I am trying to read a medical imaging data which is in .tif format using Octave . It so happens that only software from https://fiji.sc/ has the ability to read the medical images I have. A sample of the image that I am referring is this one. This image is readable in.tif format only in fiji. The image can also be converted to jpg image. Only after data points is visible to other image editing software. Now the issue is , I want to load it into octave and read it - at the moment it is not possible. The imshow() function in octave is not allowing me to visualize the given .tif file.
So, if anybody has experience in reading such file formats please let me know. Thanks.
Your linked image is a 16bit grayscale image, see $ gm identify -verbose hello.tif. So lets load it into GNU Octave:
img = imread ("hello.tif");
hist (img(:), 200); # show histogram
Ah!, the main information of your image is in the range 0-600 (probably the image aquisition system used had 11 or 12bit resolution), so lets scale and print this part as color encoded (viridis) image:
imagesc (img, [0 600])
colorbar
Is this what you want? Of course we can also use a gray colormap, try: colormap gray
If this still doesn't fit your need you should really explain what you expect to see....
imread() relies on image magic to do the conversion, some versions of which can only read TIFF in 8-bit mode (giving a warning message), but when and how this happens I do not know.
It works for me using a .raw ṕicture converted to .tif in Fiji. I am specifically interested in several spectral analysis from my pictures which are taken illuminating with 660 and 850nm.
Related
New to Juypter, trying to use it with Latex. Everything works fine except for the images. I used this tutorial: https://www.youtube.com/watch?v=m3o1KXA1Rjk&t=149s
Png Images are fine in markdown, i.e
But LaTex cannot determine size of png images. If I save the image as pdf I get the same issue. If I save the image as eps then LaTex complains that it cannot convert eps to pdf.
Has anyone had this issue? Anyone know how to solve it?
PNG images always contain the size in pixels.
Optionally, they can include a chunk of data named pHYs. This contains the resolution of the image. If this chuck is present, you should be able to find the actual text pHYs in the file.
If this chunk is missing from the PNG file, the scale of the image can not be found.
If you are on a UNIX-like operating system you could use grep or hexdump to check for the text pHYs in the PNG file. The identify program from the ImageMagick suite also can display the resolution of PNG images.
Note that there is an error in the video. The author first uses latex and then pdflatex three times. That is not a good idea, since they have different capabilities w.r.t. graphics. Stick with pdflatex.
I am trying to open GeoTIFF file in ImageJ. It is opened as blank black image. But I want the view as its JPEG converted image. Please If anyone can help me. I want to process that image for Oil Spill Detection.
I would recommend using the Fiji distribution of ImageJ. It includes the Bio-Formats importer which supports a huge number of image formats. It looks like it has support for GeoTIFF tags, as well.
Also, sometimes images "look" black but aren't truly. See this FAQ entry.
I need to calculate the image width and height from the actual image file, so I'm reading the image with open file. so I have bunch of characters and numbers and everything that seems meaningless and they are presenting rgb information probably.
I just want to calculate the size of the image with the raw file information
I am programming in Erlang language but the code in any language will help as we are working with raw file as long as we don't use built-in libraries.
Thank you all in advance for help
I found the answer by going to details of each format,
So it works like this
JPG : you can find the width and height after the bytes "255,192,0,17,8" after that its the information for size
PNG : you can find it after "IHDR"
GIF : you can find it after "GIF89a"
there are information for more but this is the most common image types on internet
Thank you all for your time
I assume when you say 'raw' you mean you only have the pixel values.
In this case there isn't always a way to know the width and height.
Say you read 400 pixels. In this case a valid image side may be any whole factorization of 400, e.g. 1x400, 2x200, 4x100, 8x50, 20x20 etc. and transposed as well.
Not to mention the fact that many image formats include some padding for pixel rows that are not multiples of 4, 8 or 16...
The way it is coded in the image file depend on the image type, which hopefully is also coded in the image file. you can have a look at the question Getting Image size of JPEG from its binary for an example with JPEG coding.
If your data is unknown, use Octave and load the image. Then take a look at this page:
http://www.gnu.org/software/octave/doc/interpreter/Displaying-Images.html
for commands to display images. Hopefully with some manipulation it will work. This works for raw images, though there are specific decoders. Once you understand how the image is, you can write the equivalent C code.
I'm running Embedded Linux on an evaluation kit (Zoom OMAP35x Torpedo Development Kit). The board has an LCD and I would like to be able to take screen shots convert them into a gif or png. I can get the raw data by doing the following: "cp /dev/fb0 screen.raw", but I am stumped on how to convert the image into a gif or png format.
I played around with convert from ImageMagick (example: "convert -depth 8 -size 240x320 rgb:./screen.raw -swap 0,2 -separate -combine screen.png"), but have been unable to get an image that looks right.
Does anyone know of any other tools that I could try out? Or does anyone have tips for using ImageMagick?
Take a look at fbgrab, an application that does just that (it saves the framebuffer content as a png).
You can simply capture the framebuffer to a file and open it in any raw image viewer or try online eg: https://rawpixels.net/
cat /dev/fb0 > fbdump
It might not be possible / easy to do it directly with ImageMagick.
