir paths containgin RegExp chars in
convert_TextGridCollection() (fixes #207)
emuR 2.2.0
- compete rewrite of hierarchical queries + requeries (now using CTEs)
+ clean-up of the EQL engine
serve() -> save bundle performance bump due to
SQLite transaction improvement + using prep. statementsserve() function now downloads current release .zip
instead of cloning repo to save time and bandwidth- fixed a few more
readr:: file vs path parameter
warnings
- using
readr::write_lines() function in
export_TextGridCollection() to better support UTF-8
symbols
- added
create_spectrogram_image_as_raster function that
used the EMU-webApp JavaScript code to draw a spectrogram as a
raster
bug fixes
- fixed invalid TextGrid export on empty levels
emuR 2.1.1
load_emuDB() performance bump due to SQLite transaction
improvement + using prep. statementscreate_itemsInLevel() now supports items of type
SEGMENT- added deprecated/not recommended texts to , and help pages (fixes
#234)
bug fixes
- implemented first version of
delete_itemsInLevel()
requery_seq() now returns correct attribute label
vs. the level attribute- fixed
In rbind(names(params), unlist(params, recursive = F)): number of columns of result is not a multiple of vector length (arg 1)
warning in runBASwebservice_maus() with
httr::upload_file()
- added missing
() to return statement
- no emuDBcache needed for
rename_emuDB()
emuR 2.1.0
- implemented
write_bundleList() and
read_bundleList() functions
- new
bundleListName serve() parameter
implemented
- added warning to
serve() when either bundleComments or
bundleFinishedEditing is set to true and no bundleListName was set
(closes #268)
- implemented
onTheFlyFunction parameter for
get_trackdata() which allows users to implement their own
functions (input: path to wav file; output tibble/data.frame that has a
column called "frame_time")
- converting factors into characters in
get_trackdata()
and normalize_length() (closes #224 and #223)
add_perspective() now sets "restrictions"
-> "showPerspectivesSidebar" to true to
make the side bar visiblenormalize_length() now doesn’t throw tibble 3.0.0
warnings any morequery() RegEx operators =~ now using
SQLites native support (wasn’t available in earlier versions)- replaced RCurl with httr dep
- moved some dependencies to
Suggests field in
DESCRIPTION file
- removed vignette stubs
bug fixes
- try catching rounding errors of sample rate and start time in
get_trackdata()
emuR 2.0.4
export_seglistToTxtCollection() now zero pads file
names (should fix #219)- implemented
write_bundleList() and
read_bundleList() functions
- new
bundleListName serve() parameter
implemented
bug fixes
- using
rstudioapi::translateLocalUrl() for ws connection
url to permit RStudio to connect
- fixed bug in duplicate levels (bad level name insert into items
table) that was causing the items array in the JSON file to stay
empty
serve() working outside of RStudio again (overlooked
that rstudioapi::translateLocalUrl() needs RStudio)- improved error formatting in
load_emuDB() and
export_TextGridCollection
- fixed
rename_bundles() issue with sub-string matching
of names (fixes #220)
requery_hier() works with non-main attributes again
(always returned levels main attribute labels)
emuR 2.0.2
- changed default
resultTypes to "tibble"
(query(), requery_hier(),
requery_seq(), get_trackdata())
- changed url in printed output of serve to https
serve() doesn’t block the R console any more- suppressing requery differing length warnings in
runBASwebservice_* functions
requery_hier() now persists the input segment list
length by inserting NA rows for missing segments- depricated vignettes are now stubs only (== empty containing notice
pointing to the EMU-SDMS manual)
- implemented
rename_bundles() function
- better
times_norm calculation for
normalize_length()
- better error message when empty or non existing session is passed
into
add_files()
serve() useViewer parameter now
implemented and the default.serve() now uses a single server to host the EMU-webApp
and provide the websocket server for the emuDBserve() now works within RStudio when it is run as a
web application
bug fixes
emuR 1.1.2
- rewrite of
list_files() that leads to massive speed
bump
- implemented
convert_wideToLong() function to convert
trackdata tibble objects to their long form representation (useful for
spectral analysis)
query() sub-function now sets perl = TRUE
arguments in regexp call when using
sessionPattern and bundlePattern (useful for
e.g. for negative look-around
bundlePattern = "^((?!msajc003).)*$")- implemented
export_seglistToTxtCollection()
- normalize length now also using
list() with
do.call(rbind, res_list)
- implemted new
runMINNI boolean parameter in
runBASwebservice_all()
bug fixes
- https default on
serve()
- fixed problems of
calcFreqs = T in
convert_wideToLong() (possibly caused by newer version of
dplyr?)
