added python based tsvplot
This commit is contained in:
Ville Rantanen
@@ -1 +1 @@
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../tsv/tsvplot
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../tsv/tsvplot.py
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41
tsv/tsvplot
41
tsv/tsvplot
@@ -1,33 +1,52 @@
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#!/bin/bash
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[[ -z "$3" ]] && {
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_helpexit() {
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self=$( basename $0 )
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echo "Plot2D for console.
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Arguments
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tsvplot FILE xCol yCol [plotStyle] [preBlock]
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$self FILE xCol yCol [-X] [plotStyle] [preBlock]
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e.g. tsvplot cal.tsv 2 4
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or tsvplot cal.tsv Area Weight \"with lines;\" \"set title 'test plot';\"
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e.g. $self cal.tsv 2 4
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or $self cal.tsv Area Weight \"with lines;\" \"set title 'test plot';\"
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preBlock may contain any GNUPlot commands.
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plotStyle contains any plotting style commands.
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-X use X11 instead of console
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Requires csvkit and gnuplot
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"
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exit
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}
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fbase=$( basename "$1" )
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if [ $# -lt 3 ]; then _helpexit; fi
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csvcut -t -c "$2,$3" "$1" | gnuplot -e "
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set term dumb $(tput cols) $(tput lines) enhanced;
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POS=0
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POSADJUST=0
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for (( i=1; i<=$#; i++ )); do
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POS=$(( $i + $POSADJUST ))
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[[ ${!i} = "-h" ]] && _helpexit
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[[ ${!i} = "help" ]] && _helpexit
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[[ ${!i} = "-X" ]] && PLOTTERM=" " && POSADJUST=$(( $POSADJUST - 1 )) && continue
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[[ $POS -eq 1 ]] && FILE="${!i}"
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[[ $POS -eq 2 ]] && XCOL="${!i}"
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[[ $POS -eq 3 ]] && YCOL="${!i}"
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[[ $POS -eq 4 ]] && STYLE="${!i}"
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[[ $POS -eq 5 ]] && PRE="${!i}"
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done
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fbase=$( basename "$FILE" )
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[[ -z "$PLOTTERM" ]] && PLOTTERM="set term dumb $(tput cols) $(tput lines) enhanced;"
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[[ -z "$PRE" ]] && PRE="set title '$fbase';"
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csvcut -t -c "$XCOL,$YCOL" "$FILE" | gnuplot -p -e "$PLOTTERM
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set datafile separator \",\";
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set xlabel '$2';
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$5
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plot '<cat' using 1:2 title '$fbase $3' $4"
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set xlabel '$XCOL';
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set ylabel '$YCOL';
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$PRE
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plot '<cat' using 1:2 title '' $STYLE"
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[[ $? -ne 0 ]] && {
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echo -n "Possible columns: "
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head -n 1 "$1" | tr \\t ,
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head -n 1 "$FILE" | tr \\t ,
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} || {
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true
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}
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224
tsv/tsvplot.py
Executable file
224
tsv/tsvplot.py
Executable file
@@ -0,0 +1,224 @@
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#!/usr/bin/env python
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#
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# Copyright 2016 Ville Rantanen
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#
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# This program is free software: you can redistribute it and/or modify it
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# under the terms of the GNU Lesser General Public License as published
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# by the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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from __future__ import print_function
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import sys, os, math, csv, subprocess
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from argparse import ArgumentParser
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'''Plot CSV files with GNUPLOT.'''
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__author__ = "Ville Rantanen"
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__version__ = "0.1"
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def get_data_scatter(opts):
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reader=csv.DictReader(open(os.path.join(*opts.csv),'rb'), dialect=csv.excel_tab, lineterminator="\n")
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data=[]
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try:
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for row in reader:
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data.append(",".join([row[c] for c in opts.columns]))
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except KeyError,ME:
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print("Column {} not found.".format(ME),file=sys.stderr)
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print("Columns in the file:"+",".join(reader.fieldnames),file=sys.stderr)
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sys.exit(1)
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return "\n".join(data)
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def get_data_histogram(opts):
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reader=csv.DictReader(open(os.path.join(*opts.csv),'rb'), dialect=csv.excel_tab, lineterminator="\n")
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data=[]
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try:
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for row in reader:
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try:
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f=float(row[opts.columns[0]])
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data.append(row[opts.columns[0]])
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except ValueError:
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continue
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except KeyError,ME:
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print("Column {} not found.".format(ME),file=sys.stderr)
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print("Columns in the file:"+",".join(reader.fieldnames),file=sys.stderr)
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sys.exit(1)
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return "\n".join(data)
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def get_stats(opts):
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reader=csv.DictReader(open(os.path.join(*opts.csv),'rb'), dialect=csv.excel_tab, lineterminator="\n")
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values_min=float('nan')
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values_max=-float('nan')
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values_n=0
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try:
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for row in reader:
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try:
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f=float(row[opts.columns[0]])
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except ValueError:
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continue
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values_n+=1
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values_min=min(f,values_min)
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values_max=max(f,values_max)
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except KeyError,ME:
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print("Column {} not found.".format(ME),file=sys.stderr)
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print("Columns in the file:"+",".join(reader.fieldnames),file=sys.stderr)
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sys.exit(1)
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return (values_min,values_max,values_n)
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def get_plotterm(opts):
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if opts.X11:
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plotterm=""
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else:
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(height,width)=termsize()
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if opts.height:
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height=opts.height
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if opts.width:
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width=opts.width
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height+=2
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plotterm="set term dumb {0} {1} enhanced;".format(width,height)
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return plotterm
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def get_histogram_template(opts):
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plotterm=get_plotterm(opts)
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(vmin,vmax,vnum)=get_stats(opts)
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if opts.bins:
