def render_text(self, text,file_type='png', width=0, height=0,color="Black"):
surface = None
width=int(width)
height=int(height)
text= text.decode("utf-8")
filename = str(uuid.uuid1())[0:5]+"."+file_type
outputfile = os.path.join(self.tmp_folder, filename )
if file_type == 'png':
surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, int(width), int(height))
if file_type == 'svg':
surface = cairo.SVGSurface(outputfile,int(width),int(height))
if file_type == 'pdf':
surface = cairo.PDFSurface(outputfile,int(width),int(height))
context = cairo.Context(surface)
try:
text = hyphenator.getInstance().hyphenate(text,u'\u00AD')
except:
print("error while hyphenating. Proceeding without Hyphenation")
width = int(width)
font_size = 10
left_margin = 10
top_margin = 10
position_x = left_margin
position_y = top_margin
rgba = get_color(color)
context.set_source_rgba (rgba.red,rgba.green,rgba.blue,rgba.alpha)
pc = pangocairo.CairoContext(context)
paragraph_layout = pc.create_layout()
paragraph_font_description = pango.FontDescription()
paragraph_font_description.set_family("Serif")
paragraph_font_description.set_size((int)(int(font_size) * pango.SCALE))
paragraph_layout.set_font_description(paragraph_font_description)
if width>0:
paragraph_layout.set_width((int)((width-2*left_margin) * pango.SCALE))
paragraph_layout.set_justify(True)
paragraph_layout.set_text(text+"\n")
context.move_to(position_x, position_y)
pango_layout_iter = paragraph_layout.get_iter();
line_width = 0
while not pango_layout_iter.at_last_line():
first_line = True
context.move_to(position_x, position_y)
while not pango_layout_iter.at_last_line() :
ink_rect, logical_rect = pango_layout_iter.get_line_extents()
line = pango_layout_iter.get_line_readonly()
has_next_line=pango_layout_iter.next_line()
# Decrease paragraph spacing
if ink_rect[2] == 0 : #It is para break
dy = font_size / 2
position_y += dy
if not first_line:
self.context.rel_move_to(0, dy)
else:
xstart = 1.0 * logical_rect[0] / pango.SCALE
context.rel_move_to(xstart, 0)
if width >0 and height > 0 :
pc.show_layout_line( line)
line_height = (int)(logical_rect[3] / pango.SCALE)
line_width = (int)(logical_rect[2] / pango.SCALE)
context.rel_move_to(-xstart, line_height )
position_y += line_height
first_line = False
if width==0 or height==0:
if width==0:
width = line_width
if height==0:
height = position_y
return self.render_text(text,file_type, width + 2.5*left_margin, height,color)
if file_type == 'png':
surface.write_to_png(outputfile)
else:
context.show_page()
return "modules/render/tmp/"+filename
knownCommands["c"] = circle
knownCommands["translate"] = translate
knownCommands["stroke"] = stroke
# knownCommands["rotate"] = rotate
def parseCommand(ctx, cmd, values):
global knownCommands
if cmd in knownCommands:
knownCommands[cmd](ctx, values)
else:
print("skipping task " + cmd + ", ".join([str(x) for x in values]))
f = open(sys.argv[1], 'r')
filename = sys.argv[1] + ".svg"
surface = cairo.SVGSurface(filename, 8.5 * 300, 11 * 300)
context = cairo.Context(surface)
for line in f:
ll = line.split(" ")
cmd = ll[0]
vals = [float(x) for x in ll[1:]]
parseCommand(context, cmd, vals)
context.stroke()
symlink_force(filename, "latest.svg")
@property
def start(self):
return (radius * math.cos(self.start_theta)) + cx, (radius * math.sin(self.start_theta)) + cy
@property
def end(self):
return (radius * math.cos(self.end_theta)) + cx, (radius * math.sin(self.end_theta)) + cy
# mults = arange(2, n_lines // 2, .002)
# for n in mults:
# hue_start += .001
n = multiplier
lines = [Line(i, angle_step * i - math.pi, angle_step * ((i * n) % n_lines) - math.pi) for i in range(n_lines)]
with cairo.SVGSurface('logo.svg', width, height) as surface:
# with cairo.ImageSurface(cairo.FORMAT_ARGB32, width, height) as surface:
ctx = cairo.Context(surface)
ctx.set_line_width(1)
# ctx.set_font_size(8)
# r1 = cairo.RadialGradient(cx, cy, 50, cx, cy, radius)
# r1.add_color_stop_rgb(1, .1, .1, .1)
# r1.add_color_stop_rgb(0, .05, .05, .05)
# ctx.set_source(r1)
# ctx.rectangle(0, 0, width, height)
# ctx.fill()
for line in lines:
# ctx.set_source_rgba(0, 0, 0, 1)
# radius += 8
# ctx.move_to(*line.start)
# ctx.show_text(str(line.place or n_lines))
message('rendering: %s -> %s...' % (pname, outfilename))
view = View(diagram.canvas)
view.painter = ItemPainter()
tmpsurface = cairo.ImageSurface(cairo.FORMAT_ARGB32, 0, 0)
tmpcr = cairo.Context(tmpsurface)
view.update_bounding_box(tmpcr)
tmpcr.show_page()
tmpsurface.flush()
w, h = view.bounding_box.width, view.bounding_box.height
if options.format == 'pdf':
surface = cairo.PDFSurface(outfilename, w, h)
elif options.format == 'svg':
surface = cairo.SVGSurface(outfilename, w, h)
elif options.format == 'png':
surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, int(w+1), int(h+1))
else:
assert False, 'unknown format %s' % options.format
cr = cairo.Context(surface)
view.matrix.translate(-view.bounding_box.x, -view.bounding_box.y)
view.paint(cr)
cr.show_page()
if options.format == 'png':
surface.write_to_png(outfilename)
surface.flush()
surface.finish()
InputMotif.close()
#Create three lists pertaining to the colors that will be used to represent each individual motif
red = []
green = []
blue = []
for motif in motifs:
red.append(random.randint(0, 100) / 100)
green.append(random.randint(0, 100) / 100)
blue.append(random.randint(0, 100) / 100)
############################
#Create our base x and y draw values and initiate our cairo surface by the calculated values
x = 25 #This can be used to tune how far fromt he margin we wish to start our images/writing
y = 0
surface = cairo.SVGSurface(FileName + ".svg", entrylength + (x * 2),
(nlines * 50) + 50)
context = cairo.Context(surface)
context.set_font_size(8)
#Draw a legend of what each motif color means
n = 25 #Decides how far down the y acis we wish to start our legend
for motif, r, g, b in zip(motifs, red, green, blue):
if n == 25:
n = draw_legend(r, g, b, n, motif)
else:
n = draw_legend(r, g, b, n, motif)
############################
#The way we will draw the exons will be to first draw an entire line to signify the whole gene (introns) then for each position in which
#an upper case character was found (exon), we will draw a vertical line. Then we will look at the motifs and draw different
