def read_iqms(feat_file):
""" Reads in the features """
bids_comps = list(BIDS_COMP.keys())
x_df = pd.read_csv(feat_file,
index_col=False,
dtype={col: str
for col in bids_comps})
# Find present bids bits and sort by them
bids_comps_present = list(
set(x_df.columns.ravel().tolist()) & set(bids_comps))
x_df = x_df.sort_values(by=bids_comps_present)
# Remove sub- prefix in subject_id
x_df.subject_id = x_df.subject_id.str.lstrip('sub-')
# Remove columns that are not IQMs
feat_names = list(x_df._get_numeric_data().columns.ravel())
for col in bids_comps:
try:
feat_names.remove(col)
except ValueError:
pass
for col in feat_names:
if col.startswith(('size_', 'spacing_', 'Unnamed')):
feat_names.remove(col)
return x_df, feat_names, bids_comps_present
def combine_datasets(inputs, rating_label="rater_1"):
mdata = []
for dataset_x, dataset_y, sitename in inputs:
sitedata, _ = read_dataset(
dataset_x,
dataset_y,
rate_label=rating_label,
binarize=True,
site_name=sitename,
)
sitedata["database"] = [sitename] * len(sitedata)
if "site" not in sitedata.columns.ravel().tolist():
sitedata["site"] = [sitename] * len(sitedata)
mdata.append(sitedata)
mdata = pd.concat(mdata)
all_cols = mdata.columns.ravel().tolist()
bids_comps = list(BIDS_COMP.keys())
bids_comps_present = list(set(mdata.columns.ravel().tolist()) & set(bids_comps))
bids_comps_present = [bit for bit in bids_comps if bit in bids_comps_present]
ordered_cols = bids_comps_present + ["database", "site", "rater_1"]
ordered_cols += sorted(list(set(all_cols) - set(ordered_cols)))
return mdata[ordered_cols]
def _run_interface(self, runtime):
out_file = self._gen_outfile()
if isdefined(self.inputs.root):
self._out_dict = self.inputs.root
root_adds = []
for key, val in list(self.inputs._outputs.items()):
if not isdefined(val) or key == 'trait_added':
continue
if not self.expr.match(key) is None:
root_adds.append(key)
continue
key, val = _process_name(key, val)
self._out_dict[key] = val
for root_key in root_adds:
val = self.inputs._outputs.get(root_key, None)
if isinstance(val, dict):
self._out_dict.update(val)
else:
IFLOGGER.warn(
'Output "%s" is not a dictionary (value="%s"), '
'discarding output.', root_key, str(val))
id_dict = {}
for comp in list(BIDS_COMP.keys()):
comp_val = getattr(self.inputs, comp, None)
if isdefined(comp_val) and comp_val is not None:
id_dict[comp] = comp_val
if self.inputs.modality == 'bold':
id_dict['qc_type'] = 'func'
elif self.inputs.modality == 'T1w':
id_dict['qc_type'] = 'anat'
if self._out_dict.get('metadata', None) is None:
self._out_dict['metadata'] = {}
self._out_dict['metadata'].update(id_dict)
with open(out_file, 'w') as f:
f.write(
json.dumps(self._out_dict,
sort_keys=True,
indent=2,
ensure_ascii=False))
return runtime
def read_iqms(feat_file):
"""Read in a features table."""
