def __init__(self, **kwargs):
# These should go through the setters
self.inroot = kwargs.get('inroot', DEF_INROOT)
self.outroot = kwargs.get('outroot', DEF_OUTROOT)
self.sweepmode = kwargs.get('sweep', False)
self.analysis = kwargs.get('analysis', ANAL_DEFAULT)
self._plot_dpi = kwargs.get('plot_dpi',
None) #Defaults based on matplotlibrc file
self._plot_dim = kwargs.get('plot_dim', 'width=6cm')
self._plot_fontsize = kwargs.get('fontsize', 18)
# Ticksize defaults to 15 btw
self.rname = kwargs.get('rname', '')
self.overwrite = kwargs.get('overwrite', False)
# Configure logger
verbosity = kwargs.get('verbosity', 'warning')
trace = kwargs.get('trace', False)
# Pop kwargs['params'] for output below
self.params = kwargs.pop('params', None)
# Add logging later; consider outdirectory conflicts
self.build_outroot()
configure_logger(screen_level=verbosity,
name=__name__,
logfile=op.join(self.outroot, 'runlog.txt'),
mode='w')
# Output the parameters
self._run_params_file = op.join(self.outroot, 'runparameters.tex')
with open(self._run_params_file, 'w') as f:
# Hacky way to write latex section from raw string literals
f.write(r'\subsection{Script Parameters}')
f.write(r'\fboxsep5mm')
f.write(
r'\fcolorbox{black}{yellow}{\vbox{\hsize=10cm \noindent \scriptsize '
)
f.write(latex_multicols(self.params, title='PyUvVis Parameters'))
f.write(latex_multicols(kwargs, 'Analysis Parameters'))
f.write('}}')
if self._plot_dpi > 600:
logger.warn('Plotting dpi is set to %s. > 600 may result in slow'
' performance.')
# Used for storing variables in reports/matlab other uses
self._run_summary = ''
self._csv_paths = []
def __init__(self, **kwargs):
# These should go through the setters
self.inroot = kwargs.get('inroot', DEF_INROOT)
self.outroot = kwargs.get('outroot', DEF_OUTROOT)
self.sweepmode = kwargs.get('sweep', False)
self.analysis = kwargs.get('analysis', ANAL_DEFAULT)
self._plot_dpi = kwargs.get('plot_dpi', None) #Defaults based on matplotlibrc file
self._plot_dim = kwargs.get('plot_dim', 'width=6cm')
self._plot_fontsize = kwargs.get('fontsize', 18)
# Ticksize defaults to 15 btw
self.rname = kwargs.get('rname', '')
self.overwrite = kwargs.get('overwrite', False)
# Configure logger
verbosity = kwargs.get('verbosity', 'warning')
trace = kwargs.get('trace', False)
# Pop kwargs['params'] for output below
self.params = kwargs.pop('params', None)
# Add logging later; consider outdirectory conflicts
self.build_outroot()
configure_logger(screen_level=verbosity, name = __name__,
logfile=op.join(self.outroot, 'runlog.txt'), mode='w')
# Output the parameters
self._run_params_file = op.join(self.outroot, 'runparameters.tex')
with open(self._run_params_file, 'w') as f:
# Hacky way to write latex section from raw string literals
f.write(r'\subsection{Script Parameters}')
f.write(r'\fboxsep5mm')
f.write(r'\fcolorbox{black}{yellow}{\vbox{\hsize=10cm \noindent \scriptsize ')
f.write(latex_multicols(self.params, title='PyUvVis Parameters'))
f.write(latex_multicols(kwargs, 'Analysis Parameters'))
f.write('}}')
if self._plot_dpi > 600:
logger.warn('Plotting dpi is set to %s. > 600 may result in slow'
' performance.')