#colored horizontal lines through each respective site
def render(options):
# create view
if (options.view):
columns = options.viewcolumns.split(',')
if (options.extracolumns):
columns += options.extracolumns.split(',')
create_views(options.dsn, options.dbprefix, options.viewprefix,
options.viewhstore, columns, options.date)
# create map
m = mapnik.Map(options.size[0], options.size[1])
# load style
mapnik.load_map(m, options.style)
# create projection object
prj = mapnik.Projection(
"+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +no_defs +over"
)
#c0 = prj.forward(Coord(bbox[0],bbox[1]))
#c1 = prj.forward(Coord(bbox[2],bbox[3]))
#e = Box2d(c0.x,c0.y,c1.x,c1.y)
# map bounds
if hasattr(mapnik, 'Box2d'):
bbox = mapnik.Box2d(*options.bbox)
else:
bbox = mapnik.Envelope(*options.bbox)
# project bounds to map projection
e = mapnik.forward_(bbox, prj)
# zoom map to bounding box
m.zoom_to_box(e)
options.file = options.file + "." + options.type
if (options.type in ("png", "jpeg")):
s = mapnik.Image(options.size[0], options.size[1])
elif cairo_exists and type == "svg":
s = cairo.SVGSurface(options.file, options.size[0], options.size[1])
elif cairo_exists and type == "pdf":
s = cairo.PDFSurface(options.file, options.size[0], options.size[1])
elif cairo_exists and type == "ps":
s = cairo.PSSurface(options.file, options.size[0], options.size[1])
else:
print "invalid image type"
print
parser.print_help()
sys.exit(1)
mapnik.render(m, s)
if isinstance(s, mapnik.Image):
view = s.view(0, 0, options.size[0], options.size[1])
view.save(options.file, options.type)
elif isinstance(s, cairo.Surface):
s.finish()
if (options.view):
drop_views(options.dsn, options.viewprefix)
def setup_svg(self):
self.surface = cairo.SVGSurface(self.fullpath, self.width, self.height)
return cairo.Context(self.surface)
sumY = sumY + sums[1]
sumX = sumX / len(magnets)
sumY = sumY / len(magnets)
p.resetForce()
p.setForce(sumX, sumY)
p.update()
p.edges()
if t % 8 == 0:
p.draw(context)
p.setLastPos()
# Call the main function
if __name__ == '__main__':
if fileFormat == 'PNG':
surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, width, height)
context = cairo.Context(surface)
main()
filename = uuid.uuid4().hex[:8]
surface.write_to_png('Images/Magnetic_Flow/' + str(filename) + '.png')
elif fileFormat == 'SVG':
filename = uuid.uuid4().hex[:8]
surface = cairo.SVGSurface(
'Images/Magnetic_Flow/0-svg/' + str(filename) + '.svg', width,
height)
context = cairo.Context(surface)
main()
surface.finish()
options.ozi.write(prepare_ozi(bbox, size[0], size[1], options.output)) if options.wld: options.wld.write(prepare_wld(bbox, size[0], size[1])) # export image m.aspect_fix_mode = mapnik.aspect_fix_mode.GROW_BBOX; m.resize(size[0], size[1]) m.zoom_to_box(bbox) outfile = options.output if options.output == '-': outfile = tempfile.TemporaryFile(mode='w+b') if need_cairo: if HAS_CAIRO: surface = cairo.SVGSurface(outfile, size[0], size[1]) if fmt == 'svg' else cairo.PDFSurface(outfile, size[0], size[1]) mapnik.render(m, surface, scale_factor, 0, 0) surface.finish() else: mapnik.render_to_file(m, outfile, fmt) else: if options.tiles == 1: im = mapnik.Image(size[0], size[1]) mapnik.render(m, im, scale_factor) im.save(outfile, fmt) else: # we cannot make mapnik calculate scale for us, so fixing aspect ratio outselves rdiff = (bbox.maxx-bbox.minx) / (bbox.maxy-bbox.miny) - size[0] / size[1] if rdiff > 0: bbox.height((bbox.maxx - bbox.minx) * size[1] / size[0]) elif rdiff < 0:
motif_pos_dict[(GCAUG_start_pos, GCAUG_end_pos)] = GCAUG_motif_key
for catag in catag_rgx.finditer(line):
#print(catag.start(), catag.end(), catag.group())
catag_start_pos = catag.start()
catag_end_pos = catag.end()
catag_motif_key = catag.group()
motif_pos_dict[(catag_start_pos, catag_end_pos)] = catag_motif_key
return (motif_pos_dict)
m_list = parse_motif_file(m)
parse_motif_file(m)
surface = cairo.SVGSurface("motif_plot.svg", 800, 500)
context = cairo.Context(surface)
context.move_to(50, 10)
context.show_text("Motif Legend:")
context.set_line_width(20)
context.set_source_rgb(1, .1, .1)
context.move_to(50, 25)
context.line_to(100, 25)
context.show_text(m_list[0])
context.stroke()
context = cairo.Context(surface)
context.set_line_width(20)
context.set_source_rgb(.32, .60, 0.1)
context.move_to(50, 50)
context.line_to(100, 50)
context.show_text(m_list[1])
for w in walkers:
if walkers[i].id != w.id and walkers[
i - 1].id != w.id and walkers[i].connect != w.id:
if walkers[i].intersect(w.p0, w.p1) or walkers[i].edges():
stopDrawing = True
break
if stopDrawing:
break
walkers[i].draw(context)
# Call the main function and save an image
if __name__ == '__main__':
if fileFormat == 'PNG':
surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, width, height)
context = cairo.Context(surface)
main()
fileName = uuid.uuid4().hex[:8]
surface.write_to_png("Images/Line_Walker/" + str(fileName) + ".png")
elif fileFormat == 'SVG':
fileName = uuid.uuid4().hex[:8]
surface = cairo.SVGSurface(
"Images/Line_Walker/0-svg/" + str(fileName) + ".svg", width,
height)
context = cairo.Context(surface)
main()
context.finish()
# Clear path to parent.
pc = c.parent
if pc != None and pc != True:
p = self.cells[pc]
c.remove_wall(pc)
p.remove_wall(cc)
# Add the neighbors to the open list.
neighbors = [n for n in c.neighbors if not self.cells[n].visited()]
for n in neighbors:
self.cells[n].visit(cc)
stack += neighbors
# Shuffle for next round.
random.shuffle(stack)
# Make the maze.
maze = Maze(20)
maze.drill()
# Render the maze.
surface = cairo.SVGSurface("maze.svg", dim, dim)
ctx = cairo.Context(surface)
ctx.set_tolerance(0.01)
ctx.set_line_width(0.5)
ctx.set_source_rgb(0, 0, 0)
maze.render(ctx)
ctx.stroke()
r'([A-Z]+)',
str(sequence)).span(1)[0] #Records start and end position of exon
exon_end = re.search(r'([A-Z]+)', str(sequence)).span(1)[1]
for elem in motif_dict:
motif_mark[elem] = []
for match in re.finditer(
elem,
str(sequence).upper()): #Again records motifs
motif_mark[elem].append(match.start())
seq_motif[header] = motif_mark
seq_exon[header] = (exon_start, exon_end)
#The two lines above record the motifs and exons for this specific sequence in dictionaries where the keys are the header of the sequence and the values are the motif start
#position dictionary and exon start and end positions.
