Changelog

3.7

• Add the new class Array to handle data like numpy arrays
• Add a new module for doing mathematics: mathematics.py
• Apply new convention for selectLines, rmsLines and calLines: one range per line instead of a list of ranges

3.6

• Implement feature requested in redmine #1888
• Fix bug due to error precision (cf redmine #1888) and refactor

3.5

• New feature: plotBestModel can plot selected lines (redmine #1429)

3.4.2

• Fix log_mode issue

3.4.1

• New feature: The best physical model can be saved with the function saveBestPhysicalModel

3.4

• Force ratioAtCutOff < 1 and reducePhysicalParam > 1
• Fix database access
• Fix a possible issue when reducePhysicalParam is an integer

3.3.5

• Bugfix: geometry is incorrect in the LineAnalysis Panel in MCMC (redmine #1358)
• Fix the computation of the dof
• Fix initComponentsForMCMC
• Fix log_mode issue with initComponentsForMCMC
• Write the value of the collisioners with the exponential format in the output file
• Fix collision files issue in Radex with MCMC
• Bugfix: plotting the best model with telescope crashes
• New feature: Selection of telescopes with ranges of lines
• Bugfix: Collisioner value is not handled correctly with log_mode in RADEX with MCMC
• Bugfix in MCMC with Radex
• Rename rangesNotExcluded -> rangesSelected

3.3

• Fix a bug: OverflowError when math.log10(0)
• Allow Range(“*”, “*”).
• Use lower case letters for the column names of the output file
• Remove outputConcatFile
• Replace: (fileName, extensionName, suffixName) -> inputFile
• New feature: selectedLines accepts “-” as a key
• Massive renaming: notExcludedLines -> selectedLines, rangesNotExcluded -> selectedRange
• weightLines is not provided by the user anymore but. All its values are set to 1.0
• In MCMC, the chi2 value passed to compute the chi2Reduced is not divided by the number of points anymore
• Remove function: displayNbOfModels. Generalize request of confirmation
• Display a confirmation panel if warning is True and a message in the console if False
• Bugfix: the interacting is not set correctly in MCMC
• Display a warning when some lines selected are not used because they don’t have enough pooints
• Divide chi2 per line by number of points rather than by user-defined weight
• Hardcode chi2Max to 1e20 to always allow determination of the best parameters
• Fix computation of chi2 and reduced chi2
• Explain clearly the issue when no optimal param can be determined
• Fix MCMC with RADEX model
• Cancel division by the total weight in the computation of the reduced chi2Min
• Fix computation of the reduced chi2Min
• Check if the provided ranges are valid
• Better warning message before the computation
• Write the value in the output file not the log10 of the value (in MCMC only)
• Sort the parameters (“nmol”, “tex”, “tkin”, “fwhm”, “size”, “vlsr”, “iso”)
• Define a more flexible the way for the user to select the lines with ranges and indexes
• Fix computation of the reduced minimal chi2 displayed per model in the console
• Print a message telling the user if lines were not taken into account
• Bugfix: select the lines with enough points to prevent irrelevant computations
• WIP: Determine which line must be used or not
• Include continuum in the computation of the chi2
• Bugfix: chi2 computed correctly taking into account the weight when the whole spectrum is selected
• Change initial minimal chi2: 1e9 -> 1e16
• Implement isoUnique in MCMC
• Bugfix: Divide chi2 by weight
• Bugfix: weight is used correctly in the computation of reduced chi2
• Bugfix: weightLines is passed to computeChi2Reduced
• Weight the chi2 per line
• Make reducePhysicalParam optional
• Introduce weightLines
• Make cutOff and ratioAtCutOff mandatory
• Modify the computation of the reduced chi2 taking into account the number of independent points. Introduce the ratioAtCutOff
• Add iso to alpha in MCMC
• Check calLines, rmsLines and notExcludedLines
• Set a new way of defining rmsLines
• Fix bug with reducePhysicalParam
• The user can define a reducing factor for every parameter
• Move cutoff to the function computeChi2MinUsingMCMC
• Set new parameters: cutoff for fac and calLines (calibration of the lines)
• Remove alphaMaximal and alphaOptimal from Component
• Change the way fac and alpha are calculated
• Fix initialization of the computation
• Make bestParameters identical in RG and MCMC
• Add the keyword lineNumber for selecting the line to be plotted
• Improve data output and display message
• Bugfix: Nmol and Vlsr are correctly placed in the output file
• Use temp instead of tex
• Simplify the launch of module
• Remove useless prints and prints the number of model the same way as RG

