def test_graphics():
f = Figure(data=None, position=None)
f.add_image(filename="", width=r"0.8\textwidth", placement=r"\centering")
f.add_caption(caption="")
# Subfigure
s = SubFigure(data=None, position=None, width=r"0.45\linewidth", seperate_paragraph=False)
s.add_image(filename="", width="r\linewidth", placement=None)
s.add_caption(caption="")
# Matplotlib
plot = MatplotlibFigure(data=None, position=None)
x = [0, 1, 2, 3, 4, 5, 6]
y = [15, 2, 7, 1, 5, 6, 9]
pyplot.plot(x, y)
plot.add_plot(width=r"0.8\textwidth", placement=r"\centering")
plot.add_caption(caption="I am a caption.")
# Quantities
Quantity(quantity=1 * pq.kg)
Quantity(quantity=1 * pq.kg, format_cb=lambda x: str(int(x)))
def test_graphics():
f = Figure(data=None, position=None)
f.add_image(filename='', width=r'0.8\textwidth', placement=r'\centering')
f.add_caption(caption='')
repr(f)
# Subfigure
s = SubFigure(data=None, position=None, width=r'0.45\linewidth')
s.add_image(filename='', width='r\linewidth',
placement=None)
s.add_caption(caption='')
repr(s)
# Matplotlib
plot = Figure(data=None, position=None)
x = [0, 1, 2, 3, 4, 5, 6]
y = [15, 2, 7, 1, 5, 6, 9]
pyplot.plot(x, y)
plot.add_plot(width=r'0.8\textwidth', placement=r'\centering')
plot.add_caption(caption='I am a caption.')
repr(plot)
def add_figure(self,file=None,caption=None,width='240px'):
""" 添加图形
:param str file: 图形文件路径
:param str caption: 图形标题
:param str width: 图形宽度
:return: 无返回值
"""
graph = Figure(position='h!')
graph.add_image(file, width=width)
if caption is not None:
graph.add_caption(caption)
self.doc.append(graph)
def test_graphics():
f = Figure(data=None, position=None)
f.add_image(filename="", width=r"0.8\textwidth", placement=r"\centering")
f.add_caption(caption="")
# Subfigure
s = SubFigure(data=None, position=None, width=r"0.45\linewidth", separate_paragraph=False)
s.add_image(filename="", width="r\linewidth", placement=None)
s.add_caption(caption="")
# Matplotlib
plot = Figure(data=None, position=None)
x = [0, 1, 2, 3, 4, 5, 6]
y = [15, 2, 7, 1, 5, 6, 9]
pyplot.plot(x, y)
plot.add_plot(width=r"0.8\textwidth", placement=r"\centering")
plot.add_caption(caption="I am a caption.")
def pile_report(self, pile, pile2, F, factor=1.25):
"""添加桩基长度计算内容"""
self.soil = pile.soil
llist = pl.get_l(self.soil, pile.d, F, factor, pile.h1, pile.rho,
pile.t, pile.k2, pile2.type, pile2.completion)
ra_1, ra_2 = pl.pile_l(llist, self.soil, pile.d, F, pile.h1, pile.rho,
pile.t, pile.k2, pile2.type, pile2.completion)
if ra_1.max() > ra_2.max():
ptype = '摩擦桩'
ra = ra_1.max()
else:
ptype = '端承桩'
ra = ra_2.max()
t1 = f'''桩基直径：$d={pile.d:.2f}\,m$\n
桩基周长：$u={pile.u:.2f}\,m$\n
桩基截面积：$A_p={pile.pd:.2f}\,m^2$\n
桩基密度：$\gamma={pile.rho:.1f}\,kN/m^3$\n
容许承载力随深度的修正系数：$k_2={pile.k2:.1f}$\n
各土层加权平均重度：$\gamma_2={self.soil.rho:.1f}\,kN/m^3$\n
清底系数：$m_0={pile.m0:.1f}$
'''
t2 = '根据规范5.3.3可得，摩擦桩单桩承载力为'
m1 = ['[R_a]', '=\\frac{1}{2}u\\sum_{i=1}^nq_{ik}l_i+A_pq_r']
t3 = '根据规范5.3.4可得，端承桩单桩承载力为'
m2 = [
'[R_a]=', 'c_1A_pf_{rk}', '+u\\sum_{i=1}^mc_{2i}h_if_{rki}',
'+\\frac{1}{2}\\xi_su\sum_{i=1}^nl_iq_{ik}'
]
t4 = '考虑桩身自重与置换土重，桩基承载力为'
m3 = ['R_a', '=[R_a]-G_p+G_s']
t5 = '代入不同长度桩长，可得摩擦桩与端承桩承载力如下图所示'
t6 = '不同桩长具体承载力如下表所示'
t7 = f'由上述分析可知，当桩长为{max(llist)}m时，{ptype}承载力为{ra:.0f}kN，安全系数为{ra/F:.2f}，桩基承载力可满足规范要求。'
with self.doc.create(Section('地基基本情况')):
with self.doc.create(LongTabu("p{4cm}XXXXX")) as soil_table:
header_row1 = self.soil.prop.columns.to_list()[:-1]
soil_table.add_hline()
soil_table.add_row(header_row1, mapper=[bold])
soil_table.add_hline()
for i in self.soil.prop.index:
soil_table.add_row(self.soil.prop.iloc[i].to_list()[:-1])
soil_table.add_hline()
with self.doc.create(Section('桩基及其他参数取值')):
self.doc.append(NoEscape(t1))
with self.doc.create(Section('桩长计算')):
self.doc.append(t2)
self.doc.append(Math(data=m1, escape=False))
self.doc.append(NoEscape('\n'))
self.doc.append(t3)
self.doc.append(Math(data=m2, escape=False))
self.doc.append(NoEscape('\n'))
self.doc.append(t4)
self.doc.append(Math(data=m3, escape=False))
self.doc.append(NoEscape('\n'))
self.doc.append(t5)
with self.doc.create(Figure(position='htbp')) as plot:
plot.add_plot(width=NoEscape(r'1\textwidth'), dpi=300)
self.doc.append(NoEscape('\n'))
self.doc.append(t6)
with self.doc.create(LongTable('p{1.5cm}|ll|ll')) as pll:
pll.add_hline()
pll.add_row(['桩长', '摩擦桩承载力', '安全系数', '端承桩承载力', '安全系数'])
pll.add_hline()
for i, j in enumerate(llist):
pll.add_row([
j, f'{ra_1[i]:.0f}', f'{ra_1[i]/F:.2f}',
f'{ra_2[i]:.0f}', f'{ra_2[i]/F:.2f}'
])
pll.add_hline()
self.doc.append(t7)
hlines=True,
cells=None,
escape=False)
# MultiColumn/MultiRow.
t.add_row((MultiColumn(size=2, align='|c|', data='MultiColumn'), ))
t.add_row((MultiRow(size=2, width='*', data='MultiRow'), ))
# Command
c = Command(command='documentclass',
arguments=None,
options=None,
packages=None)
# Figure
f = Figure(data=None, position=None)
f.add_image(filename='', width=r'0.8\textwidth', placement=r'\centering')
f.add_caption(caption='')
# Subfigure
s = SubFigure(data=None,
position=None,
width=r'0.45\linewidth',
seperate_paragraph=False)
s.add_image(filename='', width='r\linewidth', placement=None)
s.add_caption(caption='')
def create(self):
try:
self.status['text'] = 'Загрузка, подождите'
self.root.update()
# Настройки отступов, языка
geometry_options = {
"tmargin": "2cm",
"lmargin": "3cm",
"rmargin": "1.5cm",
"bmargin": "2cm"
}
doc = Document(geometry_options=geometry_options)
doc.packages.add(
Package('grffile',
options=['encoding', 'filenameencoding=utf8']))
doc.packages.add(Package('babel', options=['russian']))
# Вставляем логотип МИРЭА
image_filename = os.path.join(os.path.dirname(__file__),
'логотип.png')
with doc.create(Figure(position='h!')) as logo:
logo.add_image(image_filename, width='80px')
# Обложка
doc.change_length(r"\TPHorizModule", "1mm")
doc.change_length(r"\TPVertModule", "1mm")
with doc.create(MiniPage(width=r"\textwidth")) as page:
# Центральная часть обложки
with page.create(TextBlock(180, 0, 0)):
page.append(Command('centering'))
page.append('МИНОБРНАУКИ РОССИИ\n')
page.append(
'Федеральное государственное бюджетное образовательное учреждение высшего образования\n'
)
page.append(
MediumText(
bold(
'«МИРЭА - Российский Технологический Университет»\n'
)))
page.append(LargeText(bold('РТУ МИРЭА\n')))
page.append(LineBreak())
page.append(
MediumText(
bold(
'Институт комплексной безопасности и специального приборостроения\n'
)))
page.append(LineBreak())
page.append(
'Кафедра КБ-8 «Информационное Противоборство»\n')
page.append(LineBreak())
page.append(LineBreak())
page.append(LineBreak())
page.append(LargeText('Отчёт\n'))
page.append(f'{str(self.entry1.get())}\n')
# Правая часть обложки
with page.create(TextBlock(80, 88, 120)):
if self.your_var.get() == 0:
page.append('Выполнил:\n')
page.append(
f'Студент {str(self.entry2.get())} курса\n')
else:
page.append('Выполнила:\n')
page.append(
f'Студентка {str(self.entry2.get())} курса\n')
page.append(f'Группа {str(self.entry3.get())}\n')
page.append(f'Шифр {str(self.entry4.get())}\n')
page.append(f'{str(self.entry5.get())}\n')
page.append(LineBreak())
page.append(LineBreak())
if self.var.get() == 0:
page.append('Проверил:\n')
else:
page.append('Проверила:\n')
page.append(f'{str(self.entry6.get())}\n')
# Нижний колонтитул
header = PageStyle("header")
with header.create(Foot("C")):
header.append(f'Москва, {time.now().timetuple().tm_year}\n')
doc.preamble.append(header)
doc.change_document_style("header")
doc.generate_pdf("title", clean_tex=False)
self.status['text'] = 'Готово!'
except FileNotFoundError as e:
self.status['text'] = str(e)
def generate_latex_document(trackers: List[Tracker],
sequences: List[Sequence],
results,
storage: Storage,
build=False,
multipart=True):
order_marks = {1: "first", 2: "second", 3: "third"}
def format_cell(value, order):
cell = format_value(value)
if order in order_marks:
cell = Command(order_marks[order], cell)
return cell
logger = logging.getLogger("vot")
table_header, table_data, table_order = extract_measures_table(
trackers, results)
plots = extract_plots(trackers, results)
doc = Document(page_numbers=True)
doc.preamble.append(Package('pgf'))
doc.preamble.append(Package('xcolor'))
doc.preamble.append(Package('fullpage'))
doc.preamble.append(NoEscape(read_resource("commands.tex")))
doc.preamble.append(
UnsafeCommand('newcommand',
r'\first',
options=1,
extra_arguments=r'{\color{red} #1 }'))
doc.preamble.append(
UnsafeCommand('newcommand',
r'\second',
options=1,
extra_arguments=r'{\color{green} #1 }'))
doc.preamble.append(
UnsafeCommand('newcommand',
r'\third',
options=1,
extra_arguments=r'{\color{blue} #1 }'))
if multipart:
container = Chunk()
generate_symbols(container, trackers)
with storage.write("symbols.tex") as out:
container.dump(out)
doc.preamble.append(Command("input", "symbols.tex"))
else:
generate_symbols(doc.preamble, trackers)
doc.preamble.append(Command('title', 'VOT report'))
doc.preamble.append(
Command('author', 'Toolkit version ' + toolkit_version()))
doc.preamble.append(Command('date', datetime.datetime.now().isoformat()))
doc.append(NoEscape(r'\maketitle'))
if len(table_header[2]) == 0:
logger.debug("No measures found, skipping table")
else:
# Generate data table
with doc.create(LongTable("l " *
(len(table_header[2]) + 1))) as data_table:
data_table.add_hline()
data_table.add_row([" "] + [
MultiColumn(c[1], data=c[0].identifier)
for c in merge_repeats(table_header[0])
])
data_table.add_hline()
data_table.add_row([" "] + [
MultiColumn(c[1], data=c[0].title)
for c in merge_repeats(table_header[1])
])
data_table.add_hline()
data_table.add_row(
["Tracker"] +
[" " + c.abbreviation + " " for c in table_header[2]])
data_table.add_hline()
data_table.end_table_header()
data_table.add_hline()
for tracker, data in table_data.items():
data_table.add_row([
UnsafeCommand("Tracker",
[tracker.reference, TRACKER_GROUP])
] + [
format_cell(x,
order[tracker] if not order is None else None)
for x, order in zip(data, table_order)
])
for experiment, experiment_plots in plots.items():
if len(experiment_plots) == 0:
continue
doc.append(Section("Experiment " + experiment.identifier))
for title, plot in experiment_plots:
with doc.create(Figure(position='htbp')) as container:
if multipart:
plot_name = plot.identifier + ".pdf"
with storage.write(plot_name, binary=True) as out:
plot.save(out, "PDF")
container.add_image(plot_name)
else:
container.append(insert_figure(plot))
container.add_caption(title)
if build:
temp = tempfile.mktemp()
logger.debug("Generating to tempourary output %s", temp)
doc.generate_pdf(temp, clean_tex=True)
storage.copy(temp + ".pdf", "report.pdf")
else:
with storage.write("report.tex") as out:
doc.dump(out)
def test_graphics():
f = Figure(data=None, position=None)
f.add_image(filename='', width=r'0.8\textwidth', placement=r'\centering')
f.add_caption(caption='')
repr(f)
# Subfigure
s = SubFigure(data=None, position=None, width=r'0.45\linewidth')
s.add_image(filename='', width='r\linewidth', placement=None)
s.add_caption(caption='')
repr(s)
# Matplotlib
plot = Figure(data=None, position=None)
x = [0, 1, 2, 3, 4, 5, 6]
y = [15, 2, 7, 1, 5, 6, 9]
pyplot.plot(x, y)
plot.add_plot(width=r'0.8\textwidth', placement=r'\centering')
plot.add_caption(caption='I am a caption.')
