So I went out and took some pictures of an eagle flying, and I thought they would have been great photos. But after getting home and loading the RAW image, and doing some editing, I exported the image to a .jpg, and I noticed a great amount of noise, particularly in the sky.
I used the following settings:
This is the picture on Flickr:
What went wrong? How do I fix it in the future?
Some of the below repeats parts of other answers. Apologies for that...
The higher the ISO, and the longer the shutterspeed, the more noise you're going to get.
Some cameras are better than others. Cameras with larger sensors tend to have lower noise and better high ISO performance. A high end full frame 35 mm DSLR with good high iso performance would make a big difference.
Given your current setup, shoot with the fastest lens you can get, with the lowest ISO you can. You might try using a larger aperture.
The good news is that the noisy parts of your image are out-of-focus.
If it were my shot I would open the raw image in Photoshop, select the bird and the tree, and then invert the selection to select the sky and apply moderate gaussian blur to the sky. That would hide the noise quite effectively. You could also use the same technique to select the sky and then apply a variety of other noise reduction techniques, but for an out-of-focus sky, blurring would be easy, effective, and give very natural-looking results.
I downloaded your image and took the liberty of doing what I describe. Here is a 100% crop of just the eagle so you can see the effect:
I would NOT use global noise-reduction software, as that tends to destroy detail in the parts of the image you want (the bird and the trees.)
In addition to Crowley's suggestions note that you can use noise reduction software selectively to improve the appearance of the image, while leaving the important detail alone. In your case I'd select the background and just do noise reduction on that.
Noise often is not as noticeable in prints as it is on screen. My experience is that software tends to exaggerate the appearance of noise and a print would not show it. Keep this in mind.
Also note that in images like these you often have to trade noise for a high shutter speed. Without the high shutter speed you get motion blur, so it's a tricky balance and sometimes you have to accept that the noise is a necessary evil. I'd agree with Crowley's observation that you could have used a slower shutter speed ( 1/1000th would have gained you two stop, which would equate to dropping ISO to about 200 where noise would be much reduced ).
What went wrong is that you underexposed the picture. The result you pulled from the raw file only used a portion of the sensor range. That amplified the noise, as if you were using a higher ISO setting.
In this case, 1/4000 second is rather extreme, although you haven't said how long the lens was or whether you had a tripod, vibration reduction, or something to lean the camera against.
As to how to fix this next time, that depends on what limits you were up against. I would look for ways to allow a longer shutter speed and a wider aperture. Using a tripod or vibration reduction could help with the shutter speed. Maybe twice the time wouldn't add significant blur even without changing anything. As for the f-stop, you don't really have a depth of field problem, so wider shouldn't cause much trouble with the picture you show.
Basically, give your sensor more light, and it's inherent noise will be less compared to the image light level.
The higher ISO you use, the higher amplification is used to calculate colour intensities. The higher amplification is used, the higher noise leaks to the resultin file.
You have several options to reduce noise next time:
From the EXIF file we can see that the maximum aperture available was F/6.3, this would have allowed you to reduce the ISO to about 400 at about the same shutter time. That would have reduced to noise quite a bit, perhaps at the expense of some unsharpness at the edges of the field of view. Noise reduction algorithms can be used to reduce the noise you are left with as mentioned in the other answers. An alternative method is to take a burst of many pictures, and then to do image stacking where you mask out the moving object, in this case the bird. When taking pictures of fast moving object you tend to take many pictures in quick succession, so you may have additional pictures of the background.
Using the free of charge program Hugin, you can align the pictures where you mask out the bird, align these and take the average to get rid of the noise in the background, and then add the bird back from one of the pictures.
There are lots of different post-processing tools for noise reduction available.
A great free noise reduction tool that I have been using is Dfine from Google's Nik Collection. You can find it here : https://www.google.com/nikcollection/products/dfine/
In addition to applying a slight gaussian blur, you might try applying some chroma noise reduction if you have the option. If you have the option, you could also reduce any applied sharpening. This may make the sky look more even on the whole, and if done in moderation won't detract from the detail of the eagle.
Here's an example with a 2.0px gaussian blur and a slight amount of chroma noise reduction using Photoshop and Camera Raw:
The image is oversharpened, which emphasizes the noise. Blue usually contains most noise, so your sky appears noisy. Turn down the global sharpening and sharpen the bald eagle locally. If that is not enough, reduce noise in the blue channel or selected sky.
If i understand your question correctly, you are asking what you should do differently during the shooting: Make sure you capture the bird in a way that does not require additional sharpening. That may require a better lens, better AF, fast sequence where you can select the best shot, better technique...
Zooming in on the eagle, it looks like the image underwent significant sharpening because the eagle has a 'halo'. Sharpening the image might also introduce the sort of grain that appears in the blue patch when the algorithm tries to enhance detail that isn't there.
Sometimes these effects are considered an over-sharpening of the image. Sharpening is probably best done with a strong consideration of the scale at which the image will be viewed. The 'grain' and 'halo' in the photo are less noticeable when displayed at a small size.
The best way to 'fix' the problem is to avoid it by applying sharpening more selectively. Perhaps using masks or simply using less sharpening. Non-descructive RAW editors such as Lightroom, Rawtherapee, and Darktable make playing around and experimenting with settings easier (in so far as not changing the original image makes changes reversible).
