def createTitle():
doc.preamble.append(pylatex.Command('title', 'Superphreak'))
doc.preamble.append(pylatex.Command('author', 'Douglas Luman'))
doc.preamble.append(pylatex.Command('date', '2016'))
doc.append(pylatex.utils.NoEscape(r'\maketitle'))
doc.generate_pdf('title', clean_tex=False)
def create_doc(title, with_tikz=False):
logging.info("Creating PDF...")
doc = pylatex.Document(geometry_options={'margin': '1.5cm'})
doc.packages.append(pylatex.Package('hyperref'))
doc.packages.append(pylatex.Package('amssymb'))
doc.packages.append(pylatex.Package('amsmath'))
doc.packages.append(pylatex.Package('float'))
doc.packages.append(
pylatex.Package('caption', {
'labelformat': 'empty',
'justification': 'centering'
}))
#doc.packages.append(pylatex.Package('todonotes'))
# I don't think these are needed
#doc.packages.append(pylatex.Package('needspace'))
#doc.packages.append(pylatex.Package('pgfplots'))
if with_tikz:
doc.packages.append(pylatex.Package('tikz'))
doc.preamble.append(
pylatex.Command('usetikzlibrary', 'decorations.markings'))
doc.preamble.append(pylatex.Command('usetikzlibrary', 'fit'))
doc.preamble.append(pylatex.Command('usetikzlibrary', 'plotmarks'))
doc.preamble.append(pylatex.Command('title', title))
doc.preamble.append(pylatex.Command('date', ''))
doc.append(pylatex.NoEscape(r"\maketitle"))
doc.append(pylatex.NoEscape(r"\tableofcontents"))
doc.append(pylatex.NoEscape(r"\newpage"))
doc.append(
pylatex.NoEscape(r"\captionsetup[subfigure]{labelformat=empty}"))
return doc
def _gen_title(self):
"""Add metadata to preamble and `\\\\maketitle` to body."""
date = pl.NoEscape(r'\today')
self.doc.preamble.append(pl.Command('title', self.args['title']))
self.doc.preamble.append(pl.Command('author', self.args['author']))
self.doc.preamble.append(pl.Command('date', date))
self.doc.append(pl.NoEscape(r'\maketitle'))
def _add_headers(self):
"""Add the `pagestyle` command and the headers/footers to the preamble."""
self.doc.preamble.append(pl.Command('pagestyle', 'fancy'))
self.doc.preamble.append(pl.Command('fancyhf', ' '))
for pos, val in self.args['heads'].items():
if val:
self.doc.preamble.append(pl.Command(pos, val))
def __init__(self, name, number, bank):
self.name = name
self.number = number
self.bank = bank
geometry_options = {
"tmargin": "35mm",
"lmargin": "25mm",
"textwidth": "160mm",
"textheight": "237mm",
}
self.doc = tex.Document(f"AccountReport_{self.name}",
documentclass="article",
document_options=['10pt', "a4paper"],
geometry_options=geometry_options,
lmodern=False)
self.doc.preamble.append(
tex.NoEscape(r"\renewcommand{\familydefault}{\sfdefault}"))
self.doc.preamble.append(tex.Command('usepackage', 'helvet'))
self.doc.preamble.append(
tex.Command('usepackage', arguments='placeins', options="section"))
self.addHeader()
self.doc.preamble.append(tex.Command('title', "Financial Report"))
# self.doc.preamble.append(Command('bank', 'Anonymous author'))
self.doc.preamble.append(tex.Command('date', tex.NoEscape(r'\today')))
def dumps(self):
name_short = self.name_short
if name_short is None:
name_short = self.acronym
command = pylatex.Command(
command='newacro',
arguments=[self.acronym, ],
options=[name_short],
extra_arguments=[pylatex.NoEscape(self.name_full), ]
).dumps()
command += pylatex.Command(
command='newcommand',
arguments=[pylatex.NoEscape('\\' + self.acronym), pylatex.NoEscape(r'\ac{' + self.acronym + '}')],
).dumps()
if self.plural:
command += pylatex.Command(
command='newcommand',
