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Merge pull request #562 from NASA-AMMOS/jr-561
Improvements to bulk_tiles and added quantize_colormap #561
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,20 @@ | ||
| # quantize_colormap.py | ||
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| ```shell | ||
| usage: quantize_colormap.py [-h] [-c COLORMAP] [-i INPUT] [-n NODATA] [-o OUTPUT_DIR] [-0] [-m] | ||
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| Generate quantized MPL colormaps from tiff files. | ||
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| options: | ||
| -h, --help show this help message and exit | ||
| -c COLORMAP, --colormap COLORMAP | ||
| matplotlib colormap to use | ||
| -i INPUT, --input INPUT | ||
| TIFF file or directory containing raw input TIFF files | ||
| -n NODATA, --nodata NODATA | ||
| nodata value | ||
| -o OUTPUT_DIR, --output_dir OUTPUT_DIR | ||
| Directory containing output colormaps | ||
| -0, --ignore_zeroes Ignore zero and under values | ||
| -m, --ignore_min Ignore min value | ||
| ``` |
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| #!/usr/bin/env python3 | ||
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| import os | ||
| import sys | ||
| import argparse | ||
| import glob | ||
| import matplotlib as mpl | ||
| import matplotlib.pyplot as plt | ||
| from matplotlib import cm | ||
| import numpy as np | ||
| from osgeo import gdal | ||
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| # https://matplotlib.org/stable/gallery/color/colormap_reference.html | ||
| cmaps = [('Perceptually Uniform Sequential', [ | ||
| 'viridis', 'plasma', 'inferno', 'magma', 'cividis']), | ||
| ('Sequential', [ | ||
| 'Greys', 'Purples', 'Blues', 'Greens', 'Oranges', 'Reds', | ||
| 'YlOrBr', 'YlOrRd', 'OrRd', 'PuRd', 'RdPu', 'BuPu', | ||
| 'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', 'YlGn']), | ||
| ('Sequential (2)', [ | ||
| 'binary', 'gist_yarg', 'gist_gray', 'gray', 'bone', 'pink', | ||
| 'spring', 'summer', 'autumn', 'winter', 'cool', 'Wistia', | ||
| 'hot', 'afmhot', 'gist_heat', 'copper']), | ||
| ('Diverging', [ | ||
| 'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', | ||
| 'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic']), | ||
| ('Cyclic', ['twilight', 'twilight_shifted', 'hsv']), | ||
| ('Qualitative', [ | ||
| 'Pastel1', 'Pastel2', 'Paired', 'Accent', | ||
| 'Dark2', 'Set1', 'Set2', 'Set3', | ||
| 'tab10', 'tab20', 'tab20b', 'tab20c']), | ||
| ('Miscellaneous', [ | ||
| 'flag', 'prism', 'ocean', 'gist_earth', 'terrain', 'gist_stern', | ||
| 'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg', | ||
| 'gist_rainbow', 'rainbow', 'jet', 'turbo', 'nipy_spectral', | ||
| 'gist_ncar'])] | ||
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| class MplColorHelper: | ||
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| def __init__(self, cmap_name, start_val, stop_val): | ||
| self.cmap_name = cmap_name | ||
| self.cmap = plt.get_cmap(cmap_name) | ||
| self.norm = mpl.colors.Normalize(vmin=start_val, vmax=stop_val) | ||
| self.scalarMap = cm.ScalarMappable(norm=self.norm, cmap=self.cmap) | ||
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| def get_rgb(self, val): | ||
| return self.scalarMap.to_rgba(val) | ||
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| def quantize_colormap_from_tiff(tiff, output_dir, colormap, nodata, ignore_zeroes, ignore_min): | ||
| print('Processing', tiff) | ||
| output_file = output_dir + '/' + os.path.basename(tiff).split('.')[0] + '.txt' | ||
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| # open the dataset and retrieve raster data as an array | ||
| dataset = gdal.Open(tiff) | ||
