def __init__(self, width=None, height=None):
"""
Compositor creator function
"""
# Main SVG initialization
self.__mainSVG = None
if ((height != None) and (width != None)):
self.__mainSVG = st.SVGFigure(width, height)
else:
self.__mainSVG = st.SVGFigure()
self.__SVGS = {}
def test_create_svg_figure():
svg_fig = transform.SVGFigure()
assert "svg" in svg_fig.to_str().decode("ascii")
svg_fig = transform.SVGFigure(Unit("2px"), Unit("2px"))
assert "svg" in svg_fig.to_str().decode("ascii")
svg_fig = transform.SVGFigure(2, 3)
assert "svg" in svg_fig.to_str().decode("ascii")
svg_fig = transform.SVGFigure("2", "3")
assert "svg" in svg_fig.to_str().decode("ascii")
def main(args):
fig = sg.SVGFigure("22cm", "25cm")
fig1 = sg.fromfile(args.gene_counts)
fig2 = sg.fromfile(args.mpc_dist)
fig3 = sg.fromfile(args.fg_roc)
fig4 = sg.fromfile(args.clinvar_roc)
plot1 = fig1.getroot()
plot2 = fig2.getroot()
plot3 = fig3.getroot()
plot4 = fig4.getroot()
plot1.moveto(0, 20, scale=0.75)
plot2.moveto(400, 0, scale=0.75)
plot3.moveto(0, 390, scale=0.7)
plot4.moveto(410, 390, scale=0.7)
# add text labels
txt1 = sg.TextElement(25, 20, "a", size=12, weight="bold")
txt2 = sg.TextElement(400, 20, "b", size=12, weight="bold")
txt3 = sg.TextElement(25, 390, "c", size=12, weight="bold")
txt4 = sg.TextElement(400, 390, "d", size=12, weight="bold")
fig.append([plot1, plot2, plot3, plot4])
fig.append([txt1, txt2, txt3, txt4])
fig.save(args.out)
def plot_depth(save_path=None):
plot_depth_abs(save_path + "_abs.svg")
plot_depth_diff(save_path + "_diff.svg")
fig = sg.SVGFigure("8.38cm", "13.2cm")
abs_fig = sg.fromfile(save_path + "_abs.svg")
abs_plot = abs_fig.getroot()
diff_fig = sg.fromfile(save_path + "_diff.svg")
diff_plot = diff_fig.getroot()
abs_plot.moveto(3.319, 11, scale=1.25)
diff_plot.moveto(0, 247, scale=1.25)
text = functools.partial(sg.TextElement,
size=12,
weight="bold",
font="freesans")
A = text(11.6, 24, "A")
B = text(11.6, 241, "B")
fig.append([abs_plot, diff_plot])
fig.append(A)
fig.append(B)
fig.save(save_path + ".svg")
figutils.figutils.svg_to_pdf(svg_path=save_path + ".svg",
pdf_path=save_path + ".pdf")
def combine_figs(*labeled_figs, unit="px"):
"""Combines the given figures horizontally."""
# Assumes all figures have the same height and use the same size units
plots = []
labels = []
cur_offset = 0
for fig, label in labeled_figs:
plot = fig.getroot()
plot.moveto(cur_offset, 0)
plots.append(plot)
width = int(fig.width.strip(unit))
left_label_offset = 0.0125 * width
top_label_offset = 0.0375 * width
font_size = 0.03 * width
text = sg.TextElement(left_label_offset + cur_offset,
top_label_offset, label, size=font_size)
labels.append(text)
cur_offset += width
height = labeled_figs[0][0].height
combined_fig = sg.SVGFigure(cur_offset, height)
combined_fig.append(plots)
combined_fig.append(labels)
return combined_fig
def write(self):
label = click.style('Cards Processed', fg='yellow')
with click.progressbar(self.data, label=label, show_eta=True) as data:
for card in data:
self.layout = sg.fromfile(self.getLayout())
output_file = os.path.join(self.dir,
'%05d.svg' % card['number'])
numbers = []
for k in card['card'].keys():
numbers = numbers + card['card'][k]
w, h = self.layout.get_size()
c = sg.SVGFigure(w, h)
c.append(self.layout)
fillables = self.getFillables()
for i in range(len(numbers)):
fillable = fillables[i]
number = numbers[i]
txt = sg.TextElement(
fillable['x'] +
(fillable['width'] -
Writer.FONT_SIZE * Writer.H_FACTOR) / 2,
fillable['y'] +
(fillable['height'] +
Writer.FONT_SIZE * Writer.V_FACTOR) / 2,
"%02d" % number,
size=Writer.FONT_SIZE,
weight="bold",
font="Helvetica")
c.append(txt)
c.save(output_file)
print click.style('\nCards written to %s' % self.dir, fg='blue') + '\n'
def put_list_of_figs_to_svg_fig(FIGS, CAP_SIZE=14,\
fig_name="fig.svg", visualize=True,\
transparent=True):
""" take a list of figures and make a """
label = list(string.ascii_uppercase)[:len(FIGS)]
fig = sg.SVGFigure("21cm", "29.7cm") # A4 figure
PLOT_LIST, LABEL_LIST = [], []
for i in range(len(FIGS)):
ff = 'f.svg'
FIGS[i].savefig(ff, format='svg', transparent=transparent)
fig1 = sg.fromfile(ff)
plot = fig1.getroot()
plot.moveto(10. * i, 10. * i, scale=1.)
