def test_pull_doc_examples(self):
"""
Pull out WCON examples from all .MD files and validate them.
"""
cur_path = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', '..', '..'))
md_paths = [
glob.glob(os.path.join(x[0], '*.md')) for x in os.walk(cur_path)
]
md_paths = [x for x in md_paths if x != []]
# Flatten, since the lists might be nested
md_paths = list(flatten(md_paths))
for md_path in md_paths:
print("Checking for JSON code in %s " % md_path)
with open(md_path, 'r') as f:
md_string = f.read()
# Find all code examples
code_snippets = md_string.split('```')[1::2]
# Consider only JSON code examples
JSON_snippets = [
s[4:] for s in code_snippets if s[:4] == 'JSON'
]
for i, JSON_snippet in enumerate(JSON_snippets):
print("Testing JSON code snippet %i from %s" %
(i + 1, md_path))
JSON_snippet = JSON_snippet.replace('\n', '')
JSON_snippet = JSON_snippet.replace('\r', '')
WCONWorms.load(StringIO(JSON_snippet))
def test_pull_doc_examples(self):
"""
Pull out WCON examples from all .MD files and validate them.
"""
cur_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
'..', '..', '..'))
md_paths = [glob.glob(os.path.join(x[0], '*.md'))
for x in os.walk(cur_path)]
md_paths = [x for x in md_paths if x != []]
# Flatten, since the lists might be nested
md_paths = list(flatten(md_paths))
for md_path in md_paths:
print("Checking for JSON code in %s " % md_path)
with open(md_path, 'r') as f:
md_string = f.read()
# Find all code examples
code_snippets = md_string.split('```')[1::2]
# Consider only JSON code examples
JSON_snippets = [s[4:] for s in code_snippets
if s[:4] == 'JSON']
for i, JSON_snippet in enumerate(JSON_snippets):
print("Testing JSON code snippet %i from %s" %
(i + 1, md_path))
JSON_snippet = JSON_snippet.replace('\n', '')
JSON_snippet = JSON_snippet.replace('\r', '')
WCONWorms.load(StringIO(JSON_snippet))
def test_chunks(self):
"""
Test load_from_file with two or more chunks
"""
# Define our chunks
chunks = []
chunks.append(
('{"files":{"current":"0.wcon", "prev":null,'
'"next":["1.wcon", "2.wcon"]},'
'"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":"3", "t":[1.3], '
'"x":[[3,4]], "y":[[5.4,3]]}]}'))
chunks.append(('{"units":{"t":"s","x":"mm","y":"mm"},'
'"files":{"current":"1.wcon", "prev":["0.wcon"],'
'"next":["2.wcon"]},'
'"data":[{"id":"3", "t":[1.4], '
'"x":[[5,1]], "y":[[15.4,3]]}]}'))
chunks.append(
('{"units":{"t":"s","x":"mm","y":"mm"},'
'"files":{"current":"2.wcon", "prev":["1.wcon", "0.wcon"],'
'"next":null},'
'"data":[{"id":"3", "t":[1.5], '
'"x":[[8,4.2]], "y":[[35.4,3]]}]}'))
# Create filenames for our chunks
chunk_filenames = [''] * len(chunks)
for (chunk_index, chunk) in enumerate(chunks):
chunk_filenames[chunk_index] = \
'test_chunk_' + str(chunk_index) + '.wcon'
# Save these chunks as files
for (chunk_index, chunk) in enumerate(chunks):
with open(chunk_filenames[chunk_index], 'w') as outfile:
outfile.write(chunk)
# First load one of them
worm_combined_manually = WCONWorms.load(StringIO(chunks[0]))
# Then merge the others sequentially to the first one
for chunk in chunks[1:]:
worm_chunk = WCONWorms.load(StringIO(chunk))
worm_combined_manually += worm_chunk
# Validate that the chunks together are __eq__ to the files
# that find each other through their "files" object
for chunk_filename in chunk_filenames:
# Worm from files that found each other through
# the "files" object
worm_from_files = WCONWorms.load_from_file(chunk_filename)
self.assertEqual(worm_from_files, worm_combined_manually)
# Delete the files created
for chunk_filename in chunk_filenames:
os.remove(chunk_filename)
def test_arrayed_software(self):
WCONWorms.load(StringIO('{ "units":{"t":"s", "x":"mm", "y":"mm"}, '
'"data":[], "metadata":{'
'"software":[{"name":"a"}, '
'{"name":"b"}]} }'))
# With "settings" field
WCONWorms.load(StringIO('{ "units":{"t":"s", "x":"mm", "y":"mm"}, '
'"data":[], "metadata":{'
'"software":[{"name":"a", "settings": '
'{"h": 5}}, {"name":"b"}]} }'))
def test_merge_commutativity(self):
worm1 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
worm2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"}, '
'"data":[{"id":4, "t":1.5, "x":[5,2], "y":[1.4,6]}]}'))
merged = worm1 + worm2
# merged.save_to_file('pythonMerged.wcon', pretty_print=True)
merged2 = worm2 + worm1
# merged2.save_to_file('pythonMerged2.wcon', pretty_print=True)
self.assertNotEqual(worm1, worm2)
self.assertEqual(merged, merged2)
def test_empty_aspect_size(self):
