def collect(
self, blocks, template_name, outdir, rstdir, builddir, srcdir, content, display_options, tracker_id, links={}
):
"""collect one or more matplotlib figures and
1. save as png, hires-png and pdf
2. save thumbnail
3. insert rendering code at placeholders in output
returns a map of place holder to placeholder text.
"""
fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats(display_options)
all_formats = [default_format] + additional_formats
# create all the images
for figman in fig_managers:
# create all images
figid = figman.num
outname = "%s_%02d" % (template_name, figid)
for id, format, dpi in all_formats:
outpath = os.path.join(outdir, "%s.%s" % (outname, format))
try:
figman.canvas.figure.savefig(outpath, dpi=dpi)
except:
s = Utils.collectExceptionAsString("Exception running plot %s" % outpath)
warnings.warn(s)
return []
# if format=='png':
# thumbdir = os.path.join(outdir, 'thumbnails')
# try:
# os.makedirs(thumbdir)
# except OSError:
# pass
# thumbfile = str('%s.png' % os.path.join(thumbdir, outname) )
# captionfile = str('%s.txt' % os.path.join(thumbdir, outname) )
# if not os.path.exists(thumbfile):
# # thumbnail only available in matplotlib >= 0.98.4
# try:
# figthumb = image.thumbnail(str(outpath), str(thumbfile), scale=0.3)
# except AttributeError:
# pass
# outfile = open(captionfile,"w")
# outfile.write( "\n".join( content ) + "\n" )
# outfile.close()
# create the text element
rst_output = Utils.buildRstWithImage(
outname,
outdir,
rstdir,
builddir,
srcdir,
additional_formats,
tracker_id,
links,
display_options,
default_format,
)
map_figure2text["#$mpl %i$#" % figid] = rst_output
return map_figure2text
def collect( self,
blocks,
template_name,
outdir,
rstdir,
rst2rootdir,
rst2builddir,
rst2srcdir,
content,
display_options,
linked_codename,
tracker_id):
'''collect one or more matplotlib figures and
1. save as png, hires-png and pdf
2. save thumbnail
3. insert rendering code at placeholders in output
returns a map of place holder to placeholder text.
'''
fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats()
all_formats = [default_format,] + additional_formats
urls = Utils.asList( Utils.PARAMS["report_urls"] )
# create all the images
for figman in fig_managers:
# create all images
figid = figman.num
for id, format, dpi in all_formats:
outname = "%s_%02d" % (template_name, figid)
outpath = os.path.join(outdir, '%s.%s' % (outname, format))
try:
figman.canvas.figure.savefig( outpath, dpi=dpi )
except:
s = exception_to_str("Exception running plot %s" % outpath)
warnings.warn(s)
return []
if format=='png':
thumbdir = os.path.join(outdir, 'thumbnails')
try:
os.makedirs(thumbdir)
except OSError:
pass
thumbfile = str('%s.png' % os.path.join(thumbdir, outname) )
captionfile = str('%s.txt' % os.path.join(thumbdir, outname) )
if not os.path.exists(thumbfile):
# thumbnail only available in matplotlib >= 0.98.4
try:
figthumb = image.thumbnail(str(outpath), str(thumbfile), scale=0.3)
except AttributeError:
pass
outfile = open(captionfile,"w")
outfile.write( "\n".join( content ) + "\n" )
outfile.close()
# create the text element
rst_output = ""
# for image directive - image path is relative from rst file to external build dir
imagepath = re.sub( "\\\\", "/", os.path.join( rst2builddir, outname ) )
# for links - path is from rst file to internal root dir
# one rst file for all
relative_imagepath_rst = re.sub( "\\\\", "/", os.path.join( rst2rootdir, template_name ) )
relative_imagepath_img = re.sub( "\\\\", "/", os.path.join( rst2rootdir, outname ) )
linked_text = relative_imagepath_rst + ".txt"
if Config.HTML_IMAGE_FORMAT:
id, format, dpi = Config.HTML_IMAGE_FORMAT
template = '''
.. htmlonly::
.. image:: %(linked_image)s
%(display_options)s
[%(code_url)s %(rst_url)s %(data_url)s %(extra_images)s]
'''
linked_image = imagepath + ".%s" % format
extra_images=[]
for id, format, dpi in additional_formats:
extra_images.append( "`%(id)s <%(relative_imagepath_img)s.%(format)s>`__" % locals())
if extra_images: extra_images = " " + " ".join( extra_images)
else: extra_images = ""
# construct additional urls
code_url, data_url, rst_url, table_url = "", "", "", ""
if "code" in urls:
code_url = "`code <%(linked_codename)s>`__" % locals()
if "data" in urls:
data_url = "`data </data/%(tracker_id)s>`__" % locals()
if "rst" in urls:
rst_url = "`rst <%(linked_text)s>`__" % locals()
rst_output += template % locals()
# treat latex separately
if Config.LATEX_IMAGE_FORMAT:
id, format, dpi = Config.LATEX_IMAGE_FORMAT
template = '''
.. latexonly::
.. image:: %(linked_image)s
%(display_options)s
'''
linked_image = imagepath + ".%s" % format
rst_output += template % locals()
map_figure2text[ "#$mpl %i$#" % figid] = rst_output
return map_figure2text
def collect( self,
blocks,
template_name,
outdir,
rstdir,
rst2rootdir,
rst2builddir,
rst2srcdir,
content,
display_options,
linked_codename,
tracker_id):
'''collect one or more R figures from all active devices
and
1. save as png, hires-png and pdf
2. save thumbnail
3. insert rendering code at placeholders in output
returns a map of place holder to placeholder text.
