problem with opening dicom file containing private tags from SIEMENS overcome with gdcmconv

[Janusz Pachucki]

The Java crashed when attempting opening dicom file whether using Weasis, dcm2txt or other dcm4che utilities.
It took me some time to figure out solution which I would like to share with others.

This is an output from dcm2txt
...
2332:(0029,0010) LO #18 [SIEMENS CSA HEADER] Private Creator Data Element
2362:(0029,0011) LO #22 [SIEMENS MEDCOM HEADER] Private Creator Data Element
2396:(0029,1008) UN #6 [SOM 5 ] ?
2414:(0029,1009) UN #12 [VA10A 971201] ?
2438:(0029,1010) UN #640 [\00\00\04\00LT\0A\001\004\004\005\000\00\00\00\05\00
3090:(0029,1140) UN #-1 ?
3102:>(FFFE,E000) #-1 Item
3110:>(0029,0010) LO #20053 [ SIEMENS MEDCOM HEADER )A UN
SOM 5 TPOS)
dcm2txt: Failed to dump /home/janusz/tmp/17/DCM/S0001/SE0001/IM00001: null
java.io.EOFException
    at org.dcm4che2.io.DicomInputStream.readFully(DicomInputStream.java:351)
    at org.dcm4che2.io.DicomInputStream.readBytes(DicomInputStream.java:651)
...

The same happen with other Java program DicomBrowser. 

The file can be opened with gdcmdump, gdcmraw or gdcmconv linux utility and more when converted by gdcmconv easily opened by Weasis or other dcm4che utilities.

Since gdcmconv uses only single file name I propose to run python script:

import os
import subprocess

output_dir = "/home/janusz/tmp2"
source_dir = "/home/janusz/tmp1"

for root, dirs, files in os.walk(source_dir):
    for name in files:
        file = name
        ext = root
        extfile = ext.replace("/", ".")
        subprocess.call(["gdcmconv" , "-i" , ext+"/"+file , "-o" , output_dir+"/C"+extfile+"."+file])
        print(extfile)
print('Job done.')