PLOT_LIST.append(plot)
txt = sg.TextElement(10.*i, 10.*i, label[i%26],\
size=CAP_SIZE, weight="bold")
LABEL_LIST.append(txt)
fig.append(PLOT_LIST)
fig.append(LABEL_LIST)
fig.save(fig_name)
if visualize:
os.system('eog ' + fig_name)
os.system('rm f.svg')
def draw_logo(file_path_or_matrix,
out_path,
unit_width,
unit_height,
revcomp=False,
words=100,
mode='KDIC'):
if os.path.isfile(file_path_or_matrix):
if file_path_or_matrix.endswith('.pcm'):
mode = 'KDIC'
elif file_path_or_matrix.endswith('.ppm'):
mode = 'freq'
else:
raise ValueError(file_path_or_matrix,
' should ends with ".pcm" or ".ppm"')
lines = []
with open(file_path_or_matrix) as f:
for line in f:
if line.startswith('>'):
continue
try:
lines.append(list(map(float,
line.strip('\n').split('\t'))))
except ValueError:
lines.append(list(map(float, line.strip('\n').split(' '))))
else:
lines = file_path_or_matrix
m, heights = get_heights(lines, mode=mode, words=words)
get_revcomp = {
'A': 'T',
'T': 'A',
'C': 'G',
'G': 'C',
}
if os.path.isdir(out_path):
if os.path.isfile(file_path_or_matrix):
out_path = os.path.join(
out_path, '{}{}.svg'.format(
os.path.splitext(os.path.basename(file_path_or_matrix))[0],
'_revcomp' if revcomp else ''))
else:
out_path = os.path.join(
out_path, 'matrix{}.svg'.format('_revcomp' if revcomp else ''))
fig = transform.SVGFigure("{}".format(m * unit_width),
"{}".format(unit_height))
for pos, pack in enumerate(heights[::-1] if revcomp else heights):
current_height = 0
for letter, height in renorm(pack):
# Draw letter with offset of pos*unit_width, current_height*unit_height and height of height*unit_height
place_letter_on_svg(
fig,
get_letter_svg_by_name(
get_revcomp[letter] if revcomp else letter), unit_width,
pos * unit_width, (1 - current_height - height) * unit_height,
height * unit_height)
current_height += height
fig.save(out_path)
def plot_cross_relationship(all_results,
graph_loc,
prediction_loc,
size=4.6,
dpi=300,
ext='pdf',
plot_dir=None):
assert ext in ['pdf', 'svg'], 'Must use svg or pdf'
tmp_dir = '/tmp/'
plot_corr_heatmap(all_results, size=size / 3, plot_dir=tmp_dir, ext='svg')
plot_glasso_edge_strength(all_results,
graph_loc,
size / 4,
plot_dir=tmp_dir,
ext='svg')
plot_cross_within_prediction(prediction_loc,
size / 4,
plot_dir=tmp_dir,
ext='svg')
fig1 = sg.fromfile('/tmp/data_correlations.svg')
fig2 = sg.fromfile('/tmp/cross_prediction.svg')
fig3 = sg.fromfile('/tmp/glasso_edge_strength.svg')
width = float(fig1.get_size()[0][:-2])
height = float(fig2.get_size()[1][:-2])
fig = sg.SVGFigure(width * 2.5, height)
fig.root.set("viewbox", "0 0 %s %s" % (width * 2, height))
plot1 = fig1.getroot()