surface = cairo.SVGSurface(
"plot.svg", longest_seq + 200,
200 * len(sequence_dict)) #establishes the surface for plotting
context = cairo.Context(surface)
context.select_font_face("Arial", cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
start_height = 25
for seq in sequence_dict:
context.set_source_rgb(0, 0, 0)
context.set_line_width(1)
context.move_to(50, start_height)
context.set_font_size(20)
context.show_text(seq)
start_height += 50
context.move_to(50, start_height)
context.line_to(len(sequence_dict[seq]) + 50, start_height)
context.stroke()
#by default iupac_conversions dictionary creates DNA motif sequences
new_dna_motif.append("".join(i))
#replace every thymine with uracil for the RNA motif sequences
new_rna_motif.append("".join(i).replace("T", "U"))
#add all possible motif sequences into respective dictionaries
DNA[motif] = new_dna_motif
RNA[motif] = new_rna_motif
#return dictionaries
return DNA, RNA
DNA, RNA = motif_maker(motif_file)
#for each fasta file run the program on it
for file in fasta_files:
#extract file name for use in naming plot
figname = re.findall('(.*)\.fa', file)[0] + ".svg"
#create a pycairo surface
surface = cairo.SVGSurface(figname, 1000, 150 * (number_of_genes + 1))
#create context on the pycairo surface
context = cairo.Context(surface)
geneGroups = parser(file, context)
legend = Legend(DNA)
legend.draw(context)
context.stroke()
surface.finish()
self.inputs = inputs
self.x = None
self.y = None
for t in range(len(tiers)):
for pm, _, inputs in tiers[t]:
tid = pm["typeID"]
mat = Mat(t, tid, pm["typeName"], inputs)
mats[tid] = mat
mat_tiers[t].append(mat.tid)
# Set up Cairo for drawing. Origin is in upper-left corner.
height = SIDE
width = round(ASPECT * SIDE)
surface = cairo.SVGSurface("pi-chart.svg", width, height)
ctx = cairo.Context(surface)
ctx.select_font_face("sans-serif", cairo.FontSlant.NORMAL,
cairo.FontWeight.BOLD)
font_face = ctx.get_font_face()
ctx.set_line_width(1.2)
# Set up column widths and heights.
col_margin = 0.05 * width
row_margin = 0.05 * height
gutter_width = 0.15 * width
ncols = len(mat_tiers)
row_maxwidth = [None] * ncols
nrow = [None] * ncols
font_height = 0.0
font_ascent = 0.0
def _render_one(self, config, tmpdir, renderer_cls, output_format,
output_filename, osm_date, file_prefix):
LOG.debug('Rendering to %s format...' % output_format.upper())
dpi = layoutlib.commons.PT_PER_INCH
config.output_format = output_format
renderer = renderer_cls(self._db, config, tmpdir, dpi, file_prefix)
if output_format == 'png':
try:
dpi = int(self._parser.get('rendering', 'png_dpi'))
except configparser.NoOptionError:
dpi = OCitySMap.DEFAULT_RENDERING_PNG_DPI
w_px = int(
layoutlib.commons.convert_mm_to_dots(config.paper_width_mm,
dpi))
h_px = int(
layoutlib.commons.convert_mm_to_dots(config.paper_height_mm,
dpi))
if w_px > 25000 or h_px > 25000:
LOG.warning(
"%d DPI to high for this paper size, using 72dpi instead" %
dpi)
dpi = layoutlib.commons.PT_PER_INCH
# as the dpi value may have changed we need to re-create the renderer
renderer = renderer_cls(self._db, config, tmpdir, dpi, file_prefix)
# As strange as it may seem, we HAVE to use a vector
# device here and not a raster device such as
# ImageSurface. Because, for some reason, with
# ImageSurface, the font metrics would NOT match those
# pre-computed by renderer_cls.__init__() and used to
# layout the whole page
w_px = int(
layoutlib.commons.convert_pt_to_dots(renderer.paper_width_pt,
dpi))
h_px = int(
layoutlib.commons.convert_pt_to_dots(renderer.paper_height_pt,
dpi))
LOG.debug("Rendering PNG into %dpx x %dpx area at %ddpi ..." %
(w_px, h_px, dpi))
surface = cairo.PDFSurface(None, w_px, h_px)
elif output_format == 'svg':
surface = cairo.SVGSurface(output_filename,
renderer.paper_width_pt,
renderer.paper_height_pt)
surface.restrict_to_version(cairo.SVGVersion.VERSION_1_2)
elif output_format == 'svgz':
surface = cairo.SVGSurface(gzip.GzipFile(output_filename, 'wb'),
renderer.paper_width_pt,
renderer.paper_height_pt)
surface.restrict_to_version(cairo.SVGVersion.VERSION_1_2)
elif output_format == 'pdf':
surface = cairo.PDFSurface(output_filename,
renderer.paper_width_pt,
renderer.paper_height_pt)
surface.restrict_to_version(cairo.PDFVersion.VERSION_1_5)
surface.set_metadata(cairo.PDFMetadata.CREATOR,
'MyOSMatic <https://print.get-map.org/>')
surface.set_metadata(cairo.PDFMetadata.TITLE, config.title)
surface.set_metadata(
cairo.PDFMetadata.AUTHOR,
"Copyright © 2018 MapOSMatic/OCitySMap developers. \n" +
"Map data © 2018 OpenStreetMap contributors (see http://osm.org/copyright)"
)
surface.set_metadata(
cairo.PDFMetadata.SUBJECT,
renderer.description) # TODO add style annotations here
surface.set_metadata(cairo.PDFMetadata.KEYWORDS,
"OpenStreetMap, MapOSMatic, OCitysMap")
elif output_format == 'ps':
surface = cairo.PSSurface(output_filename, renderer.paper_width_pt,
renderer.paper_height_pt)
elif output_format == 'ps.gz':
surface = cairo.PSSurface(gzip.GzipFile(output_filename, 'wb'),
renderer.paper_width_pt,
renderer.paper_height_pt)
elif output_format == 'csv':
# We don't render maps into CSV.
return
else:
raise ValueError( \
'Unsupported output format: %s!' % output_format.upper())
renderer.render(surface, dpi, osm_date)
LOG.debug('Writing %s...' % output_filename)
if output_format == 'png':
surface.write_to_png(output_filename)
surface.finish()
def draw_a_gene(gene_objects, gene_nums, margin, motif_ext, motif_colors, svg_name):
# initialize surface
surface = cairo.SVGSurface(svg_name, 1000, 1000)
context = cairo.Context(surface)
# make a figure title
context.set_source_rgb(0, 0, 0)
context.set_font_size(30)
context.select_font_face("Arial", cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
context.move_to(margin, 40)
context.show_text("Motif Finder Results")
context.stroke()
# iterate through all genes
for gene_num,gene_obj in zip(gene_nums, gene_objects):
# draw gene title
context.set_source_rgb(0, 0, 0)
context.set_font_size(15)
context.select_font_face("Arial", cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
context.move_to(margin, gene_num-25)
context.show_text(gene_obj.fasta_header)
context.stroke()
# draw gene length
context.set_line_width(3)
context.move_to(margin, gene_num)
context.line_to(gene_obj.end, gene_num)
context.stroke()
# draw exons
context.set_line_width(15)
for exon in gene_obj.exons:
e0 = exon[0]
e1 = exon[1]
context.move_to(e0 + margin, gene_num)
context.line_to(e1 + margin, gene_num)
context.stroke()
# draw motifs
#context.scale (10000, 10000)
for motif in gene_obj.motif_coordinates.keys():
#context.set_source_rgb(52, 235, 207)
red = motif_colors[motif][0]
green = motif_colors[motif][1]
blue = motif_colors[motif][2]
for coord in gene_obj.motif_coordinates[motif]:
# coord = (start, stop)
m0 = coord[0]
m1 = coord[1]
# draw line at motif
context.set_line_width(15)
context.set_source_rgba(red, green, blue, .5)
context.move_to(m0+margin, gene_num)
context.line_to(m1+margin, gene_num)
context.stroke()
# make motif legend
start_legend = max(gene_nums) + 40
for motif in motif_colors.keys():
# get rgb colors
red = motif_colors[motif][0]
green = motif_colors[motif][1]
blue = motif_colors[motif][2]
#draw label
context.set_source_rgb(0, 0, 0)
context.set_font_size(15)
context.select_font_face("Arial", cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
context.move_to(margin+60, start_legend+3)
context.show_text(motif)
context.stroke()
# draw line color
# draw line at motif
context.set_line_width(10)
context.set_source_rgb(red, green, blue)
context.move_to(margin, start_legend)
context.line_to(margin + 50, start_legend)
context.stroke()
start_legend += 20
surface.finish()
def drawing(gene_objects, output_name, pallete, sequence_file, motif_file,
motifs):
'''
All functions for the pycairo graphic
Takes in each of the gene objects (with exons and motifs stored), the name of the file to
write to, the color pallete, the original motifs in IUPAC form, and the names of the
input files.
