Skip to content

SpotlightView module

SpotlightView

Bases: widgets.DOMWidget

Source code in evince/spotlight.py 
 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
@widgets.register
class SpotlightView(widgets.DOMWidget):
    # Name of the widget view class in front-end
    _view_name = Unicode('SpotlightView').tag(sync=True)

    # Name of the widget model class in front-end
    _model_name = Unicode('SpotlightModel').tag(sync=True)

    # Name of the front-end module containing widget view
    _view_module = Unicode('evince').tag(sync=True)

    # Name of the front-end module containing widget model
    _model_module = Unicode('evince').tag(sync=True)


    # Version of the front-end module containing widget view
    _view_module_version = Unicode(NPM_PACKAGE_RANGE).tag(sync=True)
    # Version of the front-end module containing widget model
    _model_module_version = Unicode(NPM_PACKAGE_RANGE).tag(sync=True)


    pos = tl.List([1,2,3]).tag(sync=True)
    radius = tl.List([]).tag(sync=True)
    init = tl.Bool(False).tag(sync=True)
    masses = tl.List([]).tag(sync=True)
    colors = tl.List([]).tag(sync=True)
    box = tl.List([]).tag(sync=True)
    bonds = tl.List([]).tag(sync=True)
    transparent_bubbles = tl.Bool(False).tag(sync=True)


    window_scale = tl.Float().tag(sync=True)
    window_scale_height = tl.Float().tag(sync=True)
    window_scale_width = tl.Float().tag(sync=True)

    #fxaa
    fxaa = tl.Bool(False).tag(sync=True)

    #camera / dof
    dof = tl.Bool(False).tag(sync=True)
    focus = tl.Float().tag(sync=True)
    aperture = tl.Float().tag(sync=True)
    max_blur = tl.Float().tag(sync=True)

    #sao controls
    sao = tl.Bool(False).tag(sync=True)
    saoScale = tl.Float().tag(sync=True)
    saoBias = tl.Float().tag(sync=True)
    saoIntensity = tl.Float().tag(sync=True)
    saoKernelRadius = tl.Int().tag(sync=True)
    saoMinResolution = tl.Float().tag(sync=True)
    saoBlur = tl.Bool(False).tag(sync=True)
    saoBlurRadius = tl.Int().tag(sync=True)
    saoBlurStdDev = tl.Float().tag(sync=True)
    saoBlurDepthCutoff = tl.Float().tag(sync=True)

    #colorscheme
    additive = tl.Bool(False).tag(sync=True)

    bg_color = tl.List([]).tag(sync=True)

    def __init__(self, b, window_scale_height = 0.5, window_scale_width=0.75, window_scale = 1.0, fxaa = True, sao  =False, dof = False, additive = False, bg_color = [1.0, 1.0, 1.0], focus = 10, aperture = 0.001, max_blur = 0.01, bonds = [], saoScale = 100 ,saoBias = .1,saoIntensity = .1,saoKernelRadius = 10,saoMinResolution = .5,saoBlur = False,saoBlurRadius = 50,saoBlurStdDev = 1.0,saoBlurDepthCutoff = 0.05, realism = False, radius_scale = 1.0, transparent_bubbles = False, colors = []):

        self.sao = sao
        self.saoScale = saoScale
        self.saoBias = saoBias
        self.saoIntensity = saoIntensity
        self.saoKernelRadius = saoKernelRadius
        self.saoMinResolution = saoMinResolution
        self.saoBlur = saoBlur
        self.saoBlurRadius = saoBlurRadius
        self.saoBlurStdDev = saoBlurStdDev
        self.saoBlurDepthCutoff = saoBlurDepthCutoff

        self.window_scale_height = window_scale_height
        self.window_scale_width = window_scale_width
        self.window_scale = window_scale



        self.fxaa = fxaa

        self.dof = dof 

        super().__init__() # execute init of parent class, append:


        self.focus = focus
        self.aperture = aperture
        self.max_blur = max_blur

        self.transparent_bubbles = transparent_bubbles

        self.additive = additive
        self.bg_color = bg_color
        pos = np.zeros((b.pos.shape[1],3), dtype = float)
        pos[:, :b.pos.shape[0]] = b.pos.T
        self.pos = pos.tolist()
        self.bonds = bonds
        self.box = b.size.tolist()
        nc = 20
        self.radius = [1.0 for i in range(b.pos.shape[0])]
        self.colors = colors
        if len(self.colors)<b.n_bubbles:
            self.colors = np.array((interp1d(np.linspace(0,1,nc), np.random.uniform(0,1,(3, nc)) )(b.masses/b.masses.max()).T), dtype = float).tolist()

        if realism:
            self.radius = (radius_scale*get_vwv_radius_from_atomic_number(b.masses)).tolist()
            self.colors = colorscheme(b.masses).T.tolist()

        self.masses = b.masses.tolist()
        self.init = True #trigger frontend init

    def save(self, filename, title = ""):
        """
        Save a standalone html embedding of the view
        """
        embed.embed_minimal_html(filename, [self], title)

save(filename, title='')

