I am working on a dataset that has two features, real and imaginary impedances. I applied data-to-image conversion using MTF in order to represent each one as an image (50x50). I was thinking of creating a 3-D image (50x50x2). I tried doing
Image = np.array([tag_gadf_re[0],tag_gadf_im[0]])
where tag_gadf_re[0] and tag_gadf_im[0] are the real and imaginary impedance image arrays. However, I tried saving the image using:
plt.imsave("Directory", Image)
However, I am getting the following error:
ValueError: Third dimension must be 3 or 4
Also note that the shape of Image is (2x50x50), when it should be (50x50x2). The solution seems simple, but I am a bit lost in the process. How can I combine both arrays appropriately and save the image, or do I need a 3rd layer in order to appropriately represent it as an RGB image?
If you want to store data as an image you need to be aware of its type and range so that you can choose an appropriate format. You also need to be aware of whether you can tolerate a "lossy" format which, when read, will not return identical values to those you stored.
If your data is integer and 16-bit or less, you can store it in a PNG. If it's multi-channel and 16-bit, you'll come unstuck with PIL. You can use tifffile though to store a 2-channel TIFF - maybe that can be greyscale + transparency or maybe 2 IFDs.
If your data is floating point, you pretty much have to use TIFF, PFM or EXR format. Again, tifffile can do this for you.
tifffile is here.
wand can also do whatever tifffile can do.
Of course, you might choose to represent your two arrays/images as one above the other in a double-height image. It's your data.
Related
I am working on bayer raw(.raw format) image domain where I need to edit the pixels according to my needs(applying affine matrix) and save them back .raw format.so There are two sub-problems.
I am able to edit pixels but can save them back as .raw
I am using a robust library called rawpy that allows me to read pixel values as numpy array, while I try to save them back I am unable to persist the value
rawImage = rawpy.imread('Filename.raw') // this gives a rawpy object
rawData = rawImage.raw_image //this gives pixels as numpy array
.
.//some manipulations performed on rawData, still a numpy array
.
imageio.imsave('newRaw.raw', rawData)
This doesn't work, throws error unknown file type. Is there a way to save such files in .raw format.
Note: I have tried this as well:-
rawImageManipulated = rawImage
rawImageManipulated.raw_image[:] = rawData[:] //this copies the new
data onto the rawpy object but does not save or persists the values
assigned.
Rotating a bayer image - I know rawpy does not handle this, nor does any other API or Library acc to my knowledge. The existing image rotation Apis of opencv and pillow alter the sub-pixels while rotating. How do I come to know? After a series of small rotations(say,30 degrees of rotation 12 times) when I get back to a 360 degree of rotation the sub-pixels are not the same when compared using a hex editor.
Are there any solutions to these issues? Am I going in the wrong direction? Could you please guide me on this. I am currently using python i am open to solutions in any language or stack. Thanks
As far as I know, no library is able to rotate an image directly in the Bayer pattern format (if that's what you mean), for good reasons. Instead you need to convert to RGB, and back later. (If you try to process the Bayer pattern image as if it was just a grayscale bitmap, the result of rotation will be a disaster.)
Due to numerical issues, accumulating rotations spoils the image and you will never get the original after a full turn. To minimize the loss, perform all rotations from the original, with increasing angles.
I am a bit confused about when an image is gamma encoded/decoded and when I need to raise it to a gamma function.
Given an image 'boat.jpg' where the colour representation is labeled 'sRGB'. My assumption is that the pixel values are encoded in the file by raising the arrays to ^(1/2.2) during the save process.
When I import the image into numpy using scikit-image or opencv I end up with a 3-dim array of uint8 values. Do these values need to be raised to ^2.2 in order to generate a histogram of the values, or when I apply the imread function, does that map the image into linear space in the array?
from skimage import data,io
boat = io.imread('boat.jpg')
if you get your image anywhere on the internet, it has gamma 2.2.
unless the image has an image profile encoded, then you get the gamma from that profile.
imread() reads the pixel values 'as-is', no conversion.
there's no point converting image to gamma 1.0 for any kind of the processing, unless you specifically know that you have to. basically, nobody does that.
As you probably know, skimage uses a handful of different plugins when reading in images (seen here). The values you get should not have to be adjusted...that happens under the hood. I would also recommend you don't use the jpeg file format because you lose data with the compression.
OpenCV (as of v 4) usually does the gamma conversion for you, depending on the image format. It appears to do it automatically with PNG, but it's pretty easy to test. Just generate a 256x256 8-bit color image with a linear color ramps along x and y, then check to see what the pixel values at given image coords. If the sRGB mapping/unmapping is done correctly at every point, x=i should have pixel value i and so on. If you imwrite to PNG in OpenCV, it will convert to sRGB, tag that in the image format, and GIMP or whatever will happily decode it back back to linear.
Most image files are stored as sRGB, and there's a tendency for most image manipulation APIs to handle it correctly, since well, if they didn't, they'd work wrong most of the time. In the odd instance where you read an sRGB file as linear or vice versa, it will make a significant difference though, especially if you're doing any kind of image processing. Mixing up sRGB and linear causes very significant problems, and you will absolutely notice it if it gets messed up; fortunately, the software world usually handles it automagically in the file read/write stage so casual app developers don't usually have to worry about it.
