src/figures/cantilever-data/extract_f_v_k_data.sh

   1 #!/bin/bash
   2 #
   3 # Extract v,f,k data.  Ignore index, temperature, etc.
   4
   5 set -e # exit immediately on failed command
   6 set -o pipefail # pipes fail if any stage fails
   7
   8 BASE_DATA_DIR="$HOME/rsrch/data"
   9 SCALED_DATA_DIR="scaled_unfold"
  10 CALIBRATION_DATA_DIR="calibration"
  11
  12 EXTRACT_UNFOLDS="$HOME/src/lab/analysis/sawmodel/extract_unfolds.py"
  13 SCALE_UNFOLD="$HOME/src/lab/analysis/sawtooth_worming-0.1/scale_unfold.py"
  14
  15 DATA_DAYS[8]=20090114
  16 #DATA_DAYS[9]=20090128   # No good sawteeth
  17 DATA_DAYS[10]=20090203
  18 #DATA_DAYS[11]=20090211  # No good sawteeth
  19 DATA_DAYS[12]=20090212
  20 DATA_DAYS[13]=20090214
  21 DATA_DAYS[14]=20090219
  22 DATA_DAYS[15]=20090222
  23
  24 echo -e "#Unfolding force (pN)\tUnfolding rate (nm/s)\tSpring constant (pN/nm)\tLoading rate (pN/s)\tDatafile"
  25
  26 function NotEmpty ()
  27 {
  28     NAME=$1
  29     VALUE=$2
  30     if [ -z "$VALUE" ]; then
  31         echo "Error parsing"
  32         echo "$UNFOLD_LINE"
  33         echo "$NAME not defined.  File format must have changed."
  34         exit 1
  35     fi
  36 }
  37
  38 FIELD_INDEX=""
  39 function FieldIndex ()
  40 {
  41     LINE="$1"
  42     TITLE_REGEXP="$2"
  43     FIELD_INDEX=`echo "$LINE" | sed 's/\t/\n/g' | grep -n "$TITLE_REGEXP" | cut -d: -f1`
  44 }
  45
  46 for DAY in ${DATA_DAYS[*]}
  47 do
  48     echo "---Processing day $DAY---" >&2
  49     DATAFILE_FIELD=""
  50     FORCE_FIELD=""
  51     LAST_DATAFILE="" # Caching for efficiency
  52     while read UNFOLD_LINE
  53     do
  54         echo "Parsing '$UNFOLD_LINE'" >&2
  55         if [ "${UNFOLD_LINE:0:1}" == "#" ] ; then
  56             # reading the header line
  57             FieldIndex "$UNFOLD_LINE" "Datafile"
  58             DATAFILE_FIELD="$FIELD_INDEX"
  59             FieldIndex "$UNFOLD_LINE" "Force (pN)"
  60             FORCE_FIELD="$FIELD_INDEX"
  61             FieldIndex "$UNFOLD_LINE" "Stiffness (pN/nm)"
  62             STIFFNESS_FIELD="$FIELD_INDEX"
  63             NotEmpty 'Datafile field' "$DATAFILE_FIELD"
  64             NotEmpty 'Force field' "$FORCE_FIELD"
  65             NotEmpty 'Stiffness field' "$STIFFNESS_FIELD"
  66             continue
  67         fi
  68         NotEmpty "$DAY extraction header" "$DATAFILE_FIELD"
  69         DATAFILE=`echo "$UNFOLD_LINE" | cut -f $DATAFILE_FIELD`
  70         NotEmpty 'Datafile' "$DATAFILE"
  71         DATAFILE="$BASE_DATA_DIR/$SCALED_DATA_DIR/$DATAFILE"
  72         UNFOLDING_FORCE=`echo "$UNFOLD_LINE" | cut -f $FORCE_FIELD`
  73         NotEmpty 'Unfolding force' "$UNFOLDING_FORCE"
  74         STIFFNESS=`echo "$UNFOLD_LINE" | cut -f $STIFFNESS_FIELD`
  75         NotEmpty 'Stiffness' "$STIFFNESS"
  76         if [ "$DATAFILE" != "$LAST_DATAFILE" ]; then
  77             UNFOLDING_RATE=`sed -n 's/^Unfold rate (nm\/s):\t//p' "${DATAFILE}_param"`
  78             NotEmpty 'Unfolding rate' "$UNFOLDING_RATE"
  79             SPRING_CONSTANT_STRING=`$SCALE_UNFOLD --print-k "$DATAFILE"`
  80             NotEmpty 'Spring constant string' "$SPRING_CONSTANT_STRING"
  81             SPRING_CONSTANT_N_PER_M=`echo "$SPRING_CONSTANT_STRING" | sed -n 's/ N\/m$//p'`
  82             NotEmpty 'Spring constant (N/m)' "$SPRING_CONSTANT_N_PER_M"
  83             SPRING_CONSTANT=`echo "print ($SPRING_CONSTANT_N_PER_M * 1e3)" | python`
  84             NotEmpty 'Spring constant (pN/nm)' "$SPRING_CONSTANT"
  85         fi
  86         LOADING_RATE=`python -c "print $STIFFNESS * $UNFOLDING_RATE"` # pN/s
  87         echo -e "$UNFOLDING_FORCE\t$UNFOLDING_RATE\t$SPRING_CONSTANT\t$LOADING_RATE\t$DATAFILE"
  88         LAST_DATAFILE="$DATAFILE"
  89     done < <(cd $BASE_DATA_DIR/$SCALED_DATA_DIR/ && $EXTRACT_UNFOLDS ${DAY}_select_fit.xml)
  90 done
  91
  92 exit 0