def draw_pedigree(pedigree, out_file, plot_params=fp.PlotParams(), colors=fp.DEFAULT_COLORS,
add_dummy=False, identifier='id', labels=None):
'''Draw pedigree to file (EPS/PNG/...).'''
extension = util.file_ext(out_file)
if not extension in ['eps', 'png']:
raise ValueError('Unsupported file extension ''%s''' % (extension,))
coord_params = fp.CoordParams()
coord_params.algorithm = 'default'
# Create famplot input file
# TODO: replace writing to a temp file by a copy constructor fp.Pedigree(our Pedigree) and
# pass it instead of prefix
tempdir = tempfile.mkdtemp()
famplot_file = tempdir + '/file.fpl'
eps_file = out_file if extension == 'eps' else tempdir + '/file.eps'
to_pedfiddler(pedigree, famplot_file, add_dummy=add_dummy, identifier=identifier, labels=labels)
p = fp.draw_pedigree(famplot_file, coord_params, plot_params, colors, eps_file)
# Convert EPS to PNG/other supported formats by the Image library
if extension != 'eps':
with open(eps_file, 'rb') as eps:
img = Image.open(eps)
img.save(out_file)
# Clean up
shutil.rmtree(tempdir)
return p
def test_draw_pedigree_hardcoded(self):
'''Test drawing a pedigree as an EPS file using hard-coded positions.'''
coord_params = fp.CoordParams()
coord_params.algorithm = 'hardcoded'
coord_params.coord_file = TestFamPlot.__PEDIGREE_POSITIONS
coord_params.balance_marriages = False
out = tempfile.NamedTemporaryFile(suffix='.eps', delete=False)
ped_info = fp.draw_pedigree(TestFamPlot.__PEDIGREE, coord_params,
fp.PlotParams(), fp.DEFAULT_COLORS, out)
expected_coord = TestFamPlot.__read_coord_dict(coord_params.coord_file)
test_util.assert_positions_almost_equal(ped_info.coord_dict,
expected_coord,
decimal=10,
err_msg='Wrong coordinates')
def test_generation_number(self):
'''Test calculating generation numbers..'''
ped = fp.read_pedigree(TestFamPlot.__PEDIGREE_UNBALANCED)
ped_info = fp.PedigreeInfo(ped)
cp = fp.CoordParams()
cp.algorithm = 'default'
fp.compute_coords(ped_info, cp)
assert_equal(ped_info.gen_dict, {
1: 0,
2: 0,
3: 1,
4: 1,
5: 1,
6: 2,
7: 2,
8: 3
}, 'Wrong generation numbers')
def __test_draw_pedigree_default(self, infile):
'''Test drawing a pedigree as an EPS file using the default node placement.'''
coord_params = fp.CoordParams()
coord_params.algorithm = 'default'
out = tempfile.NamedTemporaryFile(suffix='.eps', delete=True)
ped_info = fp.draw_pedigree(infile, coord_params, fp.PlotParams(),
fp.DEFAULT_COLORS, out)
#expected_coord = TestFamPlot.__read_coord_dict(TestFamPlot.__PEDIGREE_POSITIONS)
# Positions are not unique; they depend on ordering person lists within the default algorithm
# test_util.assert_positions_almost_equal(ped_info.coord_dict, expected_coord,
# decimal=10, err_msg='Wrong coordinates')
# print '==============================================='
# print ped_info.pprint()
# print '==============================================='
for info in ped_info.data.itervalues():
self.assertTrue(info.coord[0] >= 0 and info.coord[1] >= 0,
'Unset coordinate at node %s' % (info.name, ))
return ped_info
#!/usr/bin/env python
'''
============================================================
Plot the nbhrs1298 pedigree.
Created on August 16, 2012
@author: Oren Livne <*****@*****.**>
============================================================
'''
import impute as im, famplot as fp
p = im.io.read_npz(im.itu.NBHRS1298_STAGE4)
in_file = 'NBHRS1298_STAGE4.txt'
im.pt.to_pedfiddler(p.pedigree, in_file)
coord_params = fp.CoordParams()
coord_params.algorithm = 'default'
out = 'NBHRS1298_STAGE4.eps'
# out = tempfile.NamedTemporaryFile(suffix='.eps', delete=False)
ped_info = fp.draw_pedigree(in_file, coord_params,
fp.PlotParams(), fp.DEFAULT_COLORS, out)