arguments=[pylatex.NoEscape('\\' + self.acronym + 's'), pylatex.NoEscape(r'\acp{' + self.acronym + '}')],
).dumps()
if self.short:
command += pylatex.Command(
command='newcommand',
arguments=[pylatex.NoEscape('\\' + self.acronym + 'Short'), pylatex.NoEscape(r'\acs{' + self.acronym + '}')],
).dumps()
return command
def ImprLtxPresEjecMat(self, doc):
#doc.append(u"\\subportadilla{Presupuestos Generales}{Presupuesto de ejecución material}" + '\n')
chapter = pylatex_utils.Chapter(
title=u'Presupuesto de ejecución material', numbering=False)
chapter.append(pylatex.Command('cleardoublepage'))
center = pylatex.Center()
center.append(pylatex_utils.LargeCommand())
center.append(pylatex.utils.bold(u'Presupuesto de Ejecución Material'))
center.append(pylatex_utils.largeCommand())
chapter.append(center)
chapter.append(pylatex.VerticalSpace('2cm'))
self.subcapitulos.ImprLtxResumen(chapter, "", False)
chapter.append(
pylatex.utils.bold(u'Presupuesto de Ejecución Material:'))
chapter.append(pylatex.Command('dotfill'))
chapter.append(pylatex.utils.bold(self.getLtxPriceString()))
chapter.append(pylatex.VerticalSpace('0.5cm'))
chapter.append(pylatex.NewLine())
chapter.append(
u'Asciende el presente presupuesto de ejecución material a la expresada cantidad de: '
)
chapter.append(
pylatex_utils.textsc(
basic_types.to_words(self.getRoundedPrice(), False) +
' euros.'))
chapter.append(pylatex_utils.input('firmas'))
doc.append(chapter)
def make_table_file(
name: str,
strings_per_bar: tuple,
title_per_bar=None,
available_columns_per_bar=None,
) -> None:
if not available_columns_per_bar:
available_columns_per_bar = tuple(37 for i in strings_per_bar)
if title_per_bar is None:
title_per_bar = tuple([
"Fret positions for bar {0}".format(idx + 1)
for idx in range(len(strings_per_bar))
])
tables = tuple(
make_string_table(strings, available_columns=available_columns)
for strings, available_columns in zip(strings_per_bar,
available_columns_per_bar))
doc = pylatex.Document(document_options=["landscape", "a4paper"])
doc.preamble.append(pylatex.Command("usepackage", arguments="lscape"))
doc.preamble.append(pylatex.Command("usepackage", arguments="xcolor"))
doc.preamble.append(
pylatex.NoEscape(r"\usepackage[a4paper,bindingoffset=0.2in,%"))
doc.preamble.append(
pylatex.NoEscape(r"left=0.5cm,right=1cm,top=1.5cm,bottom=1cm,%"))
doc.preamble.append(pylatex.NoEscape(r"footskip=.25in]{geometry}"))
doc.preamble.append(pylatex.NoEscape(r"\pagenumbering{gobble}"))
for title, table in zip(title_per_bar, tables):
# doc.append(pylatex.utils.bold(pylatex.LargeText(title)))
doc.append(pylatex.LargeText(pylatex.utils.bold(title)))
doc.append(table)
doc.generate_pdf(name)
doc.generate_tex(name)
def writePriceTableTwoIntoLatexDocument(self, doc):
part = pylatex_utils.Part("Cuadro de precios no. 2")
part.append(pylatex.Command('parttoc'))
part.append(pylatex.Command('setcounter{chapter}{0}'))
super(Obra, self).writePriceTableTwoIntoLatexDocument(part, 'root')
part.append(pylatex.Command('input{firmas}'))
doc.append(part)
def generate_latex(dataset1, dataset2, output):
doc = pl.Document(page_numbers=True,
geometry_options={
"tmargin": "1cm",
"lmargin": "1cm"
})
doc.packages.append(pl.Package('booktabs'))
doc.preamble.append(
pl.Command('title', 'VH/VL Packing for Gradient Boosted Regression'))
doc.preamble.append(pl.Command('author', 'Veronica A. Boron'))
doc.append(pl.NoEscape(r'\maketitle'))
doc.append(
'This document summarizes results for predicting VHVL packing angles using Gradient Boosted Regression via the \
Scikit Learn framework.')
