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20 hours ago •
holoviz
holoviz
Issues with using custom matplotlib colormap
I'm having two issues:
- When using
xarray.hvplot.quadmesh, I'm unable to use a a customLinearSegmentedColormapunless I register it with with matplotlib and call it that way.
- I'm able to use a custom registered matplotlib colormap in one of my conda environments (running Python 3.10.5), but not the other (running Python 3.8.13). This is the same exact code as successfully plotted above:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/IPython/core/formatters.py:973, in MimeBundleFormatter.__call__(self, obj, include, exclude)
970 method = get_real_method(obj, self.print_method)
972 if method is not None:
--> 973 return method(include=include, exclude=exclude)
974 return None
975 else:
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/core/dimension.py:1294, in Dimensioned._repr_mimebundle_(self, include, exclude)
1287 def _repr_mimebundle_(self, include=None, exclude=None):
1288 """
1289 Resolves the class hierarchy for the class rendering the
1290 object using any display hooks registered on Store.display
1291 hooks. The output of all registered display_hooks is then
1292 combined and returned.
1293 """
-> 1294 return Store.render(self)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/core/options.py:1426, in Store.render(cls, obj)
1424 data, metadata = {}, {}
1425 for hook in hooks:
-> 1426 ret = hook(obj)
1427 if ret is None:
1428 continue
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/ipython/display_hooks.py:277, in pprint_display(obj)
275 if not ip.display_formatter.formatters['text/plain'].pprint:
276 return None
--> 277 return display(obj, raw_output=True)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/ipython/display_hooks.py:253, in display(obj, raw_output, **kwargs)
251 elif isinstance(obj, (HoloMap, DynamicMap)):
252 with option_state(obj):
--> 253 output = map_display(obj)
254 elif isinstance(obj, Plot):
255 output = render(obj)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/ipython/display_hooks.py:141, in display_hook.<locals>.wrapped(element)
139 try:
140 max_frames = OutputSettings.options['max_frames']
--> 141 mimebundle = fn(element, max_frames=max_frames)
142 if mimebundle is None:
143 return {}, {}
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/ipython/display_hooks.py:201, in map_display(vmap, max_frames)
198 max_frame_warning(max_frames)
199 return None
--> 201 return render(vmap)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/ipython/display_hooks.py:68, in render(obj, **kwargs)
65 if renderer.fig == 'pdf':
66 renderer = renderer.instance(fig='png')
---> 68 return renderer.components(obj, **kwargs)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/renderer.py:398, in Renderer.components(self, obj, fmt, comm, **kwargs)
395 embed = (not (dynamic or streams or self.widget_mode == 'live') or config.embed)
397 if embed or config.comms == 'default':
--> 398 return self._render_panel(plot, embed, comm)
399 return self._render_ipywidget(plot)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/renderer.py:405, in Renderer._render_panel(self, plot, embed, comm)
403 doc = Document()
404 with config.set(embed=embed):
--> 405 model = plot.layout._render_model(doc, comm)
406 if embed:
407 return render_model(model, comm)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/panel/viewable.py:505, in Renderable._render_model(self, doc, comm)
503 if comm is None:
504 comm = state._comm_manager.get_server_comm()
--> 505 model = self.get_root(doc, comm)
507 if config.embed:
508 embed_state(self, model, doc,
509 json=config.embed_json,
510 json_prefix=config.embed_json_prefix,
511 save_path=config.embed_save_path,
512 load_path=config.embed_load_path,
513 progress=False)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/panel/viewable.py:556, in Renderable.get_root(self, doc, comm, preprocess)
539 """
540 Returns the root model and applies pre-processing hooks
541
(...)
553 Returns the bokeh model corresponding to this panel object
554 """
555 doc = init_doc(doc)
--> 556 root = self._get_model(doc, comm=comm)
557 if preprocess:
558 self._preprocess(root)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/panel/layout/base.py:146, in Panel._get_model(self, doc, root, parent, comm)
144 if root is None:
145 root = model
--> 146 objects = self._get_objects(model, [], doc, root, comm)
147 props = dict(self._init_params(), objects=objects)
148 model.update(**self._process_param_change(props))
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/panel/layout/base.py:131, in Panel._get_objects(self, model, old_objects, doc, root, comm)
129 else:
130 try:
--> 131 child = pane._get_model(doc, root, model, comm)
132 except RerenderError:
133 return self._get_objects(model, current_objects[:i], doc, root, comm)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/panel/pane/holoviews.py:265, in HoloViews._get_model(self, doc, root, parent, comm)
263 plot = self.object
264 else:
--> 265 plot = self._render(doc, comm, root)
267 plot.pane = self
268 backend = plot.renderer.backend
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/panel/pane/holoviews.py:342, in HoloViews._render(self, doc, comm, root)
339 if comm:
340 kwargs['comm'] = comm
--> 342 return renderer.get_plot(self.object, **kwargs)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/bokeh/renderer.py:70, in BokehRenderer.get_plot(self_or_cls, obj, doc, renderer, **kwargs)
63 @bothmethod
64 def get_plot(self_or_cls, obj, doc=None, renderer=None, **kwargs):
65 """
