This repository has been archived by the owner on Nov 9, 2023. It is now read-only.
/
test_colors.py
359 lines (302 loc) · 14.3 KB
/
test_colors.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
#!/usr/bin/env python
# file test_colors.py
__author__ = "Rob Knight and Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project" # consider project name
__credits__ = ["Jesse Stombaugh"] # remember to add yourself
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
from numpy import array
from StringIO import StringIO
from os.path import exists
from collections import defaultdict
from unittest import TestCase, main
from numpy.testing import assert_almost_equal
from os import remove
from random import choice, randrange
import shutil
from qiime.colors import (Color, rgb_tuple_to_hsv, mage_hsv_tuple_to_rgb,
combine_map_label_cols, process_colorby,
linear_gradient, natsort, make_color_dict, color_dict_to_objects,
iter_color_groups, get_group_colors,
get_color, color_groups, string_to_rgb,
get_map, map_from_coords, sample_color_prefs_and_map_data_from_options,
taxonomy_process_prefs, get_qiime_hex_string_color)
class ColorTests(TestCase):
"""Tests of the Color class"""
def setUp(self):
"""Color init should take name, coords, colorspace"""
self.black = Color('black', (0, 0, 0))
self.red = Color('red', (255, 0, 0))
self.pink = Color('pink', (100, 0, 0))
self.green = Color('green', (0, 255, 0))
def test_str(self):
"""Color init and string representation should give correct result"""
self.assertEqual(str(self.black), 'black:#000000')
self.assertEqual(str(self.red), 'red:#ff0000')
self.assertEqual(str(self.pink), 'pink:#640000')
def test_toRGB(self):
"""Color toRGB should give correct r, g, b tuple (range 0-255)"""
self.assertEqual(self.black.toRGB(), (0, 0, 0))
self.assertEqual(self.red.toRGB(), (255, 0, 0))
self.assertEqual(self.pink.toRGB(), (100, 0, 0))
def test_toMage(self):
"""Color toMage should give correct string using h, s, v tuple"""
self.assertEqual(self.black.toMage(), '@hsvcolor {black} 0.0 0.0 0.0')
self.assertEqual(self.red.toMage(), '@hsvcolor {red} 0.0 100.0 100.0')
self.assertEqual(self.pink.toMage(), '@hsvcolor {pink} 0.0 100.0 39.2')
self.assertEqual(self.green.toMage(),
'@hsvcolor {green} 120.0 100.0 100.0')
def test_toHex(self):
"""Color toHex should give correct hex string"""
self.assertEqual(self.black.toHex(), '#000000')
self.assertEqual(self.red.toHex(), '#ff0000')
self.assertEqual(self.pink.toHex(), '#640000')
def test_toInt(self):
"""Color toHex should give correct hex string"""
self.assertEqual(self.black.toInt(), 0)
self.assertEqual(self.red.toInt(), 16711680)
self.assertEqual(self.pink.toInt(), 6553600)
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
"""define some top-level data"""
self.data = {}
self.data['coord'] = [['Sample1', 'Sample2'], array([[-0.2, 0.07],
[-0.04, 0.2]]), array(
[0.7, 0.6]),
array([25.00, 30.00])]
self.data[
'map'] = [['#Sample-ID', 'Day'], ['Sample1', 'Day1'], ['Sample2',
'Day1']]
self.coord_header = ["Sample1", "Sample2", "Sample3"]
self.coords = array(
[[-0.219044992, 0.079674486, 0.09233683], [-0.042258081,
0.000204041, 0.024837603], [0.080504323, -0.212014503,
-0.088353435]])
self.groups = {}
self.groups['Day1'] = ['Sample1', 'Sample2', 'Sample3']
self.pct_var = array([25.00, 30.00, 35.00])
self.coord_tups = [("1", "2"), ("3", "2"), ("1", "3")]
self.colors = {"Day1": "red1"}
self.filename = 'test_pca.txt'
self.dir_path = '/tmp/'
self.prefs = {}
self.prefs['Sample'] = {}
self.prefs['Sample']['column'] = "Day"
self.dict = defaultdict(list)
self.dict['Day1'].append('Sample1')
self.dict['Day1'].append('Sample2')
self.dict['Day1'].append('Sample3')
self.labelname = self.prefs['Sample']['column']
self.mapping = [
["Sample-ID", "Day", "Type"], ["Sample1", "Day1", "Soil"],
["Sample2", "Day1", "Soil"], ["Sample3", "Day1", "Soil"]]
self.data_color_hsv = {
#'black1': (0,0,20),
'red1': (0, 100, 100),
'blue1': (240, 100, 100),
'orange1': (28, 98, 95),
'green1': (120, 100, 50.2),
'purple1': (302, 73, 57),
'yellow1': (60, 100, 100),
'cyan1': (184, 49, 96),
'pink1': (333, 37, 96),
'teal1': (178, 42, 63),
'brown1': (36, 89, 42),
