myokit 1.35.0__py3-none-any.whl → 1.35.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- myokit/__init__.py +11 -14
- myokit/__main__.py +0 -3
- myokit/_config.py +1 -3
- myokit/_datablock.py +914 -12
- myokit/_model_api.py +1 -3
- myokit/_myokit_version.py +1 -1
- myokit/_protocol.py +14 -28
- myokit/_sim/cable.c +1 -1
- myokit/_sim/cable.py +3 -2
- myokit/_sim/cmodel.h +1 -0
- myokit/_sim/cvodessim.c +79 -42
- myokit/_sim/cvodessim.py +20 -8
- myokit/_sim/fiber_tissue.c +1 -1
- myokit/_sim/fiber_tissue.py +3 -2
- myokit/_sim/openclsim.c +1 -1
- myokit/_sim/openclsim.py +8 -11
- myokit/_sim/pacing.h +121 -106
- myokit/_unit.py +1 -1
- myokit/formats/__init__.py +178 -0
- myokit/formats/axon/_abf.py +911 -841
- myokit/formats/axon/_atf.py +62 -59
- myokit/formats/axon/_importer.py +2 -2
- myokit/formats/heka/__init__.py +38 -0
- myokit/formats/heka/_importer.py +39 -0
- myokit/formats/heka/_patchmaster.py +2512 -0
- myokit/formats/wcp/_wcp.py +318 -133
- myokit/gui/datablock_viewer.py +144 -77
- myokit/gui/datalog_viewer.py +212 -231
- myokit/tests/ansic_event_based_pacing.py +3 -3
- myokit/tests/{ansic_fixed_form_pacing.py → ansic_time_series_pacing.py} +6 -6
- myokit/tests/data/formats/abf-v2.abf +0 -0
- myokit/tests/test_datablock.py +84 -0
- myokit/tests/test_datalog.py +2 -1
- myokit/tests/test_formats_axon.py +589 -136
- myokit/tests/test_formats_wcp.py +191 -22
- myokit/tests/test_pacing_system_c.py +51 -23
- myokit/tests/test_pacing_system_py.py +18 -0
- myokit/tests/test_simulation_1d.py +62 -22
- myokit/tests/test_simulation_cvodes.py +52 -3
- myokit/tests/test_simulation_fiber_tissue.py +35 -4
- myokit/tests/test_simulation_opencl.py +28 -4
- {myokit-1.35.0.dist-info → myokit-1.35.2.dist-info}/LICENSE.txt +1 -1
- {myokit-1.35.0.dist-info → myokit-1.35.2.dist-info}/METADATA +1 -1
- {myokit-1.35.0.dist-info → myokit-1.35.2.dist-info}/RECORD +47 -44
- {myokit-1.35.0.dist-info → myokit-1.35.2.dist-info}/WHEEL +0 -0
- {myokit-1.35.0.dist-info → myokit-1.35.2.dist-info}/entry_points.txt +0 -0
- {myokit-1.35.0.dist-info → myokit-1.35.2.dist-info}/top_level.txt +0 -0
myokit/_datablock.py
CHANGED
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@@ -1148,9 +1148,13 @@ class DataBlock2d:
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data = self._2d[name]
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# Get color map
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color_map = ColorMap.get(colormap)
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+
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# Get lower and upper bounds for colormap scaling
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lower = np.min(data) if lower is None else float(lower)
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upper = np.max(data) if upper is None else float(upper)
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if upper < lower: # pragma: no cover
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upper = lower
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# Create images
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frames = []
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for frame in data:
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@@ -1687,8 +1691,8 @@ class ColorMap:
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@staticmethod
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def hsv_to_rgb(h, s, v):
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"""
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-
Converts hsv values in the range [0,1] to rgb values in the range
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[0,255].
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Converts hsv values in the range [0, 1] to rgb values in the range
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[0, 255].
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"""
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r, g, b = np.empty_like(h), np.empty_like(h), np.empty_like(h)
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i = (h * 6).astype(int) % 6
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@@ -1756,9 +1760,8 @@ class ColorMap:
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class ColorMapBlue(ColorMap):
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-
"""
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"""
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""" A plain white-to-blue colormap. """
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def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
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# Normalize floats
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f = ColorMap.normalize(floats, lower, upper)
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@@ -1781,10 +1784,27 @@ class ColorMapBlue(ColorMap):
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return out
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class ColorMapGray(ColorMap):
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""" A plain black-to-white colormap. """
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def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
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# Normalize floats
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f = 255 * ColorMap.normalize(floats, lower, upper)
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# Offset for first color in (a)rgb or rgb(a)
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m = 1 if (alpha and rgb) else 0
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# Number of bytes per float
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n = 4 if alpha else 3
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# Create output
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out = 255 * np.ones(n * len(floats), dtype=np.uint8)
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out[m + 0::n] = f
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out[m + 1::n] = f
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out[m + 2::n] = f
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return out
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class ColorMapGreen(ColorMap):
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"""
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"""
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""" A plain white-to-green colormap. """
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def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
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# Normalize floats
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f = ColorMap.normalize(floats, lower, upper)
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@@ -1808,9 +1828,8 @@ class ColorMapGreen(ColorMap):
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class ColorMapRed(ColorMap):
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"""
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"""
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""" A plain white-to-red colormap. """
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def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
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# Normalize floats
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f = ColorMap.normalize(floats, lower, upper)
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@@ -1835,7 +1854,10 @@ class ColorMapRed(ColorMap):
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class ColorMapTraditional(ColorMap):
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"""
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A traditional hue-cycling colormap.
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Probably best not to use in publications. See e.g.
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https://doi.org/10.1371/journal.pone.0199239
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"""
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def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
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# Normalize floats
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@@ -1859,6 +1881,886 @@ class ColorMapTraditional(ColorMap):
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return out
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class ColorMapCividis(ColorMap):
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"""
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A colormap using "Cividis".
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The values used by this color map are taken from supplement 3 in
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https://doi.org/10.1371/journal.pone.0199239, by Jamie R. Nuñez,
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Christopher R. Anderton, and Ryan S. Renslow.