# Worms with a segment that is empty should still parse without issue.
WCON_string = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":1, "t":[1.3,1.5],
"x":[[],[1215.11, 1216.14, 1217.12]],
"y":[[],[234.89, 265.23, 235.08]] }
]
}
"""
w = WCONWorms.load(StringIO(WCON_string))
test_path = 'test_empty_aspect.wcon'
w.save_to_file(test_path, pretty_print=True)
w_from_saved = WCONWorms.load_from_file(test_path)
self.assertEqual(w, w_from_saved)
os.remove(test_path)
def test_empty_aspect_size(self):
# Worms with a segment that is empty should still parse without issue.
WCON_string = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":1, "t":[1.3,1.5],
"x":[[],[1215.11, 1216.14, 1217.12]],
"y":[[],[234.89, 265.23, 235.08]] }
]
}
"""
w = WCONWorms.load(StringIO(WCON_string))
test_path = 'test_empty_aspect.wcon'
w.save_to_file(test_path, pretty_print=True)
w_from_saved = WCONWorms.load_from_file(test_path)
self.assertEqual(w, w_from_saved)
os.remove(test_path)
def test_merge_commutativity(self):
worm1 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
worm2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"}, '
'"data":[{"id":4, "t":1.5, "x":[5,2], "y":[1.4,6]}]}'))
merged = worm1 + worm2
# merged.save_to_file('pythonMerged.wcon', pretty_print=True)
merged2 = worm2 + worm1
# merged2.save_to_file('pythonMerged2.wcon', pretty_print=True)
self.assertNotEqual(worm1, worm2)
self.assertEqual(merged, merged2)
def test_bad_files_object(self):
"""
Test that a badly specified "files" object will fail
"""
# "this":null should be disallowed by the schema
worm_file_text1 = ((
'{"files":{"this":null, "prev":null, "next":["_1", "_2"]},'
'"units":{"t":"s","x":"mm","y":"mm"},"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
with self.assertRaises(jsonschema.exceptions.ValidationError):
WCONWorms.load(StringIO(worm_file_text1))
# "this":"" should be disallowed by the schema
worm_file_text2 = ((
'{"files":{"this":"", "prev":null, "next":["_1", "_2"]},'
'"units":{"t":"s","x":"mm","y":"mm"},"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
with self.assertRaises(jsonschema.exceptions.ValidationError):
WCONWorms.load(StringIO(worm_file_text2))
def test_merge_user_defined_constants(self):
""" This example is pulled right from the specification"""
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s", "x":"mm", "y":"mm", "@XJ z":"mm"},'
'"data":[{"id":"0", "t":[1,2], "x":[0,1], "y":[1,0],'
'"@XJ z":[3,4], "@XJ g":9.8, "@XJ f":"salmon"},'
'{"id":"0", "t":[3,4,5], "x":[1,0,1], "y":[2,3,2],'
'"@XJ z":[5,6,5], "@XJ g":9.8, "@XJ f":"cod"}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s", "x":"mm", "y":"mm", "@XJ z":"mm"},'
'"data":[{"id":"0", "t":[1,2,3,4,5], '
'"x":[0,1,1,0,1], "y":[1,0,2,3,2],'
'"@XJ z":[3,4,5,6,5], "@XJ g":9.8, '
'"@XJ f":["salmon", "salmon", "cod", "cod", "cod"]}]}'))
self.assertEqual(w1, w2)
def test_bad_files_object(self):
"""
Test that a badly specified "files" object will fail
"""
# "this":null should be disallowed by the schema
worm_file_text1 = (
('{"files":{"this":null, "prev":null, "next":["_1", "_2"]},'
'"units":{"t":"s","x":"mm","y":"mm"},"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
with self.assertRaises(jsonschema.exceptions.ValidationError):
WCONWorms.load(StringIO(worm_file_text1))
# "this":"" should be disallowed by the schema
worm_file_text2 = (
('{"files":{"this":"", "prev":null, "next":["_1", "_2"]},'
'"units":{"t":"s","x":"mm","y":"mm"},"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
with self.assertRaises(jsonschema.exceptions.ValidationError):
WCONWorms.load(StringIO(worm_file_text2))
def test_tracker_commons_and_units(self):
with self.assertRaises(ValueError):
# The JSON parser shouldn't accept this as valid JSON
# "ValueError: Expecting ',' delimiter: line 1 column 25 (char 24)"
WCONWorms.load(StringIO('{"lalala":blahblah}'))
