I am trying to read a dicom header tag in dicom file.
Now, there are two ways to read this dicom header tag.
1) Using pydicom package in python which apparently is not working well on my python installed version(python 3).
2) or when i call AFNI function 'dicom_hinfo' through command line, i can get dicom tag value. The syntax to call afni function in terminal is as follows:
dicom_hinfo -tag aaaa,bbbb filename.dcm
output:fgre
Now how should i call this dicom-info -tag aaaa,bbbb filename.dcm in python script.
I guess subprocess might work but not sure about how to use it in this case.
To get output from a subprocess, you could use check_output() function:
#!/usr/bin/env python
from subprocess import check_output
tag = check_output('dicom_hinfo -tag aaaa,bbbb filename.dcm output:fgre'.split(),
universal_newlines=True).strip()
universal_newlines=True is used to get Unicode text on Python 3 (the data is decoded using user locale's character encoding).
check_output() assumes that dicom_hinfo prints to its standard output stream (stdout). Some utilities may print to stderr or the terminal directly instead. The code could be modified to adapt to that.
Oh this was due to syntax error using Pydicom.
I wanted to access 0019, 109c tag.
Syntax should be:
ds[0x0019,0x109c].value.
not ds[aaaa,bbbb].value
Related
So, I'm writing a basic python script to use youtube-dl to download a highquality thumbnail from a video. With the command line youtube-dl, you can run "youtube-dl --list-thumbnails [LINK]" and it will output a list of different quality links to the thumbnail images. Usually the highest resolution one has 'maxresdefault' in its link. I want to be able to download this image from the command line with wget. This is the code I have so far to achieve it. I'm not familiar with regex, but according to this site: regexr.com, it should have a match in the link with 'maxresdefault'.
import subprocess
import sys
import re
youtubeoutput = subprocess.call(['youtube-dl', '--list-thumbnails', 'https://www.youtube.com/watch?v=t2U2mUtTnzY'], shell=True, stdout=subprocess.PIPE)
print(str(youtubeoutput))
imgurl = re.search("/maxresdefault/g", str(youtubeoutput)).group(0)
print(imgurl)
subprocess.run('wget', str(imgurl))
I put the print statements in there to see what the outputs were. When I run the code, I can see the youtube-dl doesn't recognize a link being in there. youtube-dl: error: You must provide at least one url. Since there's no links in the output, the re.search becomes a NoneType and it gives me an error. I don't know why youtube-dl won't recognize the link. I'm not even sure it recognizes the --list-thumnails. Could anyone help?
You've asked subprocess to use a shell (shell=True), so you would usually pass an entire command to call, like so:
youtubeoutput = subprocess.call("youtube-dl --list-thumbnails https://www.youtube.com/watch?v=t2U2mUtTnzY", shell=True, stdout=subprocess.PIPE)
But really, you may not need a shell. Try something like:
youtubeoutput = subprocess.check_output(['youtube-dl', '--list-thumbnails', 'https://www.youtube.com/watch?v=t2U2mUtTnzY'])
Note that call does not actually return the program's standard output; check_output does.
Reference
I'm confused on how exactly we should use the python sh library, specifically the sh.Command(). Basically, I wish to pass input_file_a to program_b.py and store its output in a different directory as output_file_b, how should I achieve this using the sh library in python?
If you mean input and output redirection, then see here (in) and here (out) respectively. In particular, looks like to "redirect" stdin you need to pass as argument the actual bytes (e.g. read them beforehand), in particular, the following should work according to their documentation (untested, as I don't have/work with sh - please let know if this works for you / fix whatever is missing):
import sh
python3 = sh.Command("python3")
with open(input_file_a, 'r') as ifile:
python3("program_b.py", _in=ifile.read(), _out=output_file_b)
Note that may need to specify argument search_paths for sh.Command for it to find python. Also, may need to specify full path to program_b.py file or os.chdir() accordingly.
I need to extract text from a PDF. I tried the PyPDF2, but the textExtract method returned an encrypted text, even though the pdf is not encrypted acoording to the isEncrypted method.