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"""
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_VALUES = np.array((
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(0, 32, 76),
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(0, 32, 78),
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(0, 33, 80),
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(0, 34, 81),
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(0, 35, 83),
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(0, 35, 85),
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(0, 36, 86),
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(0, 37, 88),
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(0, 38, 90),
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(0, 38, 91),
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(0, 39, 93),
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(0, 40, 95),
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(0, 40, 97),
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(0, 41, 99),
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(0, 42, 100),
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(0, 42, 102),
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(0, 43, 104),
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(0, 44, 106),
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1911
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(0, 45, 108),
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(0, 45, 109),
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(0, 46, 110),
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(0, 46, 111),
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(0, 47, 111),
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(0, 47, 111),
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(0, 48, 111),
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(0, 49, 111),
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(0, 49, 111),
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(0, 50, 110),
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(0, 51, 110),
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(0, 52, 110),
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1923
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(0, 52, 110),
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(1, 53, 110),
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(6, 54, 110),
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(10, 55, 109),
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(14, 55, 109),
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(18, 56, 109),
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(21, 57, 109),
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(23, 57, 109),
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(26, 58, 108),
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(28, 59, 108),
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(30, 60, 108),
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(32, 60, 108),
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(34, 61, 108),
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(36, 62, 108),
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(38, 62, 108),
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(39, 63, 108),
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(41, 64, 107),
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(43, 65, 107),
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(44, 65, 107),
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(46, 66, 107),
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(47, 67, 107),
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(49, 68, 107),
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(50, 68, 107),
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1946
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(51, 69, 107),
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(53, 70, 107),
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(54, 70, 107),
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(55, 71, 107),
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(56, 72, 107),
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(58, 73, 107),
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(59, 73, 107),
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(60, 74, 107),
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(61, 75, 107),
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(62, 75, 107),
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(64, 76, 107),
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(65, 77, 107),
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1958
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(66, 78, 107),
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(67, 78, 107),
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(68, 79, 107),
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(69, 80, 107),
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(70, 80, 107),
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(71, 81, 107),
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(72, 82, 107),
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(73, 83, 107),
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(74, 83, 107),
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(75, 84, 107),
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1968
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(76, 85, 107),
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1969
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(77, 85, 107),
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(78, 86, 107),
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(79, 87, 108),
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1972
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(80, 88, 108),
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1973
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(81, 88, 108),
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1974
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(82, 89, 108),
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1975
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(83, 90, 108),
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1976
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(84, 90, 108),
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1977
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(85, 91, 108),
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1978
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(86, 92, 108),
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1979
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(87, 93, 109),
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1980
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(88, 93, 109),
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1981
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(89, 94, 109),
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1982
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(90, 95, 109),
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1983
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(91, 95, 109),
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1984
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(92, 96, 109),
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1985
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(93, 97, 110),
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1986
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(94, 98, 110),
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1987
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(95, 98, 110),
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1988
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(95, 99, 110),
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1989
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(96, 100, 110),
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1990
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(97, 101, 111),
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1991
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(98, 101, 111),
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1992
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(99, 102, 111),
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1993
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(100, 103, 111),
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1994
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(101, 103, 111),
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1995
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(102, 104, 112),
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1996
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(103, 105, 112),
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1997
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(104, 106, 112),
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1998
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(104, 106, 112),
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1999
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(105, 107, 113),
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2000
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(106, 108, 113),
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2001
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(107, 109, 113),
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2002
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(108, 109, 114),
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2003
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(109, 110, 114),
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2004
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(110, 111, 114),
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2005
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(111, 111, 114),
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2006
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(111, 112, 115),
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2007
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(112, 113, 115),
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2008
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(113, 114, 115),
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2009
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(114, 114, 116),
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2010
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(115, 115, 116),
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2011
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(116, 116, 117),
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2012
