imagej MER basics - Page 15

Previous 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 Next
Author Message

Posts: 1661

Reply: 281

PostPosted: April 13, 2013 1:21 PM 


Thanks for the past year on setting up the Rover 'imagej MER basics' thread...I certainly learned a lot of very useful data.

All the best with your new camera pics.

Take care,



Posts: xxx

Reply: 282

PostPosted: April 14, 2013 4:45 PM 

Hi Hort, thanks for all the great info. when I try to compile and run new pds reader I get there errors. Using ubuntu. Thanks

/home/rick/ImageJ/plugins/ class PDS_Reader_New is public, should be declared in a file named
public class PDS_Reader_New extends ImagePlus implements PlugIn {
/home/rick/ImageJ/plugins/ warning: [deprecation] write(java.lang.String) in ij.IJ has been deprecated
IJ.write(keyword +" = " + value); // display map scale value
1 error
1 warning


Posts: xxx

Reply: 283

PostPosted: April 14, 2013 8:01 PM 

I downloaded the old PDS reader class and put it in with plugins and I still get same message but it shows up in plugin menu now and seems to work ok. Thanks for all the Mars image help you have given us all!


Posts: xxx

Reply: 284

PostPosted: April 14, 2013 8:19 PM 

Well maybe not... When try to open .img says :This does not appear to be a PDS image file

Using EDR .img file from A notebook, is this the right data product to use?

Thanks for any insight


Posts: 3465

Reply: 285

PostPosted: April 15, 2013 10:50 AM 

Try recompiling the new reader again and ignore the message and see if it works. The problem may be O/S related. The code works fine under windows. I have never used Ubuntu.

The new version of the reader was written to read the Curiosity .img files. Once the Mastcam and MAHLI files are released ( especially the Bayer images ) I am sure I will have to modify it again.


Posts: 344

Reply: 286

PostPosted: April 15, 2013 11:26 AM 

Ubuntu is a version of the Linux OS that runs on the Mac platform.

Linux is case-sensitive. The problem may possibly be that the file name is spelled in upper-case, whereas the class PDS_Reader_New is spelled in mixed-case. Try renaming the file to be (mixed-case).


Posts: xxx

Reply: 287

PostPosted: April 15, 2013 1:45 PM 

Thanks Barsoomer that fixed it! Still get a warning:

/home/rick/ImageJ/plugins/PDS_Reader_New/ warning: [deprecation] write(java.lang.String) in ij.IJ has been deprecated
IJ.write(keyword +" = " + value); // display map scale value
1 warning

But the error message is gone and it opens the .img files now! Hope they release the MastCam and MAHLI data next release. Have to wonder why they were not "ready" to release them the 20th.

Thnaks for the cool plugin and macros Hort!


Posts: 250

Reply: 288

PostPosted: June 20, 2013 5:37 AM 

The "new reader" wont open Mastcam images (img) on my system (Navcam img raw data does work with the plugin).

Horton any ideas how to open this:\\data-cluster\pds-san\ANMSL\mslpub\data\mcam\00077\0077MR0005750060103781E01_DRCL.IMG

Thats the Sol 77 "Rocknest croc" raw image... Smile


Posts: 3465

Reply: 289

PostPosted: June 20, 2013 7:06 AM 

I will have a look at what changes were made to the file to allow Mastcam, MAHLI and MARDI images.


Posts: 3465

Reply: 290

PostPosted: June 20, 2013 3:24 PM 

_RGB_a - an imagej macro to convert an RGB image to false color image.


run("RGB Stack");
run("Stack to Images");
run("Multiply...", "value=255");
run("Enhance Contrast", "saturated=0.5");
run("Multiply...", "value=255.000000");
run("Enhance Contrast", "saturated=0.5");
run("Multiply...", "value=255.000000");
run("Enhance Contrast", "saturated=0.5");
run("Merge Channels...", "red=Red green=Green blue=Blue gray=*None*");


As per usual, copy the text between the "cut lines" into a .txt file and save to the imagej macro directory.


Posts: 3465

Reply: 291

PostPosted: June 20, 2013 5:07 PM 


Why is everything so %*$(ing complicated with "big science"?