# Used for storing variables in reports/matlab other uses
self._run_summary = ''
self._csv_paths = []
import sys
import os
import os.path as op
from collections import OrderedDict
from pyuvvis.scripts.gwu_script.tex_templates import EXPERIMENT_MAIN, HEADER, \
BLANK_SECTION
import logging
logger = logging.getLogger(__name__)
from pyuvvis.logger import log, configure_logger, logclass
from pyuvvis.scripts.gwu_script import LOGO_PATH
logger = configure_logger(name=__name__)
@logclass(public_lvl='info')
class Reporter(object):
''' Report is stored as an ordered dict. Main is followed by sections. '''
def __init__(self, **kwargs):
self.overwrite = kwargs.get('overwrite', False)
# Add main experimental body from template file or blank
template_file = kwargs.get('template_file', None)
if template_file:
if not op.exists(template_file):
raise IOError("Template file %s not found!")
self.main_template = file(template_file, 'r').read()
import sys
import os
import os.path as op
from collections import OrderedDict
from pyuvvis.scripts.gwu_script.tex_templates import EXPERIMENT_MAIN, HEADER, \
BLANK_SECTION
import logging
logger = logging.getLogger(__name__)
from pyuvvis.logger import log, configure_logger, logclass
from pyuvvis.scripts.gwu_script import LOGO_PATH
logger = configure_logger(name=__name__)
@logclass(public_lvl='info')
class Reporter(object):
''' Report is stored as an ordered dict. Main is followed by sections. '''
def __init__(self, **kwargs):
self.overwrite = kwargs.get('overwrite', False)
# Add main experimental body from template file or blank
template_file = kwargs.get('template_file', None)
if template_file:
if not op.exists(template_file):
raise IOError("Template file %s not found!")
self.main_template = file(template_file, 'r').read()
def main(args=None):
if args:
if isinstance(args, basestring):
args = shlex.split(args)
sys.argv = args
parser = argparse.ArgumentParser(SCRIPTNAME,
description='GWU PyUvVis composite'
' latex report assembly script',
epilog='Additional help not found',
usage='%s --globals <command> --cmdopts' %
SCRIPTNAME)
parser.add_argument('-v',
'--verbosity',
help='Set screen logging; '
'defaults to info.',
nargs='?',
default='warning',
const='info',
metavar='')
parser.add_argument('-o', '--overwrite', action='store_true')
# parser.add_argument('-s', '--sep', metavar='',
# help='Latex section separator. Defaults to %s. '
# 'Set to None to avoid auto sub-sectioning' %SEP_DEFAULT)
# Sub Commands
subparsers = parser.add_subparsers(title='commands', metavar='', dest='op')
# TEMPLATE SUBCOMMAND
p_template = subparsers.add_parser(
'template',
usage='%s --globals <template> outpath --opts ' % SCRIPTNAME,
help='template help',
epilog='PUT EXAMPLES HERE')
p_template.add_argument(
'outpath',
metavar='outfile',
help='Name of outfile (eg foo.tex or path/to/foo.tex)')
p_template.add_argument(
'-s',
'--sections',
metavar='',
nargs='*',
help='List of sections to add.'
'or tree file. If not tree file, default section template will be "template/section" '
'section names will auto-break into subsections based on value of --sep',
default=[])
p_template.add_argument('-t', '--template_file', metavar='')
# BUILD SUBCOMMAND
p_build = subparsers.add_parser(
'build',
help='Adds latex doc header including '
'begin/close document, title, author etc...',
usage='%s --globals <build> texfile outpath --opts ' % SCRIPTNAME,
epilog='Put examples here')
p_build.add_argument('texfile',
help='Output file of %s template' % SCRIPTNAME)
p_build.add_argument(
'outpath',
metavar='outfile',
help='Name of outfile (eg foo.tex or path/to/foo.tex)')
p_build.add_argument('--title',
default='Untitled',
metavar='',
help='Title '
' in outfile')
p_build.add_argument('--author',
default='Adam Hughes',
metavar='',
help='Author in outfile')
p_build.add_argument('--email',
default='*****@*****.**',
metavar='',
help='Email in outfile')
# Compile and open
p_build.add_argument('--nocompile',
action='store_true',
help='Do not compile outfile'
' (eg latex outfile.tex)')
p_build.add_argument('--nopdf',
action='store_true',
help='When compiling,'
' will call "latex" instead of "pdflatex"')
p_build.add_argument('-c',
'--clean',
action='store_true',
help='Remove .aux, .log'
' and other latex temporary files.')