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(117, 117, 117),
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2013
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(117, 117, 117),
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2014
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(118, 118, 118),
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2015
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(119, 119, 118),
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2016
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(120, 120, 118),
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2017
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(121, 120, 119),
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2018
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(122, 121, 119),
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2019
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(123, 122, 119),
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2020
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(123, 123, 120),
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2021
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(124, 123, 120),
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2022
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(125, 124, 120),
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2023
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(126, 125, 120),
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2024
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(127, 126, 120),
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2025
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(128, 126, 120),
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2026
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(129, 127, 120),
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2027
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(130, 128, 120),
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2028
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(131, 129, 120),
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2029
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(132, 129, 120),
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2030
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(133, 130, 120),
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2031
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(134, 131, 120),
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2032
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(135, 132, 120),
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(136, 133, 120),
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(137, 133, 120),
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2035
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(138, 134, 120),
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(139, 135, 120),
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2037
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(140, 136, 120),
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2038
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(141, 136, 120),
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2039
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(142, 137, 120),
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2040
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(143, 138, 120),
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2041
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(144, 139, 120),
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2042
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(145, 140, 120),
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2043
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(146, 140, 120),
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2044
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(147, 141, 120),
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2045
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(148, 142, 120),
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2046
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(149, 143, 120),
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2047
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(150, 143, 119),
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2048
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(151, 144, 119),
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2049
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(152, 145, 119),
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2050
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(153, 146, 119),
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2051
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(154, 147, 119),
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2052
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(155, 147, 119),
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2053
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(156, 148, 119),
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2054
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(157, 149, 119),
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2055
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(158, 150, 118),
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2056
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(159, 151, 118),
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2057
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(160, 152, 118),
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2058
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(161, 152, 118),
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2059
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(162, 153, 118),
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2060
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(163, 154, 117),
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2061
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(164, 155, 117),
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2062
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(165, 156, 117),
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2063
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(166, 156, 117),
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2064
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(167, 157, 117),
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2065
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(168, 158, 116),
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2066
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(169, 159, 116),
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2067
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(170, 160, 116),
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2068
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(171, 161, 116),
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2069
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+
(172, 161, 115),
|
|
2070
|
+
(173, 162, 115),
|
|
2071
|
+
(174, 163, 115),
|
|
2072
|
+
(175, 164, 115),
|
|
2073
|
+
(176, 165, 114),
|
|
2074
|
+
(177, 166, 114),
|
|
2075
|
+
(178, 166, 114),
|
|
2076
|
+
(180, 167, 113),
|
|
2077
|
+
(181, 168, 113),
|
|
2078
|
+
(182, 169, 113),
|
|
2079
|
+
(183, 170, 112),
|
|
2080
|
+
(184, 171, 112),
|
|
2081
|
+
(185, 171, 112),
|
|
2082
|
+
(186, 172, 111),
|
|
2083
|
+
(187, 173, 111),
|
|
2084
|
+
(188, 174, 110),
|
|
2085
|
+
(189, 175, 110),
|
|
2086
|
+
(190, 176, 110),
|
|
2087
|
+
(191, 177, 109),
|
|
2088
|
+
(192, 177, 109),
|
|
2089
|
+
(193, 178, 108),
|
|
2090
|
+
(194, 179, 108),
|
|
2091
|
+
(196, 180, 108),
|
|
2092
|
+
(197, 181, 107),
|
|
2093
|
+
(198, 182, 107),
|
|
2094
|
+
(199, 183, 106),
|
|
2095
|
+
(200, 184, 106),
|
|
2096
|
+
(201, 184, 105),
|
|
2097
|
+
(202, 185, 105),
|
|
2098
|
+
(203, 186, 104),
|
|
2099
|
+
(204, 187, 104),
|
|
2100
|
+
(205, 188, 103),
|
|
2101
|
+
(206, 189, 103),
|
|
2102
|
+
(207, 190, 102),
|
|
2103
|
+
(209, 191, 102),
|
|
2104
|
+
(210, 192, 101),
|
|
2105
|
+
(211, 192, 101),
|
|
2106
|
+
(212, 193, 100),
|
|
2107
|
+
(213, 194, 99),
|
|
2108
|
+
(214, 195, 99),
|
|
2109
|
+
(215, 196, 98),
|
|
2110
|
+
(216, 197, 98),
|
|
2111
|
+
(217, 198, 97),
|
|
2112
|
+
(219, 199, 96),
|
|
2113
|
+
(220, 200, 96),
|
|
2114
|
+
(221, 201, 95),
|
|
2115
|
+
(222, 202, 94),
|
|
2116
|
+
(223, 203, 93),
|
|
2117
|
+
(224, 203, 93),
|
|
2118
|
+
(225, 204, 92),
|
|
2119
|
+
(227, 205, 91),
|
|
2120
|
+
(228, 206, 91),
|
|
2121
|
+
(229, 207, 90),
|
|
2122
|
+
(230, 208, 89),
|
|
2123
|
+
(231, 209, 88),
|
|
2124
|
+
(232, 210, 87),
|
|
2125
|
+
(233, 211, 86),
|
|
2126
|
+
(235, 212, 86),
|
|
2127
|
+
(236, 213, 85),
|
|
2128
|
+
(237, 214, 84),
|
|
2129
|
+
(238, 215, 83),
|
|
2130
|
+
(239, 216, 82),
|
|
2131
|
+
(240, 217, 81),
|
|
2132
|
+
(242, 218, 80),
|
|
2133
|
+
(243, 219, 79),
|
|
2134
|
+
(244, 220, 78),
|
|
2135
|
+
(245, 221, 77),
|
|
2136
|
+
(246, 222, 76),
|
|
2137
|
+
(247, 223, 75),
|
|
2138
|
+
(249, 224, 73),
|
|
2139
|
+
(250, 224, 72),
|
|
2140
|
+
(251, 225, 71),
|
|
2141
|
+
(252, 226, 70),
|
|
2142
|
+
(253, 227, 69),
|
|
2143
|
+
(255, 228, 67),
|
|
2144
|
+
(255, 229, 66),
|
|
2145
|
+
(255, 230, 66),
|
|
2146
|
+
(255, 231, 67),
|
|
2147
|
+
(255, 232, 68),
|
|
2148
|
+
(255, 233, 69),
|
|
2149
|
+
))
|
|
2150
|
+
|
|
2151
|
+
def __init__(self):
|
|
2152
|
+
self._n = len(self._VALUES)
|
|
2153
|
+
|
|
2154
|
+
def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
|
|
2155
|
+
# Normalize floats
|
|
2156
|
+
f = ColorMap.normalize(floats, lower, upper)
|
|
2157
|
+
# Get RGB
|
|
2158
|
+
val = self._VALUES[
|
|
2159
|
+
np.minimum(np.round(f * self._n).astype(int), self._n - 1)]
|
|
2160
|
+
# Color order
|
|
2161
|
+
rgb = (sys.byteorder == 'big') if rgb is None else rgb
|
|
2162
|
+
# Offset for first color in (a)rgb or rgb(a)
|
|
2163
|
+
m = 1 if (alpha and rgb) else 0
|
|
2164
|
+
# Number of bytes per float
|
|
2165
|
+
n = 4 if alpha else 3
|
|
2166
|
+
# Create output
|
|
2167
|
+
out = 255 * np.ones(n * len(floats), dtype=np.uint8)
|
|
2168
|
+
out[m + 0::n] = val[:, 0] if rgb else val[:, 2]
|
|
2169
|
+
out[m + 1::n] = val[:, 1]
|
|
2170
|
+
out[m + 2::n] = val[:, 2] if rgb else val[:, 0]
|
|
2171
|
+
return out
|
|
2172
|
+
|
|
2173
|
+
|
|
2174
|
+
class ColorMapViridis(ColorMap):
|
|
2175
|
+
"""
|
|
2176
|
+
A colormap using "Viridis".
|
|
2177
|
+
|
|
2178
|
+
The values used by this color map are taken from
|
|
2179
|
+
https://github.com/BIDS/colormap/blob/master/colormaps.py
|
|
2180
|
+
and were distributed under a CC0 license.
|
|
2181
|
+
|
|
2182
|
+
Viridis was designed by Eric Firing, Nathaniel J. Smith, and Stefan van der
|
|
2183
|
+
Walt.
