The RECSPE package described here is the result of a project to digitise extensive mm-wave rotational spectra of the H2O...HF hydrogen bonded complex recorded in the Nizhnii Novgorod laboratory in Russia.  Partial analysis of those spectra was published (Belov et al. J.Mol.Spectrosc. 241 (2007) 124), but the majority of the lines remained unassigned and only the paper version of those spectra survived.

        In fact the situation when a spectrum exists only in the form of a paper record and contains valuable unprocessed information is not that rare.  Such spectra are also often in the form of  chart recorder rolls.  It is very desirable to convert such spectra into a digital form that will be amenable for use with contemporary packages for graphical assignment, such as AABS.

        RECSPE is a package of programs for conversion into a usable digital form of such legacy paper spectra.  Several graphics programs (such as Inkscape) can trace a bitmap image into a vector, which is useful, but the result is still far from what we would regard as a digital spectrum.  The present package offers a complete route from legacy paper spectra to calibrated digital spectra in the form of point intensities at a uniform frequency spacing.

        Recovery of paper spectra poses some specific issues that need to be addressed, and these needed to be dealt with in the RECSPE programs:

• Frequency calibration: This is key to the usability of recovered spectra.  Many old spectra are inherently nonlinear in frequency.  Even if the spectrum was linear it is possible that nonlinearities may have crept in from uneven operation of the original recorder or distortions in the paper through folding or crumpling.
  
• Multipage spectra: If the spectra are in the form of a strip chart record then they need to be scanned to multiple images that need to be spliced together 
  

        

        Examples of paper spectra and of their conversion:

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        This is the key program in the RECSPE  package and it converts a bitmap image of a spectrum into a string of points.  If the spectrum contains a second channel with  markers or a reference spectrum then that channel can also be analysed synchronously with the main channel.  The points are assigned x,y values in pixel units.

	TRACE.FOR Source listing. TRACE.EXE Windows executable.  The program runs as specified in the trace.inp file. Launch from the command line in the directory containing the bitmaps for tracing. Two modes are possible: Manual mode: program will trace only the specified bitmap Auto mode: program will attempt to trace all .BMP files in the current directory TRACE.INP The control file for TRACE with entries for tracing the sample bitmap below.  This can be reedited as necessary. Colour values are to be established from the bitmap to be scanned by using the colour picker of any bitmap graphics program If you only want to trace one channel then specify 0 values for RGB colours of trace B Traces can be smoothed (recommended) using standard Savitsky-Golay least-squares polynomial smoothing Traces can also be differentiated for use when you might want to convert from first to second derivative lineshape.  The phase factors ensure upward central peaks. 38A.ZIP This is the full bitmap of the image shown in 38a_reduced.jpg for the H2O...HF example above.  It is quite large (>8Mb) so it has been zipped but it can be unpacked and used for testing   TRACE. 38A_SM.GLE 38A_SM_A.XY 38A_SM_B.XY One of several sets of  files for gle that will be produced by TRACE for the bitmap above.  The .XY files are the resulting traces while various additional files allow convenient viewing of the results of the tracing.  The files are produced in sets for the raw traces, smoothed traces, and differentiated traces (if specified). These three files correspond to the gle diagram shown in 38a_sm.pdf. The .XY traces are ASCII files containing in the first two columns the x,y values that will be used for further processing.  The last two columns list actual pixel coordinates of the points (top-left corner of bitmap is 0,0) for direct comparison with coordinates displayed by most graphics programs. The .XY files can be read and displayed with the SVIEW_L program of the AABS package.

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       This program splices traces for adjacent scanned pages of multipage spectra by aligning the overlap regions.  So it is necessary to exercise some foresight during the scanning process to ensure that there is sufficient overlap between adjacent pages.

       The use of the QGLE previewer from the gle package is mandatory in this case.  Once the package is installed, and SPLICE is launched then all you need to do is to click on the automatically generated file  SPLICE.GLE to view the splicing for the current parameters.

