'''
utils.py: part of the nidmviewer package
Functions to work with html templates
Copyright (c) 2014-2018, Vanessa Sochat
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
'''
import numpy as np
import contextlib
import tempfile
import nibabel
import zipfile
import urllib
import shutil
import string
import numpy
import random
import os
# Split a url to just get base
[docs]def strip_url(url,encode=True):
if encode:
return url.split("/")[-1].encode("utf-8")
else:
return url.split("/")[-1]
# Get the directory of the package
[docs]def get_package_dir():
return os.path.abspath(os.path.join(os.path.dirname(__file__)))
# Make directory
[docs]def make_dir(directory):
if not os.path.exists(directory):
os.makedirs(directory)
# Unzip static files to temporary directory
[docs]def unzip(source,dest_dir):
with zipfile.ZipFile(source, "r") as z:
z.extractall(dest_dir)
# Make temporary directory
[docs]@contextlib.contextmanager
def make_tmp_folder():
temp_dir = tempfile.mkdtemp()
yield temp_dir
shutil.rmtree(temp_dir)
# Reading Files
[docs]def read_file_lines(file_name):
filey = open(file_name,'r')
file_contents = filey.readlines()
filey.close()
return file_contents
[docs]def download_file(src,dest):
try:
requester = urllib.URLopener()
requester.retrieve(src, dest)
return True
except:
print("Cannot download %s" %src)
return False
# Filenames
[docs]def get_name(path):
return os.path.split(path)[1].split(".")[0]
[docs]def get_random_name(length=6,chars=string.ascii_uppercase + string.digits):
return ''.join(random.choice(chars) for _ in range(length))
# Generate new png paths to correspond to nifti filenames
[docs]def make_png_paths(nifti_files):
image_paths = []
for i in range(0,len(mr_files)):
image = mr_files[i]
tmp_svg = "%s/tmpbrain%s.png" %(tmp_dir,i)
make_glassbrain_image(image,tmp_svg)
image_paths.append(tmp_svg)
return image_paths
[docs]def get_extension(path):
fileparts = os.path.basename(path).split(".")
fileparts.pop(0)
return ".".join(fileparts)
# Get unique values in a list of lists
[docs]def unwrap_list_unique(list_of_lists):
uniques = []
for listy in list_of_lists:
uniques = uniques + [item for item in listy]
uniques = list(np.unique(uniques))
return uniques
# Brain image templates
[docs]def get_standard_brain(load=True):
mr_directory = get_package_dir()
brain = "%s/data/MNI152_T1_2mm_brain.nii.gz" %(mr_directory)
if load:
return nib.load(brain)
else:
return brain
# Check if nifti is empty
[docs]def is_empty(nii_file):
nii = nibabel.load(nii_file)
data = nii.get_data()
data = numpy.nan_to_num(data)
if numpy.count_nonzero(data) == 0:
return 1
return 0
[docs]def get_images(peaks,location_key):
'''get_images returns unique images for a location key from
a peaks table
'''
image_list = []
for nidm,entries in peaks.items():
nidm_directory = os.path.dirname(nidm)
for e in range(len(entries)):
if location_key in entries[e]:
brainmap = entries[e][location_key]
if brainmap not in image_list:
image_list.append(brainmap)
return image_list