Spectragryph
- optical spectroscopy software -

Functions of the Plot/Views ribbon => Click onto a button for descriptions

New view... Here you can create a new view of different types. Each view is created in an own separate tab, with a name and icon depending on its type. Each view type has its own characteristic set of inline buttons at the top (explained with their respective ribbons). The greyed out types will be implemented in future versions. Change the tab name after double-clicking on it. Change the tab order by drag&dropping tabs. Tabs can be dragged out of the main window as separate windows and docked into it again afterwards, but not all functionality is available for such separated tabs. Close view Close the current tab by clicking on the "Close View" button or the Close symbol [ x ] inside each tab header. Tabs can also be closed by the CTRL+W key shortcut.

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	View enhancements These are three ways to enhance a spectra view. The multicursor gives a collective vertical readout for all spectra at a movable x position. The additional peak labeling toolbar has many options for automated and manual labeling of peak maxima. The spectroscope view bar show the spectral as if the measured sample was viewed through a visual spectroscope.
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Multi cursor The multicursor tool gives a collective vertical readout for all spectra at one movable x position. Use the left mouse button to grip and move the dashed vertical line. The data values are shown and updated live in the rightmost area. The values are in the same order as the spectra (as seen in the legend box). The y values are shown in the same colours as the corresponding spectra. With the upper "Copy Values" button, the values are copied to the clipboard for further use. Another click onto the "Multicursor" button will remove both the vertical line as well as the right-hand value display area.

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Peak labels This function allows automated peak labeling of maxima (and minima in transmission mode). Exact peak positions are calculated by fitting a 3rd order polynom and solving the polynom equation. The vertical label line starts at the nearest x value position. Many labeling options are available: - label type: a label can consist of both a peaks x and y value, or only one of them. Several specific label types are available for special types of spectra: "LIBS" for atomic emission spectra, "XRF" for x-ray fluorescence and "Gamma" for radiation from radioactive nuclides. For each of those, elements can be chosen from a PSE table and a position tolerance can be set. See also a tutorial video. - threshold: to rule out labeling of noise-related maxima from the lower part of the spectrum, a lower limit for detecting peaks is set (default: 5% of Max-Min). - prominence: a principle borrowed from geography. A prominence of 10 will show only the most prominent peak of all, lower prominence values show more of the little peaks. Minimum is 1. - digits (x, y): define the number of relevant digits for the displayed values. - angle: use 90° for showing vertical labels, 0° for horizontal ones, and any values inbetween for inclined labels. - spectra selection: either select a single spectrum in the drop down menu or label all spectra together. In addition, by clicking on the symbol, it is possible to manually edit, remove and add labels. This manual edits are shown when the manual mode is active, and hidden when it is inactive. Manual edits are saved and reloaded when using the native Spectragryph *.sgd files. Several options are available: - remove all peak labels - remove individual peak labels - restore labels based on parameters from automated labelling - move label text position - reset label text positions - add a custom label - edit label text

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Spectroscope view To simulate the view through a visual hand-held spectroscope, based on current spectral data. Works for absorbance, transmittance and emission data. The "rainbow view" color bar is located below the spectra plot, and will move and stretch according to the plot above. Select the spectrum of interest from the right drop down box, check "activate" and the "rainbow" view gets modulated by the spectral data values. Some options available: - change the tick distance in 5 nm steps, or turn them off completely - have the "rainbow view" converted to gray scale, consisting only of brightness values - have the "rainbow view" aligned and moving with the selected spectrum, or keep it steady - Copy it to the clipboard for copy&pasting the picture to anywhere else, or - save it as BMP file

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	Tweaking plot display - With the "Stack spectra" function, you can vertically stack up to 15 spectra at once. Each one then has it's own y axis. Zooming, panning and scrolling happens simultaneously for all of them, but please use the topmost spectrum for this. - With "Scale & Shift" activated, you can shift around individual spectra (left mouse button), and also stretch/ compress them (Shift key + left mouse), without effect on the original data. Several options are available from the dropdown menu: - use only x offsets (for horizontal shifting/ stretching) - use only y offsets (for vertical shifting/ stretching) - allow x and y offsets (for shifting/ stretching in both directions) - spread all spectra evenly (for a waterfall kind of spectra display) - reset changes (go back to initial display) - make plot changes permanent (by changing the actual spectral data)	- The "Show Grid" button allows to show/hide the grid lines, which are located behind the spectra traces. From the dropdown menu, select either solid or dotted grid lines The Color button lets you select any color as plot background. It is only visible on screen, but not within printouts or exported plot images.
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	Spectra display options This area has some options for influencing the display of spectral traces. You can temporarily hide from display a selection of spectra without removing them. Line width is variable, data values can be shown as points, color sequence for consecutive spectra is changeable and after playing around, a default display can be set again.
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Flip through For large numbers of loaded spectra (some dozens, hundreds or even more), it is often helpful to not show them all at at once, but to flip through like you do with a comic book, showing only a few spectra at once. This feature is also activated on loading a large number of spectra, the threshold can be set from File > Options > Plot, Views, Spectra > Flip through. - Select the number of concurrently shown spectra at the left (default value defined form the same place in File > Options as above). - flip back and forth with the blue arrow buttons - quickly navigate through all spectra with the green slider - grabbing the start or end number below the green slider allows to change the interval size

