Visual Spec 3.9.2 - 3.9.7 - 4.0.0 - 4.1.2 - 4.1.3 - 4.1.4 - 4.2.6

Goto V4.2.6 description

Mouse Wheel

Visual Spec is now responding to mouse wheel in the two following cases:

Open an image, click in the image and use the mouse wheel to reduce or enlarge the thresholds window. A reduced window width will increase the contrast.

Open a profile, click on the profile at the position you want to keep centered. Use the mouse wheel to zoom around this position. you can always revert to the original display with the "unzoom" button. if no profile position has been indicated (by a simple click) the zoom will be centered on the middle of the profile.

Display Positions next to cursor

If you want to have the display of the X, Y position of the cursor next to it, click on the small square next to the X,Y label in the toolbar. 

If the mouse is over an image, it will display the X,Y coorinates. 

If the mouse is over a spectrum profile, it will display the pixel and its wavelength. The wavelength is zero if the profile is not calibrated.

Image sky background subtraction

If you want to subtract the sky background above and below the spectrum, there is now a new button in the toolbar

A new dialog box will be displayed

The algorithm can find automatically the spectrum if there is only one spectrum in the image. But if you un-select the Auto mode, enter the Y position of the middle of the spectrum in the image.

The sky background correction compute a column by column average value from two regions above and below the spectrum region. The width of those windows can be modified. This profile can be assimilated to the sky spectrum and is then subtracted as an offset to the entire image.

If the auto mode is selected, Visual Spec will pick two sky regions at 10 pixels above and below the profile region. 
If the auto mode is unselect, enter the Y top and bottom coordinates of the two prefered regions.

Image raw profile extraction

This function extract and display the profile of the spectrum from one image. Go in the menu Extraction>Basic profile extraction.

The dialog box is similar to the sky subtraction box. The two additional functions are the tilt correction and the binning profile extraction. If the tilt angle mode is selected, Visual Spec will compute the rotation angle along the horizontal axis. The value found will be set in the text field next to it. If unselected the text field is active and the angle value will be the one entered in the text field.

The binning auto mode will use the specific binning algorithm of Visual spec which retains only lines which contains signal. If the auto mode is unselected, a classic sum is made column by column in the region around the spectrum defines at the beginning of this process.

The raw profile is displayed in a profile document. The resulting profile is the spectral profile, but not yet calibrated. The tilt angle is corrected, but not the slant, as this is not necessary for a such basic function.

Image basic calibrated profile extraction

This function extracts, calibrates and displays the profile of the spectrum from one image. It is based on the above described steps in the raw profile extraction with the addition of a set of field to perform a basic calibration.

Go in the menu Extraction>Basic profile extraction.

A dialog box is opened. On the left, the panels have the same function as in the function above. The right panel is for the basic calibration of the raw profile. To perform a very basic calibration you need to identify 2 lines and assign the wavelength to the pixel positions.

If you turn on the display X,Y position next to the cursor, you can move it on the image and see where are the lines. In the exemple above, the H-alpha line at 6563 is visible as an absorbtion line, and the first O2 atmospheric molecular absorbtion band is also visible on the right side. The first deep line position is used.

This calibration is very basic in a sense that it used pixel position of the line center defines visually by the user. The final calibration shall be made using the barycenter or a gaussian fit of the line, and more lines maybe used to really fit the dispersion law. In this case, a spectral reference lamp spectrum is used, and not the star spectrum itself. Star lines wavelength can be modified by the object radial velocity. At 6563 angström, 45km/s RV is equivalent to 1 angström shift.

After the processing, the profile is displayed, the axis is graduated and the sampling factor is updated in the top toolbar.

I use this basic calibration extraction during my observing session. I usually process the first raw image of an object. As soon as the image is recorded, I open Visual Spec and perform the extraction. As I know the sampling factor of my instrument, I use the 1 line calibration, just indicating the H-alpha line position.

Spectrum profile basic linear calibration

The function can be found as a new button in the toolbar or in the menu spectrometry>basic calibration. A profile shall be displayed.

