read_buffer.py

import numpy as np
import re
def colorvol2points(voxels):
    points = []
    rgb    = []
    for z in range(voxels.shape[0]):
        for y in range(voxels.shape[1]):
            for x in range(voxels.shape[2]):
                color = voxels[z][y][x]
                if color[0]!=0 and color[1]!=0 and color[2]!=0:
                    points.append(np.array([x, y, z]))
                    rgb.append(color)
    points = np.vstack(points)
    rgb = np.vstack(rgb)
    return {'points':points, 'rgb':rgb}

def writeply(filename, points, rgb):
    target = open(filename, 'w')

    # write the  header
    target.write('ply\n');
    target.write('format ascii 1.0 \n')
    target.write('element vertex ' + str(points.shape[0]) + '\n')
    target.write('property float x\n')
    target.write('property float y\n')
    target.write('property float z\n')
    target.write('property uchar red\n')
    target.write('property uchar green\n')
    target.write('property uchar blue\n')
    target.write('end_header\n')

    # write the  points
    for i in range(points.shape[0]):
        target.write('%f %f %f %d %d %d\n'%(points[i,0],points[i,1],points[i,2], rgb[i,0],rgb[i,1],rgb[i,2]))
    target.close()


def color_voxel_label_to_ply(voxel, output_ply):
    points = colorvol2points(voxel)
    writeply(output_ply, points['points'], points['rgb'])
    print('output: ' + output_ply)

def read_data(filename, byteorder='>'):
    """Return image data from a raw PGM file as numpy array.

    Format specification: http://netpbm.sourceforge.net/doc/pgm.html

    """
    with open(filename, 'rb') as f:
        buffer = f.read()
    try:
        header, height, width, depth, channel, maxval = re.search(
            b"(^CV\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n])*"
            b"(\d+)\s(?:\s*#.*[\r\n]\s)*)", buffer).groups()
    except AttributeError:
        raise ValueError("File header not found: '%s'" % filename)
    #print(height)
    #print(width)
    #print(depth)
    #print(channel)
    #print(maxval)
    color_voxel= np.frombuffer(buffer,
                         dtype=np.int32,
                         count=int(height)*int(width)*int(depth)*int(channel),
                         offset=len(header)
                         ).reshape((int(height), int(width), int(depth), int(channel)))
    #print(color_voxel.shape)
    return color_voxel


color_voxel = read_data('sceneXXXX_XX.dat')
print(color_voxel)
color_voxel_label_to_ply(color_voxel, "voxel.ply")