msqms.reports.report module

msqms.reports.report module#

Generate MEG Pipeline HTML Report

Summary#

Classes:#

HtmlReport

Generate an HTML report for MEG quality metrics.

QualityReport

Generate a quality report from MEG raw data.

SummaryHtmlReport

Generate an HTML summary report for multiple MEG quality metrics.

SummaryQualityReport

Generate a summary quality report for multiple MEG files.

Functions:#

gen_quality_report

Generate HTML/JSON Report for a set of MEG Raw data.

gen_summary_quality_report

Generate a summary HTML report for multiple MEG files with quality scores distribution.

Reference#

msqms.reports.report.gen_quality_report(megfiles, outdir, report_fname='', data_type='', ftype='html')[source]#

Generate HTML/JSON Report for a set of MEG Raw data.

Parameters:

  • megfiles ([Union[str, Path]]) – Paths to the MEG files for which the quality reports will be generated.

  • outdir (Union[str, Path]) – The directory where the generated report will be saved.

  • report_fname (str) – The name of the generated report file. Default is an empty string.

  • data_type (DATA_TYPE, optional) – The type of data. Either ‘opm’ or ‘squid’. Default is an empty string.

  • ftype (str) – The format of the report file to be generated. Either ‘html’ or ‘json’. Default is ‘html’.

Returns:

A dictionary containing the quality assessment data: {

”msqm_score”: msqm_score, “details”: details, “category_scores”: category_scores

}

Return type:

dict

msqms.reports.report.gen_summary_quality_report(megfiles, outdir, report_fname='summary_report', data_type='', ftype='html')[source]#

Generate a summary HTML report for multiple MEG files with quality scores distribution.

Parameters:

  • megfiles (List[Union[str, Path]]) – List of paths to the MEG files for which the summary report will be generated.

  • outdir (Union[str, Path]) – The directory where the generated report will be saved.

  • report_fname (str) – The name of the generated summary report file. Default is “summary_report”.

  • data_type (DATA_TYPE, optional) – The type of data. Either ‘opm’ or ‘squid’. Default is an empty string.

  • ftype (str) – The format of the report file to be generated. Either ‘html’ or ‘json’. Default is ‘html’.

Returns:

A dictionary containing summary statistics for all files.

Return type:

dict

class msqms.reports.report.QualityReport(report_data, minify_html)[source]#

Bases: object

Generate a quality report from MEG raw data.

to_json(out_json_path)[source]#

Write the report to a JSON file.

Return type:

None

Parameters:

out_json_path (str or Path) – The path where the JSON report will be saved.

to_html(out_html_path)[source]#

Write the report to an HTML file.

Return type:

None

Parameters:

out_html_path (str or Path) – The path where the HTML report will be saved.

class msqms.reports.report.HtmlReport(report_data)[source]#

Bases: object

Generate an HTML report for MEG quality metrics.

get_template(template_name)[source]#

Load and return the Jinja2 template by name.

Return type:

Template

Parameters:

template_name (str) – The name of the template to load.

Returns:

The loaded template.

Return type:

jinja2.Template

gen_base_template()[source]#

Generate the base HTML template.

Returns:

The base template for the HTML report.

Return type:

jinja2.Template

gen_html_report()[source]#

Generate the full HTML report.

Returns:

The generated HTML report content.

Return type:

str

gen_nav_html()[source]#

Generate the navigation HTML component.

Returns:

The generated navigation HTML content.

Return type:

str

gen_body_html()[source]#

Generate the body HTML component.

Returns:

The generated body HTML content.

Return type:

str

render_html()[source]#

Render the complete HTML page.

Returns:

The final rendered HTML content.

Return type:

str

class msqms.reports.report.SummaryQualityReport(report_data, minify_html)[source]#

Bases: object

Generate a summary quality report for multiple MEG files.

to_json(out_json_path)[source]#

Write the summary report to a JSON file.

Return type:

None

Parameters:

out_json_path (str or Path) – The path where the JSON report will be saved.

to_html(out_html_path)[source]#

Write the summary report to an HTML file.

Return type:

None

Parameters:

out_html_path (str or Path) – The path where the HTML report will be saved.

class msqms.reports.report.SummaryHtmlReport(report_data)[source]#

Bases: object

Generate an HTML summary report for multiple MEG quality metrics.

get_template(template_name)[source]#

Load and return the Jinja2 template by name.

Return type:

Template

Parameters:

template_name (str) – The name of the template to load.

Returns:

The loaded template.

Return type:

jinja2.Template

render_html()[source]#

Render the complete HTML summary page.

Returns:

The final rendered HTML content.

Return type:

str