def table() -> pylatex.Table:
optics_single = optics.as_designed_single_channel()
model_distortion = optics_single.rays_output.distortion.model()
model_distortion_relative = optics_single.rays_output_relative.distortion.model(
)
def fmt_coeff(coeff: u.Quantity):
return kgpy.format.quantity(
a=coeff.value * u.dimensionless_unscaled,
scientific_notation=True,
digits_after_decimal=2,
)
result = pylatex.Table()
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular('ll|rr')) as tabular:
tabular.escape = False
tabular.append(
'\multicolumn{2}{l}{Coefficient} & $x\'$ & $y\'$\\\\')
tabular.add_hline()
for c, name in enumerate(model_distortion.x.coefficient_names):
tabular.add_row([
f'{name}',
f'({model_distortion.x.coefficients[c].unit:latex_inline})',
fmt_coeff(
model_distortion_relative.x.coefficients[c].squeeze()),
fmt_coeff(
model_distortion_relative.y.coefficients[c].squeeze()),
])
return result
def table() -> pylatex.Table:
result = pylatex.Table(position='!htb')
result._star_latex_name = True
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular(table_spec='llll', )) as tabular:
tabular.escape = False
tabular.add_row(
['Parameter', 'Requirement', 'Science Driver', 'Capabilities'])
tabular.add_hline()
tabular.add_row([
r'Spectral line',
r'\OV',
r'\EEs',
r'\OVion, \MgXion, \HeIion, Figure~\ref{fig:bunch}',
])
tabular.add_row([
r'Spectral sampling',
r'\spectralResolutionRequirement',
r'Broadening from \MHD\ waves',
r'\dispersionDoppler, Table~\ref{table:prescription}',
])
tabular.add_row([
r'Spatial resolution',
r'\angularResolutionRequirement (\spatialResolutionRequirement)',
r'\EEs',
r'\spatialResolutionTotal, Table~\ref{table:errorBudget}',
])
tabular.add_row([
r'\SNRShort',
r'\snrRequirement\ (\CHShort)',
r'\MHD\ waves in \CHShort',
r'\StackedCoronalHoleSNR\ ($\NumExpInStack \times \text{\detectorExposureLength}$ exp.), '
r'Table~\ref{table:counts}',
])
tabular.add_row([
r'Cadence',
r'\cadenceRequirement',
r'Torsional waves',
r'\detectorExposureLength\ eff., Section~\ref{subsec:SensitivityandCadence}',
])
tabular.add_row([
r'Observing time',
r'\observingTimeRequirement',
r'\EEs',
r'\SI{270}{\second}, Section~\ref{sec:MissionProfile}',
])
tabular.add_row([
r'\FOV\ diameter',
r'\fovRequirement',
r'Span \QSShort, \ARShort, and limb',
r'\fov, Table~\ref{table:prescription}',
])
result.add_caption(
pylatex.NoEscape(
r"""\ESIS\ instrument requirements and capabilties. Note that MTF exceeds the Rayleigh criterion of 0.109."""
))
result.append(kgpy.latex.Label('table:scireq'))
return result
def df_to_pdf(df,
out_file,
print_index=True,
debug=False,
digit_round=1,
caption=None,
comma_separated_columns=[],
gen_latex='False'):
"""
convert data frame to pdf/latex. used to create tables for paper/thesis.
"""
if digit_round is not None:
df = df.round(digit_round)
for column in comma_separated_columns:
df[column] = df[column].map('{:,}'.format)
table_columns = len(df.columns) + 1 if print_index else len(df.columns)
if gen_latex:
with open(table_path + out_file + '.tex', 'w') as f:
f.write(
df.to_latex(escape=False,
index=print_index,
column_format='c' * table_columns))
return
doc = pl.Document(documentclass='standalone', document_options='varwidth')
doc.packages.append(pl.Package('booktabs'))
with doc.create(pl.MiniPage()):
with doc.create(pl.Table(position='htbp')) as table:
table.append(pl.Command('centering'))
table.append(
pl.NoEscape(
df.to_latex(escape=False,
index=print_index,
column_format='c' * table_columns)))
if caption is not None:
table.add_caption(caption)
if debug:
return doc.dumps()
doc.generate_pdf(output_path + out_file)
def table() -> pylatex.Table:
optics_all = esis.flight.optics.as_measured()
detector = optics_all.detector
result = pylatex.Table()
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular('ccccc')) as tabular:
tabular.escape = False
tabular.add_row([
r'Channel',
r'Quad.',
r'Gain',
r'Read noise',
r'Dark current',
])
tabular.add_row([
'', '', f'({detector.gain.unit:latex_inline})',
f'({detector.readout_noise.unit:latex_inline})',
f'({detector.dark_current.unit:latex_inline})'
])
tabular.add_hline()
for i in range(detector.gain.shape[0]):
for j in range(detector.gain.shape[1]):
if j == 0:
channel_name_i = optics_all.channel_name[i]
serial_number_i = f'({detector.serial_number[i]})'
else:
channel_name_i = ''
serial_number_i = ''
tabular.add_row([
f'{channel_name_i} {serial_number_i}',
j + 1,
detector.gain[i, j].value,
detector.readout_noise[i, j].value,
f'{detector.dark_current[i, j].value:0.3f}',
])
tabular.add_hline()
result.add_caption(pylatex.NoEscape(r'\ESIS\ camera properties'))
result.append(kgpy.latex.Label('tabel:cameraProperties'))
return result
def _add_keyboard_notes(document: pylatex.Document, texts: dict,
images: dict) -> None:
document.append(
pylatex.Subsection(
title=texts["keyboard"]["title"],
label=False,
numbering=False,
))
document.append(texts["keyboard"]["text0"])
document.append(pylatex.NoEscape(r"\vspace{5mm}"))
table = pylatex.Tabular(r" l | l | p{9cm} ")
# table.add_hline()
table.add_row(*tuple(
pylatex.MediumText(column_title) for column_title in (
"Bereich",
"Beschreibung der Klänge",
"verwendete Lautsprecher",
)))
for zone_idx in range(3):
table.add_hline()
table.add_row(
_make_img(images["zone_{}".format(zone_idx)],
width=0.22,
add_figure=False),
texts["keyboard"]["zone{}sound".format(zone_idx)],
texts["keyboard"]["zone{}speaker".format(zone_idx)],
)
# table.add_hline()
document.append(pylatex.Table(data=table, position="h!"))