'''
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats()
all_formats = [default_format,] + additional_formats
urls = Utils.asList( Utils.PARAMS["report_urls"] )
devices = R["dev.list"]()
try:
maxid = max( R["dev.list"]() )
except TypeError:
return map_figure2text
for figid in range( 2, maxid+1 ):
for id, format, dpi in all_formats:
R["dev.set"]( figid )
outname = "%s_%02d" % (template_name, figid)
outpath = os.path.join(outdir, '%s.%s' % (outname, format))
if format.endswith( "png" ):
R["dev.copy"]( device = R.png,
filename = outpath,
res = dpi )
R["dev.off"]()
elif format.endswith( "svg" ):
R["dev.copy"]( device = R.svg,
filename = outpath )
R["dev.off"]()
elif format.endswith( "eps" ):
R["dev.copy"]( device = R.postscript,
file = outpath,
onefile = True )
R["dev.off"]()
else:
raise ValueError( "format '%s' not supported" % format )
if not os.path.exists( outpath ):
continue
# raise ValueError( "rendering problem: image file was not be created: %s" % outpath )
if format=='png':
thumbdir = os.path.join(outdir, 'thumbnails')
try:
os.makedirs(thumbdir)
except OSError:
pass
thumbfile = str('%s.png' % os.path.join(thumbdir, outname) )
captionfile = str('%s.txt' % os.path.join(thumbdir, outname) )
if not os.path.exists(thumbfile):
# thumbnail only available in matplotlib >= 0.98.4
try:
figthumb = image.thumbnail(str(outpath), str(thumbfile), scale=0.3)
except AttributeError:
pass
outfile = open(captionfile,"w")
outfile.write( "\n".join( content ) + "\n" )
outfile.close()
R["dev.off"](figid)
# create the text element
rst_output = ""
# for image diretive - image path is relative from rst file to external build dir
imagepath = re.sub( "\\\\", "/", os.path.join( rst2builddir, outname ) )
# for links - path is from rst file to internal root dir
relative_imagepath = re.sub( "\\\\", "/", os.path.join( rst2rootdir, outname ) )
linked_text = relative_imagepath + ".txt"
if Config.HTML_IMAGE_FORMAT:
id, format, dpi = Config.HTML_IMAGE_FORMAT
template = '''
.. htmlonly::
.. image:: %(linked_image)s
%(display_options)s
[%(code_url)s %(rst_url)s %(data_url)s %(extra_images)s]
'''
linked_image = imagepath + ".%s" % format
extra_images=[]
for id, format, dpi in additional_formats:
extra_images.append( "`%(id)s <%(relative_imagepath)s.%(format)s>`__" % locals())
if extra_images: extra_images = " " + " ".join( extra_images)
else: extra_images = ""
# construct additional urls
code_url, data_url, rst_url = "", "", ""
if "code" in urls:
code_url = "`code <%(linked_codename)s>`__" % locals()
if "data" in urls:
data_url = "`data </data/%(tracker_id)s>`__" % locals()
if "rst" in urls:
rst_url = "`rst <%(linked_text)s>`__" % locals()
rst_output += template % locals()
# treat latex separately
if Config.LATEX_IMAGE_FORMAT:
id, format, dpi = Config.LATEX_IMAGE_FORMAT
template = '''
.. latexonly::
.. image:: %(linked_image)s
%(display_options)s
'''
linked_image = imagepath + ".%s" % format
rst_output += template % locals()
map_figure2text[ "#$rpl %i$#" % figid] = rst_output
return map_figure2text
def collect( self,
blocks,
template_name,
outdir,
rstdir,
builddir,
srcdir,
content,
display_options,
tracker_id,
links = {}):
'''collect one or more R figures.