plot2 = fig2.getroot()
plot3 = fig3.getroot()
# move plots
plot2.moveto(width, 0)
plot3.moveto(width * 1.8, 0)
fig.append([plot1, plot2, plot3])
# add text
txt1 = sg.TextElement(0, height * .1, "A", size=size * 1.5, weight="bold")
txt2 = sg.TextElement(width * 1.05,
height * .1,
"B",
size=size * 1.5,
weight="bold")
txt3 = sg.TextElement(width * 1.85,
height * .1,
"C",
size=size * 1.5,
weight="bold")
fig.append([txt1, txt2, txt3])
# save
svg_file = path.join(plot_dir, 'cross_relationship.svg')
fig.save(svg_file)
if ext == 'pdf':
pdf_file = path.join(plot_dir, 'cross_relationship.pdf')
a = subprocess.Popen('cairosvg %s -o %s' % (svg_file, pdf_file),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# remove temp files
remove('/tmp/data_correlations.svg')
remove('/tmp/glasso_edge_strength.svg')
remove('/tmp/cross_prediction.svg')
def plot_point_bar_figure(figure_one_path, figure_two_path):
"""
Combines the pointplot and bargraph together using svg magic
Arguments:
figure_one_path - The pointplot figure
figure_two_path - The barplot figure
"""
fig = sg.SVGFigure("1280", "960")
fig.append([
etree.Element("rect", {
"width": "100%",
"height": "100%",
"fill": "white"
})
])
fig1 = sg.fromfile(figure_one_path)
plot1 = fig1.getroot()
plot1.moveto(22, 25, scale=1.35)
fig2 = sg.fromfile(figure_two_path)
plot2 = fig2.getroot()
plot2.moveto(662, 0, scale=1.35)
fig.append([plot1, plot2])
text_A = sg.TextElement(10, 30, "A", size=18, weight="bold")
text_B = sg.TextElement(640, 30, "B", size=18, weight="bold")
fig.append([text_A, text_B])
return fig
def main(args):
fig = sg.SVGFigure("50cm", "50cm")
fig1 = sg.fromfile(args.panel_one)
fig2 = sg.fromfile(args.uc)
fig3 = sg.fromfile(args.panel_two)
fig4 = sg.fromfile(args.clinvar)
fig5 = sg.fromfile(args.denovo)
plot1 = fig1.getroot()
plot2 = fig2.getroot()
plot3 = fig3.getroot()
plot4 = fig4.getroot()
plot5 = fig5.getroot()
plot1.moveto(0, 0, scale=0.75)
plot2.moveto(0, 150, scale=0.75)
plot3.moveto(0, 300, scale=0.75)
plot4.moveto(0, 450, scale=0.75)
plot5.moveto(0, 600, scale=0.75)
# add text labels
txt1 = sg.TextElement(25, 20, "panel one", size=12, weight="bold")
txt2 = sg.TextElement(25, 150, "uc", size=12, weight="bold")
txt3 = sg.TextElement(25, 300, "panel two", size=12, weight="bold")
txt4 = sg.TextElement(25, 450, "clinvar", size=12, weight="bold")
txt5 = sg.TextElement(25, 600, "denovo db", size=12, weight="bold")
fig.append([plot1, plot2, plot3, plot4, plot5])
fig.append([txt1, txt2, txt3, txt4, txt5])
fig.save(args.out)
def save(self, fname):
"""Save figure to SVG file.
Parameters
----------
fname : str
Full path to file.