The Linux kernel 4.2 documentation https://github.com/torvalds/linux/blob/v4.2/Documentation/fb/api.txt#45 says:
Pixels are stored in memory in hardware-dependent formats. Applications need
to be aware of the pixel storage format in order to write image data to the
frame buffer memory in the format expected by the hardware.
Formats are described by frame buffer types and visuals. Some visuals require
additional information, which are stored in the variable screen information
bits_per_pixel, grayscale, red, green, blue and transp fields.
Visuals describe how color information is encoded and assembled to create
macropixels. Types describe how macropixels are stored in memory. The following types and visuals are supported.
A list of visuals and types follows, but the description is not enough for me to understand the exact formats immediately.
But it seems likely that it might not be a format that ImageMagick will understand directly, or at least you'd have to find out the used format to decide the ImageMagick options.
I'm looking for software to create PNG8 format transparent images as per this article.
NOTE: I need a Linux solution myself, but please submit answers for other OSes.
pngquant does a good job of converting to PNG8 while preserving full transparency.
If you're size-conscious, you may also be interested in pngcrush, which can usually (losslessly) compress PNG files quite a bit.
I also needed a Linux solution and found pngnq to do a pretty good job. It seems to be designed specifically for creating 8-bit PNG images with alpha channels.
apt-get install pngnq # If on Ubuntu/Debian
For Mac: ImageOptim and ImageAlpha are GUIs that run pngcrush, pngquant, and various other normally command-line compression utilities. http://pngmini.com/
The link you provided references ImageMagick, which is an excellent toolkit for manipulating images on Linux.
Ah, if I remember correctly, when I have read this article some months ago, pngquant hadn't a Windows version. I see it has one now. So I tried it, and pngnq too.
The latter seems to do a slightly better job on the IceAlpha.png test image (from libpng.org), at the cost of a slightly bigger image (it can be post-processed with pngcrush or pngout anyway).
The dithering algorithms (the two of pngquant, the only one of pngnq) are different, and it might be worth having both tools, converting images with all algorithms and see what looks the best.
For the record, on the Windows side, IrfanView (4.10) displays these images very well (using the transparency level on each palette entry) while XnView (1.85.1) and GIMP (2.4) apply only a full transparency/opaque display, à la GIF: the light bulb given as an example in the linked article has a transparent background around it, but the orange part is fully opaque.
And the excellent utility TweakPNG shows we have a PLTE (palette, 222 entries) chunk and a tRNS (alpha values for palette colors, 222 entries) chunk. Even more, it allows to edit each palette entry, color and alpha level. It might be an interesting complementary tool for this format.
Note on IrfanView support: if it handles PNG8 correctly for transparency, it doesn't handle gamma information in PNG files: on the toucan image or the ping-pong image, I had to apply a gamma of 2.4 to get similar (lighter) colors.
Note also that IrfanView does an awful job of converting 32-bit PNG images to 256, allowing only one transparent color, which looks bad if full color was dithered!
I see that the GIMP manual states: "his “PNG8” format, like GIF, uses only one bit for transparency; only two transparency levels are possible, transparent or opaque. "
while the ISO/W3C standard states:
"The tRNS chunk specifies either alpha values that are associated with palette entries (for indexed-colour images) or a single transparent colour (for greyscale and truecolour images).". The PNG specification 1.2 added: "Although simple transparency is not as elegant as the full alpha channel, it requires less storage space and is sufficient for many common cases."
It looks like the unique transparent color is more implemented than the full transparency palette, alas. At least browsers get it right.
It depends on what exactly your original images look like.
If your images already contain 256 or fewer colors (RGBA values), you need only look at pngout (Windows) (Linux/BSD/Mac OS X ports), which you should already be using to optimize your PNG images anyway. It can't quantize images, but it can save them as 8-bit, including alpha transparency. Just pass in the /c3 (or -c3 on Linux et al.) color option to force it to save the image as PNG8.
If your images do contain more than 256 colors, you have a few more, but all less than perfect options:
Adobe Fireworks is probably the best option in terms of the resulting image quality. It will do the job if you only need to convert a few images, or if you don't mind relying on Fireworks to do the batch processing. I did find that it sometimes somehow limits the number of colors in the palette, creating a worse quality image than necessary. I don't know if that's perhaps a bug in CS3 that's been fixed in CS4.
If you're not on Windows or OS X this obviously isn't an option, and buying Fireworks just for this probably isn't worth it either.
The only alternatives I know of are the already mentioned pngquant and pngnq. I've had better luck with pngnq, but that's probably just going to depend on which quantization strategy works best on the files you're working with.
Unfortunately, I've noticed that neither of them work very well with small amounts of transparency (say, an opaque image with transparent, rounded corners).
I recommend "The GIMP" as it is possible to output in PNG8 and supports Linux/Windows. If you want a quick Windows-only solution, I also recommend IrfanView.
Microsoft Windows: Ultimate Paint (freeware and shareware
versions are available).
Both versions can save as an 8 bit transparent PNG image.
It can also save as a 4 bit PNG (16 colours). This cuts the
file size in half compared to 8 bit.
Input formats include BMP, GIF, ICO, JPG/JPEG and PNG.
The freeware edition of Ultimate Paint Standard 2.88 LE can
be downloaded directly from
http://www.ultimatepaint.com/up.zip (1.7 MB).