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
|
.. _nrn_defaults:
The appearance of NEURON's graphical windows is controlled by definitions in the file ``$(NEURONHOME)/lib/nrn.defaults`` (under MSWindows it's ``c:\nrnxx\lib\nrn.def`` where ``xx`` is the version number). This is a plain ASCII file that you can edit with a text editor.
What's $(NEURONHOME)?
Start NEURON, and at the oc> prompt type
.. code::
Python
neuronhome()
On my Linux box, this tells me that $(NEURONHOME) is
:file:`/usr/local/nrn/share/nrn`
and sure enough, ``nrn.defaults`` is in
.. code::
Python
/usr/local/nrn/share/nrn/lib
How to change the background color used in shape plots and other graphs
------------------
Change the lines
.. code::
*Scene_background: #ffffff
*Scene_foreground: #000000
to whatever you like. For example,
.. code::
Python
*Scene_background: #000000
*Scene_foreground: #ffffff
makes the background black and the axes and black traces white.
How create a custom colormap
------------
The lines
.. code::
Python
//the color map for pseudocolor plotting for 3-D cells
*shape_scale_file: $(NEURONHOME)/lib/shape.cm2
tell you which file contains the colormap that will be used (under MSWin it's ``c:\nrnxx\lib\shape.cm2``). The colormap file is read when NEURON is initially launched. If the file doesn't exist, NEURON uses a default scale.
The colormap file is plain ASCII, with one set of RGB values per line. NEURON comes with a couple of different scales in files shape.cm1 and shape.cm2.
Here's another one you might try:
.. code::
95 0 95
111 0 111
127 0 143
143 0 127
159 0 111
175 0 95
191 0 79
207 0 63
207 31 47
223 47 47
239 63 31
255 79 15
255 95 7
255 111 0
255 127 0
255 143 0
255 159 0
255 175 0
255 191 0
255 207 0
255 223 0
255 239 0
255 247 0
255 255 0
255 255 255
and yet another:
.. code::
111 0 111
143 0 127
175 0 95
207 0 63
223 47 47
255 79 15
255 111 0
255 143 0
255 175 0
255 207 0
255 239 0
255 255 0
255 255 200
but you can make up anything you like.
Before you start cooking up your own schemes, you might want to look at the following:
`"How NOT to Lie with Visualization" by Rogowitz & Treinish <https://aip.scitation.org/doi/pdf/10.1063/1.4822401>`_
`"A Rule-based Tool for Assisting Colormap Selection" by Bergman et al. <https://www.researchgate.net/publication/220943601_A_Rule-Based_Tool_for_Assisting_Colormap_Selection>`_
|