|
|
2184
|
+
"""
|
|
2185
|
+
_VALUES = np.array((
|
|
2186
|
+
(68, 1, 84),
|
|
2187
|
+
(69, 2, 86),
|
|
2188
|
+
(69, 4, 87),
|
|
2189
|
+
(69, 5, 89),
|
|
2190
|
+
(70, 7, 90),
|
|
2191
|
+
(70, 8, 92),
|
|
2192
|
+
(70, 10, 93),
|
|
2193
|
+
(71, 11, 95),
|
|
2194
|
+
(71, 13, 96),
|
|
2195
|
+
(71, 14, 98),
|
|
2196
|
+
(71, 16, 99),
|
|
2197
|
+
(72, 17, 100),
|
|
2198
|
+
(72, 19, 102),
|
|
2199
|
+
(72, 20, 103),
|
|
2200
|
+
(72, 22, 104),
|
|
2201
|
+
(72, 23, 106),
|
|
2202
|
+
(72, 24, 107),
|
|
2203
|
+
(72, 26, 108),
|
|
2204
|
+
(72, 27, 109),
|
|
2205
|
+
(72, 28, 110),
|
|
2206
|
+
(72, 30, 112),
|
|
2207
|
+
(73, 31, 113),
|
|
2208
|
+
(72, 32, 114),
|
|
2209
|
+
(72, 34, 115),
|
|
2210
|
+
(72, 35, 116),
|
|
2211
|
+
(72, 36, 117),
|
|
2212
|
+
(72, 37, 118),
|
|
2213
|
+
(72, 39, 119),
|
|
2214
|
+
(72, 40, 120),
|
|
2215
|
+
(72, 41, 121),
|
|
2216
|
+
(72, 42, 122),
|
|
2217
|
+
(72, 44, 123),
|
|
2218
|
+
(71, 45, 124),
|
|
2219
|
+
(71, 46, 125),
|
|
2220
|
+
(71, 47, 125),
|
|
2221
|
+
(71, 49, 126),
|
|
2222
|
+
(70, 50, 127),
|
|
2223
|
+
(70, 51, 128),
|
|
2224
|
+
(70, 52, 128),
|
|
2225
|
+
(70, 54, 129),
|
|
2226
|
+
(69, 55, 130),
|
|
2227
|
+
(69, 56, 130),
|
|
2228
|
+
(69, 57, 131),
|
|
2229
|
+
(68, 58, 132),
|
|
2230
|
+
(68, 60, 132),
|
|
2231
|
+
(67, 61, 133),
|
|
2232
|
+
(67, 62, 133),
|
|
2233
|
+
(67, 63, 134),
|
|
2234
|
+
(66, 64, 134),
|
|
2235
|
+
(66, 66, 135),
|
|
2236
|
+
(65, 67, 135),
|
|
2237
|
+
(65, 68, 136),
|
|
2238
|
+
(65, 69, 136),
|
|
2239
|
+
(64, 70, 136),
|
|
2240
|
+
(64, 71, 137),
|
|
2241
|
+
(63, 73, 137),
|
|
2242
|
+
(63, 74, 138),
|
|
2243
|
+
(62, 75, 138),
|
|
2244
|
+
(62, 76, 138),
|
|
2245
|
+
(61, 77, 138),
|
|
2246
|
+
(61, 78, 139),
|
|
2247
|
+
(60, 79, 139),
|
|
2248
|
+
(60, 80, 139),
|
|
2249
|
+
(59, 81, 139),
|
|
2250
|
+
(59, 83, 140),
|
|
2251
|
+
(58, 84, 140),
|
|
2252
|
+
(58, 85, 140),
|
|
2253
|
+
(57, 86, 140),
|
|
2254
|
+
(57, 87, 140),
|
|
2255
|
+
(56, 88, 141),
|
|
2256
|
+
(56, 89, 141),
|
|
2257
|
+
(55, 90, 141),
|
|
2258
|
+
(55, 91, 141),
|
|
2259
|
+
(54, 92, 141),
|
|
2260
|
+
(54, 93, 141),
|
|
2261
|
+
(53, 94, 141),
|
|
2262
|
+
(53, 95, 142),
|
|
2263
|
+
(52, 96, 142),
|
|
2264
|
+
(52, 97, 142),
|
|
2265
|
+
(52, 98, 142),
|
|
2266
|
+
(51, 99, 142),
|
|
2267
|
+
(51, 100, 142),
|
|
2268
|
+
(50, 101, 142),
|
|
2269
|
+
(50, 102, 142),
|
|
2270
|
+
(49, 103, 142),
|
|
2271
|
+
(49, 104, 142),
|
|
2272
|
+
(48, 105, 142),
|
|
2273
|
+
(48, 106, 142),
|
|
2274
|
+
(48, 107, 143),
|
|
2275
|
+
(47, 108, 143),
|
|
2276
|
+
(47, 109, 143),
|
|
2277
|
+
(46, 110, 143),
|
|
2278
|
+
(46, 111, 143),
|
|
2279
|
+
(45, 112, 143),
|
|
2280
|
+
(45, 113, 143),
|
|
2281
|
+
(45, 114, 143),
|
|
2282
|
+
(44, 115, 143),
|
|
2283
|
+
(44, 116, 143),
|
|
2284
|
+
(43, 117, 143),
|
|
2285
|
+
(43, 118, 143),
|
|
2286
|
+
(43, 119, 143),
|
|
2287
|
+
(42, 120, 143),
|
|
2288
|
+
(42, 121, 143),
|
|
2289
|
+
(42, 122, 143),
|
|
2290
|
+
(41, 123, 143),
|
|
2291
|
+
(41, 123, 143),
|
|
2292
|
+
(40, 124, 143),
|
|
2293
|
+
(40, 125, 143),
|
|
2294
|
+
(40, 126, 143),
|
|
2295
|
+
(39, 127, 143),
|
|
2296
|
+
(39, 128, 143),
|
|
2297
|
+
(39, 129, 143),
|
|
2298
|
+
(38, 130, 143),
|
|
2299
|
+
(38, 131, 143),
|
|
2300
|
+
(37, 132, 143),
|
|
2301
|
+
(37, 133, 142),
|
|
2302
|
+
(37, 134, 142),
|
|
2303
|
+
(36, 135, 142),
|
|
2304
|
+
(36, 136, 142),
|
|
2305
|
+
(36, 137, 142),
|
|
2306
|
+
(35, 138, 142),
|
|
2307
|
+
(35, 139, 142),
|