doc.append(pl.NoEscape(r'\maketitle'))
_add_data(doc, dataset1)
doc.append(pl.NoEscape(r'\newpage'))
_add_data(doc, dataset2)
doc.append(pl.NoEscape(r'\newpage'))
print('Generating PDF...')
doc.generate_pdf(output, clean_tex=False)
def sum_sample(self):
"""Summarize the analysis data and plots in a report
"""
for i in range(len(self.infiles)):
self.logger.info('\nCreating pdf for sample {} results.\n'.format(
self.sample[i]))
geometry_options = {
'tmargin': '3cm',
'bmargin': '3cm',
'rmargin': '3cm',
'lmargin': '3cm'
}
doc = px.Document(documentclass='article',
geometry_options=geometry_options)
doc.preamble.append(
px.Command('title',
'Sequencing results for sample ' + self.sample[i]))
doc.preamble.append(px.Command('date', px.NoEscape(r'\today')))
doc.append(px.NoEscape(r'\maketitle'))
with doc.create(px.Section('Genome coverage')):
#include table of results with statistics of coverage
with doc.create(px.Subsection('Coverage results')):
with doc.create(px.Tabular(table_spec='l l')) as table:
with open(self.stats_file, 'r') as stats:
table.add_hline()
stats_data = pd.read_csv(stats, sep='\t')
for num in range(len(stats_data.iloc[0])):
table.add_row([
stats_data.columns[num],
stats_data.iloc[0][num]
])
table.add_hline()
#include coverage plot
with doc.create(px.Figure(position='htb!')) as plot:
plot.add_image(self.cov_plot[i],
width=px.NoEscape(r'\linewidth'))
plot.add_caption(
'Genome coverage for sample ' + self.sample[i] +
'. Calculated using samtools depth with zero-coverage positions included.'
)
#include mismatch plot comparing the sample to the reference
with doc.create(px.Section('Comparison to reference genome')):
with doc.create(px.Figure(position='htb!')) as plot:
plot.add_image(self.basefreq_plot + '_' + self.sample[i] +
'.png',
width=px.NoEscape(r'\linewidth'))
plot.add_caption(
'Mismatch fraction per position for sample ' +
self.sample[i] +
'. Calculated compared to reference {}.'.format(
self.config['folder_locations']['ref_fasta']))
doc.generate_pdf(
filepath=os.path.join(self.outputdir, self.sample_info[i] +
'.Report'))
self.logger.info(
'\nDone creating pdf for sample {} results.\n'.format(
self.sample[i]))
def ImprCompLtxPreParc(self, otra, doc):
part = pylatex_utils.Part('Presupuestos parciales')
part.append(pylatex.Command('parttoc'))
part.append(pylatex.Command('setcounter{chapter}{0}'))
part.append(pylatex_utils.ltx_begin("landscape") + '\n')
super(Obra, self).ImprCompLtxPre(part, 'root', otra)
part.append(pylatex_utils.ltx_end("landscape") + '\n')
doc.append(part)
def append_a_lgs(doc, lsgen, eqns, vars, no_or_inf_solutions=False, homogen=False):
doc.append(pylatex.Command('item'))
doc.append(pylatex.Command('('))
doc.append(pylatex.Command('displaystyle'))
with doc.create(Array(options="t", arguments="rrrrrr")):
ue, lsg = get_a_lgs(eqns, vars, no_or_inf_solutions, homogen)
doc.append(ue)
lsgen.append(lsg)
doc.append(pylatex.Command(')'))
def append_a_lsg(doc, lsg):
doc.append(pylatex.Command('item'))
doc.append(pylatex.Command('('))
doc.append(pylatex.Command('displaystyle'))
doc.append(pylatex.NoEscape('\\mathbb{L} = \\{('))
doc.append(", ".join(
map(str, map(int, lsg))
))
doc.append(pylatex.NoEscape(')\\}'))
doc.append(pylatex.Command(')'))
def create_tikz_doc():
logging.info("Creating PDF...")