feat_file = Path(feat_file)
if feat_file.suffix == ".csv":
bids_comps = list(BIDS_COMP.keys())
x_df = pd.read_csv(feat_file,
index_col=False,
dtype={col: str
for col in bids_comps})
# Find present bids bits and sort by them
bids_comps_present = list(
set(x_df.columns.ravel().tolist()) & set(bids_comps))
bids_comps_present = [
bit for bit in bids_comps if bit in bids_comps_present
]
x_df = x_df.sort_values(by=bids_comps_present)
# Remove sub- prefix in subject_id
x_df.subject_id = x_df.subject_id.str.lstrip("sub-")
# Remove columns that are not IQMs
feat_names = list(x_df._get_numeric_data().columns.ravel())
for col in bids_comps:
try:
feat_names.remove(col)
except ValueError:
pass
else:
bids_comps_present = ["subject_id"]
x_df = pd.read_csv(feat_file,
index_col=False,
sep="\t",
dtype={"bids_name": str})
x_df = x_df.sort_values(by=["bids_name"])
x_df["subject_id"] = x_df.bids_name.str.lstrip("sub-")
x_df = x_df.drop(columns=["bids_name"])
x_df.subject_id = [
"_".join(v.split("_")[:-1]) for v in x_df.subject_id.ravel()
]
feat_names = list(x_df._get_numeric_data().columns.ravel())
for col in feat_names:
if col.startswith(("size_", "spacing_", "Unnamed")):
feat_names.remove(col)
return x_df, feat_names, bids_comps_present
def read_labels(label_file, rate_label='rate', binarize=True):
""" Reads in the labels """
# Massage labels table to have the appropriate format
bids_comps = list(BIDS_COMP.keys())
y_df = pd.read_csv(label_file,
index_col=False,
dtype={col: str
for col in bids_comps})
# Find present bids bits and sort by them
bids_comps_present = list(
set(y_df.columns.ravel().tolist()) & set(bids_comps))
y_df = y_df.sort_values(by=bids_comps_present)
y_df.subject_id = y_df.subject_id.str.lstrip('sub-')
# Convert string labels to ints
try:
y_df.loc[y_df[rate_label].str.contains('fail', case=False, na=False),
rate_label] = -1
y_df.loc[
y_df[rate_label].str.contains('exclude', case=False, na=False),
rate_label] = -1
y_df.loc[y_df[rate_label].str.contains('maybe', case=False, na=False),
rate_label] = 0
y_df.loc[y_df[rate_label].str.contains('may be', case=False, na=False),
rate_label] = 0
y_df.loc[y_df[rate_label].str.contains('ok', case=False, na=False),
rate_label] = 1
y_df.loc[y_df[rate_label].str.contains('good', case=False, na=False),
rate_label] = 1
except AttributeError:
pass
y_df[[rate_label]] = y_df[[rate_label]].apply(pd.to_numeric,
errors='raise')
if binarize:
y_df.loc[y_df[rate_label] >= 0, rate_label] = 0
y_df.loc[y_df[rate_label] < 0, rate_label] = 1
return y_df[bids_comps_present + ['site', rate_label]]
def get_bids_cols(dataframe):
""" Returns columns corresponding to BIDS bits """
bids_comps = list(BIDS_COMP.keys())
bids_comps_present = list(set(dataframe.columns.ravel().tolist()) & set(bids_comps))
return [bit for bit in bids_comps if bit in bids_comps_present]
def read_dataset(
feat_file,
label_file,
merged_name=None,
binarize=True,
site_name=None,
rate_label="rater_1",
rate_selection="random",
):
""" Reads in the features and labels """
x_df, feat_names, _ = read_iqms(feat_file)
y_df = read_labels(
label_file,
rate_label,
binarize,
collapse=True,
site_name=site_name,
rate_selection=rate_selection,
)
if isinstance(rate_label, (list, tuple)):
rate_label = rate_label[0]
# Find present bids bits and sort by them
bids_comps = list(BIDS_COMP.keys())
bids_comps_x = list(set(x_df.columns.ravel().tolist()) & set(bids_comps))
bids_comps_x = [bit for bit in bids_comps if bit in bids_comps_x]
bids_comps_y = list(set(x_df.columns.ravel().tolist()) & set(bids_comps))
bids_comps_y = [bit for bit in bids_comps if bit in bids_comps_y]
if bids_comps_x != bids_comps_y:
raise RuntimeError("Labels and features cannot be merged")
x_df["bids_ids"] = x_df.subject_id.values.copy()
y_df["bids_ids"] = y_df.subject_id.values.copy()
for comp in bids_comps_x[1:]:
x_df["bids_ids"] = x_df.bids_ids.str.cat(x_df.loc[:, comp].astype(str), sep="_")
y_df["bids_ids"] = y_df.bids_ids.str.cat(y_df.loc[:, comp].astype(str), sep="_")
