data.py

# Compatability Imports
from __future__ import print_function
from os.path import isfile, join

import segyio
from os import listdir
import numpy as np
import scipy.misc


def readSEGY(filename):
    print('Loading data cube from',filename,'with:')

    # Read full data cube
    data = segyio.tools.cube(filename)

    # Put temporal axis first
    data = np.moveaxis(data, -1, 0)

    #Make data cube fast to acess
    data = np.ascontiguousarray(data,'float32')

    #Read meta data
    segyfile = segyio.open(filename, "r")
    print('  Crosslines: ', segyfile.xlines[0], ':', segyfile.xlines[-1])
    print('  Inlines:    ', segyfile.ilines[0], ':', segyfile.ilines[-1])
    print('  Timeslices: ', '1', ':', data.shape[0])

    #Make dict with cube-info
    data_info = {}
    data_info['crossline_start'] = segyfile.xlines[0]
    data_info['inline_start'] = segyfile.ilines[0]
    data_info['timeslice_start'] = 1 #Todo: read this from segy
    data_info['shape'] = data.shape
    #Read dt and other params needed to do create a new


    return data, data_info

# Writes out_cube to a segy-file (out_filename) with same header/size as in_filename
def writeSEGY(out_filename, in_filename, out_cube):
    #Select last channel
    if type(out_cube) is list:
        out_cube = out_cube[-1]

    print('Writing interpretation to ' + out_filename)
    #Copy segy file
    from shutil import copyfile
    copyfile(in_filename, out_filename)

    # Moving temporal axis back again
    out_cube = np.moveaxis(out_cube, 0,-1)

    #Open out-file
    with segyio.open(out_filename, "r+") as src:
        iline_start = src.ilines[0]
        dtype = src.iline[iline_start].dtype
        # loop through inlines and insert output
        for i in src.ilines:
            iline = out_cube[i-iline_start,:,:]
            src.iline[i] = np.ascontiguousarray(iline.astype(dtype))

    # Moving temporal axis first again - just in case the user want to keep working on it
    out_cube = np.moveaxis(out_cube, -1, 0)

    print('Writing interpretation - Finished')
    return

#Alternative writings for slice-type
inline_alias = ['inline','in-line','iline','y']
crossline_alias = ['crossline','cross-line','xline','x']
timeslice_alias = ['timeslice','time-slice','t','z','depthslice','depth']

# Read labels from an image
def readLabels(foldername, data_info):
    files = [f for f in listdir(foldername) if isfile(join(foldername, f))]

    label_imgs = []
    label_coordinates = {}


    #Find image files in folder
    for file in files:
        if file[-3:].lower() in ['jpg','png','peg', 'bmp','gif'] and file[0] !='.':
            if True:
                tmp = file.split('_')
                slice_type = tmp[0].lower()
                tmp = tmp[1].split('.')
                slice_no = int(tmp[0])

                if slice_type not in inline_alias + crossline_alias + timeslice_alias:
                    print('File:', file, 'could not be loaded.', 'Unknown slice type')
                    continue

                if slice_type in inline_alias:
                    slice_type = 'inline'
                if slice_type in crossline_alias:
                    slice_type = 'crossline'
                if slice_type in timeslice_alias:
                    slice_type = 'timeslice'

                #Read file
                print('Loading labels for', slice_type, slice_no, 'with')
                img =  scipy.misc.imread(join(foldername, file))
                img = interpolate_to_fit_data(img, slice_type, slice_no, data_info)
                label_img = parseLabelsInImage(img)

                #Get coordinates for slice
                coords = get_coordinates_for_slice(slice_type, slice_no, data_info)

                #Loop through labels in label_img and append to label_coordinates
                for cls in np.unique(label_img):
                    if cls > -1:
                        if str(cls) not in label_coordinates.keys():
                            label_coordinates[str(cls)] = np.array(np.zeros([3,0]))
                        inds_with_cls = label_img==cls
                        cords_with_cls = coords[:, inds_with_cls.ravel()]
                        label_coordinates[str(cls)]  = np.concatenate( (label_coordinates[str(cls)] , cords_with_cls), 1)
                        print(' ', str(np.sum(inds_with_cls)), 'labels for class',str(cls))
                if len(np.unique(label_img)) == 1:
                    print(' ', 0, 'labels', str(cls))

