Transparency of NaN values grayed out


I have a recurring problem where transparent NaN values (using grdimage) in my postscript AND pdf figures that are produced by GMT get grayed out when imported into certain applications (e.g. Adobe Illustrator). Normally, I circumvent this by avoiding editing them in illustrator, as the transparency works just fine on the PDF. However, I have just recieved the proof of a paper that is about to be published and whatever program they use has this problem and has completely grayed out my bathymetry map, making the figure essentially useless and unpublishable in this form. The correct figure should look like:

The proof’s version looks like:

The output from GMT itself is fine, so I realize the issue is more with the program that is imported the file and how or whether it handles transparency, but I know of many people who have had this issue with GMT output specifically. For example, Illustrator can definitely handle transparency just fine, but not when it’s coming from a pdf made from a postscript file it seems. Is there a way to fix this within our gmt script, a certain output option, other than just a raster image? Any help with this issue is much appreciated. Thanks.

This has been a problem for GMT output and Illustrator for a long time. I have edited some figures in Adobe Illustrator, but I have to open it in Illustrator, extract the image layer into Photoshop, edit the image in Photoshop to set the transparency again and save as a PNG, then replace the image in Illustrator with the PNG that has the transparency.

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Yes, Eric’s recipe is the most likely one. The main problem is limitations in the Adobe suite to handle their own PostScript language properly. Personally, I am doing everything I can to never need to make any edits in Illustrator ever. Legends, labels, lines, whatever is better placed via GMT scripting than to fuss manually in an expensive tool with limitations. Maybe awkward at first, but down the road you save time.

Yes this is a terrible problem - Paul’s solution is definitely the best, in particular if there are several revisions…
Anyhow, If you have access to corel draw you can open the GMT generated PDF and export it as a corel generated PDF. Later you can open this PDF with Illustrator. In most cases this works but might introduce additional smaller issues such wrong degree symbols…
If you don’t have corel you can send me the file and I will give it a try.