document.append(texts["keyboard"]["text1"])
# document.append(pylatex.NoEscape(r"\vspace{3mm}"))
document.append(texts["keyboard"]["text2"])
def table_old() -> pylatex.Table:
result = pylatex.Table()
result._star_latex_name = True
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular('llrr')) as tabular:
tabular.escape = False
tabular.add_row(
[r'Element', r'Parameter', r'Requirement', r'Measured'])
tabular.add_hline()
tabular.add_row(
[r'Primary', r'RMS slope error ($\mu$rad)', r'$<1.0$', r''])
tabular.add_row([r'', r'Integration length (mm)', r'4.0', r''])
tabular.add_row([r'', r'Sample length (mm)', r'2.0', r''])
tabular.add_hline()
tabular.add_row(
[r'Primary', r'RMS roughness (nm)', r'$<2.5$', r''])
tabular.add_row([r'', r'Periods (mm)', r'0.1-6', r''])
tabular.add_hline()
tabular.add_row(
[r'Grating', r'RMS slope error ($\mu$rad)', r'$<3.0$', r''])
tabular.add_row([
r'', r'Integration length (mm)', r'2 \roy{why fewer sigfigs?}',
r''
])
tabular.add_row([r'', r'Sample length (mm)', r'1', r''])
tabular.add_hline()
tabular.add_row(
[r'Grating', r'RMS roughness (nm)', r'$<2.3$', r''])
tabular.add_row([r'', r'Periods (mm)', r'0.02-2', r''])
tabular.add_hline()
result.add_caption(
pylatex.NoEscape(r"""
Figure and surface roughness requirements compared to metrology for the \ESIS\ optics.
Slope error (both the numerical estimates and the measurements) is worked out with integration length and sample length
defined per ISO 10110."""))
result.append(kgpy.latex.Label('table:error'))
return result
def _add_data(doc: pl.Document, ds: Dataset, nr: NonRedundantization,
meth: MLMethod):
name = f'{ds.name}_{nr.name}_{meth.name}'
directory = ds.name
aVp_graph = f'{name}.jpg'
angle_dist_graph = f'{name}_angledistribution.jpg'
error_dist_graph = f'{name}_errordistribution.jpg'
sqerror_graph = f'{name}_sqerror_vs_actual.jpg'
stats_csv_all = f'{name}_stats_all.csv'
stats_csv_out = f'{name}_stats_out.csv'
actualVpred_file = os.path.join(directory, aVp_graph)
ang_dist_file = os.path.join(directory, angle_dist_graph)
error_dist_file = os.path.join(directory, error_dist_graph)
sqerror_file = os.path.join(directory, sqerror_graph)
df_all = pd.read_csv(os.path.join(directory, stats_csv_all))
df_out = pd.read_csv(os.path.join(directory, stats_csv_out))
with doc.create(pl.Section(f'Method: {ds.name}, {nr.name}, {meth.name}')):
with doc.create(pl.Subsection('Summary of method:')):
doc.append(f'Dataset: {ds.name}')
doc.append(f'\nNon-redundantization: {nr.name}')
doc.append(f'\nType of machine learning used: {meth.name}')
with doc.create(pl.Subsection('Summary of the data:')):
with doc.create(pl.Figure(position='!htbp')) as actualVpred:
actualVpred.add_image(actualVpred_file, width='300px')
actualVpred.add_caption(
'Graph showing the predicted packing angle against the actual packing angle, when using the above specified methods of non-redundetization and machine learning.'
)
with doc.create(pl.Table(position='!htbp')) as table:
table.add_caption('Summary of results for all data')
table.append(pl.Command('centering'))
table.append(pl.NoEscape(df_all.to_latex(escape=False)))
with doc.create(pl.Table(position='!htbp')) as table:
table.add_caption('Summary of results for outliers.')
table.append(pl.Command('centering'))
table.append(pl.NoEscape(df_out.to_latex(escape=False)))
with doc.create(pl.Figure(position='!htbp')) as graphs:
with doc.create(
pl.SubFigure(position='!htbp',
width=pl.NoEscape(
r'0.30\linewidth'))) as ang_dist_graph:
ang_dist_graph.add_image(ang_dist_file,
width=pl.NoEscape(r'\linewidth'))
ang_dist_graph.add_caption(
'Frequency distribution of the packing angle.')
with doc.create(
pl.SubFigure(position='!htbp',
width=pl.NoEscape(
r'0.33\linewidth'))) as error_dist_graph:
error_dist_graph.add_image(error_dist_file,
width=pl.NoEscape(r'\linewidth'))
error_dist_graph.add_caption(
'Distribution of errors calculated as the difference between the predicted and actual interface angle.'
)
with doc.create(
pl.SubFigure(position='!htbp',
width=pl.NoEscape(
r'0.33\linewidth'))) as sqerror_graph:
sqerror_graph.add_image(sqerror_file,
width=pl.NoEscape(r'\linewidth'))
sqerror_graph.add_caption(
'Squared error in predicted packing angle against actual packing angle.'
)
graphs.add_caption('Graphs for further metrics.')
def generate_latex(output):
top10 = 'top10.csv'
top10_df = pd.read_csv(top10)
top10_o = 'top10_out.csv'
top10_o_df = pd.read_csv(top10_o)
doc = pl.Document(page_numbers=True,
geometry_options={
"tmargin": "1cm",
"lmargin": "1cm"
})
doc.packages.append(pl.Package('booktabs'))
doc.preamble.append(
pl.Command('title', 'VH/VL Packing Angle Pipeline Results'))
doc.preamble.append(pl.Command('author', 'Veronica A. Boron'))
doc.append(pl.NoEscape(r'\maketitle'))
doc.append(
'This document summarizes the results obtained by running `packing_angle_pipeline.py` on various datasets.'
)
# TODO table of contents is broken and doesn't show all sections
# doc.append(pl.NoEscape(r'\tableofcontents'))
doc.append(pl.NoEscape(r'\newpage'))
with doc.create(pl.Section(f'Summary of Results')):
with doc.create(pl.Table(position='!htbp')) as table:
table.add_caption(
'Rakings of the top 20 combinations of methods, datasets, non-redundatizing, \
and correction factors. They were ranked according to a combination parameter which was calcuated \
in the following way: Combined-parameter = |(1/Pearsons coefficient)| + |mean-error| + |RMSE| + \
|RELRMSE|. The smallest combined-para value indicates a combination of low errors and \
high correlation coefficient.')
table.append(pl.Command('centering'))
table.append(pl.NoEscape(r'\resizebox{\textwidth}{!}{'))
table.append(pl.NoEscape(top10_df.to_latex(escape=False)))
table.append(pl.NoEscape(r'}'))
with doc.create(pl.Table(position='!htbp')) as table:
table.add_caption(
'Rakings of the top 20 combinations of methods, datasets, non-redundatizing, \
and correction factors for outlier prediction. They were ranked in according to a combination parameter.'
