def get_BIDSLayout_with_conf(dir_, **kwargs):
"""Get BIDSLayout with bids, derivatives, and pndni_bids configuration files loaded"""
if "pndni_bids" not in bids_config.get_option("config_paths"):
layout.add_config_paths(pndni_bids=resource_filename(
'pndniworkflows', 'config/pndni_bids.json'))
l = layout.BIDSLayout(dir_,
config=['bids', 'derivatives', 'pndni_bids'],
**kwargs)
return l
def __init__(self,
reportlets_dir,
out_dir,
run_uuid,
config=None,
subject_id=None,
out_filename='report.html',
packagename=None):
self.root = reportlets_dir
# Add a new figures spec
try:
add_config_paths(
figures=pkgrf('niworkflows', 'reports/figures.json'))
except ValueError as e:
if "Configuration 'figures' already exists" != str(e):
raise
# Initialize structuring elements
self.sections = []
self.errors = []
self.out_dir = Path(out_dir)
self.out_filename = out_filename
self.run_uuid = run_uuid
self.template_path = None
self.packagename = packagename
self.subject_id = subject_id
if subject_id is not None and subject_id.startswith('sub-'):
self.subject_id = self.subject_id[4:]
if self.subject_id is not None:
self.out_filename = 'sub-{}.html'.format(self.subject_id)
if config is None:
config = pkgrf('niworkflows', 'reports/fmriprep.yml')
self._load_config(Path(config))
def test_add_config_paths():
bids_dir = dirname(bids.__file__)
bids_json = os.path.join(bids_dir, 'layout', 'config', 'bids.json')
with pytest.raises(ValueError) as exc:
add_config_paths(test_config1='nonexistentpath.json')
assert str(exc.value).startswith('Configuration file')
with pytest.raises(ValueError) as exc:
add_config_paths(bids=bids_json)
assert str(exc.value).startswith("Configuration 'bids' already")
add_config_paths(dummy=bids_json)
config = Config.load('dummy')
assert 'subject' in config.entities
def test_add_config_paths():
bids_dir = dirname(bids.__file__)
bids_json = os.path.join(bids_dir, 'layout', 'config', 'bids.json')
with pytest.raises(ValueError) as exc:
add_config_paths(test_config1='nonexistentpath.json')
assert str(exc.value).startswith('Configuration file')
with pytest.raises(ValueError) as exc:
add_config_paths(bids=bids_json)
assert str(exc.value).startswith("Configuration 'bids' already")
add_config_paths(dummy=bids_json)
config = Config.load('dummy')
assert 'subject' in config.entities
from os import path as op
from pathlib import Path
import jinja2
import pkg_resources as pkgr
from bids.layout import add_config_paths, BIDSLayout
from ..utils import snake_to_camel
PATH_PATTERNS = [
'[sub-{subject}/][ses-{session}/][sub-{subject}_][ses-{session}_]'
'model-{model}[_run-{run}].html'
]
add_config_paths(fitlins=pkgr.resource_filename('fitlins', 'data/fitlins.json'))
def deroot(val, root):
if isinstance(val, str):
if val.startswith(root):
idx = len(root)
if val[idx] == '/':
idx += 1
val = val[idx:]
elif isinstance(val, list):
val = [deroot(elem, root) for elem in val]
elif isinstance(val, dict):
val = {key: deroot(value, root) for key, value in val.items()}
return val
Generalizes report generation across BIDS-Apps
"""
from pathlib import Path
import re
from itertools import compress
from collections import defaultdict
from pkg_resources import resource_filename as pkgrf
from bids.layout import BIDSLayout, add_config_paths
import jinja2
from nipype.utils.filemanip import copyfile
# Add a new figures spec
try:
add_config_paths(figures=pkgrf("niworkflows", "data/nipreps.json"))
except ValueError as e:
if "Configuration 'figures' already exists" != str(e):
raise
PLURAL_SUFFIX = defaultdict(str("s").format, [("echo", "es")])
SVG_SNIPPET = [
"""\
<object class="svg-reportlet" type="image/svg+xml" data="./{0}">
Problem loading figure {0}. If the link below works, please try \
reloading the report in your browser.</object>
</div>
<div class="elem-filename">
Get figure file: <a href="./{0}" target="_blank">{0}</a>
</div>
""",
Generalizes report generation across BIDS-Apps
"""
from pathlib import Path
import re
from itertools import product
from collections import defaultdict
from pkg_resources import resource_filename as pkgrf
from bids.layout import BIDSLayout, add_config_paths
import jinja2
from nipype.utils.filemanip import copyfile
# Add a new figures spec
try:
add_config_paths(figures=pkgrf('niworkflows', 'reports/figures.json'))
except ValueError as e:
if "Configuration 'figures' already exists" != str(e):
raise
PLURAL_SUFFIX = defaultdict(str('s').format, [('echo', 'es')])
SVG_SNIPPET = ["""\
<object class="svg-reportlet" type="image/svg+xml" data="./{0}">
Problem loading figure {0}. If the link below works, please try \
reloading the report in your browser.</object>
</div>
<div class="elem-filename">
Get figure file: <a href="./{0}" target="_blank">{0}</a>
</div>
""", """\
<img class="svg-reportlet" src="./{0}" style="width: 100%" />
"""Extending pyBIDS for querying TemplateFlow."""
from pkg_resources import resource_filename
from bids.layout import BIDSLayout, add_config_paths
add_config_paths(
templateflow=resource_filename("templateflow", "conf/config.json"))
class Layout(BIDSLayout):
def __repr__(self):
# A tidy summary of key properties
s = """\
TemplateFlow Layout
- Home: {}
- Templates: {}.""".format(self.root, ", ".join(sorted(self.get_templates())))
return s
"""
Extending pyBIDS
"""
from pkg_resources import resource_filename
from bids.layout import BIDSLayout, add_config_paths
add_config_paths(
templateflow=resource_filename('templateflow', 'conf/config.json'))
class Layout(BIDSLayout):
def __repr__(self):
# A tidy summary of key properties
s = """\
TemplateFlow Layout
- Home: {}
- Templates: {}.""".format(self.root, ', '.join(sorted(self.get_templates())))
return s
