Display, Annote and export analog signal images

[Malcolm Roberts]

Hi John,
I note that the flurry of discussion has died off a bit, so I thought I'd pipe up and see if we cannot get a bit of revitalisation. Subject above outlines the matter on hand. I am finding some behaviour "not as predicted" (by me), although I am prepared to accept that my logic as a geo may not be the same as others. I am testing things so I know what they do.
What am I trying to do? Output analogue images in BMP format with a variety of attributes - with and without sample position points, variety of colour schemes, titles and scale bars. I might then use these in docs or fiddle further in other programs. What I find:
1) Bitmaps exported including sample position points are exported without sample position points.
2) If I choose one colour scheme and then change to another and save as bitmap, the saved image has the colour scheme changed from and not the newly selected one. If I want the new one, I have to save another image, but there is no guarantee that I will get the colour scheme I want. I am finding this with "thermal" and "rainbow". Whatever I save is tending to always be thermal. The only way around this I can find is to copy to clipboard and paste into something. Then I get the scheme I want plus all the labelling.
3) Any tips on how to make changes to the default point and text? I am finding that in thermal, the blue is not good against dark colours.
4) And finally, is this behaviour as it should be?

Cheers,
Malc.

[Probeman]

1) Bitmaps exported including sample position points are exported without sample position points.

Hi Malcolm,
I assume you mean these controls?



The answer is yes, this is expected. To get the overlay graphics output along with the image you should use the Copy To Clipboard button as you have been doing *or* use the Output | Save Images to BMP Files as seen here:



The nice thing about this Output menu is that in addition to the overlay graphics, it also outputs a .ACQ stage coordinate and .TXT column condition file for each image.

2) If I choose one colour scheme and then change to another and save as bitmap, the saved image has the colour scheme changed from and not the newly selected one. If I want the new one, I have to save another image, but there is no guarantee that I will get the colour scheme I want. I am finding this with "thermal" and "rainbow". Whatever I save is tending to always be thermal.

You can do it but you need to first change the default palette by selecting the palette that you want, then close the Display, Annotate, etc dialog, then open it again, and then export the selected image(s) with the new default palette.

3) Any tips on how to make changes to the default point and text? I am finding that in thermal, the blue is not good against dark colours.

There is no provision for changing the over text font and color at the moment- though it's not a bad idea...

In the meantime it is easy to open the image/GRD in Surfer using the New | Image Map menu, then add a "Post Layer" to the plot to show analytical coordinates on the image. Then you select both plots and click the "Overlay Maps" to align them to each other. It's several steps but then you have full control over everything as seen here:



I should probably write up a small Surfer macro to do this automatically, but feel free to share any efforts of your own in that direction- I would implement it right into PFE for you!

[Malcolm Roberts]

Hi John
Here's an example of where some changes might be handy. This is using rainbow. Scale bar black and can be changed. Sample name and analysis points white and cannot be changed. Latter as good as invisible. Why not make the colour change for the scale bar valid for all - text, points and etc?
Cheers,
Malc.

[John Donovan]

Here's an example of where some changes might be handy. This is using rainbow. Scale bar black and can be changed. Sample name and analysis points white and cannot be changed. Latter as good as invisible. Why not make the colour change for the scale bar valid for all - text, points and etc?

That is possible. 

I've tried to find a text color for each palette that shows up well and as you say, sometimes it doesn't for a particular image, 

Are you wedded completely to using the "rainbow" palette?  I ask, because if you just click a different palette, the text ought to "pop out" better.

Did you try replacing the default custom.fc file with the JEOLColor palette?
john

[Malcolm Roberts]

Hi John
Not yet. I was hoping to change it to something invented by me in surfer. Unfortunately as people like using the probe, I have not had a chance to give that a go, if that is, you have had a chance to add the .clr to .fc transform button.........
The rainbow pallet is spitting out some fairly awesome results....!! Here's one I have tweaked a bit....... its a piece of uraninite apparently......

[Probeman]

Not yet. I was hoping to change it to something invented by me in surfer. Unfortunately as people like using the probe, I have not had a chance to give that a go, if that is, you have had a chance to add the .clr to .fc transform button.........
The rainbow pallet is spitting out some fairly awesome results....!! Here's one I have tweaked a bit....... its a piece of uraninite apparently......