I am saving images using
import matplotlib.pyplot as plt
plt.imsave(img_path,img_arr,cmap = 'gray') #shape (512,512)
...
img = plt.imread(img_path)
and the img.shape returns a (512,512,4) whereas i expect it to only be (512,512).
I thought maybe all the channels would be the same so I could just pick one but np.allclose(img[:,:,0],img_arr)
returns false no matter which index I choose. Printing the images, they are indeed the correct ones I am comparing as they do look almost identical(by eye), but are obviously not exactly identical.
I also tried saving the images with cv2 but that seems to save a black box for some reason. loading them with cv2.imread(img_path,0) does return a (512,512) array but something seems to be lost because again, np.allclose() tells me they're different.
I wanted to know if there is a good way to save grayscale images? Every method I try seems to convert it to RBG or RGBA which is really annoying. Also, I would like to preserve the dtype (int16) of the image as downsampling it loses important information.
Thanks in advance.
You cannot preserve a bit depth of 16 bit when saving images with matplotlib with any of the default colormaps which only have 256 colors (=8 bit).
And in addition, matplotlib converts the pixel values to floats, which may be a source for rounding errors.
In total, matplotlib does not seem to be the optimal tool in case you need to get perfect accuracy.
That being said, even PIL does not seem to allow for 16 bit single channel pngs. There is a possible solution in this question, but I haven't tested it.
In any case a bulletproof way to save your array without accuracy loss is to save it with numpy, np.save("arr.npy", im_arr).
I have a large 2D array (4000x3000) saved as a numpy array which I would like to display and save while keeping the ability to look at each individual pixels.
For the display part, I currently use matplotlib imshow() function which works very well.
For the saving part, it is not clear to me how I can save this figure and preserve the information contained in all 12M pixels. I tried adjusting the figure size and the resolution (dpi) of the saved image but it is not obvious which figsize/dpi settings should be used to match the resolution of the large 2D matrix displayed. Here is an example code of what I'm doing (arr is a numpy array of shape (3000,4000)):
fig = pylab.figure(figsize=(16,12))
pylab.imshow(arr,interpolation='nearest')
fig.savefig("image.png",dpi=500)
One option would be to increase the resolution of the saved image substantially to be sure all pixels will be properly recorded but this has the significant drawback of creating an image of extremely large size (at least much larger than the 4000x3000 pixels image which is all that I would really need). It also has the disadvantage that not all pixels will be of exactly the same size.
I also had a look at the Python Image Library but it is not clear to me how it could be used for this purpose, if at all.
Any help on the subject would be much appreciated!
I think I found a solution which works fairly well. I use figimage to plot the numpy array without resampling. If you're careful in the size of the figure you create, you can keep full resolution of your matrix whatever size it has.
I figured out that figimage plots a single pixel with size 0.01 inch (this number might be system dependent) so the following code will for example save the matrix with full resolution (arr is a numpy array of shape (3000,4000)):
rows = 3000
columns = 4000
fig = pylab.figure(figsize=(columns*0.01,rows*0.01))
pylab.figimage(arr,cmap=cm.jet,origin='lower')
fig.savefig("image.png")
Two issues I still have with this options:
there is no markers indicating column/row numbers making it hard to know which pixel is which besides the ones on the edges
if you decide to interactively look at the image, it is not possible to zoom in/out
A solution that also solves the above 2 issues would be terrific, if it exists.
The OpenCV library was designed for scientific analysis of images. Consequently, it doesn't "resample" images without your explicitly asking for it. To save an image:
import cv2
cv2.imwrite('image.png', arr)
where arr is your numpy array. The saved image will be the same size as your array arr.
You didn't mention the color-model that you are using. Pngs, like jpegs, are usually 8-bit per color channel. OpenCV will support up to 16-bits per channel if you request it.
Documentation on OpenCV's imwrite is here.
Using Python's PIL module, we can read an digital image into an array of integers,
from PIL import Image
from numpy import array
img = Image.open('x.jpg')
im = array(img) # im is the array representation of x.jpg
I wonder how does PIL interpret an image as an array? First I tried this
od -tu1 x.jpg
and it indeed gave a sequence of numbers, but how does PIL interpret a color image into a 3D array?
In short, my question is that I want to know how can I get a color image's array representation without using any module like PIL, how could do the job using Python?
Well, it depends on the image format I would say.
For a .jpg, there is a complete description of the format that permits to read the image .
You can read it here
What PIL does is exactly what you did at first. But then it reads the bytes following the specifications, which allow it to transform this into a human readable format (in this case an array).
It may seem complex for JPEG, but if you take png (the version without compression) everything can seem way more simple.
For example this image
If you open it, you will see something like that :
You can see several information on top that corresponds to the header.
Then you see all those zeroes, that are the numerical representation of black pixels of the image (the top left corner).
If you open the image with PIL, you will get an array that is mostly filled with 0.
If you want to know more about the first bytes, look at the png specifications chapter 11.2.2.
You will see that some of the bytes corresponds to the width and height of the image. This is how PIL is able to create the array :).
Hope this helps !
Depends on the color mode. In PIL an image is stored as a list of integers with all channels interleaved on a per-pixel basis.
To illustrate this:
Grayscale image: [pixel1, pixel2, pixel3, ...]
RGB: [pixel1_R, pixel1_G, pixel1_B, pixel2_R, pixel_2_G, ...]
Same goes for RBGA and so on.