Changes

Version 1.2.4→ 1.2.5 (official release, available on the web site):
Version 2017-11-04 (tested with CASA Version 5.1.1 for Linux Red Hat 6 and for MAC 10.11):

  • Now, molecule names used in the Splatalogue catalogue can be used in XCLASS as well. Note, the columns in the iso ratio file have to be separated by tabs or by at least two blanks. In order to see the table used by XCLASS to translate Splatalogue names into VAMDC names execute the following command within CASA

    QueryString = "select PF_Name, PF_SPLAT_NAME from partitionfunctions order by PF_Name"
    Contents = DatabaseQuery()

    where the first column describes the VAMDC and the second column the Splatalogue names, respectively.

  • removed bugs in MCMC and Error Estimation algorithm using MCMC. Now, MAGIX computes the chi^2 values for more than one parameter vector simultaneously.

  • removed bug in corner plots used by Error Estimation algorithm using MCMC. Now the computed error is displayed properly even if the error is very small or very large.

  • removed bug in Error Estimation algorithm using INS. Now, histograms are plotted correctly.

  • removed bug in Error Estimation algorithm using Fisher matrix. Now, the covariance matrix is calculated correctly.

  • removed bug in ListDatabase function. The function can now be used within CASA.

  • removed typos in XCLASS manual.

  • Note, XCLASS creates for each (myXCLASS, myXCLASSFit, myXCLASSMapFit, myXCLASSRedoFit, and LineID) function call a new input file called "collision-partners*.out.input" which will be used in a later XCLASS release.

  • Note, in the myXCLASSMapFit function, the frequency limits (FreqMin and FreqMax) have to be specified explicitly, if parameter 'experimentalData' describes path and name of a FITS file, i.e. the frequency limits are no longer determined from the FITS file. If parameter 'experimentalData' describe path and name of a obs. xml file, everything stays the same.

  • Note, many entries in the database for CH3OH have been changed. So many test cases have new reference results.

Version 1.2.3→ 1.2.4 (official release, available on the web site):
Version 2017-06-16 (tested with CASA Version 4.7.2 for Linux Red Hat 6 and for MAC 10.11):

  • removed bug in the myXCLASSMapFit function: parameter images for molfit parameters of foreground components are now created correctly

  • add Band 6 ALMA data set of IRAS 16293 as new test case for myXCLASSMapFit function (updated test case description as well)

  • improved installation script and improved handling in XCLASS python scripts of absolute path definitions of XCLASS subdirectories

  • improved XCLASS tutorial

  • updated XCLASS manual.
     

Version 1.2.2→ 1.2.3 (official release, available on the web site):
Version 2017-05-17 (tested with CASA Version 4.7.2 for Linux Red Hat 6 and for MAC 10.11):

  • improved GetTransition function: Now, a modeled spectra can be added to the observational data as well. The frequency can now be selected with the right mouse button. Using the key shortcuts "0", "1", and "2" the contents of the database around the selected frequency is sorted by transition frequency, lower energy or Einstein A coefficient

  • removed bug in the myXCLASSMapFit function: The definition of the global v_LSR parameter is now handled correctly

  • removed bug in the myXCLASSFit function: The iso ratio file is now also handled correctly if no observational xml file is used.

  • removed bug in the myXCLASSFit function: If no obs. xml file is used, usage of iso ratio file is now corrected.

  • removed bug in LineID function: The definition of the global v_LSR parameter is now handled correctly.

  • updated XCLASS manual.
     

Version 1.2.1 → 1.2.2 (official release, available on the web site):
Version 2016-12-05 (tested with CASA Version 4.7.0 for Linux Red Hat 6 and for MAC 10.11):

  • improved installation script to check, if python packages and compilers are available and checks if compilation was successfully.

  • installation script was modified so that XCLASS works now with CASA Version 4.7.0 for Linux Red Hat 6 as well.

  • included the possibility to define the XCLASS root directory in the .bashrc file using the XCLASSRootDir environment variable. Manual was updated.

  • removed bug in MAGIX, the tag <ValueEmptyOutputFile> is now handled correctly.

  • removed bug in Genetic algorithm: If <UseNewRange> tag is selected, the new ranges contain now always the optimized parameter values corrsponding to the best sites. Additionally, a buffer underflow detection is included.

  • removed bug in the XML import routine. Now, the subroutine guarantees that the tags <error>, <lowlimit> and <uplimit> in the instance xml-file are not empty.

  • the function LoadASCIIFile is now able to import FITS files as well. Manual was updated.

  • removed bug in XCLASS core routine, n_H column density definition in the molfit file is now handled correctly.

  • removed bug in XCLASS core routine, if beta is given in the molfit file, it was not fitted correctly.

  • removed bug in conversion of measurement set files to FITS files. Note, names of MS files/directories has to end with ".ms"!!! (In xml files, the corresponding import filter has to be set to "xclassfits"!)

  • removed bug in the FITS import and export subroutines and fits2dat.py script: The cos correction for the R.A. coordinate was not taken into account.

  • removed bug in the myXCLASSMapFit and myXCLASSMapRedoFit functions: The cos correction was not taken into account properly, which cased an offset in the R.A. direction.

  • removed errors in XCLASS manual.