	SPLICE.FOR Source listing. SPLICE.EXE Windows executable. The program is to be launched from the command line in the directory containing the traces. For the input file as below you will see the following screen.  At the same time a file SPLICE.GLE is generated and you need to click on that in order to preview the splicing with QGLE. After these preliminaries you need to manually hunt around for the best splicing parameters, by typing in the option number and its value. SPLICE.INP The control file.  This can be reedited as necessary and the entries shown are for the sample case below. If you specify only one channel conversion and generic file names MOLNAM and MOLNAM1 then SPLICE expects to find files MOLNAM.XY and MOLNAM1.XY.  If two channel conversion is specified then SPLICE expects to find MOLNAM_A.XY + MOLNAM_B.XY and MOLNAM1_A.XY + MOLNAM1_B.XY. The first block of the splicing options controls the QGLE display, while the last three parameters control the splicing.  The crucial aligning parameter is the x-axis overlap width but you may also need to change the other two parameters. Once you are satisfied that optimum splicing has been reached you need to exit SPLICE by pressing ENTER, when the parameters in SPLICE.INP will be updated.  The contents of this file underneath the top block will be copied over so that commenting/previous versions of parameters can be kept there. 38a_dif_a.xy 38a_dif_b.xy 38b_dif_a.xy 38b_dif_b.xy The traces for spectrum 38a (channel a and b) and for spectrum 38b (channel a and b) to be spliced using the input file above SPLICE.PDF Illustration of the display that you will see in the QGLE viewer of gle on launching SPLICE with the data above.   You can see that there is some x-axis misalignment that can be corrected by changing the value of parameter number 6. 38ab_a.xy 38ab_b.xy The traces resulting from optimum splicing of the data above, channel A is SO2, channel B is H2O...HF.

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        This program assigns the frequency axis to a trace, which can be either directly from  TRACE, or result from splicing with SPLICE.  Frequency is recalculated in a straightforward linear conversion based on coordinates of two points.  For a spectrum that is known to be nonlinear this is really a zero order operation to make subsequent handling easier.  If the spectrum is linear then this may be all that you need to do.

        You need to load the traced spectrum into SVIEW_L and measure two lines (or features) to determine their X-coordinates for use in calibration.  These X-coordinates and the known true frequencies of these two points are then to be written to the file MOLNAM.FPT, where MOLNAM is the generic name used for files associated with this spectrum.

	FZERO.FOR Source listing. FZERO.EXE Windows executable, to be used from the command line.  The program will: first try to convert file MOLNAM.XY (single channel mode). if there is no MOLNAM.XY  then the program will try to convert files  MOLNAM_A.XY and MOLNAM_B.XY (two channel mode) MEOH04_SM.XY Uncalibrated trace for the example methanol spectrum as shown in meoh_04_uncal.pdf MEOH04_SM.FPT The file with the two calibration points for the above. MEOH04_SM.SPE The resulting file corresponding to meoh_04_cal.pdf 38ab.FPT The file with the two calibration points for the H2O...HF+SO2 example discussed in the description of SPLICE.   38ab_a.SPE 38ab_b.SPE The files resulting from addition of the zero order frequency axis to files 38ab_a.xy and 38ab_b.xy from the SPLICE example

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        This program merges all traces with assigned frequency scale into a single spectrum. The operation is as follows:

1. frequency sorted list of basic properties spectra in the current directory is produced
2. the spectra are unified to a common frequency grid (defined by the internal parameter FSTEP) and each spectrum  SPECNAM.SPE is converted to U_SPECNAM.SPE
   
3. all U_ spectra spectra are then merged into two files, U_A.SPE containing all A channel spectra, and U_B.SPE containing all B channel spectra.
   

	MERGE.FOR The source listing. MERGE.EXE Windows executable to be launched from the command line in the directory containing the spectra. Note that: spectral files are to have  extension .SPE and are to be in the two column ASCII standard as produced by FZERO  no spaces are allowed in file names data points have to be equidistant in frequency missing parts are filled with zeroes, overlapping parts are connected at the middle of the overlap region LIST Listing of the spectra found and processed by MERGE. This file is identical in format tho the LIST file required by the AABS package for displaying the ranges of spectra available for analysis. This listing summarises all constituent spectra from the H2O...HF project that were combined into one single spectrum. u_A.spe u_B.spe The result of operation of MERGE on files 38ab_a.SPE and 38ab_b.SPE obtained above with FZERO.  The files were converted to the 0.5 MHz frequency grid and if more spectra were available then those would have been merged into these two output files.