doc = pylatex.Document(documentclass='standalone',
document_options=['crop', 'tikz'])
doc.packages.append(pylatex.Package('tikz'))
doc.preamble.append(
pylatex.Command('usetikzlibrary', 'decorations.markings'))
doc.preamble.append(pylatex.Command('usetikzlibrary', 'fit'))
doc.preamble.append(pylatex.Command('usetikzlibrary', 'plotmarks'))
return doc
def append_a_det(doc, lsgen, m=0, n=0, misproportion_possible=False):
doc.append(pylatex.Command('item'))
doc.append(pylatex.Command('('))
doc.append(pylatex.Command('displaystyle'))
with doc.create(Array(options="t", arguments="rrrrrr")):
if misproportion_possible:
[m, n] = [random.randint(2, 3, 4) for _ in range(2)]
A = rand_nice_numbers(m, n)
doc.append(pylatex.NoEscape(make_matr_tex(A)))
lsgen.append(np.linalg.det(A))
doc.append(pylatex.Command(')'))
def append_a_matr(doc, lsgen, m=0, p=0, n=0, misproportion_possible=False):
doc.append(pylatex.Command('item'))
doc.append(pylatex.Command('('))
doc.append(pylatex.Command('displaystyle'))
with doc.create(Array(options="t", arguments="rrrrrr")):
if misproportion_possible:
[m, p, n] = [random.randint(2, 3) for _ in range(3)]
ue, lsg = get_a_matr(m, p, n, misproportion_possible)
doc.append(ue)
lsgen.append(lsg)
doc.append(pylatex.Command(')'))
def _init_doc(self, name, add_date=True):
doc = pyl.Document(name, geometry_options=geometry_options)
doc.packages.append(pyl.Package('hyperref'))
doc.preamble.append(pyl.Command('title', f'Supplementary Figures for {name}'))
if add_date:
doc.preamble.append(pyl.Command('date', pyl.NoEscape(r'\today')))
else:
doc.preamble.append(pyl.Command('date', pyl.NoEscape(r'')))
doc.append(pyl.NoEscape(r'\maketitle'))
doc.append(pyl.NewPage())
return doc
def append_a_lsg(doc, lsg):
doc.append(pylatex.Command('item'))
doc.append(pylatex.Command('('))
doc.append(pylatex.Command('displaystyle'))
if lsg.__class__ == np.float64:
doc.append(str(int(round(lsg))))
elif lsg.__class__ == np.ndarray:
if (lsg == np.array([[0]])).all():
doc.append("Keine Lösung")
else:
with doc.create(Array(options="t", arguments="rrrrrr")):
doc.append(pylatex.NoEscape(make_matr_tex(lsg)))
doc.append(pylatex.Command(')'))
def render_table_cell_latex(cell, c, top_space, btm_space, widths):
cell = cell.walk(links_to_table_notes)
cell_wrapper = lc.Span()
content = utils.panflute2output(cell.content, format="latex")
style = ""
if cell.heading == 1:
style = "\\sffamily "
elif cell.heading == 2:
style = "\\sffamily\\small "
content = style + content
cell_width = widths[c]
if cell.col_span > 1:
cell_width = sum(widths[c:c + cell.col_span])
minipage = pl.MiniPage(
width="{}\\columnwidth".format(cell_width),
pos="t",
align="left",
content_pos="t",
)
minipage.append(pl.Command("setstretch", arguments="0.6"))
if cell.vertical:
minipage.append(lc.RotateBox(pl.NoEscape(content)))
else:
minipage.append(pl.NoEscape(content))
cell_wrapper.append(pl.Command("noindent"))
cell_wrapper.append(minipage)
if c == 0:
if top_space:
