API

myXCLASS

# import myXCLASS function
from xclass import task_myXCLASS

myXCLASSCore(MolfitsFileName = "",
             MolfitFileName = None,
             ObsXMLFileName = None,
             FreqMin = 1.0,
             FreqMax = 1.e8,
             FreqStep = 1.0,
             TelescopeSize = None,
             BMIN = None,
             BMAJ = None,
             BPA = None,
             Redshift = None,
             Inter_Flag = False,
             t_back_flag = True,
             tBack = 0.0,
             tSlope = 0.0,
             N_H = 0.0,
             beta_dust = 0.0,
             kappa_1300 = 0.0,
             DustFileName = "",
             BackgroundFileName = "",
             ContPhenFuncID = None,
             ContPhenFuncParam1 = None,
             ContPhenFuncParam2 = None,
             ContPhenFuncParam3 = None,
             ContPhenFuncParam4 = None,
             ContPhenFuncParam5 = None,
             NumModelPixelXX = 100,
             NumModelPixelYY = 100,
             LocalOverlapFlag = False,
             NoSubBeamFlag = False,
             dbFileName = "",
             CheckMoleculeInDB = True,
             RestFreq = 0.0,
             vLSR = 0.0,
             EmAbsFlag = False,
             EmAbsPATH = None,
             printFlag = None,
             SpectrumOnlyFlag = False)

The function models a spectrum by solving the radiative transfer equation for an isothermal object in one dimension, called detection equation.

The files produced by a myXCLASS function call are copied to a so-called “job-directory” located in the XCLASS interface working directory path-of-XCLASS/run/myXCLASS/! The name of a job directory for a myXCLASS run is made up of four components: The first part consists of the phrase “job_” whereas the second and third part describe the date and the time stamp (hours, minutes, seconds) of the function execution, respectively. The last part indicates a so-called job ID which is composed of the so-called PID followed by a four digit random integer number to create a really unambiguous job number, e.g.

path-of-XCLASS/run/myXCLASS/job__25-07-2013__12-02-03__189644932/

Input parameters:

• MolfitsFileName: path and name of the molfit file, see Sect. “The molfit file”.
  
  

• MolfitFileName: (optional) alias of MolfitsFileName, (default: None).
  
  

• ObsXMLFileName: (optional) path and name of an obs. xml file, (default: None), see Sect. “Observational xml file” for a detailed description. The obs. xml file can be used to create a synthetic spectrum for each frequency range.

  Note, the name of the xml file has to end with ".xml".
  
  

• FreqMin: start frequency of simulated spectrum (in MHz), (default: 1).
  
  

• FreqMax: end frequency of simulated spectrum (in MHz), (default: \(10^8\)).
  
  

• FreqStep: step frequency of simulated spectrum (in MHz), (default: 1).
  
  

• vLSR: velocity (local standard of rest) in km s\(^{-1}\) (default: 0) 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\(_{\rm LSR}\) parameter. For example, the user defines v\(_{\rm LSR}\) = 20 km/s, and the molfit file describes CH\(_3\)CN with one component and v\(_{\rm off}^{\rm molfit}\) = 2 km/s, XCLASS uses v\(_{\rm off}\) = v\(_{\rm LSR}\) + v\(_{\rm off}^{\rm molfit}\) = 20 km/s + 2 km/s = 22 km/s for the calculation of the spectra.

  Additionally, XCLASS considers the v\(_{\rm LSR}\) 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\(_{\rm LSR}\) (e.g. to describe lines in high-red-shifted 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.
  
  

• TelescopeSize: for single dish observations (Inter_Flag = False): TelescopeSize describes the size of telescope (in m), (default: 1); for interferometric observations (Inter_Flag = True): TelescopeSize describes the interferometric beam FWHM size (in arcsec), (default: 1).
  
  

• BMIN: (optional) Beam minor axis length (in arsec) (default: None), see Sect. “Sub-beam description”.
  
  

• BMAJ: (optional) Beam major axis length (in arsec) (default: None), see Sect. “Sub-beam description”.
  
  

• BPA: (optional) Beam position angle (in degree) (default: None), see Sect. “Sub-beam description”.
  
  

• Redshift: (optional) red shift (dimensionless), (default: None) NOT YET AVAILABLE!
  
  

• Inter_Flag (True/False): defines, if single dish (False) or interferometric observations (True) are described, (default: False).
  
  

• t_back_flag (True/False): defines, if the user defined background temperature \(T_{\rm bg}\) and temperature slope \(T_{\rm slope}\) given by the input parameters tBack and tSlope describe the continuum contribution completely (t_back_flag = True) or not (t_back_flag = False) (default: True).
  
  

• tBack background temperature (in K), (default: 0).
  
  

• tSlope temperature slope (dimensionless), (default: 0).
  
  

• BackgroundFileName (optional) path and name of file describing the background as function of frequency (in MHz), (default: None).
  
  

• N_H (optional) Hydrogen column density (in cm\(^{-2}\)), (default: 0.0), see Sect. “Dust contribution”.
  
  

• beta_dust (optional) spectral index for dust (dimensionless), (default: 0.0), see Sect. “Dust contribution”.
  
  

• kappa_1300 (optional) kappa at 1.3 mm (cm\(^2 \,\)g\(^{-1}\)), (default: 0.0), see Sect. “Dust contribution”.
  
  

• DustFileName (optional) path and name of file describing optical depth of dust as function of frequency (in MHz), (default: None), see Sect. “Dust contribution”.
  
  

• ContPhenFuncID: (optional) describes which phenomenological function is used to describe the continuum (default: None), see Sect. “Phenomenological continuum description”.
  
  

• ContPhenFuncParam1: (optional) first parameter for phenomenological function describing the continuum (default: None), see Sect. “Phenomenological continuum description”.
  
  

• ContPhenFuncParam2: (optional) second parameter for phenomenological function describing the continuum (default: None), see Sect. “Phenomenological continuum description”.
  
  

• ContPhenFuncParam3: (optional) third parameter for phenomenological function describing the continuum (default: None), see Sect. “Phenomenological continuum description”.
  
  

• ContPhenFuncParam4: (optional) fourth parameter for phenomenological function describing the continuum (default: None), see Sect. “Phenomenological continuum description”.
  
  

• ContPhenFuncParam5: (optional) fifth parameter for phenomenological function describing the continuum (default: None), see Sect. “Phenomenological continuum description”.
  
  

• iso_flag: use isotopologues (True/False). If iso_flag is set to True isotopologues defined in the iso ratio file are used (default: False).
  
  

• IsoTableFileName: (has to be given only if iso_flag is set to True): path and file name of an ASCII file including the iso ratios between certain molecules. The so-called “iso ratio file” defines the iso ratios between molecules. The ASCII file consists of three columns, where the first two columns indicates the molecules, respectively. The third column defines the ratio for both molecules. The columns are separated by blanks or tabs. So, the names of the molecules must not contain blanks. Comments have to be marked with the “%” sign, i.e. all characters on the right side of a “%” sign are ignored.

  The myXCLASSFit function offers the possibility to optimize the ratios between isotopologues as well. For that purpose, the user has to add two additional columns on the right indicating the lower and the upper limit of a certain ratio, respectively. A detailed description of the iso ratio file is given in Sect. “The iso ratio file”.
  
  

• NumModelPixelXX: (optional) used for sub-beam modeling, describes the number of model pixels used in x-direction (default: 100), see Sect. “Sub-beam description”.
  
  

• NumModelPixelYY: (optional) used for sub-beam modeling, describes the number of model pixels used in y-direction (default: 100), see Sect. “Sub-beam description”.
  
  

• LocalOverlapFlag (True/False): (optional) take local overlap into account (default: False), see Sect. “Local-overlap of neighboring lines”.
  
  

• NoSubBeamFlag (True/False): (optional) do not use sub-beam description into (default: False), see Sect. “Sub-beam description”, i.e. XCLASS uses the old source description, see Sect. “Simple 1-d description”.
  
  

• dbFilename: (optional) path and name of a database file, which is used instead of the default file cdms_sqlite.db stored in directory Database/, (default: None).
  
  

• RestFreq: rest frequency in MHz (default: 0). (If this parameter is unequal zero, the intensity is also plotted against velocity (in km s\(^{-1}\)) using parameter vLSR, see above.
  
  

• EmAbsFlag (True/False): (optional) flag indicating that emission and absorption as function of frequency are stored (default: False)
  
  

• EmAbsPATH: (optional) path containing files describing functions emission / absorption (default: None).
  
  

• CheckMoleculeInDB (True/False): (optional) check, if molecules included in molfit file have transitions within given frequency range (default: True)
  
  

• printFlag (True/False): (optional) flag for printing messages to the screen (default: True)
  
  

• SpectrumOnlyFlag (True/False): (optional) flag indicating that only the spectra (and no optical depth etc.) are calculated (default: False)

Output parameters:

• myXCLASSspectrum: contains the calculated myXCLASS spectrum

  If RestFreq is unequal zero, the myXCLASS function adds a column to the output parameter myXCLASSspectrum which contains the velocities. So, for a rest frequency unequal zero, the parameter myXCLASSspectrum represents a python array with three columns, where the first column describes the frequencies, the second column describes the velocities and the third column the corresponding intensities.
  
  

• myXCLASSlog: contains the corresponding log file
  
  

• myXCLASSTrans: (python) list containing the transition frequencies (in MHz) from the last myXCLASS run, the Doppler-shifted transition frequencies (in MHz), the corresponding absolute and integrated intensities (in K), the energy of the lower level (in K and K MHz), the upper state degeneracy, the Einstein A coefficient (in s\(^{-1}\)), and the molecule names within the defined range
  
  

• myXCLASSIntOptical: contains intensities and optical depths for each molecule and component. Depending on the local-overlap flag, i.e. if local-overlap is taken into account or not, the intensities and optical depths are given for each component or for each distance, see Sect. “Local-overlap of neighboring lines”.

