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#!/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__ = "1.4.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
from numpy import array
from StringIO import StringIO
from os.path import exists
from collections import defaultdict
from cogent.util.unit_test import TestCase, main
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)
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))
self.assertFloatEqual(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))
self.assertFloatEqual(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)
#run tests if called from command line
if __name__ == "__main__":
main()
|