Outputs a SVG. Each fasta sequence from the input file gets its own drawing. The drawings
are depicted as the same size, but exon and motif bounds are scaled in size relative to the
length of the gene. Each gene drawing shows the exons as grey boxes and introns as straight dark lines.
Motifs are represented by colored boxes spanning the window which matched the motif.
A key is provided at the bottom to associate motifs with their color.
The original file names are written to the output for record keeping.
'''
#determine how many genes need to be represented
gene_count = len(gene_objects) + 1
#height for each gene
base_height = 100
#dimensions of total output, scaled for number of genes
width, height = 600, base_height * (gene_count + 1)
#name of output
filename = output_name + ".svg"
#leaving whitespace for ease of viewing
left_indent = width * .1
#width of gene in visual, relative to width of whole image
gene_width = width * .8
with cairo.SVGSurface(filename, width, height) as surface:
#create visual object
context = cairo.Context(surface)
#which gene were on, used for scaling height coordinates
gene_count = 1
for gene in gene_objects:
#make a straight line for each gene
context.set_source_rgb(0, 0, 0)
x1, y1 = width * .1, base_height * .5 + base_height * gene_count
x2, y2 = width * .9, base_height * .5 + base_height * gene_count
context.set_line_width(1)
context.move_to(x1, y1)
context.line_to(x2, y2)
#add the name of each gene/fasta entry above the visual
x3, y3 = width * .09, base_height * .1 + base_height * gene_count
context.move_to(x3, y3)
gene_name = gene + " {} BP".format(
len(gene_objects[gene].sequence))
context.show_text(gene_name)
context.stroke()
#find length of gene to scale motifs and exons accordingly
gene_length = len(gene_objects[gene].sequence)
#add the exon as a rectangle
for exon in gene_objects[gene].exons:
exon_start, exon_stop = exon
#scale the start position for the graphic
exon_x1 = (exon_start / gene_length) * gene_width + left_indent
exon_y1 = base_height * 0.3 + base_height * gene_count
exon_height = base_height * 0.4
exon_width = (exon_stop -
exon_start) / gene_length * gene_width
#make a grey box that is wider than the intron lines
context.rectangle(exon_x1, exon_y1, exon_width, exon_height)
context.set_source_rgb(.6, .6, .6)
context.fill()
#now iterating through each motif found in this sequence
for motif in gene_objects[gene].motifs:
#grabbing BP coordinates for where the motifs matched the sequence (often more than one)
for window in gene_objects[gene].motifs[motif]:
#output the motifs as boxes
re_x1 = (((window[0] / gene_length) * gene_width) +
left_indent)
re_width = (window[1] -
window[0]) / gene_length * gene_width
re_height = base_height * .2
context.rectangle(
re_x1, base_height * .4 + base_height * gene_count,
re_width, re_height)
#uses the same color for same motifs
r, g, b, a = pallete[motif]
context.set_source_rgba(r, g, b, a)
context.fill()
gene_count += 1
#adding figure title
context.move_to(width * 0.1, base_height * 0.5)
context.set_source_rgb(0, 0, 0)
context.set_font_size(10.0)
context.show_text(
"Identifying motifs described in the file '{}' found in the file '{}'"
.format(motif_file, sequence_file))
context.move_to(width * 0.1, base_height * 0.7)
context.set_source_rgb(0, 0, 0)
context.set_font_size(7.0)
context.show_text(
"Grey boxes represent exons, and colored boxes represent motifs. See motif legend below."
)
#adding the motif legend
legend_x, legend_y = left_indent, base_height * 0.2 + base_height * gene_count
legend_horiz_spacing = width * 0.2
legend_vert_spacing = base_height * 0.1
context.move_to(legend_x, legend_y - legend_vert_spacing)
context.set_font_size(10)
context.show_text("Motif legend")
motif_count = 0
line = 0
for motif in motifs:
#wrapping so 4 motifs appear in each line
if motif_count % 4 == 0:
line += 1
x1, y1 = (legend_x + (motif_count % 4) * legend_horiz_spacing), (
legend_y + legend_vert_spacing * line)
context.move_to(x1, y1)
#cute lil boxes
context.rectangle(x1, y1, base_height * 0.05, base_height * 0.05)
r, g, b, a = pallete[motifs[motif]]
context.set_source_rgba(r, g, b, a)
context.fill()
#write the original motif
x1, y1 = x1 + base_height * 0.07, y1 + base_height * 0.07
context.move_to(x1, y1)
context.set_source_rgb(0, 0, 0)
context.show_text(motifs[motif].upper())
motif_count += 1
#In cm
import cairo
width = WIDTH = height = HEIGHT = 5
PIXEL_SCALE = 100 #400 px width and height
#width, height = width_in_points, height_in_points
with cairo.SVGSurface("m_logo.svg", WIDTH * PIXEL_SCALE,
HEIGHT * PIXEL_SCALE) as surface:
ctx = cairo.Context(surface)
ctx.scale(PIXEL_SCALE, PIXEL_SCALE) #scaling
#making a M
#ctx.set_line_width(1)
ctx.set_line_width(0.1)
ctx.move_to(0, 2.5)
ctx.line_to(2.5, 0)
ctx.line_to(2.5, 2.5)
ctx.line_to(5, 2.5)
ctx.line_to(2.5, 5)
ctx.set_source_rgb(0.8, 0.5, 0.7) #color
#ctx.set_line_width(0.1)
ctx.stroke()
surface.write_to_png('m_logo.png')
import os
os.startfile("m_logo.svg")
import cairo
with cairo.SVGSurface("pycairo_generated.svg", 200, 200) as surface:
context = cairo.Context(surface)
x, y, x1, y1 = 0.1, 0.5, 0.4, 0.9
x2, y2, x3, y3 = 0.6, 0.1, 0.9, 0.5
context.scale(200, 200)
context.set_line_width(0.04)
context.move_to(x, y)
context.curve_to(x1, y1, x2, y2, x3, y3)
context.stroke()
context.set_source_rgba(1, 0.2, 0.2, 0.6)
context.set_line_width(0.02)
context.move_to(x, y)
context.line_to(x1, y1)
context.move_to(x2, y2)
context.line_to(x3, y3)
context.stroke()
import cairo
with cairo.SVGSurface("exemplo.svg", 400, 400) as surface:
c = cairo.Context(surface)
c.scale(400, 400)
c.set_line_width(1)
c.move_to(1, 1)
c.line_to(0.5, 0.5)
c.move_to(2, 2.5)
c.line_to(-0.5, -0.5)
c.set_source_rgb(0.03, 0, 1)
c.stroke()
print("Minimal distance after filtering:", min(distances))
nodes = list(set([val for sublist in edges for val in sublist]))
######## EDGES FILTERED ########
drawTree(edges=edges, nodes=leafs, title="I")
nodes.sort(key=lambda node: node.norm())
leafs = []
for N in nodes:
neighbours = [edge for edge in edges if N in edge]
if len(neighbours) == 1: # If node is a leaf
leafs.append(N)
surface = cairo.SVGSurface("after.svg", WIDTH, HEIGHT)
surface.set_document_unit(cairo.SVG_UNIT_MM)
ctx = cairo.Context(surface)
# ctx.set_source_rgb(0.2, 0.2, 0.2)
# ctx.rectangle(0, 0, WIDTH, HEIGHT)
# ctx.fill()
# ctx.set_source_rgb(1, 1, 1)
# ctx.set_line_width(1)
img = np.ones((HEIGHT, WIDTH, 3)) * 0.1
nLeafsDrawn = 0
for NODE in nodes:
def run(options):
dim_mm = None
scale = None
size = None
bbox = None
rotate = not options.norotate
if (options.ozi and options.projection.lower() != 'epsg:3857'
and options.projection != EPSG_3857):
raise Exception(
'Ozi map file output is only supported for Web Mercator (EPSG:3857). '
+ 'Please remove --projection.')