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"}, "data":[]}'))
# This should fail because "units" is required
with self.assertRaises(jsonschema.exceptions.ValidationError):
WCONWorms.load(StringIO('{"data":[]}'))
# The smallest valid WCON file (Empty data array should be fine)
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"}, "data":[]}'))
# Duplicate keys should cause the parser to fail
with self.assertRaises(KeyError):
WCONWorms.load(
StringIO('{"units":{"t":"s","t":"s","x":"mm","y":"mm"},'
'"data":[]}'))
def test_origin_offset(self):
# ox, without optional bracket
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":1.3, "ox":5000, "oy":0,'
'"x":[3,4], "y":[5.4,3]}]}'))
w2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, '
'"x":[5003,5004], "y":[5.4,3]}]}'))
self.assertEqual(w1, w2)
# oy, with optional bracket
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":1.3, "ox":0, "oy":[4000], '
'"x":[3,4], "y":[5.4,3]}]}'))
w2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, '
'"x":[3,4], "y":[4005.4,4003]}]}'))
self.assertEqual(w1, w2)
# ox and oy, without optional brackets
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":1.3, "ox":-500, "oy":4000, '
'"x":[3,4], "y":[5.4,3]}]}'))
w2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, '
'"x":[-497,-496], "y":[4005.4,4003]}]}'))
self.assertEqual(w1, w2)
# ox, with two time points
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":5000, "oy":0,'
'"x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], '
'"x":[[5003],[5004]], "y":[[5.4],[3]]}]}'))
self.assertEqual(w1, w2)
def test_tracker_commons_and_units(self):
with self.assertRaises(ValueError):
# The JSON parser shouldn't accept this as valid JSON
# "ValueError: Expecting ',' delimiter: line 1 column 25 (char 24)"
WCONWorms.load(StringIO('{"lalala":blahblah}'))
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"}, "data":[]}'))
# This should fail because "units" is required
with self.assertRaises(jsonschema.exceptions.ValidationError):
WCONWorms.load(StringIO('{"data":[]}'))
# The smallest valid WCON file (Empty data array should be fine)
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"}, "data":[]}'))
# Duplicate keys should cause the parser to fail
with self.assertRaises(KeyError):
WCONWorms.load(
StringIO(
'{"units":{"t":"s","t":"s","x":"mm","y":"mm"},'
'"data":[]}'))
def test_centroid(self):
# ox, with two time frames, with centroid
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "ox":[0,0],'
'"oy":[5000,4990], '
'"cx":[10, 11], "cy":[13, 12], "x":[[3, 5],[4, 5]],'
'"y":[[5.4, 4],[3, 2]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "cx":[10, 11],'
'"cy":[5013, 5002], '
'"x":[[3, 5],[4, 5]], "y":[[5005.4, 5004],[4993, 4992]]}]}'))
self.assertEqual(w1, w2)
# oy with no oy: assertionerror
with self.assertRaises(AssertionError):
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "oy":[5000, 5000],'
'"cx":[10, 10], "cy":[10, 10], "x":[[3,3,3],[4,4,4.2]], '
'"y":[[5.4, 5.4, 5.5],[3, 3, 7]]}]}'))
# units missing for centroid
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "ox":[5,5], "oy":[0,0],'
' "cx":[10, 10], "cy":[10, 10], "x":[[3],[4]], '
' "y":[[5.4],[3]]}]}'))
def test_origin_offset(self):
# ox, without optional bracket
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":1.3, "ox":5000, "oy":0,'
'"x":[3,4], "y":[5.4,3]}]}'))
w2 = WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, '
'"x":[5003,5004], "y":[5.4,3]}]}'))
self.assertEqual(w1, w2)
# oy, with optional bracket
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":1.3, "ox":0, "oy":[4000], '
'"x":[3,4], "y":[5.4,3]}]}'))
w2 = WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, '
'"x":[3,4], "y":[4005.4,4003]}]}'))
self.assertEqual(w1, w2)
