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- module -T: fixed -morpho cube, added -statcell and -statvox
<orientation_descriptor>, added -ori :flat, added -transform ori, made minor
fix to the objective function for tesr (does not change the result), made
minor fixes to -statface and -statpoly, made other minor fixes.
- module -M: added -transform node and ori, fixed -stateltco and -statelsetco,
added -stat{elt,elset}{1d,2d} theta, fixed nsets in 2D, added -statelt and
-statelset <orientation_descriptor>, added -statelset scaleid, added
-statelset* elts,nodenb,nodes, made minor fix to inp output, made minor fixes
and improvements.
- module -S: fixed various bugs related to the initial state, revised odf and
odfn, made minor other improvements.
- module -V: added -datacellsymbol, -datapointsymbol, -lightambient,
-lightsource, -lightdiffuse and -lightreflection options, added -space pf to
plot pole figures, added -space tree to plot a simulation directory, added
-asymptote, added -pfpole, -pfprojection, -pfmode, -pfgrid, -pfkernel,
-pfdir, -pfclustering, -pfsym and -pfshape options, renamed -imageantialias
into -povrayantialiasing, added :shape transformation to color maps, made
minor fixes.
- documentation: made minor improvements.
- general: added tutorials to documentation, fixed FORCE_BUILTIN_*
configuration options, made various installation improvements.
:data:`triclinic` triclinic (Laue group :math:`\overline{1}`) 24
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:data:`cubic` cubic 24
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:data:`hexagonal` hexagonal 1
@@ -821,29 +823,44 @@ Color Maps
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.. _color_map_for_integer_values:
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Color Map for Integer Values
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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The *color map* or *palette* used to represent integer values is defined from the above color list, by excluding colors of brightness below 0.2 and above 0.8. The brightness is defined as the average of the channel values divided by 255. The resulting list of colors is: \(1) :data:`red`, (2) :data:`green`, (3) :data:`blue`, (4) :data:`yellow`, (5) :data:`magenta`, (6) :data:`cyan`, (7) :data:`chartreuse`, (8) :data:`springgreen`, (9) :data:`olive`, (10) :data:`purple`, (11) :data:`teal`, (12) :data:`gray`, (13) :data:`deepskyblue`, (14) :data:`lawngreen`, (15) :data:`darkgray`, (16) :data:`orangered`, (17) :data:`silver`, (18) :data:`darkorange`, (19) :data:`mediumblue`, (20) :data:`indigo`, (21) :data:`lightcoral`, (22) :data:`coral`, (23) :data:`salmon`, (24) :data:`aquamarine`, (25) :data:`gold`, (26) :data:`orange`, (27) :data:`darkmagenta`, (28) :data:`darkcyan`, (29) :data:`peru`, (30) :data:`steelblue`, (31) :data:`mediumspringgreen`, (32) :data:`darkslateblue`, (33) :data:`darkgoldenrod`, (34) :data:`lightsalmon`, (35) :data:`lightskyblue`, (36) :data:`tomato`, (37) :data:`slategray`, (38) :data:`hotpink`, (39) :data:`darkkhaki`, (40) :data:`darkturquoise`, (41) :data:`mediumseagreen`, (42) :data:`mediumvioletred`, (43) :data:`violet`, (44) :data:`greenyellow`, (45) :data:`darkseagreen`, (46) :data:`rosybrown`, (47) :data:`deeppink`, (48) :data:`saddlebrown`, (49) :data:`darkviolet`, (50) :data:`dodgerblue`, (51) :data:`lightslategray`, (52) :data:`burlywood`, (53) :data:`mediumslateblue`, (54) :data:`turquoise`, (55) :data:`skyblue`, (56) :data:`mediumturquoise`, (57) :data:`tan`, (58) :data:`limegreen`, (59) :data:`darksalmon`, (60) :data:`lightsteelblue`, (61) :data:`royalblue`, (62) :data:`palegreen`, (63) :data:`crimson`, (64) :data:`mediumorchid`, (65) :data:`khaki`, (66) :data:`lightgreen`, (67) :data:`darkslategray`, (68) :data:`darkorchid`, (69) :data:`seagreen`, (70) :data:`yellowgreen`, (71) :data:`blueviolet`, (72) :data:`palevioletred`, (73) :data:`olivedrab`, (74) :data:`mediumpurple`, (75) :data:`sandybrown`, (76) :data:`darkolivegreen`, (77) :data:`mediumaquamarine`, (78) :data:`slateblue`, (79) :data:`forestgreen`, (80) :data:`midnightblue`, (81) :data:`lightseagreen`, (82) :data:`orchid`, (83) :data:`cornflowerblue`, (84) :data:`sienna`, (85) :data:`firebrick`, (86) :data:`indianred`, (87) :data:`dimgray`, (88) :data:`chocolate`, (89) :data:`brown`, (90) :data:`goldenrod`, (91) :data:`plum` and (92) :data:`cadetblue`.