)
table.append(pl.Command('centering'))
table.append(pl.NoEscape(r'\resizebox{\textwidth}{!}{'))
table.append(pl.NoEscape(top10_o_df.to_latex(escape=False)))
table.append(pl.NoEscape(r'}'))
# for ds, nr, cr in itertools.product(Dataset, NonRedundantization, Correction):
# for ds, nr, in itertools.product(Dataset, NonRedundantization):
# _add_data(doc, ds, nr, MLMethod.XvalWeka, cr)
# doc.append(pl.NoEscape(r'\newpage'))
# for tt, nr, meth, cr in itertools.product(get_all_testtrain(), NonRedundantization, MLMethod, Correction):
for tt, nr, meth in itertools.product(get_all_testtrain(),
NonRedundantization, MLMethod):
# if meth is not MLMethod.XvalWeka:
# _add_data(doc, tt.testing, nr, meth, cr)
_add_data(doc, tt.testing, nr, meth)
doc.append(pl.NoEscape(r'\newpage'))
print('Generating PDF...')
doc.generate_pdf(output, clean_tex=False)
def table() -> pylatex.Table:
optics_single = optics.as_designed_single_channel()
optics_all = esis.flight.optics.as_measured()
primary = optics_single.primary
grating = optics_single.grating
unit_length_integration = u.mm
unit_length_sample = u.mm
unit_slope_error = u.urad
unit_ripple_period = u.mm
unit_ripple = u.nm
unit_microroughness_period = u.um
unit_microroughness = u.nm
result = pylatex.Table()
result._star_latex_name = True
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular('llrr')) as tabular:
tabular.escape = False
tabular.add_row([
r'Element',
r'Parameter',
r'Requirement',
r'Measured',
])
tabular.add_hline()
tabular.add_row([
r'Primary',
f'RMS slope error ({unit_slope_error:latex_inline})',
f'{optics_single.primary.slope_error.value.to(unit_slope_error).value:0.1f}',
f'{optics_all.primary.slope_error.value.to(unit_slope_error).value:0.1f}',
])
tabular.add_row([
r'',
f'\\quad Integration length = {primary.slope_error.length_integration.to(unit_length_integration).value:0.1f}\,{unit_length_integration:latex_inline}',
r'',
r'',
])
tabular.add_row([
r'',
f'\\quad Sample length = {primary.slope_error.length_sample.to(unit_length_sample).value:0.1f}\,{unit_length_sample:latex_inline}',
r'',
r'',
])
tabular.add_row([
r'',
f'RMS roughness ({unit_ripple:latex_inline})',
f'{optics_single.primary.ripple.value.to(unit_ripple).value:0.1f}',
f'{optics_all.primary.ripple.value.to(unit_ripple).value:0.1f}',
])
tabular.add_row([
r'',
f'\quad Periods = ${primary.ripple.periods_min.to(unit_ripple_period).value:0.2f}-{primary.ripple.periods_max.to(unit_ripple_period).value:0.1f}$\\,{unit_ripple_period:latex_inline}',
r'',
r'',
])
tabular.add_row([
r'',
f'RMS microroughness ({unit_microroughness:latex_inline})',
f'{optics_single.primary.microroughness.value.to(unit_ripple).value:0.1f}',
f'{optics_all.primary.microroughness.value.to(unit_ripple).value:0.1f}',
])
tabular.add_row([
r'',
f'\quad Periods = ${primary.microroughness.periods_min.to(unit_microroughness_period).value:0.2f}-{primary.microroughness.periods_max.to(unit_microroughness_period).value:0.1f}$\\,{unit_microroughness_period:latex_inline}',
r'',
r'',
])
tabular.add_hline()
tabular.add_row([
r'Grating',
f'RMS slope error ({unit_slope_error:latex_inline})',
f'{optics_single.grating.slope_error.value.to(unit_slope_error).value:0.1f}',
f'{optics_all.grating.slope_error.value.to(unit_slope_error).value.mean():0.1f}',
])
tabular.add_row([
r'',
f'\\quad Integration length = {grating.slope_error.length_integration.to(unit_length_integration).value:0.1f}\,{unit_length_integration:latex_inline}',
r'',
r'',
])
tabular.add_row([
r'',
f'\\quad Sample length = {grating.slope_error.length_sample.to(unit_length_sample).value:0.1f}\,{unit_length_sample:latex_inline}',
r'',
r'',
])
tabular.add_row([
r'',
f'RMS roughness ({unit_ripple:latex_inline})',
f'{optics_single.grating.ripple.value.to(unit_ripple).value:0.1f}',
f'{optics_all.grating.ripple.value.to(unit_ripple).value.mean():0.1f}',
])
tabular.add_row([
r'',
f'\quad Periods = ${grating.ripple.periods_min.to(unit_ripple_period).value:0.2f}-{grating.ripple.periods_max.to(unit_ripple_period).value:0.1f}$\\,{unit_ripple_period:latex_inline}',
r'',
r'',
])
tabular.add_row([
r'',
f'RMS microroughness ({unit_microroughness:latex_inline})',
f'{optics_single.grating.microroughness.value.to(unit_ripple).value:0.1f}',
f'{optics_all.grating.microroughness.value.to(unit_ripple).value.mean():0.1f}',
])
tabular.add_row([
r'',
f'\quad Periods = ${grating.microroughness.periods_min.to(unit_microroughness_period).value:0.2f}-{grating.microroughness.periods_max.to(unit_microroughness_period).value:0.1f}$\\,{unit_microroughness_period:latex_inline}',
r'',
r'',
])
tabular.add_hline()
result.add_caption(
pylatex.NoEscape(r"""
Figure and surface roughness requirements compared to metrology for the \ESIS\ optics.
Slope error (both the numerical estimates and the measurements) is worked out with integration length and sample length
defined per ISO 10110."""))