  The intensities and optical depths are stored as follows:

  • myXCLASSIntOptical[0], contains all information about the intensities

    • myXCLASSIntOptical[0][i][0] contains the name of the \(i\)th molecule

    • myXCLASSIntOptical[0][i][1] contains the index of the component of the \(i\)th molecule

    • myXCLASSIntOptical[0][i][2] contains the intensities of the \(i\)th molecule as a 2D numpy array. Please note, the intensities for each core component \(\left[T_{\rm mb}^{i=1}\right]^{m,c}(\nu)\) and \(\left[T_{\rm mb}^{i>1}\right]^{m,c}(\nu)\) are given by different expression, depending if local-overlap is taken into account or not.

      If local-overlap is not taken into account, the intensities \(\left[T_{\rm mb}^{i=1}\right]^{m,c}(\nu)\) for components contained in the layer which is closest to the background is

      \[\begin{split}\left[T_{\rm mb}^{i=1}\right]^{m,c}(\nu) &= \Bigg[\eta \left(\theta^{m,c}\right) \left[S^{m,c}(\nu) \left(1 - e^{-\tau_{\rm total}^{m,c}(\nu)}\right) + I_{\rm bg} (\nu) \left(e^{-\tau_{\rm total}^{m,c}(\nu)} - 1\right)\right]\Bigg] \\ & \qquad + \frac{1}{N_{\rm all}^{i=1}} \, \left[I_{\rm bg} (\nu) - J_\mathrm{CMB} \right],\end{split}\]

      where \(N_{\rm all}^{i=1}\) indicates the number of all components of all molecules located in this layer. The intensities of components \(\left[T_{\rm mb}^{\rm i > 1}\right]^{m,c}\) with smaller distances are given by

      \[\left[T_{\rm mb}^{i > 1}\right]^{m,c}(\nu) = \Big[S^{m,c}(\nu) \left(1 - e^{-\tau_{\rm total}^{m,c}(\nu)}\right) + \left[T_{\rm mb}^{(i - 1)}\right]^{m,c} e^{-\tau_{\rm total}^{m,c}(\nu)}\Big].\]

      If local-overlap is taken into account, the expression for \(\left[T_{\rm mb}^{i=1}\right]^{m,c}(\nu)\) is slightly different

      (54)\[\begin{split}\left[T_{\rm mb}^{i=1}\right]^{m,c}(\nu) &= \sum_{m,c \in i} \Bigg[\eta \left(\theta^{m,c}\right) \left[S^{m,c}(\nu) \left(1 - e^{-\tau_{\rm total}^{m,c}(\nu)}\right) + I_{\rm bg} (\nu) \left(e^{-\tau_{\rm total}^{m,c}(\nu)} - 1\right)\right]\Bigg] \\ & \qquad + \frac{1}{N_{\rm all}^{i=1}} \, \left[I_{\rm bg} (\nu) - J_\mathrm{CMB} \right].\end{split}\]

      Additionally, the intensities for components at smaller distances \(\left[T_{\rm mb}^{\rm i > 1}\right]^{m,c}\) are given by

      (55)\[\left[T_{\rm mb}^{i > 1}\right]^{m,c}(\nu) = \sum_{m,c \in i} \Big[S^{m,c}(\nu) \left(1 - e^{-\tau_{\rm total}^{m,c}(\nu)}\right) + \left[T_{\rm mb}^{(i - 1)}\right]^{m,c} e^{-\tau_{\rm total}^{m,c}(\nu)}\Big].\]

    • myXCLASSIntOptical[0][i][3] contains the integrated intensities of the \(i\)th molecule.
      
      

  • myXCLASSIntOptical[1], contains all information about the optical depths.

    • myXCLASSIntOptical[1][i][0] contains the name of the \(i\)th molecule

    • myXCLASSIntOptical[1][i][1] contains the index of the component of the \(i\)th molecule

    • myXCLASSIntOptical[1][i][2] contains the optical depth of the \(i\)th molecule as a 2D numpy array. In general, the optical depths are given by

      \[\tau_l^{m,c}(\nu) = \sum_t \tau_t^{m,c}(\nu),\]

      where the sum runs over all transition \(t\) of a certain component (if local-overlap is not taken into account) or over all transitions of components, which belongs to the same distances (if local-overlap is taken into account).
      
      

• myXCLASSJobDir: absolute path of the job directory created for the current run
  
  

Note, the user is free to define different names for the output parameters. In the example describe below, we use the name "modeldata" for output parameter myXCLASSspectrum, "log" for output parameter myXCLASSlog, "TransEnergies" for output parameter myXCLASSTrans, "IntOptical" for output parameter myXCLASSIntOptical, and "jobDir" for output parameter myXCLASSJobDir.

myXCLASSFit

# import myXCLASSFit function
from xclass import task_myXCLASSFit

task_myXCLASSFit.myXCLASSFitCore(MolfitsFileName = "",
                                 MolfitFileName = None,
                                 NumberIteration = 10,
                                 AlgorithmXMLFileName = "",
                                 ObsXMLFileName = "",
                                 ObsDataFileName = None,
                                 experimentalData = None,
                                 observationalData = None,
                                 Optimizer = "magix",
                                 FastFlag = False,
                                 ChannelIntegrationFlag = True,
                                 TelescopeSize = None,
                                 BMIN = None,
                                 BMAJ = None,
                                 BPA = None,
                                 Redshift = 0.0,
                                 Inter_Flag = False,
                                 t_back_flag = True,
                                 tBack = 0.0,
                                 tSlope = 0.0,
                                 BackgroundFileName = "",
                                 N_H = 0.0,
                                 beta_dust = 0.0,
                                 kappa_1300 = 0.0,
                                 DustFileName = "",
                                 ContPhenFuncID = None,
                                 ContPhenFuncParam1 = None,
                                 ContPhenFuncParam2 = None,
                                 ContPhenFuncParam3 = None,
                                 ContPhenFuncParam4 = None,
                                 ContPhenFuncParam5 = None,
                                 iso_flag = False,
                                 IsoTableFileName = "",
                                 EmAbsPATH = None,
                                 NoSubBeamFlag = None,
                                 NumModelPixelXX = 100,
                                 NumModelPixelYY = 100,
                                 LocalOverlapFlag = None,
                                 RestFreq = 0.0,
                                 vLSR = 0.0,
                                 DictOutFlag = False)

For each run the myXCLASSFit function creates a so-called job directory located in the run directory (path-of-XCLASS-run/myXCLASSFit/) where all files created by the myXCLASSFit function are stored in. The name of this job directory is made up of four components: The first part consists of the phrase “job_” whereas the second and third part describe the date (day, month, year) and the time stamp (hours, minutes, seconds) of the function execution, respectively. The last part indicates a so-called job ID which is composed of the so-called PID followed by a four digit random integer number to create a really unambiguous job number, e.g. /path-of-XCLASS-run/myXCLASSFit/job__25-07-2013__12-02-03__189644/.

Before the fit procedure starts, the function copies the molfit, the observational data, and xml-files to the myXCLASSFit job directory. The path(s) defined in the observational xml-file are adjusted so that these paths point to the current myXCLASSFit job directory.

Please note, that the original observational xml- and data files are not modified. Only the copy of the observational xml file located in the myXCLASSFit job directory is modified!

If no observational xml-file is defined, the myXCLASSFit function creates an observational xml-file containing the settings for the different parameters in the myXCLASSFit job directory. Additionally, the function creates an ASCII file located in the myXCLASSFit job directory containing the observational data given by the parameter "observationalData". If the parameter "observationalData" defines the path and the name of an observational data file, then the data file is copied to the myXCLASSFit job directory as well. The path and the name of this ASCII file is pasted in the created observational xml file. Furthermore, the function creates automatically the algorithm and i/o control xml files, need by MAGIX, so that the user does not need to edit any xml-file.

Additionally, the myXCLASSFit function converts the column density \(N_{\rm tot}\) (and if the hydrogen column density \(N_H\) is given for each component) the hydrogen column density \(N_H\) as well to a log scale, i.e. these two densities are converted automatically to their log10 values to get a better fit. At the end of the fitting process, the log10 values are converted back to the original linear values. So, the MAGIX log files contain the log10 values of these parameters, whereas the input and output molfit file contain the linear values, respectively.

Input parameters:

• MolfitsFileName: path and name of the (extended) molfit file, see Sect. “The molfit file”
  
  

• MolfitFileName: (optional) alias of MolfitsFileName, (default: None).
  
  

• AlgorithmXMLFileName: (optional) path and name of an algorithm xml-file describing settings for an algorithm or algorithm chain, see Sect. “Algorithm xml file”.

  NOTE, if the user specify a xml file, the number of iterations given by the parameter NumberIteration is ignored. The number of iteration is then given by the xml file.
  
  

• NumberIteration: max. number of iterations (default: 10). (This parameter is ignored if a algorithm xml file is defined). If parameter Optimizer, see below, is set to 'magix', the Levenberg-Marquardt algorithm, otherwise the trf algorithm is used.
  
  

• ObsXMLFileName: (optional) path and name of an obs. xml file (recommended procedure), (default: ""), see Sect. “Observational xml file” for a detailed description.

  Note, the name of the xml file has to end with ".xml".
  
  

• ObsDataFileName: (optional) describes the observational data, if no obs. xml file is given, (default: None). There are two options for transferring the data to XCLASS:

  • the parameter describes path and name of an ASCII file called observational data file, where the first column describe the frequency (in MHz) and the second column the brightness temperature (in Kelvin)

    Please note, without using an obs. xml file, it is not possible to fit more than one data cube, simultaneously.