cell_wrapper.append(pl.Command("T"))
if btm_space:
cell_wrapper.append(pl.Command("B"))
if cell.col_span > 1:
margins = "@{}" if cell.rm_horizontal_margins else ""
multicolumn = pl.MultiColumn(cell.col_span,
align=pl.NoEscape(f"{margins}l{margins}"),
data=cell_wrapper)
return multicolumn
elif not cell.covered:
return cell_wrapper
def __init__(self, title):
super().__init__(geometry_options={
"tmargin": "1cm",
"lmargin": "1cm",
"rmargin": "1cm",
"bmargin": "2cm"})
self.preamble.append(tex.Package('graphicx'))
self.preamble.append(tex.Command('title', title))
self.preamble.append(tex.Command('author', 'Charles Wilmot'))
self.preamble.append(tex.Command('date', tex.utils.NoEscape(r'\today')))
self.append(tex.utils.NoEscape(r'\maketitle'))
self.clearpage()
self.append(tex.Command("tableofcontents"))
self.clearpage()
def _confusion_matrices(data):
for layer in data:
matrix = np.zeros((2,3))
for i_true in [1, 2, 3]:
subdata = data[layer][np.where(data[layer]['Output_number_true'] == i_true)]
for i_nn in [1, 2, 3]:
nclas = np.count_nonzero(subdata['Output_number_estimated'] == i_nn)
if i_nn == 1:
matrix[0, i_true - 1] = float(nclas) / subdata.shape[0]
else:
matrix[1, i_true - 1] += float(nclas) / subdata.shape[0]
table = latex.Tabular('r r c c c')
table.add_row('', '', '', latex.utils.bold('True'), '')
table.add_row(
'',
'',
latex.utils.bold('1'),
latex.utils.bold('2'),
latex.utils.bold('3')
)
table.add_hline()
table.append(latex.Command('addlinespace', options='3mm'))
for i in range(2):
if i == 0:
cell0 = latex.MultiRow(
# 3,
2,
data=latex.Command(
'rotatebox',
['90', latex.utils.bold('Network')],
'origin=c'
)
)
n = '1'
else:
cell0 = ''
n = '2/3'
row = [cell0, latex.utils.bold(n)]
for j in range(3):
row.append('{:.2f}'.format(matrix[i, j]))
table.add_row(row)
if i == 0:
table.append(latex.Command('addlinespace', options='4mm'))
path = 'confusion_{}.tex'.format(layer)
with open(path, 'w') as wfile:
wfile.write(table.dumps())
print ' -> wrote ' + path
def ImprLtxResumen(self, doc, sect, recurre=True):
if (self.hasQuantities()):
if (sect != 'root'):
doc.add_item(self.getTitle())
doc.append(pylatex.Command('dotfill'))
doc.append(self.getLtxPriceString())
else:
doc.append(pylatex_utils.LargeCommand())
doc.append(pylatex.utils.bold('Total'))
doc.append(pylatex.Command('dotfill'))
doc.append(pylatex.utils.bold(self.getLtxPriceString()))
doc.append(pylatex_utils.NormalSizeCommand())
if (recurre):
self.subcapitulos.ImprLtxResumen(
doc, pylatex_utils.getLatexSection(sect), recurre)
def _init_doc(self, add_date=True):
doc = pyl.Document(geometry_options=geometry_options)
doc.packages.append(pyl.Package("float"))
doc.packages.append(pyl.Package("hyperref"))
doc.preamble.append(pyl.Command("title", self.title))
if add_date:
doc.preamble.append(pyl.Command("date", pyl.NoEscape(r"\today")))
else:
doc.preamble.append(pyl.Command("date", pyl.NoEscape(r"")))
doc.append(pyl.NoEscape(r"\maketitle"))
doc.append(pyl.NewPage())