# Remove failed cases from Y, append new columns to X
y_df = y_df[y_df["bids_ids"].isin(list(x_df.bids_ids.values.ravel()))]
# Drop indexing column
del x_df["bids_ids"]
del y_df["bids_ids"]
# Merge Y dataframe into X
x_df = pd.merge(x_df, y_df, on=bids_comps_x, how="left")
if merged_name is not None:
x_df.to_csv(merged_name, index=False)
# Drop samples with invalid rating
nan_labels = x_df[x_df[rate_label].isnull()].index.ravel().tolist()
if nan_labels:
message = DROPPING_NON_NUMERICAL.format(n_labels=len(nan_labels))
config.loggers.interface.info(message)
x_df = x_df.drop(nan_labels)
# Print out some info
n_samples = len(x_df)
ds_created_message = CREATED_DATASET.format(
feat_file=feat_file, label_file=label_file, n_samples=n_samples
)
config.loggers.interface.info(ds_created_message)
# Inform about ratings distribution
labels = sorted(set(x_df[rate_label].values.ravel().tolist()))
ldist = [int(np.sum(x_df[rate_label] == label)) for label in labels]
config.loggers.interface.info(
"Ratings distribution: %s (%s, %s)",
"/".join(["%d" % x for x in ldist]),
"/".join(["%.2f%%" % (100 * x / n_samples) for x in ldist]),
"accept/exclude" if len(ldist) == 2 else "exclude/doubtful/accept",
)
return x_df, feat_names
def read_labels(
label_file,
rate_label="rater_1",
binarize=True,
site_name=None,
rate_selection="random",
collapse=True,
):
"""
Reads in the labels. Massage labels table to have the
appropriate format
"""
if isinstance(rate_label, str):
rate_label = [rate_label]
output_labels = rate_label
bids_comps = list(BIDS_COMP.keys())
y_df = pd.read_csv(
label_file, index_col=False, dtype={col: str for col in bids_comps}
)
# Find present bids bits and sort by them
bids_comps_present = get_bids_cols(y_df)
y_df = y_df.sort_values(by=bids_comps_present)
y_df.subject_id = y_df.subject_id.str.lstrip("sub-")
y_df[rate_label] = y_df[rate_label].apply(pd.to_numeric, errors="raise")
if len(rate_label) == 2:
np.random.seed(42)
ratermask_1 = ~np.isnan(y_df[[rate_label[0]]].values.ravel())
ratermask_2 = ~np.isnan(y_df[[rate_label[1]]].values.ravel())
all_rated = ratermask_1 & ratermask_2
mergey = np.array(y_df[[rate_label[0]]].values.ravel().tolist())
mergey[ratermask_2] = y_df[[rate_label[1]]].values.ravel()[ratermask_2]
subsmpl = np.random.choice(
np.where(all_rated)[0], int(0.5 * np.sum(all_rated)), replace=False
)
all_rated[subsmpl] = False
mergey[all_rated] = y_df[[rate_label[0]]].values.ravel()[all_rated]
y_df["merged_ratings"] = mergey.astype(int)
# Set default name
if collapse:
cols = [
("indv_%s" % c) if c.startswith("rater") else c
for c in y_df.columns.ravel().tolist()
]
cols[y_df.columns.get_loc("merged_ratings")] = rate_label[0]
y_df.columns = cols
output_labels = [rate_label[0]]
else:
output_labels = rate_label
output_labels.insert(0, "merged_ratings")
if binarize:
mask = y_df[output_labels[0]] >= 0
y_df.loc[mask, output_labels[0]] = 0
y_df.loc[~mask, output_labels[0]] = 1
if "site" in y_df.columns.ravel().tolist():
output_labels.insert(0, "site")
elif site_name is not None:
y_df["site"] = [site_name] * len(y_df)
output_labels.insert(0, "site")
return y_df[bids_comps_present + output_labels]
def individual_html(in_iqms, in_plots=None):
import os.path as op #pylint: disable=W0404
import datetime
from json import load
from mriqc import logging, __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports.utils import iqms2html, read_report_snippet
from mriqc.data import IndividualTemplate
from io import open #pylint: disable=W0622
report_log = logging.getLogger('mriqc.report')
def _get_details(in_iqms, modality):
in_prov = in_iqms.pop('provenance', {})
warn_dict = in_prov.pop('warnings', None)
sett_dict = in_prov.pop('settings', None)
wf_details = []
if modality == 'bold':
bold_exclude_index = in_iqms.get('dumb_trs')
if bold_exclude_index is None:
report_log.warning('Building bold report: no exclude index was found')
elif bold_exclude_index > 0:
msg = """\
<span class="problematic">Non-steady state (strong T1 contrast) has been detected in the \
first {} volumes</span>. They were excluded before generating any QC measures and plots."""