                #Add label_img to output
                label_imgs.append([label_img, slice_type, slice_no])

            #except:
            #    print('File:', file, 'could not be loaded.')
    return label_imgs, label_coordinates

# Add colors to this table to make it possible to have more classes
class_color_coding =[
    [0,0,255], #blue
    [0,255,0], #green
    [0,255,255],  #cyan
    [255,0,0], #red
    [255,0,255],  #blue
    [255,255,0]  #yellow
]

#Convert RGB image to class img
def parseLabelsInImage(img):
    label_img = np.int16(img[:,:,0])*0 -1 # -1 = no class

    #decompose color channels (#Alpha is ignored)
    r = img[:,:,0]
    g = img[:,:,1]
    b = img[:,:,2]

    #Alpha channel
    if img.shape[2] == 4:
        a = 1-img.shape[2]//255
        r = r * a
        g = g * a
        b = b * a


    tolerance = 1
    #Go through classes and find pixels with this class
    cls = 0
    for color in class_color_coding:
        #Find pixels with these labels
        inds =  (np.abs(r - color[0]) < tolerance) & \
                (np.abs(g - color[1]) < tolerance) & \
                (np.abs(b - color[2]) < tolerance)
        label_img[inds] = cls
        cls +=1

    return label_img

# Function to resize image if needed
def interpolate_to_fit_data(img, slice_type, slice_no, data_info):
    #Get wanted output size
    if slice_type == 'inline':
        n0 = data_info['shape'][0]
        n1 = data_info['shape'][2]
    elif slice_type == 'crossline':
        n0 = data_info['shape'][0]
        n1 = data_info['shape'][1]
    elif slice_type == 'timeslice':
        n0 = data_info['shape'][1]
        n1 = data_info['shape'][2]
    return scipy.misc.imresize(img, (n0,n1), interp='nearest')

# Get coordinates for slice in the full cube
def get_coordinates_for_slice( slice_type, slice_no, data_info):
    ds = data_info['shape']

    #Coordinates for cube
    x0,x1,x2 = np.meshgrid( np.linspace(0, ds[0] - 1, ds[0]),
                               np.linspace(0, ds[1] - 1, ds[1]),
                               np.linspace(0, ds[2] - 1, ds[2]),
                              indexing='ij')
    if slice_type == 'inline':
        start = data_info['inline_start']
        slice_no = slice_no - start

        x0 = x0[:, slice_no, :]
        x1 = x1[:, slice_no, :]
        x2 = x2[:, slice_no, :]
    elif slice_type == 'crossline':
        start = data_info['crossline_start']
        slice_no = slice_no - start
        x0 = x0[:, :, slice_no]
        x1 = x1[:, :, slice_no]
        x2 = x2[:, :, slice_no]


    elif slice_type == 'timeslice':
        start = data_info['timeslice_start']
        slice_no = slice_no - start
        x0 = x0[slice_no, :, :]
        x1 = x1[slice_no, :, :]
        x2 = x2[slice_no, :, :]

    #Collect indexes
    x0 = np.expand_dims(x0.ravel(), 0)
    x1 = np.expand_dims(x1.ravel(), 0)
    x2 = np.expand_dims(x2.ravel(), 0)
    coords = np.concatenate((x0,x1,x2), axis=0)

    return coords

# Return data-slice
def get_slice(data, data_info, slice_type, slice_no, window=0):

    if slice_type == 'inline':
        start = data_info['inline_start']
        slice_no = slice_no - start

        slice = data[:, slice_no-window:slice_no+window+1, :]
    elif slice_type == 'crossline':
        start = data_info['crossline_start']
        slice_no = slice_no - start
        slice = data[:, slice_no-window:slice_no+window+1, :]

    elif slice_type == 'timeslice':
        start = data_info['timeslice_start']
        slice_no = slice_no - start
        slice = data[:, slice_no-window:slice_no+window+1, :]

    return np.squeeze(slice)