[BUG/ENH] Improve generate_report method of multi-subject maskers

[ymzayek]

Is there an existing issue for this?

• I have searched the existing issues

Operating system

• Linux
• Mac
• Windows

Operating system version

• Linux Ubuntu 22.04

Python version

• 3.11
• 3.10
• 3.9
• 3.8
• 3.7

nilearn version

10.2.dev

Expected behavior

The multi-subject maskers generate_report behavior can be improved.

The MultiNiftiMasker does not support generate_report even if passed one subject. The following error is raised if called:

NameError: name 'warning_message' is not defined at line 205 column 7 in file [/home/yasmin/nilearn/nilearn/nilearn/reporting/data/html/report_body_template.html](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/nilearn/reporting/data/html/report_body_template.html)

In the case of the labels and maps multi-subject maskers, it does work with one subject. This is partly improved in PR #3935. It clarifies that generate_report is only supported with one subject. We can think of a way to support multiple subjects where you can click through the first time point of the different subjects but this could present scaling issues.

Current behavior & error messages

This is what I got:

Full Traceback

# Paste the error message here
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Input In [6], in <cell line: 7>()
      4 img = datasets.fetch_development_fmri(n_subjects=1)["func"]
      6 masker = MultiNiftiMasker()
----> 7 masker.fit(img).generate_report()

File [~/nilearn/nilearn/nilearn/maskers/nifti_masker.py:305](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/maskers/nifti_masker.py:305), in NiftiMasker.generate_report(self)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/maskers/nifti_masker.py?line=301'>302</a>](file:///home/yasmin/nilearn/nilearn/nilearn/maskers/nifti_masker.py?line=301%27%3E302%3C/a%3E) """Generate a report of the masker."""
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/maskers/nifti_masker.py?line=302'>303</a>](file:///home/yasmin/nilearn/nilearn/nilearn/maskers/nifti_masker.py?line=302%27%3E303%3C/a%3E) from nilearn.reporting.html_report import generate_report
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/maskers/nifti_masker.py?line=304'>305</a>](file:///home/yasmin/nilearn/nilearn/nilearn/maskers/nifti_masker.py?line=304%27%3E305%3C/a%3E) return generate_report(self)

File [~/nilearn/nilearn/nilearn/reporting/html_report.py:192](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/reporting/html_report.py:192), in generate_report(estimator)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=188'>189</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=188%27%3E189%3C/a%3E) if not hasattr(estimator, '_reporting_data'):
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=189'>190</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=189%27%3E190%3C/a%3E)     warnings.warn('This object has not been fitted yet ! '
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=190'>191</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=190%27%3E191%3C/a%3E)                   'Make sure to run `fit` before inspecting reports.')
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=191'>192</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=191%27%3E192%3C/a%3E)     return _update_template(
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=192'>193</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=192%27%3E193%3C/a%3E)         title='Empty Report',
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=193'>194</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=193%27%3E194%3C/a%3E)         docstring=(
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=194'>195</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=194%27%3E195%3C/a%3E)             "This report was not generated. Please `fit` the object."
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=195'>196</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=195%27%3E196%3C/a%3E)         ),
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=196'>197</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=196%27%3E197%3C/a%3E)         content=_embed_img(None),
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=197'>198</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=197%27%3E198%3C/a%3E)         overlay=None,
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=198'>199</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=198%27%3E199%3C/a%3E)         parameters={},
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=199'>200</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=199%27%3E200%3C/a%3E)         data=data,
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=200'>201</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=200%27%3E201%3C/a%3E)     )
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=202'>203</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=202%27%3E203%3C/a%3E) elif estimator._reporting_data is None:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=203'>204</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=203%27%3E204%3C/a%3E)     warnings.warn('Report generation not enabled ! '
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=204'>205</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=204%27%3E205%3C/a%3E)                   'No visual outputs will be created.')

File [~/nilearn/nilearn/nilearn/reporting/html_report.py:137](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/reporting/html_report.py:137), in _update_template(title, docstring, content, overlay, parameters, data, template_name)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=133'>134</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=133%27%3E134%3C/a%3E)     raise FileNotFoundError(f"No template {body_template_name}")
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=134'>135</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=134%27%3E135%3C/a%3E) tpl = tempita.HTMLTemplate.from_filename(str(body_template_path),
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=135'>136</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=135%27%3E136%3C/a%3E)                                          encoding='utf-8')
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=136'>137</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=136%27%3E137%3C/a%3E) body = tpl.substitute(title=title, content=content,
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=137'>138</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=137%27%3E138%3C/a%3E)                       overlay=overlay,
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=138'>139</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=138%27%3E139%3C/a%3E)                       docstring=docstring,
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=139'>140</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=139%27%3E140%3C/a%3E)                       parameters=parameters,
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=140'>141</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=140%27%3E141%3C/a%3E)                       **data)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=142'>143</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=142%27%3E143%3C/a%3E) head_template_name = 'report_head_template.html'
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=143'>144</a>](file:///home/yasmin/nilearn/nilearn/nilearn/reporting/html_report.py?line=143%27%3E144%3C/a%3E) head_template_path = resource_path.joinpath(head_template_name)