| array = dataset.ReadAsArray() | ||
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| # get min max values | ||
| min = np.min(array) | ||
| max = np.max(array) | ||
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| # remove 0 and negative values | ||
| if ignore_zeroes: | ||
| array = array[array > 0] | ||
| # remove min values | ||
| if ignore_min: | ||
| array = array[array != min] | ||
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| # use the numpy percentile function to calculate quantile thresholds | ||
| print('Calculating quantiles...') | ||
| print(max, min) | ||
| percentiles = [] | ||
| for i in np.arange(100, 0, -10).tolist(): | ||
| percentiles.append(np.percentile(array, i)) | ||
| percentiles.append(np.min(array)) | ||
| print(percentiles) | ||
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| print('Generating', output_file) | ||
| out = open(output_file, 'w+') | ||
| mch = MplColorHelper(colormap, 0, len(percentiles)) | ||
| for i in range(0, len(percentiles)): | ||
| val = percentiles[i] | ||
| rgba = (mch.scalarMap.to_rgba(len(percentiles)-1-i)) | ||
| r = round(rgba[0] * 255) | ||
| g = round(rgba[1] * 255) | ||
| b = round(rgba[2] * 255) | ||
| a = round(rgba[3] * 255) | ||
| out_str = ' '.join([str(round(val)), str(r), str(g), str(b), str(a)]) | ||
| out.write(out_str + '\n') | ||
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| if not str(nodata) == 'nv': | ||
| if float(nodata) <= min: | ||
| out.write(f'{str(nodata)} 0 0 0 0\n') | ||
| else: | ||
| out.write(f'nv 0 0 0 0\n') | ||
| out.seek(0) | ||
| print(out.read()) | ||
| out.close() | ||
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| parser = argparse.ArgumentParser(description='Generate quantized MPL colormaps from tiff files.') | ||
| parser.add_argument( | ||
| '-c', | ||
| '--colormap', | ||
| default='viridis', | ||
| dest='colormap', | ||
| help='matplotlib colormap to use', | ||
| action='store') | ||
| parser.add_argument( | ||
| '-i', | ||
| '--input', | ||
| default='Raw/', | ||
| dest='input', | ||
| help='TIFF file or directory containing raw input TIFF files', | ||
| action='store') | ||
| parser.add_argument( | ||
| '-n', | ||
| '--nodata', | ||
| dest='nodata', | ||
| default='nv', | ||
| help='nodata value', | ||
| action='store') | ||
| parser.add_argument( | ||
| '-o', | ||
| '--output_dir', | ||
| default='Colormaps/', | ||
| dest='output_dir', | ||
| help='Directory containing output colormaps', | ||
| action='store') | ||
| parser.add_argument( | ||
| '-0', | ||
| '--ignore_zeroes', | ||
| default=False, | ||
| dest='ignore_zeroes', | ||
| help='Ignore zero and under values', | ||
| action='store_true') | ||
| parser.add_argument( | ||
| '-m', | ||
| '--ignore_min', | ||
| default=False, | ||
| dest='ignore_min', | ||
| help='Ignore min value', | ||
| action='store_true') | ||
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| args = parser.parse_args() | ||
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| if not os.path.isdir(args.output_dir): | ||
| print(args.output_dir, 'is not a directory.') | ||
| sys.exit() | ||
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| if os.path.isfile(args.input): | ||
| quantize_colormap_from_tiff(args.input, args.output_dir, args.colormap, args.nodata, args.ignore_zeroes, args.ignore_min) | ||
| else: | ||
| print('Searching', args.input) | ||
| input_files = glob.glob(args.input + '*.tif*', recursive=True) | ||
| for input_file in input_files: | ||
| quantize_colormap_from_tiff(input_file, args.output_dir, args.colormap, args.nodata, args.ignore_zeroes, args.ignore_min) | ||
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| sys.exit() |