wf_details.append(msg.format(bold_exclude_index))
hmc_fsl = sett_dict.pop('hmc_fsl')
if hmc_fsl is not None:
msg = 'Framewise Displacement was computed using '
if hmc_fsl:
msg += 'FSL <code>mcflirt</code>'
else:
msg += 'AFNI <code>3dvolreg</code>'
wf_details.append(msg)
fd_thres = sett_dict.pop('fd_thres')
if fd_thres is not None:
wf_details.append(
'Framewise Displacement threshold was defined at %f mm' % fd_thres)
elif modality in ('T1w', 'T2w'):
if warn_dict.pop('small_air_mask', False):
wf_details.append(
'<span class="problematic">Detected hat mask was too small</span>')
if warn_dict.pop('large_rot_frame', False):
wf_details.append(
'<span class="problematic">Detected a zero-filled frame, has the original '
'image been rotated?</span>')
return in_prov, wf_details
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
if in_plots is None:
in_plots = []
# Extract and prune metadata
metadata = iqms_dict.pop('bids_meta', None)
mod = metadata.pop('modality', None)
prov, wf_details = _get_details(iqms_dict, mod)
file_id = [metadata.pop(k, None)
for k in list(BIDS_COMP.keys())]
file_id = [comp for comp in file_id if comp is not None]
pred_qa = None #metadata.pop('mriqc_pred', None)
config = {
'modality': mod,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': [read_report_snippet(pfile) for pfile in in_plots],
'workflow_details': wf_details,
'provenance': iqms2html(prov, 'provenance-table'),
'metadata': iqms2html(metadata, 'metadata-table'),
'pred_qa': pred_qa
}
if config['metadata'] is None:
config['workflow_details'].append(
'<span class="warning">File has no metadata</span> '
'<span>(sidecar JSON file missing or empty)</span>')
tpl = IndividualTemplate()
tpl.generate_conf(config, out_file)
report_log.info('Generated individual log (%s)', out_file)
return out_file
def individual_html(in_iqms, in_plots=None):
from os import path as op
import datetime
from json import load
from mriqc import logging, __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports import REPORT_TITLES
from mriqc.reports.utils import iqms2html, read_report_snippet
from mriqc.data import IndividualTemplate
report_log = logging.getLogger('mriqc.report')
def _get_details(in_iqms, modality):
in_prov = in_iqms.pop('provenance', {})
warn_dict = in_prov.pop('warnings', None)
sett_dict = in_prov.pop('settings', None)
wf_details = []
if modality == 'bold':
bold_exclude_index = in_iqms.get('dumb_trs')
if bold_exclude_index is None:
report_log.warning(
'Building bold report: no exclude index was found')
elif bold_exclude_index > 0:
msg = """\
<span class="problematic">Non-steady state (strong T1 contrast) has been detected in the \
first {} volumes</span>. They were excluded before generating any QC measures and plots."""
