helske / rlibeemd Goto Github PK

I came across an issue with the ceemdan() function parameter setting num_imfs. In the documentation, the default values of num_imfs=0 is said to correspond to a

maximal number of IMFs

. However, depending on other parameter settings (e.g. noise_strength), this is not necessarily the case. A residual with two non-edge extrema, which could be further decomposed, is possible.
Then (for N>3), not num_imfs=emd_num_imfs(N) (which seems to take floor(log2(N)) as the num_imfs-value), but the smallest integer which is not less than log2(N), thus, num_imfs=ceiling(log2(N)), appears to correspond to the maximal number of IMFs (meaning the residual has maximum one non-edge extremum). Whether floor(log2(N)) or ceiling(log2(N)) corresponds to the maximal number of IMFs depends on other parameter settings such as noise_strength. Maybe the number of non-edge extrema should be checked to decide on either floor(log2(N)) or ceiling(log2(N)) for num_imfs.

Attached I provide an example. An NDVI (Normalised Difference Vegetation Index) time series of length 340 (example_NDVI.txt). It is decomposed in R using ceemdan() (ceemdan_issue.txt). When setting a noise_strength=0.3, the default setting of num_imfs=0 results in a residual with two non-edge extrema.

I hope I am not missing anything/getting wrong and this information is of help. In case it is a bug, an edit would be appreciated.

These are my sessionInfo:

R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

packageVersion("Rlibeemd")
[1] ‘1.4.0’

Best, Katharina

I am wondering how to calculating and plot the spectrogram using the package of EMD and hht?

@helske Turned out, OpenMP detection does not work, at least in 1.4.3:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by Rlibeemd configure 1.4.2, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure 

## --------- ##
## Platform. ##
## --------- ##

hostname = 10.6.shared
uname -m = x86_64
uname -r = 10.8.0
uname -s = Darwin
uname -v = Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64

/usr/bin/uname -p = i386
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = Mach kernel version:
	 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64
Kernel configured for up to 8 processors.
8 processors are physically available.
8 processors are logically available.
Processor type: i486 (Intel 80486)
Processors active: 0 1 2 3 4 5 6 7
Primary memory available: 8.00 gigabytes
Default processor set: 153 tasks, 392 threads, 8 processors
Load average: 3.40, Mach factor: 4.68
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: /bin
PATH: /sbin
PATH: /usr/bin
PATH: /usr/sbin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1685: checking for gsl-config
configure:1703: found /opt/local/bin/gsl-config
configure:1715: result: /opt/local/bin/gsl-config
configure:1889: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by Rlibeemd config.status 1.4.2, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on 10.6.shared

config.status:716: creating src/Makevars

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_path_GSL_CONFIG=/opt/local/bin/gsl-config

## ----------------- ##
## Output variables. ##
## ----------------- ##

DEFS='-DPACKAGE_NAME=\"Rlibeemd\" -DPACKAGE_TARNAME=\"rlibeemd\" -DPACKAGE_VERSION=\"1.4.2\" -DPACKAGE_STRING=\"Rlibeemd\ 1.4.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
GSL_CFLAGS='-I/opt/local/include'
GSL_CONFIG='/opt/local/bin/gsl-config'
GSL_LIBS='-L/opt/local/lib -lgsl -lgslcblas'
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME='Rlibeemd'
PACKAGE_STRING='Rlibeemd 1.4.2'
PACKAGE_TARNAME='rlibeemd'
PACKAGE_URL=''
PACKAGE_VERSION='1.4.2'
PATH_SEPARATOR=':'
SHELL='/bin/sh'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
runstatedir='${localstatedir}/run'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "Rlibeemd"
#define PACKAGE_TARNAME "rlibeemd"
#define PACKAGE_VERSION "1.4.2"
#define PACKAGE_STRING "Rlibeemd 1.4.2"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""

configure: exit 0

Build is fine, but OpenMP is not used, despite being, obviously, supported by GCC.

Makevars are written like:

GSL_CFLAGS = -I/opt/local/include
GSL_LIBS = -L/opt/local/lib -lgsl -lgslcblas
PKG_LIBS=$(GSL_LIBS) $(SHLIB_OPENMP_CFLAGS)
PKG_CFLAGS=$(GSL_CFLAGS) $(SHLIB_OPENMP_CFLAGS)

And then SHLIB_OPENMP_CFLAGS are undefined. Should be -fopenmp there instead for it to work.