'gray1': (0, 0, 50.2),
'lime': (123, 99, 96),
'red2': (14, 51, 97),
'blue2': (211, 42, 85),
'orange2': (32, 46, 99),
'green2': (142, 36, 79),
'purple2': (269, 29, 75),
'yellow2': (56, 40, 100),
#'black2': (303,100,24),
'gray2': (0, 0, 75.3),
#'teal2': (192,100,24),
'red3': (325, 100, 93),
'blue3': (197, 100, 100),
#'purple3': (271,43,36),
'brown2': (33, 45, 77),
'green3': (60, 100, 50.2),
'purple4': (264, 75, 100),
#'yellow3': (60,66,75),
#'blue4': (213,45,77),
'red4': (348, 31, 74),
'teal3': (180, 100, 50.2),
#'brown3': (60,100,28),
'red5': (0, 100, 50.2),
'green4': (81, 100, 26),
#'purple5': (240,100,41),
'orange3': (26, 100, 65)
#'brown4': (25,100,20),
#'red6': (17,100,63),
#'purple6':(272,100,44)
}
self.data_color_order = ['red1', 'blue1', 'orange1', 'green1',
'purple1', 'yellow1', 'cyan1', 'pink1', 'teal1', 'brown1',
'gray1', 'lime', 'red2', 'blue2', 'orange2', 'green2',
'purple2', 'yellow2', 'gray2', 'red3', 'blue3', 'brown2',
'green3', 'purple4', 'red4', 'teal3', 'red5', 'green4',
'orange3']
self._paths_to_clean_up = []
self._dir_to_clean_up = ''
def tearDown(self):
map(remove, self._paths_to_clean_up)
if self._dir_to_clean_up != '':
shutil.rmtree(self._dir_to_clean_up)
def test_string_to_rgb(self):
"""str_to_rgb should accept a hex string and emit tuples on right scale"""
strgb = string_to_rgb # for convenience
self.assertEqual(strgb('#000000'), (0, 0, 0))
self.assertEqual(strgb('#FFFFFF'), (255, 255, 255))
self.assertEqual(strgb('#F0F0F0'), (240, 240, 240))
self.assertEqual(strgb('#AFF0AA'), (175, 240, 170))
def test_rgb_tuple_to_hsv(self):
"""rgb_tuple_to_hsv should accept and emit tuples on right scale"""
rth = rgb_tuple_to_hsv # for convenience
self.assertEqual(rth((0, 0, 0)), (0, 0, 0))
self.assertEqual(rth((255, 0, 0)), (0, 100, 100))
self.assertEqual(rth((0, 255, 0)), (120, 100, 100))
self.assertEqual(rth((0, 0, 255)), (240, 100, 100))
assert_almost_equal(rth((127, 127, 127)), (0, 0, 49.803921568627452))
def test_mage_hsv_tuple_to_rgb(self):
"""mage_hsv_to_rgb should accept and emit tuples on right scale"""
htr = mage_hsv_tuple_to_rgb # for convenience
self.assertEqual(htr((0, 0, 0)), (0, 0, 0))
self.assertEqual(htr((0, 100, 100)), (255, 0, 0))
self.assertEqual(htr((120, 100, 100)), (0, 255, 0))
self.assertEqual(htr((240, 100, 100)), (0, 0, 255))
assert_almost_equal(htr((0, 0, 49.803921568627452)), (127, 127, 127))
def test_combine_map_label_cols(self):
"""combine_map_label_cols: Combine two or more columns from the \
mapping file"""
self.combinecolorby = ['Day', 'Type']
exp = [["Sample-ID", "Day", "Type", "Day&&Type"],
["Sample1", "Day1", "Soil", "Day1Soil"],
["Sample2", "Day1", "Soil", "Day1Soil"],
["Sample3", "Day1", "Soil", "Day1Soil"]]
obs = combine_map_label_cols(self.combinecolorby, self.mapping)
self.assertEqual(obs, exp)
def test_process_colorby(self):
"""process_colorby: parses the cmd line and determines which columns \
from mapping file to color by"""
self.colorby = 'Day'
exp1 = {}
exp1['0'] = {'column': 'Day'}
obs1, obs2 = process_colorby(self.colorby, self.data)
self.assertEqual(obs1, exp1)
self.assertEqual(obs2, self.data)
def test_linear_gradient(self):
"""linear_gradient: returns linear gradient of colors"""
self.assertEqual(linear_gradient([0, 1, 2], [1, 0, 0], 5),
[[0, 1, 2],
[0.25, 0.75, 1.5],
[0.5, 0.5, 1],
[0.75, 0.25, 0.5],
[1, 0, 0]])
def test_make_color_dict(self):
"""make_color_dict: returns dict of named colors"""
self.assertEqual(
make_color_dict('red', (0, 100, 100), 'white', (0, 0, 100), 3),
{'redtowhite3_0': [0, 100, 100],
'redtowhite3_1': [0, 50, 100],
'redtowhite3_2': [0, 0, 100],
})
def test_color_dict_to_objects(self):
"""color_dict_to_objects should return color objects"""
d = {'redtowhite3_0': [0, 100, 100],
'redtowhite3_1': [0, 50, 100],
'redtowhite3_2': [0, 0, 100],
}
res = color_dict_to_objects(d)
obs = [(str(k), str(v)) for k, v in sorted(res.items())]
exp = [('redtowhite3_0', 'redtowhite3_0:#ff0000'),
('redtowhite3_1', 'redtowhite3_1:#ff7f7f'),
('redtowhite3_2', 'redtowhite3_2:#ffffff')]
self.assertEqual(obs, exp)
def test_iter_color_groups(self):
"""iter_color_groups should iterate over color groups correctly."""
