Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[DOC] Add references to HTML report #695

Merged
merged 1 commit into from
Mar 22, 2021
Merged

[DOC] Add references to HTML report #695

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
50 changes: 25 additions & 25 deletions tedana/workflows/tedana.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -632,31 +632,6 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
if verbose:
io.writeresults_echoes(catd, mmix, mask, comptable, ref_img, out_dir=out_dir)

if not no_reports:
LGR.info('Making figures folder with static component maps and '
'timecourse plots.')
# make figure folder first
if not op.isdir(op.join(out_dir, 'figures')):
os.mkdir(op.join(out_dir, 'figures'))

reporting.static_figures.comp_figures(data_oc, mask=mask,
comptable=comptable,
mmix=mmix_orig,
ref_img=ref_img,
out_dir=op.join(out_dir,
'figures'),
png_cmap=png_cmap)

if sys.version_info.major == 3 and sys.version_info.minor < 6:
warn_msg = ("Reports requested but Python version is less than "
"3.6.0. Dynamic reports will not be generated.")
LGR.warn(warn_msg)
else:
LGR.info('Generating dynamic report')
reporting.generate_report(out_dir=out_dir, tr=img_t_r)

LGR.info('Workflow completed')

RepLGR.info("This workflow used numpy (Van Der Walt, Colbert, & "
"Varoquaux, 2011), scipy (Jones et al., 2001), pandas "
"(McKinney, 2010), scikit-learn (Pedregosa et al., 2011), "
Expand Down Expand Up @@ -696,6 +671,29 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
with open(repname, 'w') as fo:
fo.write(report)

if not no_reports:
LGR.info('Making figures folder with static component maps and '
'timecourse plots.')
# make figure folder first
if not op.isdir(op.join(out_dir, 'figures')):
os.mkdir(op.join(out_dir, 'figures'))

reporting.static_figures.comp_figures(data_oc, mask=mask,
comptable=comptable,
mmix=mmix_orig,
ref_img=ref_img,
out_dir=op.join(out_dir,
'figures'),
png_cmap=png_cmap)

if sys.version_info.major == 3 and sys.version_info.minor < 6:
warn_msg = ("Reports requested but Python version is less than "
"3.6.0. Dynamic reports will not be generated.")
LGR.warn(warn_msg)
else:
LGR.info('Generating dynamic report')
reporting.generate_report(out_dir=out_dir, tr=img_t_r)

log_handler.close()
logging.root.removeHandler(log_handler)
sh.close()
Expand All @@ -706,6 +704,8 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
local_logger.removeHandler(handler)
os.remove(refname)

LGR.info('Workflow completed')


def _main(argv=None):
"""Tedana entry point"""
Expand Down