Save PSD to JPG without invisible layers - python

I would like to export a PSD file for which we put some group layers as invisible to JPG.
Currently, I tried to put the concerned group layers as invisible (by looping through the PSD layers and put the concerned group as invisible like group.visible = False) and then save that PSD.
The saved new PSD does have the concerned group layers invisible.
Later, the new PSD is converted to JPG.
However, the JPG output shows also the invisible layers.
The python code used for passing from the new saved PSD to JPG is like the same for saving (we used psd_tools).
from psd_tools import PSDImage
image= PSDImage.open(PSDFilePath)
image.save(outputPath, "JPEG")
I have also tried with the command line "convert" on linux but it has also showed the invisible layers after conversion.
So, my question is to know whether there's a way to either remove invisible layers before saving to JPG within the same script without calling a script inside PhotoShop (which requires to open instances of PhotoShop) or export it to JPG without removing with a python code or maybe a command line.
I have found the last days something that does the trick from this StackOverflow Post by adding composite(force=True)
from psd_tools import PSDImage
image= PSDImage.open(PSDFilePath)
image.composite(force=True).save(outputPath) #outputPath is expected to be a JPG file
This is pretty good for light files. However, when the PSD's size is very large like 1GB, it takes too much time.
As I would like to execute this operation on a daily basis on about > 1000 files, this would take days to be done.
So, I am always looking for another solution.
Here's a sample to a lighter file, unfortunately, I could not put the real one for professional reasons.
https://file.io/yxdDxlzMeMsA

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Resizing .nii file in Python

I am trying to resize Nii files so that my program takes less computational resources, I want to rescale them from (240,240,155) to (120,120,155). I have tried using nilearn.image.resample_img module to do so however as it is seen the image below the output is not what I would expect. Need some help to figure this out.

How to get the image torchvision.utils.save_image saves, without reading it back from disk?

from torchvision.utils import save_image
...
save_image(im, f'im_name.png')
In my case (standard mnist), using code from here, im is a Tensor:96, and save_image works.
I want that image in memory to show it in other plots, and I don't want to read it back after saving it, which seems kind of stupid.
Is there a way to separate the functionality of generating the image and of saving it?
Edit
clarification:
I want an equivalent to
save_image(im, f'im_name.png')
reread = plt.imread(f'im_name.png')
without saving the image and reading it back.
I just want the image, and I want to save it later.
the save_image function does some work, like stacking multiple images into one, converting the tensor to images of correct sizes and so on. I want only that part without the saving to disk.
About 2 weeks later, I stumbled upon the solution by accident.
grid = torchvision.utils.make_grid(im)
grid will be the image save_image was just saving.

Reading tiffs in opencv swaps top and bottom third of image

I've got a pretty strange issue. I have several tif images of astronomical objects. I'm trying to use opencv's python bindings to process them. Upon reading the image file, it appears that segments of the images are swapped or rotated. I've stripped it down to the bare minimum, and it still reproduces:
img = cv2.imread('image.tif', 0)
cv2.imwrite('image_unaltered.tif', img)
I've uploaded some samples to imgur, to show the effect. The images aren't super clear, that's the nature of preprocessed astronomical images, but you can see it:
First set:
http://imgur.com/vXzRQvS
http://imgur.com/wig99KR
Second set:
http://imgur.com/pf7tnPz
http://imgur.com/xGn9C77
The same rotated/swapped images appear if I use cv2.imShow(...) as well, so I believe it's something when I read the file. Furthermore, it persists if I save as jpg as well. Opening the original in Photoshop shows the correct image. I'm using opencv 2.4.10, on Linux Mint 17.1. If it matters, the original tifs were created with FITS liberator on windows.
Any idea what's happening here?

Why the frames of a VideoClip change when it is written to a video file?

