All files in directories

.gitignore

.DS_Store
DB*
Config*

dir.rb

#!/usr/bin/env ruby

database_dir  = ARGV[0]
config_dir    = ARGV[1]

Dir.glob("#{database_dir}/*").each do |entry|
  if File.directory?(entry) && File.exists?(File.join(entry, 'tmp/mammo_config.xml'))
    system("sh sed_mammo_substitution.sh #{entry} #{config_dir}")
  end
end

sed_mammo_substitution.sh

#!/bin/sh
PATIENT_DIR=$1  		#Path to the directory where you placed the 'DB' directory
CONFIG_DIR=$2       #Path to the directory where you placed the 'Config' directory

INPUT_MAMMO_CONFIG_XML_PATH=$PATIENT_DIR"/tmp/mammo_config.xml"
OUTPUT_MAMMO_CONFIG_XML_PATH=$PATIENT_DIR"/tmp/mammo_config_NEW.xml"

TMP_DIR=$PATIENT_DIR"/tmp/"
MAMMO_RECONSTRUCTION_DIR=$PATIENT_DIR"/media/mammo_reconstruction/"
REC_DIR=$PATIENT_DIR"/rec/"

sed -e "s;[a-zA-Z]:[A-Za-z0-9\\]*\\measures.xml;"$TMP_DIR"measures.xml;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\bodymarks.xml;"$TMP_DIR"bodymarks.xml;

        s;[a-zA-Z]:[A-Za-z0-9\\_]*\\front.jpg;"$MAMMO_RECONSTRUCTION_DIR"front.jpg;
        s;[a-zA-Z]:[A-Za-z0-9\\_]*\\right.jpg;"$MAMMO_RECONSTRUCTION_DIR"right.jpg;
        s;[a-zA-Z]:[A-Za-z0-9\\_]*\\left.jpg;"$MAMMO_RECONSTRUCTION_DIR"left.jpg;

        s;[a-zA-Z]:[A-Za-z0-9\\]*\\completebody.obj;"$REC_DIR"completebody.obj;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\completebody.k3d;"$REC_DIR"completebody.k3d;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\mammo_info.xml;"$REC_DIR"mammo_info.xml;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\rec\\thorax.obj;"$REC_DIR"thorax.obj;  
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\thorax.k3d;"$REC_DIR"thorax.k3d;  

        s;[a-zA-Z]:[A-Za-z0-9\\]*\\small.xml;"$CONFIG_DIR"small.xml;        
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\mask.png;"$CONFIG_DIR"mask.png;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\medium_uv.txt;"$CONFIG_DIR"medium_uv.txt;        
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\BreastSubdivisionTriangles.txt;"$CONFIG_DIR"BreastSubdivisionTriangles.txt;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\RGBACacheImage.mha;"$CONFIG_DIR"RGBACacheImage.mha;        
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\Config\\thorax.obj;"$CONFIG_DIR"thorax.obj;
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\flat_lateral.xml;"$CONFIG_DIR"flat_lateral.xml;        
        s;[a-zA-Z]:[A-Za-z0-9\\]*\\TrainingFeatures;"$CONFIG_DIR"TrainingFeatures;" $INPUT_MAMMO_CONFIG_XML_PATH > $OUTPUT_MAMMO_CONFIG_XML_PATH

Example: ruby dir.rb /Users/jrdi/Code/directories/DB /Users/jrdi/Code/directories/Config/