This function is vary basic. If you know the sampling factor of your instrument, you can simply assign a wavelength to a pixel value, enter the angström per pixel sampling value and get your profile calibrated. If you do not know the sampling factor, you will need to identify two lines and enter the wavelengths for each line positions in pixel, as described above.

If you turn on the "next to cursor" XY display, check where is the center of the H-alpha line. Enter the X coordinate into the box Pixel in front of the 6563 ang value, H-alpha wavelength. Enter the sampling factor, here 0.42 angström per pixel.

If you click in the Pixel box text field, then click on the profil, the X position will be automatically updated.

Click ok and the profile will be calibrated.

Remember, this is not very accurate calibration, as the center of the line is defined manually. For better performances, use the 1-line calibration function and select the line so the barycenter can de determined for better accuracy.

But you can also see the barycenter of a selected line from here.

Simply select the line you want to know the barycenter (assuming your profile is not calibrated). Click the right button of the mouse, a popup-menu will be displayed. Select the label item. The barycenter will be shown under the line.

To erase label, click on the "refresh" icon in the side toolbar.

Default profile window size

As PC screen are getting larger, the default size of a profile document at opening can be now modified. Go in the preferences menu. Select the language tab. You can enter first the width, then the height, in pixels.

Image slant and tilt

Load an image.

Click on the "angle" button. It will compute the slant or the tilt angle.

Slant

If you load a lamp spectrum, with vertical line, you can compute the slant angle by dragging the selection (right click of the mouse) around a calibration line. Make sure the rectangle is higher than its width. This will be the criteria used by Vspec to define if it has to compute a slant or a tilt angle.

The result is displayed in the infos window and the slant of the image is corrected.

Tilt

If you load an image of an object spectrum, then drag along the spectrum, with a rectangle wider than its heigth. The tilt angle will be computed and the spectrum will be tilted by this angle.

 

Note: there is no possibility in Visual Spec to save images. Those image processing functions are only for a rapid evaluation of the spectra obtained, on a single image. And as the correction can quickly be re-applied, this not critical for this purpose.

For the true image processings and profile extraction and calibration of an image sequence, see the ISIS freeware, from Christian Buil.

Image rotation

Load an image.

Click on the "rotation" button.

It will open a new dialog box.

Enter the center of the rotation in X, Y coordinates. If you want to rotate around the center of the image, then click on the checkbox Image center. If you want to use the cursor to define the rotation center, click in one of the text field X or Y, then click in the image to get the cursor position loaded.

Enter the angle of rotation in the text field below the slider. To apply it, clcik on the checkmark icon, pointed by the red arrow.

To come back to the original image, click on the "undo" blue arrow icon.

You can enter negative value, and decimal value.

If you prefer you can use the slider. Click on its small cursor and slide it. The image rotation will happen upon releasing. Each time you click again on the slider cursor, the image will re-start from the original one. It is not good to perform multiple rotation on one image. The quality will be degraded.

The rotation process will make black areas appear on the side of the image. This can disturb the good functionning of function like automatic tilt correction. Better to put then a 0 tilt value and check the tilt angle box in Basic raw profile and Basic calibrated profile.

In general, applying a rotation is not appropriate. It will degrade the resolution. It is recommanded to align at your best the spectrum at the acquisition and use the tilt function to fix the residual misalignement.

Reading bmp files

This is work in progress function, but it shall be able to read bmp files as image.

In open image menu, in the dialog box, you can select fits, pic or bmp now as image format

Reading dat files

At opening of a .dat file, check the linearity of the wavelength values. if the mean standard deviation compare to a linear graduation is greater than 10%, Visual Spec proposes to resample it. In version 3.9.7 this feature is again removed... the criteria to decide if non linear is too difficult to adjust and the message is creating bugs. So, disabled again

Export png, jpg, bmp files

You can now export the content of a profile window as png or jpg or bmp image. It will keep axes graduation and all annotations.

Add annotations on profile

This is again some work in progress... on the side of the profile window, two new buttons can be found. One to add a line and one to add a text.