wf_details.append(msg.format(bold_exclude_index))
hmc_fsl = sett_dict.pop('hmc_fsl')
if hmc_fsl is not None:
msg = 'Framewise Displacement was computed using '
if hmc_fsl:
msg += 'FSL <code>mcflirt</code>'
else:
msg += 'AFNI <code>3dvolreg</code>'
wf_details.append(msg)
fd_thres = sett_dict.pop('fd_thres')
if fd_thres is not None:
wf_details.append(
'Framewise Displacement threshold was defined at %f mm' %
fd_thres)
elif modality in ('T1w', 'T2w'):
if warn_dict.pop('small_air_mask', False):
wf_details.append(
'<span class="problematic">Detected hat mask was too small</span>'
)
if warn_dict.pop('large_rot_frame', False):
wf_details.append(
'<span class="problematic">Detected a zero-filled frame, has the original '
'image been rotated?</span>')
return in_prov, wf_details
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
# Extract and prune metadata
metadata = iqms_dict.pop('bids_meta', None)
mod = metadata.pop('modality', None)
prov, wf_details = _get_details(iqms_dict, mod)
file_id = [metadata.pop(k, None) for k in list(BIDS_COMP.keys())]
file_id = [comp for comp in file_id if comp is not None]
if in_plots is None:
in_plots = []
else:
if any(('melodic_reportlet' in k for k in in_plots)):
REPORT_TITLES['bold'].insert(3, 'ICA components')
in_plots = [(REPORT_TITLES[mod][i], read_report_snippet(v))
for i, v in enumerate(in_plots)]
pred_qa = None # metadata.pop('mriqc_pred', None)
config = {
'modality': mod,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': in_plots,
'workflow_details': wf_details,
'provenance': iqms2html(prov, 'provenance-table'),
'metadata': iqms2html(metadata, 'metadata-table'),
'pred_qa': pred_qa
}
if config['metadata'] is None:
config['workflow_details'].append(
'<span class="warning">File has no metadata</span> '
'<span>(sidecar JSON file missing or empty)</span>')
tpl = IndividualTemplate()
tpl.generate_conf(config, out_file)
report_log.info('Generated individual log (%s)', out_file)
return out_file
def individual_html(in_iqms, in_plots=None, api_id=None):
from pathlib import Path
import datetime
from json import load
from mriqc import logging, __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports import REPORT_TITLES
from mriqc.reports.utils import iqms2html, read_report_snippet
from mriqc.data import IndividualTemplate
report_log = logging.getLogger('mriqc.report')
def _get_details(in_iqms, modality):
in_prov = in_iqms.pop('provenance', {})
warn_dict = in_prov.pop('warnings', None)
sett_dict = in_prov.pop('settings', None)
wf_details = []
if modality == 'bold':
bold_exclude_index = in_iqms.get('dumb_trs')
if bold_exclude_index is None:
report_log.warning('Building bold report: no exclude index was found')
elif bold_exclude_index > 0:
msg = """\
<span class="problematic">Non-steady state (strong T1 contrast) has been detected in the \
first {} volumes</span>. They were excluded before generating any QC measures and plots."""
wf_details.append(msg.format(bold_exclude_index))
hmc_fsl = sett_dict.pop('hmc_fsl')
if hmc_fsl is not None:
msg = 'Framewise Displacement was computed using '
if hmc_fsl:
msg += 'FSL <code>mcflirt</code>'
else:
msg += 'AFNI <code>3dvolreg</code>'
wf_details.append(msg)
fd_thres = sett_dict.pop('fd_thres')
if fd_thres is not None:
wf_details.append(
'Framewise Displacement threshold was defined at %f mm' % fd_thres)
elif modality in ('T1w', 'T2w'):
if warn_dict.pop('small_air_mask', False):
wf_details.append(
'<span class="problematic">Detected hat mask was too small</span>')
if warn_dict.pop('large_rot_frame', False):
wf_details.append(
'<span class="problematic">Detected a zero-filled frame, has the original '
'image been rotated?</span>')
return in_prov, wf_details, sett_dict
in_iqms = Path(in_iqms)
with in_iqms.open() as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
