imagej MER basics - Page 2

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Author Message
Mizar


Posts: 692

Reply: 21



PostPosted: April 16, 2012 1:32 PM 

Haha the comment of the year "Readin' and chewing gum...." and a new world to discover i might add... this is great, thanks to our Horton.

Fred


Posts: 73

Reply: 22



PostPosted: April 16, 2012 2:59 PM 


I chewwin a little faster now...lol

Fred


Posts: 73

Reply: 23



PostPosted: April 16, 2012 6:07 PM 


Just to let my Professor know, I should have a couple hours tomorrow and again Wednesday. If I get jammed I will fire off questions.

I believe I speak for all when I say thank you for taking the time to instruct. Many I am sure will follow alone at home.

Thanks Brother

dx


Posts: 1661

Reply: 24



PostPosted: April 17, 2012 9:06 AM 

...a flickr try again

yt
dx

Fred


Posts: 73

Reply: 25



PostPosted: April 18, 2012 7:00 AM 


Flickr test...

Fred


Posts: 73

Reply: 26



PostPosted: April 18, 2012 7:03 AM 


Thats right!!! Thanks Professor Hort...Nothing to see here folks....

Fred


Posts: 73

Reply: 27



PostPosted: April 18, 2012 8:39 AM 

OK I went into macros. After stacking the images I get a standard R1 and AVG stack1 window open. When I prompted to record macros a window opened and I selected the R1 and avg stack. I then saved it to a folder. I got no image as of yet. Looks like some study of macros is in order. This may take a while.

Just wanted you to know where I am. The gum has been discarded.

hortonheardawho


Posts: 3465

Reply: 28



PostPosted: April 18, 2012 9:36 AM 

select Plugins / Macro / Record... immediately after the R1 and R2 file opens.

Then proceed with the processing - including the Image / Color / Stack to RGB command.

Your Macro should look something like this just before you save it:

------------------------------

run("16-bit");
run("Put Behind [tab]");
run("16-bit");
run("Images to Stack");
run("Multiply...", "stack value=255");
rename("R12");
run("Z Project...", "start=2 stop=2 projection=[Max Intensity]");
selectWindow("R12");
run("Z Project...", "start=1 stop=2 projection=[Average Intensity]");
selectWindow("R12");
run("Z Project...", "start=1 stop=1 projection=[Max Intensity]");
run("Images to Stack");
rename("RGB");
selectWindow("R12");
close();
run("Stack to RGB");
rename("R12");
selectWindow("RGB");
close();

---------------------------

Notice the use of the Image / Rename... command to "keep track" of intermediate processing windows.

Also notice the use of the Image / Type / 16 Bit command followed by a Process / Math / Multiply... by 255 to convert the images to 16 bit images. This is extremely useful for such manipulations as square root used in High Dynamic Range ( HDR ) images.

Fred


Posts: 73

Reply: 29



PostPosted: April 18, 2012 9:46 AM 

Do I type in those cammands on the first or second screen before or after I hit record.

Fred


Posts: 73

Reply: 30



PostPosted: April 18, 2012 10:00 AM 


Er.... that should be the "create" button....

dx


Posts: 1661

Reply: 31



PostPosted: April 18, 2012 2:01 PM 

horton>>>

I am trying to absorb your 17...with difficulty grabbing the images for the next step!

How many do I use in the stack and I am no where near understanding 'avg'.

Do all images in the stack have to look the same other than all 'L' or all 'R'?

Should I use Engineering Camera or the Science Camera?

Are we still working in the Pancam pics?

I am now at a standstill and slightly overwhelmed with data.

But I did get a flickr image up by following your instructions. That was a relief with thanks.

yt
dx

dx


Posts: 1661

Reply: 32



PostPosted: April 18, 2012 2:20 PM 

horton>>>

From your 20>>>Your assignment is to record, save and post your processing steps for creating a synthetic color image using the map:

(R, G, B ) = ( R2, avg(R1,R2), R1 )

Assume that the order the files have been opened is R1, R2.


How do you determine which image is R1 or R2 for each RGB?

I'm drawing a blank...other than looking at the JPL images [sub-frame EDR] and see 7 R-images[sol 2913]. Are these 7 to be stacked or just take any 2 as R1 and R2?