repr(plot)
def details():
if __name__ == '__main__':
image_filename = os.path.join(os.path.dirname(__file__), 'kitten.jpg')
logo_file = os.path.join(os.path.dirname(__file__),'sample-logo.png')
geometry_options = {"tmargin": "1cm", "lmargin": "3cm"}
doc = Document(geometry_options=geometry_options)
header = PageStyle("header")
with header.create(Head("R")):
header.append(simple_page_number())
with header.create(Foot("C")):
header.append("Center Footer")
first_page = PageStyle("firstpage")
with first_page.create(Head("L")) as header_left:
with header_left.create(MiniPage(width=NoEscape(r"0.49\textwidth"),pos='c')) as logo_wrapper
with doc.create(MiniPage(align='l')):
doc.append(LargeText(bold("INVESTMENT PROPERTY - BUY & HOLD")))
doc.append(LineBreak())
doc.append(MediumText(bold(" ")))
logo_wrapper.append(StandAloneGraphic(image_options="width=120px",
filename=logo_file))
with doc.create(Section('Home Adress')):
doc.append('Some regular text and some')
doc.append(italic('italic text. '))
doc.append('\nAlso some crazy characters: $&#{}')
with doc.create(Subsection('Math that is incorrect')):
doc.append(Math(data=['2*3', '=', 9]))
with doc.create(Subsection('Table of something')):
with doc.create(Tabular('rc|cl')) as table:
table.add_hline()
table.add_row((1, 2, 3, 4))
table.add_hline(1, 2)
table.add_empty_row()
table.add_row((4, 5, 6, 7))
a = np.array([[100, 10, 20]]).T
M = np.matrix([[2, 3, 4],
[0, 0, 1],
[0, 0, 2]])
with doc.create(Section('The fancy stuff')):
with doc.create(Subsection('Correct matrix equations')):
doc.append(Math(data=[Matrix(M), Matrix(a), '=', Matrix(M * a)]))
with doc.create(Subsection('Alignat math environment')):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'\frac{a}{b} &= 0 \\')
agn.extend([Matrix(M), Matrix(a), '&=', Matrix(M * a)])
with doc.create(Subsection('Beautiful graphs')):
with doc.create(TikZ()):
plot_options = 'height=4cm, width=6cm, grid=major'
with doc.create(Axis(options=plot_options)) as plot:
plot.append(Plot(name='model', func='-x^5 - 242'))
coordinates = [
(-4.77778, 2027.60977),
(-3.55556, 347.84069),
(-2.33333, 22.58953),
(-1.11111, -493.50066),
(0.11111, 46.66082),
(1.33333, -205.56286),
(2.55556, -341.40638),
(3.77778, -1169.24780),
(5.00000, -3269.56775),
]
plot.append(Plot(name='estimate', coordinates=coordinates))
with doc.create(Subsection('Cute kitten pictures')):
with doc.create(Figure(position='h!')) as kitten_pic:
kitten_pic.add_image(image_filename, width='120px')
kitten_pic.add_caption('Look it\'s on its back')
doc.generate_pdf('full', clean_tex=False)
spacing = '2.5in'
doc.append(
NoEscape(r'\question ' +
NoEscape(question['question'])))
doc.append(Command('vspace', spacing))
answerKey = np.append(answerKey, [-1])
else:
break
doc.append(Command('end', 'questions'))
big_code = pyqrcode.create(np.array_str(answerKey), mode='binary')
big_code.png('code.png')
with doc.create(Figure(position='b!')) as code:
code.add_image('code.png', width='50px')
doc.generate_pdf(clean_tex=False)
doc.generate_tex()
elif currentMode == 'Grade':
filename = askopenfilename()
image = cv2.imread(filename, cv2.IMREAD_GRAYSCALE)
scanner = zbar.Scanner()
results = scanner.scan(image)
for result in results:
print(result.type, result.data, result.quality, result.position)
answerKey = list(str(results[0].data.decode("utf-8"))[1:-1].split("."))
def create_report(system, curves, grid, filename):
lines = system.lines
trafos = system.trafos
buses = system.buses
geometry_options = {
"tmargin": "1cm",
"lmargin": "1cm",
"rmargin": "1cm",
"bmargin": "1cm",
"includeheadfoot": True
}
doc = Document(page_numbers=True, geometry_options=geometry_options)
doc.preamble.append(Command('usepackage', 'cmbright'))
doc.preamble.append(Command('usepackage', 'tikz'))
doc.preamble.append(Command('usepackage', 'amsmath'))
doc.preamble.append(Command('usepackage', 'graphicx'))
now = datetime.datetime.now()
doc.append('Report auto-generated by ASPy at '
'{:02d}/{:02d}/{:02d} {:02d}:{:02d}:{:02d}'.format(
now.day, now.month, now.year, now.hour, now.minute,
now.second))
wye_comm = UnsafeCommand(
'newcommand',
'\\wye',
extra_arguments=
r'\mathbin{\text{\begin{tikzpicture}[x=1pt, y=1pt, scale=2]'
r'\draw '
r'(-0.9, 0) -- (0.9, 0) '
r'(-0.6, -0.5) -- (0.6, -0.5) '
r'(-0.3, -1) -- (0.3, -1) '
r'(0, 0) -- ++(0, 1.5) -- ++(1.2, 0) coordinate (tmp)'
r'-- +(0, -2) '
r'(tmp) +(45:2) -- (tmp) -- +(135:2) ;'
r'\end{tikzpicture}}}')
why_comm = UnsafeCommand(
'newcommand',
'\\why',
extra_arguments=
r'\mathbin{\text{\begin{tikzpicture}[x=1pt, y=1pt, scale=2]'
r'\draw '
r'(1.2, 1.5) coordinate (tmp)'
r'-- +(0, -2) '
r'(tmp) +(45:2) -- (tmp) -- +(135:2) ;'
r'\end{tikzpicture}}}')
doc.append(wye_comm)
doc.append(why_comm)
doc.add_color(name="lightgray", model="gray", description="0.80")
with doc.create(Section('Buses')):
with doc.create(Subsection('Power-Flow Solution')):
with doc.create(LongTable('c|ccccccc')) as tbl:
tbl.add_hline()
tbl.add_row(
('Bus', NoEscape('$|V|$ (pu)'),
NoEscape('$\\delta$ (deg)'), NoEscape('$P_G$ (MW)'),
NoEscape('$Q_G$ (Mvar)'), NoEscape('$P_L$ (MW)'),
NoEscape('$Q_L$ (Mvar)'), NoEscape('$Z_L$ (pu)')))
tbl.add_hline()
tbl.end_table_header()
tbl.add_hline()
tbl.add_row((MultiColumn(8,
align='r',
data='Continued on Next Page'), ))
tbl.add_hline()
tbl.end_table_footer()
tbl.add_hline()
tbl.end_table_last_footer()
for i, b in enumerate(buses):
if i % 2 == 0:
color = 'lightgray'
else:
color = None
tbl.add_row(
(b.bus_id + 1, NoEscape('{:.04f}'.format(b.v)),
NoEscape('${:.02f}$'.format(b.delta * 180 / np.pi)),
NoEscape('{:.02f}'.format(b.pg * 100)),
NoEscape('{:.02f}'.format(b.qg * 100)),
NoEscape('{:.02f}'.format(b.pl * 100)),
NoEscape('{:.02f}'.format(b.ql * 100)), check_inf(
b.Z)),
color=color)
with doc.create(Subsection('Fault Calculations')):
with doc.create(LongTable('c|cccccccccc')) as tbl:
tbl.add_hline()
tbl.add_row((MultiRow(2, data='Bus'),
MultiColumn(2, align='c', data=NoEscape('TPG')),
MultiColumn(2, align='c', data=NoEscape('SLG')),
MultiColumn(4, align='c', data=NoEscape('DLG')),
MultiColumn(2, align='c', data=NoEscape('LL'))))
tbl.add_hline(2, 11)
tbl.add_row(
('', NoEscape('$I_A$ (pu)'), NoEscape('$\\delta_A$ (deg)'),
NoEscape('$I_A$ (pu)'), NoEscape('$\\delta_A$ (deg)'),
NoEscape('$I_B$ (pu)'), NoEscape('$\\delta_B$ (deg)'),
NoEscape('$I_C$ (pu)'), NoEscape('$\\delta_C$ (deg)'),
NoEscape('$I_B$ (pu)'), NoEscape('$\\delta_B$ (deg)')))
tbl.add_hline()
tbl.end_table_header()
tbl.add_hline()
tbl.add_row((MultiColumn(11,
align='r',
data='Continued on Next Page'), ))
tbl.add_hline()
tbl.end_table_footer()
tbl.add_hline()
tbl.end_table_last_footer()
for i, b in enumerate(buses):
if i % 2 == 0:
color = 'lightgray'
else:
color = None
tbl.add_row((b.bus_id + 1, check_inf(np.abs(b.iTPG)),
NoEscape('${:.02f}$'.format(
np.angle(b.iTPG) * 180 / np.pi)),
check_inf(np.abs(b.iSLG)),
NoEscape('${:.02f}$'.format(
np.angle(b.iSLG) * 180 / np.pi)),
check_inf(np.abs(b.iDLGb)),
NoEscape('${:.02f}$'.format(
np.angle(b.iDLGb) * 180 / np.pi)),
check_inf(np.abs(b.iDLGc)),
NoEscape('${:.02f}$'.format(
np.angle(b.iDLGc) * 180 / np.pi)),
check_inf(np.abs(b.iLL)),
NoEscape('${:.02f}$'.format(
np.angle(b.iLL) * 180 / np.pi))),
color=color)
with doc.create(Section('Lines')):
with doc.create(LongTable('c|cccccccc')) as tbl:
tbl.add_hline()
tbl.add_row((MultiRow(2, data='Line'),
MultiColumn(3, align='c', data='Parametrization'),
MultiColumn(2, align='c', data='Loss'),
MultiColumn(3, align='c', data='Flow')))
tbl.add_hline(2, 9)
tbl.add_row(
('', NoEscape('$R$ (\\%pu)'), NoEscape('$X_L$ (\\%pu)'),
NoEscape('$B_C$ (\\%pu)'), NoEscape('$P_{loss}$ (MW)'),
NoEscape('$Q_{loss}$ (Mvar)'), NoEscape('$P$ (MW)'),
NoEscape('$Q$ (Mvar)'), NoEscape('$I/I_{max}$ (\\%)')))
tbl.add_hline()
tbl.end_table_header()
tbl.add_hline()
tbl.add_row((MultiColumn(9,
align='r',
data='Continued on Next Page'), ))
tbl.add_hline()
tbl.end_table_footer()
tbl.add_hline()
tbl.end_table_last_footer()
for i, lt in enumerate(lines):
if i % 2 == 0:
color = 'lightgray'
else:
color = None
tbl.add_row((NoEscape('{} -- {}'.format(
lt.orig.bus_id + 1, lt.dest.bus_id + 1)),
NoEscape('{:.04f}'.format(lt.Zpu.real * 100)),
NoEscape('{:.04f}'.format(lt.Zpu.imag * 100)),
NoEscape('{:.04f}'.format(lt.Ypu.imag * 100)),
NoEscape('{:.02f}'.format(lt.Sper.real * 100)),
NoEscape('{:.02f}'.format(lt.Sper.imag * 100)),
NoEscape('{:.02f}'.format(lt.S2.real * 100)),
NoEscape('{:.02f}'.format(lt.S2.imag * 100)),
NoEscape('{:.02f}'.format(
np.abs(lt.Ia) / lt.imax * 100))),
color=color)
with doc.create(Section('Trafos')):
with doc.create(LongTable('c|cccccccc')) as tbl:
tbl.add_hline()
tbl.add_row((MultiRow(2, data='Trafo'),
MultiColumn(3, align='c', data='Parametrization'),
MultiColumn(2, align='c', data='Loss'),
MultiColumn(3, align='c', data='Flow')))
tbl.add_hline(2, 9)
tbl.add_row(
('', NoEscape('$x^+$ (\\%pu)'), NoEscape('$x^0$ (\\%pu)'),
'Configuration', NoEscape('$P_{loss}$ (MW)'),
NoEscape('$Q_{loss}$ (Mvar)'), NoEscape('$P$ (MW)'),
NoEscape('$Q$ (Mvar)'), NoEscape('$S/S_N$ (\\%)')))
tbl.add_hline()
tbl.end_table_header()
tbl.add_hline()
tbl.add_row((MultiColumn(9,
align='r',
data='Continued on Next Page'), ))
tbl.add_hline()
tbl.end_table_footer()
tbl.add_hline()
tbl.end_table_last_footer()
for i, tr in enumerate(trafos):
if i % 2 == 0:
color = 'lightgray'
else:
color = None
tbl.add_row((NoEscape('{} -- {}'.format(
tr.orig.bus_id + 1, tr.dest.bus_id + 1)),
NoEscape('{:.02f}'.format(tr.Z1.imag * 100)),
NoEscape('{:.02f}'.format(
tr.Z0.imag * 100)), get_scheme(tr),
NoEscape('{:.02f}'.format(tr.Sper.real * 100)),
NoEscape('{:.02f}'.format(tr.Sper.imag * 100)),
NoEscape('{:.02f}'.format(tr.S2.real * 100)),
NoEscape('{:.02f}'.format(tr.S2.imag * 100)),
NoEscape('{:.02f}'.format(
np.abs(tr.S2) * 1e8 / tr.snom * 100))),
color=color)
filepath = filename.strip('.pdf')
make_system_schematic(curves, grid, initial_fontsize=9)
doc.append(NewPage())
with doc.create(Section('System')):
with doc.create(Figure(position='h')) as system_pic:
system_pic.add_plot(bbox_inches='tight',
width=NoEscape('\\textwidth'))
doc.generate_pdf(filepath,
clean_tex=True,
compiler='latexmk',
compiler_args=['-pdf'])
def odstup_generator(df):
''' Funkce k vytvoření kapitoly s vypočtenými odstupy
Vstupní data musí být DataFrame o specifickém formátu o deseti
sloupcích viz níže:
df_result['Nazev/fasada', 'vyska', 'sirka', 'Samostatne']]
df_result['POP'] = POP_store_list
df_result['p_v'] = pv_list
df_result['I_avrg'] = I_tok_list
df_result['d'] = d_results
df_result['d\''] = d_results_kraj
df_result['d\'s'] = d_results_za_krajem
Funkce tvoří přímo tabulku upravenou na míru pro prezentování
odstupových vzdáleností v PBŘ zprávě
'''
'''Poznámky k tabulce'''
list_avaiable = ['Přístřešky pro auta DP3', 'Pergoly / přístřešky']
'''Práce s daty '''
data_popis = df['Samostatne'].values.tolist() # Data pro přidání popisků
df = df.drop(columns=['Samostatne'])
data_used = df.values.tolist() # Data pro tvoření tabulky
'''Přidání popisků na správné místo'''
check = []
if not data_popis:
# Zjišťuje zda je nutné přidat popisky
pass
else:
save_var = []
save_id = []
save_name = []
save_id_check = []
for i in range(0, len(data_popis)):
if data_popis[i] in list_avaiable:
check.append(i)
save_var.append(data_popis[i])
save_id_check.append(i)
count = list(range(1, len(save_var)+1))
pre = ' $^{'
suf = ')}$'
for i in range(0, len(save_var)):
count[i] = pre + str(count[i])
count[i] = str(count[i]) + suf
for n in range(0, len(save_var)):
if n == 0:
new_dict = dict(zip([save_var[n]], [count[n]]))
save_id.append(save_id_check[n])
save_name.append(save_var[n])
# new_dict = dict(zip([save_var[n]], str(count[n])))
if n > 0:
if save_var[n] in new_dict:
save_id.append(save_id_check[n])
save_name.append(save_var[n])
else:
len_dict = len(new_dict)+1
len_dict = pre + str(len_dict)
len_dict = str(len_dict) + suf
save_id.append(save_id_check[n])
save_name.append(save_var[n])
new_dict[save_var[n]] = len_dict
for i in range(0, len(save_id)):
data_used[save_id[i]][0] = NoEscape(data_used[save_id[i]][0]
+ new_dict[save_name[i]])
'''Přeměna čísel s . na čísla s ,'''
for i in range(0, len(data_used)):
data_used[i][1] = str(("%.2f" % data_used[i][1])).replace(".", ",")
data_used[i][2] = str(("%.2f" % data_used[i][2])).replace(".", ",")
data_used[i][3] = str(("%.2f" % data_used[i][3])).replace(".", ",")
data_used[i][4] = str(("%.2f" % data_used[i][4])).replace(".", ",")
data_used[i][5] = str(("%.2f" % data_used[i][5])).replace(".", ",")
data_used[i][6] = str(("%.2f" % data_used[i][6])).replace(".", ",")
data_used[i][7] = str(("%.2f" % data_used[i][7])).replace(".", ",")
data_used[i][8] = str(("%.2f" % data_used[i][8])).replace(".", ",")
'''Textová část kapitoly '''
with doc.create(Subsection('Stanovení odstupových vzdáleností')):
if kcni_system != 'nehořlavý':
doc.append(NoEscape(r'Požární zatížení je v souladu s čl. 10.4.4 normy ČSN 73 0802 vzhledem k zatřídění konstrukčního systému nově navrhované budovy ({}; zatřídění viz tabulka '.format(kcni_system)))
doc.append(NoEscape(r'\ref{PTCH}) '))
doc.append(NoEscape(r' dále zvýšeno o {} kg/m$^2$.'.format(add_pv)))
doc.append(NoEscape('\par'))
doc.append(NoEscape(r'Odstupové vzdálenosti jsou stanoveny určením vzdáleností kritického tepelného toku 18,5 kW/m$^2$ od vnějšího líce požárně otevřené plochy, a to pomocí programu pro výpočet odstupových vzdáleností, který je zmíněn v kapitole \ref{cha-1}). Výsledné hodnoty odstupových vzdáleností z tohoto programu jsou názorně zakresleny v následujícím obrázku \ref{SchemaPOP2}.'))
with doc.create(Figure(position='htb!')) as Odstup:
Odstup.add_image('images/odstup.jpg', width='160px')
Odstup.add_caption('Znázornění vypočtených hodnot')
Odstup.append(Command('label', 'SchemaPOP2'))
doc.append(NoEscape(r'Vypočtené odstupové vzdále\-nosti jsou patrné z tabulky \ref{odstup}.'))
