Write grace2images

Wish

To write a conversion script that can make a conversion script

Call to the function

When we make a dispersion analysis, we write xmgrace files.
So we want include the writing in this analysis

import the function and call it

In specific_analyses/relax_disp/disp_data.py we import the coming new writing function

We change

from lib.software.grace import write_xy_data, write_xy_header

to

from lib.software.grace import write_xy_data, write_xy_header, write_grace2images

Then we add doc string to: def plot_disp_curves(dir=None, force=None):

    """Custom 2D Grace plotting function for the dispersion curves.

    One file will be created per spin system.

to

    """Custom 2D Grace plotting function for the dispersion curves.

    One file will be created per spin system.

    A python "grace to PNG/EPS/SVG..." conversion script is created at the end

Then we add to end of file. We open the file, call your writing script and close the file.

    # Write a python "grace to PNG/EPS/SVG..." conversion script.
    # Open the file for writing.
    file_name = "grace2images.py"
    file = open_write_file(file_name, dir, force)

    # Write the file.
    write_grace2images(file=file)

    # Close the file.
    file.close()

make the writing function

In lib/software/grace.py we write the new function

def write_grace2images(file=None):
    """Write a python "grace to PNG/EPS/SVG..." conversion script..

    The makes a conversion script to image types as PNG/EPS/SVG. The conversion is looping over a directory list of *.agr files, and making function calls to xmgrace. 
    Successfull conversion of images depends on the compilation of xmgrace. The input is a list of image types which is wanted, f.ex: PNG EPS SVG. PNG is default.

    @type file:             file object
    """

    # Write to file
    # Hack for the chaos of " and ' in same string
    t="'"

    lines = [
    r'#!/usr/bin/env python',"\n"
    r"","\n"
    r'import glob, os, sys',"\n"
    r'import shlex,subprocess',"\n"
    r'import argparse',"\n"
    r'from itertools import chain',"\n"
    r"","\n"
    r"# Add functioning for argument parsing","\n"
    r"parser = argparse.ArgumentParser(description='Process grace files to images')","\n"
    r"# Add argument type. Destination instance is set to types.","\n"
    r"parser.add_argument('-g', action='store_true', dest='relax_gui', help='Make it possible to run script through relax GUI. Run by using User-functions -> script')","\n"
    r"parser.add_argument('-l', nargs='+', action='append', dest='l', help='Make in possible to run scriptif relax has logfile turned on. Run by using User-functions -> script')","\n"
    r"parser.add_argument('-t', nargs='+', action='append', dest='types', help='List image types for conversion. Execute script with: python %s -t PNG EPS ...'%(sys.argv[0]), default=[])","\n"
    r"","\n"
    r"# Lets stop the execution and print help if no arguments are passed","\n"
    r"if len(sys.argv)==1:","\n"
    r"    print('system argument is:',sys.argv)","\n"
    r"    parser.print_help()","\n"
    r"    sys.exit(1)","\n"
    r"","\n"
    r"# Parse the arguments to a Class instance object","\n"
    r"args = parser.parse_args()","\n"
    r"# If we run through the GUI, we cannot pass input arguments, so we make a default PNG option","\n"
    r"if args.relax_gui:","\n"
    r"    args.types = [['PNG']]","\n"
    r"","\n"
    r"# The instance object will contain a list of lists. We convert this to one list.","\n"
    r"types = list(chain.from_iterable(args.types))","\n"
    r"","\n"
    r"# A easy search for files with *.agt, is to use glob, which is pathnames matching a specified pattern according to the rules used by the Unix shell, not opening a shell","\n"
    r'gracefiles = glob.glob("*.agr")',"\n"
    r"","\n"
    r"# For png conversion, several parameters can be passed to xmgrace. These can be altered later afterwards, and the script rerun. ","\n"
    r"# The option for transparent is good for poster or insertion in color backgrounds. The ability for this, still depends on xmgrace compilation","\n"
    r'if "PNG" in types:',"\n"
    r'    pngpar = "png.par"',"\n"
    r"    if not os.path.isfile(pngpar):","\n"
    r'        wpngpar = open(pngpar,"w")',"\n"
    r'        wpngpar.write(r%sDEVICE "PNG" FONT ANTIALIASING on%s+"\n")'%(t,t),"\n"
    r'        wpngpar.write(r%sDEVICE "PNG" OP "transparent:on"%s+"\n")'%(t,t),"\n"
    r'        wpngpar.write(r%sDEVICE "PNG" OP "compression:9"%s+"\n")'%(t,t),"\n"
    r'        wpngpar.close()',"\n"
    r'',"\n"
    r'# Now loop over the grace files',"\n"
    r'for grace in gracefiles:',"\n"
    r'    # Get the filename without extension',"\n"
    r'    fname = grace.split(".agr")[0]',"\n"
    r'    if "PNG" in types:',"\n"
    r'        # Produce the argument string',"\n"
    r'        im_args = r"xmgrace -hdevice PNG -hardcopy -param %s -printfile %s.png %s"%(pngpar,fname,grace)',"\n"
    r'        # Split the arguments the right way, to call xmgrace',"\n"
    r'        im_args = shlex.split(im_args)',"\n"
    r'        return_code = subprocess.call(im_args)',"\n"
    r'    if "EPS" in types:',"\n"
    r'        im_args = r"xmgrace -hdevice EPS -hardcopy -printfile %s.eps %s"%(fname,grace)',"\n"
    r'        im_args = shlex.split(im_args)',"\n"
    r'        return_code = subprocess.call(im_args)',"\n"
    r'    if ("JPG" or "JPEG") in types:',"\n"
    r'        im_args = r"xmgrace -hdevice JPEG -hardcopy -printfile %s.jpg %s"%(fname,grace)',"\n"
    r'        im_args = shlex.split(im_args)',"\n"
    r'        return_code = subprocess.call(im_args)',"\n"
    r'    if "SVG" in types:',"\n"
    r'        im_args = r"xmgrace -hdevice SVG -hardcopy -printfile %s.svg %s"%(fname,grace)',"\n"
    r'        im_args = shlex.split(im_args)',"\n"
    r'        return_code = subprocess.call(im_args)',"\n"
    r'',"\n"
    r'',"\n"

    ]
    file.writelines(lines)

Test the function

Then we make a small script to call the function outside relax, to see if we get the wanted output.
We first append to system path, so we can import the modules in relax, and then change to a directory where we have stored some results.

import sys,os
sys.path.append("C:\\WinPython27\\relax_disp")
os.chdir("C:\\WinPython27\\relax_results")

import lib.software.grace
reload(lib.software.grace)

file_name = "grace2images.py"
file = open(file_name,"w")
# Write the file.
lib.software.grace.write_grace2images(file=file)
file.close()

Commit the log

See [[Category:FAQ]