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.. _color_map_for_real_values:
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Color Maps for Real Values
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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The color *map* used to represent real values is smooth and obtained by interpolation between nominal colors. `Tinycolormap <https://github.com/yuki-koyama/tinycolormap>`_ is used to generate standard color maps:
and :data:`viridis` is the default. See `Tinycolormap <https://github.com/yuki-koyama/tinycolormap>`_ for illustrations.
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Alternatively, any series of colors can be used to define a color map. Neper's legacy color map (version :math:`< 4`) is :data:`blue,cyan,yellow,green` and can be obtained using :data:`legacy`.
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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The color *map* used to represent real values is smooth and obtained by interpolation between nominal colors. `Tinycolormap <https://github.com/yuki-koyama/tinycolormap>`_ is used to generate standard color maps, and the default is :data:`viridis`. The color maps are
Alternatively, a custom color map can be provided as :data:`custom(<color1>,<color2>,...)`. Neper's legacy color map (version :math:`< 4`) is :data:`custom(blue,cyan,yellow,green)` and can also be obtained using :data:`legacy`:
Finally, it is possible to gradually fade the start of a color map, to make it starts with white. This can be done using the :data:`fade` modifier, following the syntax :data:`<colormap>:fade[(threshold)]`. The threshold ranges from 0 to 1 and is equal to 0.1 by default. Fading is applied linearly from 0 (full fading) to the threshold (no fading). Examples are show below:
Copy file name to clipboardExpand all lines: doc/fileformat.rst
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Data File
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---------
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A data file provides a number of data to be assigned to entities (seeds, cells, points, etc.). It must contain the expected number of data. It is a general, simply-formatted ASCII file that contains a fixed number of data per entity, and the data can be integers, real numbers or character strings. A real number can have an arbitrary number of digits, but the decimal mark must be :option:`.`. The data can be separated from each other by spaces, tabulators or newlines (any number as well as arbitrary combinations of them are supported). However, a good practice is to format the file with the data of one entity per line. An example of a data file containing 5 values is::
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A data file contains a number of data to be assigned to entities (seeds, cells, points, etc.). It must contain the expected number of data. It is a general, simply-formatted ASCII file that contains a fixed number of data per entity, and the data can be integers, real numbers or character strings. A real number can have an arbitrary number of digits, but the decimal mark must be :option:`.`. The data can be separated from each other by spaces, tabulators or newlines (any number as well as arbitrary combinations of them are supported). However, a good practice is to format the file with the data of one entity per line. An example of a data file containing 5 values is::
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Position File
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-------------
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A position file lists the coordinates of a given number of points. The file must contain 1 coordinate per point in 1D, 2 coordinates per point in 2D and 3 coordinates per point in 3D. While the dimension can be known from the context in which the file is read, it can also be specified by appending :data:`:dim` to the name of the position file, where :data:`dim` is the dimension. A coordinate can be an integer or real number. A real number can have an arbitrary number of digits, but the decimal mark must be :option:`.`. The coordinates can be separated from each other by spaces, tabulators or newlines (any number as well as arbitrary combinations of them are supported). However, a good practice is to format the file with one point per line. An example of a position file containing 5 points in 3D is::
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A position file contains the coordinates of a number of points. The file must contain 1 coordinate per point in 1D, 2 coordinates per point in 2D and 3 coordinates per point in 3D. While the dimension can be known from the context in which the file is read, it can also be specified by appending :data:`:dim` to the name of the position file, where :data:`dim` is the dimension. A coordinate can be an integer or real number. A real number can have an arbitrary number of digits, but the decimal mark must be :option:`.`. The coordinates can be separated from each other by spaces, tabulators or newlines (any number as well as arbitrary combinations of them are supported). However, a good practice is to format the file with one point per line. An example of a position file containing 5 points in 3D is::
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