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.
Quote from: Malcolm Roberts on March 02, 2015, 05:57:32 PM
1) Bitmaps exported including sample position points are exported without sample position points.
Hi Malcolm,
I assume you mean these controls?
(https://smf.probesoftware.com/oldpics/i59.tinypic.com/1z6efmh.jpg)
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:
(https://smf.probesoftware.com/oldpics/i62.tinypic.com/292wpx3.jpg)
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.
Quote from: Malcolm Roberts on March 02, 2015, 05:57:32 PM
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.
Quote from: Malcolm Roberts on March 02, 2015, 05:57:32 PM
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:
(https://smf.probesoftware.com/oldpics/i60.tinypic.com/2ni7ax2.jpg)
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!
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.
Quote from: Malcolm Roberts on March 12, 2015, 10:20:08 PM
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
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......
Quote from: Malcolm Roberts on March 15, 2015, 05:05:35 PM
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...
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.
Quote from: Malcolm Roberts on March 16, 2015, 05:41:04 PM
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:
(https://smf.probesoftware.com/oldpics/i62.tinypic.com/mmsutg.jpg)
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
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.
Quote from: gmorgan@ou.edu on June 10, 2015, 12:06:27 PM
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:
(https://smf.probesoftware.com/oldpics/i61.tinypic.com/2j2c55f.jpg)
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:
(https://smf.probesoftware.com/oldpics/i60.tinypic.com/15pibgz.jpg)
john
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..
Quote from: gmorgan@ou.edu on June 11, 2015, 11:53:57 AM
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!
(https://smf.probesoftware.com/oldpics/i61.tinypic.com/2s8o3v6.jpg)
And as Gareth mentioned, the complete image conditions are saved to a .txt file with the same name.
Quote from: gmorgan@ou.edu on June 11, 2015, 11:53:57 AM
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:
(https://smf.probesoftware.com/oldpics/i60.tinypic.com/292l505.jpg)
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!
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.
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.
Quote from: gmorgan@ou.edu on June 12, 2015, 05:12:10 AM
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
John/George
If I interpret correctly, the problem is that users want to place saved images in an (EDS?) Report as they go. George, is this the point???
Given what you describe, I assume that the user wants to use PFE Imaging as a Work-Around because the EDS hardware can't acquire an image? I imagine the PFE Imaging interface is designed to maximise efficiency and support operation of PFE, not to work as a generic Imaging platform, e.g. the ability to add/remove/modify important spatially referenced overlays etc. But in the spirit of Work-Arounds, here are a few suggestions:
1)You could use PeakSight Imaging? It works much like an SEM interface (of sorts).
2)You could screensnap the Imaging window and paste directly into report or into IrfanView:
-screen snap active Imaging window (rather than the desktop) is e.g. FN+ALT+PRNTSCN on my PC.
-If necessary Paste into report or Irfan (CTRL+V)
-'Save as' in Irfan (hit the S key)
Using this method, the important image parameters are retained in the panel on the left.
3)You could do similar to above, perhaps even a little faster, using a Windows7 Snip tool.
-open Snip.
-click NEW (only necessary for the second time around)
-drag
-CTRL+S to save.
4)You can use the Output | Save Images to BMP option at any time, not just the end.
-collect image
-Click Output
-Click Save Images to BMP (for the first image only you will need to set up desired overlays in Run | Display Images)
because all images are being output each time (~2 seconds per image), this will work OK unless you have lots and lots of images in one .mdb. If you get a message saying "can't paste to clipboard" just click the Cancel button at the bottom right of the log window, and try output again.
Perhaps non of the above is ideal but hopefully you can tolerate one of them until you can get EDS software imaging working.
Cheers,
Gareth
Hi George,
I still think the method of clicking the Save To Database button once for each image acquisition you want to save, and then clicking once at the end to automatically output all images to BMP files with the data bar and scale bar burned in as you want, is the easiest but Gareth's suggestions will also work.
Or how about just telling Cameca to get the darn tootin' external scan inputs working on your Sx100? That would make *everyone* happy!
Has Cameca explained to you why the external scan inputs don't work on your instrument?
john
Well, for many users I will want to use a single MDB to analyze multiple samples - say an experimental system in which multiple experiments are performed. If I wait until done and output the images in one batch from the MDB, won't the system give them image names based upon the MDB name and image in sequence rather than a sample name (and number in sequence) that I choose? (e.g., Expt#1-image#1, Expt#1-image#2, Expt#2-image#1, etc.)? So won't I then need to go back and rename all of the images (likely using a printed version for reference, if there are a lot of them) to something meaningful to the user, or perhaps just remove the name of the MDB for brevity? Talk about make-work. Admittedly, I have not yet seen what the options are for the filenames during batch export.
For a single experimental system, if I perform multiple sessions with a single MDB the batch output method would again export previously exported images. To avoid this I would need to create a new MDB for each session, but then all of the images will not be saved in the same database - so the databases as backups would not be easily searchable for a particular experiment number (I guess not a big deal), especially if the same experiment is looked at in more than one session (which does happen). So why not just be able to save each image to a chosen directory with a scale bar and a name I choose at the time of creation? (Okay, is it obvious I come from the olden times of DOS file names rather than thumbnails in a folder?)