Hi Malcolm,
Can you post the color spectrum as seen in the Classify window?  What data type is the attached uraninite in your post?

I have a .fc to .clr routine already!   But I will have to code the inverse function...

[Malcolm Roberts]

Hi John
It's default rainbow.fc with the far left-hand purple replaced by black using good 'ol Paint (image copied to clipboard and pasted into Paint............ The image is back-scattered. Nothing fancy, but it illustrates what can be done quite easily..........
Cheers,
malc.

[John Donovan]

It's default rainbow.fc with the far left-hand purple replaced by black using good 'ol Paint (image copied to clipboard and pasted into Paint............ The image is back-scattered. Nothing fancy, but it illustrates what can be done quite easily..........

Hi Malcolm,
I implemented a .CLR (Golden Software Surfer color palette) to .FC (PFE color palette) file convertor for you in the latest version of PFE:



Note that it uses the "interpolation" mode of the .FC file because the .CLR file can have 2 to 256 colors defined.

Have fun!
john

[gmorgan@ou.edu]

After acquiring an analog electron image with Acquire!|Imaging, how can one embed a scale on it that will be saved to the bitmap?
I just want to acquire a simple image and save it directly to bitmap with a scale bar (and perhaps analytical conditions), and not necessarily save it into a *.MDB or have to handle it with another program.

[Probeman]

After acquiring an analog electron image with Acquire!|Imaging, how can one embed a scale on it that will be saved to the bitmap?
I just want to acquire a simple image and save it directly to bitmap with a scale bar (and perhaps analytical conditions), and not necessarily save it into a *.MDB or have to handle it with another program.

Hi George,
There are several ways.  First, just click the Print Image button and print the image to a PDF. You'll have to first select Adobe PDF printer from the File | Print Setup menu though. Second, you can click the Copy To Clipboard button and then paste the image into any paint program, document editor, or presentation software as seen here:



But the best method I think is to set up everything the way you like it in the above Display, Export, etc Images dialog, and then use the Output | Save Images To BMP Files menu as seen here:



john

[gmorgan@ou.edu]

John,

I tried the Run|Display, Annotate option and the program didn’t see any image that wasn’t saved into the current database. So, to use this method I MUST save the image into a database (*.MDB), which I indicated in the previous message and post that I really didn’t want to have to do. I have several users that need images and EDXA, but don’t need WDS. To acquire the images on the same PC that hosts the EDXA (needed to imbed images in the EDXA reports quickly and easily) right now I have to create a database for each of them. Even so, it would be fairly easy to have a single simple database that allows me to acquire images for all such users, but then save the images with scale bars directly to BMP (or TIF, etc) without putting them in the data base, but apparently the software doesn’t allow that.?
 
So, after the Run|Display operation, to burn the scale bar into the image I must copy the image to the clipboard, and then paste it into another program in order to save it?  Unless I’m overlooking something basic, this is clumsy and will be very time consuming  (three operations to do a single task). It seems I should be able to save an image with info/scale bar to BMP (or TIF) format directly after acquisition with Automate!|Imaging, rather than subsequently have to pull it up in Run|Display, save it to clipboard, and then paste it into another program in order to save it.

Also, the information available to be included with the image seems limited – essentially just a scale bar and locations of any analyzed points on the picture (which for many users will be none). Just about any other operating system I’ve used allows a text field at the bottom to include a variety of information, for example scale bar, signal type, accelerating voltage, probe current, magnification, etc..

[John Donovan]

I tried the Run|Display, Annotate option and the program didn’t see any image that wasn’t saved into the current database. So, to use this method I MUST save the image into a database (*.MDB), which I indicated in the previous message and post that I really didn’t want to have to do. I have several users that need images and EDXA, but don’t need WDS. To acquire the images on the same PC that hosts the EDXA (needed to imbed images in the EDXA reports quickly and easily) right now I have to create a database for each of them. Even so, it would be fairly easy to have a single simple database that allows me to acquire images for all such users, but then save the images with scale bars directly to BMP (or TIF, etc) without putting them in the data base, but apparently the software doesn’t allow that.?

Hi George,
Of course, PFE can directly save an image to a file!   

