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 required images
for figman in fig_managers:
# create all images
figid = figman.num
# select the correct figure
figure = plt.figure(figid)
# save explicit formats
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 []
# insert display figure
is_html = False
script_text = None
if USE_MPLD3:
outpath = os.path.join(
outdir,
'%s.html' % (outname))
# plt.legend()
# write to file
with open(outpath, "w") as outf:
outf.write(mpld3.fig_to_html(figure))
is_html = True
elif USE_BOKEH:
outpath = os.path.join(
outdir,
'%s.html' % (outname))
is_html = True
# (try to) convert to bokeh figure
try:
# pd_job - use pandas object
# xkcd - use xkcd style
renderer = bokeh.mpl.BokehRenderer(pd_obj=True,
xkcd=False)
exporter = bokeh.mplexporter.exporter.Exporter(renderer)
exporter.run(figure)
bpl = renderer.fig
except NotImplementedError:
# fall back to matplotlib
is_html = False
if is_html:
bokeh_id = bpl._id
res = bokeh.resources.CDN
script_path = os.path.join(
'_static/report_directive/',
"%s.js" % bokeh_id)
# get js figure and html snippet
js_text, script_text = bokeh.embed.autoload_static(
bpl, res, script_path)
with open(script_path, "w") as outf:
outf.write(js_text)
with open(outpath, "w") as outf:
outf.write(script_text)
# create the text element
rst_output = Utils.buildRstWithImage(
outname,
outdir,
rstdir,
builddir,
srcdir,
additional_formats,
tracker_id,
links,
display_options,
default_format,
is_html=is_html,
text=script_text)
map_figure2text["#$mpl %i$#" % figid] = rst_output
return map_figure2text
def collect(self, blocks, figure_key="", subfig=0):
'''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 is None:
return {}
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats(
self.display_options)
all_formats = [default_format, ] + additional_formats
image_options = Utils.getImageOptions(self.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" % (self.template_name, figid)
outpath = os.path.join(self.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(self.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(self.content) + "\n")
outfile.close()
R["dev.off"](figid)
# create the text element
rst_output = Utils.buildRstWithImage(outname,
self.outdir,
self.rstdir,
self.builddir,
self.srcdir,
additional_formats,
self.tracker_id,
self.links,
self.display_options)
map_figure2text["#$rpl %i$#" % figid] = rst_output
figid = maxid
##########################################
##########################################
##########################################
# iterate over ggplot plots
for block in blocks:
if not hasattr(block, "rggplot"):
continue
pp = block.rggplot
figname = block.figname
outname = "%s_%s" % (self.template_name, figname)
for id, format, dpi in all_formats:
outpath = os.path.join(self.outdir, '%s.%s' % (outname, format))
try:
R.ggsave(outpath, plot=pp, dpi=dpi)
except rpy2.rinterface.RRuntimeError as 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,
self.outdir,
self.rstdir,
self.builddir,
self.srcdir,
additional_formats,
self.tracker_id,
self.links,
self.display_options)
map_figure2text["#$ggplot %s$#" % figname] = rst_output
return map_figure2text
def collect(self, blocks, figure_key=None, subfig=0):
'''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()
self.debug("figure_key: {}, subfig: {}: collecting {} matplotlib images".format(
figure_key, subfig, len(fig_managers)))
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats(
self.display_options)
all_formats = [default_format, ] + additional_formats
# create all required images
for figman in fig_managers:
# create all images
figid = figman.num
# select the correct figure
figure = plt.figure(figid)
# save explicit formats
outname = "%s_%s_%02d_%02d" % (self.template_name, figure_key, subfig, figid)
has_output = False
for id, format, dpi in all_formats:
outpath = os.path.join(self.outdir, '%s.%s' % (outname, format))