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Hiding spectra On clicking the spectra hiding button, a checkbox is shown next to each legend entry in the legend box . Uncheck a legend entry for hiding the corresponding spectrum. Check it for showing again. After clicking the "Hide spectra" button a second time, the legend box is shown normal, but without the unchecked spectra and legend entries. The button's dropdown menu has several options: - "Show all" checks all legend entries at once, leading to the full plot again. To be used before hiding only a few spectra. - "Hide all" unchecks all legend entries at once, leading to an empty plot. To be used before showing only a few spectra. - After a decision to not only hide but actually remove the hidden spectra, just click the "Remove hidden spectra" menu point.

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Line thickness For changing the global line width of all spectra together. Clicking one of the buttons once changes the line width by one step. There are 9 steps available, per default the second or third step is active. When changing a single spectrum's line width in the "Spectra" ribbon, this happens relative to the global line width from here. Before printing and creating image files, a line width around three is recommended.

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Points & Lines Normally, spectra are represented as lines ("Lines" option). This dropdown button allows to add small symbols at the position of the spectrum's data points ("Points & Lines" option). Or, you can show only the data points without the connecting line ("Points" option). Not to confuse with the "line type" option from the "Spectra" ribbon... Sometimes, the data point marks might be hard to see, depending on line width, x axis step width and zoom status.

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Standard lines & colours Whichever weird combinations of line color, line type, points&lines and global/ individual line width you chose, this button will set it back to standard values. That is: colors from the standard color palette, solid lines, no points, line width of two. However, all those weird combinations can be preserved for eternity by saving as Spectragryph *.sgd binary file. At least, this works for line type, width and color.

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Color palettes Here you can choose from 16 different color palettes to give distinguished colors to your spectra plot. Each palette was optimized for viewing and printing (no white, yellow, light grey color entries). Use the "Preview" button for getting a glimpse on how your spectra will look like with another palette. Press the "Apply" button to activate the selected palette. The selected palette is also used as standard palette with the "Standard Lines & Colors" function. Create a fully user-defined, customized palette with the "Add palette" button. By clicking on the color fields, you can then add individual colors and edit the palette name. It is possible to save and load custom palette files, for exchange with other users... Finally, custom palettes can be removed again with the "Remove palette" button (not possible for the 16 built-in palettes).

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Axes settings - Use the upper dropdown menus to set font type and font size for the axis titles and axis tick marks. Use the lower right down arrow for full font control. - Switch the x axis direction with "Flip axis". - Hide one or both axis titles from display with the "Show Titles" button. - Activate the display of your custom titles (to be defined by clicking onto the axis titles) with the "Custom Titles" button. - Activate the use of custom axis boundaries (to be defined by clicking onto the axes) with the "Custom Boundaries" button.

- Select your desired x and y axis type for display from these two buttons ("Change x axis" and "Change y axis"). Any spectrum can be displayed with every axis type, as long it makes sense physically and is possible mathematically. - IMPORTANT HINT: The calculations are done on the fly and do not affect the spectral data as such, only the visual display is changed! - ANOTHER IMPORTANT HINT: Axis types for spectra are assigned on loading spectrum files, based on the information inside the file (if nothing found, default types apply). These cannot be changed afterwards. Renaming axis titles is not the same as changing axis types! OK, there is one possibility: have a look at the "Interpolate, Resample" function from the Transform ribbon...

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Legend settings - Use the upper dropdown menus to set font type and font size for the legend entries. Use the lower right down arrow for full font control. - Hide/ show the legend box surrounding with the "Transparent" button - Hide/ show the legend box as such with the "Show" button - The "Floating" button switches the legend display between fixed + outside the plot and floating + inside the plot.

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	App Style -With the upper dropdown menu, choose from a wide range of historic app styles. Office 2013/ 2016 are most recommended. - The effect of choosing color for the app style is not available for Office2010 and Win7. It is strongest for "Office 2016 White". - With "Old style menu", a nearly classical pure menu is shown, you can get back by clicking onto "Switch back modern style"
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