Version 1.2.0 → 1.2.1 (official release, available on the web site):
Version 2016-09-22 (tested with CASA Version 4.6.0 for Linux Red Hat 6 and for MAC 10.11):

  • removed serious bugs in the myXCLASSMapRedoFit function. Now, the function works properly.
  • pixel coordinates for the myXCLASSMapRedoFit function can now be defined by their indices as well, see manual.
  • removed errors in the manual.
  • removed bugs in the myXCLASSMapFit function: The threshold is now handled correctly, if the intensity of the observational data cube is given in Jy/beam. Additionally, the calculated intensities are converted to jy/beam, if the observational data cube is given in Jy/beam as well.
  • now, the Genetic, MCMC, and INS algorithms offer the possibility to define the number of best sites (comparable with e.g. Bees algorithm), see manual for more details.
  • removed bug in the subroutine which sorts the chi2 log file
  • XCLASS uses the pyfits package included in astropy. If astropy is not available, XCLASS tries to import the old stand-alone pyfits package.

 

Version 1.1.9 → 1.2.0 (official release, available on the web site):
Version 2016-07-19 (tested with CASA Version 4.6.0 for Linux Red Hat 6 and  for MAC 10.11):

  • removed bug in GetTransitionParameters routine. Now, the vLSR parameter is handled correctly.
  • improved MAGIX routines to import and export FITS files.
  • removed bug in Genetic algorithm. New parameter ranges are now calculated correctly.
  • removed bug in Bees, Genetic, Levenberg-Marquardt, PSO, Nested-Sampling and Simulated-Annealing algorithm. Now, parameter values will never be printed as *****.
  • a new stand-alone version of MAGIX (version 2.0.1) is available and can be downloaded from the website:

 

Version 1.1.8 → 1.1.9 (official release, available on the web site):
Version 2016-06-24 (tested with CASA Version 4.6.0 for Linux Red Hat 6 and for MAC 10.11):

  • add MCMC as new swarm algorithm to MAGIX/XCLASS (SMP + MPI version), using the emcee package.
  • add new options to the error estimation algorithm: Now, error estimation can be done by using MCMC, Fisher-matrix or the (old) INS method, for more details see manual.
  • meaning of v_LSR input parameter has changed for myXCLASS, myXCLASSFit, local standard of rest (in km/s) USED in the calculation of the synthetic spectra, i.e. all velocity offsets described in the molfit file have to be defined relative to the v_LSR parameter. For example, the user defines v_LSR = 20 km/s, and the molfit file describes CH3CN with one component and v_off^molfit = 2 km/s, XCLASS uses v_off = v_LSR + v_off^molfit = 20 + 2 = 22 km/s for the  calculation of the spectra. Additionally, XCLASS considers the v_LSR parameter for the determination of the transition frequencies contained in the database: For each frequency range, XCLASS shifts the lowest and highest frequency by v_LSR (e.g. to describe lines in high-redshifted galaxies) and expands each range by taking the lowest and highest velocity offset defined in the molfit file into account. This offers the possibility to describe lines which are located at the edges of the frequency ranges. (For myXCLASSFit and myXCLASSMapFit function, XCLASS uses the user-defined lower and upper limits of a velocity offset parameter in the molfit file, if this parameter is fitted within a MAGIX run.) Please note, using a xml-file, the v_LSR parameter can be defined for each obs. data file!! (Note, the meaning of the parameter "RestFreq" is not changed. If the user defines a rest frequency != 0, XCLASS will add a velocity axis to the output arrays, using the v_LSR parameter.)
  • the myXCLASS function now creates output files describing the intensities and optical depths for isotopologues defined in the iso-ratio file as well. Additionally, the file "transition_energies.dat" contains now the integrated intensity for each Doppler-shifted line as well.
  • add input parameter vLSR to LineID function
  • removed bug in routine which is used for the extrapolation of the partition function. Now, temperatures above 1000 K can be fitted, correctly.
  • removed input parameters RestFreq and vLSR in the myXCLASSMapRedoFit function
  • removed bugs in Bees, PSO, Genetic, Nested-Sampling algorithm. Parameter vectors are now always within the given parameter limits
  • (really) removed bug in the myXCLASSMapFit function which produced wrong conversion results between JanskyPerBeam and Kelvin
  • (really) removed bug in test script for automatic LineID function
  • MAGIX sorting routine for .log.chi2 files ignores now entries with a chi^2 of 1.e99.
  • a new stand-alone version of MAGIX (version 2.0.0) is available and can be downloaded from the website: http://www.astro.uni-koeln.de/projects/schilke/MAGIX

 

Version 1.1.7 → 1.1.8 (official release, available on the web site):
Version 2016-05-14 (tested with CASA Version 4.5.2 for Linux Red Hat 6 and for MAC 10.11):

  • removed bug in the myXCLASSMapFit function which produced wrong conversion results between JanskyPerBeam and Kelvin for interferometric data
  • the pixel fits performed by the myXCLASSMapFit function are now stored in a subdirectory called "Pixel-Fits" within the job directory
  • update test scripts for XCLASS functions
  • removed bug in test script for automatic LineID function
  • removed bug in installation script
  • speed up MAGIX sorting routine for .log.chi2 files
  • removed bug in SMP version