if options.url:
parse_url(options.url, options)
# format should not be empty
if options.fmt:
fmt = options.fmt.lower()
elif '.' in options.output:
fmt = options.output.split('.')[-1].lower()
else:
fmt = 'png256'
need_cairo = fmt in ['svg', 'pdf']
# output projection
if options.projection.isdigit():
proj_target = mapnik.Projection('+init=epsg:{}'.format(
options.projection))
else:
proj_target = mapnik.Projection(options.projection)
transform = mapnik.ProjTransform(proj_lonlat, proj_target)
# get image size in millimeters
if options.paper:
portrait = False
if options.paper[0] == '-':
portrait = True
rotate = False
options.paper = options.paper[1:]
elif options.paper[0] == '+':
rotate = False
options.paper = options.paper[1:]
else:
rotate = True
dim_mm = get_paper_size(options.paper.lower())
if not dim_mm:
raise Exception('Incorrect paper format: ' + options.paper)
if portrait:
dim_mm = [dim_mm[1], dim_mm[0]]
elif options.size:
dim_mm = options.size
if dim_mm and options.margin:
dim_mm[0] = max(0, dim_mm[0] - options.margin * 2)
dim_mm[1] = max(0, dim_mm[1] - options.margin * 2)
# ppi and scale factor are the same thing
if options.ppi:
ppmm = options.ppi / 25.4
scale_factor = options.ppi / 90.7
else:
scale_factor = options.factor
ppmm = 90.7 / 25.4 * scale_factor
# svg / pdf can be scaled only in cairo mode
if scale_factor != 1 and need_cairo and not HAS_CAIRO:
logging.error('Warning: install pycairo for using --factor or --ppi')
scale_factor = 1
ppmm = 90.7 / 25.4
# convert physical size to pixels
if options.size_px:
size = options.size_px
elif dim_mm:
size = [int(round(dim_mm[0] * ppmm)), int(round(dim_mm[1] * ppmm))]
if size and size[0] + size[1] <= 0:
raise Exception('Both dimensions are less or equal to zero')
if options.bbox:
bbox = options.bbox
# scale can be specified with zoom or with 1:NNN scale
fix_scale = False
if options.zoom:
scale = 2 * 3.14159 * 6378137 / 2**(options.zoom + 8) / scale_factor
elif options.scale:
scale = options.scale * 0.00028 / scale_factor
# Now we have to divide by cos(lat), but we might not know latitude at this point
# TODO: division should only happen for EPSG:3857 or not at all
if options.center:
scale = scale / math.cos(math.radians(options.center[1]))
elif options.bbox:
scale = scale / math.cos(
math.radians((options.bbox[3] + options.bbox[1]) / 2))
else:
fix_scale = True
# all calculations are in EPSG:3857 projection (it's easier)
if bbox:
bbox = transform.forward(mapnik.Box2d(*bbox))
bbox_web_merc = transform_lonlat_webmerc.forward(
mapnik.Box2d(*(options.bbox)))
if scale:
scale = correct_scale(bbox, scale, bbox_web_merc, bbox)
# calculate bbox through center, zoom and target size
if not bbox and options.center and size and size[0] > 0 and size[
1] > 0 and scale:
# We don't know over which latitude range the bounding box spans, so we
# first do everything in Web Mercator.
center = transform_lonlat_webmerc.forward(
mapnik.Coord(*options.center))
w = size[0] * scale / 2
h = size[1] * scale / 2
bbox_web_merc = mapnik.Box2d(center.x - w, center.y - h, center.x + w,
center.y + h)
bbox = transform_lonlat_webmerc.backward(bbox_web_merc)
bbox = transform.forward(bbox)
# now correct the scale
scale = correct_scale(bbox, scale, bbox_web_merc, bbox)
center = transform.forward(mapnik.Coord(*options.center))
w = size[0] * scale / 2
h = size[1] * scale / 2
bbox = mapnik.Box2d(center.x - w, center.y - h, center.x + w,
center.y + h)
# reading style xml into memory for preprocessing
if options.style == '-':
style_xml = sys.stdin.read()
style_path = ''
else:
with codecs.open(options.style, 'r', 'utf-8') as style_file:
style_xml = style_file.read()
style_path = os.path.dirname(options.style)
if options.base:
style_path = options.base
if options.vars:
style_xml = xml_vars(style_xml, options.vars)
if options.layers or options.add_layers:
style_xml = reenable_layers(
style_xml,
parse_layers_string(options.layers) +
parse_layers_string(options.add_layers))
# for layer processing we need to create the Map object
# ----- BEGIN PRINTMAPS -----
# m = mapnik.Map(100, 100) # temporary size, will be changed before output
m = mapnik.Map(size[0], size[1])
# ----- END PRINTMAPS -----
mapnik.load_map_from_string(m, style_xml.encode("utf-8"), False,
style_path)
m.srs = proj_target.params()
# register non-standard fonts
if options.fonts:
for f in options.fonts:
add_fonts(f)
# get bbox from layer extents
if options.fit:
bbox = layer_bbox(m, options.fit.split(','), proj_target, bbox)
# here's where we can fix scale, no new bboxes below
if bbox and fix_scale:
scale = scale / math.cos(
math.radians(transform.backward(bbox.center()).y))
bbox_web_merc = transform_lonlat_webmerc.forward(
transform.backward(bbox))
if scale:
scale = correct_scale(bbox, scale, bbox_web_merc, bbox)
# expand bbox with padding in mm
if bbox and options.padding and (scale or size):
if scale:
tscale = scale
else:
tscale = min((bbox.maxx - bbox.minx) / max(size[0], 0.01),
(bbox.maxy - bbox.miny) / max(size[1], 0.01))
bbox.pad(options.padding * ppmm * tscale)
# bbox should be specified by this point
if not bbox:
raise Exception('Bounding box was not specified in any way')
# rotate image to fit bbox better
if rotate and size:
portrait = bbox.maxy - bbox.miny > bbox.maxx - bbox.minx
# take into consideration zero values, which mean they should be calculated from bbox
if (size[0] == 0 or size[0] > size[1]) and portrait:
size = [size[1], size[0]]
# calculate pixel size from bbox and scale
if not size:
if scale:
size = [
int(round(abs(bbox.maxx - bbox.minx) / scale)),
int(round(abs(bbox.maxy - bbox.miny) / scale))
]
else:
raise Exception(
'Image dimensions or scale were not specified in any way')
elif size[0] == 0:
size[0] = int(
round(size[1] * (bbox.maxx - bbox.minx) / (bbox.maxy - bbox.miny)))
elif size[1] == 0:
size[1] = int(
round(size[0] / (bbox.maxx - bbox.minx) * (bbox.maxy - bbox.miny)))
if options.output == '-' or (need_cairo and options.tiles > 1):
options.tiles = 1
# ----- BEGIN PRINTMAPS -----
# if max(size[0], size[1]) / options.tiles > 16384:
# raise Exception('Image size exceeds mapnik limit ({} > {}), use --tiles'.format(
# max(size[0], size[1]) / options.tiles, 16384))
# ----- END PRINTMAPS -----
# add / remove some layers
if options.layers:
