Python, Opening files in loop (dicom)

4
votes

I am currently reading in 200 dicom images manually using the code: 

ds1 = dicom.read_file('1.dcm')

so far, this has worked but I am trying to make my code shorter and easier to use by creating a loop to read in the files using this code:

for filename in os.listdir(dirName):
    dicom_file = os.path.join("/",dirName,filename)   
    exists = os.path.isfile(dicom_file) 
    print filename
    ds = dicom.read_file(dicom_file)

This code is not currently working and I am receiving the error: 

"raise InvalidDicomError("File is missing 'DICM' marker. "
dicom.errors.InvalidDicomError: File is missing 'DICM' marker. Use         
force=True to force reading

Could anyone advice me on where I am going wrong please?

2
pythonfor-loopdicom
Are there files other than .dcm files in that folder? – user812786
Sounds like one or more of the files in your directory are not of the correct type. – gkusner
Are there only ".dcm" files in the directory, or could there be other files or directories? You are checking if it is a file (exists) but then not using that information. I was anticipating seeing an "if exists:" line right after that. – RobertB
How about printing dicom_file to see if you have the path right. – tdelaney
The error seems to be that there were two .txt files in the folder with dicoms and when they were moved the code worked, thank you! I will add an if exists to ensure the problem doesn't happen again. Thank you everyone! – smailliwharas

2 Answers

3
votes

I think the line:

dicom_file = os.path.join("/",dirName,filename)

might be an issue? It will join all three to form a path rooted at '/'. For example:

os.path.join("/","directory","file")

will give you "/directory/file" (an absolute path), while:

os.path.join("directory","file")

will give you "directory/file" (a relative path)

If you know that all the files you want are "*.dcm" you can try the glob module:

import glob

files_with_dcm = glob.glob("*.dcm")

This will also work with full paths:

import glob

files_with_dcm = glob.glob("/full/path/to/files/*.dcm")

But also, os.listdir(dirName) will include everything in the directory including other directories, dot files, and whatnot

Your exists = os.path.isfile(dicom_file) line will filter out all the non files if you use an "if exists:" before reading.

I would recommend the glob approach, if you know the pattern, otherwise:

if exists:
   try:
      ds = dicom.read_file(dicom_file)
   except InvalidDicomError as exc:
      print "something wrong with", dicom_file

If you do a try/except, the if exists: is a bit redundant, but doesn't hurt...

2
votes

Try adding:

dicom_file = os.path.join("/",dirName,filename) 
if not dicom_file.endswith('.dcm'):
    continue