result.append(kgpy.latex.Label('table:error'))
return result
def table(doc: kgpy.latex.Document) -> pylatex.Table:
result = pylatex.Table()
optics_single = optics.as_designed_single_channel()
wavelength = optics_single.bunch.wavelength
index_o5 = np.nonzero(optics_single.bunch.ion == 'o_5')[0][0]
wavelength_o5 = wavelength[index_o5]
index_mg10_2 = np.nonzero(optics_single.bunch.ion == 'mg_10')[0][1]
wavelength_mg10_2 = wavelength[index_mg10_2]
intensity_o5 = [334.97, 285.77, 1018.65, 519.534
] * u.erg / u.cm**2 / u.sr / u.s
intensity_mg10 = [51.43, 2.62, 397.64, 239.249
] * u.erg / u.cm**2 / u.sr / u.s
energy_o5 = wavelength_o5.to(u.erg, equivalencies=u.spectral()) / u.photon
energy_mg10 = wavelength_mg10_2.to(u.erg,
equivalencies=u.spectral()) / u.photon
optics_single_measured = optics.as_measured_single_channel()
rays = optics_single_measured.rays_output
area = rays.intensity.copy()
area[~rays.mask] = np.nan
area = np.nansum(
area, (rays.axis.pupil_x, rays.axis.pupil_y, rays.axis.velocity_los),
keepdims=True)
area[area == 0] = np.nan
area = np.nanmean(area, (rays.axis.field_x, rays.axis.field_y)).squeeze()
area_o5 = area[0]
area_mg10 = area[2]
pixel_subtent = (optics_single.plate_scale.x *
optics_single.plate_scale.y * u.pix * u.pix).to(u.sr)
time_integration = optics_single.detector.exposure_length
counts_o5 = (intensity_o5 * area_o5 * pixel_subtent * time_integration /
energy_o5).to(u.photon)
counts_mg10 = (intensity_mg10 * area_mg10 * pixel_subtent *
time_integration / energy_mg10).to(u.photon)
counts_total = counts_o5 + counts_mg10
stack_num = 12
counts_total_stacked = counts_total * stack_num
noise_shot = np.sqrt(counts_total.value) * counts_total.unit
noise_shot_stacked = np.sqrt(
counts_total_stacked.value) * counts_total.unit
noise_read = optics_single_measured.detector.readout_noise.mean()
noise_read = noise_read * optics_single_measured.detector.gain.mean()
noise_read_o5 = (noise_read / (energy_o5 / (3.6 * u.eV / u.electron))).to(
u.photon)
noise_read_o5_stacked = stack_num * noise_read_o5
noise_total = np.sqrt(np.square(noise_shot) + np.square(noise_read_o5))
noise_total_stacked = np.sqrt(
np.square(noise_shot_stacked) + np.square(noise_read_o5_stacked))
snr = counts_total / noise_total
snr_stacked = counts_total_stacked / noise_total_stacked
label = f'1 $\\times$ {kgpy.format.quantity(time_integration, digits_after_decimal=0)} exp.'
label_stacked = f'{stack_num} $\\times$ {kgpy.format.quantity(time_integration, digits_after_decimal=0)} exp.'
doc.set_variable(
name='NumExpInStack',
value=str(stack_num),
)
doc.set_variable_quantity(
name='StackedCoronalHoleSNR',
value=snr_stacked[np.argmin(intensity_o5)],
digits_after_decimal=1,
)
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular('lrrrr')) as tabular:
tabular.escape = False
tabular.add_row([r'Source', r'\VR', r'\VR', r'\VR', r'\CDS'])
tabular.add_row(r'Solar context', r'\QSShort', r'\CHShort',
r'\ARShort', r'\ARShort')
tabular.add_hline()
tabular.add_hline()
tabular.append(f'\\multicolumn{{5}}{{c}}{{{label}}}\\\\')
tabular.add_row([
r'\OV',
] + [f'{c:0.0f}' for c in counts_o5.value])
tabular.add_row([
r'\MgXdim',
] + [f'{c:0.0f}' for c in counts_mg10.value])
tabular.add_hline()
tabular.add_row([
r'Total',
] + [f'{c:0.0f}' for c in counts_total.value])
tabular.add_row([
r'Shot noise',
] + [f'{c:0.1f}' for c in noise_shot.value])
tabular.add_row([
r'Read noise',
] + 4 * [f'{noise_read_o5.value:0.1f}'])
tabular.add_row([
r'\SNRShort',
] + [f'{c:0.1f}' for c in snr.value])
tabular.add_hline()
tabular.add_hline()
tabular.append(f'\\multicolumn{{5}}{{c}}{{{label_stacked}}}\\\\')
tabular.add_row([
'Total',
] + [f'{c:0.0f}' for c in counts_total_stacked.value])
tabular.add_row([
r'\SNRShort',
] + [f'{c:0.1f}' for c in snr_stacked.value])
tabular.add_hline()
tabular.add_hline()
result.add_caption(
pylatex.NoEscape(r"""
Estimated signal statistics per channel (in photon counts) for \ESIS\ lines in \CH, \QS, and \AR.
Note that the \SNR\ estimates are lower bounds since charge diffusion decreases the shot noise."""
))
result.append(kgpy.latex.Label('table:counts'))
return result
def tabulateAll(self):
"""
Create a table that summarises all input variables and additive
components, including the constant kernel as baseline and the final
full additive model.
"""
# 1-D variables
ks = self.best1d[:]
# Baseline: constant kernel
ks.append(self.constker)
# Additive components, if not 1-D
for k in self.summands:
if len(k.getActiveDims()) > 1:
ks.append(k)
# Full additive model, if involves more than one additive term
best = self.history[-1]
if len(self.summands) > 1:
ks.append(best)
ks.sort(key=lambda k: round(k.getNLML(), 2))
ks.sort(key=lambda k: round(k.error(), 4))
data = ks[0].data
ds = data.getDataShape()
nlml_min = round(min([k.getNLML() for k in ks]), 2)
error_min = round(min([k.error() for k in ks]), 4)
doc = self.doc
with doc.create(pl.Table(position='htbp!')) as tab:
caption_str = "Classification performance of the full model, its additive components (if any), all input variables, and the baseline."
tab.add_caption(ut.NoEscape(caption_str))
t = pl.Tabular('rlrr')
# Header
t.add_hline()
t.add_row((pl.MultiColumn(1, align='c', data='Dimensions'),
pl.MultiColumn(1, align='c', data='Kernel expression'),
pl.MultiColumn(1, align='c', data='NLML'),
pl.MultiColumn(1, align='c', data='Error')))
t.add_hline()
# Entries
for k in ks:
if k is self.constker:
row = [
ut.italic('--', escape=False),
ut.italic('$' + k.latex() + '$ (Baseline)',
escape=False),
ut.italic('{0:.2f}'.format(k.getNLML()), escape=False),
ut.italic(r'{0:.2f}\%'.format(k.error() * 100),
escape=False)
]
else:
dims = sorted(k.getActiveDims())
row = [
ut.NoEscape(', '.join([str(d + 1) for d in dims])),
ut.NoEscape('$' + k.latex() + '$'),
ut.NoEscape('{0:.2f}'.format(k.getNLML())),
ut.NoEscape(r'{0:.2f}\%'.format(k.error() * 100))
]
if round(k.getNLML(), 2) == nlml_min:
row[2] = ut.bold(row[2])
if round(k.error(), 4) == error_min:
row[3] = ut.bold(row[3])
t.add_row(tuple(row))
t.add_hline()
tab.append(ut.NoEscape(r'\centering'))
tab.append(t)
def tabulateVariables(self):
"""
Create a table that summarises all input variables.