emuR 1.1.1
bug fixes
- fixed bad column init. in
normalize_length()
column
- removed detritus LaTex files (e.g. .log, .aux) from
vignette/pics directory (as requested by CRAN
maintainer)
emuR 1.1.0
- URL encoding of bundle and session names to allow for URL string
reserved characters in bundle and session names
- error message of
get_trackdata() now contains seglist
row index if “Can not extract following”
normalize_length() now allows for additional
non-numeric columns- changed
stop() to warning() in
get_trackdata() when samplerates are inconsistent (closes
#190)
- better error message when there is a naming mismatch of
_emuDB dir _DBconfig.json
- using
sub() instead of
tools::file_path_sans_ext() to handle _ in
file extensions
query(), requery_seq() and
requery_hier() now supports the resultType
"tibble" (and get_trackdata(),
requery_seq(), requery_hier() and
serve() support them as input)serve() function now uses seglist$start
and seglist$end instead of
seglist$sample_start and
seglist$sample_end- implemented first version of
update_itemsInLevel()
(only label updates for now)
- now setting the
sample_start and
sample_end values in query results when EVENT levels are
queried (previously only start was set)
- implemented first versions of
create_links() (currently
not checking for anything), create_itemsInLevel() (only
EVENTs and ITEMs) and update_itemsInLevel() (only labels)
and delete_itemsInLevel()
list_bundles() outside of loop for performance bump in
get_trackdata()- better error message in
add_files() if no files are
found
consistentOutputType of get_trackdata() is
not set to TRUE and is reset to T if
resultType is "emuRtrackdata" or
"tibble" (fixes #203)- avoiding negative
times_rel and times_norm
values in create_emuRtrackdata() by setting them to 0
(caused by string to numeric conversion precision errors)
requery_seq() now inserts NA values for the out of
bounds rows instead of dropping them.- implemented
list_sampleRates() function
get_trackdata() is now iteratively appending to a
list() instead of into a SQLite temp table. This is a
fairly large performance boost and also fixes #206.- added deprecation warnings to vignettes (added links to manual
chapters)
bug fixes
- propper fix for “now ordering by
items_idx not by
start_start_seq_idx which led to bad label sequences (fixes
#140)”
- fixed bad indexing in
normalize_length() when sl_rowIdx
values are not a c(1, 2, 3, 4, ...) sequence
- fixed
staticContours SSFF tracks not being sent to
EMU-webApp (fixes #195)
- fixed bug with completely empty levels that caused a bad resort of
levels in
_annot.jsons in
rewrite_allAnnots()
- fixed bug in
add_files() that was using the wrong
variable (fixes #196)
- added error message when querying levels without time-bearing
sub-levels (closes #150)
- fixed bug in
create_emuRtrackdata() with handling
trackdata object of class spectral
- correct recalculation of ITEM IDs of missing levels in .hlb files
(== only present in ESPS files) in
convert_legacyEmuDB()
- fixed handling of completely empty levels in .hlb files
normalize_length() now handles various additional
column types (not just "numeric")
emuR 1.0.0
- implemented new
consistentOutputType parameter for
get_trackdata() to always return a trackdata
or emuRtrackdata object independent of what the
cut and npoints arguments are set to
- now removing
levelCanvasOrder entry in
remove_levelDefinition() (fixes #156)
