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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>
See https://github.com/G-node/nix/wiki for more information.
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 numpy as np
import nixio as nix
import matplotlib.pyplot as plt
import docutils
from PIL import Image as img
def print_metadata_table(section, ax):
columns = ['Name', 'Value']
cell_text = []
for p in section.items():
for i, v in enumerate(p[1].values):
value = str(v)
if len(value) > 30:
value = value[:30] + '...'
if i == 0:
row_data = [p[0], value]
else:
row_data = [p[0], value]
cell_text.append(row_data)
if len(cell_text) > 0:
nrows, ncols = len(cell_text)+1, len(columns)
ax.axis('off')
the_table = ax.table(cellText=cell_text,
colLabels=columns,
loc='center')
for cell in the_table.get_children():
cell.set_height(.075)
cell.set_fontsize(16)
def load_image():
image = img.open('lenna.png')
pix = np.array(image)
channels = list(image.mode)
return pix, channels
def plot_data(data_array):
img_data = np.zeros(data_array.shape)
data_array.read_direct(img_data)
img_data = np.array(img_data, dtype='uint8')
new_img = img.fromarray(img_data)
fig = plt.figure()
img_axis = fig.add_subplot(121)
img_axis.imshow(new_img)
info_axis = fig.add_subplot(122)
print_metadata_table(data_array.metadata, info_axis)
fig.subplots_adjust(left=0.075, right=0.975, bottom=0.075, top=0.975)
if docutils.is_running_under_pytest():
plt.close()
else:
fig.savefig('image_with_metadata.png')
fig.show()
def add_image_information(nix_file):
section = nix_file.create_section('Image metadata', 'image_source')
section['Original name'] = 'Lenna'
section['Journal'] = 'Playboy Magazine'
section['Year'] = 1972
section['Month'] = 'November'
section['Author'] = 'Dwight Hooker'
section['Source'] = 'http://en.wikipedia.org/wiki/File:Lenna.png#mediaviewer/File:Lenna.png'
section['Comment'] = '512x512 electronic/mechanical scan of a section of the full portrait: Alexander Sawchuk and two others[1] - The USC-SIPI image database.'
section['Model'] = 'Lena Soederberg'
return section
if __name__ == '__main__':
img_data, channels = load_image()
# create a new file overwriting any existing content
file_name = 'image_with_source_example.h5'
file = 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 = file.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
height_dim = data.append_sampled_dimension(1)
height_dim.label = "height"
width_dim = data.append_sampled_dimension(1)
width_dim.label = "width"
color_dim = data.append_set_dimension()
color_dim.labels = channels
section = add_image_information(file)
data.metadata = section
# let's plot the data from the stored information
plot_data(data)
file.close()
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