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        This program calibrates the frequency axis of the spectrum by applying a correction based on a cubic spline function fit to a predefined set of calibration points.  Alternatively, a previously determined spline function can be used, providing that it was determined for the same frequency axis (for cases when a separate reference channel was recorded).

        A prerequisite to running this program is to produce a file of frequency calibration points. For this you need to use the AABS package. The spectrum is to be displayed in SVIEW_L and the predictions with true frequencies of lines should be displayed displayed in ASCP_L.   The two program should be in linked mode ensured by the presence of a suitable SVIEW_L.INP file in the working directory.  You need to declare MOLNAM.FRE as the name of the fitting data file, where MOLNAM is the generic name for the project.  Calibration measurements should then be written to that file with the F8 option of ASCP_L.

	FRECAL.FOR The source listing. FRECAL.EXE Windows executable to be run from the command line.  The only parameter that you specify is the generic name, MOLNAM, for the files in question.  The program then expects that you have the file FRECAL.INP (as below) and have prepared: MOLNAM.SPE = the file containing the spectrum to be calibrated (in the IFPAN binary format, as written with the m option of SVIEW_L)   MOLNAM.FRE = the file with the calibration points produced with the F8 option of ASCP_L operating in linked mode with SVIEW_L. Alternatively if a run such as that described above has taken place on a reference spectrum and you have an identically recorded sample spectrum to calibrate then you can reuse the spline function MOLNAM_spline.FNC generated in the previous run by copying it to a file where the MOLNAM part of the name corresponds to that used for the sample spectrum. The primary output file will be MOLNAM_frecal.SPE.containing a two column ASCII version for the spectrum for the same points as in the input spectrum, but with frequency of each point recalculated according to the calibration function.  This point spacing in this spectrum will NOT be equidistant in frequency, so you can convert to equidistant frequency spacing with SVIEW_L FRECAL.INP The control file for FRECAL.  In the presence of noise affecting the calibration points a simple cubic spline function fit may not be the  optimum solution.  You therefore have the option of interpolating additional points that will reduce spline function excursions, and also of smoothing the correction function.  The best solution is to use a mixture of these techniques. A.SPE Spectrum for the SO2 channel in H2O...HF spectra used as a worked example for the complete RECSPE procedure.  This file is a direct conversion to binary format made with SVIEW_L of spectrum u_A.spe obtained above with MERGE. A.FRE The calibration points for this spectrum determined by using the AABS package with spectrum A.SPE, as above, and linelists for SO2 from the  CDMS database.  Linelists for the ground states of the parent and isotopic species, and for the bending satellite in the parent were loaded. The calibration points do not have to be in any particular order, but  FRECAL will sort them in frequency. A_FRECAL.SPE The main result of operation of FRECAL on the two files above (without the use of interpolation and smoothing).  This is a frequency calibrated spectrum in ASCII standard.  The file also contains an additional third column listing  the original frequencies.  Note that the points in this  spectrum are NOT equidistant in frequency but this spectrum can be read and converted to equal frequency increments with SVIEW_L A.GLE A_calpts.out A_spline.out Additional files produced by of FRECAL that allow viewing of the spline function used for the calibration.  Spline functions are powerful tools but are susceptible to experimental errors in declared points.  The sensitivity is particularly high for points very close together and it is recommended that a check for unexpected spline function excursions is made. A_spline.pdf The spline function diagram produced with the 'export' option of  QGLE from the three files above.  The lowest and highest frequency  points have zero correction because they were already calibrated, in the process of defining the zero order frequency scale in FZERO. B.SPE B_spline.fnc The two files necessary for calibration of the spectrum in the H2O...HF channel: the file B.SPE is a binary version of u_B.spe obtained above with MERGE.  It is necessary to ensure that the first point in this spectrum is at the at the same frequency as in the reference spectrum. the file B_spline.fnct is a binary file containing the spline function that was generated during calibration of the SO2 channel.  It is just a copy of the file A_spline.fnc generated during that operation. B_FRECAL.SPE The frequency calibrated H2OHF spectrum at 321GHz.

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