out_file = str(Path(in_iqms.with_suffix(".html").name).resolve())
# Extract and prune metadata
metadata = iqms_dict.pop('bids_meta', None)
mod = metadata.pop('modality', None)
prov, wf_details, _ = _get_details(iqms_dict, mod)
file_id = [metadata.pop(k, None)
for k in list(BIDS_COMP.keys())]
file_id = [comp for comp in file_id if comp is not None]
if in_plots is None:
in_plots = []
else:
if any(('melodic_reportlet' in k for k in in_plots)):
REPORT_TITLES['bold'].insert(3, ('ICA components', 'ica-comps'))
in_plots = [(REPORT_TITLES[mod][i] + (read_report_snippet(v), ))
for i, v in enumerate(in_plots)]
pred_qa = None # metadata.pop('mriqc_pred', None)
config = {
'modality': mod,
'dataset': metadata.pop('dataset', None),
'bids_name': in_iqms.with_suffix("").name,
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': in_plots,
'workflow_details': wf_details,
'webapi_url': prov.pop('webapi_url'),
'webapi_port': prov.pop('webapi_port'),
'provenance': iqms2html(prov, 'provenance-table'),
'md5sum': prov['md5sum'],
'metadata': iqms2html(metadata, 'metadata-table'),
'pred_qa': pred_qa
}
if config['metadata'] is None:
config['workflow_details'].append(
'<span class="warning">File has no metadata</span> '
'<span>(sidecar JSON file missing or empty)</span>')
tpl = IndividualTemplate()
tpl.generate_conf(config, out_file)
report_log.info('Generated individual log (%s)', out_file)
return out_file
def _run_interface(self, runtime):
out_file = self._gen_outfile()
if isdefined(self.inputs.root):
self._out_dict = self.inputs.root
root_adds = []
for key, val in list(self.inputs._outputs.items()):
if not isdefined(val) or key == 'trait_added':
continue
if not self.expr.match(key) is None:
root_adds.append(key)
continue
key, val = _process_name(key, val)
self._out_dict[key] = val
for root_key in root_adds:
val = self.inputs._outputs.get(root_key, None)
if isinstance(val, dict):
self._out_dict.update(val)
else:
IFLOGGER.warn(
'Output "%s" is not a dictionary (value="%s"), '
'discarding output.', root_key, str(val))
id_dict = {}
for comp in list(BIDS_COMP.keys()):
comp_val = getattr(self.inputs, comp, None)
if isdefined(comp_val) and comp_val is not None:
id_dict[comp] = comp_val
# Predict QA from IQMs and add to metadata
if self.inputs.modality == 'T1w':
from pkg_resources import resource_filename as pkgrf
import numpy as np
from mriqc.classifier.cv import CVHelper
cvhelper = CVHelper(load_clf=pkgrf('mriqc',
'data/rfc-nzs-full-1.0.pklz'),
n_jobs=1)
features = tuple(
[self._out_dict.get(key, None) for key in cvhelper.ftnames])
id_dict['mriqc_pred'] = int(
cvhelper.predict(np.array([features]))[0])
id_dict['modality'] = self.inputs.modality
if self.inputs.save_extra:
from mriqc import __version__ as version
id_dict['version'] = version
id_dict['software'] = 'mriqc'
if self._out_dict.get('metadata', None) is None:
self._out_dict['metadata'] = {}
self._out_dict['metadata'].update(id_dict)
with open(out_file, 'w') as f:
f.write(
json.dumps(self._out_dict,
sort_keys=True,
indent=2,
ensure_ascii=False))
return runtime
def _run_interface(self, runtime):
out_file = self._gen_outfile()
if isdefined(self.inputs.root):
self._out_dict = self.inputs.root
root_adds = []
for key, val in list(self.inputs._outputs.items()):
if not isdefined(val) or key == "trait_added":
continue
if not self.expr.match(key) is None:
root_adds.append(key)
continue
key, val = _process_name(key, val)
self._out_dict[key] = val
for root_key in root_adds:
val = self.inputs._outputs.get(root_key, None)
if isinstance(val, dict):
self._out_dict.update(val)
else:
config.loggers.interface.warning(
'Output "%s" is not a dictionary (value="%s"), '
"discarding output.",
root_key,
str(val),
)
# Fill in the "bids_meta" key
id_dict = {}
for comp in list(BIDS_COMP.keys()):