#SUMMARY SUBCOMMAND (not implemented)
#p_summary = subparsers.add_parser('summary', help='summary help')
#p_summary.add_argument('texfile')
ns = parser.parse_args()
# No logfile implemented
configure_logger(screen_level='debug', name=__name__)
logger.info('Namespace is: %s' % ns)
reporter = Reporter(**ns.__dict__) # Is this ok?
if ns.op == 'template':
reporter.output_template(ns.outpath)
elif ns.op == 'build':
reporter.make_report(ns.texfile, ns.outpath)
# If compiling, choose pdflatex or latex
if not ns.nocompile:
if not ns.nopdf:
latex_type = 'pdflatex'
else:
latex_type = 'latex'
# Run latex or pdflatex twice to ensure contents load
os.system('%s %s' % (latex_type, ns.outpath))
os.system('%s %s' % (latex_type, ns.outpath))
# Cleanup latex .toc/.log/.aux files of outfile
if ns.clean:
outdir, outname = op.split(op.abspath(ns.outpath))
outname = op.splitext(outname)[0]
for ext in ['toc', 'log', 'aux', 'out']:
wastefile = op.join(outdir, outname + '.' + ext)
if op.isfile(wastefile):
logger.info('Cleaning up file: "%s"' % wastefile)
os.remove(wastefile)
else:
NotImplemented
def main():
ns = parse()
configure_logger(screen_level="info", name=__name__)
logger.info("Logging initialized: set to info")
outfile = op.abspath(op.join(SECTIONREPORTSDIR, OUTNAME))
if op.exists(outfile) and not ns.overwrite:
raise IOError("%s ALREADY EXISTS. Remove or rerun with -o flag." % outfile)
# Get all files; warn if directories found
infiles = files_in_dir(SECTIONREPORTSDIR)
## Execute any outstanding tex files
# if ns.runtexs:
# texfiles = [f for f in infiles if ext(f) == '.tex']
## Don't run sweavetree.tex, only other tex files
# if outfile in texfiles:
# texfiles.remove( outfile )
## pdflatex on all files
# for tf in texfiles:
# logger.info('Twice executing "pdflatex %s"' % tf)
## Switch wd of auxilarry files will be written to .
# wd = os.getcwd()
# os.chdir(SECTIONREPORTSDIR)
# os.system('pdflatex %s' % tf )
# os.system('pdflatex %s' % tf )
# os.chdir(wd)
## Regenerate files list as files have been udpated
# infiles = files_in_dir(SECTIONREPORTSDIR)
# Sort pdfs and make .tex snippet
pdfs = [op.abspath(f) for f in infiles if ext(f) == ".pdf"]
if not pdfs:
raise AttributeError('NO PDFS FOUND IN "%s"' % SECTIONREPORTSDIR)
pdfs.sort()
# Consider making different styles
with open(outfile, "w") as o:
for idx, filename in enumerate(pdfs):
# Take filename, replace '_' with '/' and remove .pdf to make section title
# /foo/bar/f1_npsam.pdf ---> f1/npsam
secname = op.basename(filename).replace("_", "-").replace(".pdf", "")
outfile = op.join(SECTIONREPORTSDIR, op.basename(filename))
if idx == 0:
sectionheading = "\section{Sectional Data Analysis}\subsection{%s}" % secname
else:
sectionheading = "\subsection{%s}" % secname
o.write("\includepdf[pages=1, offset=25 0, pagecommand=%s]{%s}\n" % (sectionheading, outfile))
o.write("\includepdf[pages=2-,pagecommand={}]{%s}\n" % outfile)
o.close()
logger.info("%s written." % outfile)
# Compile main report
if ns.pdf:
texfiles = [f for f in files_in_dir(".") if ext(f) == ".tex"]
if len(texfiles) > 1:
logger.critical(
"There are more than one .tex files in this current" " directory. Am not going to compile them..."