'''Ověření zda je možné přidat popisky + přidání popisků'''
if len(check) > 0:
doc.append(Command('begin', 'ThreePartTable'))
doc.append(Command('begin', 'TableNotes'))
doc.append(NoEscape('\small'))
for key in new_dict.keys():
pre_str = '\item '
if key == 'Pergoly / přístřešky':
loc_str = ' Odstupová vzdálenost z domnělých stěn otevřených přístřešků je spočtena pomocí normové křivky pro vnější požár. Maximální teplota požáru je tedy v tomto případě 658$^o$C. Požární zatížení je stanoveno pomocí čl. 10.4.4 normy ČSN 73 0802.'
string = new_dict[key]
doc.append(NoEscape(pre_str + string + loc_str))
if key == 'Přístřešky pro auta DP3':
loc_str = ' Odstupová vzdálenost od otevřeného přístřešku pro auta je stanovena na základě čl. I.3.1 normy ČSN 73 0804. Uvažováno je s ekvivalentní dobou požáru 30 minut (zde označeno jako p$_v$ = 30 kg/m$^2$). s výškou přístřešku 1,5 m a skutečnou délkou přístřešku.'
string = new_dict[key]
doc.append(NoEscape(pre_str + string + loc_str))
if len(check) > 0:
doc.append(Command('end', 'TableNotes'))
with doc.create(LongTable("lcccccccc", pos=['htb'])) as data_table:
doc.append(Command('caption', 'Odstupové vzdálenosti od objektu'))
doc.append(Command('label', 'odstup'))
doc.append(Command('\ '))
data_table.append
data_table.add_hline()
data_table.add_row([" ", "Výška", "Šířka", "POP",
NoEscape('$p_v$'), NoEscape('$I_{avrg}$'), "d", "d\'", NoEscape("d\'$_s$")])
data_table.add_row([" ", "[m]", "[m]", NoEscape('[\%]'), NoEscape('[kg/m$^2$]'),
NoEscape('[kW/m$^2$]'), "[m]", "[m]", "[m]"])
data_table.add_hline()
data_table.end_table_header()
for i in range(0, len(data_used)):
if i == 0:
# \multicolumn{9}{l}{\textbf{1. nadzemní podlaží - POP společné}}\\
data_table.add_row((MultiColumn(9, align='l', data=utils.bold(df_popis[i])),))
if i > 0 and df_popis[i] != df_popis[i-1]:
data_table.add_hline()
data_table.add_row((MultiColumn(9, align='l', data=utils.bold(df_popis[i])),))
if (i) % 2 == 0:
data_table.add_row(data_used[i], color="Hex")
elif (i) % 2 != 0:
data_table.add_row(data_used[i])
data_table.add_hline()
if len(check) > 0:
doc.append(NoEscape('\insertTableNotes'))
if len(check) > 0:
doc.append(Command('end', 'ThreePartTable'))
def main():
# copy diagram
subprocess.run(["cp", "-r", dp.diagram_path, dp.latex_pics_path])
# copy diagram velocity only for begin and last
for root, dirnames, filenames in os.walk(dp.f_momentum_mass_field_path):
# if not empty
if filenames:
sorted_filenames = natural_sort(filenames)
first_filename = sorted_filenames[0]
last_filename = sorted_filenames[-1]
copy_filenames = [first_filename, last_filename]
for filename in copy_filenames:
filepath = os.path.join(root, filename)
f_copy_path = filepath.replace(dp.diagram_path,
dp.latex_pics_path)
subprocess.run(["cp", filepath, f_copy_path])
os.chdir(dp.latex_path)
doc = Document(default_filepath=dp.latex_path + "plots")
doc.packages.append(Package('placeins', "section"))
#breakpoint()
with doc.create(Section("Simulation Plot")):
doc.append("Width= " + str(rr.log_variable["width_wall_dp_unit"]) +
" diameter")
doc.append("\nHeight= " +
str(rr.log_variable["z_length_create_dp_unit"]) +
" diameter")
doc.append("\nPeriodic length in shear direction = " +
str(rr.log_variable["x_period_dp_unit"]) + " diameter")
doc.append("\nSavage_number = " + str(rr.log_variable["Sa"]))
doc.append("\nV_wall = " + str(
float(rr.log_variable["in_velocity"]) /
float(rr.log_variable["dp"])) + " diameter/second")
list_plot_no_errorbar = [
("Coord1", "mv_1"),
]
list_plot_errorbar = [
("I_12", "mu_12_middle"),
("I_tensor", "mu_tensor_12"),
("strain", "I_12"),
("strain", "mu_12_middle"),
("strain", "I_tensor"),
("strain", "mu_tensor_12"),
("strain", "fraction"),
("strain", "velocity_1"),
("strain", "velocity_2"),
("strain", "velocity_3"),
("strain", "strain_rate_21_middle"),
("strain", "strain_rate_31_middle"),
("strain", "strain_rate_22_middle"),
("strain", "strain_rate_32_middle"),
("strain", "strain_rate_23_middle"),
("strain", "strain_rate_33_middle"),
("strain", "stress_11"),
("strain", "stress_22"),
("strain", "stress_33"),
("strain", "stress_12"),
("strain", "stress_13"),
("strain", "stress_23"),
("fraction", "mu_12_middle"),
("fraction", "I_12"),
("fraction", "mu_tensor_12"),
("fraction", "I_tensor"),
("strain", "fraction"),
("strain", "inwall_stress_1"),
("strain", "inwall_stress_2"),
("strain", "inwall_stress_3"),
("strain", "outwall_stress_1"),
("strain", "outwall_stress_2"),
("strain", "outwall_stress_3"),
("strain", "zbottom_stress_1"),
("strain", "zbottom_stress_2"),
("strain", "zbottom_stress_3"),
]
for (x_name, y_name) in list_plot_no_errorbar:
folder_name = y_name + "_" + x_name + "/"
folder_path = dp.latex_pics_path + "diagram/n_ave_51/" + folder_name
onlyfilepaths = [
os.path.join(folder_path, f) for f in os.listdir(folder_path)
if os.path.isfile(os.path.join(folder_path, f))
]
pic_path_list = natural_sort(onlyfilepaths)
subsection_title = y_name + " vs. " + x_name
#breakpoint()
with doc.create(Subsection(subsection_title.replace('_middle',
''))):
for pic_path in pic_path_list:
with doc.create(Figure(position='h!')) as pic:
#breakpoint()
pic.add_image(pic_path)
pic.add_caption(NoEscape("\label{fig:epsart}"))
doc.append(NoEscape("\\FloatBarrier"))
for (x_name, y_name) in list_plot_errorbar:
folder_name = y_name + "_" + x_name + "/"
folder_path = dp.latex_pics_path + "diagram/n_ave_51/" + folder_name
onlyfilepaths = [
os.path.join(folder_path, f) for f in os.listdir(folder_path)
if os.path.isfile(os.path.join(folder_path, f))
]
pic_path_list = natural_sort(onlyfilepaths)
folder_path = dp.latex_pics_path + "diagram/n_ave_51/" + folder_name + "errorbar/"
onlyfilepaths = [
os.path.join(folder_path, f) for f in os.listdir(folder_path)
if os.path.isfile(os.path.join(folder_path, f))
]
pic_path_list_errorbar = natural_sort(onlyfilepaths)
subsection_title = y_name + " vs. " + x_name
#breakpoint()
with doc.create(Subsection(subsection_title.replace('_middle',
''))):
for pic_path in pic_path_list:
with doc.create(Figure(position='h!')) as pic:
#breakpoint()
pic.add_image(pic_path)
pic.add_caption(NoEscape("\label{fig:epsart}"))
doc.append(NoEscape("\\FloatBarrier"))
with doc.create(
Subsection(
subsection_title.replace('_middle', '') +
" (with errorbar)")):
for pic_path in pic_path_list_errorbar:
with doc.create(Figure(position='h!')) as pic:
pic.add_image(pic_path)
pic.add_caption(NoEscape("\label{fig:epsart}"))
doc.append(NoEscape("\\FloatBarrier"))
doc.generate_pdf(clean_tex=False)
os.chdir(rr.lammps_directory)
Mal_y_pos = np.arange(len(Mal_obj))
#______________________________________
geometry_options = {"margin":"0.5in"}
doc = Document('matplotlib_ex-dpi', geometry_options=geometry_options,documentclass='report', document_options=['12pt, notitlepage'])
#doc.preamble.append(NoEscape(r'\linespread{1.8}'))
Command('linespread','1.6')
# doc.append('Introduction.')
# with doc.create(Section('I am a section')):
# doc.append('Take a look at this beautiful plot:')
with doc.create(Figure(position='h!')) as plotgrid:
#first graph
plt.bar(y_pos, benchMark, align='center', alpha=0.5)
plt.bar(y_pos, unconInvest,bottom=benchMark, align='center', alpha=1, color="#f3e151")
plt.xticks(y_pos, objects,fontsize=9, rotation=30)
plt.ylabel('USD bn')
plt.title('Brazil')
with doc.create(SubFigure(position='b',width=NoEscape(r'0.5\linewidth'))) as Leftplot:
Leftplot.add_plot(width=NoEscape(r'\linewidth'), dpi=300)
plt.clf()
#Second graph
plt.bar(mex_y_pos, mex_benchMark, align='center', alpha=0.5)
plt.bar(mex_y_pos, mex_unconInvest,bottom=mex_benchMark, align='center', alpha=1, color="#f3e151")
plt.xticks(mex_y_pos, mex_obj, fontsize=9, rotation=30)
with doc.create(MiniPage(align='l')):
#doc.append(NoEscape(r"\noindent\rule{\textwidth}{1pt}"))
#doc.append(NewLine())
doc.append('Name : ' + str(sub_info.Name[0]))
doc.append('\nAge: ' + str(sub_info.Age[0]))
doc.append('\nGender: ' + str(sub_info.Gender[0]))
doc.append('\nUH Id: ' + str(sub_info.UHID[0]))
doc.append('\nDate: ' + d2)
doc.append(LineBreak())
doc.append(NoEscape(r"\noindent\rule{\textwidth}{1pt}"))
doc.append(NewLine())
doc.append(LineBreak())
with doc.create(MiniPage(align='c')):
doc.append(LargeText(bold('Vowel Triangle Analysis Report')))
# Analysis result and image
with doc.create(Section('Vowel Triangle Analysis')):
with doc.create(Figure(position='h!')) as img_plot:
img_plot.add_image(img1, width='300px')
img_plot.add_caption('Vowel Triangle PLot')
with doc.create(Subsection('Vowel Triangle')):
doc.append('Area : ' + str(area))
doc.append(NoEscape(r"\pagebreak[4]"))
# saving the pdf and tex
doc.generate_pdf(filepath='media/VT.report1', clean_tex=False)
def plot_show(caption, width=r'0.5\textwidth', *args, **kwargs):
fig = Figure(position='htbp')
fig.add_plot(width=NoEscapeStr(width), *args, **kwargs)
fig.add_caption(NoEscapeStr(caption))
return fig
def writeFigure(doc, figname, soru_sayisi, scale):
with doc.create(Figure(position="h!")) as fig:
width = NoEscape(r"{}\textwidth".format(scale))
fig.add_image(settings.fig_path + figname, width=width)
fig.add_caption("Soru "+ str(soru_sayisi))
def dessiner(doc, chemin):
for photo in os.listdir(chemin):
with doc.create(Section('Showing subfigures')):
image_filename = os.path.join(chemin, photo)
with doc.create(Figure(width=NoEscape(r'\linewidth'))) as frog:
frog.add_image(image_filename, width=NoEscape(r'\linewidth'))
itemize.add_item("the second item")
itemize.add_item("the third etc")
# you can append to existing items
itemize.append(Command("ldots"))
if __name__ == '__main__':
# Basic document
doc = Document('basic')
fill_document(doc)
# Document with `\maketitle` command activated
doc = Document()
image_filename = os.path.join(os.path.dirname(__file__), 'final.png')
with doc.create(Figure(position='h!')) as logo:
logo.add_image(image_filename, width='300px')
doc.preamble.append(Command('title', 'note-o-matic Summary'))
doc.preamble.append(Command('author', 'Generated using note-o-matic'))
doc.preamble.append(Command('date', NoEscape(r'\today')))
doc.append(NoEscape(r'\maketitle'))
fill_document(doc)
# Add stuff to the document
with doc.create(Section('Your notes - reworked.')):
doc.append('uwu')
doc.generate_pdf('note-o-maticSummary',
clean_tex=False,
compiler='/Library/TeX/texbin/pdflatex')
rev_c = {"A": "T", "C": "G", "G": "C", "T": "A", "$": "$"}
colors = ["red", "green", "blue", "yellow"]
def create_figure(seq, interval_dict, query):
seq_fig = tikz_matrix("seq", body([seq, "".join(rev_c[c] for c in seq)]))
query_fig = tikz_matrix("q", body([query]), "below=of seq")
rec_1 = r"\node[color=%s, draw, dashed, rounded corners, fit=(seq-1-%s) (seq-1-%s)] {};"
rec_2 = r"\node[color=%s, draw, dashed, rounded corners, fit=(seq-2-%s) (seq-2-%s)] {};"
rec_q = r"\node[color=%s, draw, dashed, rounded corners, fit=(q-1-%s) (q-1-%s)] {};"
lines = []
N = len(seq)
i = 0
for (s, e), (intervals, reverse_intervals) in interval_dict.iteritems():
lines.append(rec_q % (colors[i], s + 1, e))
for (start, end) in intervals:
lines.append(rec_1 % (colors[i], start + 1, end))
for start, end in reverse_intervals:
lines.append(rec_2 % (colors[i], N - end + 1, N - start))
i += 1
content = seq_fig + "\n" + query_fig + "\n" + "\n".join(lines)
content = content.replace("$", r"\$")
return content
if __name__ == "__main__":
fig = Figure("memfig", "memfigs")
fig.write(create_figure("ATTCT", {1: ([(0, 3), (2, 5)], [(1, 3)])}))
def save_latex(self,
uiObj,
Design_Check,
reportsummary,
filename,
rel_path,
Disp_2d_image,
Disp_3d_image,
module=''):
companyname = str(reportsummary["ProfileSummary"]['CompanyName'])
companylogo = str(reportsummary["ProfileSummary"]['CompanyLogo'])
groupteamname = str(reportsummary["ProfileSummary"]['Group/TeamName'])
designer = str(reportsummary["ProfileSummary"]['Designer'])
projecttitle = str(reportsummary['ProjectTitle'])
subtitle = str(reportsummary['Subtitle'])
jobnumber = str(reportsummary['JobNumber'])
client = str(reportsummary['Client'])
does_design_exist = reportsummary['does_design_exist']
osdagheader = '/ResourceFiles/images/Osdag_header_report.png'