"""
ks = self.best1d[:]
ks.append(self.constker)
ks.sort(key=lambda k: round(k.getNLML(), 2))
ks.sort(key=lambda k: round(k.error(), 4))
data = ks[0].data
ds = data.getDataShape()
nlml_min = round(min([k.getNLML() for k in ks]), 2)
error_min = round(min([k.error() for k in ks]), 4)
doc = self.doc
with doc.create(pl.Table(position='htbp!')) as tab:
tab.add_caption(ut.NoEscape("Input variables"))
t = pl.Tabular('rlrrrcrr')
# Header
t.add_hline()
t.add_row(('', '', pl.MultiColumn(3, align='c', data='Statistics'),
pl.MultiColumn(3,
align='c',
data='Classifier Performance')))
t.add_hline(start=3, end=8)
t.add_row((pl.MultiColumn(1, align='c', data='Dimension'),
pl.MultiColumn(1, align='c', data='Variable'),
pl.MultiColumn(1, align='c', data='Min'),
pl.MultiColumn(1, align='c', data='Max'),
pl.MultiColumn(1, align='c', data='Mean'),
pl.MultiColumn(1, align='c', data='Kernel'),
pl.MultiColumn(1, align='c', data='NLML'),
pl.MultiColumn(1, align='c', data='Error')))
t.add_hline()
# Entries
for k in ks:
if k is self.constker:
row = [
ut.italic('--', escape=False),
ut.italic('Baseline', escape=False),
ut.italic('--', escape=False),
ut.italic('--', escape=False),
ut.italic('--', escape=False),
ut.italic(k.shortInterp(), escape=False),
ut.italic('{0:.2f}'.format(k.getNLML()), escape=False),
ut.italic(r'{0:.2f}\%'.format(k.error() * 100),
escape=False)
]
else:
dim = k.getActiveDims()[0]
row = [
dim + 1, data.XLabel[dim],
'{0:.2f}'.format(ds['x_min'][dim]),
'{0:.2f}'.format(ds['x_max'][dim]),
'{0:.2f}'.format(ds['x_mu'][dim]),
k.shortInterp(),
ut.NoEscape('{0:.2f}'.format(k.getNLML())),
ut.NoEscape(r'{0:.2f}\%'.format(k.error() * 100))
]
if round(k.getNLML(), 2) == nlml_min:
row[6] = ut.bold(row[6])
if round(k.error(), 4) == error_min:
row[7] = ut.bold(row[7])
t.add_row(tuple(row))
t.add_hline()
tab.append(ut.NoEscape(r'\centering'))
tab.append(t)
sentence = f'The project has a loss of ${-1 * SDCF:,.0f}.'
# Create document
doc = pl.Document()
doc.packages.append(pl.Package('booktabs'))
# Add preamble
doc.preamble.append(pl.Command('title', report_title))
doc.preamble.append(pl.Command('author', repot_author))
doc.preamble.append(pl.Command('date', pl.NoEscape(r'\today')))
doc.append(pl.NoEscape(r'\maketitle'))
# Create section 1
with doc.create(pl.Section('Data')):
doc.append('The cash flow data is as follows.')
with doc.create(pl.Table(position='htbp')) as table:
table.add_caption('Cash Flow')
table.append(pl.Command('centering'))
table.append(
pl.NoEscape(df_original.to_latex(escape=False, index=False)))
# Create section 2
with doc.create(pl.Section('Conclusion')):
doc.append(sentence)
# Create section 3
with doc.create(pl.Section('Appendix')):
doc.append('The discounted cash flow is shown in the table below.')
with doc.create(pl.Table(position='htbp')) as table:
table.add_caption('Discounted Cash Flow')
table.append(pl.Command('centering'))
def table(doc: kgpy.latex.Document) -> pylatex.Table:
requirements = esis.optics.design.requirements()
optics_single = optics.as_designed_single_channel()
opt = esis.optics.design.final(**optics.error_kwargs)
wavelength = optics_single.bunch.wavelength
index_o5 = np.nonzero(optics_single.bunch.ion == 'o_5')[0][0]
wavelength_o5 = wavelength[index_o5]
# opt = esis.optics.design.final(
# pupil_samples=101,
# # pupil_is_stratified_random=True,
# field_samples=11,
# all_channels=False,
# )
# psf_diffraction = opt.system.psf_diffraction
# plt.figure()
# plt.imshow(psf_diffraction.data[5,~0,..., 0].T, aspect='auto')
#
# print('position', psf_diffraction.grid.position)
# print('position', psf_diffraction.grid.position.points.x.shape)
# print('position', psf_diffraction.grid.position.points.y.shape)
# opt.psf_diffraction
opt.mtf_diffraction
plt.show()
# rays_grating = opt.system.raytrace[opt.system.surfaces_all.flat_local.index(opt.grating.surface)]
# rays_grating.pupil_hist2d(bins=100)
# plt.show()
frequency_requirement = 1 / requirements.resolution_angular
def calc_mtf(optics: esis.optics.Optics):
rays = optics.rays_output
mtf, frequency = rays.mtf(
bins=200,
frequency_min=frequency_requirement,
)
print('mtf', mtf.mean())
print('frequency', frequency)
mtf = np.take(a=mtf, indices=[index_o5], axis=rays.axis.wavelength)
print('mtf', mtf.mean())
mtf = np.mean(
mtf.value, axis=rays.axis.field_xy, keepdims=True,
where=mtf != 0) << mtf.unit
print('mtf', mtf.mean())
frequency = frequency.take(indices=[index_o5],
axis=rays.axis.wavelength)
frequency = np.mean(frequency, axis=rays.axis.field_xy, keepdims=True)
plt.figure()
plt.imshow(mtf.squeeze().T)
with astropy.visualization.quantity_support():
plt.figure()
plt.plot(
frequency.x.take(indices=0, axis=rays.axis.pupil_x).squeeze(),
mtf.take(indices=0, axis=rays.axis.pupil_x).squeeze())
plt.plot(
frequency.y.take(indices=0, axis=rays.axis.pupil_y).squeeze(),
mtf.take(indices=0, axis=rays.axis.pupil_y).squeeze())
mtf = np.take(a=mtf, indices=[0], axis=rays.axis.pupil_x)
print('mtf', mtf.mean())
index_frequency_requirement = np.argmax(frequency.y.take(
indices=[0], axis=rays.axis.pupil_x) >= frequency_requirement,
axis=rays.axis.pupil_y)
index_frequency_requirement = np.expand_dims(
index_frequency_requirement, axis=rays.axis.pupil_y)
print('index frequency requirement', index_frequency_requirement.shape)