|
2308
|
+
(35, 139, 142),
|
|
2309
|
+
(34, 140, 142),
|
|
2310
|
+
(34, 141, 142),
|
|
2311
|
+
(34, 142, 141),
|
|
2312
|
+
(33, 143, 141),
|
|
2313
|
+
(33, 144, 141),
|
|
2314
|
+
(33, 145, 141),
|
|
2315
|
+
(32, 146, 141),
|
|
2316
|
+
(32, 147, 141),
|
|
2317
|
+
(32, 148, 140),
|
|
2318
|
+
(32, 149, 140),
|
|
2319
|
+
(31, 150, 140),
|
|
2320
|
+
(31, 151, 140),
|
|
2321
|
+
(31, 152, 139),
|
|
2322
|
+
(31, 153, 139),
|
|
2323
|
+
(31, 154, 139),
|
|
2324
|
+
(31, 155, 139),
|
|
2325
|
+
(31, 156, 138),
|
|
2326
|
+
(31, 156, 138),
|
|
2327
|
+
(31, 157, 138),
|
|
2328
|
+
(31, 158, 137),
|
|
2329
|
+
(31, 159, 137),
|
|
2330
|
+
(31, 160, 137),
|
|
2331
|
+
(31, 161, 136),
|
|
2332
|
+
(31, 162, 136),
|
|
2333
|
+
(32, 163, 135),
|
|
2334
|
+
(32, 164, 135),
|
|
2335
|
+
(32, 165, 134),
|
|
2336
|
+
(33, 166, 134),
|
|
2337
|
+
(33, 167, 134),
|
|
2338
|
+
(34, 168, 133),
|
|
2339
|
+
(34, 169, 133),
|
|
2340
|
+
(35, 170, 132),
|
|
2341
|
+
(36, 170, 131),
|
|
2342
|
+
(37, 171, 131),
|
|
2343
|
+
(38, 172, 130),
|
|
2344
|
+
(38, 173, 130),
|
|
2345
|
+
(39, 174, 129),
|
|
2346
|
+
(40, 175, 128),
|
|
2347
|
+
(41, 176, 128),
|
|
2348
|
+
(43, 177, 127),
|
|
2349
|
+
(44, 178, 126),
|
|
2350
|
+
(45, 179, 126),
|
|
2351
|
+
(46, 180, 125),
|
|
2352
|
+
(48, 180, 124),
|
|
2353
|
+
(49, 181, 123),
|
|
2354
|
+
(50, 182, 123),
|
|
2355
|
+
(52, 183, 122),
|
|
2356
|
+
(53, 184, 121),
|
|
2357
|
+
(55, 185, 120),
|
|
2358
|
+
(56, 186, 119),
|
|
2359
|
+
(58, 187, 118),
|
|
2360
|
+
(60, 187, 118),
|
|
2361
|
+
(61, 188, 117),
|
|
2362
|
+
(63, 189, 116),
|
|
2363
|
+
(65, 190, 115),
|
|
2364
|
+
(67, 191, 114),
|
|
2365
|
+
(68, 192, 113),
|
|
2366
|
+
(70, 193, 112),
|
|
2367
|
+
(72, 193, 111),
|
|
2368
|
+
(74, 194, 110),
|
|
2369
|
+
(76, 195, 109),
|
|
2370
|
+
(78, 196, 108),
|
|
2371
|
+
(80, 197, 106),
|
|
2372
|
+
(82, 197, 105),
|
|
2373
|
+
(84, 198, 104),
|
|
2374
|
+
(86, 199, 103),
|
|
2375
|
+
(88, 200, 102),
|
|
2376
|
+
(90, 200, 101),
|
|
2377
|
+
(92, 201, 99),
|
|
2378
|
+
(95, 202, 98),
|
|
2379
|
+
(97, 203, 97),
|
|
2380
|
+
(99, 203, 95),
|
|
2381
|
+
(101, 204, 94),
|
|
2382
|
+
(103, 205, 93),
|
|
2383
|
+
(106, 206, 91),
|
|
2384
|
+
(108, 206, 90),
|
|
2385
|
+
(110, 207, 89),
|
|
2386
|
+
(113, 208, 87),
|
|
2387
|
+
(115, 208, 86),
|
|
2388
|
+
(117, 209, 84),
|
|
2389
|
+
(120, 210, 83),
|
|
2390
|
+
(122, 210, 81),
|
|
2391
|
+
(125, 211, 80),
|
|
2392
|
+
(127, 212, 78),
|
|
2393
|
+
(130, 212, 77),
|
|
2394
|
+
(132, 213, 75),
|
|
2395
|
+
(135, 213, 74),
|
|
2396
|
+
(137, 214, 72),
|
|
2397
|
+
(140, 215, 71),
|
|
2398
|
+
(142, 215, 69),
|
|
2399
|
+
(145, 216, 67),
|
|
2400
|
+
(147, 216, 66),
|
|
2401
|
+
(150, 217, 64),
|
|
2402
|
+
(153, 217, 62),
|
|
2403
|
+
(155, 218, 61),
|
|
2404
|
+
(158, 218, 59),
|
|
2405
|
+
(160, 219, 57),
|
|
2406
|
+
(163, 219, 55),
|
|
2407
|
+
(166, 220, 54),
|
|
2408
|
+
(168, 220, 52),
|
|
2409
|
+
(171, 221, 50),
|
|
2410
|
+
(174, 221, 49),
|
|
2411
|
+
(176, 222, 47),
|
|
2412
|
+
(179, 222, 45),
|
|
2413
|
+
(182, 222, 43),
|
|
2414
|
+
(184, 223, 42),
|
|
2415
|
+
(187, 223, 40),
|
|
2416
|
+
(190, 224, 38),
|
|
2417
|
+
(192, 224, 37),
|
|
2418
|
+
(195, 224, 35),
|
|
2419
|
+
(198, 225, 34),
|
|
2420
|
+
(201, 225, 32),
|
|
2421
|
+
(203, 225, 31),
|
|
2422
|
+
(206, 226, 29),
|
|
2423
|
+
(209, 226, 28),
|
|
2424
|
+
(211, 226, 27),
|
|
2425
|
+
(214, 227, 26),
|
|
2426
|
+
(216, 227, 26),
|
|
2427
|
+
(219, 227, 25),
|
|
2428
|
+