"""
element = _transform.SVGFigure(self.width, self.height)
element.append(self)
element.save(os.path.join(CONFIG['figure.save_path'], fname))
def dumps(self):
# the default .tostr() function fails to return the same text .dump() would return
element = _transform.SVGFigure(self.width, self.height)
element.append(self)
out = etree.tostring(element.root, xml_declaration=True,
standalone=True,
pretty_print=True)
# but even this doesn't make it. The encoding must be changed to UTF-8 (otherwise svgexport fails)
out = out.replace("version='1.0'", 'version="1.0"')
out = out.replace("encoding='ASCII'", 'encoding="UTF-8"')
return out
def test_svg_figure_writes_width_height_and_view_box():
svg_fig = transform.SVGFigure(Unit("400mm"), Unit("300mm"))
with NamedTemporaryFile() as f1:
svg_fig.save(f1.name)
with open(f1.name) as f2:
written_content = f2.read()
assert 'width="400.0mm"' in written_content
assert 'height="300.0mm"' in written_content
assert 'viewBox="0 0 400.0 300.0"' in written_content
def makeSVG(output,sc=0.435,W2=680/2 ,H1=300):
#create new SVG figure
fig = sg.SVGFigure("19.05cm", "22.86cm")
# load matpotlib-generated figures
figA2 = sg.fromfile(output+os.sep+'FigureB_histXY.svg')
figA1= sg.fromfile(output+os.sep+'FigureA_histXY.svg')
figB4 = sg.fromfile(output+os.sep+'angle_hist.svg')
figB=[]
for n in [u'ext__Bacteria_Rad25_1_3', u'ext__IngredientC_1_1', u'ext__snake']:
fig2 = sg.fromfile(output+os.sep+n+"_histXY_labels.svg")
figB.append(fig2)
figB.append(figB4)
# W2 = 680/2
# H1 = 350
# get the plot objects
plot1 = figA1.getroot()
plot1.moveto(5, 0, scale=sc)
plot2 = figA2.getroot()
plot2.moveto(W2, 0, scale=sc)
plot3 = figB[0].getroot()
plot3.moveto(5, H1, scale=sc)
plot4 = figB[1].getroot()
plot4.moveto(W2, H1, scale=sc)
plot5 = figB[2].getroot()
plot5.moveto(5, H1*2, scale=sc)
plot6 = figB[3].getroot()
plot6.moveto(W2, H1*2, scale=sc)
# add text labels
txt1 = sg.TextElement(25,20, "A.1", size=12, weight="bold")
txt2 = sg.TextElement(W2+5,20, "A.2", size=12, weight="bold")
txt3 = sg.TextElement(25,20+H1, "B.1", size=12, weight="bold")
txt4 = sg.TextElement(W2+5,20+H1, "B.2", size=12, weight="bold")
txt5 = sg.TextElement(25,20+H1*2, "B.3", size=12, weight="bold")
txt6 = sg.TextElement(W2+5,20+H1*2, "B.4", size=12, weight="bold")
# append plots and labels to figure
fig.append([plot1, plot2])
fig.append([plot3, plot4])
fig.append([plot5, plot6])
fig.append([txt1, txt2])
fig.append([txt3, txt4])
fig.append([txt5, txt6])
# save generated SVG files
fig.save(output+os.sep+"fig_final.svg")
def main():
svgs = files_to_svg_dict(
["A.svg", "B.svg", "C.svg", "D.svg", "E.svg", "F.svg"])
rescale(svgs)
change_positions(svgs)
full_width = sum([svgs[i].width for i in ['A', 'E']])
full_height = sum([svgs[i].height for i in ['A', 'B', 'C', 'D']])
fig = sg.SVGFigure(full_width, full_height)
text = letter_annotations(svgs)
fig.append([s.data for s in svgs.values()])
fig.append(text)
fig.save("combined.svg")
def combine_svg_verbose(in_brainmask, in_segmentation, in_artmask, in_headmask,
in_airmask, in_bgplot):
import os.path as op
import svgutils.transform as svgt
import svgutils.compose as svgc
import numpy as np
hspace = 10
wspace = 10
#create new SVG figure
in_mosaics = [
in_brainmask, in_segmentation, in_artmask, in_headmask, in_airmask
]
