tem_to_iv.py

#!/usr/bin/env python

# -*- coding: utf-8 -*-

# Imports
from skimage import io

import pandas as pd

import fastparquet as fp

import numpy as np

import os

import tempfile

def readTiff(filename):
    """Read data from the tiff file and return a Pandas dataframe"""
    filenamePrefix = os.path.splitext(os.path.basename(filename))[0]

    im = io.imread(filename)

    print(im.shape[2], im.shape[1], im.shape[0])
    dataSize = im.shape[0] * im.shape[1] * im.shape[2]
    imgdata1d = im.reshape(dataSize)
    data = {
        'index': range(dataSize),
        'value': imgdata1d.astype(np.int32),
    }

    df = pd.DataFrame(data)

    return df


def writeParquet(inputFilename, df):
    """Export Pandas dataframe as Parquet"""
    filenamePrefix = os.path.splitext(os.path.basename(inputFilename))[0]
    outFilepath = os.path.join(tempfile.gettempdir(), ''.join([filenamePrefix, '.parq']))
    fp.write(outFilepath, df, compression='GZIP')
    print outFilepath	
    return outFilepath



if __name__ == "__main__":

    import argparse

    parser = argparse.ArgumentParser(description='Script to convert data in tiff format to Parquet format')
    parser.add_argument('--tiff', dest='filename', help='input tiff file')
    parser.add_argument('--hdfs', dest='hdfsroot', help='HDFS root for data upload')
    args = parser.parse_args()

    # Read TIFF file and convert it into a Pandas dataframe
    df = readTiff(args.filename)

    # Export dataframe as parquet
    outFilepath = writeParquet(args.filename, df)