# ox and oy, without optional brackets
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":1.3, "ox":-500, "oy":4000, '
'"x":[3,4], "y":[5.4,3]}]}'))
w2 = WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, '
'"x":[-497,-496], "y":[4005.4,4003]}]}'))
self.assertEqual(w1, w2)
# ox, with two time points
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":5000, "oy":0,'
'"x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], '
'"x":[[5003],[5004]], "y":[[5.4],[3]]}]}'))
self.assertEqual(w1, w2)
def test_load_from_file(self):
"""
Test that .load_from_file works identically to .load
"""
worm_file_text3 = ((
'{"units":{"t":"s","x":"mm","y":"mm"},"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
# STREAM
worm_from_stream = WCONWorms.load(StringIO(worm_file_text3))
# FILE
with open("test.wcon", 'w') as outfile:
outfile.write(worm_file_text3)
worm_from_file = WCONWorms.load_from_file("test.wcon")
os.remove("test.wcon")
# COMPARISON
self.assertEqual(worm_from_file, worm_from_stream)
def test_load_from_file(self):
"""
Test that .load_from_file works identically to .load
"""
worm_file_text3 = (
('{"units":{"t":"s","x":"mm","y":"mm"},"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
# STREAM
worm_from_stream = WCONWorms.load(StringIO(worm_file_text3))
# FILE
with open("test.wcon", 'w') as outfile:
outfile.write(worm_file_text3)
worm_from_file = WCONWorms.load_from_file("test.wcon")
os.remove("test.wcon")
# COMPARISON
self.assertEqual(worm_from_file, worm_from_stream)
def test_metadata(self):
WCON_string1 = \
"""
{
"metadata":{
"lab":{"location":"CRB, room 5020",
"name":"Behavioural Genomics" },
"who":"Firstname Lastname",
"timestamp":"2012-04-23T18:25:43.511Z",
"temperature":23.8,
"humidity":40.3,
"dish":{ "type":"petri", "size":35, "units":"mm" },
"food":"none",
"media":"agarose",
"sex":"hermaphrodite",
"stage":"adult",
"age":66.8,
"strain":"CB4856",
"image_orientation":"imaged onto agar",
"protocol":"text description of protocol",
"software":{
"tracker":{"name":"Software Name",
"version":"1.3.0"},
"featureID":"@OMG"
},
"settings":
"Any valid string with hardware and software configuration details"
},
"units":{"t":"s", "x":"mm", "y":"mm", "humidity":"%",
"temperature":"C", "age":"h"},
"data":[
{ "id":1, "t":1.3, "x":[7.2, 5], "y":[0.5, 0.86] }
]
}
"""
w1 = WCONWorms.load(StringIO(WCON_string1))
self.assertEqual(w1.metadata["strain"], "CB4856")
self.assertEqual(w1.metadata["dish"]["size"], 35)
def test_metadata(self):
WCON_string1 = \
"""
{
"metadata":{
"lab":{"location":"CRB, room 5020",
"name":"Behavioural Genomics" },
"who":"Firstname Lastname",
"timestamp":"2012-04-23T18:25:43.511Z",
"temperature":23.8,
"humidity":40.3,
"dish":{ "type":"petri", "size":35, "units":"mm" },
"food":"none",
"media":"agarose",
"sex":"hermaphrodite",
"stage":"adult",
"age":66.8,
"strain":"CB4856",
"image_orientation":"imaged onto agar",
"protocol":"text description of protocol",
"software":{
"tracker":{"name":"Software Name",
"version":"1.3.0"},
"featureID":"@OMG"
},
"settings":
"Any valid string with hardware and software configuration details"
},
"units":{"t":"s", "x":"mm", "y":"mm", "humidity":"%",
"temperature":"C", "age":"h"},
"data":[
{ "id":1, "t":1.3, "x":[7.2, 5], "y":[0.5, 0.86] }
]
}
"""
w1 = WCONWorms.load(StringIO(WCON_string1))
self.assertEqual(w1.metadata["strain"], "CB4856")
self.assertEqual(w1.metadata["dish"]["size"], 35)
def test_origin_offset(self):
# ox and oy
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":"1", "t":[1.3], "ox":[-500], "oy":[4000], '
'"x":[[3,4]], "y":[[5.4,3]]}]}'))
w2 = WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":"1", "t":[1.3], '
'"x":[[-497,-496]],'
'"y":[[4005.4,4003]]}]}'))
self.assertEqual(w1, w2)
# ox with two time points
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "ox":[5000, 5000],'
'"oy":[0, 0],'