66 Given a HoloViews Viewable return a corresponding plot instance.
67 Allows supplying a document attach the plot to, useful when
68 combining the bokeh model with another plot.
69 """
---> 70 plot = super().get_plot(obj, doc, renderer, **kwargs)
71 if plot.document is None:
72 plot.document = Document() if self_or_cls.notebook_context else curdoc()
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/renderer.py:240, in Renderer.get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
237 defaults = [kd.default for kd in plot.dimensions]
238 init_key = tuple(v if d is None else d for v, d in
239 zip(plot.keys[0], defaults))
--> 240 plot.update(init_key)
241 else:
242 plot = obj
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/plot.py:949, in DimensionedPlot.update(self, key)
947 if len(self) == 1 and ((key == 0) or (key == self.keys[0])) and not self.drawn:
948 return self.initialize_plot()
--> 949 item = self.__getitem__(key)
950 self.traverse(lambda x: setattr(x, '_updated', True))
951 return item
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/plot.py:432, in DimensionedPlot.__getitem__(self, frame)
430 if isinstance(frame, int) and frame > len(self):
431 self.param.warning("Showing last frame available: %d" % len(self))
--> 432 if not self.drawn: self.handles['fig'] = self.initialize_plot()
433 if not isinstance(frame, tuple):
434 frame = self.keys[frame]
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/geoviews/plotting/bokeh/plot.py:111, in GeoPlot.initialize_plot(self, ranges, plot, plots, source)
109 def initialize_plot(self, ranges=None, plot=None, plots=None, source=None):
110 opts = {} if isinstance(self, HvOverlayPlot) else {'source': source}
--> 111 fig = super(GeoPlot, self).initialize_plot(ranges, plot, plots, **opts)
112 if self.geographic and self.show_bounds and not self.overlaid:
113 from . import GeoShapePlot
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/bokeh/element.py:1397, in ElementPlot.initialize_plot(self, ranges, plot, plots, source)
1394 self.handles['y_range'] = plot.y_range
1395 self.handles['plot'] = plot
-> 1397 self._init_glyphs(plot, element, ranges, source)
1398 if not self.overlaid:
1399 self._update_plot(key, plot, style_element)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/bokeh/element.py:1341, in ElementPlot._init_glyphs(self, plot, element, ranges, source)
1339 else:
1340 style = self.style[self.cyclic_index]
-> 1341 data, mapping, style = self.get_data(element, ranges, style)
1342 current_id = element._plot_id
1344 with abbreviated_exception():
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/geoviews/plotting/bokeh/plot.py:171, in GeoPlot.get_data(self, element, ranges, style)
169 if self._project_operation and self.geographic:
170 element = self._project_operation(element, projection=self.projection)
--> 171 return super(GeoPlot, self).get_data(element, ranges, style)
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/bokeh/raster.py:90, in RasterPlot.get_data(self, element, ranges, style)
88 mapping = dict(image='image', x='x', y='y', dw='dw', dh='dh')
89 val_dim = element.vdims[0]
---> 90 style['color_mapper'] = self._get_colormapper(val_dim, element, ranges, style)
91 if 'alpha' in style:
92 style['global_alpha'] = style['alpha']
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/bokeh/element.py:1913, in ColorbarPlot._get_colormapper(self, eldim, element, ranges, style, factors, colors, group, name)
1908 if isinstance(cmap, list) and len(cmap) != ncolors:
1909 raise ValueError('The number of colors in the colormap '
1910 'must match the intervals defined in the '
1911 'color_levels, expected %d colors found %d.'
