Qualitative X-Ray Maps outputs

[KVenance]

I have acquired qualitative X-ray maps on a large number of monazite grains with ProbeImage.  While acquiring, I set it to the thermal colour scheme.  Is it possible to export them as thermal or rainbow, rather than grey-scale?  I realize that I can save in thermal/rainbow from CalcImage, but that (I think) I need to do map by map and I have hundreds of them.
 
Also, I don't see how (in ProbeImage or CalcImage) to show the intensity scale next to the element map and can one adjust the scale such that it is consistent within a sample in order to compare element intensities amongst grains in a particular sample?
Thank you,
Katherine

[John Donovan]

Remember, qualitative x-ray maps are simply x-ray maps that have not yet been quantified!      

See this for batch mode output in CalcImage:

https://probesoftware.com/smf/index.php?topic=191.msg6791#msg6791

This batch output processing doesn't really work for qualitative x-ray maps, as we really don't have much support for raw intensity x-ray maps.  But why would you not quantify them?  It's easy!  Now that you have the x-ray maps it is a simple matter to acquire some standards (and MAN curves if you didn't acquire off-peak maps) in Probe for EPMA. 

Then from CalcImage you can output net intensity maps if you really want, but full quant maps are so much better, and you just need some standards acquired in Probe for EPMA using the same elements, spectrometers, crystals, etc.

To modify the default palette in CalcImage see the Image Processing menu.

Does this help?  Please let me know.

[John Donovan]

I realize that I can save in thermal/rainbow from CalcImage, but that (I think) I need to do map by map and I have hundreds of them. 

Katherine,
You can also use the Window | Output Currently Displayed Images to Surfer menu to output all currently loaded images in CalcImage to Surfer output.

https://probesoftware.com/smf/index.php?topic=912.msg5911#msg5911

This will allow you to output raw x-ray maps with intensity scales and beam current notated.

[JonF]

Although quantitative maps would be better, I've altered a macro that I use in ImageJ for you (based on a macro that Ben Buse uploaded).

As you've got hundreds of maps, it would be best to sort the files in to folders of elements (assuming all were taken under the same conditions) - simply go to the top folder that contains all the maps and search for the elements one by one, then copy and paste them in to a new folder.

Then you can use CalcImage to convert all of the files (one folder/element at a time) to a format you can use in ImageJ/R/Matlab etc with the Convert > Convert All PrbImg Files in Folder to ASCII.

Once you got the maps sorted by element and as ASCII .TXT files, you can then run the attached macro in ImageJ/Fiji for each of the folders (in ImageJ, go to Plugins > Macros > Install then Plugins > Macro > ProbeImage_Output_v2_presetMinMax to run the macro).
Just navigate to the first element folder and select it, then select an output folder (just press select again if you want the outputs in the same folder), enter the pixel size for the maps (again, assuming they're all the same?) and press OK, then select the lookup table of choice (16 colours is probably closest to the Rainbow LUT), then OK the next window and enter the preset minimum and maximum levels you want to use for this element.

ImageJ will then cycle through all the images and add scale bars and colour scales to each image and save them as .jpg files.

Repeat this process for all of your elements/folders. If you want to reassemble your maps by sample, just search through the directory again filtering by sample/run number and copy and paste the .jpg files in to a sample directory.


Hope this helps.

[Probeman]

Jon's suggestion using Buse's modified macro is a good idea.

Another method which might save you some mouse clicks is to create a dummy CalcImage project by using a dummy Probe for EPMA MDB file (without standards for quantification). The idea being to use the Create (New) Project Wizard menu to simply load/convert many PrbImg files (acquired with Probe Image) into a dummy CalcImage project. The reason being you'll only need to select one PrbImg file from each map acquisition set, to load all of the other maps from that acquisition.

Then once the PrbImg files are converted to GRD files, you can simply use the Window | Output Currently Displayed Images to Surfer menu to output all currently loaded images in CalcImage to a Surfer project, using the 1, 4 or 9 maps per page option in CalcImage.

Finally once the GRD files are converted to Surfer project pages (by running the Surfer .BAS script(s)), you can adjust the color and/or intensity scales on each x-ray map image by opening the .SRF Surfer project file in Surfer and using the color scale and Z data scaling options.

Having your raw intensity (or quant) maps in Surfer gives one plenty of options for other output customization as well, and you won't need to edit any scripts.

[KVenance]

Thank you for all the suggestions.  Sorry about the late reply, I got some flu bug shortly after posting and I've been laid up since then.  I will take a look at these options soon.
Katherine