def generateStatsHTML(graph,statsFilePath = "stats.html",postStatsFilePath = "postStats.html"): #Generates the Stats HTML section
firstLevel = checkFirstLevel(graph)
softwareLabelNum = queryVersionNum(graph)
softwareLabelNumList = addQueryToList(softwareLabelNum)
stats = document(title="FSL Viewer") #Creates initial html page (stats)
stats += h1("Sample FSL Viewer")
stats += ul(li(a("Stats", href="stats.html")), li("-"),li(a("Post Stats", href = "postStats.html")))
stats += h2("Stats")
stats += hr()
stats += h3("Analysis Methods")
if askSpm(graph) == True: #Checks if SPM was used
stats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/)." % softwareLabelNumList[1])
elif askFsl(graph) == True: #Checks if FSL was used
fslFeatVersion = queryFslFeatVersion(graph)
stats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)." % (fslFeatVersion[0], softwareLabelNumList[1]))
stats += hr()
stats += h3("Design Matrix")
designMatrixLocation = queryDesignMatrixLocation(graph)
stats += a(img(src = designMatrixLocation[1], style = "border:5px solid black", border = 0), href = designMatrixLocation[0]) #Adds design matrix image (as a link) to html page
statsFile = open(statsFilePath, "x")
print(stats, file = statsFile) #Prints html page to a file
statsFile.close()
def _add_item(self, pocket_item: PocketItem) -> None:
"""Add a pocket item to the HTML report page
Args:
pocket_item (PocketItem):
Returns:
None
"""
self.doc.add(tags.h3(pocket_item.title, cls="defaultfontfamily"))
# Add bullets
pocket_item_description = tags.ul()
pocket_item_description += tags.li(
"Link: ",
tags.a(pocket_item.url, href=pocket_item.url),
cls="defaultfontfamily",
)
pocket_item_description += tags.li(
"Tags: ",
", ".join([elem for elem in pocket_item.tags]),
cls="defaultfontfamily",
)
pocket_item_description += tags.li(
"Time added: ",
pocket_item.convert_datetime_to_string(pocket_item.time_added),
cls="defaultfontfamily",
)
self.doc.add(pocket_item_description)
def render(self):
if len(self.highlights) == 0 \
and len(self.notes) == 0 \
and len(self.bookmarks) == 0:
return
with div():
h2(self.title)
if self.authors is not None:
p(f'Authors: {self.authors}')
p(f'File: {self.file_name}')
if len(self.bookmarks) > 0:
h3('Bookmarks')
with ol():
for bookmark in self.bookmarks:
with li():
bookmark.render()
if len(self.highlights) > 0:
h3('Highlights')
with ol():
for highlight in self.highlights:
with li():
highlight.render()
if len(self.notes) > 0:
h3('Notes')
with ol():
for note in self.notes:
with li():
note.render()
def __init__(self, subtitle=''):
self.doc = dominate.document(self.site_name)
self.subtitle = subtitle if subtitle else self.__class__.__name__
self.on_ready_scriptage = []
with self.doc.head:
for css in self.cssfiles.split():
self._link_css(css)
for scripturl in self.scripturls:
tags.script(crossorigin="anonymous", src=scripturl)
self.script_list = tags.script().children
with self.doc.body.add(tags.div(cls="container")):
self.header = tags.div(id="header")
with self.header.add(tags.h2()):
tags.a(self.site_name, href='/', id="site_name")
tags.h3(self.subtitle, id="subtitle")
with tags.ul(id="status", style=self.status_style):
for msg in flask.get_flashed_messages():
tags.li(msg)
self.content = tags.div(id="content")
self.footer = tags.div(id="footer")
with self.footer:
tags.a("Latest", href=url_for("list_latest"))
tags.a("Back to the Front", href="/")
tags.a("Catalog",
href=url_for("show_catalog_page"),
onclick="shift_edit(event, this)")
tags.a("Register", href=url_for('loginbp.new_user'))
tags.label("")
if flask_login.current_user.is_authenticated:
tags.a(f"Log out", href=url_for('loginbp.logout'))
else:
tags.a(f"Login", href=url_for('loginbp.login'))
def makeHtml(path, fileName, sitename, authorname, usecss, usejs):
doc = dominate.document(title=sitename)
with doc.head:
if (usecss.lower() == "y"):
link(rel='stylesheet', href='style.css')
if (usejs.lower() == "y"):
script(type='text/javascript', src='script.js')
with meta():
attr(author=authorname)
with doc:
with div(id='header').add(ol()):
for i in ['home', 'about', 'contact']:
li(a(i.title(), href='/%s.html' % i))
with div():
attr(cls='body')
p('Lorem ipsum..')