# mtf = np.take(a=mtf, indices=[index_frequency_requirement], axis=rays.axis.pupil_y)
mtf = np.take_along_axis(mtf,
indices=index_frequency_requirement,
axis=rays.axis.pupil_y)
print('mtf', mtf.mean())
print('mtf.shape', mtf.shape)
return mtf.squeeze()
mtf_nominal = calc_mtf(opt)
accumulator = dict(mtf=1 * u.dimensionless_unscaled, )
def add_mtf(
tabular: pylatex.Tabular,
name_major: str = '',
name_minor: str = '',
value_str: str = '',
mtf: u.Quantity = 0 * u.dimensionless_unscaled,
):
accumulator['mtf'] *= mtf
tabular.add_row([
name_major,
name_minor,
value_str,
f'',
f'',
f'{mtf.value:0.3f}',
])
def add_optics(
tabular: pylatex.Tabular,
optics: typ.Union[esis.optics.Optics,
typ.Tuple[esis.optics.Optics,
esis.optics.Optics]],
name_major: str = '',
name_minor: str = '',
value: typ.Optional[typ.Union[u.Quantity,
typ.Tuple[u.Quantity,
u.Quantity]]] = None,
value_format_kwargs: typ.Optional[typ.Dict[str, typ.Any]] = None,
remove_nominal_mtf: bool = True):
if value_format_kwargs is None:
value_format_kwargs = dict(
digits_after_decimal=3,
scientific_notation=False,
)
if not isinstance(optics, esis.optics.Optics):
optics_min, optics_max = optics
mtf_min, mtf_max = calc_mtf(optics_min), calc_mtf(optics_max)
if mtf_max < mtf_min:
mtf = mtf_max
else:
mtf = mtf_min
if value is not None:
value_min, value_max = value
if value_max == -value_min:
value_str = f'$\\pm${kgpy.format.quantity(value_max, **value_format_kwargs)}'
else:
raise NotImplementedError
else:
value_str = ''
else:
mtf = calc_mtf(optics)
if value is not None:
value_str = f'{kgpy.format.quantity(value, **value_format_kwargs)}'
else:
value_str = ''
if remove_nominal_mtf:
mtf = mtf / mtf_nominal
add_mtf(
tabular=tabular,
name_major=name_major,
name_minor=name_minor,
value_str=value_str,
mtf=mtf,
)
opt = esis.optics.design.final(**optics.error_kwargs)
# print(calc_mtf(opt_err))
# rays_err = opt_err.rays_output
# # rays_err.position.z = np.broadcast_to(rays_err.wavelength, rays_err.position.shape, subok=True).copy()
# # rays_err.position = rays_err.distortion.model(inverse=True)(rays_err.position).to(u.arcsec)
#
# mtf, frequency = rays_err.mtf(
# bins=200,
# frequency_min=frequency_requirement,
# )
#
# index_freq = np.argmax(frequency.y == frequency_requirement)
# print('index_freq', index_freq)
#
# mtf[mtf == 0] = np.nan
# mtf = np.nanmean(mtf, axis=(rays_err.axis.field_x, rays_err.axis.field_y))[..., 0, 0]
# print('mtf', mtf[0, index_freq])
#
# print(mtf.shape)
#
# plt.figure()
# plt.imshow(mtf.T)
# # plt.show()
#
# with astropy.visualization.quantity_support():
# plt.figure()
# plt.plot(frequency.x, mtf[0])
# plt.plot(frequency.y, mtf[..., 0])
#
# plt.show()
units_psf = u.pix
plate_scale = optics_single.plate_scale
focal_length_effective = optics_single.magnification.y * optics_single.primary.focal_length
opt = esis.optics.design.final(**optics.error_kwargs)
system_psf = np.nanmean(opt.rays_output.spot_size_rms[..., 0, :])
frequency_mtf_arcsec = 0.5 * u.cycle / u.arcsec
frequency_mtf = frequency_mtf_arcsec * plate_scale.y / u.cycle
def to_mtf(psf_size: u.Quantity):
psf_size = psf_size / np.sqrt(2)
alpha = 1 / (2 * psf_size**2)
return np.exp(-(np.pi * frequency_mtf)**2 / alpha)
# return np.exp(-(2 * np.pi * frequency_mtf * psf_size) ** 2)
def to_pix(value: u.Quantity):
return value / (optics_single.detector.pixel_width / u.pix)
def from_pix(value: u.Quantity):
return value * (optics_single.detector.pixel_width / u.pix)
primary_slope_error = optics_single.primary.slope_error.value
primary_slope_error_psf = focal_length_effective * np.tan(
2 * primary_slope_error)
primary_slope_error_psf /= optics_single.detector.pixel_width / u.pix
opt_primary_decenter_x_max = optics.error_primary_decenter_x_max()
opt_primary_decenter_x_min = optics.error_primary_decenter_x_min()
opt_primary_decenter_y_max = optics.error_primary_decenter_y_max()
opt_primary_decenter_y_min = optics.error_primary_decenter_y_min()
distance_grating_to_detector = (
optics_single.detector.transform.translation_eff -
optics_single.grating.transform.translation_eff).length
grating_slope_error = optics_single.grating.slope_error.value
grating_slope_error_psf = distance_grating_to_detector * np.tan(
2 * grating_slope_error)
grating_slope_error_psf /= optics_single.detector.pixel_width / u.pix
opt_grating_translation_x_min = optics.error_grating_translation_x_min()
opt_grating_translation_x_max = optics.error_grating_translation_x_max()
opt_grating_translation_y_min = optics.error_grating_translation_y_min()
opt_grating_translation_y_max = optics.error_grating_translation_y_max()
opt_grating_translation_z_min = optics.error_grating_translation_z_min()
opt_grating_translation_z_max = optics.error_grating_translation_z_max()
opt_grating_roll_min = optics.error_grating_roll_min()
opt_grating_roll_max = optics.error_grating_roll_max()
opt_grating_radius_min = optics.error_grating_radius_min()
opt_grating_radius_max = optics.error_grating_radius_max()
opt_grating_ruling_density_min = optics.error_grating_ruling_density_min()
opt_grating_ruling_density_max = optics.error_grating_ruling_density_max()
opt_grating_ruling_spacing_linear_min = optics.error_grating_ruling_spacing_linear_min(
)
opt_grating_ruling_spacing_linear_max = optics.error_grating_ruling_spacing_linear_max(
)
opt_grating_ruling_spacing_quadratic_min = optics.error_grating_ruling_spacing_quadratic_min(
