I'm trying to open a zipped nifty file using nibabel library (as nib) and the following code:
img = nib.load (nifti_file)
img_data = img.get_data ()
where nifti_file is a variable with the path to the file in the same directory.
On the second line, there is an out-of-memory error that happens 60% of the time randomly while I try running those two lines.
I have enough memory space on my computer so I'm not sure why this happens and also as I mentioned sometimes it simply works.
Related
I am using the keras.preprocessing.image ImageDataGenerator to stream images from a folder on my hard drive. It works mostly, but the code randomly throws an error when accessing images. The error message looks like this:
img = pil_image.open(path)
File "C:\Program Files\Anaconda3\envs\py35_cv2_nb_tf\lib\site-packages\PIL\Image.py", line 2452, in open
% (filename if filename else fp))
OSError: cannot identify image file 'd:/workspace/cat_dog/train\\cats\\666.jpg'
But I think it is misleading, since:
sometimes it goes through the whole batch without any problem. When the crash occurs, it always happens at a different image.
there is nothing obviously wrong with the cat666 image
but after the crash, the file remains locked
Any ideas? I have already removed all meta-data from the images.
You should use your path string variable as raw string, use r as prefix to evaluate the variable as raw string.
path = r'd:/workspace/cat_dog/train/cats666.jpg'
I would like to read a tif file with basically the following code:
import matplotlib.pyplot as plt
filename = 'test.tif'
plt.imread(filename)
This results in the following error message (just the last lines):
File ".../miniconda2/lib/python2.7/site-packages/PIL/Image.py", line 692, in tobytes
self.load()
File ".../miniconda2/lib/python2.7/site-packages/PIL/TiffImagePlugin.py", line 1013, in load
return super(TiffImageFile, self).load()
File ".../miniconda2/lib/python2.7/site-packages/PIL/ImageFile.py", line 204, in load
decoder.setimage(self.im, extents)
ValueError: tile cannot extend outside image
When I open the tif image with imagemagick's display and save it without making changes, everything works normally.
Nevertheless, I think it could a problem with my python environment/version, as my colleague who's working with the same code and the same files did not have this problem.
I tried many files and it ends in the same for all of them. I am aware that, for this mini example, I could make a workaround or use e.g. gdal (which works fine). But as these lines are just a part of a larger code and are supposed to work for new files immediately, I would like to have a real solution.
I am working with openSUSE 11.4, conda 4.3.23, Python 2.7.13, matplotlib 2.0.2 .
This could be a duplicate of Value Error in reading tif image with pil in python?. Due to the lack of specific information there, I open a new question. Sorry if that's the wrong way - my first post here...
Remark: I see that my tif file gets uploaded as png here. Is there a way to change that?
I am writing a simple program that reads and does some operations with a series of images. One of the input images has some faults (I think it's the result of disconnecting thumb drive during data transfer).
So the only statement involving the input image that does not cause the program to freeze is cv2.imread(). The moment my program reaches any statement that involves the input, it freezes. I tried putting these statements in try-catch blocks (so that error is thrown and this image is skipped) but nothing changes. Is there anything I can do to make my program see the error in the input then ignore it and go to the next image instead of freezing?
As per OpenCV doc:
The function imread loads an image from the specified file and returns it. If the image cannot be read (because of missing file, improper permissions, unsupported or invalid format), the function returns an empty matrix ( Mat::data==NULL ).
Therefore, just check for None value, for example:
for fname in fnames:
img = cv2.imread(fname)
if img is None:
continue
# Do your processing here
I'm not entirely sure why this is happening but I am in the process of making a program and I am having tons of issues trying to get opencv to open images using imread. I keep getting errors saying that the image is 0px wide by 0px high. This isn't making much sense to me so I searched around on here and I'm not getting any answers from SO either.
I have taken about 20 pictures and they are all using the same device. Probably 8 of them actually open and work correctly, the rest don't. They aren't corrupted either because they open in other programs. I have triple checked the paths and they are using full paths.
Is anyone else having issues like this? All of my files are .jpgs and I am not seeing any problems on my end. Is this a bug or am I doing something wrong?
Here is a snippet of the code that I am using that is reproducing the error on my end.
imgloc = "F:\Kyle\Desktop\Coinjar\Test images\ten.png"
img = cv2.imread(imgloc)
cv2.imshow('img',img)
When I change the file I just adjust the name of the file itself the entire path doesn't change it just refuses to accept some of my images which are essentially the same ones.
I am getting this error from a later part of the code where I try to use img.shape
Traceback (most recent call last):
File "F:\Kyle\Desktop\Coinjar\CoinJar Test2.py", line 14, in <module>
height, width, depth = img.shape
AttributeError: 'NoneType' object has no attribute 'shape'
and I am getting this error when I try to show a window from the code snippet above.