if not os.path.exists("./" + path):
os.makedirs("./" + path)
f = open("./" + path + "/" + fileName, 'w+')
f.write(str(doc))
f.close()
if (usejs.lower() == "y"):
if not os.path.exists("./" + sitename + "/js"):
os.makedirs("./" + sitename + "/js")
if (usecss.lower() == "y"):
if not os.path.exists("./" + sitename + "/css"):
os.makedirs("./" + sitename + "/css")
def append_list(self, *items):
with self.doc.body:
with ul() as unorderedList:
for item in items:
if type(item) is list:
self.append_list(*item)
else:
li(item)
def generateMainHTML(graph,mainFilePath = "Main.html", statsFilePath = "stats.html", postStatsFilePath = "postStats.html"): #Generates the main HTML page
main = document(title="FSL Viewer")
main += h1("Sample FSL Viewer")
main += ul(li(a("Stats", href="stats.html")), li("-"),li(a("Post Stats", href = "postStats.html")))
mainFile = open(mainFilePath, "x")
print(main, file = mainFile)
mainFile.close()
def visit_Navbar(self, node):
nav = tags.nav(cls="navbar navbar-expand-lg navbar-dark bg-primary")
with nav:
tags.span(node.title, cls="navbar-brand")
with tags.div(id='navbarColor01', cls="collapse navbar-collapse"):
with tags.ul(cls='navbar-nav mr-auto'):
for item in node.items:
tags.li(self.visit(item))
return nav
def report_list_group(self, items, **kwargs):
"""
Creates a list group. Each arg is a line
:param str title: Title of the section
:param list items: Each arg passed will be treated as a new list item
:param bool section: Kwarg Set to True to append the cards section to the preceding section. Default is false
:param tuple alert: Kwarg Create a dismissable alert box. First value of tuple is the color, and the second is the message
:param tuple reference: Kwarg Adds a small button which hrefs to a user supplied link. Is a tuple. First value is color, second is link
:param dict badge: Kwarg Adds badges. Key is the color, and value is the message.
:param str custom_html: Insert raw html to be added to the end of the section
:param dict modal: Create a modal. Is a dictionary. Valid keys are button, title and content
:raises NoValidTag: Raises not valid tag
Example:
>>> r += report.report_list_group('First entry', 'Second entry', ...)
"""
if not kwargs.get('title'):
raise rng.NotValidTag('Need a title')
title = kwargs.get('title')
if not isinstance(items, list):
raise rng.NotValidTag('Items have to be in the form of a list')
if 'section' in kwargs:
style = rng.CSSControl.sticky_section_css
else:
style = rng.CSSControl.css_overflow
with tag.div(
_class="jumbotron container context reportng-list-group-class",
style=style) as r:
t = tag.h1(title,
id="%s" % rng.HelperFunctions.id_with_random(5, title))
# creates a reference button with link
if 'reference' in kwargs:
t.add(rng.HelperFunctions.ref_button(kwargs.get('reference')))
# creates dismissable alert box
if 'alert' in kwargs:
rng.HelperFunctions.make_alert(kwargs.get('alert'))
with tag.ul(_class="list-group"):
for i in range(len(items)):
tag.li(
items[i],
_class=
"list-group-item d-flex justify-content-between align-items-center text-primary"
)
if 'badge' in kwargs:
rng.HelperFunctions.create_badges(kwargs.get('badge'))
if 'custom_html' in kwargs:
raw(kwargs.get('custom_html'))
if 'modal' in kwargs:
if isinstance(kwargs.get('modal'), dict):
rng.HelperFunctions.make_modals(title.replace(' ', ''),
kwargs.get('modal'))
return rng.HelperFunctions.convert_to_string(r)
def generateHtml():
with open(path.join(current_dir, '../changelog/', 'storage.json'),
'r') as f:
data = json.load(f)[::-1]
doc = document(title='Changelog - lkellar.org')
articles = []
with doc.head:
tags.link(rel='stylesheet', href='style.css')
tags.meta(charset="UTF-8")
tags.meta(name="description",
content="A log of all changes made on lkellar.org")
tags.meta(name="viewport",
content="width=device-width, initial-scale=1")
tags.link(rel="alternate",