3.2

• Rename the script to LineAnalysisScripting (RG and MCMC included)
• Add Plot.py
• Implement plotRates
• Bugfix adding initializations for lists: variations, rates, thetas, iterIndexes
• Add alphaMaximal, alphaOptimal, chi2Optimal keywords for MCMC
• Fix the computation of chi2 with the functions extracted from ScriptLineAnalysisRG
• Removes chi2min and keeps chi2Min
• Refactor: use Plot to plot the scatter plot for the rates
• MCMC is fully functional
• Bugfix: plotBestModel works properly when run from the command line

3.1

• New feature: new syntax for notExcludedLines
• notExcludedLines and rangesNotExcluded -> notExcludedLines
• Implement conversions to MHz and km/s (FrequencyScale)
• Implement convertion to MHz from km/s, cm-1, micrometer
• Remove keyword unit and delta that will be contained in Range
• Add Range class
• Formalize the calculation of the number of models in fct of isoUnique
• Define new rules for exclusions
• Allow to set both excludedLines and rangesNotExcluded at the same time
• Bugfix: Prevent the division by zero when the dof = nbPointsUsed for the chi2MinReduced
• Set keyword outputFile
• Set keyword inputDir and outputDir instead of workingDir
• Rescale ranges when necessary
• Finish implementation of the conversion user inputs into the correct unit
• Use the vlsr of the data for the shift rather than the vlsr of the user
• Rename: freqsNotExcluded -> rangesNotExcluded, freqsExcluded -> rangesExcluded
• A different tuningBand can be applied from plotBestModel
• Fix chi2 computation using vlsrRange
• Take into account the deltaV and vlsr in the chi2 computation on a selected frequency range
• Take into account the user start index (1) instead of the logic start index (0)

2.9.9.3

• Set warning message when the freqs specified are not subsets of the speciifed lines
• Bugfix: freqsExcluded is determined properly
• Set warning message when all the lines are excluded
• Set warning message when freqsNotExcluded and freqsExcluded are both defined
• Fix issue with freqsNotExcluded and freqsExcluded
• Fix MCMC
• Bugfix: Fix bad condition when more than 1 freq to be not excluded are provided
• Improve theta, alpha parameters...
• Add ScriptLineAnalysisMCMC
• Feature implemented: Don’t take into account collision parameters in LTE mode
• Fix telescope check
• Remove n (H2 density) from component
• Add tbg and n as new extra parameters in the components
• Fix a bug when no chi2 < chi2Min was found
• plotBestModel and plotChi2Contour return a variable
• Add quantun numbers: jup, kup, lup, mup
• Display automatically the ContourPlotProduct in CASSIS standalone
• Fix header display in the output file
• Replace “_” with “-” in the collisioners in the output file
• Collisioners start with a lower letter in the output file
• Bugfix: interacting = True with many components
• Display the detail about the number of values per parameter if warning is True
• Change UserInputs.telescopes -> UserInputs.telescope
• Check the telescopes in the inputs of the user
• Check the continuum file existence
• Bugfix: If min == max et nstep != 1, nstep must be set to 1
• Add new keyword iMin and set the title of the outputFile
• the temp parameter is renamed tex or tkin regarding the selected model
• Implement concatenation of the input data files for the plot of the best model
• New feature: warning keyword
• New implementation for isoUnique
• Filter only the models where the isotopic ratios are similar
• Introduce overSampling option in plotBestModel
• Fix condition on freqsNotExcluded
• Replace freqsExcluded with freqsNotExcluded
• Fix the number of lines to be processd
• excludedLines and notExcludedLines are handled properly
• Radex model works
• plotBestModel accepts the moltag instead of an index
• Add geometry and interacting parameters in the components
• Improve display of the information in the console
• Introduce collision parameters for RADEX
• Use specific module to prevent error precisions
• Bugfix with log_mode

2.9.9.2

• Bug fixes
• Implementation of the MCMC method
• Implementation of the RG method
• Initial version