Click on the line button. Move the cursor where you want the line to start. Keep the mouse left button pressed and move to the end of the line. Release. If you want to modify the line, click on it and move one the 2 small dark dot. If you want to erase, click and press suppress buttton. If you want to add another line, click again on the line toolbar button.

Click on the A text button. Move the cursor where you want to put text. Replace the default text by yours. To select an annotation, click in it. Keep the left button pressed and move the text to another place. If you click on the small black dot you can resize the text. If you click with the right mouse button in a text selected you can change the text position (left, right or center) and change the police and color. If you want to erase the text, select it by clicking in it and press the suppress button.

Edit utilities files

Visual spec is using some text file as utilities like the intru_text.txt file which is used to record all your instrument names or the observation site. You can also have direct access to the pgm (scripting) files or gnuplot templates etc...

In the assistant menu (a profile shall be opened) go to the edit menu and pick the file you want to edit. It will search and open notepad.exe to open the file.

As a result the selected file will be opened. You can edit the changes and save it. In the list_instru.txt case, add a new instrument and it will be shown in the drop down list of instrument when exporting as fit for BeSS (ctrl W)

Automatic telluric lines suppression

This is a test. This function iterates (slowly) on the region 6540nm - 6552nm to eliminates the telluric lines. If the profile is perfectly calibrated (aligned with telluric lines to eliminate) this gives some pretty good result. But not all the lines can be corrected, some overshoot can be seen. This can be improved in the future.

V4.0.0

Equivalent Witdh

3 new way to compute Equivalent Width are now available in the menu Spectrometry

- EW lin : from the limit of the selection, compute the average of the 20 pixels before the beginning of the selection and the average of 20 pixels after the end of the selection. Defines the continuum as a line defined by the two above computed averages. Which lineraized the continuum below the line, which may have a slope.

- EW cst fit: from the limit of the selection, compute the average of the 20 pixels before the beginning of the selection and the average of 20 pixels after the end of the selection. Compute the avearge of the two above average and defines the continuum as a constant line.

- EW cst 1: consider the continuum around the selection is already normalized to 1, no continuum fit

For all EW computation, compute the Signa to noise ratio from the region defined as continuum for scaling to 1 operation. See in Preferences menu, tab continuum. Then compute the EW error using the formula from Chalabaev, A. and Maillard, J.P. (1983)

It shall be noted that these 3 EW command are also available as console & script commands: leq, leqc and leq1

V4.0.5

Improved BeSS check

In this version the BeSS validation check function includes now some tests on the profile wavelength domain and propose different ways to check the validity of the spectrum.

If the range is large, Balmer lines are diplayed instead of telluric lines.

If it does not include H-alphe, He lines can be displayed.

This function is developped to assist the BeSS administrators to check the submitted spectra. Use it and see if you can become an admin in the future...

Verif Atm cal

This function checks the accuracy of the calibration using 6 telluric lines around H-alpha region. It displays the shift onthe graph.

In this example above, a shift of 0.1 angström would be appropriate

V4.1.2

Opened file list

This function opens a new window with the list of all the opened files under the current session of Vspec. It is useful if a lot of files are opened and you are looking for a specific one, without clicking on the profile window bar to get to the profile name.

You can get quickly into it hitting the F4 keypad button as a shortcut.

Click on the file name you are interested in to bring the profile window on top of all the opened profiles. Click on the small red cross to close this window.

Elements line lists

In this version, 3 new list of lines are selectable from the elements dialog box. Those are kindly provided by François Teyssier.

- Neb Plan, refer to a list of lines generally encountered in Planetary nebula spectra

- WR, refers to a list of lines generally encountered in Worl Rayet stars

- symb, referes to a list of lines generally encountered in symbiotic stars

To get access to this new lists, open the Elements, click on the top right dropdown box and scroll to see them

Stack and Y shift, time

When you open the Stack and Shift Y dialog box, you can the see the options to stack respecting the scale of time of the list of profiles. If you pick this option, the profiles displayed in the vspec desk will copy and paste in the current profile selected. An offset will be added to each profile intensities in regard to their date and time. The earlier profile will be at the bottom and the latest at the top with the highest offset added. You can adjust the "overlap" by playing with the Y offset constant.