title="Changelog Feed",
type="application/json",
href="https://lkellar.org/changelog/feed.json")
with doc:
with tags.nav().add(tags.ol()):
with tags.li():
tags.a("Home", href="../")
tags.li("Changelog")
with tags.main():
tags.h1('Changelog')
for entry in data:
tags.hr()
article_content = tags.article()
with article_content:
tags.h2(
f'{entry["title"]} - {entry["date"].split("T")[0]}',
id=f'{entry["title"]} - {entry["date"]}'.replace(
' ', ''.lower()))
list_content = tags.ul()
with list_content:
for line in entry['items']:
line = urls.sub(r'<a href="\2">\1</a>', line)
tags.li(raw(line))
articles.append((f'{entry["title"]} - {entry["date"]}'.replace(
' ', ''.lower()), list_content.render(), entry["date"],
entry['title']))
with open(path.join(current_dir, '../changelog/', 'index.html'), 'w') as f:
f.write(doc.render())
generateFeed(articles)
def new_user(form, ws_url, errors=None):
title = 'New User'
d = _doc(title)
with d:
with t.form(action=form.action, method='post'):
with t.fieldset():
t.legend(title)
_errors(errors)
with t.ol(cls='step_numbers'):
with t.li():
t.p('First, create a one-word username for yourself (lowercase, no spaces)...'
)
_text_input(
*form.nv('new_username'),
('required', 'autofocus'), {
'pattern': valid.re_username,
'oninput': 'check_username(this.value)'
}, 'Type new username here',
_invalid(valid.inv_username,
form.invalid('new_username')))
_invalid(valid.inv_username_exists, False,
'username_exists_message')
with t.li():
t.p("Next, invent a password; type it in twice to make sure you've got it..."
)
_text_input('password',
None, ('required', ),
{'pattern': valid.re_password},
'Type new password here',
_invalid(valid.inv_password,
form.invalid('password')),
type_='password')
_text_input('password_confirmation',
None, ('required', ),
None,
'Type password again for confirmation',
_invalid(
valid.inv_password_confirmation,
form.invalid('password_confirmation'),
'password_match_message'),
type_='password')
with t.li():
t.p("Finally, type in an email address that can be used if you ever need a password reset (optional, but this may be very useful someday!)..."
)
_text_input(
*form.nv('email'), None,
{'pattern': valid.re_email},
'Type email address here',
_invalid(valid.inv_email, form.invalid('email')))
t.input_(type="submit", value="Done!")
t.script(_js_validate_new_user_fields())
t.script(_js_check_username(ws_url))
return d.render()
def slide_indicator(num):
"""
Helper function that controls how image slide count works
"""
with tag.ol(_class="carousel-indicators") as o:
for cnt in range(num):
if cnt == 0:
tag.li(data_target="#carousel_controls",
data_slide_to="0", _class="active")
else:
tag.li(data_target="#carousel_controls",
data_slide_to="%s" % str(cnt))
return o
def render_comment(self, row: Row):
"""Render description column."""
comment = row.get('comment', '') or ''
if comment:
yield raw(comment)
if row['prov_value'] is None:
return
see_also_links = list(
map(
operator.itemgetter('link'),
self.query(
'''
SELECT ?link WHERE {
$node rdfs:seeAlso ?link .
OPTIONAL {
$node octa:position ?position .
}
}
ORDER BY ?position
''',
node=row['prov_value'],
),
), )
if see_also_links:
yield ul(
li(render(
node=link,
octiron=self.octiron,
), ) for link in see_also_links)
def _pagerlink(self,
page: int,
text: str,
extra_attributes: Optional[dict[str, Any]] = None):
anchor = super(Page, self)._pagerlink(page, text)
extra_attributes = extra_attributes or {}
return str(tags.li(anchor, **extra_attributes))
def visit_LogIn(self, node):
item = tags.li()
inner = item.add(tags.a(href=node.get_url(), _class="nav-image"))
inner.add(tags.img(src=url_for("static", filename="sso_login.png")))
if node.active:
item['class'] = 'active'
return item
def author(self):
authors = self.octiron.query('''
SELECT ?name ?url WHERE {
?page adr:author [
schema:name ?name ;
schema:url ?url
] .
