def __init__(self,
plate_image,
new=False,
categories=None,
tags='PlateMeasurement',
well_dimensions=(8, 12),
configuration_path='config',
plate_design=None,
pixel_intensities=False):
Treant.__init__(self, plate_image, categories=categories, tags=tags)
# store the image name provided in the categories, if there is one
if 'ImageFileName' in self.categories.keys():
self.image_name = self.categories['ImageFileName']
elif 'IMAGEFILENAME' in self.categories.keys():
self.image_name = self.categories['IMAGEFILENAME']
# store the (rows,cols) of the plate
self.well_dimensions = well_dimensions
# calculate and store the total number of wells
self.number_of_wells = self.well_dimensions[0] * self.well_dimensions[1]
# store the path and name of the plate
self.configuration_path = '/'.join(('..', configuration_path))
self.plate_design = plate_design
# remember whether we will be analysing and keeping the pixel intensities etc
self.pixel_intensities = pixel_intensities
def test_regen(self, tags, categories, tmpdir):
"""Test regenerating Treant.
- create Treant
- modify Treant a little
- create same Treant (should regenerate)
- check that modifications were saved
"""
with tmpdir.as_cwd():
C1 = Treant('regen', tags=tags, categories=categories)
C2 = Treant('regen') # should be regen of C1
if tags is not None:
for tag in tags:
assert tag in C2.tags
if categories is not None:
for cat, val in categories.items():
assert cat in C2.categories
assert C2.categories[cat] == val
assert C1 == C2
# they point to the same file, but they are not the same object
assert C1 is not C2
def test_gen_methods(self, tmpdir):
"""Test the variety of ways we can generate a new Treant
1. ``Treant('treant')``, where 'treant' is not an existing file or
directory path
2. ``Treant('treant')``, where 'treant' is an existing directory
without Treant state files inside
3. ``Treant('/somedir/treant')``, where 'treant' is not an existing
file or directory in 'somedir'
4. ``Treant('/somedir/treant')``, where 'treant' is an existing
directory in 'somedir' without any Treant state files inside
"""
with tmpdir.as_cwd():
# 1
t1 = Treant('newone')
assert os.path.exists(t1._treantdir)
# 2
os.mkdir('another')
t2 = Treant('another')
assert os.path.exists(t2._treantdir)
# 3
t3 = Treant('yet/another')
assert os.path.exists(t3._treantdir)
# 4
os.mkdir('yet/more')
t4 = Treant('yet/more')
assert os.path.exists(t4._treantdir)
def test_cmp(self, tmpdir):
"""Test the comparison of Treants when sorting"""
with tmpdir.as_cwd():
c1 = Treant('a')
c2 = Treant('b')
c3 = Treant('c')
assert sorted([c3, c2, c1]) == [c1, c2, c3]
assert c1 <= c2 < c3
assert c3 >= c2 > c1
def basic_treant(self, tmpdir):
# treant with tags and cats, in tmpdir
with tmpdir.as_cwd():
t1 = Treant('Rincewind')
t1.tags.add('magical')
t1.categories.add({'colour': 'octarine'})
yield t1
def test_gen_OSError(self, tmpdir):
with tmpdir.as_cwd():
with mock.patch('os.makedirs') as mp:
mp.sideeffect = OSError(os.errno.ENOSPC, 'Mock - disk full')
with pytest.raises(OSError) as error:
t = Treant('new')
t.tags.add('worthless')
assert error.errno == os.errno.ENOSPC
def test_gen_OSError13(self, tmpdir):
with tmpdir.as_cwd():
with mock.patch('os.makedirs') as mp:
mp.sideeffect = OSError(os.errno.EACCES, 'Mock - disk full')
with pytest.raises(OSError) as error:
t = Treant('new')
t.tags.add('worthless')
assert error.errno == os.errno.EACCES
assert ("Permission denied; cannot create 'new'"
in str(error))
def test_init_treant(tmpdir):
pool = mp.Pool(processes=4)
num = 73
# TODO: eventually want this to work without initing the treant
# here
init_treant(tmpdir, ['bark'])
for i in range(num):
pool.apply_async(init_treant, args=(tmpdir, ['run_{}'.format(i)]))
pool.close()
pool.join()
with tmpdir.as_cwd():
tf = Treant('sprout')
assert len(tf.tags) == num + 1
def test_tags_setting(self, tmpdir):
"""Test that we can set tags with lists or sets, or with Tags
objects.
"""
with tmpdir.as_cwd():
# set with a list
t1 = Treant('maple')
t1.tags = ['sprout', 'deciduous']
assert t1.tags == {'sprout', 'deciduous'}
# set with a set
t2 = Treant('elm')
t2.tags = {'sprout', 'deciduous'}
assert t2.tags == {'sprout', 'deciduous'}
# set with a Tags object
t3 = Treant('sequoia')
t3.tags = t2.tags
assert t3.tags == {'sprout', 'deciduous'}
def test_init_from_Tree(self, tmpdir):
with tmpdir.as_cwd():
tree = dtr.Tree('this')
t = Treant(tree)
assert t.path == tree.path
def test_tags_set_behavior(self, tmpdir):
with tmpdir.as_cwd():
# 1
t1 = Treant('maple')
t1.tags.add(['sprout', 'deciduous'])
# 2
t2 = Treant('sequoia')
t2.tags.add(['sprout', 'evergreen'])
tags_union = t1.tags | t2.tags
for t in ['sprout', 'deciduous', 'evergreen']:
assert t in tags_union
tags_intersect = t1.tags & t2.tags
assert 'sprout' in tags_intersect
for t in ['deciduous', 'evergreen']:
assert t not in tags_intersect
tags_diff = t1.tags - t2.tags
assert 'deciduous' in tags_diff
for t in ['sprout', 'evergreen']:
assert t not in tags_diff
tags_symm_diff = t1.tags ^ t2.tags
for t in ['deciduous', 'evergreen']:
assert t in tags_symm_diff
assert 'sprout' not in tags_symm_diff
# 3
t3 = Treant('oak')
t3.tags.add(['deciduous'])
# Test set membership
assert t1.tags <= t1.tags
assert not t1.tags < t1.tags
assert t1.tags == t1.tags
assert not t1.tags < t3.tags
assert t1.tags > t3.tags
# test TypeErrors in Tags
# type_error_msg = "Operands must be AggTags, Tags, or a set."
with pytest.raises(TypeError) as e:
('tree') == t1.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
t1.tags < ('tree')
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
('tree') - t1.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
t1.tags - ('tree')
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
('tree') | t1.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
t1.tags | ('tree')
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
('tree') & t1.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
t1.tags & ('tree')
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
('tree') ^ t1.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
t1.tags ^ ('tree')
def init_treant(tmpdir, tags):
with tmpdir.as_cwd():
tf = Treant('sprout', tags=tags)
return tf
def pokefile(treantpath, string):
"""Add a number of tags to a Treant."""
treant = Treant(treantpath)
treant.tags.add(* ["{}_{}".format(string, i) for i in range(100)])
def treant(tmpdir):
with tmpdir.as_cwd():
t = Treant('sprout')
return t