Loading DICOM files in Python

[dejana....@gmail.com]

Hello,

I am new with pydicom, so I have some problems with it.

For Python 3.4, pydicom 0.99, when I try loading DICOM files, I get this error:

import dicom
import os
import numpy

PathDicom = "C:\Python34\Baza"
lstFilesDCM = []  # create an empty list
for dirName, subdirList, fileList in os.walk(PathDicom):
    for filename in fileList:
        if ".dcm" in filename.lower():  # check whether the file's DICOM
            lstFilesDCM.append(os.path.join(dirName,filename))

# Get ref file
RefDs = dicom.read_file(lstFilesDCM[0])

# Load dimensions based on the number of rows, columns, and slices (along the Z axis)
ConstPixelDims = (int(RefDs.Rows), int(RefDs.Columns), len(lstFilesDCM))

# Load spacing values (in mm)
ConstPixelSpacing = (float(RefDs.PixelSpacing[0]), float(RefDs.PixelSpacing[1]), float(RefDs.SliceThickness))


ERROR:
C:\Python34\python.exe C:/Users/041213/PycharmProjects/untitled1/Dejana.py
Traceback (most recent call last):
  File "C:/Users/041213/PycharmProjects/untitled1/Dejana.py", line 13, in <module>
    RefDs = dicom.read_file(lstFilesDCM[0])
IndexError: list index out of range

If someone could help me with this, I would really appreciate. 

Or if someone could help me how do I load DICOM files in general?

Sorry for a long post,

Greetings,

Dejana

[Jonathan Suever]

Dejana,

The issue does not appear to be a problem with pydicom. Instead, it seems that lstFilesDCM is an empty list (i.e. your script didn't find any files ending in ".dcm" in the specified folder) therefore when you try to access the first element using lstFilesDCM[0] it fails resulting in the IndexError ("list index out of range").

-Jonathan

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[dejana....@gmail.com]

Yes, I understand that, but the problem is that is not an empty file, it consists of 20 dcm files.

Even when I use the most simple code, it won't work.
For example:

import dicom

filePath="C:\Python34\Lib\site-packages\dicom\testfiles"
ds=dicom.read_file(filePath[0])

Error is: 

C:\Python34\python.exe C:/Users/041213/PycharmProjects/D/Deki.py Traceback (most recent call last):

 File "C:/Users/041213/PycharmProjects/D/Deki.py", line 4, in

    ds=dicom.read_file(filePath[0]) 

File "C:\Python34\lib\site-packages\dicom\filereader.py", line 589, in read_file 

    fp = open(fp, 'rb') FileNotFoundError: [Errno 2]

 No such file or directory: 'C'

[Aditya Panchal]

You may want to escape your filePath as a raw string due to the single backslashes on Windows masquerading as escape characters:

filePath=r"C:\Python34\Lib\site-packages\dicom\testfiles"

So you need to insert an 'r' before the string.

Otherwise you'll need to double backslash your file path.

Adit

--

[Eli Stevens (Gmail)]

Also, the code you gave is incorrect:

filePath="C:\Python34\Lib\site-packages\dicom\testfiles"
ds=dicom.read_file(filePath[0])

Here, filePath[0] is just "C" since it's a string, not a list of strings.

I recommend starting to print out the repr of values you are passing
into APIs to make sure they're what you expect. Gives you quick
feedback about stuff. That would have caught the backslash issue too.

Cheers,
Eli

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