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bins=opts.bins
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else:
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bins=math.ceil(math.sqrt(vnum))
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if not opts.X11:
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(height,width)=termsize()
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if opts.width:
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width=opts.width
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bins=min(int(float(width)/4),bins)
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template='''{}
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set datafile separator ",";
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set xlabel '{}';
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Min = {};
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Max = {};
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n = {:f};
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width = (Max-Min)/n;
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set boxwidth width absolute;
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bin(x) = width*(floor((x-Min)/width)+0.5) + Min;
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{}
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plot '<cat' u (bin($1)):(1.0) smooth freq title '' {};
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'''.format(
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plotterm,
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opts.columns[0],
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vmin,vmax,bins,
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opts.pre,
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opts.style
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)
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return template
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def get_scatterplot_template(opts):
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plotterm=get_plotterm(opts)
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template = '''{}
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set datafile separator ",";
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set xlabel '{}';
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set ylabel '{}';
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{}
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plot '<cat' using 1:2 title '' {};'''.format(
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plotterm,
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opts.columns[0],
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opts.columns[1],
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opts.pre,
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opts.style
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)
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return template
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def run_gnuplot(opts, template, get_data):
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p = subprocess.Popen(['gnuplot','-p','-e',template], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
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comm=p.communicate(input=get_data(opts))
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for l in comm[0].split("\n"):
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if not l.strip()=="":
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print(l)
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if p.returncode>0:
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print(template)
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print('='*25)
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print(comm[1])
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return(p.returncode)
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def which(program):
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import os
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def is_exe(fpath):
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return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
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fpath, fname = os.path.split(program)
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if fpath:
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if is_exe(program):
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return program
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else:
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for path in os.environ["PATH"].split(os.pathsep):
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exe_file = os.path.join(path, program)
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if is_exe(exe_file):
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return exe_file
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return None
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def setup_options():
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''' Setup the command line options '''
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parser=ArgumentParser(description="Plot CSV columns to 2D scatter plot, or a histogram. Uses GNUPLOT command line utility to draw plots.")
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parser.add_argument("-v","--version",action='version', version=__version__)
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parser.add_argument("-c",action="store",dest="columns",type=str,required=True,
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help="Column name for histogram, or comma separated list of two names for scatter plot. First column is the x-axis.")
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parser.add_argument("-d",action="store",dest="delimiter",default="\t",
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help="File delimiter, default [tab].")
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parser.add_argument("-n",action="store",type=int,dest="bins",default=False,
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help="Bins for histograms. Default: min( console_width/4,sqrt(len(values)) )")
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parser.add_argument("-p",action="store",dest="pre",default="",
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help="Gnuplot commands to execute before plotting.")
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parser.add_argument("-s",action="store",dest="style",default=None,
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help="Plotting style, e.g. 'with lines'. Defaults to points for 2D plot, boxes for histogram.")
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parser.add_argument("--width",action="store",type=int,dest="width",default=False,
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help="Console width. Default: fullscreen")
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parser.add_argument("--height",action="store",type=int,dest="height",default=False,
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help="Console height. Default: fullscreen")
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parser.add_argument("-X",action="store_true",dest="X11",default=False,
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help="Show plot in X11 window, instead of console.")
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parser.add_argument("-D",action="store_true",dest="debug",default=False,
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help="Print commands before execution")
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parser.add_argument("csv",type=str,action="store",
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help="CSV file to plot")
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options=parser.parse_args()
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options.columns=[c.strip() for c in options.columns.split(",")]
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if len(options.columns)>2:
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parser.error("Only two columns supported.")
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options.csv=os.path.split(options.csv)
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if not options.style:
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if len(options.columns)==1:
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options.style="with boxes;"
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else:
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options.style="pt '*'"
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return options
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def termsize():
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try:
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rows, columns = os.popen('stty size', 'r').read().split()
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except:
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(rows,columns)=(25,80)
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return (int(rows),int(columns))
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if not which('gnuplot'):
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print('You don\'t seem to have "gnuplot" installed!')
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sys.exit(1)
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opts=setup_options()
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if len(opts.columns)==1:
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template=get_histogram_template(opts)
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get_data=get_data_histogram
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else:
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template=get_scatterplot_template(opts)
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get_data=get_data_scatter
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if opts.debug:
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print(template)
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rc=run_gnuplot(opts, template, get_data)
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sys.exit(rc)
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@@ -45,7 +45,7 @@ then usage
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exit 1
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fi
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which ncsv &> /dev/null || ( echo ncsv required: "https://code.google.com/p/nicecsv/"; exit 1 )
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which ncsv &> /dev/null || ( echo ncsv required: "https://bitbucket.org/MoonQ/ncsv"; exit 1 )
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which csvcut &> /dev/null || ( echo csvkit required: "https://csvkit.readthedocs.org/"; exit 1 )
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if [ -z "$LABEL" ]
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