shasum_checker.sh

#!/bin/bash
# finds the nifti files in the subject sub folders
# gets sha26sum values and sorts according to the file names
# prints only the sha256sum values to the output file.


# Function to find the base directory containing both src and data
find_basedir() {
    # to store the dir variable
    local dir="$1" 
    #to create a search loop for base directiory
    while [[ "$dir" != "/" ]]; do  
        # if there is src and data set this as the base directory
        if [[ -d "$dir/src" && -d "$dir/data" ]]; then 
            # to print the base directory
            echo "$dir"
            return
        fi
        # to set the directory to the parent directory
        dir=$(dirname "$dir")
    done
    echo "Base directory not found"
}

# Determining the base directory using the 'find_basedir' function

BASEDIR=$(find_basedir "$(pwd)")
# without this part script does not stop because it needs to exit, exit 1 does that.
if [[ "$BASEDIR" == "Base directory not found" ]]; then
    echo "Error: Base directory not found."
    exit 1
fi

# Define paths relative to the base directory
SRCDIR="$BASEDIR/src"
DATADIR="$BASEDIR/data" #where all data is stored
OUTPUTDIR="$DATADIR/output" #where spm outputs are stored
# Reference folder is the folder which contains all results from batch interface step by step
# All other folders will be compared with this.
REFERENCEDIR="$DATADIR/MoAEpilot" 
# Output folder of the batch interface
BATCHDIR="$OUTPUTDIR/MoAEpilot_bids_batch" 
# Output folder of the script interface
SCRIPTDIR="$OUTPUTDIR/MoAEpilot_bids_script"  

# first level analysis output comparison

FL_GUI="$OUTPUTDIR/first_level_analysis_gui"
FL_SCRIPT="$OUTPUTDIR/first_level_analysis_script"


##Event Related data

# face_rep images preprocessing reference folder
FACEGUIDIR="$DATADIR/face_rep_gui" 
# script results face_rep images preprocessing 
FACESCRIPTDIR="$DATADIR/face_rep_script"  

#Categorical Modelling Results
EVENTCATGUI="$OUTPUTDIR/event_related_gui/categorical"

EVENTCATSCRIPT="$OUTPUTDIR/event_related_script/categorical"

#Parametric Modelling Results 
EVPARAMGUI="$OUTPUTDIR/event_related_gui/parametric"

EVPARAMSCRIPT="$OUTPUTDIR/event_related_script/parametric"



RESULTSDIR="$BASEDIR/results"



# defining file extension to search for the defined file extension 
file_extension=".nii"

#Now we are looking for the nifti files in the functional and anatomical subfolders
# calculating their shasums 
# and storing them in a file with the same name as the subfolder.

calculate_shasums() {
    local input_folder="$1"
    local output_file="${input_folder%.*}_shasums.txt" #to create the output file accordingly

    # Initialize an array to store all SHA256 sums
    shasums=()

    # Find files with the specified extension in the input folder and its subfolders
    # IFS is to set filed separator actually not used here just keeping it to have it for the future
    while IFS= read -r -d '' file; do
        # Calculate sha256sum, print only the first column and sort the output 
        sha_sum=$(sha256sum "$file" | awk '{print $1}' | sort)
        
        # This is to append the sha256 sum to the array
        shasums+=("$sha_sum")
# this one liner looks for the files containing the 'file_extension' in the folder and prints.
    done < <(find "$input_folder" -type f -name "*$file_extension" -print0)

    # Print all SHA256 sums to the output file
    printf "%s\n" "${shasums[@]}" > "$output_file"
}

compare_shasums() {
# loading text files  
local output_file="$RESULTSDIR/basecomparison_result.txt"
local reference="$1"
local file1="$2"
# compare the loaded text files below
if cmp -s "$reference" "$file1";
then
   echo "SHA256sums are identical for $reference and $file1" >> "$output_file"
else
   echo "SHA256sums are not identical for $reference and $file1" >> "$output_file"
fi
}
##############################################################
# Iterate over the REFERENCE folder to calculate shasums for all the nifti files'
# THIS NEEDS TO BE DONE ONCE FOR THE REFERENCE FOLDER 
# It is recommended to run it once then comment it out.
# lock your reference folder and reference txt to avoid overwriting.
# COMMENT OUT THE FOLLOWING 3 LINES OF THE CODE BELOW TO GET THE SHASUMS OF THE REFERENCE FOLDER 
##############################################################
#for ref_subfolder in "$REFERENCEDIR"; do
#    calculate_shasums "$ref_subfolder"
#done
##############################################################


# TO CALCULATE THE SHASUMS
# Iterate over BATCH folder to calculate shasums for all nifti files'

for batch_subfolder in "$BATCHDIR"; do
    calculate_shasums "$batch_subfolder"
done

# Iterate over SCRIPT folder to calculate shasums for all nifti files'
for script_subfolder in "$SCRIPTDIR"; do
    calculate_shasums "$script_subfolder"
done

for flgui_subfolder in "$FL_GUI"; do
    calculate_shasums "$flgui_subfolder"
done

for flsc_subfolder in "$FL_SCRIPT"; do
    calculate_shasums "$flsc_subfolder"
done

for fagui_subfolder in "$FACEGUIDIR"; do
    calculate_shasums "$fagui_subfolder"
done

for fascript_subfolder in "$FACESCRIPTDIR"; do
    calculate_shasums "$fascript_subfolder"
done


for eventcatgui_subfolder in "$EVENTCATGUI"; do
    calculate_shasums "$eventcatgui_subfolder"
done

for eventcatscript_subfolder in "$EVENTCATSCRIPT"; do
    calculate_shasums "$eventcatscript_subfolder"
done

for evparamgui_subfolder in "$EVPARAMGUI"; do
    calculate_shasums "$evparamgui_subfolder"
done

for evparamscript_subfolder in "$EVPARAMSCRIPT"; do
    calculate_shasums "$evparamscript_subfolder"
done

# TO COMPARE THE SHASUMS WITH EACH OTHER
reference_file="$DATADIR/MoAEpilot_shasums.txt"
batch_file="$DATADIR/MoAEpilot_batch_shasums.txt"
script_file="$DATADIR/MoAEpilot_script_shasums.txt"

reference_file2="$OUTPUTDIR/first_level_analysis_gui_shasums.txt"
flsc_file="$OUTPUTDIR/first_level_analysis_script_shasums.txt"

reference_txt="$DATADIR/face_rep_gui_shasums.txt"
script_txt="$DATADIR/face_rep_script_shasums.txt"

referencesha="$OUTPUTDIR/categorical_gui_shasums.txt" 
scriptsha="$OUTPUTDIR/categorical_script_shasums.txt"

referencesha="$OUTPUTDIR/categorical_gui_shasums.txt" 
scriptsha="$OUTPUTDIR/categorical_script_shasums.txt"

refpamsha="$OUTPUTDIR/parametric_gui_shasums.txt"
scriptpamsha="$OUTPUTDIR/parametric_script_shasums.txt"


compare_shasums "$batch_file" "$reference_file"
compare_shasums "$script_file" "$reference_file"
compare_shasums "$batch_file" "$script_file"

compare_shasums "$flsc_file" "$reference_file2"

compare_shasums "$script_txt" "$reference_txt"

compare_shasums "$referencesha" "$scriptsha"
compare_shasums "$refpamsha" "$scriptpamsha"
# With this experiment we showed that we can reproduce same
# results using SPM12 gui, batch and script interfaces for 
# preprocessing and analysis steps. 
### END OF THE SCRIPT ###