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Merge pull request #162 from rwblair/issue155
Issue155 [WIP]
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| { | ||
| "sub_reports": | ||
| [ | ||
| { | ||
| "name": "Skull Strippings", | ||
| "elements": | ||
| [ | ||
| { | ||
| "name": "t1_stripped_overlay", | ||
| "file_pattern": "t1_stripped_overlay", | ||
| "title": "Skull Stripped T1", | ||
| "description": "Stripped T1 placed over an image of the unstripped T1" | ||
| }, | ||
| { | ||
| "name": "sbref_stripped_overlay", | ||
| "file_pattern": "sbref_stripped_overlay", | ||
| "title": "Skull Stripped Sbref", | ||
| "description": "Unwarped and stripped sbref with a background image of an unwarped sbref" | ||
| }, | ||
| { | ||
| "name": "fmap_magnitude_stripped_overlay", | ||
| "file_pattern": "fmap_magnitude_stripped_overlay", | ||
| "title": "Skull Stripped Field Map Magnitude", | ||
| "description": "Stripped fieldmap magnitude estimated phase-difference image and one or more magnitude images corresponding to two or more gradient echo sequence acquisitions" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Registration Outputs", | ||
| "elements": | ||
| [ | ||
| { | ||
| "name": "sbref_to_t1", | ||
| "file_pattern": "sbref_to_t1", | ||
| "title": "Sbref to T1", | ||
| "description": "Corrected sbref image registred into t1 space." | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| <?xml version="1.0" encoding="utf-8" ?> | ||
| <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | ||
| <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> | ||
| <head> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | ||
| <meta name="generator" content="Docutils 0.12: http://docutils.sourceforge.net/" /> | ||
| <title></title> | ||
| <style type="text/css"> | ||
| </style> | ||
| </head> | ||
| <body> | ||
|
|
||
|
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|
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| {% for sub_report in sub_reports %} | ||
| <h2>{{ sub_report.name }}</h2> | ||
| {% for elem in sub_report.elements %} | ||
| {{ elem.name }} | ||
| {% for image in elem.files_contents %} | ||
| {{ image }} | ||
| {% endfor %} | ||
| {% endfor %} | ||
| {% endfor %} | ||
|
|
||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| from __future__ import unicode_literals | ||
|
|
||
| import codecs | ||
| import json | ||
| import re | ||
| import os | ||
| from os.path import join, exists, basename, dirname | ||
|
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| import jinja2 | ||
| from pkg_resources import resource_filename as pkgrf | ||
|
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| class Element(object): | ||
|
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| def __init__(self, name, file_pattern, title, description): | ||
| self.name = name | ||
| self.file_pattern = re.compile(file_pattern) | ||
| self.title = title | ||
| self.description = description | ||
| self.files = [] | ||
| self.files_contents = [] | ||
|
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|
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| class SubReport(object): | ||
|
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| def __init__(self, name, elements, **kwargs): | ||
| self.name = name | ||
| self.elements = [] | ||
| for e in elements: | ||
| element = Element(**e) | ||
| self.elements.append(element) | ||
|
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| def generate_sub_report(self, report): | ||
| env = jinja2.Environment( | ||
| loader=jinja2.FileSystemLoader(searchpath='/'), | ||
| trim_blocks=True, lstrip_blocks=True | ||
| ) | ||
| sub_report_tpl = env.get_template('{}_tpl.html'.format(self.name)) | ||
| sub_report_render = sub_report_tpl.render | ||
| return sub_report_render | ||
|
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| class Report(object): | ||
|
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| def __init__(self, path, config, out_dir, out_filename='report.html'): | ||
| self.root = path | ||
| self.sub_reports = [] | ||
| self._load_config(config) | ||
| self.out_dir = out_dir | ||
| self.out_filename = out_filename | ||
|
|
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| def _load_config(self, config): | ||
| if isinstance(config, str): | ||
| config = json.load(open(config, 'r')) | ||
|
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| for e in config['sub_reports']: | ||
| sub_report = SubReport(**e) | ||
| self.sub_reports.append(sub_report) | ||
|
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| self.index() | ||
|
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| def index(self): | ||
| for root, directories, filenames in os.walk(self.root): | ||
| for f in filenames: | ||
| f = join(root, f) | ||
| for sub_report in self.sub_reports: | ||
| for element in sub_report.elements: | ||
| if element.file_pattern.search(f) and f.split('.')[-1] == 'svg': | ||
| element.files.append(f) | ||
| with open(f) as fp: | ||
| content = fp.read() | ||
| content = '\n'.join(content.split('\n')[1:]) | ||
| element.files_contents.append(content) | ||
|
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| def generate_report(self): | ||
| searchpath = pkgrf('fmriprep', '/') | ||
| env = jinja2.Environment( | ||
| loader=jinja2.FileSystemLoader(searchpath=searchpath), | ||
| trim_blocks=True, lstrip_blocks=True | ||
| ) | ||
| report_tpl = env.get_template('viz/report.tpl') | ||
| report_render = report_tpl.render(sub_reports=self.sub_reports) | ||
| with open(os.path.join(self.out_dir, self.out_filename), 'w') as fp: | ||
| fp.write(report_render) | ||
| return report_render |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| from pkg_resources import resource_filename as pkgrf | ||
|
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| from reports import Report | ||
|
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| if __name__ == '__main__': | ||
| path = pkgrf('fmriprep', '../out/images/') | ||
| out_dir = pkgrf('fmriprep', '../out/') | ||
| config = pkgrf('fmriprep', 'viz/config.json') | ||
| report = Report(path, config, out_dir) | ||
| for sub_report in report.sub_reports: | ||
| for element in sub_report.elements: | ||
| print(element.files) | ||
| print(element.title) | ||
| print(report.generate_report()) |
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