filter_layers(m, parse_layers_string(options.layers))
if options.add_layers or options.hide_layers:
select_layers(m, parse_layers_string(options.add_layers),
parse_layers_string(options.hide_layers))
# ----- BEGIN PRINTMAPS -----
# logging.debug('scale=%s', scale)
# logging.debug('scale_factor=%s', scale_factor)
# logging.debug('size=%s,%s', size[0], size[1])
# logging.debug('bbox=%s', bbox)
# logging.debug('bbox_wgs84=%s', transform.backward(bbox) if bbox else None)
# logging.debug('layers=%s', ','.join([l.name for l in m.layers if l.active]))
print('scale={}'.format(scale))
print('scale_factor={}'.format(scale_factor))
print('size={},{}'.format(size[0], size[1]))
print('bbox={}'.format(bbox))
print('bbox_wgs84={}'.format(transform.backward(bbox) if bbox else None))
print('layers=' + ','.join([l.name for l in m.layers if l.active]))
# ----- END PRINTMAPS -----
# ----- BEGIN PRINTMAPS -----
if options.info:
quit()
# ----- END PRINTMAPS -----
# generate metadata
if options.ozi:
options.ozi.write(
prepare_ozi(bbox, size[0], size[1], options.output, transform))
if options.wld:
options.wld.write(prepare_wld(bbox, size[0], size[1]))
# export image
m.aspect_fix_mode = mapnik.aspect_fix_mode.GROW_BBOX
# ----- BEGIN PRINTMAPS -----
# m.resize(size[0], size[1])
# ----- END PRINTMAPS -----
m.zoom_to_box(bbox)
outfile = options.output
if options.output == '-':
outfile = tempfile.TemporaryFile(mode='w+b')
if need_cairo:
if HAS_CAIRO:
if fmt == 'svg':
surface = cairo.SVGSurface(outfile, size[0], size[1])
else:
surface = cairo.PDFSurface(outfile, size[0], size[1])
mapnik.render(m, surface, scale_factor, 0, 0)
surface.finish()
else:
mapnik.render_to_file(m, outfile, fmt)
else:
if options.tiles == 1:
im = mapnik.Image(size[0], size[1])
mapnik.render(m, im, scale_factor)
im.save(outfile, fmt)
else:
# we cannot make mapnik calculate scale for us, so fixing aspect ratio outselves
rdiff = (bbox.maxx - bbox.minx) / (bbox.maxy -
bbox.miny) - size[0] / size[1]
if rdiff > 0:
bbox.height((bbox.maxx - bbox.minx) * size[1] / size[0])
elif rdiff < 0:
bbox.width((bbox.maxy - bbox.miny) * size[0] / size[1])
scale = (bbox.maxx - bbox.minx) / size[0]
width = max(32, int(math.ceil(1.0 * size[0] / options.tiles)))
height = max(32, int(math.ceil(1.0 * size[1] / options.tiles)))
m.resize(width, height)
m.buffer_size = TILE_BUFFER
tile_cnt = [
int(math.ceil(1.0 * size[0] / width)),
int(math.ceil(1.0 * size[1] / height))
]
logging.debug('tile_count=%s %s', tile_cnt[0], tile_cnt[1])
logging.debug('tile_size=%s,%s', width, height)
# ----- BEGIN PRINTMAPS -----
# tmp_tile = '{:02d}_{:02d}_{}'
tmp_tile = '{}_{:02d}_{:02d}'
# ----- END PRINTMAPS -----
tile_files = []
for row in range(0, tile_cnt[1]):
for column in range(0, tile_cnt[0]):
logging.debug('tile=%s,%s', row, column)
tile_bbox = mapnik.Box2d(
bbox.minx + 1.0 * width * scale * column,
bbox.maxy - 1.0 * height * scale * row,
bbox.minx + 1.0 * width * scale * (column + 1),
bbox.maxy - 1.0 * height * scale * (row + 1))
tile_size = [
width if column < tile_cnt[0] - 1 else size[0] -
width * (tile_cnt[0] - 1),
height if row < tile_cnt[1] - 1 else size[1] - height *
(tile_cnt[1] - 1)
]
m.zoom_to_box(tile_bbox)
im = mapnik.Image(tile_size[0], tile_size[1])
mapnik.render(m, im, scale_factor)
# ----- BEGIN PRINTMAPS -----
# tile_name = tmp_tile.format(row, column, options.output)
tile_name = tmp_tile.format(options.output, row, column)
# ----- END PRINTMAPS -----
im.save(tile_name, fmt)
if options.just_tiles:
# write ozi/wld for a tile if needed
if '.' not in tile_name:
tile_basename = tile_name + '.'
else:
tile_basename = tile_name[0:tile_name.rindex('.') +
1]
if options.ozi:
with open(tile_basename + 'ozi', 'w') as f:
f.write(
prepare_ozi(tile_bbox, tile_size[0],
tile_size[1],
tile_basename + '.ozi',
transform))
if options.wld:
with open(tile_basename + 'wld', 'w') as f:
f.write(
prepare_wld(tile_bbox, tile_size[0],
tile_size[1]))
else:
tile_files.append(tile_name)
if not options.just_tiles:
# join tiles and remove them if joining succeeded
import subprocess
result = subprocess.call([
IM_MONTAGE, '-geometry', '+0+0', '-tile', '{}x{}'.format(
tile_cnt[0], tile_cnt[1])
] + tile_files + [options.output])
if result == 0:
for tile in tile_files:
os.remove(tile)
if options.output == '-':
if sys.platform == "win32":
# fix binary output on windows
import msvcrt
msvcrt.setmode(sys.stdout.fileno(), os.O_BINARY)
outfile.seek(0)
sys.stdout.write(outfile.read())
outfile.close()
import cairo
with cairo.SVGSurface("example.svg", 200, 200) as surface:
c = cairo.Context(surface)
c.scale(200, 200)
c.set_line_width(0.05)
c.move_to(1, 1)
c.line_to(0.5, 0, 5)
c.move_to(2, 1)
c.line_to(-0.5, 0, 5)
c.set_source_rgb(0, 0, 1)
c.stroke()
def _prim_add_food(self, name, media, calories, protein, carbohydrates,
fiber, fat):
# Add a new food item to the palette
palette = make_palette('food',
colors=["#FFFFFF", "#A0A0A0"],
help_string=_('Palette of foods'))
# We need to convert the media into two svgs, one for the
# palette and one for the block.
filepath = None
if media is not None and os.path.exists(media.value):
filepath = media.value
elif self.tw.running_sugar: # datastore object
from sugar.datastore import datastore
try:
dsobject = datastore.get(media.value)
except:
debug_output("Couldn't find dsobject %s" % (media.value),
self.tw.running_sugar)
if dsobject is not None:
filepath = dsobject.file_path
if filepath is None:
self.tw.showlabel('nojournal', filepath)
return
pixbuf = None
try:
pixbufsmall = gtk.gdk.pixbuf_new_from_file_at_size(
filepath, 40, 40)
pixbufoff = gtk.gdk.pixbuf_new_from_file_at_size(filepath, 40, 40)
except:
self.tw.showlabel('nojournal', filepath)
debug_output("Couldn't open food image %s" % (filepath),
self.tw.running_sugar)
return
def _draw_pixbuf(cr, pixbuf, x, y, w, h):
# Build a gtk.gdk.CairoContext from a cairo.Context to access
# the set_source_pixbuf attribute.
cc = gtk.gdk.CairoContext(cr)
cc.save()
# center the rotation on the center of the image
cc.translate(x + w / 2., y + h / 2.)
cc.translate(-x - w / 2., -y - h / 2.)