doc.append(pyl.Command("tableofcontents"))
doc.append(pyl.NewPage())
return doc
def add_hline(document):
if self.has_label:
cmd = r"\cline{" + "2-{0}".format(self.amount_elements +
1) + "}"
document.append(pylatex.NoEscape(cmd))
else:
document.append(pylatex.Command("hline"))
def add_page3(self):
doc = self.m_doc
doc.append("Influence of mesocrystal height")
doc.append(pl.VerticalSpace("2cm"))
doc.append("\n")
with doc.create(
pl.MiniPage(width=r"0.2\textwidth",
height=r"0.25\textwidth",
content_pos='t')):
lines = data.split("\n")
with doc.create(pl.Tabular('l l', row_height=0.8)) as table:
myfont = [mono, tiny]
for l in lines:
parts = l.split(":")
print(parts)
if len(parts) == 2:
table.add_row(parts[0], parts[1], mapper=myfont)
elif len(parts) == 1:
table.add_hline()
table.add_row((l, " "), mapper=myfont)
doc.append("\n")
with doc.create(
pl.MiniPage(width=r"0.8\textwidth",
height=r"0.25\textwidth",
content_pos='t')):
doc.append(
pl.Command('includegraphics',
options='scale=0.8',
arguments='meso.png'))
doc.append("\n")
doc.append(pl.NewPage())
def add2document(self, doc) -> None:
with doc.create(pylatex.Section(self.name)):
for table in self.tables:
table.add2document(doc)
doc.append(pylatex.NoEscape(""))
doc.append(pylatex.Command("newline"))
doc.append(pylatex.NoEscape(""))
doc.append(
pylatex.Command(
"vspace",
arguments="{0}mm".format(
self.VERTICAL_SPACE_BETWEEN_TABLE),
))
doc.append(pylatex.NoEscape(""))
doc.append(pylatex.Command("newline"))
doc.append(pylatex.NoEscape(""))
def addHeader(self):
# Add document header
header = tex.PageStyle("header",
header_thickness=1,
footer_thickness=1)
# Create left header
with header.create(tex.Head("L")):
header.append(f"Account name: {self.name}")
header.append(tex.LineBreak())
header.append(f"IBAN: {self.number}")
# Create right header
with header.create(tex.Head("R")):
header.append(self.bank)
# Create left footer
with header.create(tex.Foot("L")):
header.append("Econicer - Financial Report")
# Create right footer
with header.create(tex.Foot("R")):
header.append("Page ")
header.append(tex.Command("thepage"))
self.doc.preamble.append(header)
self.doc.change_document_style("header")
def addYearlyReports(self, plotPaths):
for i, (year, paths) in enumerate(plotPaths.items()):
self.addYearSection(year, paths)
if (i + 1) % 2 == 0:
self.doc.append(tex.Command("newpage"))
def ImprLtxPre(self, doc, sect):
'''Imprime presupuestos parciales.'''
if (self.hasQuantities()):
if (sect != 'root'):
doc.append(pylatex.Section(self.getTitle()))
self.quantities.ImprLtxPre(doc, self.getTitle())
self.subcapitulos.ImprLtxPre(doc,
pylatex_utils.getLatexSection(sect))
if self.subcapitulos:
doc.append(pylatex.Command('noindent'))
doc.append(pylatex_utils.largeCommand())
doc.append(
pylatex.utils.bold('Total: ' + self.getTitle() + ' '))
doc.append(pylatex.Command('dotfill'))
doc.append(pylatex.utils.bold(self.getLtxPriceString()))
doc.append(pylatex.NewLine())
doc.append(pylatex_utils.NormalSizeCommand())
