diff --git a/phys2bids/cli/run.py b/phys2bids/cli/run.py
index 0eb6cdf46..50da14e5a 100644
--- a/phys2bids/cli/run.py
+++ b/phys2bids/cli/run.py
@@ -190,7 +190,8 @@ def _get_parser():
default=False,
)
optional.add_argument(
- "-report", "--report",
+ "-report",
+ "--report",
dest="make_report",
action="store_true",
help="Generate a report with the data and generated folder structure. "
@@ -198,7 +199,7 @@ def _get_parser():
default=False,
)
optional.add_argument("-v", "--version", action="version", version=("%(prog)s " + __version__))
-
+
parser._action_groups.append(optional)
return parser
diff --git a/phys2bids/reporting/__init__.py b/phys2bids/reporting/__init__.py
index 107d3aba2..adeeb7218 100644
--- a/phys2bids/reporting/__init__.py
+++ b/phys2bids/reporting/__init__.py
@@ -1 +1 @@
-"""Visual reporting tools for inspecting phys2bids workflow outputs."""
\ No newline at end of file
+"""Visual reporting tools for inspecting phys2bids workflow outputs."""
diff --git a/phys2bids/reporting/assets/main.css b/phys2bids/reporting/assets/main.css
index 426336395..a5b9886bb 100644
--- a/phys2bids/reporting/assets/main.css
+++ b/phys2bids/reporting/assets/main.css
@@ -99,4 +99,4 @@ html, body {
.main{
margin-top: 100px;
margin-left: 100px;
-}
\ No newline at end of file
+}
diff --git a/phys2bids/reporting/html_report.py b/phys2bids/reporting/html_report.py
index 698325aeb..49dd4f251 100644
--- a/phys2bids/reporting/html_report.py
+++ b/phys2bids/reporting/html_report.py
@@ -4,9 +4,10 @@
from os.path import join
from pathlib import Path
from string import Template
-from bokeh.plotting import figure, ColumnDataSource
+
from bokeh.embed import components
from bokeh.layouts import gridplot
+from bokeh.plotting import ColumnDataSource, figure
from phys2bids import _version
@@ -33,14 +34,17 @@ def _save_as_html(log_html_path, log_content, qc_html_path):
Saves the html file
"""
resource_path = Path(__file__).resolve().parent
- head_template_name = 'report_log_template.html'
+ head_template_name = "report_log_template.html"
head_template_path = resource_path.joinpath(head_template_name)
- with open(str(head_template_path), 'r') as head_file:
+ with open(str(head_template_path), "r") as head_file:
head_tpl = Template(head_file.read())
- html = head_tpl.substitute(version=_version.get_versions()['version'],
- log_html_path=log_html_path, log_content=log_content,
- qc_html_path=qc_html_path)
+ html = head_tpl.substitute(
+ version=_version.get_versions()["version"],
+ log_html_path=log_html_path,
+ log_content=log_content,
+ qc_html_path=qc_html_path,
+ )
return html
@@ -67,16 +71,18 @@ def _update_fpage_template(tree_string, bokeh_id, bokeh_js, log_html_path, qc_ht
"""
resource_path = Path(__file__).resolve().parent
- body_template_name = 'report_plots_template.html'
+ body_template_name = "report_plots_template.html"
body_template_path = resource_path.joinpath(body_template_name)
- with open(str(body_template_path), 'r') as body_file:
+ with open(str(body_template_path), "r") as body_file:
body_tpl = Template(body_file.read())
- body = body_tpl.substitute(tree=tree_string,
- content=bokeh_id,
- javascript=bokeh_js,
- version=_version.get_versions()['version'],
- log_html_path=log_html_path,
- qc_html_path=qc_html_path)
+ body = body_tpl.substitute(
+ tree=tree_string,
+ content=bokeh_id,
+ javascript=bokeh_js,
+ version=_version.get_versions()["version"],
+ log_html_path=log_html_path,
+ qc_html_path=qc_html_path,
+ )
return body
@@ -94,13 +100,13 @@ def _generate_file_tree(out_dir):
tree_string: String with the tree of files in directory
"""
# prefix components:
- space = ' '
- branch = '│ '
+ space = " "
+ branch = "│ "
# pointers:
- tee = '├── '
- last = '└── '
+ tee = "├── "
+ last = "└── "
- def tree(dir_path: Path, prefix: str = ''):
+ def tree(dir_path: Path, prefix: str = ""):
"""Generate tree structure.