'"x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], '
'"x":[[5003],[5004]], "y":[[5.4],[3]]}]}'))
self.assertEqual(w1, w2)
# ox specified not for each time frame should as of version 1.2
# raise an error
with self.assertRaises(jsonschema.exceptions.ValidationError):
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "ox":5000, "oy":0,'
'"x":[[3],[4]], "y":[[5.4],[3]]}]}'))
# Try the same but wrap our single origin points in brackets
# (should still fail)
with self.assertRaises(AssertionError):
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":"1", "t":[1.3,1.4], "ox":[5000], "oy":[0],'
'"x":[[3],[4]], "y":[[5.4],[3]]}]}'))
def test_data2(self):
WCON_string = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":1, "t":[1.3,1.5],
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]] }
]
}
"""
self._validate_from_schema(WCON_string)
WCONWorms.load(StringIO(WCON_string))
# Test that extra features are ignored
WCON_string1 = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08], "ignorethat":"yes" },
{ "id":1, "t":[1.3,1.5], "ignorethis": 12,
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]] }
]
}
"""
self._validate_from_schema(WCON_string1)
w = WCONWorms.load(StringIO(WCON_string1))
# TODO: test that "ignorethis" and "ignorethat" are not present in w
# order permuted from previous example
WCON_string2 = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":1, "t":[1.3,1.5],
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]] },
{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] }
]
}
"""
self._validate_from_schema(WCON_string2)
WCONWorms.load(StringIO(WCON_string2))
# Origin values
WCON_string3 = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm", "ox":"mm", "oy":"mm"},
"data":[{ "id":1, "t":[1.3,1.5],
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]],
"ox":5000, "oy":0 },
{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08]},
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] }
]
}
"""
self._validate_from_schema(WCON_string3)
WCONWorms.load(StringIO(WCON_string3))
def test_arrayed_software(self):
WCONWorms.load(
StringIO('{ "units":{"t":"s", "x":"mm", "y":"mm"}, '
'"data":[], "metadata":{'
'"software":[{"name":"a"}, '
'{"name":"b"}]} }'))
def test_data2(self):
WCON_string = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":1, "t":[1.3,1.5],
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]] }
]
}
"""
self._validate_from_schema(WCON_string)
WCONWorms.load(StringIO(WCON_string))
# Test that extra features are ignored
WCON_string1 = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08], "ignorethat":"yes" },
{ "id":1, "t":[1.3,1.5], "ignorethis": 12,
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]] }
]
}
"""
self._validate_from_schema(WCON_string1)
w = WCONWorms.load(StringIO(WCON_string1))
# TODO: test that "ignorethis" and "ignorethat" are not present in w
# order permuted from previous example
WCON_string2 = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm"},
"data":[{ "id":1, "t":[1.3,1.5],
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]] },
{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] },
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] }
]
}
"""
self._validate_from_schema(WCON_string2)
WCONWorms.load(StringIO(WCON_string2))
# Origin values
WCON_string3 = \
"""
{
"units":{"t":"s", "x":"mm", "y":"mm", "ox":"mm", "oy":"mm"},
"data":[{ "id":1, "t":[1.3,1.5],
"x":[[1,1,1],[1215.11, 1216.14, 1217.12]],
"y":[[2,2,2],[234.89, 265.23, 235.08]],
"ox":5000, "oy":0 },
{ "id":2, "t":1.4, "x":[125.11, 126.14, 117.12],
"y":[23.3, 22.23, 21135.08] },
{ "id":1, "t":1.4, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08]},
{ "id":2, "t":1.5, "x":[1215.11, 1216.14, 1217.12],
"y":[234.89, 265.23, 235.08] }
]
}
"""
self._validate_from_schema(WCON_string3)