Save a standalone html embedding of the view

Source code in evince/spotlight.py 
186
187
188
189
190
def save(self, filename, title = ""):
    """
    Save a standalone html embedding of the view
    """
    embed.embed_minimal_html(filename, [self], title)

colorscheme(masses)

Default CPK-colorscheme for atoms source: https://sciencenotes.org/molecule-atom-colors-cpk-colors/

Source code in evince/spotlight.py 
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
def colorscheme(masses):
    """
    Default CPK-colorscheme for atoms
    source: https://sciencenotes.org/molecule-atom-colors-cpk-colors/
    """
    colors = np.array([[255, 217, 204, 194, 255, 144,  48, 255, 144, 179, 171, 138, 191,
        240, 255, 255,  31, 128, 143,  61, 230, 191, 166, 138, 156, 224,
        240,  80, 200, 125, 194, 102, 189, 255, 166,  92, 112,   0, 148,
        148, 115,  84,  59,  36,  10,   0, 192, 255, 166, 102, 158, 212,
        148,  66,  87,   0, 112, 255, 217, 199, 163, 143,  97,  69,  48,
         31,   0,   0,   0,   0,   0,  77,  77,  33,  38,  38,  23, 208,
        255, 184, 166,  87, 158, 171, 117,  66,  66,   0, 112,   0,   0,
          0,   0,   0,  84, 120, 138, 161, 179, 179, 179, 189, 199, 204,
        209, 217, 224, 230, 235],
       [255, 255, 128, 255, 181, 144,  80,  13, 224, 227,  92, 255, 166,
        200, 128, 255, 240, 209,  64, 255, 230, 194, 166, 153, 122, 102,
        144, 208, 128, 128, 143, 143, 128, 161,  41, 184,  46, 255, 255,
        224, 194, 181, 158, 143, 125, 105, 192, 217, 117, 128,  99, 122,
          0, 158,  23, 201, 212, 255, 255, 255, 255, 255, 255, 255, 255,
        255, 255, 230, 212, 191, 171, 194, 166, 148, 125, 102,  84, 208,
        209, 184,  84,  89,  79,  92,  79, 130,   0, 125, 171, 186, 161,
        143, 128, 107,  92,  92,  79,  54,  31,  31,  13,  13,   0,   0,
          0,   0,   0,   0,   0],
       [255, 255, 255,   0, 181, 144, 248,  13,  80, 245, 242,   0, 166,
        160,   0,  48,  31, 227, 212,   0, 230, 199, 171, 199, 199,  51,
        160,  80,  51, 176, 143, 143, 227,   0,  41, 209, 176,   0, 255,
        224, 201, 181, 158, 143, 140, 133, 192, 143, 115, 128, 181,   0,
        148, 176, 143,   0, 255, 199, 199, 199, 199, 199, 199, 199, 199,
        199, 156, 117,  82,  56,  36, 255, 255, 214, 171, 150, 135, 224,
         35, 208,  77,  97, 181,   0,  69, 150, 102,   0, 250, 255, 255,
        255, 255, 255, 242, 227, 227, 212, 212, 186, 166, 135, 102,  89,
         79,  69,  56,  46,  38]])/510.0


    return interp1d(np.arange(1,colors.shape[1]+1), colors,bounds_error=False,fill_value = [1.0,1.0,1.0])(masses)

extract_bonds(b, btype=2)

Extract harmonic oscillator interactions (btype == 2) from a bubblebbox.mdbox object

returns a bonds-list for spotlightviewer

Source code in evince/spotlight.py 
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
def extract_bonds(b, btype = 2):
    """
    Extract harmonic oscillator interactions (btype == 2) from 
    a bubblebbox.mdbox object

    returns a bonds-list for spotlightviewer
    """
    bonds = []
    for i in range(b.n_bubbles):
        for j in range(i+1, b.n_bubbles):
            if b.interactions[i,j,0] == 2.0:
                #print("Harmonmic", i,j)
                bonds.append([i,j])

    return bonds