# Add document header
geometry_options = {
"top": "5cm",
"hmargin": "2cm",
"headheight": "100pt",
"footskip": "100pt",
"bottom": "5cm"
}
doc = Document(geometry_options=geometry_options, indent=False)
doc.packages.append(Package('amsmath'))
doc.packages.append(Package('graphicx'))
doc.packages.append(Package('needspace'))
doc.append(pyl.Command('fontsize', arguments=[8, 12]))
doc.append(pyl.Command('selectfont'))
doc.add_color('OsdagGreen', 'RGB', '153,169,36')
doc.add_color('PassColor', 'RGB', '153,169,36')
doc.add_color('Red', 'RGB', '255,0,0')
doc.add_color('Green', 'RGB', '0,200,0')
doc.add_color('FailColor', 'HTML', '933A16')
header = PageStyle("header")
# Create center header
with header.create(Head("C")):
with header.create(Tabularx('|l|p{4cm}|l|X|')) as table:
table.add_hline()
# MultiColumn(4)
table.add_row((
MultiColumn(
2,
align='|c|',
data=('' if companylogo is '' else StandAloneGraphic(
image_options="height=0.95cm",
filename=companylogo))),
MultiColumn(2,
align='|c|',
data=[
'Created with',
StandAloneGraphic(
image_options="width=4.0cm,height=1cm",
filename=rel_path + osdagheader)
]),
))
table.add_hline()
table.add_row(('Company Name', companyname, 'Project Title',
projecttitle),
color='OsdagGreen')
table.add_hline()
table.add_row(
('Group/Team Name', groupteamname, 'Subtitle', subtitle),
color='OsdagGreen')
table.add_hline()
table.add_row(('Designer', designer, 'Job Number', jobnumber),
color='OsdagGreen')
table.add_hline()
table.add_row(
('Date', time.strftime("%d /%m /%Y"), 'Client', client),
color='OsdagGreen')
table.add_hline()
# Create right footer
with header.create(Foot("R")):
header.append(NoEscape(r'Page \thepage'))
#
# doc.preamble.append(header)
# doc.change_document_style("header")
# Add Heading
# with doc.create(MiniPage(align='c')):
doc.preamble.append(header)
doc.change_document_style("header")
with doc.create(Section('Input Parameters')):
with doc.create(
LongTable('|p{5cm}|p{2.5cm}|p{1.5cm}|p{3cm}|p{3.5cm}|',
row_height=1.2)) as table:
table.add_hline()
for i in uiObj:
# row_cells = ('9', MultiColumn(3, align='|c|', data='Multicolumn not on left'))
if i == "Selected Section Details" or i == KEY_DISP_ANGLE_LIST or i == KEY_DISP_TOPANGLE_LIST or i == KEY_DISP_CLEAT_ANGLE_LIST:
# if type(uiObj[i]) == list:
continue
if type(uiObj[i]) == dict:
table.add_hline()
sectiondetails = uiObj[i]
image_name = sectiondetails[KEY_DISP_SEC_PROFILE]
Img_path = '/ResourceFiles/images/' + image_name + '.png'
if (len(sectiondetails)) % 2 == 0:
# merge_rows = int(round_up(len(sectiondetails),2)/2 + 2)
merge_rows = int((len(sectiondetails) / 2)) + 2
else:
merge_rows = round_up((len(sectiondetails) / 2), 2)
if (len(sectiondetails)) % 2 == 0:
sectiondetails[''] = ''
a = list(sectiondetails.keys())
# index=0
for x in range(1, (merge_rows + 1)):
# table.add_row("Col.Det.",i,columndetails[i])
if x == 1:
table.add_row((
MultiRow(
merge_rows,
data=StandAloneGraphic(
image_options=
"width=5cm,height=5cm",
filename=rel_path + Img_path)),
MultiColumn(2, align='|c|', data=a[x]),
MultiColumn(2,
align='|c|',
data=sectiondetails[a[x]]),
))
elif x <= 4:
table.add_row((
'',
MultiColumn(2,
align='|c|',
data=NoEscape(a[x])),
MultiColumn(2,
align='|c|',
data=NoEscape(
sectiondetails[a[x]])),
))
else:
table.add_row((
'',
NoEscape(a[x]),
sectiondetails[a[x]],
NoEscape(a[merge_rows + x - 4]),
sectiondetails[a[merge_rows + x - 4]],
))
table.add_hline(2, 5)
elif uiObj[i] == "TITLE":
table.add_hline()
table.add_row((MultiColumn(
5,
align='|c|',
data=bold(i),
), ))
table.add_hline()
elif i == 'Section Size*':
table.add_hline()
table.add_row((
MultiColumn(
3,
align='|c|',
data=i,
),
MultiColumn(2,
align='|c|',
data="Ref List of Input Section"),
))
table.add_hline()
elif len(str(uiObj[i])) > 55 and type(
uiObj[i]) != pyl.math.Math:
str_len = len(str(uiObj[i]))
loop_len = round_up((str_len / 55), 1, 1)
for j in range(1, loop_len + 1):
b = 55 * j + 1
if j == 1:
table.add_row((
MultiColumn(3,
align='|c|',
data=MultiRow(loop_len,
data=i)),
MultiColumn(2,
align='|c|',
data=uiObj[i][0:b]),
))
else:
table.add_row((
MultiColumn(3,
align='|c|',
data=MultiRow(loop_len,
data="")),
MultiColumn(2,
align='|c|',
data=uiObj[i][b - 55:b]),
))
table.add_hline()
else:
table.add_hline()
table.add_row((
MultiColumn(3, align='|c|', data=NoEscape(i)),
MultiColumn(2, align='|c|', data=uiObj[i]),
))
table.add_hline()
for i in uiObj:
if i == 'Section Size*' or i == KEY_DISP_ANGLE_LIST or i == KEY_DISP_TOPANGLE_LIST or i == KEY_DISP_CLEAT_ANGLE_LIST:
with doc.create(Subsection("List of Input Section")):
# with doc.create(LongTable('|p{8cm}|p{8cm}|', row_height=1.2)) as table:
with doc.create(Tabularx('|p{4cm}|X|',
row_height=1.2)) as table:
table.add_hline()
table.add_row((
MultiColumn(
1,
align='|c|',
data=i,
),
MultiColumn(1,
align='|X|',
data=uiObj[i].strip("[]")),
))
# str_len = len(uiObj[i])
# loop_len = round_up((str_len/100),1,1)
# table.add_hline()
# for j in range(1,loop_len+1):
# b= 100*j+1
# if j ==1:
# table.add_row((MultiColumn(1, align='|c|', data=i, ),
# MultiColumn(1, align='|X|', data=uiObj[i][0:b]),))
# else:
# table.add_row((MultiColumn(1, align='|c|', data=" ", ),
# MultiColumn(1, align='|X|', data=uiObj[i][b-100:b]),))
table.add_hline()
doc.append(
pyl.Command('Needspace', arguments=NoEscape(r'10\baselineskip')))
doc.append(NewPage())
count = 0
with doc.create(Section('Design Checks')):
with doc.create(
Tabularx(
r'|>{\centering}p{12.5cm}|>{\centering\arraybackslash}X|',
row_height=1.2)) as table:
table.add_hline()
# Fail = TextColor("FailColor", bold("Fail"))
# Pass = TextColor("PassColor", bold("Pass"))
if does_design_exist != True:
table.add_row(bold('Design Status'),
color_cell("Red", bold("Fail")))
else:
table.add_row(bold('Design Status'),
color_cell("OsdagGreen", bold("Pass")))
table.add_hline()
for check in Design_Check:
if check[0] == 'SubSection':
if count >= 1:
# doc.append(NewPage())
doc.append(
pyl.Command(
'Needspace',
arguments=NoEscape(r'10\baselineskip')))
with doc.create(Subsection(check[1])):
#########################
# if uiObj== "WELDImage":
# table.add_hline()
# table.add_row((MultiColumn(5, align='|c|', data=bold(i), ),))
# table.add_hline()
# else:
#########################
with doc.create(LongTable(check[2], row_height=1.2)
) as table: # todo anjali remove
table.add_hline()
table.add_row(
('Check', 'Required', 'Provided', 'Remarks'),
color='OsdagGreen')
table.add_hline()
table.end_table_header()
table.add_hline()
count = count + 1
elif check[0] == "Selected":
if count >= 1:
# doc.append(NewPage())
doc.append(
pyl.Command(
'Needspace',
arguments=NoEscape(r'10\baselineskip')))
with doc.create(Subsection(check[1])):
with doc.create(LongTable(check[2],
row_height=1.2)) as table:
table.add_hline()
for i in uiObj:
# row_cells = ('9', MultiColumn(3, align='|c|', data='Multicolumn not on left'))
print(i)
if type(
uiObj[i]
) == dict and i == 'Selected Section Details':
table.add_hline()
sectiondetails = uiObj[i]
image_name = sectiondetails[
KEY_DISP_SEC_PROFILE]
Img_path = '/ResourceFiles/images/' + image_name + '.png'
if (len(sectiondetails)) % 2 == 0:
# merge_rows = int(round_up(len(sectiondetails),2)/2 + 2)
merge_rows = int(
round_up((len(sectiondetails) /
2), 1, 0) + 2)
else:
merge_rows = int(
round_up((len(sectiondetails) /
2), 1, 0) + 1)
print('Hi',
len(sectiondetails) / 2,
round_up(len(sectiondetails), 2) / 2,
merge_rows)
if (len(sectiondetails)) % 2 == 0:
sectiondetails[''] = ''
a = list(sectiondetails.keys())
# index=0
for x in range(1, (merge_rows + 1)):
# table.add_row("Col.Det.",i,columndetails[i])
if x == 1:
table.add_row((
MultiRow(
merge_rows,
data=StandAloneGraphic(
image_options=
"width=5cm,height=5cm",
filename=rel_path +
Img_path)),
MultiColumn(2,
align='|c|',
data=NoEscape(
a[x])),
MultiColumn(
2,
align='|c|',
data=NoEscape(
sectiondetails[a[x]])),
))
elif x <= 4:
table.add_row((
'',
MultiColumn(2,
align='|c|',
data=NoEscape(
a[x])),
MultiColumn(
2,
align='|c|',
data=sectiondetails[a[x]]),
))
else:
table.add_row((
'',
NoEscape(a[x]),
sectiondetails[a[x]],
NoEscape(a[merge_rows + x -
4]),
sectiondetails[a[merge_rows +
x - 4]],
))
table.add_hline(2, 5)
table.add_hline()
count = count + 1
else:
if check[3] == 'Fail':
table.add_row((NoEscape(check[0])), check[1], check[2],
TextColor("Red", bold(check[3])))
else:
table.add_row((NoEscape(check[0])), check[1], check[2],
TextColor("OsdagGreen", bold(check[3])))
table.add_hline()
# 2D images
if len(Disp_2d_image) != 0:
if module == KEY_DISP_BCENDPLATE or module == KEY_DISP_BB_EP_SPLICE:
if does_design_exist and sys.platform != 'darwin':
doc.append(NewPage())
weld_details = rel_path + Disp_2d_image[0]
detailing_details = rel_path + Disp_2d_image[1]
stiffener_details = rel_path + Disp_2d_image[2]
with doc.create(Section('2D Drawings (Typical)')):
with doc.create(Figure()) as image:
image.add_image(weld_details,
width=NoEscape(r'0.7\textwidth'),
placement=NoEscape(r'\centering'))
image.add_caption(
'Typical Weld Details -- Beam to End Plate Connection'
)
# doc.append(NewPage())
with doc.create(Figure()) as image_2:
image_2.add_image(
detailing_details,
width=NoEscape(r'0.7\textwidth'),
placement=NoEscape(r'\centering'))
image_2.add_caption('Typical Detailing')
# doc.append(NewPage())
with doc.create(Figure()) as image_3:
image_3.add_image(
stiffener_details,
width=NoEscape(r'0.9\textwidth'),
placement=NoEscape(r'\centering'))
image_3.add_caption('Typical Stiffener Details')
# doc.append(NewPage())
elif module == KEY_DISP_BASE_PLATE:
if does_design_exist and sys.platform != 'darwin':
doc.append(NewPage())
bp_sketch = rel_path + Disp_2d_image[0]
bp_detailing = rel_path + Disp_2d_image[1]
bp_weld = rel_path + Disp_2d_image[2]
bp_anchor = rel_path + Disp_2d_image[3]
bp_key = rel_path + Disp_2d_image[4]
with doc.create(Section('2D Drawings (Typical)')):
with doc.create(Figure()) as image_1:
image_1.add_image(
bp_sketch,
width=NoEscape(r'1.0\textwidth'),
placement=NoEscape(r'\centering'))
image_1.add_caption('Typical Base Plate Details')
# doc.append(NewPage())
with doc.create(Figure()) as image_2:
image_2.add_image(
bp_detailing,
width=NoEscape(r'1.0\textwidth'),
placement=NoEscape(r'\centering'))
image_2.add_caption('Typical Base Plate Detailing')
# doc.append(NewPage())
with doc.create(Figure()) as image_3:
image_3.add_image(
bp_weld,
width=NoEscape(r'1.0\textwidth'),
placement=NoEscape(r'\centering'))
image_3.add_caption('Typical Weld Details')
# doc.append(NewPage())
with doc.create(Figure()) as image_4:
image_4.add_image(
bp_anchor,
width=NoEscape(r'0.5\textwidth'),
placement=NoEscape(r'\centering'))
image_4.add_caption('Typical Anchor Bolt Details')
# doc.append(NewPage())
if len(Disp_2d_image[-1]) > 0:
with doc.create(Figure()) as image_5:
image_5.add_image(
bp_key,
width=NoEscape(r'0.9\textwidth'),
placement=NoEscape(r'\centering'))
image_5.add_caption(
'Typical Shear Key Details')
# doc.append(NewPage())
if does_design_exist and sys.platform != 'darwin':
doc.append(NewPage())
Disp_top_image = "/ResourceFiles/images/top.png"
Disp_side_image = "/ResourceFiles/images/side.png"
Disp_front_image = "/ResourceFiles/images/front.png"
view_3dimg_path = rel_path + Disp_3d_image
view_topimg_path = rel_path + Disp_top_image
view_sideimg_path = rel_path + Disp_side_image
view_frontimg_path = rel_path + Disp_front_image
with doc.create(Section('3D Views')):
with doc.create(
Tabularx(
r'|>{\centering}X|>{\centering\arraybackslash}X|',
row_height=1.2)) as table:
view_3dimg_path = rel_path + Disp_3d_image
view_topimg_path = rel_path + Disp_top_image
view_sideimg_path = rel_path + Disp_side_image
view_frontimg_path = rel_path + Disp_front_image
table.add_hline()
table.add_row([
StandAloneGraphic(image_options="height=4cm",
filename=view_3dimg_path),
StandAloneGraphic(image_options="height=4cm",
filename=view_topimg_path)
])
table.add_row('(a) 3D View', '(b) Top View')
table.add_hline()
table.add_row([
StandAloneGraphic(image_options="height=4cm",
filename=view_sideimg_path),
StandAloneGraphic(image_options="height=4cm",
filename=view_frontimg_path)
])