  • the parameter describes a 2d numpy array, where the first column describes the frequency (in MHz) and the second column the brightness temperature (in Kelvin).
    
    

• experimentalData: (optional) alias of ObsDataFileName, (default: None)
  
  

• observationalData: is deprecated.
  
  

The following parameters are needed, if parameter ObsDataFileName is used instead of parameter ObsXMLFileName:

• vLSR: source velocity (local standard of rest) in km s\(^{-1}\) (default: 0).
  
  

• TelescopeSize: for single dish observations (Inter_Flag = False): TelescopeSize describes the size of telescope (in m), (default: 1); for interferometric observations (Inter_Flag = True): TelescopeSize describes the interferometric beam FWHM size (in arcsec), (default: 1).
  
  

• BMIN: (optional) Beam minor axis length (in arcsec) (default: None)
  
  

• BMAJ: (optional) Beam major axis length (in arcsec) (default: None)
  
  

• BPA: (optional) Beam position angle (in degree) (default: None)
  
  

• Redshift: (optional) red shift (dimensionless), (default: None)
  
  

• Inter_Flag (True/False): defines, if single dish (False) or interferometric observations (True) are described, (default: False).
  
  

• t_back_flag (True/False): defines, if the user defined background temperature \(T_{\rm bg}\) and temperature slope \(T_{\rm slope}\) given by the input parameters tBack and tSlope describe the continuum contribution completely (t_back_flag = True) or not (t_back_flag = False) (default: True).
  
  

• tBack background temperature (in K), (default: 0).
  
  

• tSlope temperature slope (dimensionless), (default: 0).
  
  

• BackgroundFileName (optional) path and name of file describing the background as function of frequency (in MHz), (default: None).
  
  

• N_H (optional) Hydrogen column density (in cm\(^{-2}\)), (default: None).
  
  

• beta_dust (optional) spectral index for dust (dimensionless), (default: None).
  
  

• kappa_1300 (optional) kappa at 1.3 mm (cm\(^2 \,\)g\(^{-1}\)), (default: None).
  
  

• DustFileName (optional) path and name of file describing dust contribution (default: "").
  
  

• ContPhenFuncID: (optional) describes which phenomenological function is used to describe the continuum (default: None).
  
  

• ContPhenFuncParam1: (optional) first parameter for phenomenological function describing the continuum (default: None).
  
  

• ContPhenFuncParam2: (optional) second parameter for phenomenological function describing the continuum (default: None).
  
  

• ContPhenFuncParam3: (optional) third parameter for phenomenological function describing the continuum (default: None).
  
  

• ContPhenFuncParam4: (optional) fourth parameter for phenomenological function describing the continuum (default: None).
  
  

• ContPhenFuncParam5: (optional) fifth parameter for phenomenological function describing the continuum (default: None).
  
  

• iso_flag: use isotopologues (True/False). If the flag is set to True isotopologues defined in the iso ratio file are taken into account, (default: False).
  
  

• IsoTableFileName (has to be given only if iso_flag is set to True): path and name of an ASCII file including the iso ratios between certain molecules. A detailed description of the iso ratio file is given in Sect. “The iso ratio file”. If no file name is given (default), the so-called iso-flag is set to False.
  
  

  NOTE, if the parameter observationalData defines a relative path, the path has to be defined relative to the current working directory!
  
  

• NumModelPixelXX: (optional) used for sub-beam modeling, describes the number of pixels used in x-direction (default: 100).
  
  

• NumModelPixelYY: (optional) used for sub-beam modeling, describes the number of pixels used in y-direction (default: 100).
  
  

• LocalOverlapFlag (True/False): (optional) take local overlap into account (default: False), see Sect. “Local-overlap of neighboring lines”.
  
  

• NoSubBeamFlag (True/False): (optional) do not use sub-beam description (default: False), see Sect. “Sub-beam description”.
  
  

The following parameter is needed to add a velocity axis to the output array model_values, see below:

• RestFreq: rest frequency in MHz (default: 0).
  
  

The myXCLASSFit function offers the possibility to use two different optimization packages: 'magix' or 'scipy', providing different optimization algorithms, see Sect. .

• Optimizer: package used for optimization ('magix' and 'scipy') (default: 'magix').

  Note, the optimization package used different fit algorithms. A list of the fit algorithms for each optimization package and the corresponding settings in the algorithm xml file is given in Sect. “Algorithm xml file”.
  
  

• FastFlag is deprecated.
  
  

• ChannelIntegrationFlag: (only for optimizer 'scipy') flag indicating usage of channel integration (default: False).
  
  

Finally, the results of the myXCLASSFit function can be exported in two different ways

• DictOutFlag: flag indicating, that all return parameters are collected in a dictionary (default: False).

Output parameters:

Please note, the user is free to define different names for the output parameters.

If the input parameter DictOutFlag is set to False, the myXCLASSFit function returns the results to the following three output parameters:

• input_file: the contents of the molfit file containing the parameters for the best fit.
  
  

• model_values: the model function values for each data point, which correspond to the best fit.

  If RestFreq is unequal zero, the myXCLASSFit function adds a column to the output parameter model_values which contains the velocities. So, for a rest frequency unequal zero, the parameter model_values represents a python array with three columns, where the first column describes the frequencies, the second column describes the velocities and the third column the corresponding intensities.
  
  

• JobDir: absolute path of the job directory created for the current run.
  
  

Please note, if more than one algorithm is used, the output parameters input_file and model_values contain all input files and model function values of all results, i.e. input_file[0] contains the molfit file and model_values[0] the model function values for the first applied fit algorithm.

The order of the results, i.e. the name of the molfit file, which correspond to input_file[0], is printed to the screen.

If the input parameter DictOutFlag is set to True, the myXCLASSFit function exports the results to a python dictionary, e.g. OutDict, containing the following items:

• "JobDir": describes path of the current job directory, i.e. OutDict["JobDir"] is the path and name of the current job directory.
  
  

• "MolfitFileNames": is a python list indicating all used molfit file names, describing the optimized fit parameters after the application of a certain optimization algorithm.
  
  

• "MolfitFilesContent": list of the corresponding molfit file contents,
  
  

• "IsoRatioFileNames": list of iso ratio file names indicating the optimized fit parameters after the application of a certain optimization algorithm,
  
  

• "IsoRatioFilesContent": list of the corresponding iso ratio file contents,
  
  

• "ListOfSpectraFileNames": list of spectra file names after the application of a certain optimization algorithm,
  
  

• "ListOfSpectraFilesContent": list of numpy arrays describing the optimized spectra after the application of a certain optimization algorithm,
  
  

• "BestMolfitFileName": name of the molfit file of the best fit
  
  

• "BestMolfitFileContent": content of the molfit file corresponding to the best fit,
  
  

• "BestIsoRatioFileName": name of the iso ratio file of the best fit,
  
  

• "BestIsoRatioFileContent": content of the iso ratio file which belongs to the best fit,
  
  

• "BestSpectraFileNames": path and name of file describing the spectra of the best result,
  
  

• "BestSpectraFilesContent": spectra of best fit.
  
  

Note, if only one algorithm is applied, the content of the items "MolfitFileNames" and "BestMolfitFileName" etc. are identical.

myXCLASSMapFit

# import myXCLASSMapFit function
from xclass import task_myXCLASSMapFit

myXCLASSMapFitCore(MolfitsFileName = "",
                   MolfitFileName = None,
                   AlgorithmXMLFileName = "",
                   AlgorithmXMLFile = "",
                   NumberIteration = 50,
                   NumberProcessors = 4,
                   ObsXMLFileName = "",
                   ObsDataFileName = "",
                   experimentalData = "",
                   FastFitFlag = True,
                   FullFitFlag = False,
                   ChannelIntegrationFlag = False,
                   clusterdef = None,
                   daskFlag = False,
                   ParallelMethod = "process",
                   regionFileName = "",
                   FITSImageMaskFileName = "",
                   Threshold = None,
                   EstimateContinuumFlag = False,
                   EstimateConNumParts = 20,
                   EstimateConNumEntireCubeFlag = True,
                   UsePreviousResults = None,
                   DataSmoothValue = 0.0,
                   ParameterMapDir = None,
                   ParamMapIterations = 1,
                   ParamSmoothMethodParam = 1.0,
                   ParamSmoothMethod = "uniform",
                   FreqMin = None,
                   FreqMax = None,
                   TelescopeSize = None,
                   BMIN = None,
                   BMAJ = None,
                   BPA = None,
                   Redshift = None,
                   Inter_Flag = False,
                   t_back_flag = True,
                   tBack = 0.0,
                   tSlope = 0.0,
                   N_H = 0.0,
                   beta_dust = 0.0,
                   kappa_1300 = 0.0,
                   DustFileName = "",
                   BackgroundFileName = "",
                   ContPhenFuncID = None,
                   ContPhenFuncParam1 = None,
                   ContPhenFuncParam2 = None,
                   ContPhenFuncParam3 = None,
                   ContPhenFuncParam4 = None,
                   ContPhenFuncParam5 = None,
                   iso_flag = False,
                   IsoTableFileName = "",
                   NumModelPixelXX = 100,
                   NumModelPixelYY = 100,
                   LocalOverlapFlag = False,
                   NoSubBeamFlag = False,
                   EmAbsPATH = None,
                   RestFreq = 0.0,
                   vLSR = 0.0,
                   ZipDirFlag = False,
                   DoParameterEstimationFlag = False,
                   InternalParameterList = {},
                   JobDir = None,
                   NameOfFunction = None)

In contrast to the myXCLASSFit function, the myXCLASSMapFit function fits a complete (FITS) data cube 1 Here, the myXCLASSMapFit function reads in the data cube(s), extracts the spectra for each pixel and fits these spectra separately using an user-defined optimization algorithm. The myXCLASSMapFit function provides three different fitting procedures: "fast", "full", and "normal". The first two methods allow accelerated fitting without MAGIX and instead provide an interface to the SciPy [Virtanen_et_al_2020] optimization functions described in Sect. “Algorithm xml file”.

