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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Copyright © 2014 German Neuroinformatics Node (G-Node)
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted under the terms of the BSD License. See
LICENSE file in the root of the Project.
Author: Jan Grewe <jan.grewe@g-node.org>
We use the "Lenna" image in this tutorial.
"Lenna" by Original full portrait: "Playmate of the Month". Playboy
Magazine. November 1972, photographed by Dwight Hooker.This 512x512
electronic/mechanical scan of a section of the full portrait:
Alexander Sawchuk and two others[1] - The USC-SIPI image
database. Via Wikipedia -
http://en.wikipedia.org/wiki/File:Lenna.png#mediaviewer/File:Lenna.png
"""
import nixio as nix
import numpy as np
from PIL import Image as img
import docutils
def load_image():
image = img.open('lenna.png')
pix = np.array(image)
channels = list(image.mode)
return pix, channels
def draw_rect(img_data, position, extent):
img_data[position[0]:position[0] + extent[0], position[1], :] = 255
img_data[position[0]:position[0] + extent[0], position[1] + extent[1], :] = 255
img_data[position[0], position[1]:position[1] + extent[1], :] = 255
img_data[position[0] + extent[0], position[1]:position[1] + extent[1], :] = 255
def plot_data(tag):
data_array = tag.references[0]
img_data = np.zeros(data_array.shape)
data_array.read_direct(img_data)
img_data = np.array(img_data, dtype='uint8')
# positions and extents are double by default, need to convert to int
pos = tuple(map(int, tag.position))
ext = tuple(map(int, tag.extent))
draw_rect(img_data, pos, ext)
new_img = img.fromarray(img_data)
if not docutils.is_running_under_pytest():
# new_img.save("../images/single_roi.png")
new_img.show()
def main():
img_data, channels = load_image()
# create a new file overwriting any existing content
file_name = 'single_roi.nix'
f = nix.File.open(file_name, nix.FileMode.Overwrite)
# create a 'Block' that represents a grouping object. Here, the recording session.
# it gets a name and a type
block = f.create_block("block name", "nix.session")
# create a 'DataArray' to take the sinewave, add some information about the signal
data = block.create_data_array("lenna", "nix.image.rgb", data=img_data)
# add descriptors for width, height and channels
data.append_sampled_dimension(1, label="height")
data.append_sampled_dimension(1, label="width")
data.append_set_dimension(labels=channels)
# create a Tag, position and extent must be 3-D since the data is 3-D
position = [250, 250, 0]
extent = [30, 100, 3]
tag = block.create_tag('Region of interest', 'nix.roi', position)
tag.extent = extent
tag.references.append(data)
# let's plot the data from the stored information
plot_data(tag)
f.close()
if __name__ == '__main__':
main()
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