WCONWorms.load(StringIO(WCON_string3))
def test_centroid(self):
# ox, with two time frames, with centroid
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":0, "oy":5000, "cx":10, '
'"cy":10, "x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":5010, '
'"x":[[-7],[-6]], "y":[[-4.6],[-7]]}]}'))
self.assertEqual(w1, w2)
# oy with no oxy: assertionerror
with self.assertRaises(AssertionError):
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "oy":5000,'
'"cx":10, "cy":10, "x":[[3, 3, 3],[4, 4, 4.2]], '
'"y":[[5.4, 5.4, 5.5],[3, 3, 7]]}]}'))
# ox, with two time frames, three articulation points, with centroid
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":0, "oy":5000, "cx":10, '
'"cy":10, "x":[[3, 3, 3],[4, 4, 4.2]], '
'"y":[[5.4, 5.4, 5.5],[3, 3, 7]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":5010, '
'"x":[[-7,-7,-7],[-6,-6,-5.8]], '
'"y":[[-4.6,-4.6,-4.5],[-7,-7,-3]]}]}'))
self.assertEqual(w1, w2)
# ox and centroid, different in different time frames
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox": 0, '
'"oy":[5000, 1000], "cx":10, '
'"cy":10, "x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":[5010, 1010], '
'"x":[[-7],[-6]], "y":[[-4.6],[-7.0]]}]}'))
self.assertEqual(w1, w2)
# ox and centroid, different in different time frames
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":0, "oy":[5000, 1000],'
'"cx":10, "cy":10, "x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":[5010, 1010], '
'"x":[[-7],[-6]], "y":[[-4.6],[-7]]}]}'))
self.assertEqual(w1, w2)
# units missing for centroid
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":5000, "oy":0,'
' "cx":10, "cy":10, "x":[[3],[4]], '
' "y":[[5.4],[3]]}]}'))
def test_data1(self):
# Single-valued 't' subelement should be fine
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
# Two values for 'x' but four values for 'y': error
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4], '
'"y":[5.4,3,1,-3]}]}'))
# Two values for 't' but 3 for 'x' and 'y': error
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":[1.3,8], '
'"x":[3,4,5], "y":[5.4,3,5]}]}'))
# Duplicated segments are OK if there are no differences
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
# Duplicated time indices are OK if the earlier entry was for a
# different worm
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":2, "t":1.3, "x":[3,4], "y":[5.4,3]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
# Duplicated time indices are OK if the earlier entry had those entries
# missing
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, "x":[null,null], "y":[null,null]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
# Error if data from a later segment conflicts with earlier segments
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.5,3]}]}'))
def test_data1(self):
# Single-valued 't' subelement should be fine
WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
# Two values for 'x' but four values for 'y': error
with self.assertRaises(AssertionError):
WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4], '
'"y":[5.4,3,1,-3]}]}'))
# Two values for 't' but 3 for 'x' and 'y': error
with self.assertRaises(AssertionError):
WCONWorms.load(StringIO('{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":3, "t":[1.3,8], '
'"x":[3,4,5], "y":[5.4,3,5]}]}'))
# Duplicated segments are OK if there are no differences
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
# Duplicated time indices are OK if the earlier entry was for a
# different worm
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":2, "t":1.3, "x":[3,4], "y":[5.4,3]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
# Duplicated time indices are OK if the earlier entry had those entries
# missing
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, "x":[null,null], "y":[null,null]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]}]}'))