figs = [svgt.fromfile(f) for f in in_mosaics]
roots = [f.getroot() for f in figs]
nfigs = len(figs)
sizes = [(int(f.width[:-2]), int(f.height[:-2])) for f in figs]
maxsize = np.max(sizes, axis=0)
minsize = np.min(sizes, axis=0)
bgfile = svgt.fromfile(in_bgplot)
bgscale = (maxsize[1] * 2 + hspace) / int(bgfile.height[:-2])
bgsize = (int(bgfile.width[:-2]), int(bgfile.height[:-2]))
bgfileroot = bgfile.getroot()
totalsize = (minsize[0] + hspace + int(bgsize[0] * bgscale),
nfigs * maxsize[1] + (nfigs - 1) * hspace)
fig = svgt.SVGFigure(
svgc.Unit(totalsize[0]).to('cm'),
svgc.Unit(totalsize[1]).to('cm'))
yoffset = 0
for i, r in enumerate(roots):
xoffset = 0
if sizes[i][0] == maxsize[0]:
xoffset = int(0.5 * (totalsize[0] - sizes[i][0]))
r.moveto(xoffset, yoffset)
yoffset += maxsize[1] + hspace
bgfileroot.moveto(minsize[0] + wspace,
3 * (maxsize[1] + hspace),
scale=bgscale)
fig.append(roots + [bgfileroot])
out_file = op.abspath('fig_final.svg')
fig.save(out_file)
return out_file
def north_arrow(img_file_in: Path,
img_file_out: Path = None,
rotation_angle=0):
if img_file_out is None:
img_file_out = img_file_in.parent / f"{img_file_in.name[:-4]}_north_arrow.svg"
arrow_fig_path = Path(__file__).parent.parent / "north_arrow.svg"
# load matpotlib-generated figures
fig1 = sg.fromfile(str(img_file_in))
fig2 = sg.fromfile(str(arrow_fig_path))
#create new SVG figure
fig = sg.SVGFigure(fig1.get_size())
w, h = get_fig_size(fig1)
# get the plot objects
plot1 = fig1.getroot()
plot2 = fig2.getroot()
print(fig2.get_size())
x_label = 0.9 * w
y_label = 0.8 * h
kx = 0.5 * 0.05
ky = 0.05
plot2.scale_xy(x=kx, y=ky)
w_fig2, h_fig2 = get_fig_size(fig2)
plot2.moveto(x_label - w_fig2 * kx / 2, y_label)
print(fig2.get_size())
n_text = sg.TextElement(0.9 * w,
0.8 * h,
"N",
size=12,
weight="bold",
anchor="middle")
fig.append([plot1, plot2])
fig.append([
n_text,
])
fig.set_size(fig1.get_size())
fig.save(str(img_file_out))
def plot_resp_amp_rois(save_path=None, loc_mask=True):
conf = ul_sens_fmri.config.get_conf()
conf.ana = ul_sens_analysis.config.get_conf()
if loc_mask:
# subjects x va x img x pres (U,L) x src (A, B)
amp_data = np.load(
os.path.join(conf.ana.base_group_dir,
"ul_sens_group_amp_data.npy"))
else:
# subjects x va x img x pres (U,L) x src (A, B)
amp_data = np.load(
os.path.join(conf.ana.base_group_dir,
"ul_sens_group_amp_ret_roi_data.npy"))
# average over images
amp_data = np.mean(amp_data, axis=2)
for i_va in xrange(len(conf.ana.roi_names)):
plot_amps_visual_area(save_path + "_" + str(i_va) + ".svg",
amp_data[:, i_va, ...], conf.ana.roi_names[i_va])
fig = sg.SVGFigure("13.7cm", "3.56cm")
v1_fig = sg.fromfile(save_path + "_0.svg")
v1_plot = v1_fig.getroot()
v1_plot.moveto(0, 0, scale=1.25)
v2_fig = sg.fromfile(save_path + "_1.svg")
v2_plot = v2_fig.getroot()
v2_plot.moveto(170, 0, scale=1.25)
v3_fig = sg.fromfile(save_path + "_2.svg")
v3_plot = v3_fig.getroot()
v3_plot.moveto(170 * 2, 0, scale=1.25)
fig.append([v1_plot, v2_plot, v3_plot])
fig.save(save_path + ".svg")
figutils.svg_to_pdf(svg_path=save_path + ".svg",
pdf_path=save_path + ".pdf")
def plot_point_bar_figure(figure_one_path, figure_two_path):
"""
Combines the pointplot and bargraph together using svg magic
Arguments:
figure_one_path - The pointplot figure
figure_two_path - The barplot figure
"""
fig1 = sg.fromfile(figure_one_path)