(222, 228, 25),
|
|
2429
|
+
(224, 228, 24),
|
|
2430
|
+
(227, 228, 24),
|
|
2431
|
+
(229, 229, 25),
|
|
2432
|
+
(232, 229, 25),
|
|
2433
|
+
(235, 229, 26),
|
|
2434
|
+
(237, 230, 27),
|
|
2435
|
+
(240, 230, 28),
|
|
2436
|
+
(242, 230, 29),
|
|
2437
|
+
(245, 231, 30),
|
|
2438
|
+
(247, 231, 32),
|
|
2439
|
+
(249, 231, 33),
|
|
2440
|
+
(252, 232, 35),
|
|
2441
|
+
(254, 232, 37),
|
|
2442
|
+
))
|
|
2443
|
+
|
|
2444
|
+
def __init__(self):
|
|
2445
|
+
self._n = len(self._VALUES)
|
|
2446
|
+
|
|
2447
|
+
def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
|
|
2448
|
+
# Normalize floats
|
|
2449
|
+
f = ColorMap.normalize(floats, lower, upper)
|
|
2450
|
+
# Get RGB
|
|
2451
|
+
val = self._VALUES[
|
|
2452
|
+
np.minimum(np.round(f * self._n).astype(int), self._n - 1)]
|
|
2453
|
+
# Color order
|
|
2454
|
+
rgb = (sys.byteorder == 'big') if rgb is None else rgb
|
|
2455
|
+
# Offset for first color in (a)rgb or rgb(a)
|
|
2456
|
+
m = 1 if (alpha and rgb) else 0
|
|
2457
|
+
# Number of bytes per float
|
|
2458
|
+
n = 4 if alpha else 3
|
|
2459
|
+
# Create output
|
|
2460
|
+
out = 255 * np.ones(n * len(floats), dtype=np.uint8)
|
|
2461
|
+
out[m + 0::n] = val[:, 0] if rgb else val[:, 2]
|
|
2462
|
+
out[m + 1::n] = val[:, 1]
|
|
2463
|
+
out[m + 2::n] = val[:, 2] if rgb else val[:, 0]
|
|
2464
|
+
return out
|
|
2465
|
+
|
|
2466
|
+
|
|
2467
|
+
class ColorMapInferno(ColorMap):
|
|
2468
|
+
"""
|
|
2469
|
+
A colormap using "Viridis".
|
|
2470
|
+
|
|
2471
|
+
The values used by this color map are taken from
|
|
2472
|
+
https://github.com/BIDS/colormap/blob/master/colormaps.py
|
|
2473
|
+
and were distributed under a CC0 license.
|
|
2474
|
+
|
|
2475
|
+
Viridis was designed by Eric Firing, Nathaniel J. Smith, and Stefan van der
|
|
2476
|
+
Walt.
|
|
2477
|
+
"""
|
|
2478
|
+
_VALUES = np.array((
|
|
2479
|
+
(0, 0, 4),
|
|
2480
|
+
(1, 0, 5),
|
|
2481
|
+
(1, 1, 6),
|
|
2482
|
+
(1, 1, 8),
|
|
2483
|
+
(2, 1, 10),
|
|
2484
|
+
(2, 2, 12),
|
|
2485
|
+
(2, 2, 14),
|
|
2486
|
+
(3, 2, 16),
|
|
2487
|
+
(4, 3, 18),
|
|
2488
|
+
(4, 3, 21),
|
|
2489
|
+
(5, 4, 23),
|
|
2490
|
+
(6, 4, 25),
|
|
2491
|
+
(7, 5, 27),
|
|
2492
|
+
(8, 6, 29),
|
|
2493
|
+
(9, 6, 32),
|
|
2494
|
+
(10, 7, 34),
|
|
2495
|
+
(11, 7, 36),
|
|
2496
|
+
(12, 8, 38),
|
|
2497
|
+
(13, 8, 41),
|
|
2498
|
+
(14, 9, 43),
|
|
2499
|
+
(16, 9, 45),
|
|
2500
|
+
(17, 10, 48),
|
|
2501
|
+
(18, 10, 50),
|
|
2502
|
+
(20, 11, 53),
|
|
2503
|
+
(21, 11, 55),
|
|
2504
|
+
(22, 11, 58),
|
|
2505
|
+
(24, 12, 60),
|
|
2506
|
+
(25, 12, 62),
|
|
2507
|
+
(27, 12, 65),
|
|
2508
|
+
(28, 12, 67),
|
|
2509
|
+
(30, 12, 70),
|
|
2510
|
+
(31, 12, 72),
|
|
2511
|
+
(33, 12, 74),
|
|
2512
|
+
(35, 12, 77),
|
|
2513
|
+
(36, 12, 79),
|
|
2514
|
+
(38, 12, 81),
|
|
2515
|
+
(40, 11, 83),
|
|
2516
|
+
(42, 11, 85),
|
|
2517
|
+
(43, 11, 87),
|
|
2518
|
+
(45, 11, 89),
|
|
2519
|
+
(47, 10, 91),
|
|
2520
|
+
(49, 10, 93),
|
|
2521
|
+
(51, 10, 94),
|
|
2522
|
+
(52, 10, 96),
|
|
2523
|
+
(54, 9, 97),
|
|
2524
|
+
(56, 9, 98),
|
|
2525
|
+
(58, 9, 99),
|
|
2526
|
+
(59, 9, 100),
|
|
2527
|
+
(61, 9, 101),
|
|
2528
|
+
(63, 9, 102),
|
|
2529
|
+
(64, 10, 103),
|
|
2530
|
+
(66, 10, 104),
|
|
2531
|
+
(68, 10, 105),
|
|
2532
|
+
(69, 10, 105),
|
|
2533
|
+
(71, 11, 106),
|
|
2534
|
+
(73, 11, 107),
|
|
2535
|
+
(74, 12, 107),
|
|
2536
|
+
(76, 12, 108),
|
|
2537
|
+
(78, 13, 108),
|
|
2538
|
+
(79, 13, 108),
|
|
2539
|
+
(81, 14, 109),
|
|
2540
|
+
(83, 14, 109),