I used install.packages("codetools") to install the parallel version to get the error "clang: error: unsupported option '-fopenmp'" LLVM has posted a fix for this at http://blog.llvm.org/2015/05/openmp-support_22.html. It will require making the installation code aware of its environment and acting accordingly.

Here's the command and the following error messages. I know the formatting is a little goofy: R colored its responses red.

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rlibeemd.so RcppExports.o bemd.o bemdR.o ceemdan.o ceemdanR.o eemdR.o eemd_routine.o emd.o emd_num_imfsR.o error.o extrema.o extremaR.o gslErrorHandlerOff.o printError.o spline.o version.o workspace.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

clang-7: error: no such file or directory: '/Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib'
make: *** [Rlibeemd.so] Error 1
ERROR: compilation failed for package ‘Rlibeemd’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rlibeemd’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rlibeemd’
Error: Failed to install 'Rlibeemd' from GitHub:
  (converted from warning) installation of package ‘/var/folders/j1/f2wn1_k51dl2_wgn8m0b5m_00000gn/T//Rtmplmblob/filed2d4c395e77/Rlibeemd_1.4.1.tar.gz’ had non-zero exit status

I don't think this will be difficult, given the short MATLAB source code available at http://bioingenieria.edu.ar/grupos/ldnlys/metorres/metorres_files/ceemdan_v2014.m.

Reference: Colominas MA, Schlotthauer G, Torres ME. "Improve complete ensemble EMD: A suitable tool for biomedical signal processing," Biomedical Signal Processing and Control, vol. 14, pp. 19-29 (2014)

From latest CRAN checks:

src/Makevars.in: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
src/Makevars.in: it is not portable to include multiple SHLIB_OPENMP_*' macros in PKG_LIBS

I tried several combinations of CFLAGS and CXXFLAGS no luck. At the moment it seems that I have to disable OpenMP with CRAN version and add a startup message which points to github for parallel version...

CRAN recommends installing from GH, but no 1.4.3 here.

https://cran.r-project.org/web/packages/Rlibeemd/index.html
vs
https://github.com/helske/Rlibeemd/tags

devtools::install_github("helske/Rlibeemd")
Downloading GitHub repo helske/Rlibeemd@HEAD
checking for file ‘/tmp/RtmptW0VkH/remotes777d3cfa4949/helske-Rlibeemd-a237af ✔ checking for file ‘/tmp/RtmptW0VkH/remotes777d3cfa4949/helske-Rlibeemd-a237af 1/DESCRIPTION’
─ preparing ‘Rlibeemd’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘Rlibeemd_1.4.1.tar.gz’

Installing package into ‘/home/lasorte/R_Libs’
(as ‘lib’ is unspecified)

• installing source package ‘Rlibeemd’ ...
  ** using staged installation
  checking for gsl-config... /home/lasorte/appdir/bin/gsl-config
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/lasorte/R_Libs/Rcpp/ include" -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_ SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecor d-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
  gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I"/home/lasorte/R_Libs/Rcpp/in clude" -I/usr/local/include -I/home/lasorte/appdir/include -fopenmp -fpic -O2 - g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --pa ram=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c bemd.c -o bemd.o
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/lasorte/R_Libs/Rcpp/ include" -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_ SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecor d-gcc-switches -m64 -mtune=generic -c bemdR.cpp -o bemdR.o
  In file included from bemdR.cpp:4:
  bemd.h:23:10: fatal error: gsl/gsl_errno.h: No such file or directory
  #include <gsl/gsl_errno.h>
  ^~~~~~~~~~~~~~~~~
  compilation terminated.
  make: *** [bemdR.o] Error 1
  ERROR: compilation failed for package ‘Rlibeemd’
• removing ‘/home/lasorte/R_Libs/Rlibeemd’
  Error: Failed to install 'Rlibeemd' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmptW0VkH/file777d2b59 7194/Rlibeemd_1.4.1.tar.gz’ had non-zero exit status