cc.set_source_pixbuf(pixbuf, x, y)
cc.rectangle(x, y, w, h)
cc.fill()
cc.restore()
if self.tw.running_sugar:
path = os.path.join(get_path(self.tw.activity, 'instance'),
'output.svg')
else:
path = TMP_SVG_PATH
svg_surface = cairo.SVGSurface(path, 40, 40)
cr_svg = cairo.Context(svg_surface)
_draw_pixbuf(cr_svg, pixbufsmall, 0, 0, 40, 40)
cr_svg.show_page()
svg_surface.flush()
svg_surface.finish()
destination = os.path.join(self.tw.path, 'plugins', 'food', 'images',
name.encode('ascii') + 'small.svg')
check_output(['mv', path, destination],
'problem moving %s to %s' % (path, destination))
pixbufsmall = gtk.gdk.pixbuf_new_from_file_at_size(destination, 40, 40)
self.tw.media_shapes[name.encode('ascii') + 'small'] = pixbufsmall
svg_surface = cairo.SVGSurface(path, 40, 40)
cr_svg = cairo.Context(svg_surface)
_draw_pixbuf(cr_svg, pixbufoff, 0, 0, 40, 40)
cr_svg.show_page()
svg_surface.flush()
svg_surface.finish()
destination = os.path.join(self.tw.path, 'plugins', 'food', 'images',
name.encode('ascii') + 'off.svg')
check_output(['mv', path, destination],
'problem moving %s to %s' % (path, destination))
# Now that we have the images, we can make the new block
self._make_polynominal(palette,
name.encode('ascii'),
name,
[calories, protein, carbohydrates, fiber, fat],
expand=(15, 15))
pixbufoff = gtk.gdk.pixbuf_new_from_file_at_size(destination, 40, 40)
self.tw.media_shapes[name.encode('ascii') + 'off'] = pixbufoff
# Show the new block
self.tw.show_toolbar_palette(palette_name_to_index('food'),
regenerate=True)
# Finally, we need to save new food item to a database so it
# loads next time.
food = name.encode('ascii')
self.food_dictionary[food] = {}
self.food_dictionary[food]['name'] = name
self.food_dictionary[food]['calories'] = calories
self.food_dictionary[food]['protein'] = protein
self.food_dictionary[food]['carbohydrates'] = carbohydrates
self.food_dictionary[food]['fiber'] = fiber
self.food_dictionary[food]['fat'] = fat
path = os.path.join(self.tw.path, 'plugins', 'food', 'food.db')
data_to_file(self.food_dictionary, path)
return
def _save(self, fo, format, **kwargs):
# save PDF/PS/SVG
orientation = kwargs.get('orientation', 'portrait')
dpi = 72
self.figure.dpi = dpi
w_in, h_in = self.figure.get_size_inches()
width_in_points, height_in_points = w_in * dpi, h_in * dpi
if orientation == 'landscape':
width_in_points, height_in_points = (height_in_points,
width_in_points)
if format == 'ps':
if not cairo.HAS_PS_SURFACE:
raise RuntimeError('cairo has not been compiled with PS '
'support enabled')
surface = cairo.PSSurface(fo, width_in_points, height_in_points)
elif format == 'pdf':
if not cairo.HAS_PDF_SURFACE:
raise RuntimeError('cairo has not been compiled with PDF '
'support enabled')
surface = cairo.PDFSurface(fo, width_in_points, height_in_points)
elif format in ('svg', 'svgz'):
if not cairo.HAS_SVG_SURFACE:
raise RuntimeError('cairo has not been compiled with SVG '
'support enabled')
if format == 'svgz':
filename = fo
if is_string_like(fo):
fo = open(fo, 'wb')
fo = gzip.GzipFile(None, 'wb', fileobj=fo)
surface = cairo.SVGSurface(fo, width_in_points, height_in_points)
else:
warnings.warn("unknown format: %s" % format)
return
# surface.set_dpi() can be used
renderer = RendererCairo(self.figure.dpi)
renderer.set_width_height(width_in_points, height_in_points)
renderer.set_ctx_from_surface(surface)
ctx = renderer.ctx
if orientation == 'landscape':
ctx.rotate(npy.pi / 2)
ctx.translate(0, -height_in_points)
# cairo/src/cairo_ps_surface.c
# '%%Orientation: Portrait' is always written to the file header
# '%%Orientation: Landscape' would possibly cause problems
# since some printers would rotate again ?
# TODO:
# add portrait/landscape checkbox to FileChooser
self.figure.draw(renderer)
show_fig_border = False # for testing figure orientation and scaling
if show_fig_border:
ctx.new_path()
ctx.rectangle(0, 0, width_in_points, height_in_points)
ctx.set_line_width(4.0)
ctx.set_source_rgb(1, 0, 0)
ctx.stroke()
ctx.move_to(30, 30)
ctx.select_font_face('sans-serif')
ctx.set_font_size(20)
ctx.show_text('Origin corner')
ctx.show_page()
surface.finish()
def export_cb (self, event):
maxx, maxy = self.MainArea.get_max_area ()
x, y, width, height, bitdepth = self.MainArea.window.get_geometry ()
glade = Gtk.Builder()
glade.add_from_file(utils.get_data_file_name('labyrinth.glade'))
dialog = glade.get_object ('ExportImageDialog')
box = glade.get_object ('dialog_insertion')
fc = Gtk.FileChooserWidget(Gtk.FileChooserAction.SAVE)
box.pack_end (fc)
filter_mapping = [ (_('All Files'), ['*']),
(_('PNG Image (*.png)'), ['*.png']),
(_('JPEG Image (*.jpg, *.jpeg)'), ['*.jpeg', '*.jpg']),
(_('SVG Vector Image (*.svg)'), ['*.svg']),
(_('PDF Portable Document (*.pdf)'), ['*.pdf']) ]
for (filter_name, filter_patterns) in filter_mapping:
fil = Gtk.FileFilter ()
fil.set_name(filter_name)
for pattern in filter_patterns:
fil.add_pattern(pattern)
fc.add_filter(fil)
fc.set_current_name ("%s.png" % self.main_window.title)
rad = glade.get_object ('rb_complete_map')
rad2 = glade.get_object ('rb_visible_area')
self.spin_width = glade.get_object ('width_spin')
self.spin_height = glade.get_object ('height_spin')
self.spin_width.set_value (maxx)
self.spin_height.set_value (maxy)
self.spin_width.set_sensitive (False)
self.spin_height.set_sensitive (False)
rad.connect ('toggled', self.toggle_range, width, height,maxx,maxy)
fc.show ()
while 1:
# Cheesy loop. Break out as needed.
response = dialog.run()
if response == Gtk.ResponseType.OK:
ext_mime_mapping = { 'png':'png', 'jpg':'jpeg', 'jpeg':'jpeg', \
'svg':'svg', 'pdf':'pdf' }
filename = fc.get_filename()
ext = filename[filename.rfind('.')+1:]
try:
mime = ext_mime_mapping[ext]
break
except KeyError:
msg = Gtk.MessageDialog(self, Gtk.DialogFlags.DESTROY_WITH_PARENT, Gtk.MessageType.ERROR, Gtk.ButtonsType.OK, \
_("Unknown file format"))
msg.format_secondary_text (_("The file type '%s' is unsupported. Please use the suffix '.png',"\
" '.jpg' or '.svg'." % ext))
msg.run ()
msg.destroy ()
else:
dialog.destroy ()
return
true_width = int (self.spin_width.get_value ())
true_height = int (self.spin_height.get_value ())
native = not rad.get_active ()
dialog.destroy ()
if mime in ['png', 'jpg']:
self.save_as_pixmap(filename, mime, true_width, true_height, bitdepth, native)
else:
surface = None
if mime == 'svg':
surface = cairo.SVGSurface(filename, true_width, true_height)
elif mime == 'pdf':
surface = cairo.PDFSurface(filename, true_width, true_height)
self.save_surface(surface, true_width, true_height, native)
SetRGB(self.color)
c.rectangle(self.x, self.y, self.w, self.h)
if self.fill:
c.fill()
else:
c.stroke()
self.x = self.xLambda(self.x, self.dx)
self.y = self.yLambda(self.y, self.dy)
self.w = self.yLambda(self.w, self.dw)
self.w = self.yLambda(self.h, self.dh)
FRAMES_PER_SECOND = 24
WIDTH = 600
HEIGHT = 600
s = cairo.SVGSurface("surface.svg", WIDTH, HEIGHT)
c = cairo.Context(s)
# rectangle1 : background rectangle that condenses into the center
# rectangle2 : background rectangle that expands from the center
# rectangle3u : quick vertical line that shoots up and expands across the screen horizontally
# rectangle3r : quick vertical line that shoots right and expands across the screen vertically
# rectangle3d : quick vertical line that shoots down and expands across the screen horizontally
# rectangle3l : quick vertical line that shoots left and expands across the screen vertically
colors = FormatColors(
["edf2fb", "e2eafc", "d7e3fc", "ccdbfd", "c1d3fe", "b6ccfe", "abc4ff"])
keyPressInfo = json.loads(open("keypressinfo.json").read())
keyPresses = json.loads(open("keypresses.json").read())
def main():
"""Main function"""
