Is better to use `itk.imread(dir)` than `itk.imread(file_list)`?

Beginner Questions
,
1

I made an experiment about the itk.imread function, and found something interesting.

I putted .dcm files with the same series ID in a directory. And then convert the dicom data into nii.gz format. Here come the difference:

Code-1: random shuffled files

import os
import itk
import random

dir_path = "./20210718_010_NECK_T1W_mDIXON_TRA+C/"
results_path = "./results/"

filenames = os.listdir(dir_path)
random.shuffle(filenames)
filenames = [os.path.join(dir_path, f) for f in filenames]
image = itk.imread(filenames)
itk.imwrite(image, results_path + "image_shuffle.nii.gz")

Here is the result visualized in ITK-SNAP:

image
image1932Ă—1274 430 KB

It obviously showed a chaotic scene.

But if I try to convert it by passing a dir parameter, it worked well.

Code-2:

import itk

dir_path = "/mnt/pc/Chenq_team/HuangData/MR/935294/20210718_010_NECK_T1W_mDIXON_TRA+C/"
results_path = "./results/"

image = itk.imread(dir_path)
itk.imwrite(image, results_path + "image.nii.gz")

In fact, I didn’t mean to bring in random to say the there is a bug in ITK.

Instead, I encountered a similar scenario while processing the dicom data. In order to describe my problem, I gave the above two simple examples.

So my question is: Why does itk.imread affected by the order of passing file_list parameter?

2

And here is the normal visualization in Code-2.

image
image1930Ă—1474 443 KB

3

What I do agree with, is that this function gives the programmer a lot of convenience and space for free play.

4

If you give the function a list of filenames, it uses the order in the list to construct the volume. If you give it a directory, it uses DICOM-specific rules to sort the list of files so they have the “expected” order.

3 Likes
5

How can I use the rules to sort my filenames by myself? If I read a series of dicom files in a unstructured folder, it may be necessary to sort by myself.

6

In this example the line fileNames = namesGenerator.GetFileNames(seriesIdentifier) uses DICOM-specific classes to sort the file names. You can use that for your own purposes, or sort the filenames using some other rules or heuristics, and then pass that list of filenames to reader.SetFileNames(fileNames), or using more dense and simpler syntax of itk.imread(fileNames).

7

If you want to learn the rules, take a look at the source code (e.g. itkGDCMSeriesFileNames.cxx
and gdcmSerieHelper), or maybe something like this?