If you do not close this dialog box and you go back to the profile window to click on the display axis button, the Y-axis will be automatically graduated with the date and not the intensities. On the X-axis, the doppler display will also be automatically activated. Make sure the reference wavelength is correctly set. If you need, you can fine adjust using the Format>Graphics... dialog box.

Line analysis

This item brings a new set of functions to go further in assisting you to analyse your spectrum. It deserves a specific page on this, so click here to get a deep review of the capabilities.

For planetary nebula this assistant will help to compute temperature and electronic densities as long as you have the right lines on your spectrum. It will guide to go directly to the line of interest and get a measure of them.

For symbiotic, the tool will only help you to go easely to spectral lines of interest to register their Equivalent Width. This will allow you to perform time analysis by collecting spectra at different date and time.

This assistant assumes the spectra are properly calibrated.

V4.1.3

BeSS query

This is an addition to the BeSS query dialog box. Once the files list if retrieved, we have a new option list to open only the spectra by month or by year. To open the selected files, as previously, click on the button with the big icone.

Film composer

This function generates a png image made of the thumbnails of the profiles opened in the desktop of Vspec. You fisrt need to have a set of profiles opened and properly formatted. Use the window>tile function and the tool>comparison function to format all the profiles with the same scale and proper axis and informations displayed.

To access to the function click on the menu Assistant, item film composer.

The function will re-displayed the profiles according to the settings in the film composer dialog box from last session.

Change the width or height of the thumbnail by entering values in the corresponding fields. You can also change the number of thumbnails per line. Click on generate to have the new values taken into account. You can also choose to have the thumbnails ordered by ascending of descending dates.

When you are satisfied, click on Export button. You can select the directory and the name. By default, a new directory named "composer" is created in the root directory of Vspec.exe

All individual thumbnails are stored by default in this "composer" directory, as bmp file. From time to time it can be good to erase the accumulated files.

As a result, you will have the following .png file

Another way to generate thumbnails is to use the web page generator function. It creates a full web page with graphics created by gnuplot.

V4.1.4

Directory favoris        

In the dialog box to open profiles, few icons have been added

- the change of the working directory

- direct access to the working directory

- the move to the directory of the Vspec.exe application

Instrumental Response assistant    

This new assistant is aimed to help in the sequence of operations to compute an instrumental response from a reference star. This is not to correct objects of the instrumental response but here to generate it.

You first need to load the acquired spectrum of the reference star from which you have an "ideal" profile, and a A-type or B-Type spectral class.

You access this assistant in the menu "Assistant" when the reference profile is opened.

A new dialog box will open and the name of the profile which will be used to generate the instrumentale response. It is recommended to have only this spectrum opened in the Visual Spec desktop.

In this assistant the frame with grey arrow are optional, the one with the green arrow are mandatory.

If you need to know the spectral type of your reference star, you have a quick access to the CDS site, with a direct access to the standard CDS query.

The first mandatory step to generate the instrumental response is the next step.

You fisrt need to have on your disk the "already corrected profile" for your reference star. Vspec offers the Pickles database by default. You will pick the right "ideal" profile which matches the best the spectral type of your reference star. For Vega, an A0V.

Christian Buil offers an additionel set of reference spectra with his ISIS software. You can directly installed the data base where you want. If you install it as isis_database in the vspec.exe directory, then Vspec detects it and propose 4 news options in the select reference spectrum frame. If the directory is not present, then the names will disabled.

To select the "ideal" spectrum select the database and click on the green arrow

Select the file from the list proposed. In this example, we have taken Regulus as the reference star during the observing session. It is in the UVES database.

Click on open when the uves_regulus.dat file is selected. The profil will be added to the profile window as a new profile. As you can see below the UVES profile in purple is slighly shifted from the acquired profile. The optional tool to shift it and match the acquired profile is provided. This is sometimes necessary. But you shall also questionned yourself about the accuracy of your wavelength calibration. (Before extracting the response a good check is to check telluric lines with the H2O function.)