As far as getting the scan issue solved, we still don't know the problem. I am still waiting (expected it last week) for a cable to allow connection of external scan control directly through the scanning board (I believe will bypass internal scanning). Until I get that, and some instruction, I may not know if the problem is with one or two control IC's on the scanning board, or if a whole new scanning board is needed (and/or if a service visit is needed). Now, if you want to send me ~$15K for a new scanning board and another ~$10-15K for a service call we might can get this solved quickly and without actual diagnosis. I guess it's still remotely possible, however, that we will never get external scan control....?
Quote from: gmorgan@ou.edu on June 16, 2015, 09:28:08 AM
Well, for many users I will want to use a single MDB to analyze multiple samples - say an experimental system in which multiple experiments are performed. If I wait until done and output the images in one batch from the MDB, won't the system give them image names based upon the MDB name and image in sequence rather than a sample name (and number in sequence) that I choose? (e.g., Expt#1-image#1, Expt#1-image#2, Expt#2-image#1, etc.)? So won't I then need to go back and rename all of the images (likely using a printed version for reference, if there are a lot of them) to something meaningful to the user, or perhaps just remove the name of the MDB for brevity? Talk about make-work. Admittedly, I have not yet seen what the options are for the filenames during batch export.
Hi George,
Good questions!
Of course you can analyze any number of samples and associated images in a single MDB file. That said, the Output | Save All Images To BMP Files menu automatically names the image file names based on both the image name and the sample name. To make this process as easy as possible be sure to try and name the image the same as the sample that you want associated with the image. This is easy if you create a new sample and then open the Imaging window, where it loads the image name based on the current sample.
Of course you can also double-click each image name in the image list and edit it to your heart's content!
But if you want to acquire all the images *before* you create the samples, be sure to name the images using the same name that you will utilize for the samples themselves. That way you can utilize this feature to "synchronize" the images with their associated samples as described in this post here:
http://smf.probesoftware.com/index.php?topic=138.msg559#msg559
I sometimes just create the digitized sample in the Automate! window (with or without any digitized points just yet), then I just click the Digitize Image button to automatically load the Imaging window with the image name loaded using the current automated sample name. On the other hand if you click the Imaging button from Acquire! it loads the image name with the current sample name. The software is trying to make this easy!
Quote from: gmorgan@ou.edu on June 16, 2015, 09:28:08 AM
For a single experimental system, if I perform multiple sessions with a single MDB the batch output method would again export previously exported images. To avoid this I would need to create a new MDB for each session, but then all of the images will not be saved in the same database - so the databases as backups would not be easily searchable for a particular experiment number (I guess not a big deal), especially if the same experiment is looked at in more than one session (which does happen). So why not just be able to save each image to a chosen directory with a scale bar and a name I choose at the time of creation? (Okay, is it obvious I come from the olden times of DOS file names rather than thumbnails in a folder?)
Hey, I resemble that remark! I come from the olden times of DOS myself!
Well, you can easily create a new MDB for each session using the Load File Setup button, and in the same folder (or not) as the previous MDB file. That way (in both cases) you won't be outputting the previously acquired images each time you output the new ones... hey you wanted flexible, you got flexible!
Quote from: gmorgan@ou.edu on June 16, 2015, 09:28:08 AM
As far as getting the scan issue solved, we still don't know the problem. I am still waiting (expected it last week) for a cable to allow connection of external scan control directly through the scanning board (I believe will bypass internal scanning). Until I get that, and some instruction, I may not know if the problem is with one or two control IC's on the scanning board, or if a whole new scanning board is needed (and/or if a service visit is needed). Now, if you want to send me ~$15K for a new scanning board and another ~$10-15K for a service call we might can get this solved quickly and without actual diagnosis. I guess it's still remotely possible, however, that we will never get external scan control....?
Sorry, I don't understand. You already have external scan generation in the Thermo box... Cameca just needs to fix the external scan inputs on your instrument, correct? What did Gareth and Edgar say? They're both real good at this type of troubleshooting...
Edit by John: just to clarify, since you are acquiring images in PFE using the Cameca internal scan generator and the Thermo scan generator is (presumably) working, the trouble must be between the Thermo cables and the Cameca scan coils. But I'm no hardware guy!
Someone recently asked about adding a scale bar to an already acquired image. Just use the Run | Display, Annotate and Export Analog Signal Image menu dialog as seen here:
(https://smf.probesoftware.com/gallery/1_13_09_20_9_36_43.png)
And if you want to save the displayed image with a scale bar, point labels, etc. just use the save To Clipboard button as seen here:
(https://smf.probesoftware.com/gallery/1_13_09_20_1_19_23.png)
Then paste it into any imaging app and then save it to any image format you prefer.
I use Paint dot net which is very easy to use and does all the image processing and editing things I need to do:
https://www.getpaint.net/
We recently add the pixel intensity value to the cursor:
(https://smf.probesoftware.com/gallery/1_05_03_25_1_48_31.png)
This was done to help us calibrate the WDS Bragg defocus correction here:
https://smf.probesoftware.com/index.php?topic=1545.msg13246#msg13246
But maybe someone else will find another use for this new feature!