table.add_row('(c) Side View', '(d) Front View')
table.add_hline()
# with doc.create(Figure(position='h!')) as view_3D:
# view_3dimg_path = rel_path + Disp_3d_image
# # view_3D.add_image(filename=view_3dimg_path, width=NoEscape(r'\linewidth'))
#
# view_3D.add_image(filename=view_3dimg_path,width=NoEscape(r'\linewidth,height=6.5cm'))
#
# view_3D.add_caption('3D View')
with doc.create(Section('Design Log')):
doc.append(
pyl.Command('Needspace',
arguments=NoEscape(r'10\baselineskip')))
logger_msgs = reportsummary['logger_messages'].split('\n')
for msg in logger_msgs:
if ('WARNING' in msg):
colour = 'blue'
elif ('INFO' in msg):
colour = 'OsdagGreen'
elif ('ERROR' in msg):
colour = 'red'
else:
continue
doc.append(TextColor(colour, '\n' + msg))
try:
doc.generate_pdf(filename, compiler='pdflatex', clean_tex=False)
except:
pass
def generateLatex(phrases, key, result, flag):
geometry_options = {"tmargin": "1cm", "lmargin": "3cm", "rmargin": "3cm"}
doc = Document(geometry_options=geometry_options)
if(flag == "E"):
with doc.create(Section('Encyption Input')):
doc.append('Text: ' + "".join(phrases) + "\n")
doc.append('Key: ' +key)
with doc.create(Section("Matrix Mltiplications")):
for phrase in phrases:
M = createEncryptMatrix(key)
messageMatrix = np.array([[getCapitalAlphaMod(phrase[0]),getCapitalAlphaMod(phrase[1]),getCapitalAlphaMod(phrase[2])]]).astype("float64").T
doc.append(Math(data=[r'1/' + str(26), Matrix(M), Matrix(messageMatrix), '=', Matrix(getModMatrix(M @ messageMatrix))]))
doc.append("\n")
doc.append("Encrypted chunk: " + getStringFromMatrix(getModMatrix(M @ messageMatrix)))
with doc.create(Section('Encyption Result')):
doc.append('Cipher: ' + result)
elif(flag == "D"):
image_filename = './LookupHill.png'
with doc.create(Section('Introduction')):
doc.append('In this project, I implement a 3 × 3 Hill Cipher Machine in Python. This machine automatically generates LaTex reports to decipher user-input step by step. \n')
doc.append('We will be deciphering: ' + "".join(phrases) + ' using the key: ' + key + '. \n')
with doc.create(Section("Enryption Matrix")):
with doc.create(Figure(position='h!')) as lookup_hill:
lookup_hill.add_image(image_filename, width='120px')
lookup_hill.add_caption('Lookup Table of Hill Cipher')
doc.append('We use the Lookup Table above to create the Encryption Matrix below. \n')
M = createEncryptMatrix(key)
doc.append(Math(data=[Matrix(M)]))
with doc.create(Section("Encryption Matrix Mod 26 Inverse")):
'''iM = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
E21E31 = iM.copy()
E21E31[(1,0)] = -1 * (augM[(1,0)]/augM[(0,0)])
E21E31[(2,0)] = -1 * (augM[(2,0)]/augM[(0,0)])
augM = E21E31.dot(augM)
E32 = iM.copy()
E32[(2,1)] = -1 * (augM[(2,1)]/augM[(1,1)])
augM = E32.dot(augM)
E23E13 = iM.copy()
E23E13[(1,2)] = -1 * (augM[(1,2)]/augM[(2,2)])
E23E13[(0,2)] = -1 * (augM[(0,2)]/augM[(2,2)])
augM = E23E13.dot(augM)
E12 = iM.copy()
E12[(0,1)] = -1 * (augM[(0,1)]/augM[(1,1)])
augM = E12.dot(augM)
det = augM[(0,0)] * augM[(1,1)] * augM[(2,2)]
if(det == 0 or math.isnan(det)):
raise ValueError("Matrix Non-Invertible")
#print("Det: " + str(det))
if(egcd(int(round(det)), 26)[0] != 1):
raise ValueError("Key Matrix determinent not co-prime with 26")
#print("Mod inv of det: " + str(modinv(det, 26)))
D = iM.copy()
D[(0,0)] = 1/augM[(0,0)]
D[(1,1)] = 1/augM[(1,1)]
D[(2,2)] = 1/augM[(2,2)]
augM = D.dot(augM)
#Here are the additional steps needed to find the modular inverse of a matrix
augM = augM * det
augM = augM * modinv(int(round(det)), 26)
modAugM = getModMatrix(augM[0:, 3:])
return modAugM'''
invMat = gaussianInverseMod26(createEncryptMatrixAug(key))
doc.append(Math(data=[Matrix(invMat)]))
doc.append("\n")
with doc.create(Section("Matrix Multiplications")):
for phrase in phrases:
M = invMat
#print(M)
messageMatrix = np.array([[getCapitalAlphaMod(phrase[0]),getCapitalAlphaMod(phrase[1]),getCapitalAlphaMod(phrase[2])]]).astype("float64").T
doc.append(Math(data=[Matrix(M), Matrix(messageMatrix), '=', Matrix(getModMatrix(M @ messageMatrix))]))
doc.append("\n")
doc.append("Decrypted chunk: " + getStringFromMatrix(getModMatrix(M @ messageMatrix)))
with doc.create(Section('Decryption Result')):
doc.append('Plaintext: ' + result)
doc.generate_pdf('full', clean_tex=False)
subprocess.call(['open', 'full.pdf'])
def gen_graphs(self, visu):
'''
function calls the graphs methods to draw from the visualization
module according to use preferences
takes as input a visualizer object
'''
# start Graphs Section in the report #
self.doc.append(NoEscape(r'\leftskip=0pt'))
with self.doc.create(Section('Graphs', numbering=False)):
# uncomment after generating predictions
if not self.regression:
# Confusion Matrix #
self.doc.append(NoEscape(r'\leftskip=20pt'))
with self.doc.create(
Subsection('Confusion Matrix', numbering=False)):
self.doc.append(NoEscape(r'\leftskip=40pt'))
with self.doc.create(
Figure(position='htbp')
) as conf_mat_plot: # Create new Figure in tex
# get image path from the visualizer
file_name = visu.gen_conf_mat(
target_names=self.target_names,
predictions=self.predictions,
y=self.y_train,
dpi=300)
conf_mat_plot.add_image(file_name,
width=NoEscape(r'1\textwidth'))
self.doc.append(NoEscape(r'\pagebreak')) #start new page
# ROC Curve #
self.doc.append(NoEscape(r'\leftskip=20pt'))
with self.doc.create(Subsection('ROC Curve', numbering=False)):
self.doc.append(NoEscape(r'\leftskip=40pt'))
with self.doc.create(
Figure(position='htbp'
)) as ROC_plot: # Create new Figure in tex
# y_tr = self.y_train
y_ts = self.y_train
file_name = visu.gen_roc_curve(
probabilities=self.probabilities,
y=y_ts,
target_names=self.target_names)
ROC_plot.add_image(file_name,
width=NoEscape(r'1.2\textwidth'))
self.doc.append(NoEscape(r'\pagebreak')) #start new page
# Feature importance #
self.doc.append(NoEscape(r'\leftskip=20pt'))
with self.doc.create(
Subsection('Feature Importance', numbering=False)):
self.doc.append(NoEscape(r'\leftskip=40pt'))
with self.doc.create(Figure(position='htbp')) as imp_plot:
file_name = visu.gen_feature_imp(
regression=self.regression,
X=self.X_train,
y=self.y_train)
imp_plot.add_image(file_name,
width=NoEscape(r'1.2\textwidth'))
self.doc.append(NoEscape(r'\pagebreak')) #start new page
if self.experiments.iloc[0][0] == 'ensembleSelection':
# Word Cloud #
self.doc.append(NoEscape(r'\leftskip=20pt'))
with self.doc.create(
Subsection('Models Cloud', numbering=False)):
self.doc.append(NoEscape(r'\leftskip=40pt'))
with self.doc.create(
Figure(position='htbp')) as cloud_plot:
file_name = visu.gen_word_cloud(self.experiments)
cloud_plot.add_image(file_name,
width=NoEscape(r'1.2\textwidth'))
def fill_document(doc):
with doc.create(Section('Section 9.1', numbering=False)):
with doc.create(Subsection('8', numbering=False)):
with doc.create(
Enumerate(enumeration_symbol=r"\alph*)",
options={'start': 1})) as enum:
enum.add_item('5')
enum.add_item('3')
enum.add_item('7')
enum.add_item(NoEscape('$\sqrt{49+25}\\approx 8.6$'))
enum.add_item(NoEscape('$\sqrt{9+25}\\approx 5.8$'))
enum.add_item(NoEscape('$\sqrt{49+9}\\approx 7.6$'))
with doc.create(Subsection('12', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'radius = \sqrt{(\sqrt{1^2+2^2})^2+3^2} &= \sqrt{14} \\')
agn.append(r'(x-1)^2+(y-2)^2+(z-3)^2 &= (\sqrt{14})^2\\')
agn.append(r'(x-1)^2+(y-2)^2+(z-3)^2 &= 14')
with doc.create(Subsection('14', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'x^2+8x+y^2-6y+z^2+2z &= -17\\')
agn.append(r'(x+4)^2-16+(y-3)^2-9+(z+1)^2-1 &= -17\\')
agn.append(r'(x+4)^2+(y-3)^2+(z+1)^2 &= -17 +16+9+1\\')
agn.append(r'(x+4)^2+(y-3)^2+(z+1)^2 &= 9\\')
doc.append(
'The equation represents a sphere with center (-4,3,-1) and radius = 3'
)
with doc.create(Subsection('16', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'3(x^2+y^2+z^2) &=10+6y+12z\\')
agn.append(r'x^2+y^2+z^2 &=\frac{10}{3}+2y+4z\\')
agn.append(r'x^2+y^2-2y+z^2-4z &=\frac{10}{3}\\')
agn.append(r'x^2+(y-1)^2-2+(z-2)^2-4 &=\frac{10}{3}\\')
agn.append(r'x^2+(y-1)^2+(z-2)^2 &=\frac{10}{3}+2+4\\')
agn.append(r'x^2+(y-1)^2+(z-2)^2 &=\frac{28}{3}\\')
doc.append(
'The equation represents a sphere with center (0,1,2) and radius ='
)
doc.append(NoEscape('$2\sqrt{\\frac{7}{3}}$'))
with doc.create(Subsection('21-32', numbering=False)):
with doc.create(
Enumerate(enumeration_symbol=r"\arabic*)",
options={'start': 21})) as enum:
enum.add_item(
'The vertical plane that lies over the line given by x=5 in the xy-plane'
)
enum.add_item(
'The vertical plane that lies over the line given by y=-2 in the xy-plane'
)
enum.add_item(
'The subspace containing all numbers smaller than the plane that goes through y=8'
)
enum.add_item(
'The subspace containing all numbes larger than the vertical plane that lies over the line given by x=-3 in the xy-plane'
)
enum.add_item(
'The subspace contained between (and including) the xy-planes that pass through z=0 and z=6'
)
enum.add_item(
'The cup-shaped shell defined by spinning the parabola given by '
)
doc.append(NoEscape('$z^2=1$'))
doc.append(' spun around the z-axis')
enum.add_item(
'The circle that lies in the xy-plane and is centered at (0,0,-1) and has a radius = 2'
)
enum.add_item(
'The cylindrical shell of radius = 4 that is centered around the x-axis'
)
enum.add_item(
'The subspace contained within the sphere centered at (0,0,0) with radius '
)
doc.append(NoEscape('$\leq\sqrt{3}$'))
enum.add_item(
'The plane that extends out from the line given by x=z')
enum.add_item(
'The subspace that is outside the sphere centered at (0,0,1) with a radius of 1'
)
with doc.create(Subsection('38', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\sqrt{(x+1)^2+(y-5)^2+(z-3)^2} &= 2\sqrt{(x-6)^2+(y-2)^2+(z+2)^2}\\'
)
agn.append(
r'x^2+2x+1+y^2-10y+25+z^2-6z+9 &= 4(x^2-12x+36+y^2-4y\\ \
&\textnormal{ }+4+z^2+4z+4)\\')
agn.append(
r'4x^2-x^2-48x-2x+4y^2-y^2-16y+10y+4z^2-z^2+16z+6z &= -141\\'
)
agn.append(r'3x^2-50x+3y^2-6y+3z^2+22z &=-141\\')
agn.append(
r'x^2-\frac{50}{3}x+y^2-2y+z^2+\frac{22}{3}z &=-47\\')
agn.append(
r'(x-\frac{25}{3})^2+(y-1)^2+(z-\frac{11}{3})^2 &=-47+\frac{625}{9}+\frac{121}{9}\\'
)
agn.append(
r'(x-\frac{25}{3})^2+(y-1)^2+(z-\frac{11}{3})^2 &=\frac{323}{9}\\'
)
doc.append('The center is (25/3, 1, 11/3) and the radius is ')
doc.append(NoEscape('$\\frac{\\sqrt{323}}{3}$'))
with doc.create(Section('Section 9.2', numbering=False)):
with doc.create(Subsection('22', numbering=False)):
doc.append(
NoEscape(
'$\\langle \\frac{-6}{\\sqrt{6}}, \\frac{12}{\\sqrt{6}}, \\frac{6}{\\sqrt{6}}\\rangle$'
))
with doc.create(Subsection('28', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'wind = &\langle 50cos(\frac{7\pi}{4}), 50sin(\frac{7\pi}{4}) \rangle \
\\plane = &\langle 250cos(\frac{\pi}{6}), 250sin(\frac{\pi}{6}) \rangle\\'
)
agn.append(
r'true course = \langle 251.86, 89.64\rangle \textnormal{ and } & \
ground speed = \sqrt{251.86^2 + 89.64^2} = 267.34\\')
with doc.create(Subsection('38', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'\vec{i} = & \langle 1,0,0 \rangle\\')
agn.append(r'\vec{j} = & \langle 0,1,0 \rangle\\')
agn.append(r'\vec{k} = & \langle 0,0,1 \rangle\\')
agn.append(
r'\vec{v} = & \langle a\vec{i},b\vec{j},c\vec{k} \rangle\\'
)
agn.append(
r'hypotenuse = \rvert\rvert v\rvert\rvert = & \sqrt{a^2+b^2+c^2}\\'
)
agn.append(r'cos\alpha = & \frac{a}{\sqrt{a^2+b^2+c^2}}\\')
agn.append(r'cos\beta = & \frac{b}{\sqrt{a^2+b^2+c^2}}\\')
agn.append(r'cos\gamma = & \frac{c}{\sqrt{a^2+b^2+c^2}}\\')
agn.append(
r'cos^2\alpha + cos^2\beta + cos^2\gamma = & \frac{a^2}{a^2+b^2+c^2} + \
\frac{b^2}{a^2+b^2+c^2} + \frac{c^2}{a^2+b^2+c^2}\\'
)
agn.append(r'cos^2\alpha + cos^2\beta + cos^2\gamma = & 1\\')
with doc.create(Subsection('43', numbering=False)):
with doc.create(Figure(position='h!')) as triangle_pic:
image_filename = os.path.join(os.path.dirname(__file__),
'tri1.jpg')
triangle_pic.add_image(image_filename, width='255px')
def make_pdf(self, jobid, filename, dirname):
"""
Makes a PDF for a given job id. It retrieves data from Prometheus HTTP API and calls make_plot() as well as make_pie() in order to make the graphs
and display resource usage to users.