Here is the final shift

Next step is to now generate the response. 

This will perform the division and configure Vspec for the continuum extraction

Refer to the standard operations of this mode. I will show here the most used workflow.

Remove the artefact produce by the telluric lines

When all are removed, run the smoothing function

Adjust the fit with the cursor of the smoothing function.

When fit is ok, click on the OK button. The orange profile will be moved as the intensity profile, to be ready for saving.

Last step is then to enter the response file name and click on the green button to save the file. By default a file name is proposed.

To exit the assistant, click on the red cross

V4.2.6

Mendeleiev table button

If a profile file is opened, and if the profile is correctly calibrated in wavelength, then you can display the table of element from Mendeleiev. This function is also avaible from the element list window.

A new window will open and display the table. In this example, the profile is a B-type star (Be star) and you can expect to see at this temperature spectral lines from Hydrogene and maybe Helium.

Click on the symbol of the hydrogene H and Helium He. The spectral which correspond to the element will be displayed in the coler of the frame clicked. Here, Hydrogene is in green and Helium is in orange. As expected you can see good matches.

If you want to improve the superimposition of the Hydrogene line for example, select the serie of the Hydrogene. You can try using the mouse to click on one of the green line or go in the serie dropdown list and select it. Then go on the side of the profile window and click on the Up arrow to increase the scale of the line. The match with Balmer lines is even more obvious.

Adding quick labels        

The popup context menu can be displayed by clicking the right mouse button when the cursor is over the image section of a profile window. Select the serie you want to add the date in the graph.

Click on the popup menu and select Label date. The date will be added with the same color than the serie.

As this is a text object, you can select and drag it where you want. You have a similar quick label item in the popup menu to add the name of the object: label name

You can export your image in png format with the save as and select png in the format, or just click on the camera icon on the right side of the profile window.

Copy/Paste contextual        

To copy and paste a serie from a profile window onto another one you can use the toolbar button or now just use the shortcut in the popup contextual menu. Right click in the image section of the profile and select the copy item.

Select another profile window, rigth click in the image section and select the paste item.

Renaming list as sequence        

It can interesting to create a sequence like i-1, i-2... i-n from a list of spectra for a same object but at different date of observations. The sequence name i-n can for example be used in ISIS to generate an animation or a 2D image spectrogram interpolated.

Fiirst load all the profile in fits format (can be Vo table from BeSS database too). Make sure date and time are correctly filled. Go in the Assistant menu and select Rename list

A new dialog will be displayed. It will show the list of the file and will prompt you to enter the generic name. You do not need to add "-" at the end of the generic name, Vspec will added for you. Then click on OK.

The files will be duplicated under the new name i-1, i-2, ... and will be stored in your default working directory.

Comparison tool with new doppler format         

To compare spepctra, it is important to display the profiles with the same format. The powerful tool "comparison" is designed for this. First display the set of profiles you want to compare. Then go in the tool menu and select comparison...

The format proposed by default are Normalization (scaling...) using the wavelength range defined in your preferences settings. Adjust to maximum will detect the maximum intensity across all profiles and pick this value as the maximum Y scale for all profiles.

X common setting will detect the common wavelength range across all the spectra to display all of them at the same X-axis scale.

Display axis will force the display of the axis for all spectra.

Not set by default are the Axe X Doppler, to force the X axis display in doppler scale, the reference wavelength is the one in the graphics options, and the 1000km/s check will force all the Xaxis to be scale from -1000km/s to +1000km/s.

In addition on the right side, you can decide wich labels to add on each profile: date and time, only date, observer name, object name.

It can be useful to refine some axis adjustments before going to the film composer. Go in the graphic settings (double click in the image section, or shortcut Ctrl+G, or menu Edit item graphic, or the two icons in the toolbar with two small arrows). in the Xaxis tab you can check the lambda value which is the reference value to compute doppler shift.

On the Y axis tab, you can see a box called "force". This will preset the ticks and major ticks set to have 0.2 between each tick and no ticks label on major tick.

never forget to click on Apply button. ok button will simply keep the current state and close the box.