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Utilities to visualise and create matplotlib colormaps and various color codecs

License: BSD 3-Clause "New" or "Revised" License

Python 20.12% Jupyter Notebook 79.88%

colormap's Introduction

Hi there

🔭 I’m currently actively working on Sequana and also maintaining BioServices, Damona, Fitter, colormap, spectrum, Bioconvert and easydev.
I'm currently leading the bioinformatics and data management activities of the Biomics NGS platform (biomics.pasteur.fr) building pipelines and tools for production.
👯 I’m looking to collaborate on BioConvert, BioServices and Damona and of course Sequana. Would you be interested to take the lead on Spectrum, fitter, colormap, please let me know.

colormap's People

Contributors

Stargazers

Watchers

Forkers

alexsavio fergui mvrozanti akronix mshriver eumiro

colormap's Issues

impor pbl on some systems

looks like this code in version 0.9.5 is causing trouble on some systems (python 2.7.3)

     36 c = Colormap()
---> 37 colormap_names = c.colormaps + c.diverging_black
     38 # create an alias to test_colormap methiod
     39 test_colormap = c.test_colormap
http://www.bioconductor.org/packages/release/bioc/html/MEIGOR.html

improve api for cmap_builder

cmap_builder('red_black_yellow')

if not found in standard cmap, split by underscore and create linear cmap

Interaction issue between GDSCTools, Reports and Colormap

I've got an issue when running the test suite of GDSCTools. There are many ways to fix it, but I think the most natural fix is in the colormap package, hence this issue. Feel free to move it to one of the other repos if you think that's more appropriate.

The fix I'm proposing is that the cmap_builder-function should check if there is only one parameter given and it is already a matplotlib cmap, it should simply return that cmap.

A solution would look roughly like this:

from matplotlib.colors import Colormap as MPLColormap
...
def cmap_builder(name, name2=None, name3=None):
    ...
    elif name in c.colormaps:
        return c.cmap(name)
    elif isinstance(name, MPLColormap):   # Proposed addition
        return name

This issue arises from the following code:
In GDCTools.anova_results:

class ANOVAResults(object):
    ....
    def get_html_table(...):
        ....
        cmap_clip = cmap_builder('#ffffff', '#0070FF')
        ...
        html.add_bgcolor(this, cmap_clip, mode='clip', threshold=clip_threshold)

The add_bgcolor comes from reports.HTMLTable class:

    def add_bgcolor(self, colname, cmap='copper', mode='absmax', threshold=2):
        ....
        cmap = cmap_builder(cmap)

So this last cmap_builder gets called with an object that's already a matplotlib colormap.

If you're happy with the above solution, I can submit a PR. If you want to fix it in Reports or GDSCTools, please let me know.

how to build colormap

hello, i confused about how to create a colormap using the exists colormap like 'RdYIGn', and then i want to give it a value, and it come back me a color value, so i can use this color to opencv for draw points.
The purpose i use colormap is to enable my points'color change according to it's x value.
Thanks!

Required module easydev not installed through pip

$ pip install colormap
$ python3

>>> import colormap
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/bers/.local/lib/python3.8/site-packages/colormap/__init__.py", line 31, in <module>
    from . import colors
  File "/home/bers/.local/lib/python3.8/site-packages/colormap/colors.py", line 26, in <module>
    from easydev.tools import check_param_in_list, swapdict, check_range
ModuleNotFoundError: No module named 'easydev'

name provided nipy_spectral is not recognised when trying to build for Python 3.8

Hi,
Debian is moving to Python3.8 and I'm trying to update the Debian package of colormap. Unfortunately I get a build time test error:

test_get_cmap.test_get_cmap ... ERROR

======================================================================
ERROR: test_get_cmap.test_get_cmap
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/build/python-colormap-1.0.2/.pybuild/cpython3_3.8_colormap/build/test/test_get_cmap.py", line 7, in test_get_cmap
    get_cmap("nipy_spectral")
  File "/build/python-colormap-1.0.2/.pybuild/cpython3_3.8_colormap/build/colormap/get_cmap.py", line 57, in cmap_builder
    raise ValueError(txt)
ValueError: name provided nipy_spectral is not recognised.
 valid name can be found in colormap.colormap_names

----------------------------------------------------------------------
Ran 13 tests in 0.168s

FAILED (errors=1)

Any idea how to fix this?
BTW, it would help if you would tag colormap releases also on Github (not only on PyPI).
Kind regards; Andreas.

matplotlib 3.1.0 removed mlab

https://matplotlib.org/3.1.0/api/api_changes.html#matplotlib-mlab-removals

This leads to errors like

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-515-01410588794d> in <module>
      1 mycmap = c.cmap_linear('red', 'white', 'green(w3c)')
----> 2 c.test_colormap(mycmap)

~/miniconda3/envs/cfd/lib/python3.7/site-packages/colormap/colors.py in test_colormap(self, cmap)
    932             cmap = self.get_cmap_heat()
    933         import numpy as np
--> 934         from pylab import clf, pcolor, colorbar, show, linspace, axis
    935         A, B = np.meshgrid(linspace(0, 10, 100), linspace(0, 10, 100))
    936         clf()

~/miniconda3/envs/cfd/lib/python3.7/site-packages/pylab.py in <module>
----> 1 from matplotlib.pylab import *
      2 import matplotlib.pylab
      3 __doc__ = matplotlib.pylab.__doc__

~/miniconda3/envs/cfd/lib/python3.7/site-packages/matplotlib/pylab.py in <module>
    231 ## We are still importing too many things from mlab; more cleanup is needed.
    232 
--> 233 from matplotlib.mlab import (
    234     amap, base_repr, binary_repr, bivariate_normal, center_matrix, csv2rec,
    235     demean, detrend, detrend_linear, detrend_mean, detrend_none, dist,

ImportError: cannot import name 'amap' from 'matplotlib.mlab' (~/miniconda3/envs/cfd/lib/python3.7/site-packages/matplotlib/mlab.py)

How is this different then the colormaps already provided in matplotlib?

matplotlib already has colormap functionality; I see that you're already using it (https://github.com/cokelaer/colormap/blob/master/src/colormap/colors.py#L717).

What functionality does this library provide that isn't already in matplotlib?

"TypeError: string indices must be integers" when using predefined colormaps

Hello. I have this code:

from colormap import Colormap
c = Colormap()
mycmap = c.cmap('YlGnBu')

When I run that, I get the following error on the last line:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/akronix/.pyenv/versions/wikichron/lib/python3.6/site-packages/colormap/colors.py", line 860, in cmap
    index = np.linspace(0, 1, len(colors['red']))
TypeError: string indices must be integers

However, it does work if I create a colormap with key RGB values:

from colormap import Colormap
c = Colormap() 
mycmap = c.cmap( {'red':[1,1,0], 'green':[0,1,.39], 'blue':[0,1,0]})

The versions I'm using of the related packages are:

colormap==1.0.2
numpy==1.17.2

Any idea how to fix it or why I'm getting this error while other people are not?

from colormap import Colormap
c = Colormap()
mycmap = c.cmap_linear('red', 'black', 'green')
cmap = c.test_colormap(mycmap)