Parameters
----------
jobid : integer,
Slurm job's ID
filename : string
File name to save the figure
dirname : string
directory name to save the file
"""
geometry_options = {"right": "2cm", "left": "2cm"}
fname = CWD + "pdf/" + str(jobid) + "_summary"
doc = Document(fname, geometry_options=geometry_options)
metrics = ("jobs_cpu_percent", "jobs_rss", "jobs_read_mb",
"jobs_write_mb")
doc.preamble.append(
Command("title", "Plots for job " + str(self.__jobid)))
doc.preamble.append(Command("date", NoEscape(r"\today")))
doc.append(NoEscape(r"\maketitle"))
doc.append(
"This pdf contains plots/pie charts which are representative of your job's usage of HPC resources on CC clusters"
)
doc.append(NewPage())
for item in metrics:
self.make_plot(item, filename, dirname, True)
with doc.create(Section("Plot for " + Y_LABELS[item])):
with doc.create(Figure(position="htbp")) as plot:
plot.add_plot(width=NoEscape(r"1\textwidth"))
plot.add_caption(Y_LABELS[item] + " variation with time")
if item == "jobs_cpu_percent":
doc.append(
"The dashed line on this plot shows the lowest acceptable bound for CPU usage for a job with as many cores as yours"
)
doc.append(NewPage())
plt.close()
metrics = ("jobs_user_time", "jobs_system_time")
title = [Y_LABELS[metric] for metric in metrics]
self.make_pie(metrics, filename, dirname, True)
with doc.create(Section("Pie chart for " + " vs ".join(title))):
with doc.create(Figure(position="htbp")) as plot:
plot.add_plot(width=NoEscape(r"1\textwidth"))
plot.add_caption(", ".join(title) + " proportions")
doc.append(NewPage())
plt.close()
metrics = ("jobs_cpu_time_core", )
self.make_pie(metrics, filename, dirname, True)
with doc.create(
Section("Pie chart for " + Y_LABELS[metrics[0]] +
" per core")):
with doc.create(Figure(position="htbp")) as plot:
plot.add_plot(width=NoEscape(r"1\textwidth"))
plot.add_caption(Y_LABELS[metrics[0]] + " proportions")
doc.append(NewPage())
plt.close()
doc.generate_pdf(clean_tex=False)
with doc.create(Section('The fancy stuff')):
with doc.create(Subsection('Correct matrix equations')):
doc.append(Math(data=[Matrix(M), Matrix(a), '=', Matrix(M * a)]))
with doc.create(Subsection('Beautiful graphs')):
with doc.create(TikZ()):
plot_options = 'height=6cm, width=6cm, grid=major'
with doc.create(Axis(options=plot_options)) as plot:
plot.append(Plot(name='model', func='-x^5 - 242'))
coordinates = [
(-4.77778, 2027.60977),
(-3.55556, 347.84069),
(-2.33333, 22.58953),
(-1.11111, -493.50066),
(0.11111, 46.66082),
(1.33333, -205.56286),
(2.55556, -341.40638),
(3.77778, -1169.24780),
(5.00000, -3269.56775),
]
plot.append(Plot(name='estimate', coordinates=coordinates))
with doc.create(Subsection('Cute kitten pictures')):
with doc.create(Figure(position='h!')) as kitten_pic:
kitten_pic.add_image(image_filename, width='120px')
kitten_pic.add_caption('Look it\'s on its back')
doc.generate_pdf('full')
with doc.create(Subsection('Summary Table')):
with doc.create(LongTabu(fmt, spread="0pt")) as data_table:
header_row = ['Experiment runs', 'Average Throughput(million events/second)']
data_table.add_row(header_row, mapper=[bold])
data_table.add_hline()
data_table.add_empty_row()
data_table.end_table_header()
# Iterates through throughput array and no_file_array and append rescpective run and throughput in the row
for x, y in np.c_[no_of_file, throughput]:
row = [x, y]
data_table.add_row(row)
doc.append(NoEscape(r'\newpage'))
# append graph into the pdf report
with doc.create(Subsection("Graph")):
with doc.create(Figure(position='h!')) as throughput_chart:
throughput_chart.add_image(throughput_image_dir, width='450px')
with doc.create(Subsection("results")):
doc.append("Over all throughput average (million events/seconds) of")
doc.append(NoEscape(r'\space'))
doc.append(path)
doc.append(NoEscape(r'\space'))
doc.append("is")
doc.append(NoEscape(r'\space'))
doc.append(final_throughput_avg)
doc.append(NoEscape(r'\newpage'))
# latency summary table and chart for latency
with doc.create(
t.add_hline(start=None, end=None)
t.add_row(cells=(1, 2), escape=False)
t.add_multicolumn(size=2, align='|c|', content='Multicol', cells=None,
escape=False)
t.add_multirow(size=3, align='*', content='Multirow', hlines=True, cells=None,
escape=False)
# Command
c = Command('documentclass', arguments=None, options=None, packages=None)
# Figure
f = Figure(data=None, position=None)
f.add_image(filename='', width=r'0.8\textwidth', placement=r'\centering')
f.add_caption('')
# Numpy
v = VectorName(name='')
M = np.matrix([[2, 3, 4],
[0, 0, 1],
[0, 0, 2]])
m = Matrix(matrix=M, name='', mtype='p', alignment=None)
# Package
p = Package(name='', base='usepackage', options=None)
def _document_models(self) -> None:
"""Add model summaries to the traceability document.
"""
with self.doc.create(Section("Models")):
for model in humansorted(self.system.network.models,
key=lambda m: m.model_name):
if not isinstance(model, (tf.keras.Model, torch.nn.Module)):
continue
self.doc.append(NoEscape(r'\FloatBarrier'))
with self.doc.create(Subsection(f"{model.model_name}")):
if isinstance(model, tf.keras.Model):
# Text Summary
summary = []
model.summary(line_length=92,
print_fn=lambda x: summary.append(x))
summary = "\n".join(summary)
self.doc.append(Verbatim(summary))
with self.doc.create(Center()):
self.doc.append(
HrefFEID(FEID(id(model)), model.model_name))
# Visual Summary
# noinspection PyBroadException
try:
file_path = os.path.join(
self.resource_dir,
"{}_{}.pdf".format(self.report_name,
model.model_name))
dot = tf.keras.utils.model_to_dot(
model, show_shapes=True, expand_nested=True)
# LaTeX \maxdim is around 575cm (226 inches), so the image must have max dimension less than
# 226 inches. However, the 'size' parameter doesn't account for the whole node height, so
# set the limit lower (100 inches) to leave some wiggle room.
dot.set('size', '100')
dot.write(file_path, format='pdf')
except Exception:
file_path = None
print(
f"FastEstimator-Warn: Model {model.model_name} could not be visualized by Traceability"
)
elif isinstance(model, torch.nn.Module):
if hasattr(model, 'fe_input_spec'):
# Text Summary
# noinspection PyUnresolvedReferences
inputs = model.fe_input_spec.get_dummy_input()
self.doc.append(
Verbatim(
pms.summary(
model.module if
self.system.num_devices > 1 else model,
inputs,
print_summary=False)))
with self.doc.create(Center()):
self.doc.append(
HrefFEID(FEID(id(model)),
model.model_name))
# Visual Summary
# Import has to be done while matplotlib is using the Agg backend
old_backend = matplotlib.get_backend() or 'Agg'
matplotlib.use('Agg')
# noinspection PyBroadException
try:
# Fake the IPython import when user isn't running from Jupyter
sys.modules.setdefault('IPython', MagicMock())
sys.modules.setdefault('IPython.display',
MagicMock())
import hiddenlayer as hl
with Suppressor():
graph = hl.build_graph(
model.module if
self.system.num_devices > 1 else model,
inputs)
graph = graph.build_dot()
graph.attr(
rankdir='TB'
) # Switch it to Top-to-Bottom instead of Left-to-Right
# LaTeX \maxdim is around 575cm (226 inches), so the image must have max dimension less
# than 226 inches. However, the 'size' parameter doesn't account for the whole node
# height, so set the limit lower (100 inches) to leave some wiggle room.
graph.attr(size="100,100")
graph.attr(margin='0')
file_path = graph.render(
filename="{}_{}".format(
self.report_name, model.model_name),
directory=self.resource_dir,
format='pdf',
cleanup=True)
except Exception:
file_path = None
print(
"FastEstimator-Warn: Model {} could not be visualized by Traceability"
.format(model.model_name))
finally:
matplotlib.use(old_backend)
else:
file_path = None
self.doc.append(
"This model was not used by the Network during training."
)
if file_path:
with self.doc.create(Figure(position='ht!')) as fig:
fig.append(
Label(
Marker(name=str(FEID(id(model))),
prefix="model")))
fig.add_image(
os.path.relpath(file_path,
start=self.save_dir),
width=NoEscape(
r'1.0\textwidth,height=0.95\textheight,keepaspectratio'
))
fig.add_caption(
NoEscape(
HrefFEID(FEID(id(model)),
model.model_name).dumps()))
def fill_document(doc):
with doc.create(Section('Basic Concept Problems', numbering=True)):
# Question 1: prove the pythagorean theorem
with doc.create(Figure(position='h!')) as pythagorean_pic:
image_filename = os.path.join(os.path.dirname(__file__),
'pythagorean.jpg')
pythagorean_pic.add_image(image_filename, width='350px')
# Question 2: prove the law of cosines
with doc.create(Figure(position='h!')) as tri_pic:
image_filename = os.path.join(os.path.dirname(__file__),
'triangle.jpg')
tri_pic.add_image(image_filename, width='100px')
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'&\textnormal{Given a triangle with sides A, B, and C }')
agn.append(
r'\textnormal{with height h and an angle } \theta\\')
agn.append(
r'& \textnormal{we know that the left triangle will}')
agn.append(r'\textnormal{ have the property } m^2+h^2=B^2\\')
agn.append(
r'&\textnormal{and the right triangle will have the property }'
)
agn.append(
r' h^2 + n^2 = C^2\\ &\textnormal{by the pythagorean theorem.}'
)
agn.append(r'\textnormal{ Therefore:}\\')
agn.append(r'&n = A - m\\')
agn.append(r'&\textnormal{and } h^2 + (A-m)^2 = C^2\\')
agn.append(r'&B^2-m^2+A^2-2Am+m^2 = C^2\\')
agn.append(
r'&\textnormal{Furthermore, we know } cos\theta = \frac{m}{B}\\'
)
agn.append(r'&\textnormal{Therefore:}\\')
agn.append(r'&B^2+A^2 -2ABcos\theta = C^2')
with doc.create(Section('9.3', numbering=False)):
with doc.create(Subsection('20', numbering=False)):
with doc.create(Figure(position='h!')) as tri2_pic:
image_filename = os.path.join(os.path.dirname(__file__),
'tri2.jpg')
tri2_pic.add_image(image_filename, width='150px')
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'\vec{u} &= <-2,3,2>\\')
agn.append(r'\vec{v} &= <3,-2,-4>\\')
agn.append(r'\vec{w} &= <1,1,-2>\\')
agn.append(r'\textnormal{The angle at D:} \\')
agn.append(
r'<-2,3,2>\cdot<1,1,-2> &=\|<-2,3,2>\| \|<1,1,-2>\|cosd\\'
)
agn.append(r'-3 &= \sqrt{17}\sqrt{6}cosd\\')
agn.append(r'cos^-1(\frac{-3}{\sqrt{102}}) &= d\\')
agn.append(r'd & \approx{107.28}^\circ\\')
agn.append(r'\textnormal{The angle at E:} \\')
agn.append(
r'-(<-2,3,2>)\cdot<3,-2,-4> &=\|<-2,3,2>\| \|<3,-2,-4>\|cose\\'
)
agn.append(r'20 &= \sqrt{17}\sqrt{29}cose\\')
agn.append(r'cos^-1(\frac{20}{\sqrt{493}}) &= e\\')
agn.append(r'e & \approx{25.74}^\circ\\')
agn.append(r'\textnormal{The angle at F:} \\')
agn.append(
r'-(<1,1,-2>)\cdot-(<3,-2,-4>) &=\|<1,1,-2>\| \|<3,-2,-4>\|cosf\\'
)
agn.append(r'9 &= \sqrt{6}\sqrt{29}cosf\\')
agn.append(r'cos^-1(\frac{9}{\sqrt{174}}) &= f\\')
agn.append(r'f & \approx{46.98}^\circ\\')
# projections
with doc.create(Subsection('30', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'\|a\| &= \sqrt{5}\\')
agn.append(
r'comp_a b &= \frac{a \cdot b}{\|a\|} = \frac{-4+2}{\sqrt{5}} = \frac{-2}{\sqrt{5}}\\'
)
agn.append(r'\textnormal{The vector projection is:}\\')
agn.append(
r'proj_a b &= \frac{-2}{\sqrt{5}}\frac{<1,2>}{\sqrt{5}} = \frac{-2}{5} <1,2>\\'
)
agn.append(r'proj_a b &= <\frac{-2}{5}, \frac{-4}{5}>')
with doc.create(Subsection('31', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'a = <2,-1,4> & \textnormal{ and } b = <0,1,\frac{1}{2}>\\'
)
agn.append(r'\| a \| &= \sqrt{4+1+16} = \sqrt{21}\\')
agn.append(
r'comp_a b &= \frac{a \cdot b}{\sqrt{21}} = \frac{1}{\sqrt{21}}\\'
)
agn.append(r'\textnormal{The vector projection is:}\\')
agn.append(
r'proj_a b &= \frac{1}{\sqrt{21}}\frac{<2,-1,4>}{\sqrt{21}} = \frac{1}{21}<2,-1,4>\\'
)
agn.append(
r'proj_a b &= <\frac{2}{21},\frac{-1}{21},\frac{4}{21}>\\')
with doc.create(Subsection('43', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\intertext{Let all sides of the cube be length = 1, and let the edges lie along the x, y, z axis}\\'
)
agn.append(
r'\text{The diagonal vector, }\vec{d}\text{ from (0,0,0) to (1,1,1) = <1,1,1>}\\'
)
agn.append(
r'\text{Let the unit vector } \vec{k} = <0,0,1> \text{be a side.}\\'
)
agn.append(
r'\text{The angle between } \vec{d} \text{ and } \vec{k} \text{ is:}\\'
)
agn.append(
r'cos\theta &= \frac{<0,0,1> \cdot <1,1,1>}{\|u\|\|v\|}\\')
agn.append(r'&= \frac{0+0+1}{\sqrt{1}\sqrt{3}}\\')
agn.append(r'&= \frac{1}{\sqrt{3}} \\')
agn.append(r'\theta &= cos^-1 \frac{1}{\sqrt{3}}\\')
agn.append(r'&= 54.74^\circ')
with doc.create(Subsection('46', numbering=False)):
with doc.create(Figure(position='h!')) as ang_pic:
image_filename = os.path.join(os.path.dirname(__file__),
'ang1.jpg')
ang_pic.add_image(image_filename, width='150px')
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'cos\alpha &= \frac{a \cdot c}{\|a\| \|c\|}\\')
agn.append(