# sanitize figure size for Agg.
if figure.get_figwidth() > 32768 or figure.get_figheight() > 32768:
warnings.warn(
"figure size unexpected large {} x {}, "
"patching to 10x10 inches".format(
figure.get_figwidth(), figure.get_figheight()))
figure.set_size_inches(10, 10)
try:
figman.canvas.figure.savefig(outpath, dpi=dpi)
except Exception as ex:
s = Utils.collectExceptionAsString(
"exception raised while building plot '%s': %s" %
(outpath, str(ex)))
warnings.warn(s)
continue
has_output = True
if not has_output:
warnings.warn("no output for '%s'" % outpath)
continue
# insert display figure
is_html = False
script_text = None
if HAVE_MPLD3 and \
Utils.PARAMS.get("report_mpl", None) == "mpld3":
outpath = os.path.join(
self.outdir,
'%s.html' % (outname))
# plt.legend()
# write to file
with open(outpath, "w") as outf:
outf.write(mpld3.fig_to_html(figure))
is_html = True
elif HAVE_BOKEH and \
Utils.PARAMS.get("report_mpl", None) == "bokeh":
outpath = os.path.join(
self.outdir,
'%s.html' % (outname))
is_html = True
# (try to) convert to bokeh figure
try:
bokeh_figure = bokeh.mpl.to_bokeh(figure,
use_pandas=True,
xkcd=False)
except NotImplementedError:
# fall back to matplotlib
is_html = False
if is_html:
bokeh_id = bokeh_figure._id
res = bokeh.resources.CDN
script_path = os.path.join(
'_static/report_directive/',
"%s.js" % bokeh_id)
# get js figure and html snippet
js_text, script_text = bokeh.embed.autoload_static(
bokeh_figure, res, script_path)
with open(script_path, "w") as outf:
outf.write(js_text)
with open(outpath, "w") as outf:
outf.write(script_text)
# release memory
plt.close(figure)
# create the text element
rst_output = Utils.buildRstWithImage(
outname,
self.outdir,
self.rstdir,
self.builddir,
self.srcdir,
additional_formats,
self.tracker_id,
self.links,
self.display_options,
default_format,
is_html=is_html,
text=script_text)
if figure_key is None:
f = figid
else:
f = "{}.{}".format(figure_key, figid)
map_figure2text["#$mpl {}$#".format(f)] = rst_output
return map_figure2text
def collect(self, blocks, figure_key=None, subfig=0):
'''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()
self.debug("figure_key: {}, subfig: {}: collecting {} matplotlib images".format(
figure_key, subfig, len(fig_managers)))
map_figure2text = {}
# determine the image formats to create
default_format, additional_formats = Utils.getImageFormats(
self.display_options)
all_formats = [default_format, ] + additional_formats
# create all required images
for figman in fig_managers:
# create all images
figid = figman.num
# select the correct figure
figure = plt.figure(figid)
# save explicit formats
outname = "%s_%s_%02d_%02d" % (self.template_name, figure_key, subfig, figid)
has_output = False
for id, format, dpi in all_formats:
outpath = os.path.join(self.outdir, '%s.%s' % (outname, format))
# sanitize figure size for Agg.
if figure.get_figwidth() > 32768 or figure.get_figheight() > 32768:
warnings.warn(
"figure size unexpected large {} x {}, "
"patching to 10x10 inches".format(
figure.get_figwidth(), figure.get_figheight()))
figure.set_size_inches(10, 10)
try:
figman.canvas.figure.savefig(outpath, dpi=dpi)
except Exception as ex:
s = Utils.collectExceptionAsString(
"exception raised while building plot '%s': %s" %
(outpath, str(ex)))
warnings.warn(s)
continue
has_output = True
if not has_output:
warnings.warn("no output for '%s'" % outpath)
continue
# insert display figure
is_html = False
script_text = None
# release memory
plt.close(figure)
# create the text element
rst_output = Utils.buildRstWithImage(
outname,
self.outdir,
self.rstdir,
self.builddir,
self.srcdir,
additional_formats,
self.tracker_id,
self.links,
self.display_options,
default_format,
is_html=is_html,
text=script_text)
if figure_key is None:
f = figid
else:
f = "{}.{}".format(figure_key, figid)
map_figure2text["#$mpl {}$#".format(f)] = rst_output
return map_figure2text