First of all just as a reminder, PFE automatically saves all data to the MDB file, the one exception being video images because of course they can be large and usually one's first attempt needs some level adjustment, so that is why we have the Save To Database button there in the Imaging window for this purpose. And if you forget to save the image to the PFE database, the software will confirm that before it releases the information to "heat".  But normally we want to document everything!

That said, I can't see how creating a database just for saving images is onerous in any way!  It's just a click on the File | New menu, select a file, and click Ok, Ok. 

In any case, you do not have to first save your images to a PFE database (though why not?), because there is a Save As button as seen here that you can use to save your image to a file without saving it to the PFE database, though again- why not save it? Bits are cheap!



And as Gareth mentioned, the complete image conditions are saved to a .txt file with the same name.

Also, the information available to be included with the image seems limited – essentially just a scale bar and locations of any analyzed points on the picture (which for many users will be none). Just about any other operating system I’ve used allows a text field at the bottom to include a variety of information, for example scale bar, signal type, accelerating voltage, probe current, magnification, etc..

If you want PFE to save the image with a "databar", you will need to click the Save To Database button and then export it from the PFE database after selecting the Plot Data Bar checkbox as seen here:



Or perhaps even easier, just save all images to the PFE database and then just give your users the PFE database (and .BIM file).  They can download the PFE installer and then they can annotate and export to their hearts content!  And they can export dozens or hundreds of images in one click using the Output | Save Images To BMP Files menu as I mentioned above!

Now I know that you are trying to do this for SEM users that don't need any WDS data, but if that is the case, then just have then use the Thermo NSS application for simple video imaging!  I'd rather not try and compete in the SEM app world!

[Gseward]

George,

I have  a few users that have similar imaging-only needs, so I am somewhat familiar with the issue.  So, although you don't want to create a database, in reality you already have - because you have to create a database (and a sample) before the Imaging option is available.

All my users have a folder and I prefer to create a new .mdb for each user and each session; I like to think of this method as an excuse to not keep a lab notebook! If you don't want to archive the images in the database, or have a .mdb for each user, you might consider having a generic Imaging.mdb: Collect images for a given session, spew them all out it one go using Output | Save Images to BMP files, then next session simply create a new .mdb and overwrite the previous one. Seems like a shame to throw-away a good back-up (and the ability to modify the overlays in the future), but perhaps there are good reasons that one might not want to keep the .mdb.

Gareth

p.s. If you don't see the 'Plot Data Bar' checkbox  (shown in Johns post above) in your 'Display Probe Image Data' window, you will need to update PFE.

   

[gmorgan@ou.edu]

Yes, there is a Save As button, but that option doesn't save the scale bar or other information on the image.
So, still, to get an image with information a user can deal with, the stored image must be called up in the Run|Display option, copied to the clipboard, and pasted into another application, or else wait until the session is finished and export them all at once. When doing EDXA reports or images for more than one user in a session, this is still clumsy. I don't think it appropriate to make remote users in different parts of the world need to download the PFE installer in order to retrieve their images from a database; they come to me to get data, not work.
Why can't a button for "Save As with Overlay" be added? That way, regardless of whether the images are stored in the database, the operator doesn't have to stop what he/she is doing and perform gymnastics to get the results out in a format a client can make use of.

[John Donovan]

Yes, there is a Save As button, but that option doesn't save the scale bar or other information on the image.
So, still, to get an image with information a user can deal with, the stored image must be called up in the Run|Display option, copied to the clipboard, and pasted into another application, or else wait until the session is finished and export them all at once. When doing EDXA reports or images for more than one user in a session, this is still clumsy. I don't think it appropriate to make remote users in different parts of the world need to download the PFE installer in order to retrieve their images from a database; they come to me to get data, not work.
Why can't a button for "Save As with Overlay" be added? That way, regardless of whether the images are stored in the database, the operator doesn't have to stop what he/she is doing and perform gymnastics to get the results out in a format a client can make use of.

Hi George,
I thought you were trying to reduce your work load!?

So you'd rather have to click the OK button in the file Save As dialog, when saving each image for dozens or hundreds of images, than just click the Run | Output All Images To BMP Files menu one time?

I really don't see your point- why not just click the Output | Save All Images To BMP Files menu once when your imaging session is complete and then you'll automatically have the data bar and scale bar burned into each image exactly as you like...  are Gareth and I missing something here?
john