Traceback (most recent call last):
File "F:\Kyle\Desktop\Coinjar\CoinJar Test2.py", line 11, in <module>
cv2.imshow('img',img)
error: ..\..\..\..\opencv\modules\highgui\src\window.cpp:261: error: (-215) size.width>0 && size.height>0 in function cv::imshow
Probably you have problem with special meaning of \ in text - like \t or \n
Use \\ in place of \
imgloc = "F:\\Kyle\\Desktop\\Coinjar\\Test images\\ten.png"
or use prefix r'' (and it will treat it as raw text without special codes)
imgloc = r"F:\Kyle\Desktop\Coinjar\Test images\ten.png"
EDIT:
Some modules accept even / like in Linux path
imgloc = "F:/Kyle/Desktop/Coinjar/Test images/ten.png"
From my experience, file paths that are too long (OS dependent) can also cause cv2.imread() to fail.
Also, when it does fail, it often fails silently, so it is hard to even realize that it failed, and usually something further the the code will be what sparks the error.
Hope this helps.
Faced the same problem on Windows: cv.imread returned None when reading jpg files from a subfolder. The same code and folder structure worked on Linux.
Found out that cv.imread processes the same jpg files, if they are in the same folder as the python file.
My workaround:
copy the image file to the python file folder
use this file in cv.imread
remove redundant image file
import os
import shutil
import cv2 as cv
image_dir = os.path.join('path', 'to', 'image')
image_filename = 'image.jpg'
full_image_path = os.path.join(image_dir, image_filename)
image = cv.imread(full_image_path)
if image is None:
shutil.copy(full_image_path, image_filename)
image = cv.imread(image_filename)
os.remove(image_filename)
...
I had i lot of trouble with cv.imread() not finding my Image. I think i tryed everything involving changing the path. The os.path.exists(file_path) function also gave me back a True.
I finaly solved the problem by loading the images with imageio.
img = imageio.imread('file_path')
This also loads the img in a numpy array and you can use funktions like cv.matchTemplate() on this object. But i would recomment if u are doing stuff with multiple images that you then read all of them with imageio because i found diffrences in the arrays produced by .imread() from the two libs (opencv, imageio) on a File both of them could open.
I hope i could help someone
Take care to :
try imread() with a reliable picture,
and the correct path in your context like (see Kyle772 answer). For me either //or \.
I lost a couple of hours trying with 2 images saved from a left click in a browser. As soon as I took a personal camera image, it works fine.
Spyder screen shot
#context windows10 / anaconda / python 3.2.0
import cv2
print(cv2.__version__) # 3.2.0
imgloc = "D:/violettes/Software/Central/test.jpg" #this path works fine.
# imgloc = "D:\\violettes\\Software\\Central\\test.jpg" this path works fine also.
#imgloc = "D:\violettes\Software\Central\test.jpg" #this path fails.
img = cv2.imread(imgloc)
height, width, channels = img.shape
print (height, width, channels)
python opencv image-loading imread
I know that the question is already answered but in case anybody still is not able to load images with imread. It may be because there are letters in the string path witch imread does not accept.
For exmaple umlauts and diacritical marks.
My suggestion for everyone facing the same problem is to try this:
cv2.imshow("image", img)
The img is keyword. Never forget.
When you get error like this AttributeError: 'NoneType' object has no attribute 'shape'
Try with new_image=image.copy
I need open an image, verify the image, then reopen it (see last sentence of below quote from PIL docs)
im.verify()
Attempts to determine if the file is broken, without actually decoding
the image data. If this method finds any problems, it raises suitable
exceptions. This method only works on a newly opened image; if the
image has already been loaded, the result is undefined. Also, if you
need to load the image after using this method, you must reopen the
image file.
This is what I have in my code, where picture is a django InMemoryUploadedFile object:
img = Image.open(picture)
img.verify()
img = Image.open(picture)
The first two lines work fine, but I get the following error for the third line (where I'm attempting to "reopen" the image):
IOError: cannot identify image file
What is the proper way to reopen the image file, as the docs suggest?
This is no different than doing
f = open('x.png')
Image.open(f)
Image.open(f)
The code above does not work because PIL advances in the file while reading its first few bytes to (attempt to) identify its format. Trying to use a second Image.open in this situation will fail as noted because now the current position in the file is past its image's header. To confirm this, you can verify what f.tell() returns. To solve this issue you have to go back to the start of the file either by doing f.seek(0) between the two calls to Image.open, or closing and reopening the file.
Try doing a del img between the verify and second open.