r'&= \frac{a \cdot (\|a\|b+\|b\|a))}{\|a\| \|c\|}\\')
agn.append(
r'&= \frac{a \cdot \|a\|a \cdot b + \|b\|a \cdot a}{\|a\| \|c\|}\\'
)
agn.append(
r'&= \frac{\|a\|a \cdot b + \|b\| \|a\|^2}{\|a\| \|c\|}\\')
agn.append(r'&= \frac{a \cdot b + \|b\| \|a\|}{\|c\|}\\')
agn.append(r'cos\beta &= \frac{b \cdot c}{\|b\| \|c\|}\\')
agn.append(
r'&= \frac{b \cdot (\|a\|b+\|b\|a))}{\|b\| \|c\|}\\')
agn.append(
r'&= \frac{\|a\| b \cdot b + \|b\|a \cdot b}{\|b\| \|c\|}\\'
)
agn.append(
r'&= \frac{\|a\| \|b\|^2 + \|b\| a \cdot b}{\|b\| \|c\|}\\'
)
agn.append(r'&= \frac{\|a\| \|b\| + a \cdot b}{\|c\|}\\')
agn.append(
r'\textnormal{Now we can see that } cos \alpha = cos \beta\\'
)
agn.append(
r' \frac{a \cdot b + \|b\| \|a\|}{\|c\|} &= \frac{\|a\| \|b\| + a \cdot b}{\|c\|}\\'
)
with doc.create(Section('9.4', numbering=False)):
with doc.create(Subsection('20', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\intertext{The cross product is orthogonol to both i+j+k and 2i+k:}\\'
)
agn.append(
r'i+j+k = <1,1,1> & \textnormal{ and } 2i+k = <2,0,1>\\')
agn.append(
r'<1,1,1>\times <2,0,1> &= (1-0) \vec{i}+(2-1) \vec{j}+(0-2) \vec{k}\\'
)
agn.append(r'<1,1,1>\times <2,0,1> &= <1,1,-2>\\')
agn.append(
r'\intertext{Divide by the magnitude to find the unit vector:}\\'
)
agn.append(
r'\textnormal{unit vector } &= \frac{<1,1,-2>}{\sqrt{1+1+4}}\\'
)
agn.append(
r'&= <\frac{1}{\sqrt{6}},\frac{1}{\sqrt{6}},\frac{-2}{\sqrt{6}}>\\'
)
agn.append(
r'\intertext{The second unit vector would be the negative of the first:}\\'
)
agn.append(
r'&= <\frac{-1}{\sqrt{6}},\frac{-1}{\sqrt{6}},\frac{2}{\sqrt{6}}>\\'
)
with doc.create(Subsection('22', numbering=False)):
with doc.create(Figure(position='h!')) as para_pic:
image_filename = os.path.join(os.path.dirname(__file__),
'para1.jpg')
para_pic.add_image(image_filename, width='150px')
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\vec{u} = <2,5,0> \textnormal{ and } \vec{v} = <0,1,3>\\'
)
agn.append(r'A &= \|<2,5,0> \times <0,1,3>\| \\')
agn.append(r'A &= \|<-15,6,-2>\| \\')
agn.append(r'A &= \sqrt{265}')
with doc.create(Subsection('24', numbering=False)):
with doc.create(Subsection('a)', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\vec{PQ} = <1,2,1> \textnormal{ and } \vec{PR} = <5,0,-2>\\'
)
agn.append(
r'\textnormal{The vector orthogonol to the plane = } \vec{PQ} \times \vec{PR}\\'
)
agn.append(r'\vec{PQ} \times \vec{PR} = <-5,7,-10>\\')
with doc.create(Subsection('b)', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'A &= \frac{\|<-5,7,-10>\|}{2}\\')
agn.append(r'A &= \frac{\sqrt{174}}{2} \approx 6.6')
with doc.create(Subsection('33', numbering=False)):
with doc.create(Subsection('a)', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'd &= \|b\|sin\theta\\')
agn.append(r'&=\frac{\|a\|}{\|a\|}\|b\|sin\theta\\')
agn.append(r'&= \frac{\|a\|\|b\|sin\theta}{\|a\|}\\')
agn.append(r'&= \frac{\|a \times b\|}{\|a\|}\\')
with doc.create(Subsection('b)', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\vec{a} = <-1,-2,-1> \textnormal{ and } \vec{b} = <1, -5, -7>\\'
)
agn.append(
r'd &= \frac{\|<-1,-2,-1> \times <1, -5, -7>\|}{\sqrt{1+4+1}}\\'
)
agn.append(r'&= \frac{\|<9,-15,7>\|}{\sqrt{6}}\\')
agn.append(r'&= \frac{\sqrt{355}}{\sqrt{6}}\\')
agn.append(r'd & \approx 7.69\\')
with doc.create(Section('9.5', numbering=False)):
with doc.create(Subsection('2', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\textnormal{vector equation } &= <6,-5,2> + t<1,3,\frac{-2}{3}>\\'
)
agn.append(r'&= <6+t, -5+3t, 2+\frac{-2}{3}t>\\')
agn.append(r'\textnormal{The parametric equations are:}\\')
agn.append(r'x(t) &= 6+t\\')
agn.append(r'y(t) &= -5+3t\\')
agn.append(r'z(t) &= 2+\frac{-2}{3}t\\')
with doc.create(Subsection('5', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(r'x(t) &= 1+t\\')
agn.append(r'y(t) &= 3t\\')
agn.append(r'z(t) &= 6+t\\')
with doc.create(Subsection('10', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\vec{n_1} = <1,2,3> \textnormal{ and } \vec{n_2} = <1,-1,1>\\'
)
agn.append(
r'<1,2,3> \times <1,-1,1> \textnormal{is a line parallel to the line of intersection.}\\'
)
agn.append(r'<1,2,3> \times <1,-1,1> = <5,2,-3>\\')
agn.append(
r'\textnormal{Plug in z=0 to solve x, y and find a point on the line of intersection}\\'
)
agn.append(r'x+2y=1 \textnormal{ and } x-y &=1\\')
agn.append(r'\textnormal{This gives us } 3y &= 0 \\')
agn.append(
r'\textnormal{Therefore (1,0,0) lies on the line of intersection and the symmetric equations are:}\\'
)
agn.append(r'\frac{x-1}{5} &= \frac{y}{2} = \frac{-z}{3}\\')
agn.append(r'\textnormal{And the parametric equations are:}\\')
agn.append(r'x(t) &= 1+5t\\')
agn.append(r'y(t) &= 2t\\')
agn.append(r'z(t) &= -3t\\')
with doc.create(Subsection('18', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\textnormal{Check ratio of coefficients to test if parallel:}\\'
)
agn.append(r'\frac{1}{-1} = \frac{3}{1} = \frac{-1}{3}\\')
agn.append(
r'-1 \neq 3 \neq -3 \textnormal{therefore the lines are NOT parallel}\\'
)
agn.append(
r'\textnormal{Solve system of equations to test if intersecting:}\\'
)
agn.append(r'1 +2t &= -1+s\\')
agn.append(r'3t &= 4+s\\')
agn.append(r'2-t &= 1+3s\\')
agn.append(r'\textnormal{Solve the first equation for t:}\\')
agn.append(r'2t &=-2+s\\')
agn.append(r't &= -1 + \frac{s}{2}\\')
agn.append(r'\textnormal{Plug into the second equation:}\\')
agn.append(r'3(-1+\frac{s}{2}) = 4+s\\')
agn.append(r'-3+\frac{3s}{2} = 4+s\\')
agn.append(r'\frac{s}{2} = 7\\')
agn.append(r's = 14\\')
agn.append(
r'\textnormal{Plug s=14 this into the equation for t:}\\')
agn.append(r't=-1+\frac{14}{2} = -6\\')
agn.append(
r'\textnormal{Plug s=14 and t=-6 into the third equation:}\\'
)
agn.append(r'2+-6 = 1+3(14)\\')
agn.append(
r'-4 \neq 43 \textnormal{therefore the lines do not intersect.}\\'
)
agn.append(
r'\textnormal{Since the lines are not parallel and do not intersect, they must be skew.}\\'
)
with doc.create(Subsection('25', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'P(0,1,1) \textnormal{ and }Q(1,0,1) \textnormal{ and }R(1,1,0)\\'
)
agn.append(r'\vec{PQ} = <1-0,0-1,1-1> &= <1,-1,0>\\')
agn.append(r'\vec{PR} = <1-0,1-1,0-1> &= <1,0,-1>\\')
agn.append(
r'\textnormal{Take the cross product to get the coefficients of the plane equation:}\\'
)
agn.append(r'<1,-1,0> \times <1,0,-1> = <1,1,1> \\')
agn.append(
r'\textnormal{Use P as the point for the equation of the plane:}\\'
)
agn.append(r'1(x-0)+1(y-1)+1(z-1) &= 0\\')
agn.append(r'x+y+z &=2\\')
with doc.create(Subsection('27', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\textnormal{The points P(6,0,-2) and Q(4,3,7) are on the plane.}\\'
)
agn.append(
r'\textnormal{Set t=1 to get a third point on the plane, R(2,8,11)}\\'
)
agn.append(r'\vec{PQ} = <4-6,3-0,7-(-2)> = <-2,3,9>\\')
agn.append(r'\vec{PR} = <2-6,8-0,11-(-2)> = <-4,8,13>\\')
agn.append(
r'\textnormal{Take the cross product to get the coefficients of the plane equation:}\\'
)
agn.append(r'<-2,3,9> \times <-4,8,13> = <-33,-10,-4>\\')
agn.append(
r'\textnormal{Use P as the point for the equation of the plane:}\\'
)
agn.append(r'-33(x-6)+-10(y-0)+-4(z+2) &= 0\\')
agn.append(r'-33x+198-10y-4z-8 &= 0\\')
agn.append(r'-33x-10y-4z &= -190')
with doc.create(Subsection('32', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\textnormal{Let Q be the plane that we are looking for.}\\'
)
agn.append(
r'\textnormal{Set z=0 to get a point on the line of intersection:}\\'
)
agn.append(r'(1,3,0)\\')
agn.append(
r'\textnormal{To get a normal vector for Q, take the cross product of two vectors parallel to Q.}\\'
)
agn.append(
r'\textnormal{The normal vector of the plane perpendicular to Q is parallel to Q:}\\'
)
agn.append(r'<1,1,-2>\\')
agn.append(
r'\textnormal{Get a second vector parallel to Q by taking the cross product of the normal vectors }\\'
)
agn.append(
r'\textnormal{of the two planes that form the line of intersection that Q passes through.}\\'
)
agn.append(r'<1,0,-1> \times <0,1,2> &= <1,-2,1>\\')
agn.append(
r'\textnormal{Now take the cross product of these two vectors:}\\'
)
agn.append(r'<1,1,-2> \times <1,-2,1> &= <-3,-3,-3>\\')
agn.append(
r'\textnormal{Plug these into the plane equation:}\\')
agn.append(r'-3(x-1)-3(y-3)-3(z-0) &= 0\\')
agn.append(r'-3x+3-3y+9-3z &= 0\\')
agn.append(r'-3x-3y-3z &= -12\\')
agn.append(r'-3(x+y+z) &= -12\\')
agn.append(r'x+y+z &= 4\\')
with doc.create(Subsection('56', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'd &= \frac{|1(6)+(-2)(0)+(-4)(-2) + (-8)|}{\sqrt{1^2+(-2)^2+(-4)^2}}\\'
)
agn.append(r'&= \frac{|6+8-8|}{\sqrt{21}}\\')
agn.append(r'&= \frac{6}{\sqrt{21}}\\ ')
agn.append(r'd &\approx 1.31\\')
with doc.create(Subsection('58', numbering=False)):
with doc.create(Alignat(numbering=False, escape=False)) as agn:
agn.append(
r'\textnormal{To find the distance we need a point on one plane.}\\'
)
agn.append(
r'\textnormal{Plug in z=0 to the first equation.}\\')
agn.append(r'0 &= 4y - 2x\\')
agn.append(r'y &= \frac{1}{2}x\\')
agn.append(
r'\textnormal{Therefore the point (2,1,0) is on the first plane.}\\'
)
agn.append(
r'\textnormal{Now we can use the distance formula.}\\')
agn.append(
r'd &= \frac{|3(2) + -6(1) + 9(0) + -1|}{\sqrt{3^2+(-6)^2+9^2}}\\'
)
agn.append(r'&= \frac{|6-6-1|}{\sqrt{126}}\\')
agn.append(r'&= \frac{1}{\sqrt{126}}\\')
agn.append(r'd & \approx .09\\')
def append_cross_section_figure(self, doc, tpdf):
with doc.create(Section(tpdf.step_split)):
with doc.create(Figure(position='H')) as fig_sectransv:
fig_sectransv.add_image("figs\\sectransv", width='500px')
fig_sectransv.add_caption(NoEscape(tpdf.figure_label))
def report(context, json_report, json_varreport, rulegraph_img):
config = json_report
sample_config = json.load(open(json_report))
var_config = json.load(open(get_config(json_varreport)))
tex_path = os.path.abspath(
os.path.join(sample_config["analysis"]["analysis_dir"],
"delivery_report"))
if not rulegraph_img:
rulegraph_img = sample_config['analysis']['dag']
os.makedirs(tex_path, exist_ok=True)
geometry_options = {
"head": "40pt",
"headheight": "130pt",
"headsep": "1cm",
"margin": "1.5cm",
"bottom": "1.5cm",
"includeheadfoot": True
}
doc = Document(geometry_options=geometry_options)
doc.packages.append(Package('lscape'))
doc.packages.append(Package('longtable'))
doc.packages.append(Package('float'))
doc.packages.append(Package('caption', options='labelfont=bf'))
doc.append(
NoEscape(
r'\captionsetup[table]{labelsep=space, justification=raggedright, singlelinecheck=off}'
))
#Add first page style
first_page = PageStyle("header", header_thickness=1)
#Add Header
with first_page.create(Head("C")) as mid_header:
with mid_header.create(
MiniPage(width=NoEscape(r"0.2\textwidth"),
pos='c')) as logo_wrapper:
logo_file = os.path.join(os.path.dirname(__file__), '..',
'assests/cg.png')
logo_wrapper.append(
StandAloneGraphic(image_options="width=50px",
filename=logo_file))
with mid_header.create(
Tabularx(
"p{3cm} p{2cm} X X p{4cm} p{3cm}",
width_argument=NoEscape(r"0.8\textwidth"))) as mid_table:
mid_table.add_row(
[MultiColumn(6, align='r', data=simple_page_number())])
mid_table.add_row([
MultiColumn(6,
align='c',
data=MediumText("Molecular report on"))
])
mid_table.add_row([
MultiColumn(6,
align='c',
data=MediumText(get_sample_name(config)))
])
mid_table.add_empty_row()
mid_table.add_row([
'gender', "NA", " ", " ", 'Sample recieved:',
sample_config['analysis']['date']['sample_received']
])
mid_table.add_row([
'tumor type', "NA", " ", " ", 'Analysis completion:',
sample_config['analysis']['date']['analysis_finish']
])
mid_table.add_row([
'analysis type', "NA", " ", " ", 'PDF Report date:',
datetime.now().strftime("%Y-%m-%d %H:%M")
])
mid_table.add_row(
['sample type', "NA", " ", " ", 'Delivery date', "NA"])
mid_table.add_row([
'sample origin', "NA", " ", " ", 'Analysis:',
r'BALSAMIC v' + sample_config['analysis']['BALSAMIC']
])
doc.preamble.append(first_page)
#End First page
# doc.preamble.append(
# Command(
# 'title',
# NoEscape(r'BALSAMIC v' + sample_config["analysis"]["BALSAMIC"] +
# r'\\ \large Developer Report')))
# doc.preamble.append(
# Command('author', 'Patient ID: ' + get_sample_name(config)))
# doc.preamble.append(Command('date', NoEscape(r'\today')))
# doc.append(NoEscape(r'\maketitle'))
doc.change_document_style("header")
with doc.create(Section(title='Analysis report', numbering=True)):
with doc.create(
Subsection('Summary of variants and variant callers',
numbering=True)):
doc.append(
"Placeholder for text about BAM alignment metrics and variant callers. Here comes the info on reads, "
+
"QC metrics, align metrics, and general sample information. preferabily in table format."