These optimization algorithms are described in an algorithm xml file, see Sect. “Algorithm xml file”. In principle, it is also possible to combine algorithms, i.e. to start with a global optimization algorithm and use the results of this algorithm as input for a local optimization algorithm such as "trf". In contrast to the myXCLASSFit function, all optimization algorithms are not parallelized, i.e. the optimization procedure for a single pixel uses only one core.

If the algorithm XML file contains a definition for the number of processors (cores) for an optimization algorithm, this number now defines the number of pixels that are fitted simultaneously. If more processor cores are defined than are available on the computer, XCLASS reduces the number to the number of available processors (cores) minus one. If no algorithm xml file is used, the myXCLASSMapFit function uses the trf algorithm with four cores and performs no more than 50 iterations.

With the "fast" method (applied by default), the myXCLASSMapFit function uses simplified versions of the XCLASS core functions to compute the synthetic spectra used for the optimization algorithms. These simplified functions are able to compute the contribution of molecules and recombination lines in LTE in conjunction with dust contributions. Additionally, it is possible to arrange the components according to the distance parameter along the line-of-sight, see Sect. “Stacking”. In contrast to the "fast" method, the "full" method uses the full XCLASS core routines, which is why it is possible to use sub-beam description Sect. “Sub-beam description. Compared to the "fast" method mentioned above, this fitting procedure is computationally more complex, so the fitting takes a little more time. Finally, the "normal" method provides an interface to the MAGIX optimization package, similar to the myXCLASSFit function. This fitting procedure requires a lot of I/O to the hard disk, which is why it is much slower compared to the previously mentioned procedures.

For each run the myXCLASSMapFit function creates a so-called job directory, where the name of a job directory is made up of four components: The first part of the name consists of the phrase "job_" whereas the second part describes the date (day, month, year), the third part the time stamp (hours, minutes, seconds) of the function execution. The last part describes a so-called job ID which is composed of the so-called PID followed by a four digit random integer number to create a really unambiguous job number, e.g.

/path-of-XCLASS-run/myXCLASSMapFit/job__25-07-2013__12-02-03__189644932/.

If the "normal" fitting method is selected, the myXCLASSMapFit function creates a subdirectory within this job directory called "Pixel-Fits/, which contains further subdirectories for each pixel, where the names of these subdirectories are made up of the values (in degrees) for the right ascension and for the declination, respectively, e.g. "83.65498__-5.24258". Additionally, the indices of the corresponding pixel are added as well separated by “_-_”, e.g. "83.65498__-5.24258__1_-_2". All output files, created by MAGIX for this pixel are stored in this subdirectory. If the user applies the Levenberg-Marquardt algorithm, the myXCLASSMapFit function uses the parameter given in the molfit file as initial guess for all pixels in the first row of the selected region.

At the end of the whole fit procedure, the myXCLASSMapFit function creates FITS images for each optimized parameter, where each pixel corresponds to the value of the optimized parameter taken from the best fit for this pixel. The name of each parameter FITS image consists of the phrase "BestResult" followed by the name of the parameter, e.g. T_rot for the rotation temperature etc, the name of the corresponding molecule, and finally by the index of the related component. For example, the FITS file

BestResult___parameter__T_rot___molecule__CH3OH_v=0____component__1.fits,

describes the optimized excitation (rotation) temperature of the first component of molecule “CH\(_3\)OH,v=0” for each pixel of the selected fit region. In addition to the parameter maps, the myXCLASSMapFit function creates one FITS image, where each pixel corresponds to the \(\chi^2\) value of the best fit, i.e. the quality of the fit, for the corresponding pixel.

Furthermore, the myXCLASSMapFit function creates FITS cubes for each used algorithm and fitted data cube, where each pixel contains the modeled spectrum. The name of these FITS cubes ends with the expression "__model.out.fits". (If more than one fit algorithm was used, this expression is extended by the respective name of the optimization algorithm). If more than one frequency range was used for a given FITS cube, the name of the corresponding FITS cube describing the synthetic spectra also contains the frequency limits (in MHz), i.e.

name-of-FITS-file__MinFreq_-_MaxFreq__MHz__model.out.fits.

The FITS files, which end with ".chi2.out.fits", describe the \(\chi^2\) function for each pixel. In addition, the myXCLASSMapFit function converts the following parameters N_tot, EM_RRL, nHcolumn_cont_dust, and nHcolumn to a log scale, i.e. these parameter values are converted automatically to their log10 values to get a better fit. At the end of the fitting process, the log10 values are converted back to the original linear values. So, the MAGIX log files contain the log10 values of these parameters, whereas the input and output molfit files contain the linear values, respectively.

The myXCLASSMapFit function offers the possibility to use a so-called cluster consisting of at least two computers. The nodes (computers) of the cluster are defined by the input parameter clusterdef, see below. Unfortunately, due to problems with the used parallelization packages, cluster computation with more than one computer is currently not possible.

The myXCLASSMapFit function can handle FITS cubes (and images) for background and dust files as well, i.e. the user can specify the path and name of a FITS cube describing the background (or dust) spectrum for each pixel and frequency range. If a FITS image is provided instead of a cube, the corresponding spectrum is automatically generated for the required frequency points. If a background spectrum is given in Jy/beam, XCLASS automatically converts the intensities to Kelvin. The FITS cubes (or images) need not to cover the entire region. Where no background (or dust) file is given, no background (or dust) spectrum is used.

Input parameters:

• MolfitsFileName: path and name of the extended molfit file, see Sect. “The molfit file”.
  
  

• MolfitFileName: (optional) alias of MolfitsFileName, (default: None).
  
  

• FastFitFlag: (optional) flag indicating fast fitting, (default: True).
  
  

• FullFitFlag: (optional) full fit flag, (default: False). If FastFitFlag and FullFitFlag are set to False, normal fitting is applied.
  
  

• ChannelIntegrationFlag: (optional, for full fitting method only) flag indicating channel integration (default: False).
  
  

• AlgorithmXMLFileName: (optional) path and name of an algorithm xml-file describing settings for an algorithm or algorithm chain, see Sect. “Algorithm xml file”.

  NOTE, if the user specify a xml file, the number of iterations given by the parameter NumberIteration is ignored. The number of iteration is then given by the xml file.
  
  

• AlgorithmXMLFile: (optional) alias of AlgorithmXMLFileName.
  
  

• NumberIteration: (only necessary if no algorithm xml and no cluster file is given) max. number of iterations (default: 50).
  
  

• NumberProcessors: (optional) max. number of cores, only used if no algorithm xml file is applied (default: 4).
  
  

• clusterdef: path and name of a file describing a cluster, (default: "").

  In order to start the myXCLASSMapFit function on a multi-computer cluster, a so-called “cluster configuration file” is required. The following requirements are necessary for all nodes which are included in the cluster:

  1. Password-less ssh access from the controller (user) machine to all other nodes included in the cluster.

     NOTE: This is not necessary when using only “localhost”, i.e. if the cluster is deployed only on the machine where XCLASS is running.

  2. XCLASS interface and gfortran (with OpenMP/OpenMPI) is installed on all nodes of the cluster.

  3. The XCLASS job directory must be located in a shared file-system, accessible from all nodes comprising the cluster, and mounted in the same path of the file-system.

     NOTE: If the cluster contains computers with different operating systems, e.g. Linux and MAC OS, the user has to define the different paths of the XCLASS interface directories.

  Example of a “cluster configuration file” used for the myXCLASSMapFit function:

  # cluster configuration file
  # node      number of cores      path of XCLASS interface
  anu,        2
  lugal,      3
  

  In the example described above, the nodes “anu” and “lugal” will be used with two (three) cores, respectively.
  
  

• regionFileName: (optional) path and name of a so-called ds9 2 region file, (default: "").
  
  

• FITSImageMaskFileName: (optional) path and name of a FITS image used for masking. Here, each pixel with a real numerical value, i.e. which is not NaN, is fitted, (default: "").
  
  

• Threshold: defines a threshold for a pixel. If the spectrum of a pixel has an max. intensity lower than the value defined by this parameter the pixel is not fitted (ignored), (default: None).

  Please note, the value for the Threshold parameter has to be given in the same unit than the spectrum in the FITS file.

  NOTE, if an observational xml-file is used, the user can define different threshold values for each frequency range by using the tag <Threshold>. Please note, that the tag <Threshold> has to be given for each frequency range. If tag <Threshold> is defined in the xml file, the value of the input parameter Threshold is ignored.
  
  

• EstimateContinuumFlag: (optional) flag indicating continuum estimation using the statcont [SanchezMonge_et_al_2018] package (default: False).
  
  

• EstimateConNumParts: (optional) number of sub-parts used for continuum estimation to describe non-constant continuum levels as well, (default: 20). In order to estimate the continuum level, the obs. data (of each pixel) are divided into \(n\) (=EstimateConNumParts) equidistant parts to which statcont is applied. Now, the obs. data within each part is replaced by the corresponding continuum level located at the center of each part. Afterwards, the well-known expression

  \[I_{\rm bg} (\nu) = T_{\rm bg} \cdot \left(\frac{\nu}{\nu_{\rm min}} \right)^{T_{\rm slope}}\]

  is fitted to these data points to achieve the parameters \(T_{\rm bg}\) and \(T_{\rm slope}\).
  