serve() method now uses GET to deliver media files to
the EMU-webApp. This avoids the base64 conversion overhead and is a
quite significant load time improvement- explicit error message in
convert_legacyEmuDB() when
invalid redundant links are found
- better error message in BPF parser
convert_legacyEmuDB() automatically converts
.ssd media files to .wav and normalizes the
annotations to start at 0 (only if attr(ssd,‘startTime’) is not 0).- added
sort() S3 method for emuRsegs
objects
- checking for badly sorted
emuRsegs in
requery_hier() and requery_seq()
functions
create_emuRtrackdata() returns a simple
data.frame object not a data.table objectemuRtrackdata object now contains a
times_norm (normalized time values between 0 and 1 for each
segment) column by default- added note to
print.emuRsegs() to give the user a hint
about missing columns
- implemented
print.emuRtrackdata() to avoid overly
verbose output
- implemented
normalize_length() function as S3 function
to normalize the length of each segment in an emuRtrackdata
object
- added
absolute_file_path column to output of
list_files()
- query engine does not rely on label index in label array any more
(updated
convert_queryResultToEmuRsegs() to use
resultAttrDef instead of labelIdx). Closes
#164.
- added
browser argument to serve() function
which is passed on to utils::browseURL() function
requery_seq() now uses start_item_seq_idx
and end_item_seq_idx of seglist instead of
start_item_id and start_item_id to simplify
function- implemented
check_emuDBhandle() function that is used
on every exported function that takes a emuDBhandle as an
argument to check if the handle is still valid (closes #176)
- implemented
"tibble" as resultType option
in get_trackdata(). This will probably replace the
"emuRtrackdata" option in future (it contains exactly the
same data/columns).
- prechecking if attribute definition is already defined (closes
#182)
get_trackdata() now uses temporary SQL tables to store
the intermediate results (massive performance gains!). Removed
nrOfAllocationRows parameter as this is no longer needed as
no matrix is used to store the intermediate results. (also closes
#125)convert_TextGridCollectio() using
dir.exists() instead of file.exists() to check
dirs- all read operations now use the readr package (avoids encoding
problems like #187)
list_attributeDefinitions() now allows for a name
vector to be passed in- rewrite of
rewrite_allAnnots() functions for faster
rewrites of _annot.json files to disk
- improved cleanup in testing DBconfig functions
- now ordering by
items_idx not by
start_start_seq_idx which led to bad label sequences (fixes
#140)
bug fixes
- fixed problem of updating cache. Didn’t handle
data.frame object that was thought to be a vector
correctly!
- fixed a bug in the BPF export function, which meant that WAVE files
were only copied into one session
- added missing
$ in pattern arguments in
list.files call in list_files (fixes
#170)
- not adding ssffTrackDefinition to DBconfig if user input is no
(closes #171)
- fixed bad
seq_start_seq_idx and
seq_seq_idx returned by requery_seq() (fixes
#183)
- fixed bad
seq_start_seq_idx returned by internal
query_databaseHier() function
- fixed bad sorting of
requery_seq()/requery_hier() when
calcTimes = F (still sorted by start_sample
instead of the correct seq_idx)
- added
readr::parse_character() to data received in
serve() as this is recoded in windows (fixes #188).