1912 % (ncolors, len(cmap)))
-> 1913 palette = process_cmap(cmap, ncolors, categorical=categorical)
1914 if isinstance(self.color_levels, list):
1915 palette, (low, high) = color_intervals(palette, self.color_levels, clip=(low, high))
File /storage/work/cnd5285/miniconda/envs/uviz/lib/python3.8/site-packages/holoviews/plotting/util.py:911, in process_cmap(cmap, ncolors, provider, categorical)
909 palette = colorcet_cmap_to_palette(cmap, ncolors, categorical)
910 else:
--> 911 raise ValueError("Supplied cmap %s not found among %s colormaps." %
912 (cmap,providers_checked))
913 else:
914 try:
915 # Try processing as matplotlib colormap
ValueError: Supplied cmap FLUT CIMSS not found among matplotlib, bokeh, or colorcet colormaps.
Successful environment (Python 3.10.5):
bokeh 2.4.3 py310hff52083_0 conda-forge
holoviews 1.14.9 pyhd8ed1ab_0 conda-forge
hvplot 0.8.1 py_0 pyviz
Failed environment (Python 3.8.13):
bokeh 2.4.3 pyhd8ed1ab_3 conda-forge
holoviews 1.15.1 py_0 pyviz
hvplot 0.8.1 py_0 pyviz
Hi @cdeciampa ! Could you provide with your issue a minimal reproducible example with code for us to copy/paste and run to try to reproduce the problem you describe? That would help tremendously!
import os
import glob
import numpy as np
import xarray as xr
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.colors import LinearSegmentedColormap
import hvplot.xarray
parent_28km_dir = "/path/to/28km/model/output/netCDFs"
h3p_files = glob.glob(os.path.join(parent_28km_dir, '*.h3.*.nc'))
h3pr_ds = xr.open_mfdataset([f for f in h3p_files if 'remap' in f])
def T_to_FLUT(T, unit='K'):
if unit == 'C':
T += 273.15
sigma = 5.6693E-8
olr = sigma*(T**4)
return olr
# Normalized CIMSS outgoing longwave radiation flux colormap
bw_colors = [(0, '#BCBCBC'), (1, '#000000')]
bw_cmp = LinearSegmentedColormap.from_list('FLUT bw', bw_colors, N=435)
levels = np.array([T_to_FLUT(temp, 'C') for temp in [-110, -105, -87.5, -80, -70, -60, -50, -35, -27.5, -22.5]])
fracs = levels-T_to_FLUT(-110, 'C')
rainbow_colors = [(0, '#0febff'), # cyan
((fracs[1]/fracs[-1]), '#7f007f'), # purple
((fracs[2]/fracs[-1]), '#e5e4e5'), # white
((fracs[3]/fracs[-1]), '#000000'), # black
((fracs[4]/fracs[-1]), '#ff0000'), # red
((fracs[5]/fracs[-1]), '#FFFF00'), # yellow
((fracs[6]/fracs[-1]), '#00FF00'), # green
((fracs[7]/fracs[-1]), '#000073'), # navy
(1, '#00ffff')] # cyan
rainbow_cmp = LinearSegmentedColormap.from_list('FLUT colors', rainbow_colors, N=184)
bws = plt.get_cmap(bw_cmp)
bws_colors = bws(np.linspace(0, 1, 435))
rainbow = plt.get_cmap(rainbow_cmp)
r_colors = rainbow(np.linspace(0, 1, 184))
all_colors = np.vstack((r_colors, bws_colors))
flut_cimss = LinearSegmentedColormap.from_list('FLUT_CIMSS', all_colors)
# Registers as matplotlib colormap
mpl.colormaps.register(flut_cimss, name='FLUT_CIMSS', force=True)
h3pr_ds.FLUT.isel(time=7).hvplot.quadmesh('lon', 'lat', geo=True, rasterize=True, dynamic=False,
clim=(T_to_FLUT(-110, 'C'), T_to_FLUT(55, 'C')),
cmap = 'FLUT_CIMSS', coastline='10m', frame_width=500)
Unfortunately @cdeciampa I won't be able to run this code without having the files you use. So either you could share with me one file or you could modify your script to generate data instead of relying on reading files.
I'm sharing two files so you don't need to modify xr.open_mfdataset and should be able to run the code as-is. They're small files, ~4 mb each.
test_files.zip
Thanks for sharing the test files. I'll just note that the glob pattern didn't work with these files and that the dataset has not FLUT variable. Yet I was able to reproduce the second problem reported by replacing FLUT by PRECC. It seems that HoloViews doesn't correctly retrieve the list of Matplotlib colormaps, I'll open an issue on HoloViews.
On the first issue, I realize that cmap isn't documented anywhere on the website, I'm not sure what types it accepts so one would first need to document what it accepts.