)
opt_grating_ruling_spacing_quadratic_max = optics.error_grating_ruling_spacing_quadratic_max(
)
opt_detector_translation_x_min = optics.error_detector_translation_x_min()
opt_detector_translation_x_max = optics.error_detector_translation_x_max()
opt_detector_translation_y_min = optics.error_detector_translation_y_min()
opt_detector_translation_y_max = optics.error_detector_translation_y_max()
opt_detector_translation_z_min = optics.error_detector_translation_z_min()
opt_detector_translation_z_max = optics.error_detector_translation_z_max()
rays = opt.system.rays_input.copy()
rays.position = np.broadcast_to(rays.position,
opt.rays_output.position.shape,
subok=True).copy()
rays.position[~opt.rays_output.mask] = np.nan
rays_min = np.nanmin(rays.position,
axis=(rays.axis.pupil_x, rays.axis.pupil_y))
rays_max = np.nanmax(rays.position,
axis=(rays.axis.pupil_x, rays.axis.pupil_y))
rays_range = np.nanmean(rays_max - rays_min)
detector_x = np.linspace(-1, 1, 100) / 2 * u.pix
diffraction_intensity = np.sinc(rays_range.x / wavelength_o5 * u.rad *
np.sin(detector_x * opt.plate_scale.x))**2
model = astropy.modeling.fitting.LevMarLSQFitter()(
model=astropy.modeling.models.Gaussian1D(),
x=detector_x,
y=diffraction_intensity,
)
diffraction_limit = np.sqrt(2) * model.stddev.quantity
accumulator = dict(
psf_size_squared=0 * u.pix**2,
mtf=1 * u.dimensionless_unscaled,
mtf_actual=1 * u.dimensionless_unscaled,
)
def add_row_basic(
tabular: pylatex.Tabular,
optics: typ.Union[esis.optics.Optics, typ.Tuple[esis.optics.Optics,
esis.optics.Optics]],
name_major: str = '',
name_minor: str = '',
value_str: str = '',
psf_size: u.Quantity = 0 * u.um,
mtf_actual: u.Quantity = 1.0 * u.dimensionless_unscaled,
):
mtf = to_mtf(psf_size)
tabular.add_row([
name_major,
name_minor,
value_str,
f'{psf_size.to(u.pix).value:0.2f}',
f'{(psf_size * optics.plate_scale.y).to(u.arcsec).value:0.2f}',
f'{mtf.value:0.3f}',
f'{mtf_actual.value:0.3f}',
])
accumulator['psf_size_squared'] += np.square(psf_size)
accumulator['mtf_actual'] *= mtf_actual
accumulator['mtf'] *= mtf
def add_row(
tabular: pylatex.Tabular,
optics: typ.Union[esis.optics.Optics, typ.Tuple[esis.optics.Optics,
esis.optics.Optics]],
name_major: str = '',
name_minor: str = '',
value: typ.Optional[typ.Union[u.Quantity,
typ.Tuple[u.Quantity,
u.Quantity]]] = None,
digits_after_decimal: int = 3,
scientific_notation: bool = False,
remove_nominal_psf: bool = True,
):
format_kwargs = dict(
digits_after_decimal=digits_after_decimal,
scientific_notation=scientific_notation,
)
if not isinstance(optics, esis.optics.Optics):
optics_min, optics_max = optics
psf_size_min = np.nanmean(
optics_min.rays_output.spot_size_rms[..., 0, :])
psf_size_max = np.nanmean(
optics_max.rays_output.spot_size_rms[..., 0, :])
if psf_size_max > psf_size_min:
optics = optics_max
else:
optics = optics_min
if value is not None:
value_min, value_max = value
if value_max == -value_min:
value_str = f'$\\pm${kgpy.format.quantity(value_max, **format_kwargs)}'
else:
raise NotImplementedError
else:
value_str = ''
else:
if value is not None:
value_str = f'{kgpy.format.quantity(value, **format_kwargs)}'
else:
value_str = ''
psf_size = np.nanmean(optics.rays_output.spot_size_rms[..., 0, :])
mtf_actual = calc_mtf(optics)
print('mtf actual', mtf_actual)
if remove_nominal_psf:
psf_size = np.nan_to_num(
np.sqrt(np.square(psf_size) - np.square(system_psf)))
mtf_actual = mtf_actual / mtf_nominal
add_row_basic(
tabular=tabular,
optics=optics,
name_major=name_major,
name_minor=name_minor,
value_str=value_str,
psf_size=psf_size,
mtf_actual=mtf_actual,
)
def ptp_to_rms(value: u.Quantity) -> u.Quantity:
return value / np.sqrt(8)
result = pylatex.Table()
result._star_latex_name = True
with result.create(pylatex.Center()) as centering:
with centering.create(pylatex.Tabular('ll|rrrrr')) as tabular:
tabular.escape = False
tabular.add_row([
r'Element',
r'',
r'Tolerance',
f'$\\sigma$ ({units_psf:latex_inline})',
f'$\\sigma$ ({u.arcsec:latex_inline})',
r'\MTF\ from $\sigma$',
r'\MTF\ actual ',
])
tabular.add_hline()
add_row(
tabular=tabular,
optics=opt,
name_major='System',
name_minor='Aberration',
remove_nominal_psf=False,
)
add_row_basic(
tabular=tabular,
optics=opt,
name_minor='Diffraction',
psf_size=diffraction_limit,
)
add_row_basic(
tabular=tabular,
optics=opt,
name_minor='Thermal drift',
psf_size=ptp_to_rms(opt.sparcs.pointing_drift /
opt.plate_scale.x *
opt.detector.exposure_length),
)
tabular.add_hline()
add_row_basic(
tabular=tabular,
optics=opt,
name_major='Primary',
name_minor='RMS Slope error',
value_str=
f'{kgpy.format.quantity(primary_slope_error, digits_after_decimal=1)}',
psf_size=primary_slope_error_psf,
mtf_actual=opt.primary.mtf_degradation_factor,
)
add_row(
tabular=tabular,
optics=(
opt_primary_decenter_x_min,
opt_primary_decenter_x_max,
),
name_minor='Translation $x$',
value=(
-opt_primary_decenter_x_min.primary.translation_error.
value.xy.length,
opt_primary_decenter_x_max.primary.translation_error.value.
xy.length,
),
digits_after_decimal=0,
)
add_row(
tabular=tabular,
optics=(
opt_primary_decenter_y_min,
opt_primary_decenter_y_max,
),
name_minor='Translation $y$',
value=(
-opt_primary_decenter_y_min.primary.translation_error.
value.xy.length,
opt_primary_decenter_y_max.primary.translation_error.value.