emuR 0.2.3
- tweaked
runBASwebservice_maus(); improved performance
for presegmented bundles
- performance bump for
fapply() by preallocating result
matrix
- performance bump for
trapply() by preallocating result
matrix
- performance bump for
mel.spectral() by preallocating
result matrix
- performance bump for
bark.spectral() by preallocating
result matrix
- updated DBI calls to comply with the latest best practices (using
DBI::dbExecute() instead of DBI::dbGetQuery()
for non-SELECT queries)
- BPF collection exporter documented and now public
bug fixes
export_TextGridCollection() now handles partial
includes of bundle and session names correctly (issue #147)- added missing check if
anagestConfig is defined to
rename_attributeDefinition()
- setting useBytes to T to avoid reencoding under windows
- fixed bug in
add_ssffTrackDefinition() that was trying
to access fp which was renamed in a refactor to
filesDf
- fixed export to autodetect S3 methods (cbind & rbind for
trackdata)
emuR 0.2.2
- some changes to the parameter names in the BAS webservice
functions
- convert_txtCollection and convert_BPFCollection now name topmost
item “bundle”
- added functions to set and get level descriptions in DBconfig
- BAS webservice functions now perform a cache update prior to
departure
- added multiple perspectives to ae demo database
- choosing explicit paths with intersecting hierarchies now
possible
- remove levelDef & linkDef now implement force parameters
- new function convert_txtCollection converts plain text collections
into single-node emuDB
- new functions runBASwebservice_* that call various BAS webservices
from inside emuR
- NULLing out empty DFs on list_level/linkDefs for more consistent
API
newLinkDefType argument implemented in
autobuild_linkFromTimes() to generate linkDefinition if so
desired- automatically removing superlevel from
levelCanvasOrder
if convertSuperlevel is set to TRUE in
autobuild_linkFromTimes()
bug fixes
- wrapped
readChars in enc2utf8 to avoid
encodings issues on windows
- updating label table correctly on add_attributeDefinition()
(#138)
- runBASwebservice_maus / minni / all now no longer ignore unlinked
items (idx -1) but treat them as linkless segments
- commented out
cat() in train() function be
be less verbose
- BAS webservice calls now get their own temp directories (UUID
based). This avoids race conditions when several scripts are running in
parallel.
- convert_txtCollection now treats perspectives as array (as it
should)
emuR 0.2.1
- added new
EMUwebAppConfig -> perspectives -> signalCanvases -> minMaxValLims
config option to emuDB vignette
- requery_hier + requery_seq now implement the same
timeRefSegmentLevel parameter as query (#135)
bug fixes
- fixed requery_hier() bug of requery on same attribute
definition
- fixed requery_hier() bug of requery on same level but different
attribute definition
emuR 0.2.0
- rewrite of query engine to not require links_ext table any more (==
redundant links)
- calcTimes parameter added to query() / requery_seq() /
requery_hier() to make calculating times optional (extreme performance
boost if no times have to be calculated)
- rewrite of annotJSONcharToBundleAnnotDFs() for faster loads emuDBs
containing large annotJSONs
- replaced tidyjson as annot.json parser with own solution at tidyjson
didn’t scale well on larger annotation files
- added verbose parameter to export_TextGridCollection()
- improved pre-check of dir exists in export_TextGridCollection()
- added new replace_itemLabels function
- improved export_TextGridCollection() doc
- improved replace_itemLables() speed
- implemented rename_emuDB() (#116)
- implemented duplicate_level() (#113)
- implemented linkDuplicates parameter in duplicate_level()
- autobuild_linkFromTimes() speed improvements
- FUNCQ queries (start(),end(), medial()) now additionally support
TRUE & FALSE and T & F values (vs. 0 & 1)
- added attrDefNames column to list_levelDefinitions() output
- can now deal with read only emuDBs by copying the cache to tempdir()
and making it writable for the user
- added start_item_seq_idx and end_item_seq_idx to emuRsegs
object
- added start_item_seq_idx and end_item_seq_idx type values to all
intermediate result tables
- added optional function to reduce hierarchical query results to left
and right most children only (large performance gain on calcTimes =
T)
- rewriting annot.json files now updates MD5 sums as well (avoids
unnecessary reload on next load_emuDB)
- rewriting annot.json files now writes all (including empty /
missing) attributeDef. labels
bug fixes
- fixed bad DBconfig gen. on add_perspective
- fixed list_linkDefinitions() returning strings as factors
- fixed bad error message when passing in ITEM levels to
autobuild_linkFromTimes()
- fixed incorrect handling of DBconfig when writeToFS was set to FALSE
(writeToFS is now called rewriteAllAnnots)
emuR 0.1.9
- also allowing “time =” in TextTiers
- “levels of type ‘EVENT’ are not allowed to be super levels (==
parents) in a domination relationship” constraint enforced in
add_linkDefinition
- added “MEDIAFILE_SAMPLES” as constant name to access audio samples
to get_trackdata() function
- improved error message to include tgPath in
create_DBconfigFromTextGrid function
- no integer return value returned by create_emuRdemoData() any more!