obs = iter_color_groups(self.mapping, self.prefs)
obs1 = list(obs)
obs_label = obs1[0][0]
obs_groups = obs1[0][1]
obs_colors = obs1[0][2]
obs_data_colors = obs1[0][3]
obs_data_color_order = obs1[0][4]
data_colors = color_dict_to_objects(self.data_color_hsv)
self.assertEqual(obs_label, self.labelname)
self.assertEqual(obs_groups, self.dict)
self.assertEqual(obs_colors, self.colors)
self.assertEqual(obs_data_colors.keys(), data_colors.keys())
# Need to iterate through color object, since they has different ids
# assigned each time using color_dict_to_objects
for key in data_colors:
self.assertEqual(obs_data_colors[key].toHex(),
data_colors[key].toHex())
self.assertEqual(obs_data_color_order, self.data_color_order)
def test_get_group_colors(self):
"""get_group_colors should iterate over color groups correctly."""
data_colors = color_dict_to_objects(self.data_color_hsv)
exp = (self.colors, data_colors, self.data_color_order)
obs = get_group_colors(self.groups, self.colors, data_colors,
self.data_color_order)
self.assertEqual(obs, exp)
def test_get_color(self):
"""get_color should get colors by several means"""
sgc = lambda x: str(get_color(x))
self.assertEqual(sgc('red1'), 'red1:#ff0000')
self.assertEqual(sgc(('red1', '#00cc00')), 'red1:#00cc00')
self.assertEqual(sgc(('red1', (120, 100, 50))), 'red1:#007f00')
self.assertRaises(ValueError, sgc, 'xyz')
def test_color_groups(self):
"""color_groups should iterate over color groups correctly."""
data_colors = color_dict_to_objects(self.data_color_hsv)
exp = None
obs = color_groups(self.groups, data_colors, self.data_color_order)
self.assertEqual(obs, exp)
def test_make_color_dict(self):
"""make_color_dict: returns dict of named colors"""
self.assertEqual(
make_color_dict('red', (0, 100, 100), 'white', (0, 0, 100), 3),
{'redtowhite3_0': [0, 100, 100],
'redtowhite3_1': [0, 50, 100],
'redtowhite3_2': [0, 0, 100],
})
def test_process_colorby(self):
"""process_colorby: parses the cmd line and determines which columns \
from mapping file to color by"""
self.colorby = 'Day'
exp1 = {}
exp1['Day'] = {'column': 'Day'}
obs1, obs2 = process_colorby(self.colorby, self.data)
self.assertEqual(obs1, exp1)
self.assertEqual(obs2, self.data)
def test_taxonomy_process_prefs(self):
"""taxonomy_process_prefs should return a taxonomy prefs file"""
taxonomy_levels = [2, 3, 4]
exp1 = {}
exp1['level_2'] = {'column': '2'}
exp1['level_3'] = {'column': 3, 'colors':
{'a': ('red', (0, 100, 100))}}
obs1 = taxonomy_process_prefs(taxonomy_levels, exp1)
exp2 = {}
exp2['2'] = {'column': '2', 'colors': {}}
exp2['3'] = {'column': '3', 'colors': {'a': ('red', (0, 100, 100))}}
exp2['4'] = {'column': '4', 'colors': {}}
self.assertEqual(obs1, exp2)
def test_get_qiime_hex_string_color(self):
"""Test colors are retreved correctly from the QIIME colors"""
# regular indices are supported
self.assertEqual(get_qiime_hex_string_color(0), '#ff0000')
self.assertEqual(get_qiime_hex_string_color(1), '#0000ff')
# if there's an overflow, test it rolls-over accordingly
self.assertEqual(get_qiime_hex_string_color(87), '#ff0000')
self.assertEqual(get_qiime_hex_string_color(100), '#7da9d8')
# test it raises an exception for negative values
self.assertRaises(AssertionError, get_qiime_hex_string_color, -1)
# run tests if called from command line
if __name__ == "__main__":
main()