)
doc.append("\n")
summary_tables = ["TMB", "VarClass", "VarCaller", "VarCallerClass"]
for i in summary_tables:
shellcmd = [
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"..", "..", "scripts/VariantReport.R")
]
shellcmd.extend([
"--infile", sample_config["vcf"]["merged"]["SNV"],
"--genomeSize", sample_config["bed"]["genome_size"],
"--type", "latex", "--mode", i, "--outfile",
os.path.join(tex_path,
sample_config['analysis']['sample_id'])
])
print(" ".join(shellcmd))
outTab = subprocess.check_output(shellcmd)
doc.append(
NoEscape(
outTab.decode('utf-8').replace("\\centering",
"\\small")))
doc.append(NoEscape(r'\normalsize'))
doc.append(NewPage())
with doc.create(Subsection("Summary of MVL report", numbering=True)):
doc.append(
"Placeholder for general description of MVL settings. A mention to summary "
+
"pipeline, summary of MVL settings. Gene coverage for identified genes should go here. Figures!"
)
outCov = dict()
cmd_param = defaultdict(list)
J = defaultdict(list)
for i in var_config["filters"]:
cmd_param["TUMOR_DP"].append(
var_config["filters"][i]["TUMOR"]["DP"])
cmd_param["TUMOR_AD"].append(
var_config["filters"][i]["TUMOR"]["AD"])
cmd_param["TUMOR_AFmax"].append(
var_config["filters"][i]["TUMOR"]["AF_max"])
cmd_param["TUMOR_AFmin"].append(
var_config["filters"][i]["TUMOR"]["AF_min"])
cmd_param["TUMOR_inMVL"].append(
var_config["filters"][i]["in_mvl"])
cmd_param["var_type"].append(",".join(
["SNP", "INDEL", "MNP", "OTHER"]))
cmd_param["varcaller"].append(",".join(
var_config["filters"][i]["variantcaller"]))
cmd_param["ann"].append(
",".join(var_config["filters"][i]["annotation"]["SNV"]) +
"," +
",".join(var_config["filters"][i]["annotation"]["INDEL"]))
cmd_param["name"].append(i.replace("_", "\_"))
cmd_param["outfile_tex"].append(tex_path + "/" + i + ".tex")
cmd_param["outfile_gene"].append(tex_path + "/" + i +
".genelist")
for i in cmd_param:
J[i] = ";".join(cmd_param[i])
shellcmd = [
os.path.join(os.path.dirname(os.path.abspath(__file__)), "..",
"..", "scripts/VariantReport.R")
]
shellcmd.extend([
"--infile", "'" + sample_config["vcf"]["merged"]["SNV"] + "'",
"--dp", "'" + J["TUMOR_DP"] + "'", "--tumorad",
"'" + J["TUMOR_AD"] + "'", "--afmax",
"'" + J["TUMOR_AFmax"] + "'", "--afmin",
"'" + J["TUMOR_AFmin"] + "'", "--inMVL",
"'" + J["TUMOR_inMVL"] + "'", "--exclusiveSets", "TRUE",
"--vartype", "'" + J["var_type"] + "'", "--varcaller",
"'" + J["varcaller"] + "'", "--ann", "'" + J["ann"] + "'",
"--name", "'" + J["name"] + "'", "--type", "latex"
])
subprocess.check_output(
" ".join(shellcmd +
["--outfile", "'" + J["outfile_tex"] + "'"]),
shell=True)
print(" ".join(shellcmd +
["--outfile", "'" + J["outfile_tex"] + "'"]))
subprocess.check_output(" ".join(shellcmd + [
"--outfile", "'" + J["outfile_gene"] + "'", "--exportGene", "T"
]),
shell=True)
for c, i in enumerate(var_config["filters"]):
with doc.create(
Subsubsection(var_config["filters"][i]["name"],
numbering=True)):
print(cmd_param["outfile_tex"])
fname = cmd_param["outfile_tex"][c]
if os.stat(fname).st_size > 10:
#get gene list
with open(cmd_param["outfile_gene"][c]) as myfile:
genes = myfile.read().replace('\n', '')
with open(fname, 'r') as myfile:
data = myfile.read() #.replace('\n', '')
#doc.append(NoEscape(r'\begin{landscape}'))
#longtable instead of tabular makes the table span multiple pages, but the header doesn't span. Occasionally
#the alignment also is messed up. There must be a hidden package conflict OR general alignment issues.
#doc.append(NoEscape(varreport.replace("{tabular}","{longtable}")))
doc.append(
NoEscape(
data.replace("\\centering", "\\scriptsize")))
for s in sample_config["bed"]["exon_cov"]:
shellcmd = [
os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"..", "scripts/CoverageRep.R")
]
shellcmd.extend([
"--infile",
sample_config["bed"]["exon_cov"][s],
"--genename", genes, "--name",
s.replace("_", "\_"), "--type", "latex"
])
outCov = subprocess.check_output(shellcmd)
doc.append(
NoEscape(
outCov.decode('utf-8').replace(
"\\centering", "\\scriptsize")))
#doc.append(NoEscape(r'\end{landscape}'))
else:
doc.append("No variants were found for this filter")
# doc.append(NoEscape(r'\normalsize'))
doc.append(NewPage())
with doc.create(Subsection('Coverage report')):
for s in sample_config["bed"]["target_cov"]:
with doc.create(Figure(position='h!')) as cov_img:
covplot = ".".join(
[os.path.join(tex_path, s), "Coverage.pdf"])
shellcmd = [
os.path.join(
os.path.dirname(os.path.abspath(__file__)), "..",
"..", "scripts/CoveragePlot.R")
]
shellcmd.extend([
"--infile", sample_config["bed"]["target_cov"][s],
"--outfile", covplot, "--title",
s.replace("_", "\_")
])
subprocess.check_output(shellcmd)
cov_img.add_image(covplot, width='450px')
cov_img.add_caption('Coverage report for sample ' +
s.replace("_", "\_"))
doc.append(NewPage())
with doc.create(Subsection('Analysis pipeline')):
with doc.create(Figure(position='h!')) as pipeline_img:
pipeline_img.add_image(rulegraph_img, width='450px')
pipeline_img.add_caption('BALSAMIC pipeline')
doc.append(NewPage())
with doc.create(Section(title="Appendix", numbering=True)):
with doc.create(Subsection("MVL settings", numbering=True)):
fmt = "p{3cm}" * (len(var_config["filters"]) + 1)
with doc.create(Tabular(fmt)) as data_table:
header_row1 = [""]
for i in var_config["filters"]:
header_row1.append(var_config["filters"][i]["name"])
data_table.add_hline()
data_table.add_row(header_row1,
mapper=[bold],
color="lightgray")
data_table.add_hline()
data_table.add_empty_row()
column = list(var_config["filters"][next(
iter(var_config["filters"]))]["TUMOR"].keys())
for i in column:
row = [i]
for j in var_config["filters"]:
row.append(var_config["filters"][j]["TUMOR"][i])
data_table.add_row(row)
row = ["MVL"]
for i in var_config["filters"]:
row.append(var_config["filters"][i]["in_mvl"])
row = ["Variantcallers"]
for i in var_config["filters"]:
row.append("\n".join(
var_config["filters"][i]["variantcaller"]))
data_table.add_row(row)
data_table.add_hline()
with doc.create(
Subsection("Bioinformatic tool in pipeline", numbering=True)):
doc.append(
"The following Bioinformatic tools were used in the analysis:\n\n"
)
with doc.create(Tabular("p{4cm}p{4cm}")) as data_table:
data_table.add_hline()
conda_env = glob.glob(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
"..", "..", "conda_yaml/*.yaml"))
pkgs = get_package_split(conda_env)
data_table.add_row(["Package", "Version"], color="lightgray")
data_table.add_hline()
data_table.add_row(
["BALSAMIC", sample_config['analysis']['BALSAMIC']])
for k, v in pkgs.items():
data_table.add_row([k, v])
doc.append(NewPage())
print(tex_path)
doc.generate_tex(os.path.join(tex_path, get_sample_name(config)))
# doc.generate_pdf(
# os.path.join(tex_path, get_sample_name(config)), clean_tex=False)
shellcmd = [
"pdflatex", "-output-directory=" + tex_path,
os.path.join(tex_path, get_sample_name(config)) + ".tex", "1>",
"/dev/null"
]
#generate_pdf doesn't run AUX files properly and ends up with incorrect total page numbers. So subprocess for
#pdflatex is called twice instead.
print(" ".join(shellcmd))
subprocess.run(" ".join(shellcmd), shell=True)
subprocess.run(" ".join(shellcmd), shell=True)
def result_to_score(arr,
doc,
arr_name="",
n_class=5,
sort="asc",
sigma=2.5,
iqr_factor=1.5,
outliers_method="z-score"):
'''
convert continuous value to ranged score
:param str arr: input result array
:param sec: pylatex document object
:param str arr_name: array name
:param str n_class: number of score classes
:param str sort: "asc" or "dsc", order of the class count with ascending or descending order
:param float sigma: standard deviation of the data in z-score outliers removal
:param float iqr_factor: factor for iqr outliers removal
:param str outliers_method: "z-score" or "iqr"
:type sigma: float
:return: arr score: array of converted score
:rtype: None
'''
# remove outliners
if outliers_method == "z-score":
z = np.abs(stats.zscore(arr))
arr_filtered = arr[(z < sigma)]
elif outliers_method == "iqr":
Q1 = np.quantile(arr, 0.25)
Q3 = np.quantile(arr, 0.75)
IQR = Q3 - Q1
arr_filtered = arr[~((arr < (Q1 - iqr_factor * IQR)) |
(arr > (Q3 + iqr_factor * IQR)))]
plt.clf()
n, bins, patches = plt.hist(x=arr_filtered,
bins=n_class,
color='#607c8e',
alpha=0.7,
rwidth=0.9)
plt.grid(axis='y', alpha=0.75)
plt.xlabel('Value')
plt.ylabel('Frequency')
# plt.title(arr_name)
maxfreq = n.max()
# Set a clean upper y-axis limit.
plt.ylim(ymax=np.ceil(maxfreq / 10) * 10 if maxfreq % 10 else maxfreq + 10)
# print(n, bins, patches)
# convert result to score
score = np.zeros_like(arr)
if sort == "asc":
for i in range(n_class):
if i == 0:
score[arr < bins[1]] = 1
elif i == n_class - 1:
score[arr > bins[n_class - 1]] = n_class
else:
score[~((arr < bins[i]) | (arr > bins[i + 1]))] = i + 1
elif sort == "dsc":
for i in reversed(range(n_class)):
if i == 0:
score[arr > bins[n_class - 1]] = 1
elif i == n_class - 1:
score[arr < bins[1]] = n_class
else:
score[~((arr < bins[::-1][i + 1]) |
(arr > bins[::-1][i]))] = i + 1
with doc.create(Figure(position='htbp')) as plot:
plot.add_plot(dpi=300)
plot.add_caption(arr_name)
with doc.create(Center()) as centered:
table_format = "c|"
for i in range(n_class):
table_format += "c"
with centered.create(Tabular(table_format)) as table:
table.add_row(['severity score'] + [i + 1 for i in range(n_class)])
table.add_hline(1, n_class + 1)
table.add_row(['range'] + [
"{:.2f}-{:.2f}".format(bins[i], bins[i + 1])
for i in reversed(range(n_class))
])
table.add_row(['count'] + [str(int(value)) for value in n])
doc.append(basic.NewPage())
return score
import os
from pylatex import Document, PageStyle, Head, Foot, Section, Subsection, Tabular, Math, TikZ, Axis, \
Plot, Figure, Matrix, Alignat, StandAloneGraphic, MiniPage, LineBreak, Center, Command
from pylatex.utils import italic, bold, NoEscape
image_filename = os.path.join(os.path.dirname(__file__), 'Invoices\sus_header.png')
geometry_options = {"tmargin": "1cm", "lmargin": "1cm"}
doc = Document(geometry_options=geometry_options)
with doc.create(Figure(position='h!')) as sus_pic:
sus_pic.add_image(image_filename, width='550px')
doc.append(Command('noindent'))
doc.append(Command('textbf', 'asdasdasd'))
doc.append(Command('linebreak'))
doc.append(Command('textbf', 'asdasdasd'))
doc.generate_pdf('test', clean_tex=False, compiler='pdflatex')