fig2 = sg.fromfile(figure_two_path)
fig1_width_size = np.round(float(fig1.root.attrib["width"][:-2]) * 1.33, 0)
fig1_height_size = np.round(
float(fig1.root.attrib["height"][:-2]) * 1.33, 0)
fig2_width_size = np.round(float(fig2.root.attrib["width"][:-2]) * 1.33, 0)
fig2_height_size = np.round(
float(fig2.root.attrib["height"][:-2]) * 1.33, 0)
fig = sg.SVGFigure(
Unit((fig1_width_size + fig2_width_size) - 360),
Unit(min(fig1_height_size, fig2_height_size) - 50),
)
fig.append([
etree.Element("rect", {
"width": "100%",
"height": "100%",
"fill": "white"
})
])
plot1 = fig1.getroot()
plot1.moveto(10, 30)
plot2 = fig2.getroot()
plot2.moveto(fig1_width_size - 160, 12)
text_A = sg.TextElement(10, 30, "A", size=18, weight="bold")
text_B = sg.TextElement(fig1_width_size - 160,
30,
"B",
size=18,
weight="bold")
fig.append([plot1, plot2, text_A, text_B])
return fig
def output_qr(self):
'''Combine plots into single SVG'''
try:
self._create_plots_qr()
except AttributeError as e: # We never got data to encode, and never produced a qrcode. Nothing to ouput.
return None
fig = sg.SVGFigure(self.qr_size * self.scale_factor,
self.qr_size * self.scale_factor)
try: # Logo and background are set
self._create_plots_logo()
fig.append([self.plot_qr, self.plot_background, self.plot_logo
]) # Order Matters. First is lowest z-index.
except AttributeError as e: # We never got a logo svg, just ouput a qr code.
fig.append(self.plot_qr) # Just a qr code
return fig.to_str() # Can only save to a file or be cast into a string
def register_sketches(skname1, sk1, skname2, sk2, mp1=1, mp2=1):
def parse_line(elem):
return ((float(elem.get('x1')), float(elem.get('y1'))),
(float(elem.get('x2')), float(elem.get('y2'))))
print _get_MP(skname1, sk1, mp1)
# Get mounting points guide lines
up1 = parse_line(sk1.find_id('MP_' + skname1 + '_' + str(mp1) + '_u').root)
rg1 = parse_line(sk1.find_id('MP_' + skname1 + '_' + str(mp1) + '_r').root)
up2 = parse_line(sk2.find_id('MP_' + skname2 + '_' + str(mp2) + '_u').root)
rg2 = parse_line(sk2.find_id('MP_' + skname2 + '_' + str(mp2) + '_r').root)
# Compute scales to make the two figures match in size
fig1scale = geomutils.line_len(up1)
fig2scale = geomutils.line_len(up2)
midscale = (fig1scale + fig2scale) / 2. # The average of the two scales
fig1_normscale = fig1scale / midscale
fig2_normscale = fig2scale / midscale
print '--scales-->', fig1scale, fig2scale
print '--normscales-->', fig1_normscale, fig2_normscale
# 2D displacement of the second figure
displacement = (up1[0][0] * fig2_normscale - up2[0][0] * fig1_normscale,
up1[0][1] * fig2_normscale - up2[0][1] * fig1_normscale)
# Get the plot objects
plot1 = sk1.getroot()
plot2 = sk2.getroot()
plot1.moveto(0, 0, scale=fig2_normscale)
plot2.moveto(0 + displacement[0],
0 + displacement[1],
scale=fig1_normscale)
# Rotation
plot1.rotate(-90 - geomutils.line_angle(up1), up1[0][0], up1[0][1])
plot2.rotate(-90 - geomutils.line_angle(up2), up2[0][0], up2[0][1])
# TODO: Flip if needed
# Create new SVG figure
fig = sg.SVGFigure("1500px", "1500px") # FIXME: hardcoded size
# Append plots and labels to figure
fig.append([plot1, plot2])
return fig
def generate_figures(self, fname, highlight=None):
_image_len = self.width / self.row
self.__subimages = [(s,
moldraw(s,
size=(_image_len, _image_len),
highlight_atoms=highlight))