  

• EstimateConNumEntireCubeFlag: (optional) flag indicating that the continuum estimation is done for the entire spectral range of the corresponding FITS cube and not only for the local frequency range, (default: True).
  
  

• DataSmoothValue: (optional) smooth factor (=0, no smoothing is performed) used for spectral smoothing, (default: 0.0). Here each pixel is convolved with a Gaussian whose width is given by this parameter.
  
  

• UsePreviousResults: Please note, this parameter is no longer used.
  
  

• ParamMapIterations: (optional) number of iterations to smooth parameter maps, (default: 1).

  A value greater 1 indicates a parameter map smoothing procedure, i.e. after finishing the first myXCLASSMapFit run, the created parameters maps are smoothed using the method and parameter described by ParamSmoothMethodParam and ParamSmoothMethod. The values of the smoothed parameter maps are used in a second myXCLASSMapFit run, where the parameters in the molfit files at each fitted pixel position are updated by the values of the smoothed maps. The whole procedure is repeated as many times as indicated by ParamMapIterations. The names of the FITS files describing the parameter maps are extended by the phrase "_____Iter__n.fits", where \(n\) indicates the current iteration, The FITS files ending with \(n=\)ParamMapIterations describe the final parameter maps.
  
  

• ParamSmoothMethodParam: (optional) parameter used for smoothing the parameter map(s), see input parameter ParamSmoothMethod, (default: 1.0)
  
  

• ParamSmoothMethod: (optional) SciPy method ("gaussian", "uniform", "median") used for parameter map smoothing, (default: "uniform").

  • For "gaussian", SciPy’s multidimensional Gaussian filter 3 is used, where ParamSmoothMethodParam indicates the standard deviation for Gaussian kernel (in pixel) which is assumed to be equal for both axes.

  • For "uniform", SciPy’s multidimensional uniform filter 4 is applied, where ParamSmoothMethodParam describes the sizes (in pixel) of the uniform filter which is equal for both axes.

  • For "median", SciPy’s multidimensional median filter 5 is utilized, where ParamSmoothMethodParam defines the sizes (in pixel) of the median filter which is equal for both axes.
    
    

• DoParameterEstimationFlag: is deprecated
  
  

• InternalParameterList: is deprecated
  
  

• ParameterMapDir: (optional) path of a directory containing FITS images describing parameter maps to update the parameter defined in the molfit file (or iso ratio file) for each pixel (default: None). By using this parameter the user can modify the content of the molfit file, defined by input parameter MolfitsFileName, for each pixel. Therefore, the name of the FITS image file describing a parameter map has to consists of the name of the molfit parameter (e.g. N_tot), which has to be updated, the name of the molecule, and the corresponding component number. The different settings has to be separated by "___". The definition of the parameter name has to start with the phrase "parameter__" followed by the name of the parameter, i.e. the name has to be "source_size", "source_radius", "s_radius", "source_center_x", "s_off_x", "source_center_y", "s_off_y", "T_rot", "T_e", "T_cont_dust", "T_dOff", "T_dSlope", "N_tot", "EM_RRL", "nHcolumn_cont_dust", "nHcolumn", "V_width, "V_width_Gauss", "V_off", "beta_cont_dust", "kappa_cont_dust", "kappa", "beta", "ContFuncID_param_1", "ContPhenFuncParam1", "ContFuncID_param_2", "ContPhenFuncParam2", "ContFuncID_param_3", "ContPhenFuncParam3", "ContFuncID_param_4", "ContPhenFuncParam4", "ContFuncID_param_5", "ContPhenFuncParam5". Additionally, the name of the molecule has to start with phrase "molecule__" followed by the name of the molecule, where the characters (";", ",", "'", "(", ")", "#") has to be replaced by "_". Finally, the definition of the component number has to start with "component__" followed by an integer number. For example, we want to use a FITS image describing the velocity offsets for the first component of CH\(_3\)CN,v=0 for each pixel of the selected region. The name of the corresponding FITS file is "parameter__V_off___molecule__CH3CN_v=0____component__1.fits".

  In order to define iso ratios for a specific isotopologue, the name of the parameter has to be set to "isoratio" and the name of the molecule has to indicate the corresponding isotopologue. The part, which describes the component has to be removed, e.g. "parameter__isoratio___molecule__C-13H3CN_v=0_.fits".

• ObsXMLFileName: (optional) path and name of an obs. xml file (recommended procedure), (default: ""), see Sect. “Observational xml file” for a detailed description.

  Note, the name of the xml file has to end with ".xml".
  
  

• ObsDataFileName: (optional) path and name of a file describing a 3d or 4d FITS data cube.

  Note, the name of the data file has to end with ".fits".

  If the intensities of a data cube are given in Jy/beam, the myXCLASSMapFit function converts the intensities to Kelvin using the following expression 6 [Rohlfs_Wilson_1996]

  \[T_{\rm mb} (\nu) = \frac{c^2 \cdot S_\nu}{2 \, k_B \, \nu^2 \, \Omega} \cdot 10^{-26},\]

  where \(S_\nu\) describes the intensity at a certain frequency \(\nu\) in Jy/beam and \(c\) and \(k_B\) represents the speed of light and the Boltzmann constant, respectively. Additionally, \(\Omega\) indicates the solid angle of the beam and can be expressed under the assumption that the beam can be approximated by a two-dimensional, elliptical Gaussian function \(G(\alpha, \beta)\)

  \[\Omega = \iint G(\alpha, \beta) \, d\alpha \, d \beta = {\rm BMAJ} \cdot {\rm BMIN} \cdot \frac{\pi}{4 \, \ln(2)},\]

  where BMAJ and BMIN indicate the FWHM of the beam major and minor axis length in arcsec, respectively 7.

  Please note, without using an obs. xml file, it is not possible to fit more than one data cube, simultaneously.

• experimentalData: (optional) alias of ObsDataFileName, (default: None)
  
  

The following parameters are needed, if parameter ObsDataFileName is used instead of parameter ObsXMLFileName:

• FreqMin: start frequency of simulated spectrum (default: 0).

  Please note, in contrast to previous XCLASS releases, the min. and max. frequency has to be defined! Additionally, the step size, i.e. the difference between two frequencies is taken from the FITS header.
  
  

• FreqMax: end frequency of simulated spectrum (default: 0).
  
  

• vLSR: velocity (local standard of rest) in km s\(^{-1}\) (default: 0) used in the calculation of the synthetic spectra
  
  

• TelescopeSize: for single dish observations (Inter_Flag = False): TelescopeSize describes the size of telescope (in m), (default: 1); for interferometric observations (Inter_Flag = True): TelescopeSize describes the interferometric beam FWHM size (in arcsec), (default: 1).
  
  

• BMIN: (optional) beam minor axis length (in arcsec), (default: None).

  Note, in the header of FITS files, the beam minor and major axis lengths are often given in degrees and not in arcsec, i.e. the values have to be divided by 3600.
  
  

• BMAJ: (optional) beam major axis length (in arcsec), (default: None).
  
  

• BPA: (optional) beam position angle (in degree), (default: None).
  
  

• Redshift: (optional) red shift (dimensionless), (default: None).
  
  

• Inter_Flag (True/False): defines, if single dish (False) or interferometric observations (True) are described, (default: False).
  
  

• t_back_flag (True/False): defines, if the user defined background temperature \(T_{\rm bg}\) and temperature slope \(T_{\rm slope}\) given by the input parameters tBack and tSlope describe the continuum contribution completely (t_back_flag = True) or not (t_back_flag = False) (default: True).
  
  

• tBack background temperature (in K), (default: 0.0).
  
  

• tSlope temperature slope (dimensionless), (default: 0.0).
  
  

• BackgroundFileName (optional) path and name of file describing the background as function of frequency (in MHz), (default: None).
  
  

• N_H (optional) Hydrogen column density (in cm\(^{-2}\)), (default: 0.0).
  
  

• beta_dust (optional) spectral index for dust (dimensionless), (default: 0.0).
  
  

• kappa_1300 (optional) kappa at 1.3 mm (cm\(^2 \,\)g\(^{-1}\)), (default: 0.0).
  
  

• DustFileName (optional) path and name of file describing dust contribution, (default: None).
  
  

• ContPhenFuncID: (optional) describes which phenomenological function is used to describe the continuum, (default: None).
  
  

• ContPhenFuncParam1: (optional) first parameter for phenomenological function describing the continuum, (default: None).
  
  

• ContPhenFuncParam2: (optional) second parameter for phenomenological function describing the continuum,(default: None).
  
  

• ContPhenFuncParam3: (optional) third parameter for phenomenological function describing the continuum, (default: None).
  
  

• ContPhenFuncParam4: (optional) fourth parameter for phenomenological function describing the continuum,(default: None).
  
  

• ContPhenFuncParam5: (optional) fifth parameter for phenomenological function describing the continuum, (default: None).
  
  

• iso_flag: use isotopologues (True/False). If iso_flag is set to True isotopologues defined in the iso ratio file are used, (default: False).
  
  

• IsoTableFileName (has to be given only if iso_flag is set to True): path and name of an ASCII file including the iso ratios between certain molecules. A detailed description of the iso ratio file is given in Sect. “The iso ratio file”. If no file name is given (default), the so-called iso-flag is set to False.

  NOTE, if the given path is a relative path, i.e. the path does not start with /, this path has to be defined relative to the current working directory!
  
  

• NumModelPixelXX: (optional) used for sub-beam modeling, Sect. “Sub-beam description”, describes the number of pixels used in x-direction, (default: 100).
  
  

• NumModelPixelYY: (optional) used for sub-beam modeling, Sect. “Sub-beam description”, describes the number of pixels used in y-direction, (default: 100).
  