}
''',
page=self.iri)
if not authors:
return ''
if len(authors) < 2:
author, = authors
dom = tags.li(
tags.a(
tags.strong('Author: '),
author['name'],
cls='md-nav__link',
href=author['url'],
target='_blank',
),
cls='md-nav__item',
)
return str(dom)
raise ValueError('page has too many authors!')
def visit_Subgroup(self, node):
if not self._in_dropdown:
node_id = sha1(str(id(node)).encode()).hexdigest()
li = tags.li(_class='dropdown')
if node.active:
li['class'] = 'active'
a = li.add(
tags.a(href='javascript:void(0);', _class='dropdown-toggle'))
a.add(tags.i(_class='fa fa-fw fa-arrows-v'))
a.add(node.title)
a['data-toggle'] = 'collapse'
a['data-target'] = '#' + node_id
a['role'] = 'button'
a['aria-haspopup'] = 'true'
a['aria-expanded'] = 'false'
if hasattr(node, 'icon') and node.icon != None:
a.add(tags.i(_class='fa fa-fw fa-%s' % node.icon))
ul = li.add(tags.ul(_class='collapse', id=node_id))
active = node.active
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
if item.active:
active = True
self._in_dropdown = False
if active == True:
li['class'] = 'sub_active'
ul['class'] = 'collapse in'
return li
else:
raise RuntimeError('Cannot render nested Subgroups')
def visit_View(self, node):
item = tags.li()
item.add(tags.a(node.text, href=node.get_url(), title=node.text))
if node.active:
item["class"] = "active"
return item
def visit_Subgroup(self, node):
if not self._in_dropdown:
li = tags.li(_class='dropdown')
if node.active:
li['class'] = 'active'
a = li.add(tags.a(href='#', _class='dropdown-toggle'))
if node.icon is not None:
a.add(tags.i(_class=str(node.icon)))
a.add(tags.span(node.title))
else:
a.add_raw_string(node.title)
a['data-toggle'] = 'dropdown'
a['role'] = 'button'
a['aria-haspopup'] = 'true'
a['aria-expanded'] = 'false'
a.add(tags.span(_class='caret'))
ul = li.add(tags.ul(_class='dropdown-menu'))
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
self._in_dropdown = False
return li
else:
raise RuntimeError('Cannot render nested Subgroups')
def visit_View(self, node):
item = tags.li()
item.add(tags.a(node.text, href=node.get_url(), title=node.text))
if node.active:
item['class'] = 'active'
return item
def get_html_forms(self, datatset_name_form=True):
"""generates html forms for all the metadata elements associated with this logical file
type
:param datatset_name_form If True then a form for editing dataset_name (title) attribute is
included
"""
root_div = div()
with root_div:
if datatset_name_form:
self._get_dataset_name_form()
keywords_div = div(cls="col-sm-12 content-block",
id="filetype-keywords")
action = "/hsapi/_internal/{0}/{1}/add-file-keyword-metadata/"
action = action.format(self.logical_file.__class__.__name__,
self.logical_file.id)
delete_action = "/hsapi/_internal/{0}/{1}/delete-file-keyword-metadata/"
delete_action = delete_action.format(
self.logical_file.__class__.__name__, self.logical_file.id)
with keywords_div:
legend("Keywords")
with form(id="id-keywords-filetype",
action=action,
method="post",
enctype="multipart/form-data"):
input(id="id-delete-keyword-filetype-action",
type="hidden",
value=delete_action)
with div(cls="tags"):
with div(id="add-keyword-wrapper", cls="input-group"):
input(id="txt-keyword-filetype",
cls="form-control",
placeholder="keyword",
type="text",
name="keywords")
with span(cls="input-group-btn"):
a("Add",
id="btn-add-keyword-filetype",
cls="btn btn-success",
type="button")
with ul(id="lst-tags-filetype",
cls="custom-well tag-list"):
for kw in self.keywords:
with li(cls="tag"):
span(kw)
with a():
span(
cls=
"glyphicon glyphicon-remove-circle icon-remove"
)
p("Duplicate. Keywords not added.",
id="id-keywords-filetype-msg",
cls="text-danger small",
style="display: none;")
self.get_extra_metadata_html_form()
self.get_temporal_coverage_html_form()
return root_div
def construct_list_items(violations) -> Iterable[li]:
"""Construct list items."""
