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POMatplotlib: Colorize grayscale image using another image
 

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  1. POMatplotlib: Colorize grayscale image using another image
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    <p>I have a black and white <strong>spectrum</strong> that I want to colorize <img src="https://i.imgur.com/nQpzvUo.png" alt="spectrum"> using this <strong>colorize</strong> image. <img src="https://i.imgur.com/v27kjsY.png?1" alt="colors"></p> <p>Adapting the method given here: <a href="https://stackoverflow.com/questions/18718101/applying-different-color-map-to-mask">Applying different color map to mask</a>, I obtain a final colorized image, but it lacks the features of the <strong>spectrum</strong> (see comments in code for a link to the picture <em>finalimage</em>).</p> <p>My code is given here (with the hosted images in the comments since I cannot display all of them here):</p> <pre><code>import numpy as np import matplotlib.pyplot as plt import pyfits wavemap = "FITS/wavemap.fits.gz" spectrum = "FITS/phxspectra.fits.gz" image = pyfits.getdata(spectrum) colors = pyfits.getdata(wavemap) mask = colors &gt; 0 colors_ma = np.ma.array(colors, mask=~mask) kwargs = {'interpolation': 'none', 'vmin': colors[mask].min(), 'vmax': colors.max(), 'origin': 'lower', 'alpha' : 0.5} plt.imshow(image, cmap=plt.cm.Greys_r, interpolation='none', origin='lower') plt.imshow(colors_ma, cmap=plt.cm.jet, **kwargs) plt.show() #![spectrum](http://i.imgur.com/nQpzvUo.png) #![spectrumfeatures](http://i.imgur.com/MTQ9yMl.png) #![colorize](http://i.imgur.com/v27kjsY.png?1) #![finalimage](http://i.imgur.com/MmnM9qK) #![finalimagefeatures](http://i.imgur.com/t5PoJiE.png) </code></pre> <p>If I lower the alpha value, the features of the <strong>spectrum</strong> show better, but the colors are very dim. If I increase the alpha value, then the colors show much better, but the features of the <strong>spectrum</strong> do not show.</p> <p>How can I get the features of the <strong>spectrum</strong> <em>AND</em> the colors from the <strong>colorize</strong> image without trading off one for the other?</p>
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    1. COI don't understand what you are trying to achieve....What are these arrays physically (I assume some sort of astro data)? Is the spectrum array just a vertical gradient sampled along the streaks?
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    2. COI'm sorry, I realize the naming convention is very confusing. Physically, the arrays are 2d spectrums. For the **spectrum** array, each value is a luminance or intensity value. For the **colorize** array, coordinate values give the wavelength, or color, of the image, which results in the rainbow gradient.
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    3. COWhat are the axes? wave length and time? k and omega? what does the white in the second image you posted mean?
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