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:184](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:184), in Template.substitute(self, *args, **kw)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=181'>182</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=181%27%3E182%3C/a%3E) if self.namespace:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=182'>183</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=182%27%3E183%3C/a%3E)     ns.update(self.namespace)
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=183'>184</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=183%27%3E184%3C/a%3E) result, defs, inherit = self._interpret(ns)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=184'>185</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=184%27%3E185%3C/a%3E) if not inherit:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=185'>186</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=185%27%3E186%3C/a%3E)     inherit = self.default_inherit

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:195](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:195), in Template._interpret(self, ns)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=192'>193</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=192%27%3E193%3C/a%3E) parts = []
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=193'>194</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=193%27%3E194%3C/a%3E) defs = {}
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=194'>195</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=194%27%3E195%3C/a%3E) self._interpret_codes(self._parsed, ns, out=parts, defs=defs)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=195'>196</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=195%27%3E196%3C/a%3E) if '__inherit__' in defs:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=196'>197</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=196%27%3E197%3C/a%3E)     inherit = defs.pop('__inherit__')

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:223](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:223), in Template._interpret_codes(self, codes, ns, out, defs)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=220'>221</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=220%27%3E221%3C/a%3E)     out.append(item)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=221'>222</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=221%27%3E222%3C/a%3E) else:
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=222'>223</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=222%27%3E223%3C/a%3E)     self._interpret_code(item, ns, out, defs)

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:240](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:240), in Template._interpret_code(self, code, ns, out, defs)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=237'>238</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=237%27%3E238%3C/a%3E) elif name == 'cond':
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=238'>239</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=238%27%3E239%3C/a%3E)     parts = code[2:]
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=239'>240</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=239%27%3E240%3C/a%3E)     self._interpret_if(parts, ns, out, defs)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=240'>241</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=240%27%3E241%3C/a%3E) elif name == 'expr':
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=241'>242</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=241%27%3E242%3C/a%3E)     parts = code[2].split('|')

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:296](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:296), in Template._interpret_if(self, parts, ns, out, defs)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=293'>294</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=293%27%3E294%3C/a%3E)     result = True
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=294'>295</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=294%27%3E295%3C/a%3E) else:
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=295'>296</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=295%27%3E296%3C/a%3E)     result = self._eval(part[2], ns, pos)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=296'>297</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=296%27%3E297%3C/a%3E) if result:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=297'>298</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=297%27%3E298%3C/a%3E)     self._interpret_codes(part[3], ns, out, defs)

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:319](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:319), in Template._eval(self, code, ns, pos)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=316'>317</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=316%27%3E317%3C/a%3E) e.args = (self._add_line_info(arg0, pos),)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=317'>318</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=317%27%3E318%3C/a%3E) if PY3:
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=318'>319</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=318%27%3E319%3C/a%3E)     raise(e)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=319'>320</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=319%27%3E320%3C/a%3E) else:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=320'>321</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=320%27%3E321%3C/a%3E)     raise (exc_info[1], e, exc_info[2])

File [~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:305](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/~/nilearn/nilearn/nilearn/externals/tempita/__init__.py:305), in Template._eval(self, code, ns, pos)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=302'>303</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=302%27%3E303%3C/a%3E) try:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=303'>304</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=303%27%3E304%3C/a%3E)     try:
--> <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=304'>305</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=304%27%3E305%3C/a%3E)         value = eval(code, self.default_namespace, ns)
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=305'>306</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=305%27%3E306%3C/a%3E)     except SyntaxError as e:
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=306'>307</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=306%27%3E307%3C/a%3E)         raise SyntaxError(
    <a href='[file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=307'>308</a>](file:///home/yasmin/nilearn/nilearn/nilearn/externals/tempita/__init__.py?line=307%27%3E308%3C/a%3E)             'invalid syntax in expression: %s' % code)

File <string>:1, in <module>

NameError: name 'warning_message' is not defined at line 205 column 7 in file [/home/yasmin/nilearn/nilearn/nilearn/reporting/data/html/report_body_template.html](https://file+.vscode-resource.vscode-cdn.net/home/yasmin/nilearn/nilearn/nilearn/reporting/data/html/report_body_template.html)

Code to reproduce

Steps and code to reproduce bug

# Paste your code here
from nilearn import datasets
from nilearn.maskers import MultiNiftiMasker

img = datasets.fetch_development_fmri(n_subjects=1)["func"]

masker = MultiNiftiMasker()
masker.fit(img).generate_report()

[Remi-Gau]

fixed by #4001