You mentioned in your 17 that there is no RGB in Pancam images...now what? Synthetic images are from the 'R' images as you stated.

I know to look at the 'R' images but that's it.

The AHAAAA has stopped!

yt
dx

Fred


Posts: 73

Reply: 33



PostPosted: April 18, 2012 3:11 PM 


When I hit pluggins/macros/run I get this error:

Macro or script not found
J/New folder2/R12.tex

dx


Posts: 1661

Reply: 34



PostPosted: April 18, 2012 3:30 PM 

Well here is the next assignment...took me awhile...did not realize there is a Z-Project name in the drop down...I was naming the file Z-Project to merge the R1 and R2 and then when inserted into the color merge got BLUE image...then also did not notice that R2 comes before R1 in the merge columns...I guess that gave me the Blue images.

Thanks horton...

yt
dx

dx


Posts: 1661

Reply: 35



PostPosted: April 18, 2012 3:34 PM 

...I will keep working these JPL files into something I am confident with or at least until I am confident to tackle the 'macro'.

That was 2.5 hours figuring that one out!!!

All the best horton.

yt
dx


Fred


Posts: 73

Reply: 36



PostPosted: April 18, 2012 3:42 PM 


Dang, break time, smok'em if you got'em...

Fred


Posts: 73

Reply: 37



PostPosted: April 18, 2012 3:54 PM 


Er...You mind posting your proceesing steps. It was afterall part of the assignment. I need help and aint too proud to ask...

dx


Posts: 1661

Reply: 38



PostPosted: April 18, 2012 4:36 PM 

Ok>>>

Using horton's steps for a SYNTHETIC' image that I was sure I was lost in...but I endured to get that image in my 34 above.

Went to the JPL site and opened the Pancam images.

Selected Sol 2913 and grabbed the first 2 R images. When you open the image and right click it will see the file has R1 way to the right. Save it.
And when you chose the next image beside it to open you will see R2 way to the right. Save it.

You now have the R1 and R2 images...I believe you can do this for all 7 R images that follow these 2 , which is what I am working on now-just to see what I get as a colored image.

Now you want to merge R1 and R2 to create the 'GREEN' -middle color in r G b.

So to do this open imagej.

Open your 2 saved R1 and R2 files. You will now have 2 neat looking images from the JPL site on your monitor.

Follow horton's step to merge the 2 images forming the 'GREEN' image in R 'G' B.

This merge forms the GREEN filter for the color dropdown next step.

R1 you have.
R2 you have.
avg you will have.

Now you have the formula: R1, avg[R1, R2] R2

But in Horton's 20 he says its: R2, avg[R1, R2] R1...somehow the R's are reversed positions-that's what through me off for I ended up with BLUE images. So I switched the 2 R's around and when merged in color got the correct image.

I also set Z-Projection to 'Average' Intensity. I played with that for several colored images and saw results I wouldn't publish.

For Color Merge I placed the R2 first as in horton's formula, then the Green merge you amde, then R1. I left the Gray as NONE...I'm playing with that too.

That's it.

Took me awhile but got it worked out.

yt
dx


Fred


Posts: 73

Reply: 39



PostPosted: April 18, 2012 5:03 PM 


I got the same thing using the formula. It had no imput from Macros or anything else. Seem like we left out what should somehow have been included....

hortonheardawho


Posts: 3465

Reply: 40



PostPosted: April 18, 2012 5:39 PM 

There was a little "gotcha" in the reply 28 problem: The order of the file opens was not "convenient" for a direct (R, G, B ) = (R2, avg(R1,R2), R1) map - so the "right" order was created with the Z Project commands:

run("Z Project...", "start=2 stop=2 projection=[Max Intensity]");
selectWindow("R12");
run("Z Project...", "start=1 stop=2 projection=[Average Intensity]");
selectWindow("R12");
run("Z Project...", "start=1 stop=1 projection=[Max Intensity]");

The "runs" in the macro in reply 28 is an exact sequence of menu clicks necessary to solve the problem.

Once you are familiar with the imagej command menu layout then the macros tell you exactly what you have to do.

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