© 2016: Dr. Friedrich Menges Software-Entwicklung Spectroscopy Ninja | Spectrometer Hardware | Spectragryph Software Imprint
[Spectroscopy Ninja]
Spectroscopy
Ninja
presents:
[SpectraGryph]

Spectragryph
- optical spectroscopy software -

Contact & Connect: academia.edu Tumblr: Haunted by spectra Facebook: Spectroscopy Ninja LinkedIn: my professional self! Twitter: Spectroscopy Ninja Xing: another professional resume ResearchGate: my academic self send an email youtube channel for Spectroscopy Ninja
...
About Testimonials Download Licenses Contact News
File Transform Analyze Fluorescence/ EEM Evaluate Automate Identify Acquire

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

New view...
 

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.

Close the currently selected tab by clicking on the right Close symbol [ x ]. 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.

<jump back to top>
 

click for details
click for details
click for details

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 labeling of peak maxima. The spectroscope view bar show the spectral as if the measured sample was viewed through a visual spectroscope.
<jump back to top>

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)

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.


<jump back to view enhancements> <jump back to top>

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.
- 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. Turn it off by choosing prominence=0.
- 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.
<jump back to view enhancements> <jump back to top>

Spectroscope view


To simulate the view through a visual hand-held spectroscope, based on current spectral data. Works for absorbance, transmittance and emission data. Emission spectra have to be normalized first. The "rainbow view" color bar is located below the spectra plot, and will move and stretch concurrently to the plot above. If this didn't happen, please click onto it once. 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
<jump back to view enhancements> <jump back to top>
 

Tweaking plot display

- With the 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.
- The button allows to show/hide the grid lines, which are located behind the spectra traces.
The Color button let's you select any color as plot background. It is only visible on screen, but not within printouts or exported plot images.
<jump back to top>
 
Hide Spectra Line thickness
Standard Lines
Color Palettes
Points/Lines

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.
<jump back to top>

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.
<jump back to spectra display> <jump back to top>

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.
<jump back to spectra display> <jump back to top>

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.
<jump back to spectra display> <jump back to top>

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.

In a future software version, there will be ways to create color gradient palettes, as well as completely user-defined color palettes.
<jump back to spectra display> <jump back to top>

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.
<jump back to spectra display> <jump back to top>
 

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".
- Activate the display of your custom titles (set by clicking onto the axis titles) with the "Custom Titles" button.
- Hide one or both axis titles from display with the "Show Titles" 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!
  <jump back to top>
 

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.
  <jump back to top>
 

App Style

-With the upper dropdown menu, choose from a wide range of historic app styles. Office 2013/ 2016 are most recommended. The app styles named after older Office versions required some changes layout, leading to a reduced feature set in the "File" menu. Sorry for this.
- The effect of choosing color for the app style is not available for all of them. 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"
  <jump back to top>

 

© 2001-2017: Friedrich Menges. Last Change: 27 February, 2019
Privacy statement: this website has no 3rd party cookies, it will neither track nor analyze you. No Google Analytics. No paid advertising. No selling of user data. No fuss. No shit. Only useful content for Spectroscopy Ninjas.