Plots are collected from all active devices.
Plots are also collected from result-blocks
containing a 'ggplot' attribute.
1. save as png, hires-png and pdf
2. save thumbnail
3. insert rendering code at placeholders in output
returns a map of place holder to placeholder text.
'''
# disable plotting if no rpy installed
if R == None: return {}
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats( display_options )
all_formats = [default_format,] + additional_formats
image_options = Utils.getImageOptions( display_options )
##########################################
##########################################
##########################################
# iterate over devices
devices = R["dev.list"]()
try:
maxid = max( R["dev.list"]() )
except TypeError:
maxid = 0
for figid in range( 2, maxid+1 ):
for id, format, dpi in all_formats:
R["dev.set"]( figid )
outname = "%s_%02d" % (template_name, figid)
outpath = os.path.join(outdir, '%s.%s' % (outname, format))
if format.endswith( "png" ):
# for busy images there is a problem with figure margins
# simply increase dpi until it works.
R["dev.set"]( figid )
width = height = 480 * dpi / 80
x = 0
while 1:
try:
R["dev.copy"]( device = R.png,
filename = outpath,
res = dpi,
width = width,
height = height )
R["dev.off"]()
except rpy2.rinterface.RRuntimeError:
width *= 2
height *= 2
if x < 5:
continue
break
elif format.endswith( "svg" ):
R["dev.copy"]( device = R.svg,
filename = outpath )
R["dev.off"]()
elif format.endswith( "eps" ):
R["dev.copy"]( device = R.postscript,
paper = 'special',
width = 6,
height = 6,
file = outpath,
onefile = True )
R["dev.off"]()
elif format.endswith( "pdf" ):
R["dev.copy"]( device = R.pdf,
paper = 'special',
width = 6,
height = 6,
file = outpath,
onefile = True )
R["dev.off"]()
else:
raise ValueError( "format '%s' not supported" % format )
if not os.path.exists( outpath ):
continue
# raise ValueError( "rendering problem: image file was not be created: %s" % outpath )
if format=='png':
thumbdir = os.path.join(outdir, 'thumbnails')
try:
os.makedirs(thumbdir)
except OSError:
pass
thumbfile = str('%s.png' % os.path.join(thumbdir, outname) )
captionfile = str('%s.txt' % os.path.join(thumbdir, outname) )
if not os.path.exists(thumbfile):
# thumbnail only available in matplotlib >= 0.98.4
try:
figthumb = image.thumbnail(str(outpath), str(thumbfile), scale=0.3)
except AttributeError:
pass
outfile = open(captionfile,"w")
outfile.write( "\n".join( content ) + "\n" )
outfile.close()
R["dev.off"](figid)
# create the text element
rst_output = Utils.buildRstWithImage( outname,
outdir,
rstdir,
builddir,
srcdir,
additional_formats,
tracker_id,
links,
display_options )
map_figure2text[ "#$rpl %i$#" % figid] = rst_output
figid = maxid
##########################################
##########################################
##########################################
# iterate over ggplot plots
for xblocks in blocks:
for block in xblocks:
if not hasattr( block, "rggplot" ): continue
pp = block.rggplot
figname = block.figname
outname = "%s_%s" % (template_name, figname)
for id, format, dpi in all_formats:
outpath = os.path.join(outdir, '%s.%s' % (outname, format))
try:
R.ggsave( outpath, plot = pp, dpi = dpi )
except rpy2.rinterface.RRuntimeError, msg:
raise
# width, height = 3 * dpi, 3 * dpi
# if format.endswith( "png"):
# R.png( outpath,
# width = width,
# height = height )
# elif format.endswith( "svg" ):
# R.svg( outpath )
# elif format.endswith( "eps" ):
# R.postscript( outpath )
# elif format.endswith( "pdf" ):
# R.pdf( outpath )
#R.plot( pp )
# R["dev.off"]()
# create the text element
rst_output = Utils.buildRstWithImage( outname,
outdir,
rstdir,
builddir,
srcdir,
additional_formats,
tracker_id,
links,
display_options )
map_figure2text[ "#$ggplot %s$#" % figname] = rst_output