)
elif len(texfiles) == 0:
logger.warn("No tex files found in current directory: --pdf option ignored use")
else:
maintexfile = texfiles[0]
os.system("pdflatex %s" % maintexfile)
os.system("pdflatex %s" % maintexfile)
# \includepdf[pages=1,pagecommand=\section{Sectional Data Analysis}
# \subsection{Fiber1/NPSAM}]{foo.pdf}
# \includepdf[pages=2,pagecommand={}]{foo.pdf}
# Clean up temporary tex files IN SWEAVESECTIONS
if ns.clean:
logger.warn("Removing all files of types %s in %s" % (TEMPFILES, SECTIONREPORTSDIR))
for filename in infiles:
if ext(filename) in TEMPFILES:
os.remove(filename)
logger.warn("Removing all files of types %s in CURRENT DIRECTORY" % TEMPFILES)
for filename in files_in_dir("."):
if ext(filename) in TEMPFILES:
os.remove(filename)
def main(args=None):
if args:
if isinstance(args, basestring):
args=shlex.split(args)
sys.argv = args
parser = argparse.ArgumentParser(SCRIPTNAME, description='GWU PyUvVis composite'
' latex report assembly script', epilog='Additional help not found',
usage='%s --globals <command> --cmdopts' % SCRIPTNAME)
parser.add_argument('-v', '--verbosity', help='Set screen logging; '
'defaults to info.', nargs='?',
default='warning', const='info', metavar='')
parser.add_argument('-o', '--overwrite', action='store_true')
# parser.add_argument('-s', '--sep', metavar='',
# help='Latex section separator. Defaults to %s. '
# 'Set to None to avoid auto sub-sectioning' %SEP_DEFAULT)
# Sub Commands
subparsers = parser.add_subparsers(title='commands', metavar='', dest='op')
# TEMPLATE SUBCOMMAND
p_template = subparsers.add_parser('template',
usage = '%s --globals <template> outpath --opts ' % SCRIPTNAME,
help='template help',
epilog='PUT EXAMPLES HERE')
p_template.add_argument('outpath', metavar='outfile',
help='Name of outfile (eg foo.tex or path/to/foo.tex)')
p_template.add_argument('-s', '--sections', metavar='', nargs='*', help='List of sections to add.'
'or tree file. If not tree file, default section template will be "template/section" '
'section names will auto-break into subsections based on value of --sep',
default=[])
p_template.add_argument('-t', '--template_file', metavar='')
# BUILD SUBCOMMAND
p_build = subparsers.add_parser('build', help='Adds latex doc header including '
'begin/close document, title, author etc...',
usage = '%s --globals <build> texfile outpath --opts ' % SCRIPTNAME,
epilog='Put examples here')
p_build.add_argument('texfile', help='Output file of %s template' % SCRIPTNAME)
p_build.add_argument('outpath', metavar='outfile',
help='Name of outfile (eg foo.tex or path/to/foo.tex)')
p_build.add_argument('--title', default='Untitled', metavar='', help='Title '
' in outfile')
p_build.add_argument('--author', default='Adam Hughes', metavar='',
help='Author in outfile')
p_build.add_argument('--email', default='*****@*****.**', metavar='',
help='Email in outfile')
# Compile and open
p_build.add_argument('--nocompile', action='store_true', help='Do not compile outfile'
' (eg latex outfile.tex)' )
p_build.add_argument('--nopdf', action='store_true', help='When compiling,'
' will call "latex" instead of "pdflatex"')
p_build.add_argument('-c', '--clean', action = 'store_true', help='Remove .aux, .log'
' and other latex temporary files.')
#SUMMARY SUBCOMMAND (not implemented)
#p_summary = subparsers.add_parser('summary', help='summary help')
#p_summary.add_argument('texfile')
ns = parser.parse_args()
# No logfile implemented
configure_logger(screen_level='debug', name=__name__)
logger.info('Namespace is: %s' % ns)
reporter = Reporter(**ns.__dict__) # Is this ok?
if ns.op == 'template':
reporter.output_template(ns.outpath)
elif ns.op == 'build':
reporter.make_report(ns.texfile, ns.outpath)
# If compiling, choose pdflatex or latex
if not ns.nocompile:
if not ns.nopdf:
latex_type = 'pdflatex'
else:
latex_type = 'latex'
# Run latex or pdflatex twice to ensure contents load
os.system('%s %s' % (latex_type, ns.outpath) )
os.system('%s %s' % (latex_type, ns.outpath) )
# Cleanup latex .toc/.log/.aux files of outfile
if ns.clean:
outdir, outname = op.split(op.abspath(ns.outpath))
outname = op.splitext(outname)[0]
for ext in ['toc', 'log', 'aux', 'out']:
wastefile = op.join(outdir, outname + '.' + ext)
if op.isfile(wastefile):
logger.info('Cleaning up file: "%s"' % wastefile)
os.remove(wastefile)
else:
NotImplemented