for s in self.__smiles]
_fig = sg.SVGFigure(str(self.width), str(self.height))
_subfigs = [
sg.fromfile(ff[1]) for ff in self.__subimages if ff[1] is not None
]
_labels = range(len(_subfigs))
_plots = [ff.getroot() for ff in _subfigs]
_x_coord = 0
_y_coord = 0
_final_coords = []
for sf in _plots:
if _x_coord + (self.width % self.row) == self.width:
_x_coord = 0
_y_coord += 1.25 * _image_len
sf.moveto(_x_coord, _y_coord, scale=1.0)
_final_coords.append((_x_coord, _y_coord))
_x_coord += _image_len
else:
sf.moveto(_x_coord, _y_coord, scale=1.0)
_final_coords.append((_x_coord, _y_coord))
_x_coord += _image_len
_txt = [
sg.TextElement(loc[0] + _image_len / 2,
loc[1] + 1.1 * _image_len,
str(n + 1),
size=36,
weight='bold',
font='Arial')
for loc, n in zip(_final_coords, _labels)
]
_fig.append(_plots)
_fig.append(_txt)
_fig.save(fname)
def draw(self):
import svgutils.transform as sg
import sys
fig = sg.SVGFigure(self.width, self.height)
n = self.height * self.width * self.density / 2500
random.shuffle(f)
x = f[:int(n)]
fig1 = sg.fromfile(x[0])
fig2 = sg.fromfile(x[1])
plot1 = fig1.getroot()
plot2 = fig2.getroot()
plot2.moveto(50, 50, scale=0.5)
fig.append([plot1, plot2])
fig.save("fig_final.svg")
def transform(setup, infile, outfile, checkfile=None):
width = f"{setup.bot_width}"
height = f"{setup.bot_height}"
fig = sg.SVGFigure(width=width, height=height)
print(f"Width: {setup.bot_width}")
print(f"Fig: {fig}")
fig.root.set('height', height)
fig.root.set('width', width)
svg = sg.fromfile(infile)
drawing = svg.getroot()
scale, x, y = get_placement(setup, svg)
drawing.moveto(x, y, scale)
fig.append([drawing])
fig.save(outfile)
if checkfile:
label_setup(fig, setup, text=False)
fig.save(checkfile)
def saveSVG(self, drawing, filename=None, path=None):
# compute canvas size
[xMin, yMin, width, height], strokeWidth = drawing.getViewBox()
# create SVG
svg = sg.SVGFigure(str(width) + "mm", str(height) + "mm")
svg.root.set("viewBox", "%s %s %s %s" % (xMin, yMin, width, height))
svgLines = []
for line in drawing.polylines:
# custom path creation
points = " ".join(
map(lambda x: "{:.3f},{:.3f}".format(x[0], -x[1]),
line.getPoints()))
linedata = etree.Element(
sg.SVG + "polyline", {
"points": points,
"stroke-width": str(strokeWidth),
"stroke-linecap": "square",
"stroke": line.color,
"fill": "none"
})
svgLines.append(sg.FigureElement(linedata))
g = sg.GroupElement(svgLines, {'id': "root"})
svg.append(g)
# save generated SVG files
if not (path):
path = self.rootPath
if not (filename):
filename = drawing.filename
filename = re.sub(
r"[^(a-zA-Z0-9\-_)]+", "_", filename
) # make sure that only safe characters are used for filename
mkpath(path)
filepath = os.path.join(path, filename) + ".svg"
drawing.filename = filename
drawing.path = path
drawing.url = self.pathToURL(filepath)
logging.info("drawing.path: " + drawing.path)
logging.info("drawing.url: " + drawing.url)
svg.save(filepath)
def compose_svg_figure(figure_spec, filename, size, display=False):
"""Compose a figure from multiple SVG components.
Parameters
----------
figure_spec : dict
Structure describing subfigures to compose (see below).
filename : str
File name to save composed SVG
size : tuple
Size of final SVG document like ("16cm", "10cm")
display : bool
If True, display the complete SVG in Jupyter notebook.