  

• LocalOverlapFlag: (optional) flag indicates if local-overlap description is used or not, see Sect. “Local-overlap of neighboring lines”, (default: False).
  
  

• NoSubBeamFlag (True/False): (optional) do not use sub-beam description (default: False), see Sect. “Sub-beam description”, i.e. XCLASS uses the old source description, see Sect. “Simple 1-d description”.

Output parameters:

• JobDir: absolute path of the job directory created for the current run.
  
  

myXCLASSMapRedoFit

# import myXCLASSMapRedoFit function
from xclass import task_myXCLASSMapRedoFit

myXCLASSMapRedoFitCore(JobNumber = None,
                       PixelList = [],
                       JobPath = "",
                       MaskFileName = "",
                       Threshold = None,
                       MolfitsFileName = "",
                       MolfitFileName = None,
                       EstimateContinuumFlag = False,
                       EstimateConNumParts = 20,
                       EstimateConNumEntireCubeFlag = True,
                       DataSmoothValue = 0.0,
                       NumberIteration = 50,
                       NumberProcessors = 2,
                       AlgorithmXMLFile = "",
                       AlgorithmXMLFileName = "",
                       clusterdef = "",
                       FastFitFlag = True,
                       FullFitFlag = False,
                       ChannelIntegrationFlag = False,
                       daskFlag = False,
                       FreqMin = None,
                       FreqMax = None,
                       t_back_flag = True,
                       tBack = 0.0,
                       tSlope = 0.0,
                       N_H = 0.0,
                       beta_dust = 0.0,
                       kappa_1300 = 0.0,
                       DustFileName = "",
                       BackgroundFileName = "",
                       ContPhenFuncID = None,
                       ContPhenFuncParam1 = None,
                       ContPhenFuncParam2 = None,
                       ContPhenFuncParam3 = None,
                       ContPhenFuncParam4 = None,
                       ContPhenFuncParam5 = None,
                       iso_flag = False,
                       IsoTableFileName = "",
                       NumModelPixelXX = 100,
                       NumModelPixelYY = 100,
                       LocalOverlapFlag = False,
                       NoSubBeamFlag = True,
                       EmAbsPATH = None)

This function offers the possibility to redo one or more so called pixel fits of a previous myXCLASSMapFit run. The function performs fits for the selected pixels and recreates the different parameter maps using the new optimized parameter values together with the corresponding FITS cube(s) describing the synthetic spectra for all selected pixels. The names of these maps are created in the same way as described in Sect. “myXCLASSMapFit”. In addition, the myXCLASSMapRedoFit function renames the files describing the parameter maps from the previous call of the myXCLASSMapFit function by replacing the end of the each filename ".fits" by the phrase "__REDO-OLD.fits". The user has to define the pixel coordinates, which should be re-fitted, the job number of the previous myXCLASSMapFit run, and the new molfit file.

Input parameters:

• JobNumber: job number of a previous myXCLASSMapFit run which should be improved.
  
  

• PixelList: list of all pixel coordinates which should be re-fitted. (These pixel coordinates are used to identify the pixel directories created by the selected myXCLASSMapFit call, see Sect. “myXCLASSMapFit”). Each coordinate consists of two numbers separated by a comma, where the first number corresponds to the right ascension and second to the declination. Different pixel coordinates are enclosed by squared brackets and separated by commas. For example, we want to refit the pixels 83.2013422325, -15.1345324232 and 83.1111111111, -15.2211111111. The PixelList parameter has to be defined as follow

  PixelList = [[83.2013422325, -15.1345324232],
               [83.1111111111, -15.2211111111]]
  

  Please note, that these coordinates are used to identify the pixel directories in the selected myXCLASSMapFit job directory, i.e. the values defined in the PixelList parameter have to be included in the names of the corresponding pixel directories. For example, we want to refit the pixel with pixel directory 83.2013422325__-15.1345324232__1_-_3. In order to identify this pixel the PixelList parameter can be defined as

  PixelList = [[83.2013422325, -15.1345324232]]
  

  Additionally, the myXCLASSMapRedoFit function offers the possibility to define the indices of the pixels which should be refitted. In the example described above, the PixelList parameter can be defined as

  PixelList = [[1, 3]]
  

  to identify the pixel 83.2013422325, -15.1345324232.
  
  

• JobPath: (optional) path of job directory for application of the myXCLASSMapFit function, (default: "").
  
  

• MaskFileName: (optional) path and name of a FITS image used for masking. Here, each pixel with a real numerical value, i.e. which is not NaN, is fitted, (default: "").
  
  

• Threshold: defines a threshold for a pixel (default: None). If the spectrum of a pixel has a max. intensity lower than the value defined by this parameter the pixel is not fitted (ignored).
  
  

• MolfitsFileName: path and name of the extended molfit file.
  
  

• MolfitFileName: (optional) alias of MolfitsFileName, (default: None).
  
  

• EstimateContinuumFlag: (optional) flag indicating continuum estimation, (default: False).
  
  

• EstimateConNumParts: (optional) number of sub parts used for continuum estimation, (default: 20).
  
  

• EstimateConNumEntireCubeFlag: (optional) flag indicating that continuum estimation is done for the entire spectral range, (default: True).
  
  

• DataSmoothValue: (optional) smooth factor (=0, no smoothing is performed) used for smoothing obs. data, (default: 0.0).
  
  

• NumberIteration: max. number of iterations, (default: 50).
  
  

• NumberProcessors: (optional, only used if no alg. xml file is defined) number of cores, (default: 2).
  
  

• AlgorithmXMLFileName: path and name of an algorithm xml-file, (default: "").. (A relative path has to be defined relative to the current working directory!)
  
  

• AlgorithmXMLFile: (optional) alias of AlgorithmXMLFileName.
  
  

• FastFitFlag: (optional) flag indicating usage of fast-fitting method, (default: True).
  
  

• FullFitFlag: (optional) flag indicating usage of full-fitting method, (default: False).
  
  

• ChannelIntegrationFlag: (optional, for full-fitting method only) flag indicating channel integration, (default: False).
  
  

• FreqMin: new start frequency of simulated spectrum, (default: 0).
  
  

• FreqMax: new end frequency of simulated spectrum, (default: 0).
  
  

• t_back_flag (True/False): defines, if the user defined background temperature \(T_{\rm bg}\) and temperature slope \(T_{\rm slope}\) given by the input parameters tBack and tSlope describe the continuum contribution completely (t_back_flag = True) or not (t_back_flag = False), (default: True).
  
  

• tBack background temperature (in K), (default: 0).
  
  

• tSlope temperature slope (dimensionless), (default: 0).
  
  

• BackgroundFileName (optional) path and name of file describing the background as function of frequency (in MHz), (default: None).
  
  

• N_H (optional) Hydrogen column density (in cm\(^{-2}\)), (default: None).
  
  

• beta_dust (optional) spectral index for dust (dimensionless), (default: None).
  
  

• kappa_1300 (optional) kappa at 1.3 mm (cm\(^2 \,\)g\(^{-1}\)), (default: None).
  
  

• DustFileName (optional) path and name of file describing dust contribution (default: "").
  
  

• ContPhenFuncID: (optional) describes which phenomenological function is used to describe the continuum, (default: None).
  
  

• ContPhenFuncParam1: (optional) first parameter for phenomenological function describing the continuum, (default: None).
  
  

• ContPhenFuncParam2: (optional) second parameter for phenomenological function describing the continuum, (default: None).
  
  

• ContPhenFuncParam3: (optional) third parameter for phenomenological function describing the continuum, (default: None).
  
  

• ContPhenFuncParam4: (optional) fourth parameter for phenomenological function describing the continuum, (default: None).
  
  

• ContPhenFuncParam5: (optional) fifth parameter for phenomenological function describing the continuum, (default: None).
  
  

• iso_flag: use isotopologues (True/False). If iso_flag is set to True isotopologues defined in the iso ratio file are used, (default: False).
  
  

• IsoTableFileName (has to be given only if iso_flag is set to True): path and name of an ASCII file including the iso ratios between certain molecules. A detailed description of the iso ratio file is given in Sect. “The iso ratio file”. If no file name is given (default), the so-called iso-flag is set to False.

  NOTE, if the given path is a relative path, i.e. the path does not start with /, this path has to be defined relative to the current working directory!
  
  

• NumModelPixelXX: (optional) used for sub-beam modeling, describes the number of pixels used in x-direction, (default: 100).
  
  

• NumModelPixelYY: (optional) used for sub-beam modeling, describes the number of pixels used in y-direction, (default: 100).
  
  

• LocalOverlapFlag (True/False): (optional) take local overlap into account (default: False), see Sect. “Local-overlap of neighboring lines”.
  
  

• NoSubBeamFlag (True/False): (optional) do not use sub-beam description (default: False), see Sect. “Sub-beam description”.
  
  

Output parameters:

• None
  
  

DatabaseQuery

# import DatabaseQuery function
from xclass import task_DatabaseQuery

DatabaseQuery(QueryString)

This function sends a given SQL query string to the XCLASS database.

Input parameters:

• QueryString: the query string (default ” “).

Output parameters:

• Contents: contains the screen output of the query command.

  Please note, the user is free to define a different name for the output parameter.
  
  

UpdateDatabase

# import UpdateDatabase function
from xclass import task_UpdateDatabase

UpdateDatabase(DBUpdateNew,
               ForceRRLAdd = False,
               RRLMaxN = 900,
               RRLMaxDeltaN = 6)

This function updates the XCLASS database file located in the directory Database from spectroscopic databases connected to the Virtual Atomic and Molecular Datacentre, VAMDC (www.vamdc.eu). Currently, data access to the CDMS database and the JPL catalog, is supported.