It was implicitly returned from wrassp function call…
- improved the slow overlap checking function in the BPF parser (is
now O(n) instead of O(n^2))
- fixed col naming problems for new (unreleased) RSQLite version
- added export_TextGridCollection() function
- improved doc for get_trackdata
- constant naming of EMU-SDMS vs EMU_SDMS in various files
- rewriting all annotation file on add_levelDefinition,
remove_levelDefinition
bug fixes
- fixed problem in conversion to JSON with empty items array (object
‘{}’ vs array ‘[]’)
- fixed problem of keywords “number” | “time” | “xmin” | … in labels
causing TextGrid parser to fail
- fixed problem with to lax RegEx in TextGrid parser
- fixed validation problem with missing levels regarding types
emuR 0.1.8
- get_trackdata with onTheFly calculation now reuses AsspDataObj if
the current utterance is the same as the previous (large performance
gain especially on long audio files)
- checking if DBconfig exists for better error message if ‘name’ field
is not set correctly in DBconfig
- setting PRAGMA temp_store = 2; for SQLite connections
- not extracting tables to R if no RegEx needed to create filtered_tmp
tables (performance gain when querying large emuDBs)
- convert_BPFCollection can now assigns the same label to more than
one item when unifying tiers
- newline at the end of load_emuDB if no redundant links are
built
- queries using dominates operator ‘^’ don’t use linksExt table
anymore -> large performances benefits
- only using _filtered_tmp tables if RegEx patterns are used
- changed primary key on items table which leads to massive
performance gains (deleting _emuDBcache.sqlite required)
bug fixes
- fixed error handling of create_emuRtrackdata + added @export to roxygen doc
- invalid annotJSONs generated by import_mediaFiles fixed
- convert_TextGridCollection can now handle nested folders again
- invalid UUIDs in DBConfig produced by convert_BPFCollection. Also
added additional unit test to detect this.
- list_bundles uses session argument again
- fixed “Expression tree is too large (maximum depth 1000)” error in
get_trackdata with long emuRsegs lists
emuR 0.1.7
- R depends version bump to 3.2.0 (as requested by CRAN
maintainer)
- updated testthat::expect_less_than to expect_lt calls (due to
deprecated warnings)
- Using new .keep_all = T parameter of dplyr
- removed legacy version of EQL vignette (overlooked as inst/doc was
in .gitignore)
emuR 0.1.6
- skipping in-depth thorough tests on CRAN for query and autobuild SQL
functions
emuR 0.1.5
- fixed problem of interm_res_tables already being present with
queries that have multiple recursion depth on both sides of either ->
or ^ operand (e.g. query (ae , “[[[Phonetic = n -> Phonetic =z] ->
Phonetic = S ] ^ [Text = friends -> Text = she]]”))
- fixed bad URL in README.md
- added CITATION file
emuR 0.1.3.9000
- renamed SQL tables & columns from camel case to underscore
notation
- variable SQL backend implementation
emuR 0.1.2.9000
- multiple check fixes on various platforms
emuR 0.1.1.9000
serve problem with internalVars bug fixed- file locking problem that caused vignettes to fail under windows
problem fixed
emuR 0.1.0.9000
- massive refactor of all functions that used to refer to an emuDB by
name and optionally by its UUID. They now use the new emuDBhandle object
that is now returned by the
load_emuDB() function.
convert_XXX_to_emuDB() functions renamed to
convert_XXX()