comp_val = getattr(self.inputs, comp, None)
if isdefined(comp_val) and comp_val is not None:
id_dict[comp] = comp_val
id_dict["modality"] = self.inputs.modality
if isdefined(self.inputs.metadata) and self.inputs.metadata:
id_dict.update(self.inputs.metadata)
if self._out_dict.get("bids_meta") is None:
self._out_dict["bids_meta"] = {}
self._out_dict["bids_meta"].update(id_dict)
if isdefined(self.inputs.dataset):
self._out_dict["bids_meta"]["dataset"] = self.inputs.dataset
# Fill in the "provenance" key
# Predict QA from IQMs and add to metadata
prov_dict = {}
if isdefined(self.inputs.provenance) and self.inputs.provenance:
prov_dict.update(self.inputs.provenance)
if self._out_dict.get("provenance") is None:
self._out_dict["provenance"] = {}
self._out_dict["provenance"].update(prov_dict)
with open(out_file, "w") as f:
f.write(
json.dumps(
self._out_dict,
sort_keys=True,
indent=2,
ensure_ascii=False,
))
return runtime
def gen_html(csv_file, mod, csv_failed=None, out_file=None):
import os.path as op
from os import remove
from shutil import copy
import datetime
from pkg_resources import resource_filename as pkgrf
from mriqc import __version__ as ver
from mriqc.data import GroupTemplate
from mriqc.utils.misc import check_folder
if version_info[0] > 2:
from io import StringIO as TextIO
else:
from io import BytesIO as TextIO
QCGROUPS = {
'T1w': [(['cjv'], None), (['cnr'], None), (['efc'], None),
(['fber'], None), (['wm2max'], None),
(['snr_csf', 'snr_gm', 'snr_wm'], None),
(['snrd_csf', 'snrd_gm', 'snrd_wm'], None),
(['fwhm_avg', 'fwhm_x', 'fwhm_y', 'fwhm_z'], 'mm'),
(['qi_1', 'qi_2'], None), (['inu_range', 'inu_med'], None),
(['icvs_csf', 'icvs_gm', 'icvs_wm'], None),
(['rpve_csf', 'rpve_gm', 'rpve_wm'], None),
(['tpm_overlap_csf', 'tpm_overlap_gm',
'tpm_overlap_wm'], None),
([
'summary_bg_mean', 'summary_bg_stdv', 'summary_bg_k',
'summary_bg_p05', 'summary_bg_p95'
], None),
([
'summary_csf_mean', 'summary_csf_stdv', 'summary_csf_k',
'summary_csf_p05', 'summary_csf_p95'
], None),
([
'summary_gm_mean', 'summary_gm_stdv', 'summary_gm_k',
'summary_gm_p05', 'summary_gm_p95'
], None),
([
'summary_wm_mean', 'summary_wm_stdv', 'summary_wm_k',
'summary_wm_p05', 'summary_wm_p95'
], None)],
'T2w': [(['cjv'], None), (['cnr'], None), (['efc'], None),
(['fber'], None), (['wm2max'], None),
(['snr_csf', 'snr_gm', 'snr_wm'], None),
(['snrd_csf', 'snrd_gm', 'snrd_wm'], None),
(['fwhm_avg', 'fwhm_x', 'fwhm_y', 'fwhm_z'], 'mm'),
(['qi_1', 'qi_2'], None), (['inu_range', 'inu_med'], None),
(['icvs_csf', 'icvs_gm', 'icvs_wm'], None),
(['rpve_csf', 'rpve_gm', 'rpve_wm'], None),
(['tpm_overlap_csf', 'tpm_overlap_gm',
'tpm_overlap_wm'], None),
([
'summary_bg_mean', 'summary_bg_stdv', 'summary_bg_k',
'summary_bg_p05', 'summary_bg_p95'
], None),
([
'summary_csf_mean', 'summary_csf_stdv', 'summary_csf_k',
'summary_csf_p05', 'summary_csf_p95'
], None),
([
'summary_gm_mean', 'summary_gm_stdv', 'summary_gm_k',
'summary_gm_p05', 'summary_gm_p95'
], None),
([
'summary_wm_mean', 'summary_wm_stdv', 'summary_wm_k',
'summary_wm_p05', 'summary_wm_p95'
], None)],
'bold': [
(['efc'], None),
(['fber'], None),
(['fwhm', 'fwhm_x', 'fwhm_y', 'fwhm_z'], 'mm'),
(['gsr_%s' % a for a in ['x', 'y']], None),
(['snr'], None),
(['dvars_std', 'dvars_vstd'], None),
(['dvars_nstd'], None),
(['fd_mean'], 'mm'),
(['fd_num'], '# timepoints'),
(['fd_perc'], '% timepoints'),
(['spikes_num'], '# slices'),
(['gcor'], None),
(['tsnr'], None),
(['aor'], None),
(['aqi'], None),
([
'summary_bg_mean', 'summary_bg_stdv', 'summary_bg_k',
'summary_bg_p05', 'summary_bg_p95'
], None),
([
'summary_fg_mean', 'summary_fg_stdv', 'summary_fg_k',
'summary_fg_p05', 'summary_fg_p95'
], None),
]
}
def_comps = list(BIDS_COMP.keys())
dataframe = pd.read_csv(csv_file,
index_col=False,
dtype={comp: object
for comp in def_comps})