|
|
2541
|
+
(84, 15, 109),
|
|
2542
|
+
(86, 15, 110),
|
|
2543
|
+
(87, 16, 110),
|
|
2544
|
+
(89, 17, 110),
|
|
2545
|
+
(91, 17, 110),
|
|
2546
|
+
(92, 18, 110),
|
|
2547
|
+
(94, 18, 111),
|
|
2548
|
+
(95, 19, 111),
|
|
2549
|
+
(97, 20, 111),
|
|
2550
|
+
(99, 20, 111),
|
|
2551
|
+
(100, 21, 111),
|
|
2552
|
+
(102, 21, 111),
|
|
2553
|
+
(103, 22, 111),
|
|
2554
|
+
(105, 23, 111),
|
|
2555
|
+
(107, 23, 111),
|
|
2556
|
+
(108, 24, 111),
|
|
2557
|
+
(110, 24, 111),
|
|
2558
|
+
(111, 25, 111),
|
|
2559
|
+
(113, 25, 110),
|
|
2560
|
+
(115, 26, 110),
|
|
2561
|
+
(116, 27, 110),
|
|
2562
|
+
(118, 27, 110),
|
|
2563
|
+
(119, 28, 110),
|
|
2564
|
+
(121, 28, 110),
|
|
2565
|
+
(123, 29, 109),
|
|
2566
|
+
(124, 29, 109),
|
|
2567
|
+
(126, 30, 109),
|
|
2568
|
+
(127, 31, 109),
|
|
2569
|
+
(129, 31, 108),
|
|
2570
|
+
(130, 32, 108),
|
|
2571
|
+
(132, 32, 108),
|
|
2572
|
+
(134, 33, 107),
|
|
2573
|
+
(135, 33, 107),
|
|
2574
|
+
(137, 34, 107),
|
|
2575
|
+
(138, 34, 106),
|
|
2576
|
+
(140, 35, 106),
|
|
2577
|
+
(142, 36, 105),
|
|
2578
|
+
(143, 36, 105),
|
|
2579
|
+
(145, 37, 105),
|
|
2580
|
+
(146, 37, 104),
|
|
2581
|
+
(148, 38, 104),
|
|
2582
|
+
(150, 38, 103),
|
|
2583
|
+
(151, 39, 102),
|
|
2584
|
+
(153, 40, 102),
|
|
2585
|
+
(154, 40, 101),
|
|
2586
|
+
(156, 41, 101),
|
|
2587
|
+
(158, 41, 100),
|
|
2588
|
+
(159, 42, 100),
|
|
2589
|
+
(161, 43, 99),
|
|
2590
|
+
(162, 43, 98),
|
|
2591
|
+
(164, 44, 98),
|
|
2592
|
+
(165, 45, 97),
|
|
2593
|
+
(167, 45, 96),
|
|
2594
|
+
(169, 46, 95),
|
|
2595
|
+
(170, 46, 95),
|
|
2596
|
+
(172, 47, 94),
|
|
2597
|
+
(173, 48, 93),
|
|
2598
|
+
(175, 49, 92),
|
|
2599
|
+
(176, 49, 92),
|
|
2600
|
+
(178, 50, 91),
|
|
2601
|
+
(179, 51, 90),
|
|
2602
|
+
(181, 51, 89),
|
|
2603
|
+
(182, 52, 88),
|
|
2604
|
+
(184, 53, 87),
|
|
2605
|
+
(185, 54, 86),
|
|
2606
|
+
(187, 54, 85),
|
|
2607
|
+
(188, 55, 85),
|
|
2608
|
+
(190, 56, 84),
|
|
2609
|
+
(191, 57, 83),
|
|
2610
|
+
(193, 58, 82),
|
|
2611
|
+
(194, 59, 81),
|
|
2612
|
+
(196, 60, 80),
|
|
2613
|
+
(197, 60, 79),
|
|
2614
|
+
(198, 61, 78),
|
|
2615
|
+
(200, 62, 77),
|
|
2616
|
+
(201, 63, 76),
|
|
2617
|
+
(203, 64, 75),
|
|
2618
|
+
(204, 65, 74),
|
|
2619
|
+
(205, 66, 72),
|
|
2620
|
+
(207, 67, 71),
|
|
2621
|
+
(208, 68, 70),
|
|
2622
|
+
(209, 69, 69),
|
|
2623
|
+
(211, 70, 68),
|
|
2624
|
+
(212, 72, 67),
|
|
2625
|
+
(213, 73, 66),
|
|
2626
|
+
(214, 74, 65),
|
|
2627
|
+
(216, 75, 64),
|
|
2628
|
+
(217, 76, 62),
|
|
2629
|
+
(218, 77, 61),
|
|
2630
|
+
(219, 79, 60),
|
|
2631
|
+
(220, 80, 59),
|
|
2632
|
+
(221, 81, 58),
|
|
2633
|
+
(223, 82, 57),
|
|
2634
|
+
(224, 84, 56),
|
|
2635
|
+
(225, 85, 54),
|
|
2636
|
+
(226, 86, 53),
|
|
2637
|
+
(227, 88, 52),
|
|
2638
|
+
(228, 89, 51),
|
|
2639
|
+
(229, 90, 50),
|
|
2640
|
+
(230, 92, 48),
|
|
2641
|
+
(231, 93, 47),
|
|
2642
|
+
(232, 95, 46),
|
|
2643
|
+
(233, 96, 45),
|
|
2644
|
+
(234, 98, 43),
|
|
2645
|
+
(235, 99, 42),
|
|
2646
|
+
(235, 101, 41),
|
|
2647
|
+
(236, 102, 40),
|
|
2648
|
+
(237, 104, 38),
|
|
2649
|
+
(238, 105, 37),
|
|
2650
|
+
(239, 107, 36),
|
|
2651
|
+
(240, 109, 35),
|
|
2652
|
+
(240, 110, 33),
|
|
2653
|
+
(241, 112, 32),
|
|
2654
|
+
(242, 113, 31),
|
|
2655
|
+
(242, 115, 30),
|
|
2656
|
+
(243, 117, 28),
|
|
2657
|
+
(244, 118, 27),
|
|
2658
|
+
(244, 120, 26),
|
|
2659
|
+
(245, 122, 24),
|
|
2660
|
+
(246, 123, 23),
|
|
2661
|
+
(246, 125, 22),
|
|
2662
|
+
(247, 127, 20),
|
|
2663
|
+
(247, 129, 19),