for violation in violations:
yield li(
strong(code(violation['code'])),
a(violation['title'], href=violation['url']),
)
def visit_View(self, node):
item = tags.li()
a = item.add(tags.a(node.text, href=node.get_url(), title=node.text))
if hasattr(node, 'icon') and node.icon != None:
a.add(tags.i(_class='fa fa-fw fa-%s' % node.icon))
if node.active:
item['class'] = 'active'
return item
def dict_html(container, query, dict_, source, target):
container.add(div(query, cls='word'))
container.add(div(raw(
f'{langs[source]} -> {langs[target[0]]}'), cls='lang'))
for w in dict_:
def_box = container.add(div()).add(ul())
defin = dict_[w]
def_box.add(li(f'{w} ({defin["word_type"]})'.lower(),
cls='definition'))
synonyms = def_box.add(ol())
for syn in defin['variants']:
if not syn[1]:
synonyms.add(li(syn[0], cls='synonyms'))
else:
syn_word = synonyms.add(li(f'{syn[0]} ',
cls='synonyms has_example'))
syn_word.add(sup(syn[1]))
def visit_SuperGroup(self, node):
li = tags.li(_id=sanitise_for_css(node.title.text), _class="parent")
if node.title.active:
li['class'] = 'parent active'
a = li.add(tags.a(node.title.text, href=node.title.get_url()))
ul = tags.ul(*[self.visit(item) for item in node.items])
ul2 = li.add(ul)
return li
def visit_View(self, node):
item = tags.li()
item.add(tags.a(node.text, _class='nav-link', href=node.get_url(), title=node.text))
if node.active:
item['class'] = 'nav-item active'
else:
item['class'] = 'nav-item'
return item
def create_page(self):
# Open plots directory
if not os.path.isdir(self.get_output('plots')):
os.mkdir(self.get_output('plots'))
# Create HTML page
self.doc = dom.document(title='BBPipe plots page')
with self.doc.head:
dtg.link(rel='stylesheet', href='style.css')
dtg.script(type='text/javascript', src='script.js')
with self.doc:
dtg.h1("Pipeline outputs")
dtg.h2("Contents:", id='contents')
lst = dtg.ul()
lst += dtg.li(dtg.a('Bandpasses', href='#bandpasses'))
lst += dtg.li(dtg.a('Coadded power spectra', href='#coadded'))
lst += dtg.li(dtg.a('Null tests', href='#nulls'))
lst += dtg.li(dtg.a('Likelihood', href='#like'))
def visit_LogIn(self, node):
item = tags.li()
inner = item.add(
tags.a(href=node.get_url(), _class="nav-image"))
inner.add(
tags.img(src=url_for("static", filename="sso_login.png")))
if node.active:
item['class'] = 'active'
return item
def visit_Link(self, node):
if self._in_dropdown:
return tags.a(node.text,
href=node.get_url(),
_class='dropdown-item')
item = tags.li(_class='nav-item')
item.add(tags.a(node.text, href=node.get_url(), _class='nav-link'))
return item
def add(self, *items, active=False):
added = []
_items = parse_into_single_tuple(items)
for item in _items:
_type = getattr(type(item), 'tagname', None)
if _type is 'li' or isinstance(item, li):
super().add(item)
added.append(item)
else:
if active is True:
element = super().add(li(item, _class='active', style='float:left;'))
else:
element = super().add(li(item, style='float:left;'))
added.append(element)
if len(added) == 1:
return added[0]
else:
return tuple(added)
def visit_Link(self, node):
if hasattr(node, '_in_dropdown'):
item = tags.a(node.text,
href=node.get_url(),
_class="dropdown-item")
else:
item = tags.li(_class="nav-item")
item.add(tags.a(node.text, href=node.get_url(), _class="nav-link"))
return item
def visit_Link(self, node):
a = tags.a(href=node.get_url())
if node.icon is not None:
a.add(tags.i(_class=str(node.icon)))
a.add(tags.span(node.text))
else:
a.add_raw_string(node.text)
li = tags.li()
li.add(a)
return li
def visit_Navbar(self, node):
kwargs = {'_class': 'navbar'}
kwargs.update(self.kwargs)
cont = tags.nav(**kwargs)
ul = cont.add(tags.ul())
for item in node.items:
ul.add(tags.li(self.visit(item)))
return cont
def visit_Subgroup(self, node):
group = tags.ul(_class='subgroup')
title = tags.span(node.title)
if node.active:
title.attributes['class'] = 'active'
for item in node.items:
group.add(tags.li(self.visit(item)))
return tags.div(title, group)
def add_footnote_to_output(paragraphs):
with tags.li():
for (para) in paragraphs:
for (run) in para.runs:
style = footer.get_style(run)
if style == "bolded":
with tags.span(run.text):
tags.attr(cls="sub-subject_small")
else:
with tags.span(run.text):
tags.attr(cls="definition_small")
tags.br()
def visit_Subgroup(self, node):
if not self._in_dropdown:
li = tags.li(_class='dropdown')
if node.active:
li['class'] = 'active'
a = li.add(tags.a(node.title, href='#', _class='dropdown-toggle'))