id_labels = list(set(def_comps) & set(dataframe.columns.ravel().tolist()))
dataframe['label'] = dataframe[id_labels].apply(_format_labels, axis=1)
nPart = len(dataframe)
failed = None
if csv_failed is not None and op.isfile(csv_failed):
MRIQC_REPORT_LOG.warn('Found failed-workflows table "%s"', csv_failed)
failed_df = pd.read_csv(csv_failed, index_col=False)
cols = list(set(id_labels) & set(failed_df.columns.ravel().tolist()))
try:
failed_df = failed_df.sort_values(by=cols)
except AttributeError:
#pylint: disable=E1101
failed_df = failed_df.sort(columns=cols)
failed = failed_df[cols].apply(myfmt, args=(cols, ),
axis=1).ravel().tolist()
csv_groups = []
datacols = dataframe.columns.ravel().tolist()
for group, units in QCGROUPS[mod]:
dfdict = {'iqm': [], 'value': [], 'label': [], 'units': []}
for iqm in group:
if iqm in datacols:
values = dataframe[[iqm]].values.ravel().tolist()
if values:
dfdict['iqm'] += [iqm] * nPart
dfdict['units'] += [units] * nPart
dfdict['value'] += values
dfdict['label'] += dataframe[['label'
]].values.ravel().tolist()
# Save only if there are values
if dfdict['value']:
csv_df = pd.DataFrame(dfdict)
csv_str = TextIO()
csv_df[['iqm', 'value', 'label', 'units']].to_csv(csv_str,
index=False)
csv_groups.append(csv_str.getvalue())
if out_file is None:
out_file = op.abspath('group.html')
tpl = GroupTemplate()
tpl.generate_conf(
{
'modality':
mod,
'timestamp':
datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version':
ver,
'csv_groups':
csv_groups,
'failed':
failed,
'boxplots_js':
open(
pkgrf(
'mriqc',
op.join('data', 'reports', 'embed_resources',
'boxplots.js'))).read(),
'd3_js':
open(
pkgrf(
'mriqc',
op.join('data', 'reports', 'embed_resources',
'd3.min.js'))).read(),
'boxplots_css':
open(
pkgrf(
'mriqc',
op.join('data', 'reports', 'embed_resources',
'boxplots.css'))).read()
}, out_file)
return out_file
def individual_html(in_iqms, in_plots=None, exclude_index=0, wf_details=None):
import os.path as op #pylint: disable=W0404
import datetime
from json import load
from mriqc import __version__ as ver
from mriqc.utils.misc import BIDS_COMP
from mriqc.reports.utils import iqms2html, anat_flags, read_report_snippet
from mriqc.data import IndividualTemplate
from mriqc import logging
from io import open #pylint: disable=W0622
report_log = logging.getLogger('mriqc.report')
report_log.setLevel(logging.INFO)
with open(in_iqms) as jsonfile:
iqms_dict = load(jsonfile)
# Now, the in_iqms file should be correctly named
fname = op.splitext(op.basename(in_iqms))[0]
out_file = op.abspath(fname + '.html')
if in_plots is None:
in_plots = []
if wf_details is None:
wf_details = []
# Extract and prune metadata
metadata = iqms_dict.pop('metadata', None)
mod = metadata.pop('modality', None)
file_id = [metadata.pop(k, None) for k in list(BIDS_COMP.keys())]
file_id = [comp for comp in file_id if comp is not None]
pred_qa = None #metadata.pop('mriqc_pred', None)
# Deal with special IQMs
if mod in ('T1w', 'T2w'):
flags = anat_flags(iqms_dict)
if flags:
wf_details.append(flags)
elif mod == 'bold':
pass
else:
RuntimeError('Unknown modality "%s"' % mod)
config = {
'modality': mod,
'sub_id': '_'.join(file_id),
'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
'version': ver,
'imparams': iqms2html(iqms_dict, 'iqms-table'),
'svg_files': [read_report_snippet(pfile) for pfile in in_plots],
'exclude_index': exclude_index,
'workflow_details': wf_details,
'metadata': iqms2html(metadata, 'metadata-table'),
'pred_qa': pred_qa
}
if config['metadata'] is None:
config['workflow_details'].append(
'<span class="warning">File has no metadata</span> '
'<span>(sidecar JSON file missing or empty)</span>')
tpl = IndividualTemplate()
tpl.generate_conf(config, out_file)
report_log.info('Generated individual log (%s)', out_file)
return out_file