# Error if data from a later segment conflicts with earlier segments
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm"},'
'"data":[{"id":1, "t":1.3, "x":[3,4], "y":[5.4,3]},'
'{"id":1, "t":1.3, "x":[3,4], "y":[5.5,3]}]}'))
def test_centroid(self):
# ox, with two time frames, with centroid
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":0, "oy":5000, "cx":10, '
'"cy":10, "x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":5010, '
'"x":[[-7],[-6]], "y":[[-4.6],[-7]]}]}'))
self.assertEqual(w1, w2)
# oy with no oxy: assertionerror
with self.assertRaises(AssertionError):
w1 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "oy":5000,'
'"cx":10, "cy":10, "x":[[3, 3, 3],[4, 4, 4.2]], '
'"y":[[5.4, 5.4, 5.5],[3, 3, 7]]}]}'))
# ox, with two time frames, three articulation points, with centroid
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":0, "oy":5000, "cx":10, '
'"cy":10, "x":[[3, 3, 3],[4, 4, 4.2]], '
'"y":[[5.4, 5.4, 5.5],[3, 3, 7]]}]}'))
w2 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":5010, '
'"x":[[-7,-7,-7],[-6,-6,-5.8]], '
'"y":[[-4.6,-4.6,-4.5],[-7,-7,-3]]}]}'))
self.assertEqual(w1, w2)
# ox and centroid, different in different time frames
w1 = WCONWorms.load(
StringIO('{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox": 0, '
'"oy":[5000, 1000], "cx":10, '
'"cy":10, "x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":[5010, 1010], '
'"x":[[-7],[-6]], "y":[[-4.6],[-7.0]]}]}'))
self.assertEqual(w1, w2)
# ox and centroid, different in different time frames
w1 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":0, "oy":[5000, 1000],'
'"cx":10, "cy":10, "x":[[3],[4]], "y":[[5.4],[3]]}]}'))
w2 = WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm",'
'"cx":"mm","cy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "cx":10, "cy":[5010, 1010], '
'"x":[[-7],[-6]], "y":[[-4.6],[-7]]}]}'))
self.assertEqual(w1, w2)
# units missing for centroid
with self.assertRaises(AssertionError):
WCONWorms.load(
StringIO(
'{"units":{"t":"s","x":"mm","y":"mm","ox":"mm","oy":"mm"},'
'"data":[{"id":1, "t":[1.3,1.4], "ox":5000, "oy":0,'
' "cx":10, "cy":10, "x":[[3],[4]], '
' "y":[[5.4],[3]]}]}'))
def test_arrayed_software(self):
WCONWorms.load(StringIO('{ "units":{"t":"s", "x":"mm", "y":"mm"}, '
'"data":[], "metadata":{'
'"software":[{"name":"a"}, '
'{"name":"b"}]} }'))
# warnings.simplefilter(action = "ignore", category = RuntimeWarning)
if __name__ == '__main__':
JSON_path = '../../tests/minimax.wcon'
w2 = WCONWorms.load_from_file(JSON_path)
w2.save_to_file('example_saved_file.WCON', pretty_print=True)
w3 = WCONWorms.load_from_file('example_saved_file.WCON')
u = MeasurementUnit.create('cm')
# io=StringIO()
# json.dump([None], io)
# io.getvalue()
if __name__ == '__main__2':
worm_file_text2 = (('{"units":{"t":"s","x":"m","y":"m"},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
w1 = WCONWorms.load(StringIO(worm_file_text2))
if __name__ == '__main__3':
w1 = WCONWorms.load(
StringIO('{"units":{},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4,4,3.2], '
'"y":[5.4,3,1,-3]}]}'))
if __name__ == '__main__':
JSON_path = '../../tests/minimax.wcon'
w2 = WCONWorms.load_from_file(JSON_path)
w2.save_to_file('example_saved_file.WCON', pretty_print=True)
w3 = WCONWorms.load_from_file('example_saved_file.WCON')
u = MeasurementUnit.create('cm')
# io=StringIO()
# json.dump([None], io)
# io.getvalue()
if __name__ == '__main__2':
worm_file_text2 = (('{"units":{"t":"s","x":"m","y":"m"},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4], "y":[5.4,3]}]}'))
w1 = WCONWorms.load(StringIO(worm_file_text2))
if __name__ == '__main__3':
w1 = WCONWorms.load(StringIO('{"units":{},'
'"data":[{"id":3, "t":1.3, '
'"x":[3,4,4,3.2], '
'"y":[5.4,3,1,-3]}]}'))