# Image surfaces provide the ability to render to memory buffers either
# allocated by cairo or by the calling code.
# List of supported surfaces: http://www.cairographics.org/manual/cairo-surfaces.html
surface = cairo.SVGSurface("fill_and_stroke.svg", WIDTH, HEIGHT)
# cairo.Context is the object that you send your drawing commands to.
context = cairo.Context(surface)
# Normalizing the canvas ([0,1],[0,1]) -> ([0,WIDTH],[0,HEIGHT])
context.scale(WIDTH, HEIGHT)
### DRAW ###
# context.set_source_rgb(0., 0., 0.)
# context.set_source_rgba(0., 0., 0., 1.)
# Sets the source pattern within context to an opaque color. This opaque color
# will then be used for any subsequent drawing operation until a new source
# pattern is set.
# The color components are floating point numbers in the range 0 to 1. If
# the values passed in are outside that range, they will be clamped.
# The default source pattern is opaque black, (that is, it is equivalent to
# cairo_set_source_rgb(context, 0.0, 0.0, 0.0)).
# Using set_source_rgb(r, g, b) is equivalent to using
# set_source_rgba(r, g, b, 1.0), and it sets your source color to use
# full opacity.
#
# context.stroke()
# The stroke() operation takes a virtual pen along the current path
# according to the current line width, line join, line cap, and dash
# settings. After cairo_stroke(), the current path will be cleared from
# the cairo context.
# See http://www.cairographics.org/manual/cairo-cairo-t.html#cairo-stroke
#
# context.fill()
# A drawing operator that fills the current path according to the current
# fill rule, (each sub-path is implicitly closed before being filled).
# After cairo_fill(), the current path will be cleared from the cairo
# context.
# See http://www.cairographics.org/manual/cairo-cairo-t.html#cairo-fill
context.set_line_width(0.03)
# WHITE BACKGROUND
context.set_source_rgb(1, 1, 1)
context.rectangle(0, 0, 1, 1)
context.fill()
# FILL...
context.set_source_rgba(1, 0.2, 0.2, 0.6)
context.rectangle(0.1, 0.1, 0.3, 0.3)
context.rectangle(0.1, 0.6, 0.3, 0.3)
context.rectangle(0.6, 0.1, 0.3, 0.3)
context.rectangle(0.6, 0.6, 0.3, 0.3)
context.fill_preserve() # <- PRESERVE PATH FOR STROKE !!!
# ...AND STROKE
context.set_source_rgb(0, 0, 0)
context.stroke()
### WRITE THE SVG FILE ###
surface.finish()
def plot_image_subregion(
raw_im,
mean_im,
absdiff_im,
roiradius,
fname,
user_coords,
scale=4.0,
view="orig",
extras=None,
):
if extras is None:
extras = {}
output_ext = os.path.splitext(fname)[1].lower()
roisize = 2 * roiradius
imtypes = ["raw", "absdiff", "mean"]
margin = 10
square_edge = roisize * scale
width = int(
round(len(imtypes) * square_edge + (len(imtypes) + 1) * margin))
height = int(round(square_edge + 2 * margin))
if output_ext == ".pdf":
output_surface = cairo.PDFSurface(fname, width, height)
elif output_ext == ".svg":
output_surface = cairo.SVGSurface(fname, width, height)
elif output_ext == ".png":
output_surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, width, height)
else:
raise ValueError("unknown output extension %s" % output_ext)
ctx = cairo.Context(output_surface)
# fill with white
ctx.set_source_rgb(1, 1, 1)
ctx.rectangle(0, 0, width, height)
ctx.fill()
user_l, user_b, user_r, user_t = user_coords
# setup transform
# calculate image boundary (user coords)
for im_idx, im in enumerate(imtypes):
if im == "raw":
display_im = raw_im
elif im == "mean":
display_im = mean_im
elif im == "absdiff":
display_im = np.clip(5 * absdiff_im, 0, 255)
# set transform - make a patch of the cairo
# device be addressed with our image space
# coords
device_l = (im_idx + 1) * margin + im_idx * square_edge
device_b = margin
ctx.identity_matrix() # reset
if view == "orig":
matrix = cairo.Matrix(
xx=scale,
yx=0,
xy=0,
yy=scale,
x0=(device_l - scale * user_l),
y0=(device_b - scale * user_b),
)
elif view == "rot -90":
matrix = cairo.Matrix(
xx=0,
yx=scale,
xy=scale,
yy=0,
x0=(device_l - scale * user_b),
y0=(device_b - scale * user_l),
)
elif view == "rot 180":
matrix = cairo.Matrix(
xx=-scale,
yx=0,
xy=0,
yy=-scale,
x0=(device_l + scale * user_r),
y0=(device_b + scale * user_t),
)
else:
raise ValueError("unknown view '%s'" % view)
ctx.set_matrix(matrix)
## print 'device_l-user_l, device_b-user_b',device_l-user_l, device_b-user_b
## #ctx.translate(device_l-user_l, device_b-user_b)
## if scale!= 1.0:
## ctx.scale( scale, scale )
## #raise NotImplementedError('')
## ctx.translate(device_l-user_l, device_b-user_b)
## #print 'square_edge/roisize, square_edge/roisize',square_edge/roisize, square_edge/roisize
## #ctx.scale( roisize/square_edge, square_edge/roisize)
if 1:
in_surface = benu.numpy2cairo(display_im.astype(np.uint8))
ctx.rectangle(user_l, user_b, display_im.shape[1],
display_im.shape[0])
if 1:
ctx.save()
ctx.set_source_surface(in_surface, user_l, user_b)
ctx.paint()
ctx.restore()
else:
ctx.set_source_rgb(0, 0.3, 0)
ctx.fill()
if 0:
ctx.move_to(user_l, user_b)
ctx.line_to(user_r, user_b)
ctx.line_to(user_r, user_t)
ctx.line_to(user_l, user_t)
ctx.line_to(user_l, user_b)
ctx.close_path()
ctx.set_source_rgb(0, 1, 0)
ctx.fill()
ctx.move_to(user_l + 5, user_b + 5)
ctx.line_to(user_r - 40, user_b + 5)
ctx.line_to(user_r - 40, user_t - 40)
ctx.line_to(user_l + 5, user_t - 40)
ctx.line_to(user_l + 5, user_b + 5)
ctx.close_path()
ctx.set_source_rgb(0, 0, 1)
ctx.fill()
if output_ext == ".png":
output_surface.write_to_png(fname)
else:
ctx.show_page()
output_surface.finish()