I wrote the following code:
from moviepy.editor import *
from PIL import Image
clip= VideoFileClip("video.mp4")
video= CompositeVideoClip([clip])
video.write_videofile("video_new.mp4",fps=clip.fps)
then to check whether the frames have changed or not and if changed, which function changed them, i retrieved the first frame of 'clip', 'video' and 'video_new.mp4' and compared them:
clip1= VideoFileClip("video_new.mp4")
img1= clip.get_frame(0)
img2= video.get_frame(0)
img3= clip1.get_frame(0)
a=img1[0,0,0]
b=img2[0,0,0]
c=img3[0,0,0]
I found that a=24, b=24, but c=26....infact on running a array compare loop i found that 'img1' and 'img2' were identical but 'img3' was different.
I suspect that the function video.write_videofile is responsible for the change in array. But i dont know why...Can anybody explain this to me and also suggest a way to write clips without changing their frames?
PS: i read the docs of 'VideoFileClip', 'FFMPEG_VideoWriter', 'FFMPEG_VideoReader' but could not find anything useful...I need to read the exact frame as it was before writing in a code I'm working on. Please, suggest me a way.
Like JPEG, MPEG-4 uses lossy compression, so it's not surprising that the frames read from "video_new.mp4" are not perfectly identical to those in "video.mp4". And as well as the variations caused purely by the lossy compression there are also variations that arise due to the wide variety of encoding options that can be used by programs that write MPEG data.
If you really need to be able to read back the exact same frame data that you write then you will have to use a different file format, but be warned: your files will be huge!
The choice of video format partly depends on what the image data is like and on what you want to do with it. If the data uses 256 colours or less, and you don't intend to perform transformations on it that will modify the colours, a simple GIF anim is a good choice. But bear in mind that even something like non-integer scaling modifies colours.
If you want to analyze the image data and transform it in various ways, it makes sense to use a format with better colour support than GIF, eg a stream of PNG images, which I assume is what Zulko mentions in his answer. FWIW, there's an anim format related to PNG called MNG, but it is not well supported or widely known.
Another option is to use a stream of PPM images, or maybe even a stream of YUV data, which is useful for certain kinds of analysis and convenient if you do intend to encode as MPEG for final consumption. The PPM format is very simple and easy to work with; YUV is slightly messy since it's a raw format with no header data, so you have to keep track of the image size and resolution data yourself.
The file size of PPM or YUV streams is large, since they incorporate no compression at all, but of course they can be compressed using standard compression techniques, if you want to save a little space when saving them to disk. OTOH, typical video processing workflows that use such streams often don't bother writing them to disk: they are sent in pipelines (perhaps using named pipes), so the file size is (mostly) irrelevant.
Although such formats take up a lot of space compared to MPEG-based files, they are far superior for use as intermediate formats while performing image data analysis and transformation, since every time you write & read back MPEG you are losing a little bit of quality.
I assume that you intend to do your image data analysis and transformations using PIL/Pillow. But you can also work with PPM & YUV streams using the ffmpeg / avconv command line programs; and the ffmpeg family happily work with sets of individual image files and GIF anims, too.
You can have lossless compression with the 'png' codec:
clip.write_videoclip('clip_new.avi', codec='png')
EDIT #PM 2Ring: when you write the line above, it makes a video that is compressed using the png algortihm (I'm not sure whether each frame is a png or if it's more subtle).

Python: Import multiple images from a folder and scale/combine them into one image?

I have a script to save between 8 and 12 images to a local folder. These images are always GIFs. I am looking for a python script to combine all the images in that one specific folder into one image. The combined 8-12 images would have to be scaled down, but I do not want to compromise the original quality(resolution) of the images either (ie. when zoomed in on the combined images, they would look as they did initially)
The only way I am able to do this currently is by copying each image to power point.
Is this possible with python (or any other language, but preferably python)?
As an input to the script, I would type in the path where only the images are stores (ie. C:\Documents and Settings\user\My Documents\My Pictures\BearImages)
EDIT: I downloaded ImageMagick and have been using it with the python api and from the command line. This simple command worked great for what I wanted: montage "*.gif" -tile x4 -geometry +1+1 -background none combine.gif
If you want to be able to zoom into the images, you do not want to scale them. You'll have to rely on the image viewer to do the scaling as they're being displayed - that's what PowerPoint is doing for you now.
The input images are GIF so they all contain a palette to describe which colors are in the image. If your images don't all have identical palettes, you'll need to convert them to 24-bit color before you combine them. This means that the output can't be another GIF; good options would be PNG or JPG depending on whether you can tolerate a bit of loss in the image quality.
You can use PIL to read the images, combine them, and write the result. You'll need to create a new image that is the size of the final result, and copy each of the smaller images into different parts of it.
You may want to outsource the image manipulation part to ImageMagick. It has a montage command that gets you 90% of the way there; just pass it some options and the names of the files in the directory.
Have a look at Python Imaging Library.
The handbook contains several examples on both opening files, combining them and saving the result.
The easiest thing to do is turn the images into numpy matrices, and then construct a new, much bigger numpy matrix to house all of them. Then convert the np matrix back into an image. Of course it'll be enormous, so you may want to downsample.

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