Input parameters:

• DBUpdateNew: indicates, if, a complete SQLite3 database file is downloaded from the CDMS web server (“new”) or if the existing database file is updated (“update”) via the VAMDC infrastructure, i.e. new entries are added to the tables and existing entries are overwritten with new data. The complete SQLite3 database file is regularly updated via the VAMDC infrastructure and contains data from CDMS and JPL (default new).

• ForceRRLAdd: flag for forcing the addition and calculation of RRLs (default: False)

• RRLMaxN: max. main quantum number n for which RRLs are computed, (default: 900)

• RRLMaxDeltaN: max. Delta n for which RRLs are computed, (default: 6)

Output parameters:

• None
  
  

ListDatabase

# import ListDatabase function
from xclass import task_ListDatabase

ListDatabaseCore(FreqMin = 1.0,
                 FreqMax = 1.e8,
                 ElowMin = 0.0,
                 ElowMax = 1.e6,
                 SelectMolecule = [],
                 OutputDevice = "",
                 dbFilename = None)

This function reads in entries from the table transitions located in the SQLite3 database file and prints out the contents to the screen or file (defined by the input parameter OutputDevice). The user can limit the output by defining a minimum and maximum for the frequency (or for the lower energy) for the transitions.

Input parameters:

• FreqMin: minimum frequency (in MHz) for transitions in the transitions table (default: 0)

• FreqMax: maximum frequency (in MHz) for transitions in the transitions table (default: \(10^8\))

• ElowMin: minimum for lower energy (in K) (default: 0)

• ElowMax: maximum for lower energy (in K) (default: \(10^6\))

• SelectMolecule: a (python) list containing the names of all molecules which should be considered or a string defining the path and the name of an ASCII file including the molecules which should be selected.

  Note, if the parameter defines a relative path, this path has to be defined relative to the current working directory!

• OutputDevice: path and name of the file where the output is written to. If no file name is defined, the content of the database is written to the screen. If this parameter is set to quiet no information is printed to screen.

  Note, if the parameter defines a relative path, this path has to be defined relative to the current working directory!

• dbFilename: path and name of used database file (default: None)

Output parameters:

• Contents: content of the database (as a python array, e.g. Contents[0] contains the entries for the first molecule within the frequency/energy range).

  Note, the user is free to define a different name for the output parameter.
  
  

GetTransitions

# import GetTransitions function
from xclass import task_GetTransitions

GetTransitionsCore(obsdata = None,
                   FreqMin = None,
                   FreqMax = None,
                   SelectMolecule = [],
                   FrequencyWidth = 5,
                   ElowMin = 0,
                   ElowMax = 1.e9,
                   modeldata = None)

Similar to the ListDatabasefunction, the GetTransitions function displays information from the embedded database about transitions within a user-defined frequency range. Here, the frequency range selection is done in an interactive way. Therefore, the GetTransitions function starts a graphical user interface (GUI) which describes observational data (defined by parameter obsdata) within a frequency range defined by the parameters FreqMin and FreqMax. Additionally, the function offers the possibility to plot a synthetic spectrum (defined by parameter modeldata) of a previous myXCLASS or myXCLASSFit function call as well.

By using the mouse in combination with the right mouse button, the user defines the central frequency (blue vertical line) of the frequency range (grey vertical bar) which is used for the database query. The initial half width of this range is defined by parameter FrequencyWidth. Note, the width of the range can be enlarged (shrinked) by pressing the “+” (“-”) key. In the following, XCLASS prints out information of all transitions within the selected frequency range to the screen, starting with the transition with the lowest transition frequency. In order to sort the transitions by lower energies, the user has to press the “1” key before selecting the central frequency. Using the “2” (“3”) key, sorts the transitions by the Einstein A coefficients (by a products of upper state degeneracies and Einstein A coefficients (gA). Pressing the “0” key restores the initial order, i.e. by transition frequencies.

Additionally, the user can reduce the number of transitions by defining a lower and a upper limit for the lower energies using parameters ElowMin and ElowMax, respectively. Furthermore, the screen output can be limited to a few molecules by using parameter SelectMolecule.

Note, the GUI has to be closed to stop the function!

Input parameters:

• obsdata: 2D numpy array containing the observational data.

  Note, the data has to be given as a function of frequency (in MHz).

• modeldata: 2D numpy array containing the synthetic spectrum.

  Note, the data has to be given as a function of frequency (in MHz).

• FreqMin: minimum frequency (in MHz) for the observational data (default: None).

• FreqMax: maximum frequency (in MHz) for the observational data (default: None).

• SelectMolecule: a (python) list containing the names of all molecules which should be considered or a file name including the molecules which should be selected.

  Note, if the parameter defines a relative path, this path has to be defined relative to the current working directory!

• FrequencyWidth: defines the width of the frequency interval in MHz (selected central frequency \(\pm\)FrequencyWidth where the line information are printed out to the screen. (default: 5)

• ElowMin: minimum for lower energy (in K) (default: 0) in table transitions.

• ElowMax: maximum for lower energy (in K) (default: \(10^6\)) in table transitions.

• modeldata 2D numpy array containing the modeled data, (default: None)

  Note, the data has to be given as a function of frequency (in MHz).

Output parameters:

• None
  
  

LineID

# import LineID function
from xclass import task_LineIdentification

LineIdentificationCore(Noise = 2.0,
                       MaxOverestimationHeight = 10.0,
                       SourceName = "",
                       DefaultMolfitFile = "",
                       EstimateParamFlag = True,
                       VelBin = 2.0,
                       ElowMax = 1.e99,
                       Tolerance = 10.0,
                       TypeSelection = "all",
                       SmoothValue = 0.0,
                       MaxNumTransInFit = 1e99,
                       SelectedMolecules = [],
                       StrongMoleculeList = [],
                       MinColumnDensityEmis = 1.e8,
                       MinColumnDensityAbs = 1.e8,
                       NumberIteration = 50,
                       AlgorithmXMLFileEstParam = "",
                       AlgorithmXMLFileISO = "",
                       AlgorithmXMLFileSMF = "",
                       AlgorithmXMLFileOverAll = "",
                       ObsXMLFileName = "",
                       ObsDataFileName = None,
                       experimentalData = None,
                       vLSR = 0.0,
                       TelescopeSize = None,
                       BMIN = None,
                       BMAJ = None,
                       BPA = None,
                       Redshift = 0.0,
                       Inter_Flag = False,
                       tBack = None,
                       tSlope = None,
                       N_H = None,
                       beta_dust = None,
                       kappa_1300 = None,
                       DustFileName = "",
                       BackgroundFileName = "",
                       ContPhenFuncID = None,
                       ContPhenFuncParam1 = None,
                       ContPhenFuncParam2 = None,
                       ContPhenFuncParam3 = None,
                       ContPhenFuncParam4 = None,
                       ContPhenFuncParam5 = None,
                       NumModelPixelXX = None,
                       NumModelPixelYY = None,
                       LocalOverlapFlag = None,
                       NoSubBeamFlag = False,
                       EmAbsPATH = None,
                       clusterdef = "",
                       InternalParameterList = {})

This function identifies molecules in a given spectrum and returns a quantitative description of the data.

In general, the LineIdentification function takes all molecules into account which have at least one transition within the user-defined frequency range(s) 1. These molecules are stored into a so-called molecule list. In order to determine the contribution of each molecule, the LineIdentification function performs so-called single molecule fits for each molecule. If a molecule covers a defined fraction of the spectrum the molecule is “for now” identified and the optimized molfit file is append to a so-called overall molfit file which describes the contribution of all identified molecules. After all single molecule fits are done, the LineIdentification function performs a final fit, using the overall molfit file created before.

Input parameters:

• Noise: noise level (in K), (default: 2.0 K). All parts of the spectrum with intensities lower than the noise level are ignored.

  The usage of an observational xml file offers the possibility to specify a noise level for each frequency range. For that purpose, a tag called NoiseLevel, see below, has to be defined for each frequency range for all spectra defined in the xml file. If the definition is not given for all frequency ranges, the value defined by this parameter Noise is used instead for all frequency ranges of all spectra.
  
  

• MaxOverestimationHeight: defines the overestimation factor of the modeled single molecule spectrum (in %), (default: 10 %).

  Please note, the input parameter MaxOverestimationHeight has to be given in % and does not define the final overestimation limit directly which is given by MaxOverestimationHeight + 100 %.

  If the modeled spectrum does not overestimate the observed spectrum, the corresponding molecule is “for now” identified and the fitted molfit file is added to the overall molfit file which is used at the end of the line identification process to determine the final contribution of each molecule.
  
  

• SourceName: This parameter defines the path and the name of a source (template) molfit file which is used for the single molecule fits. Whenever the LineIdentification function fits the contribution of one of the molecules included in the source molfit file the definitions herein are used instead of the definitions in the default molfit file, see description below. This offers the possibility to fit the contribution(s) of one or more molecules with a different number of components, ranges, initial values etc. as defined in the default molfit file. In order to perform the single molecule fits for molecules which are not described by the source molfit file, the LineIdentification function uses the definitions in the default molfit file, see below.
  
  

• DefaultMolfitFile: This parameter defines the path and name of a so-called default molfit file which is used to fit the contribution of each molecule.

  The default molfit file defines for one molecule the number of components, the ranges and initial values for each parameter.

  During the line identification process the name of the (first) molecule defined in the default molfit file is replaced by the name of the current molecule.

  NOTE, if the parameter DefaultMolfitFile defines a relative path, the path has to be defined relative to the current working directory!
  
  

• Tolerance: defines the max. fraction (in %) of overestimated lines. If the fraction of overestimated lines in the result of a single molecule fit is lower than the given threshold, the corresponding molecule is “for now” identified and the optimized molfit file (and the corresponding iso ratios) are considered in the final overall fit (default: 10.0).
  