|
|
2664
|
+
(248, 130, 18),
|
|
2665
|
+
(248, 132, 16),
|
|
2666
|
+
(249, 134, 15),
|
|
2667
|
+
(249, 136, 14),
|
|
2668
|
+
(249, 137, 12),
|
|
2669
|
+
(250, 139, 11),
|
|
2670
|
+
(250, 141, 10),
|
|
2671
|
+
(250, 143, 9),
|
|
2672
|
+
(251, 145, 8),
|
|
2673
|
+
(251, 146, 7),
|
|
2674
|
+
(251, 148, 7),
|
|
2675
|
+
(252, 150, 6),
|
|
2676
|
+
(252, 152, 6),
|
|
2677
|
+
(252, 154, 6),
|
|
2678
|
+
(252, 156, 6),
|
|
2679
|
+
(252, 158, 7),
|
|
2680
|
+
(253, 160, 7),
|
|
2681
|
+
(253, 161, 8),
|
|
2682
|
+
(253, 163, 9),
|
|
2683
|
+
(253, 165, 10),
|
|
2684
|
+
(253, 167, 12),
|
|
2685
|
+
(253, 169, 13),
|
|
2686
|
+
(253, 171, 15),
|
|
2687
|
+
(253, 173, 17),
|
|
2688
|
+
(253, 175, 19),
|
|
2689
|
+
(253, 177, 20),
|
|
2690
|
+
(253, 179, 22),
|
|
2691
|
+
(253, 181, 24),
|
|
2692
|
+
(252, 183, 27),
|
|
2693
|
+
(252, 185, 29),
|
|
2694
|
+
(252, 186, 31),
|
|
2695
|
+
(252, 188, 33),
|
|
2696
|
+
(252, 190, 35),
|
|
2697
|
+
(251, 192, 38),
|
|
2698
|
+
(251, 194, 40),
|
|
2699
|
+
(251, 196, 43),
|
|
2700
|
+
(251, 198, 45),
|
|
2701
|
+
(250, 200, 48),
|
|
2702
|
+
(250, 202, 50),
|
|
2703
|
+
(250, 204, 53),
|
|
2704
|
+
(249, 206, 56),
|
|
2705
|
+
(249, 208, 58),
|
|
2706
|
+
(248, 210, 61),
|
|
2707
|
+
(248, 212, 64),
|
|
2708
|
+
(247, 214, 67),
|
|
2709
|
+
(247, 216, 70),
|
|
2710
|
+
(246, 218, 73),
|
|
2711
|
+
(246, 220, 76),
|
|
2712
|
+
(245, 222, 80),
|
|
2713
|
+
(245, 224, 83),
|
|
2714
|
+
(244, 226, 86),
|
|
2715
|
+
(244, 228, 90),
|
|
2716
|
+
(244, 229, 94),
|
|
2717
|
+
(243, 231, 97),
|
|
2718
|
+
(243, 233, 101),
|
|
2719
|
+
(243, 235, 105),
|
|
2720
|
+
(242, 237, 109),
|
|
2721
|
+
(242, 238, 113),
|
|
2722
|
+
(242, 240, 117),
|
|
2723
|
+
(242, 241, 122),
|
|
2724
|
+
(243, 243, 126),
|
|
2725
|
+
(243, 244, 130),
|
|
2726
|
+
(244, 246, 134),
|
|
2727
|
+
(244, 247, 138),
|
|
2728
|
+
(245, 249, 142),
|
|
2729
|
+
(246, 250, 146),
|
|
2730
|
+
(247, 251, 150),
|
|
2731
|
+
(249, 252, 154),
|
|
2732
|
+
(250, 253, 158),
|
|
2733
|
+
(251, 254, 162),
|
|
2734
|
+
(253, 255, 165),
|
|
2735
|
+
))
|
|
2736
|
+
|
|
2737
|
+
def __init__(self):
|
|
2738
|
+
self._n = len(self._VALUES)
|
|
2739
|
+
|
|
2740
|
+
def __call__(self, floats, lower=None, upper=None, alpha=True, rgb=None):
|
|
2741
|
+
# Normalize floats
|
|
2742
|
+
f = ColorMap.normalize(floats, lower, upper)
|
|
2743
|
+
# Get RGB
|
|
2744
|
+
val = self._VALUES[
|
|
2745
|
+
np.minimum(np.round(f * self._n).astype(int), self._n - 1)]
|
|
2746
|
+
# Color order
|
|
2747
|
+
rgb = (sys.byteorder == 'big') if rgb is None else rgb
|
|
2748
|
+
# Offset for first color in (a)rgb or rgb(a)
|
|
2749
|
+
m = 1 if (alpha and rgb) else 0
|
|
2750
|
+
# Number of bytes per float
|
|
2751
|
+
n = 4 if alpha else 3
|
|
2752
|
+
# Create output
|
|
2753
|
+
out = 255 * np.ones(n * len(floats), dtype=np.uint8)
|
|
2754
|
+
out[m + 0::n] = val[:, 0] if rgb else val[:, 2]
|
|
2755
|
+
out[m + 1::n] = val[:, 1]
|
|
2756
|
+
out[m + 2::n] = val[:, 2] if rgb else val[:, 0]
|
|
2757
|
+
return out
|
|
2758
|
+
|
|
2759
|
+
|
|
2760
|
+
ColorMap._colormaps['cividis'] = ColorMapCividis
|
|
2761
|
+
ColorMap._colormaps['inferno'] = ColorMapInferno
|
|
2762
|
+
ColorMap._colormaps['viridis'] = ColorMapViridis
|
|
2763
|
+
ColorMap._colormaps['gray'] = ColorMapGray
|
|
1862
2764
|
ColorMap._colormaps['blue'] = ColorMapBlue
|
|
1863
2765
|
ColorMap._colormaps['green'] = ColorMapGreen
|
|
1864
2766
|
ColorMap._colormaps['red'] = ColorMapRed
|