So I moved on to trying accessing a program that does the job from the command prompt, so I could call it from python with the subprocess module. I found this program called textExtract, which did the job I wanted with the following command line on cmd:
"textextract.exe" "download.pdf" /to "download.txt"
However, when I tried running it with subprocess I couldn't get a 0 return code.
Here is the code I tried:
textextract = shlex.split(r'"textextract.exe" "download.pdf" /to "download.txt"')
subprocess.run(textextract)
I already tried it with shell=True, but it didn't work.
Can anyone help me?
I was able to get the following script to work from the command line after installing the PDF2Text Pilot application you're trying to use:
import shlex
import subprocess
args = shlex.split(r'"textextract.exe" "download.pdf" /to "download.txt"')
print('args:', args)
subprocess.run(args)
Sample screen output of running it from a command line session:
> C:\Python3\python run-textextract.py
args: ['textextract.exe', 'download.pdf', '/to', 'download.txt']
Progress:
Text from "download.pdf" has been successfully extracted...
Text extraction has been completed!
The above output was generated using Python 3.7.0.
I don't know if your use of spyder on anaconda affects things or not since I'm not familiar with it/them. If you continue to have problems with this, then, if it's possible, I suggest you see if you can get things working directly—i.e. running the the Python interpreter on the script manually from the command line similar to what's shown above. If that works, but using spyder doesn't, then you'll at least know the cause of the problem.
There's no need to build a string of quoted strings and then parse that back out to a list of strings. Just create a list and pass that:
command=["textextract.exe", "download.pdf", "/to", "download.txt"]
subprocess.run(command)
All that shlex.split is doing is creating a list by removing all of the quotes you had to add when creating the string in the first place. That's an extra step that provides no value over just creating the list yourself.
I have a file name that I want to pass to a program or a bash script. For example if it's my car's picture.jpg, I have to change it to my\ car\'s picture.jpg to pass it to os.system like show my\ car\'s picture.jpg. Is there a function to do it the backslashes automatically?
You should use the subprocess module to call shell scripts from Python. Then you don't have to worry about escaping things yourself.
import subprocess
subprocess.call(['script_name', "my car's picture.jpg"])
subprocess.call() will escape everything correctly for you. If you need to read the output of the shell script, use subprocess.check_output() instead.
You can simply pass as is and use subprocess, os.system is depreciated.
c = check_output(["file","/home/padraic/Pictures/my cars' picture.png"])
print(c)
b"/home/padraic/Pictures/my cars' picture.png: PNG image data, 1366 x 768, 8-bit/color RGB, non-interlaced\n"
To call a script use check_call, if you want to pipe you can use Popen, there are lots of example in the docs linked above including replacing-os-system.
I can offer several incomplete suggestions that could be helpful to you.
Use "my car's picture.jpg" -- double quotes escape single ones
Using spaces in a UNIX file system generates only headaches. You could pass the filename inside of double-quotes.
os.system('cp "my car\'s picture" myCarPicture.jpg')
If you are using filenames with backslashes in a Windows system, use raw string
r"C:\Foo\bah\baz.jpg"
I need to enter the contents of a text (.txt) file as input for a Python (.py) file. Assuming the name of the text file is TextFile and the name of the Python file PythonFile, then the code should be as follows:
python PythonFile.py < TextFile.txt
Yet, when I try to do this in IDLE and type in
import PythonFile < TextFile,
IDLE gives me an invalid syntax message, pointing to the < sign. I tried all sorts of variations on this theme (i.e.,using or not using the file name extensions), but still got the same invalid-syntax message. How is the syntax different for input redirection in IDLE?
If it works in the command line, then why do you want to do this in IDLE? There are ways to achieve a similar result using, for example, subprocess, but a better way would be to refactor PythonFile.py so that you can call a function from it, e.g.:
>>> import PythonFile
>>> PythonFile.run_with_input('TextFile.txt')
If you post the contents of PythonFile.py, we might be able to help you do this.