a['data-toggle'] = 'dropdown'
a['role'] = 'button'
a['aria-haspopup'] = 'true'
a['aria-expanded'] = 'false'
a.add(tags.span(_class='caret'))
ul = li.add(tags.ul(_class='dropdown-menu'))
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
self._in_dropdown = False
return li
else:
raise RuntimeError('Cannot render nested Subgroups')
def visit_Subgroup(self, node):
if not self._in_dropdown:
li = tags.li(_class="dropdown")
if node.active:
li["class"] = "active"
a = li.add(tags.a(node.title, href="#", _class="dropdown-toggle"))
a["data-toggle"] = "dropdown"
a["role"] = "button"
a["aria-haspopup"] = "true"
a["aria-expanded"] = "false"
a.add(tags.span(_class="caret"))
ul = li.add(tags.ul(_class="dropdown-menu"))
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
self._in_dropdown = False
return li
else:
raise RuntimeError("Cannot render nested Subgroups")
def visit_Separator(self, node):
if not self._in_dropdown:
raise RuntimeError('Cannot render separator outside Subgroup.')
return tags.li(role='separator', _class='divider')
def visit_Link(self, node):
item = tags.li()
item.add(tags.a(node.text, href=node.get_url()))
return item
def visit_Text(self, node):
if not self._in_dropdown:
return tags.p(node.text, _class='navbar-text')
return tags.li(node.text, _class='dropdown-header')
def add_footnote_to_output(paragraphs):
text = ""
for (para) in paragraphs:
text += para.text
tags.li(text)
def visit_LinkTab(self, node):
item = tags.li()
item.add(tags.a(node.text, href=node.get_url(), target="_blank"))
return item
def generatePostStatsHTML(graph,statsFilePath = "stats.html",postStatsFilePath = "postStats.html"): #Generates Post-Stats page
voxelWise = checkHeightThreshold(graph)
clusterWise = checkExtentThreshold(graph)
softwareLabelNum = queryVersionNum(graph)
softwareLabelNumList = addQueryToList(softwareLabelNum)
statisticType = queryStatisticType(graph)
statisticType = statisticImage(statisticType[0])
statisticTypeString = statisticImageString(statisticType)
contrastName = queryContrastName(graph)
statisticMapImage = queryExcursionSetMap(graph)
postStats = document(title="FSL Viewer") #Creates initial HTML page (Post Stats)
postStats += h1("Sample FSL Viewer")
postStats += ul(li(a("Stats", href="stats.html")), li("-"),li(a("Post Stats", href = "postStats.html")))
postStats += h2("Post-stats")
postStats += hr()
postStats += h3("Analysis Methods")
if voxelWise == True: #If main threshold is Height Threshold
mainThreshValue = queryHeightThresholdValue(graph)
if askSpm(graph) == True:
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded at P = %s (corrected)" % (softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif askFsl(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)."
"%s statistic images were thresholded at P = %s (corrected)"
%(fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif clusterWise == True: #If main threshold is extent threshold
mainThreshValue = queryClusterThresholdValue(graph)
heightThreshValue = queryUHeightThresholdValue(graph)
clusterThreshType = clusterFormingThreshType(graph, statisticType)
if askSpm(graph) == True:
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded using clusters determined by %s > %s and a (corrected) "
"cluster significance of P = %s "
% (softwareLabelNumList[1], statisticTypeString, clusterThreshType, heightThreshValue[0], mainThreshValue[0]))
elif askFsl(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl). %s statistic images were thresholded "
"using clusters determined by %s > %s and a (corrected) cluster significance of P = %s"
%(fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, clusterThreshType, heightThreshValue[0], mainThreshValue[0]))
else: #If there is no corrected threshold - assume voxel wise
mainThreshValue = queryUHeightThresholdValue(graph)
if askSpm(graph) == True and askIfPValueUncorrected(graph) == True: #SPM used and threshold type is nidm_PValueUncorrected
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded at P = %s (uncorrected)" % (softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif askSpm(graph) == True and askIfOboStatistic(graph) == True: #SPM used and threshold type is obo_statistic
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded at %s = %s (uncorrected)" % (softwareLabelNumList[1], statisticTypeString, statisticType, mainThreshValue[0]))
elif askFsl(graph) == True and askIfPValueUncorrected(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)."
