Mercurial > repos > kls286 > chap_test_20230328

comparison MLaaS/mnist_img.py @ 0:cbbe42422d56 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
author kls286
date Tue, 28 Mar 2023 15:07:30 +0000
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-1:000000000000 0:cbbe42422d56
1 #!/usr/bin/env python
2 #-*- coding: utf-8 -*-
3 #pylint: disable=
4 """
5 File : mnist_img.py
6 Author : Valentin Kuznetsov <vkuznet AT gmail dot com>
7 Description:
8 """
9
10 import json
11 import gzip
12 import argparse
13 # from itertools import chain
14
15 import numpy as np
16 import matplotlib.pyplot as plt
17
18
19 def readImage(fname, fout, num_images=5, imgId=2):
20 """
21 Helper function to read MNIST image
22 """
23 image_size = 28
24 with gzip.open(fname, 'r') as fstream:
25 fstream.read(16)
26 buf = fstream.read(image_size * image_size * num_images)
27 data = np.frombuffer(buf, dtype=np.uint8).astype(np.float32)
28 data = data.reshape(num_images, image_size, image_size, 1)
29 image = np.asarray(data[imgId]).squeeze()
30 plt.imsave(fout, image)
31 print("read:", fname, "wrote:", fout, "image:", type(image), "shape:", image.shape)
32
33 def img2json(image):
34 """
35 Convert given image to JSON data format used by TFaaS
36 """
37 # values = [int(i) for i in list(chain.from_iterable(image))]
38 # values = image.tolist()
39 values = []
40 for row in image.tolist():
41 row = [int(i) for i in row]
42 vals = [[i] for i in row]
43 values.append(vals)
44 # final values should be an array of elements, e.g. single image representation
45 values = [values]
46 keys = [str(i) for i in range(0, 10)]
47 meta = {
48 'keys': keys,
49 'values': values,
50 'model': 'mnist'
51 }
52 with open('img.json', 'w') as ostream:
53 ostream.write(json.dumps(meta))
54
55
56 class OptionParser():
57 def __init__(self):
58 "User based option parser"
59 fname = "train-images-idx3-ubyte.gz"
60 self.parser = argparse.ArgumentParser(prog='PROG')
61 self.parser.add_argument("--fin", action="store",
62 dest="fin", default=fname, help=f"Input MNIST file, default {fname}")
63 self.parser.add_argument("--fout", action="store",
64 dest="fout", default="img.png", help="Output image fila name, default img.png")
65 self.parser.add_argument("--nimages", action="store",
66 dest="nimages", default=5, help="number of images to read, default 5")
67 self.parser.add_argument("--imgid", action="store",
68 dest="imgid", default=2, help="image index to use from nimages, default 2 (number 4)")
69
70 def main():
71 """
72 main function to produce image file from mnist dataset.
73 MNIST dataset can be downloaded from
74 curl -O http://yann.lecun.com/exdb/mnist/train-images-idx3-ubyte.gz
75 """
76 optmgr = OptionParser()
77 opts = optmgr.parser.parse_args()
78 num_images = int(opts.nimages)
79 imgId = int(opts.imgid)
80 img = readImage(opts.fin, opts.fout, num_images, imgId)
81
82 if __name__ == '__main__':
83 main()