[SOLVED] bash for loop for given array only accounts for one file out of two files in array

bash for loop for given array only accounts for one file out of two files in array

I have an array of two files from the find command:

[ogino@chead SIEMENS]$ DCM_FILES=($(find . -type f))

[ogino@chead SIEMENS]$ echo ${DCM_FILES[@]}
./107939/107939/DICOM/0020_20071002_104554.150005 ./100013/100013/DICOM/0002_20130723_100423.117500

I have then constructed a for loop in order to dump information in the files (via dcmdump of the dcmtk Toolbox):

[ogino@chead SIEMENS]$ for dcm in "${DCM_FILES[@]}"
do
  sd=$(dcmdump ${dcm} | grep "(0008,1030)"); 
done

However, it seems like it is only reading one DICOM file, as displayed in my output:

[ogino@chead SIEMENS]$ echo ${sd[0]}
(0008,1030) LO [RESEARCH^THOMPSON_SCHILL] # 24, 1 Unknown Tag & Data

[ogino@chead SIEMENS]$ echo ${sd[1]}

# I get a blank line for the second instance of my echo testing

[ogino@chead SIEMENS]$ echo ${sd[@]}
(0008,1030) LO [RESEARCH^THOMPSON_SCHILL] # 24, 1 Unknown Tag & Data

I tried initiating a blank array for sd before the loop, that didn't work (sd=( )), and surprisingly, indexing with dcm also didn't seem to pick up the second file ${sd[1]}...

[ogino@chead SIEMENS]$ echo ${dcm[0]}
./100013/100013/DICOM/0002_20130723_100423.117500
[ogino@chead SIEMENS]$ echo ${dcm[1]}

[ogino@chead SIEMENS]$ echo ${dcm[@]}
./100013/100013/DICOM/0002_20130723_100423.117500

Removing the variable assignment for the sd variable seems to remove the error, except, I need to store this particular output somewhere with an array, which is why I set the dcmdump command to sd in the first place.

[ogino@chead SIEMENS]$ for dcm in "${DCM_FILES[@]}"; do dcmdump ${dcm} | grep "(0008,1030)"; done
W: no data dictionary loaded, check environment variable: DCMDICTPATH
(0008,1030) LO [MRI BRAIN/MRHD]                         #  14, 1 Unknown Tag & Data
W: no data dictionary loaded, check environment variable: DCMDICTPATH
(0008,1030) LO [RESEARCH^THOMPSON_SCHILL]               #  24, 1 Unknown Tag & Data

Googling around seems to hint to me that there may be an issue with grep, but it's not so clear to me at the moment.

Is there a modification I need to make in my loop to make sure I can store both instances into an array? Any help to point me in the right direction to produce the output above with the second instance of grep

Solution

How about iterating over the indexes of your DCM_FILES array instead of the values, since you want the indexes to match in your new array anyway?

DCM_FILES=($(find . -type f))
for idx in $(seq ${#DCM_FILES[@]}) ; do
  sd[idx]=$(dcmdump ${DCM_FILES[idx]} | grep "(0008,1030)")
done
echo "${sd[@]}"