Publication quality output from SciDAVis

  • Tribo LaBoy
    Tribo LaBoy


    I would like to share with other users the only way I found to produce publication quality graphs from SciDAVis 2.4 on Windows.
    It is to use the "Export to PDF" button on the toolbar. The vector PDF file can then be imported into a recent version of Inskape and modified if that is desired.

    For a long time I tried to get publication quality out of SciDAVis, unsuccessfully. Here are the problems, which I found. They may be of interest  to other users, but most of all to the developers.

    1. PDF export from the menu : File->Export Graph. The axes and the tickmarks are a mess.

    2. PDF print using Adobe's PDF writer. The exported PDF contains bitmap elements and their resolution is quite low. These elements are the legend or text objects overlayed on the plot. I couldn't find consistency in this, which elements are converted to bitmamaps.

    3. SVG export from the menu : File->Export Graph. The produced SVG resembles the PDF export - its axes and tickmarks are around different rectangular areas. The lines and symbols look thin.

    4. EPS export  from the menu : File->Export Graph. See 1 and 3 above.

    5. Bitmap (BMP, PNG) export from the menu : File->Export Graph. The file looks like a screenshot of the graph at current screen resolution and graph size and has a black line surrounding the whole graph. Not  possible to magnifiy it without very obvious blurring and loss of detail. Unusable for publications. 

    Hope the identification of these problems is of help to the developers. SciDAVis is already a very nice plotting application, and I am glad that I have found a way to get reasonable output from it!

    Keep up the good work!

  • Tung Le
    Tung Le

    Thank you very much for your trick. The Pdf output looks much better, especially the axes and tick-marks.

    BTW, do you know the same way but applying for ESP output. The normal export way gives a not-very-good result.

    Thank you very much!

  • Tribo LaBoy
    Tribo LaBoy

    As I said, this is the ONLY way that I found for publication quality vector output put of SciDAVis. To produce an EPS file I would import the PDF into Inkscape and then export it from there. There must be a command line way to this with some tools, but I don't know it. If there is anyone knowledgeable in this area, I would also be interested. Particularly automated script conversion from PDF to SVG and PNG simultaneously …

  • Tribo LaBoy
    Tribo LaBoy

    OK, I played a little bit around and I came with a batch file for converting the PDFs into SVGs and PNG by using Inkscape. Here it is:

    -----------------------------Code start -------------------------

    REM This batch program converts the PDF files to SVG and PNG files by using Inkscape
    REM Before running this BAT-file make sure that the  F_BASE_NAMES list contains the desired pdf filenames 
    REM without the extension. Also don't forget to set INKS_PATH to the actual directory with the inkscape.exe 
    SET BatFilePath=%~dp0
    SET INKS_PATH=D:\PORT\PortApps\GRAPHICS\InkscapePortable\App\Inkscape\
    SET F_PATH=%BatFilePath%SVG_PNG\
    SET FN_EXT=pdf
    REM Loop through the filenames in F_BASE_NAMES
    FOR %%A IN (%F_BASE_NAMES%) ^
    DO %INKS_PATH%inkscape.exe --file=%F_PATH%%%A.%FN_EXT%  ^
    --export-plain-svg=%F_PATH%%%A.svg ^
    --export-area-drawing ^
    --export-dpi=300 ^

    ---------------------------------------Code end--------------------------

    Hope somebody finds this helpful

  • Me Myself
    Me Myself


    I am also in desperate need for quality output. So far I get hung up with a bug that displaces different layers, if I export PDF or SVG. I always loose a bit of one of my graphs on the top of the plot of one layer. Does anyone have good solution for making plots with multiple y-axis besides layers?

  • sashko

    in my experience the best result is produced with the right-click on the plot Export -> Layer (or Window makes no difference there is only one layer) and choose SVG format. Inkscape opens that svg, and turns out that the plot exported by this method does not suffer from the problem of displaced tick marks and axes (v 0.2.4 release) which is typical if you use File -> Export. Don't ask me why.  However, there something one should keep in mind. Looks like Inkscape and Scidavis are using different units to specify font sizes. Inkscape is using "px" (and gives you a hint about that) and Scidavis does not even tell you what it uses, but I suspect these are "pt" because when imported the font size in Inkscape relates as 16/12 to the one specified in Scidavis. None of these applications give you a choice for font size units and I'm not going to take sides, but it would be nice to have some consistency, especially because the line thickness is consistent between the programs. So as long as you keep this factor in mind and  specify your fonts right in the beginning, the workflow is very smooth.

    The method proposed by tribolaboy does not work for me unfortunately, While Inkscape can import PDF and it remains vector, some kind of font substitution and manual kerning happens, so all the labels and numbers in resulting plot end up very bold and pile on top of each other. The line thickness changes as well. It does not happens if I used the method described above.

    Other that that I'm grateful to developers for wonderful piece of software and looking forward for updates.

  • Paul

    Hi, the export of SVG format has the most excellent performance. Here is what i do:
    1. Export the graph to .svg format using File menu then export graph to .svg file;
    2. Open the .svg file in Safari, and then export to pdf using File menu to export to pdf, or using File menu to Print... then PDF;
    3. Crop the exported PDF in Preview.
    The output PDF is a vector file so it has the best quality for publication.
    Thank you!

    My computer is MacBook Pro Retina late 2012. I have tried this way in my PC computer with no success. Maybe the best way for PC export is to print the draft using a pdf printer (DoPdf, or AcrobatPdf), but there is still problems. Sometimes the figure will 'stretch out' of the paper border, and the 'scale to fit paper size' is not working in both PC and Mac.

    Last edit: Paul 2014-07-22
  • Paul

    In Windows, you can use XML2PDF WORKSTATION FREE to convert .svg file into .pdf. It is free of charge, small and handy, also a great app.