Given a directory Path object
@@ -119,9 +125,9 @@ def tree(dir_path: Path, prefix: str = ''):
# i.e. space because last, └── , above so no more |
yield from tree(path, prefix=prefix + extension)
- tree_string = ''
+ tree_string = ""
for line in tree(Path(out_dir)):
- tree_string += line + '
'
+ tree_string += line + "
"
return tree_string
@@ -145,7 +151,7 @@ def _generate_bokeh_plots(phys_in, figsize=(250, 500)):
--------
https://phys2bids.readthedocs.io/en/latest/howto.html
"""
- colors = ['#ff7a3c', '#008eba', '#ff96d3', '#3c376b', '#ffd439']
+ colors = ["#ff7a3c", "#008eba", "#ff96d3", "#3c376b", "#ffd439"]
time = phys_in.timeseries.T[0] # assumes first phys_in.timeseries is time
ch_num = len(phys_in.ch_name)
@@ -158,19 +164,20 @@ def _generate_bokeh_plots(phys_in, figsize=(250, 500)):
# build a data source for each plot, with only the data + index (time)
# for the purpose of reporting, data is downsampled 10x
# doesn't make much of a difference to the naked eye, fine for reports
- source = ColumnDataSource(data=dict(
- x=time[::downsample],
- y=timeser[::downsample]))
+ source = ColumnDataSource(data=dict(x=time[::downsample], y=timeser[::downsample]))
i = row + 1
- tools = ['wheel_zoom,pan,reset']
- q = figure(plot_height=figsize[0], plot_width=figsize[1],
- tools=tools,
- title=f' Channel {i}: {phys_in.ch_name[i]}',
- sizing_mode='stretch_both')
- q.line('x', 'y', color=colors[i - 1], alpha=0.9, source=source)
- q.xaxis.axis_label = 'Time (s)'
+ tools = ["wheel_zoom,pan,reset"]
+ q = figure(
+ plot_height=figsize[0],
+ plot_width=figsize[1],
+ tools=tools,
+ title=f" Channel {i}: {phys_in.ch_name[i]}",
+ sizing_mode="stretch_both",
+ )
+ q.line("x", "y", color=colors[i - 1], alpha=0.9, source=source)
+ q.xaxis.axis_label = "Time (s)"
# hovertool commented for posterity because I (KB) will be triumphant
# eventually
# q.add_tools(HoverTool(tooltips=[
@@ -178,9 +185,9 @@ def _generate_bokeh_plots(phys_in, figsize=(250, 500)):
# ('HELP', '100 :D')
# ], mode='vline'))
plot_list.append([q])
- p = gridplot(plot_list, toolbar_location='right',
- plot_height=250, plot_width=750,
- merge_tools=True)
+ p = gridplot(
+ plot_list, toolbar_location="right", plot_height=250, plot_width=750, merge_tools=True
+ )
script, div = components(p)
return script, div
@@ -207,27 +214,27 @@ def generate_report(out_dir, log_path, phys_in):
https://phys2bids.readthedocs.io/en/latest/howto.html
"""
# Copy assets into output folder
- pkgdir = sys.modules['phys2bids'].__path__[0]
- assets_path = join(pkgdir, 'reporting', 'assets')
- copy_tree(assets_path, join(out_dir, 'assets'))
+ pkgdir = sys.modules["phys2bids"].__path__[0]
+ assets_path = join(pkgdir, "reporting", "assets")
+ copy_tree(assets_path, join(out_dir, "assets"))
# Read log
- with open(log_path, 'r') as f:
+ with open(log_path, "r") as f:
log_content = f.read()
- log_content = log_content.replace('\n', '
')
- log_html_path = join(out_dir, 'phys2bids_report_log.html')
- qc_html_path = join(out_dir, 'phys2bids_report.html')
+ log_content = log_content.replace("\n", "
")
+ log_html_path = join(out_dir, "phys2bids_report_log.html")
+ qc_html_path = join(out_dir, "phys2bids_report.html")
html = _save_as_html(log_html_path, log_content, qc_html_path)
- with open(log_html_path, 'wb') as f:
- f.write(html.encode('utf-8'))
+ with open(log_html_path, "wb") as f:
+ f.write(html.encode("utf-8"))
# Read in output directory structure & create tree
tree_string = _generate_file_tree(out_dir)
bokeh_js, bokeh_div = _generate_bokeh_plots(phys_in, figsize=(250, 750))
html = _update_fpage_template(tree_string, bokeh_div, bokeh_js, log_html_path, qc_html_path)
- with open(qc_html_path, 'wb') as f:
- f.write(html.encode('utf-8'))
\ No newline at end of file
+ with open(qc_html_path, "wb") as f:
+ f.write(html.encode("utf-8"))
diff --git a/phys2bids/reporting/report_log_template.html b/phys2bids/reporting/report_log_template.html
index 64182d820..fb1cfb32f 100644
--- a/phys2bids/reporting/report_log_template.html
+++ b/phys2bids/reporting/report_log_template.html
@@ -30,4 +30,4 @@
$log_content
-