I am new in ITK. I wrote a small program to read image using sitk and display the image using imageJ.
import os
import SimpleITK as sitk
pathDicom = 'C://Users//clouds.png'
input = sitk.ReadImage(pathDicom)
sitk.Show( input , debugOn=True)
To link simpleITK to imageJ I set the environment variable. But I am getting following error for sitk.Show():
return _SimpleITK.Show(*args, **kwargs)
RuntimeError: Exception thrown in SimpleITK Show: C:\d\VS14-Win32-pkg\SimpleITK\Code\IO\src\sitkShow.cxx:580:
sitk::ERROR: Error in administrating child process: [Access is denied].
imageJ output is shown in the attached figure. Can someone tell what's the problem?
What version of SimpleITK are you running. It looks like it is not correctly finding the ImageJ executable. The 2nd line of the output shows that it's trying to execute 'C:\Users\Harish\fiji-win64\Fiji.app'. That's the Fiji directory, not the actual executable.
Can you try moving the Fiji.app directory to be directly inside your home directory? So move it up a directory to get rid of fiji-win64 in the path.
By default it searches there, so maybe the fiji-win64 directory is messing it up.
The other thing you can try is the SITK_SHOW_COMMAND environment variable. Set it to the full path of the ImageJ executable. That will override the search for ImageJ.
Related
Recently, I have been working on one of my python3 programs and then I wanted to to open a picture. Here is the code that I used to do it:
from PIL import Image
r = Image.open('C:/Users/sudam/OneDrive/Desktop/programming/python/projects/good night app/morning.png' )
r.show()
But as soon as I run this code,the windows photo viewer opens and gives and error saying that the specified file was moved. I tried googling this question but all of the answers I got only worked for python2, but not for python3.
Because you have whitespace in your path you need to use the r"string" format.
Also you need to use:
PIL.ImageShow.show(r)
to show your image.
It's also recommended to check if the file exist before opening any file.
You can do like this:
from pathlib import Path
from PIL import Image, ImageShow
path =r"C:/Users/sudam/OneDrive/Desktop/programming/python/projects/good night app/morning.png"
if Path(path).is_file():
r = Image.open(path)
ImageShow.show(r)
else:
print(f'{path} not exist')
I am trying to save sequence of predicted images into specific folder but its not working. Used below code and its running but not writing/saving the images into "results" folder.
save_image_path = f"results/{image_name}"
cv2.imwrite(save_image_path, cat_image)
Tried with full folder path also but its not working and error is occurring.
save_image_path = r'D:\Medical Imaging\Code\segmentation\results'
cv2.imwrite(save_image_path/{image_name}, cat_image)
Tried without extension and error is occurring.
save_image_path = r'D:\Medical Imaging\Code\segmentation\results'
cv2.imwrite(save_image_path, cat_image)
I am using pycharm IDE, Please suggest/guide if possible.
You need to spesify the file type ( ".jpg",".png",..) as;
save_image_path = f"results/{image_name}.jpg"
cv2.imwrite(save_image_path, cat_image)
I've read a couple other answers on this, but I'm still stuck. I imagine I'm doing something stupid, but this doesn't work:
import pytesseract
from PIL import Image
def tryTesseract(u):
return(pytesseract.image_to_string(Image.open(u)))
loc = 'C:\\Python\\Lineups\\558.png'
print(pytesseract)
print(tryTesseract(loc))
The first line prints:
<module 'pytesseract' from 'C:\Python\lib\site-packages\pytesseract\init.py'>
But the second prints several lines of error and culminates in:
pytesseract.pytesseract.TesseractNotFoundError: tesseract is not installed or it's not in your PATH. See README file for more information.
This seems weird if the first line works. I BELIEVE I have correctly added it to path though, and it is correctly installed, as in this screenshot:
Full error message:
Edited for exciting new error. I followed user3250052's advice and am now getting a new error (CMD window on top of Python window here:)
from PIL import Image
def tryTesseract(u):
return(pytesseract.image_to_string(Image.open(u)))
loc = os.path.join('C','Python','Lineups','558.png')
pytesseract.tesseract_cmd = r'C:\Program Files\Tesseract-OCR'
print(pytesseract)
print(tryTesseract(loc))```
That is a file not fond error.
Try
loc = os.path.join('C','Python','Lineups','558.png')
you might also need
pytesseract.tesseract_cmdloc = r'<full_path_to_your_tesseract_executable>'
Honest warning—I'm a total beginner.
I'm using Python 3.8.2 in IDLE and sometimes in Spyder.
My goal: to open an image (located in a folder) in Preview using Pillow
My code:
from PIL import Image
my_image = Image.open("flower.jpg")
my_image.show(r"/Users/User/Desktop/flower.jpg")
I run this, and it works! But it only works if the jpg is on the Desktop. I want to put the image in a folder. So I changed my last line of code to something like this:
my_image.show(r"/Users/User/Desktop/folder/flower.jpg")
I put the image in the folder, run the program, and get this error:
**FileNotFoundError: [Errno 2] No such file or directory: 'flower.jpg'**
Oddly, if I put the jpg back onto the Desktop and still use the path with "folder" in it, the program runs successfully and shows me the image.
Is this a problem with the path? How can I use Image.show() to open an image that is located somewhere other than the Desktop?
Thank you!
If you want to open and view an image using an absolute path, you'll have to change this line:
my_image = Image.open(path_to_image_dir)
You've incorrectly passed a string to PIL.Image.show. This doesn't throw an error, since PIL.Image.show happens to take an optional string parameter title, which it will use as a title in the image window. Don't pass any parameters to show, and change "flower.jpg" in the line above to the actual path.
I'm trying to read a jpg file using Pillow (Version 3.2.0) in Jupyter notebook (Python 3.4), but it fails with the following error:
OSError: broken data stream when reading image file
I'm using the following code:
from PIL import Image
im = Image.open("/path/to/image.jpeg")
im.show()
It works fine both in the interactive Python shell and using Python 2.7 instead of 3.4.
I've followed these steps already: Using Pillow with Python 3
Anyone an idea what's going on?
Looks like you're not pointing to the directory where your photo is stored.
import os
defaultWd = os.getcwd()
defaultWd # Sets your curretn wd
os.chdir(defaultWd + '\\Desktop') # Points to your photo--e.g., on Desktop
os.getcwd() # Shows change in wd
from PIL import Image
im = Image.open("Mew.jpg")
im.show() # Will plot to your default image viewing software
And another way if you don't want to change current wd:
im = Image.open(os.getcwd() + "\\Desktop\\Mew.jpg")
im.show()
And if you want to plot inline:
from matplotlib.pyplot import imshow
%matplotlib inline
inlinePic = Image.open(os.getcwd() + "\\Desktop\\Mew.jpg")
imshow(inlinePic)
Note: You may also want to simply try typing 'jpg' instead of 'jpeg' as you did above, if your image is in your current working directory. Also, if PIC is not installed, you'll get this error NameError: name 'Image' is not defined.
The problem was related to another import: I was importing Tensorflow before PIL, which caused the problem. Same issue as this one: https://github.com/scikit-image/scikit-image/issues/2000. Changing the order of the imports solved it.