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