"%s statistic images were thresholded at P = %s (uncorrected)." % (fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif askFsl(graph) == True and askIfOboStatistic(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)."
"%s statistic images were thresholded at %s = %s (uncorrected)." % (fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, statisticType, mainThreshValue[0]))
postStats += hr()
postStats += h3("Thresholded Activation Images")
postStats += hr()
i = 0
if askFsl(graph) == True:
while i < len(contrastName):
postStats += p("%s" % contrastName[i])
postStats += img(src = statisticMapImage[i])
i = i + 1
postStatsFile = open(postStatsFilePath, "x")
print(postStats, file = postStatsFile)
postStatsFile.close()
def visit_Separator(self, node):
if not self._in_dropdown:
raise RuntimeError("Cannot render separator outside Subgroup.")
return tags.li(role="separator", _class="divider")
def fix_links(html_docs_l):
# fix outbound links
print "Fixing links"
for (doc) in html_docs_l:
for (child) in doc.body.children[0].children:
if 'definition' in child.attributes.get('class', ()):
href = ""
try:
href = child.children[0].attributes.get("href")
except AttributeError as e:
pass
# it's a link - try to update it
if href:
# first, strip it of weird chars
try:
href = clean_name(href)
updated = False
if update_values_for_href(child, href):
updated = True
else:
if href[0] in (u"ה", u"ו", u"ש", u"ב", u"כ", u"ל", u"מ"):
updated = update_values_for_href(child, href[1:])
if not updated:
# failed to update - it's not a real link...
update_href_no_link(child)
except Exception as e:
pass
print e, "Exception of HREF update", href
#TODO - investigate why it happens? (it's a single corner case, I think)
def sorter(html_doc):
if html_doc.name in [u"ערכים כלליים",]:
return "FIRST"
if html_doc.name in [u"נספחות",]:
return u"תתתתתתתתתת" #last
else:
return html_doc.name
# update sections menu
for (doc) in html_docs_l:
letters_l = []
# content_menu = doc.body.children[0].children[1].children[0].children[0].children[-1].children[0].children[1]
content_menu = doc.body.children[0].children[1].children[0].children[1].children[-1]
assert content_menu['class'] == 'dropdown-menu dropdown-menu-left scrollable-menu'
with content_menu:
with tags.li():
tags.a(u"אודות", href="index.html")
with tags.li():
tags.a(u"הקדמות", href="opening_intros.html")
with tags.li():
tags.a(u"הסכמות", href="opening_haskamot.html")
with tags.li():
tags.a(u"קיצורים", href="opening_abbrev.html")
with tags.li():
tags.a(u"סימנים", href="opening_signs.html")
# if you add more entries here, please update add_menu_to_apriory_htmls(..)
with tags.li():
tags.attr(cls="divider")
sorted_html_docs_l = sorted(html_docs_l, key=sorter)
for (html_doc) in sorted_html_docs_l:
# Only if this a 'high' heading, and not just a letter - include it in the TOC
if html_doc.name != "NEW_LETTER":
with tags.li():
tags.a(html_doc.name, href=str(html_doc.index)+".html")
if doc.section == html_doc.section:
tags.attr(cls="active")
else:
# it's a letter - if it's related to me, save it
if doc.section == html_doc.section:
letters_l.append(html_doc)
with doc.body.children[-1]:
assert doc.body.children[-1]['class'] == 'container-fluid'
with tags.ul():
tags.attr(cls="pagination")
for (html_doc) in letters_l:
tags.li(tags.a(html_doc.letter, href=str(html_doc.index)+".html"))
return html_docs_l
def visit_Text(self, node):
if not self._in_dropdown:
raise RuntimeError('Cannot render label outside Subgroup')
return tags.li(node.text, _class='dropdown-header')