Each item in *figure_spec* is a dict containing::
{
'figure': <matplotlib Figure>,
'pos': (x, y),
'scale': 1.0,
'label': 'A',
'label_opts': {'size': 16, 'weight': 'bold'},
}
"""
import svgutils.transform as svg
fig = svg.SVGFigure(*size)
for item in figure_spec:
subfig = svg.from_mpl(item['figure'], savefig_kw={'bbox_inches':'tight', 'pad_inches':0})
root = subfig.getroot()
root.moveto(item['pos'][0], item['pos'][1], scale=item.get('scale', 1.0))
label = svg.TextElement(item['pos'][0], item['pos'][1], item['label'], **item.get('label_opts', {}))
fig.append([root, label])
fig.save(filename)
if display:
from IPython.display import SVG, display
display(SVG(filename=filename))
def plot_dist(save_path=None):
plot_dist_abs(save_path + "_abs.svg")
plot_dist_diff(save_path + "_diff.svg")
fig = sg.SVGFigure("8.38cm", "17.5cm")
abs_fig = sg.fromfile(save_path + "_abs.svg")
abs_plot = abs_fig.getroot()
diff_fig = sg.fromfile(save_path + "_diff.svg")
diff_plot = diff_fig.getroot()
map_fig = sg.fromfile(
os.path.join("/home/damien/science/papers/current/ns_patches/figures",
"dist/dist_map.svg"))
map_plot = map_fig.getroot()
map_plot.moveto(41, 14, scale=1)
abs_plot.moveto(0, 160.0, scale=1.25)
diff_plot.moveto(0, 395.08, scale=1.25)
text = functools.partial(sg.TextElement,
size=12,
weight="bold",
font="freesans")
A = text(11.6, 13, "A")
B = text(11.6, 162, "B")
C = text(11.6, 390, "C")
fig.append([abs_plot, diff_plot, map_plot])
fig.append(A)
fig.append(B)
fig.append(C)
fig.save(save_path + ".svg")
figutils.figutils.svg_to_pdf(svg_path=save_path + ".svg",
pdf_path=save_path + ".pdf")
def main(args=None):
parser = argparse.ArgumentParser(description="Combine SVG sample.")
parser.add_argument("input", nargs="+", help="input SVGs")
parser.add_argument("-o", "--output", help="output SVG", required=True)
options = parser.parse_args(args)
w = 0
svgs = []
for i, path in enumerate(options.input):
xml = ET.parse(path)
for elem in xml.iter(GROUP):
elem.attrib.pop("id", None)
for elem in xml.iter(SYMBOL):
elem.set("id", fixid(elem.get("id"), i))
for elem in xml.iter(USE):
elem.set(HREF, fixid(elem.get(HREF), i))
f = BytesIO()
xml.write(f)
svg = sg.fromstring(f.getvalue().decode("us-ascii"))
width = float(svg.width[:-2])
w = max(w, width)
svgs.append(svg)
h = 0
elems = []
for svg in svgs:
height = float(svg.height[:-2])
width = float(svg.width[:-2])
root = svg.getroot()
root.moveto((w - width) / 2, h)
h += height
elems.append(root)
fig = sg.SVGFigure(w, h)
fig.append(elems)
fig.save(options.output)
def combine_svg(svg_list):
"""
Composes the input svgs into one standalone svg
"""
import numpy as np
import svgutils.transform as svgt
# Read all svg files and get roots
svgs = [svgt.fromstring(f.encode('utf-8')) for f in svg_list]
roots = [f.getroot() for f in svgs]
# Query the size of each
sizes = [(int(f.width[:-2]), int(f.height[:-2])) for f in svgs]
# Calculate the scale to fit all widths
scales = [1.0] * len(svgs)
if not all([width[0] == sizes[0][0] for width in sizes[1:]]):
ref_size = sizes[0]
for i, els in enumerate(sizes):
scales[i] = ref_size[0] / els[0]
newsizes = [
tuple(size)
for size in np.array(sizes) * np.array(scales)[..., np.newaxis]
]
# Compose the views panel: total size is the width of
# any element (used the first here) and the sum of heights
totalsize = [newsizes[0][0], np.sum(newsizes, axis=0)[1]]
fig = svgt.SVGFigure(totalsize[0], totalsize[1])
yoffset = 0
for i, r in enumerate(roots):
size = newsizes[i]
r.moveto(0, yoffset, scale=scales[i])
yoffset += size[1]
fig.append(r)
return fig