First, the MSL dat files available at are also not readable with the imagej PDS reader plugin ( both EDR and RDR products). The image labels are NOT in the dat file but in separate .LBL extents

The .DAT file sizes are too small for anything but JPG files.

The corresponding EDR and RDR JPG files are in the "extras" directory:

Here is a comparison for the first file in sol 77:

from the MSL site:

from extras EDR:

from extras RDR:

The file sizes are all comparable in size: 203K for the MSL site, 229K from the extra EDR directory and 209K from the extra RDR directory.

The 12 bit data from the 1600x1200 CCD is about 2.75 MB - so the compression from the CCD to JPG is about 10x - ie, 90% of the data was thrown away.

Furthermore, the C software package provided to decode the DAT files clearly states in the documentation that lossless JPGs are NOT handled by the code. And if you compare the "original" test images with the decoded JPG images there are clearly differences.

A big yuk all around.

It doesn't look like any additional image quality will be gained from the PDS releases.

I will next have a look at what's available for the images I'm really interested in - RAW CCD RGGB Bayer images.

HOPEFULLY a straight forward 16 bit TIFF file of CCD readings will be provided. But, naah, it's NASA - and they know it.


Posts: 3465

Reply: 292

PostPosted: June 20, 2013 5:50 PM 

I forgot to mention a major difference between the EDR and RDR versions: The RDR has lens corrections ( vignetting and distortions ) and color corrections which get rid of the awful green tint of the EDR ( and MSL Raw ) images.

The RDR images are still not "white balanced". There is still a remaining very light red tint to the pictures - which gives the pictures a feeling of late aftermoon light before sunset on Earth - which I think is about right for Mars.


Posts: 3465

Reply: 293

PostPosted: June 20, 2013 7:59 PM 


The .DAT files are too small for a simple, uncompressed 12 bit RAW Bayer image. The PDL "extra" images are JPGs.

My "test" Bayer image.DAT file was 849K and the PDL RDR "extra" was a 225K JPG file.

My "test" Bayer image was from sol 19 and here is an animation comparing my Bayer processing with the PDS RDR Bayer to JPL image:

Here is a link to the comparison as an animated png file for those using Firefox. ( There are not-so-subtle color and banding differences caused by the 256 color limit in GIF files.)

I am much annoyed by this obfuscation of the data. I expected better.


Posts: xxx

Reply: 294

PostPosted: September 11, 2014 12:22 AM 

Does anyone know how to get rid of the small white vertical lines/dashes in this image.

Got rid of the small dots with despecal filter but what filter would you use to get ride of the dashes?


Posts: xxx

Reply: 295

PostPosted: September 11, 2014 12:27 AM 

Also anyone use Huggin and know what settings to use for pancam and Mastcam images?

I did a quick try and this is what I got.


Much better

Posts: xxx

Reply: 296

PostPosted: March 13, 2016 6:38 PM 

Having Hort's old post on the front page is better than that troll trash that was here!


Posts: 344

Reply: 297

PostPosted: May 11, 2016 2:05 AM 

Sometimes posts seem to get "stuck" on MRB and show up in the listing but seem to be missing when the page is opened. I have found that reloading the page URL with an '&' at the end can make the missing posts appear. But for some reason, this has to be done twice. For example loading

[link] & [link] &

should trigger any missing posts on this page.


Posts: xxx

Reply: 298

PostPosted: May 12, 2016 8:48 PM 

Testing again


Posts: 344

Reply: 299

PostPosted: May 12, 2016 10:38 PM 

Ok, to push out a stuck post on this page, I would enter

[link] &

in the address bar and load it. Then I would enter

[link] &

again and load it again. Then the stuck post shows up.

It might also work to click on this link
twice, which does the same thing.


Posts: 4

Reply: 300

PostPosted: May 13, 2016 6:55 AM 

That just worked for me Barsoomer I added & to the end of the url, let it reload and added & againg and reloaded and it pushed out the post

Previous 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 Next

Join the conversation:

Very Happy Smile Sad Surprised
Shocked Confused Cool Laughing
Mad Razz Embarassed Crying or Very Sad
Evil or Very Mad Twisted Evil Rolling Eyes Wink
Powered by MTSmileys