  

• SelectedMolecules: A (python) list defining molecules which should be excluded from or considered only by the line identification process.

  In general, the LineIdentification function considers all molecules which are included in the database within the defined frequency range(s).

  If the list contains the command words “known molecules”, the LineIdentification function adds all known molecules 1 to the list as well.

  In order to exclude a molecule from the line identification process, the name of the molecule has to start with “--“, e.g. to exclude the molecule CH3SH;v=0; the user has to define SelectedMolecules = ["--CH3SH;v=0;"].

  If the molecule names do not start with “--“, the LineIdentification function consider only these molecules.
  
  

• StrongMoleculeList: A (python) list including the strong (highly abundant) molecules which should be fitted at the beginning (default: “[]”).
  
  

• MinColumnDensityEmis: min. column density (for core lines) of an optimized component of a single molecule fit to be included in the overall molfit file (default: 0).
  
  

• MinColumnDensityAbs: min. column density (for foreground lines) of an optimized component of a single molecule fit to be included in the overall molfit file (default: 0).
  
  

• NumberIteration: max. number of iterations (default: 50). This parameter is used only if no MAGIX xml files are defined by the parameters AlgorithmXMLFile and AlgorithmXMLFileOverAll.
  
  

• AlgorithmXMLFileSMF (only necessary, if the user wants to use another fit algorithm (than Levenberg-Marquardt) for each single molecule fit): path and name of a MAGIX xml-file defining settings for an algorithm or algorithm tree has to be given. (A relative path has to be defined relative to the current working directory!)

  NOTE, if the user specify a xml file, the number of iterations given by the parameter NumberIteration is ignored. The number of iteration is then given by the xml file itself. In order to use the implemented fit algorithm (Levenberg-Marquardt) clear the AlgorithmXMLFileSMF parameter, i.e. AlgorithmXMLFileSMF = “”, and define the max. number of iterations by using parameter NumberIteration.
  
  

• AlgorithmXMLFileOverAll: only necessary, if the user wants to use another fit algorithm (than Levenberg-Marquardt) for the overall fit. Therefore, the path and name of a MAGIX xml-file defining settings for an algorithm or algorithm tree has to be given. (A relative path has to be defined relative to the current working directory!)

  For more information see description of parameter AlgorithmXMLFileSMF.
  
  

• ObsXMLFileName: (optional) path and name of an obs. xml file (recommended procedure), (default: ""), see Sect. “Observational xml file” for a detailed description.

  Note, the name of the xml file has to end with ".xml".
  
  

• ObsDataFileName: (optional) describes the observational data, if no obs. xml file is given, (default: None). There are two options for transferring the data to XCLASS:

  • the parameter describes path and name of an ASCII file called observational data file, where the first column describe the frequency (in MHz) and the second column the brightness temperature (in Kelvin)

    Please note, without using an obs. xml file, it is not possible to fit more than one data cube, simultaneously.

  • the parameter describes a 2d numpy array, where the first column describes the frequency (in MHz) and the second column the brightness temperature (in Kelvin).
    
    

• experimentalData: (optional) alias of ObsDataFileName, (default: None)
  
  

The following parameters are needed, if parameter ObsDataFileName is used instead of parameter ObsXMLFileName:

• vLSR: velocity (local standard of rest) in km s\(^{-1}\) (default: 0) used in the calculation of the synthetic spectra, see description for myXCLASS function Sect. “myXCLASS”. Please note, using a xml-file, the vLSR parameter can be defined for each obs. data file, see Sect. “myXCLASS”!
  
  

• TelescopeSize: size of telescope (default: 1).
  
  

• Inter_Flag (True/False): defines, if single dish (False) or interferometric observations (True) are described, (default: False).
  
  

• tBack: background temperature (in K), (default: 0).

  Please note, the background temperature and slope have to describe the continuum completely, i.e. t_back_flag is always set to True.
  
  

• tSlope: temperature slope (dimensionless), (default: 0).
  
  

• N_H: Hydrogen column density (in cm\(^{-2}\)), (default: 0).
  
  

• beta_dust: spectral index for dust (dimensionless), (default: 0).
  
  

• kappa_1300: dust mass opacity kappa (cm\(^2 \,\)g\(^{-1}\)), (default: 0.01).
  
  

• NumModelPixelXX: (optional) used for sub-beam modeling, describes the number of pixels used in x-direction (default: 100).
  
  

• NumModelPixelYY: (optional) used for sub-beam modeling, describes the number of pixels used in y-direction (default: 100).
  
  

• LocalOverlapFlag (True/False): (optional) take local overlap into account (default: False), see Sect. :ref:myxclass-localoverlap.
  
  

• NoSubBeamFlag (True/False): (optional) do not use sub-beam description (default: False), see Sect. “Sub-beam description”, i.e. XCLASS uses the old source description, see Sect. “Simple 1-d description”.

Finally, the last parameter is needed to start the LineIdentification function on a cluster

• clusterdef: path and name of a file containing information for the cluster as described in the CASA cookbook 10 (subsection “10.3 Parallelization control”). In contrast to CASA’s “cluster configuration file”, the LineIdentification function requires only two entries for each node: the hostname of the target node where the cluster is deployed and the number of cores (engines) separated by comma. (Comments are marked with the “#” character.) Please note, the third column can be used to define the positions of the XCLASS directory on each computer in the cluster. This is essential, if the cluster contains computers with different operating systems, e.g. Linux and MAC OS. If no path is defined, the LineIdentification function assumes that the XCLASS interface is located in the same directory as the current XCLASS interface.

  Note, a “cluster configuration file” described in the CASA cookbook can be used as well whereat the definitions for the work directories are interpreted as definition for the XCLASS directory on the different nodes of the cluster. Additionally, the definitions of RAM usage and RAM per engine are ignored.

  The following requirements are necessary for all nodes which are included in the cluster:

  1. Password-less ssh access from the controller (user) machine into all the hosts to be included in the cluster.

     NOTE: This is not necessary when using only “localhost”, i.e. if the cluster is deployed only on the machine where casapy is running.

  2. XCLASS interface, CASA and gfortran (with OpenMP) are installed on all nodes of the cluster.

  3. The XCLASS job directory must be located in a shared file-system, accessible from all nodes comprising the cluster, and mounted in the same path of the file-system.

     NOTE: If the cluster contains computers with different operating systems, e.g. Linux and MAC OS, the user has to define the different paths of the XCLASS interface directories.

  Example of a “cluster configuration file” used for the LineIdentification function:

  # cluster configuration file
  # node      number of cores      path of XCLASS interface
  anu,        2
  lugal,      3
  

  In the example described above, the nodes “anu” and “lugal” will be used with two (three) cores, respectively.

  NOTE: The total number of cores used on a node of the cluster is determined by the number of processors defined in the algorithm xml file times the number of cores defined in the “cluster configuration file”. For example, the user wants to apply the Levenberg-Marquardt algorithm with eight processors on a cluster defined in the example above. On node “anu” 16 (\(2 \times 8\)) cores and on node “lugal” 18 (\(3 \times 8\)) cores are used.
  
  

• InternalParameterList: is deprecated
  
  

Output parameters:

• IdentifiedLines: contains the optimized molfit file including the fitted parameters of all identified molecules.
  
  

• JobDir: absolute path of the job directory created for the current run.
  
  

Footnotes

1(1,2,3)

Please note, the data cube has to be given in the World Coordinate System (WCS) described in [Greisen_Calabretta_2002], [Calabretta_Greisen_2002], [Greisen_et_al_2006]. The data cubes must have a spectral axis, where the spectral axis can also be in velocity units. For the fitting procedure, the spectral axis is automatically converted to frequencies (MHz) and the intensities to Kelvin. At the end of the fitting procedure, XCLASS converts the resulting fitting cubes back to the original units.

2

See http://ds9.si.edu/site/Home.html for details.

3

https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.gaussian_filter.html

4

https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.uniform_filter.html

5

https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.median_filter.html

6

Note, here we assume that the source size is small compared to the telescope beam size.

7

If BMAJ and BMIN are not defined, we assume BMAJ = BMIN = TelescopeSize, see below. For single dish telescopes the FWHM of the beam is computed using Eq. [myXCLASS:DiffractionLimit].

10

http://casa.nrao.edu/Doc/Cookbook/casa_cookbook.pdf

References

Virtanen_et_al_2020

Virtanen, Gommers, Oliphant, Haberland, Reddy, Cournapeau, Burovski, Peterson, Weckesser, Bright, van der Walt, Brett, Wilson, Millman, Mayorov, Nelson, Jones, Kern, Larson, Carey, Polat, Feng, Moore, VanderPlas, Laxalde, Perktold, Cimrman, Henriksen, Quintero, Harris, Archibald, Ribeiro, Pedregosa, van Mulbregt, & SciPy 1.0 Contributors

SanchezMonge_et_al_2018

Sanchez-Monge, A., Schilke, P., Ginsburg, A., Cesaroni, R., & Schmiedeke, A. 2018, Astronomy & Astrophysics, 609, A101

Rohlfs_Wilson_1996

Rohlfs, K. & Wilson, T.~L. 1996, Tools of Radio Astronomy

Greisen_Calabretta_2002

Greisen, E.~W. & Calabretta, M.~R. 2002, Astronomy & Astrophysics, 395, 1061

Calabretta_Greisen_2002

Calabretta, M.~R. & Greisen, E.~W. 2002, Astronomy & Astrophysics, 395, 1077

Greisen_et_al_2006

Greisen, E., Calabretta, M., Valdes, F., & Allen, S. 2006, Astronomy & Astrophysics, 446, 747