xy.length,
),
digits_after_decimal=0,
)
tabular.add_hline()
add_row_basic(
tabular=tabular,
optics=opt,
name_major='Grating',
name_minor='RMS Slope error',
value_str=
f'{kgpy.format.quantity(grating_slope_error, digits_after_decimal=1)}',
psf_size=grating_slope_error_psf,
mtf_actual=opt.grating.mtf_degradation_factor,
)
add_row(
tabular=tabular,
optics=(
opt_grating_translation_x_min,
opt_grating_translation_x_max,
),
name_minor='Translation $x$',
value=(
-opt_grating_translation_x_min.grating.translation_error.
value.xy.length,
opt_grating_translation_x_max.grating.translation_error.
value.xy.length,
),
digits_after_decimal=0,
)
add_row(
tabular=tabular,
optics=(
opt_grating_translation_y_min,
opt_grating_translation_y_max,
),
name_minor='Translation $y$',
value=(
-opt_grating_translation_y_min.grating.translation_error.
value.xy.length,
opt_grating_translation_y_max.grating.translation_error.
value.xy.length,
),
digits_after_decimal=0,
)
add_row(
tabular=tabular,
optics=(
opt_grating_translation_z_min,
opt_grating_translation_z_max,
),
name_minor='Translation $z$',
value=(
opt_grating_translation_z_min.grating.translation_error.z,
opt_grating_translation_z_max.grating.translation_error.z,
),
digits_after_decimal=3,
)
add_row(
tabular=tabular,
optics=(
opt_grating_roll_min,
opt_grating_roll_max,
),
name_minor='Roll',
value=(
opt_grating_roll_min.grating.roll_error,
opt_grating_roll_max.grating.roll_error,
),
digits_after_decimal=3,
)
add_row(
tabular=tabular,
optics=(
opt_grating_radius_min,
opt_grating_radius_max,
),
name_minor='Radius',
value=(
opt_grating_radius_min.grating.tangential_radius_error,
opt_grating_radius_max.grating.tangential_radius_error,
),
digits_after_decimal=1,
)
add_row(
tabular=tabular,
optics=(
opt_grating_ruling_density_min,
opt_grating_ruling_density_max,
),
name_minor='Ruling density',
value=(
opt_grating_ruling_density_min.grating.
ruling_density_error,
opt_grating_ruling_density_max.grating.
ruling_density_error,
),
digits_after_decimal=1,
)
add_row(
tabular=tabular,
optics=(
opt_grating_ruling_spacing_linear_min,
opt_grating_ruling_spacing_linear_max,
),
name_minor='Linear coeff.',
value=(
opt_grating_ruling_spacing_linear_min.grating.
ruling_spacing_coeff_linear_error,
opt_grating_ruling_spacing_linear_max.grating.
ruling_spacing_coeff_linear_error,
),
digits_after_decimal=1,
scientific_notation=True,
)
add_row(
tabular=tabular,
optics=(
opt_grating_ruling_spacing_quadratic_min,
opt_grating_ruling_spacing_quadratic_max,
),
name_minor='Quadratic coeff.',
value=(
opt_grating_ruling_spacing_quadratic_min.grating.
ruling_spacing_coeff_quadratic_error,
opt_grating_ruling_spacing_quadratic_max.grating.
ruling_spacing_coeff_quadratic_error,
),
digits_after_decimal=1,
scientific_notation=True,
)
tabular.add_hline()
add_row(
tabular=tabular,
optics=(
opt_detector_translation_x_min,
opt_detector_translation_x_max,
),
name_major='Detector',
name_minor='Translation $x$',
value=(
-opt_detector_translation_x_min.detector.translation_error.
value.xy.length,
opt_detector_translation_x_max.detector.translation_error.
value.xy.length,
),
digits_after_decimal=0,
)
add_row(
tabular=tabular,
optics=(
opt_detector_translation_y_min,
opt_detector_translation_y_max,
),
name_minor='Translation $y$',
value=(
-opt_detector_translation_y_min.detector.translation_error.
value.xy.length,
opt_detector_translation_y_max.detector.translation_error.
value.xy.length,
),
digits_after_decimal=0,
)
add_row(
tabular=tabular,
optics=(
opt_detector_translation_z_min,
opt_detector_translation_z_max,
),
name_minor='Translation $z$',
value=(
opt_detector_translation_z_min.detector.translation_error.
z,
opt_detector_translation_z_max.detector.translation_error.
z,
),
digits_after_decimal=2,
)
add_row_basic(
tabular=tabular,
optics=opt,
name_minor='Charge diffusion',
psf_size=to_pix(opt.detector.charge_diffusion),
)
tabular.add_hline()
add_row_basic(
tabular=tabular,
optics=opt,
name_major=r'\SPARCSShort',
name_minor='Pointing jitter',
value_str=
f'$\\pm${kgpy.format.quantity(opt.sparcs.pointing_jitter / 2, digits_after_decimal=2)}',
psf_size=ptp_to_rms(opt.sparcs.pointing_jitter /
opt.plate_scale.x),
)
add_row_basic(
tabular=tabular,
optics=opt,
name_minor='Pointing drift',
value_str=f'{kgpy.format.quantity(opt.sparcs.pointing_drift)}',
psf_size=ptp_to_rms(opt.sparcs.pointing_drift /
opt.plate_scale.x *
opt.detector.exposure_length),
)
pointing = 10 * u.arcmin
add_row_basic(
tabular=tabular,
optics=opt,
name_minor='Roll jitter',
value_str=
f'$\\pm${kgpy.format.quantity(opt.sparcs.rlg_jitter / 2, digits_after_decimal=0)}',
psf_size=ptp_to_rms(2 * np.sin(opt.sparcs.rlg_jitter / 2) *
pointing / opt.plate_scale.x),
)
add_row_basic(
tabular=tabular,
optics=opt,
name_minor='Roll drift',
value_str=f'{kgpy.format.quantity(opt.sparcs.rlg_drift)}',
psf_size=ptp_to_rms(2 * np.sin(
opt.sparcs.rlg_drift * opt.detector.exposure_length / 2) *
pointing / opt.plate_scale.x),
)
tabular.add_hline()
tabular.add_hline()
psf_size_total = np.sqrt(accumulator['psf_size_squared'])
doc.set_variable_quantity(
name='spatialResolutionTotal',
value=2 * psf_size_total * opt.plate_scale.x,
digits_after_decimal=2,
)
add_row_basic(
tabular=tabular,
optics=opt,
name_major='Total',
psf_size=psf_size_total,
mtf_actual=accumulator['mtf_actual'],
)
result.add_caption(
pylatex.NoEscape(f"""
Imaging error budget and tolerance analysis results.
\\MTF\\ is given at {kgpy.format.quantity(frequency_mtf_arcsec, digits_after_decimal=1)}."""
))
result.append(kgpy.latex.Label('table:errorBudget'))
return result
def create_overleaf_files(overleaf):
files = []
articles = get_project_articles(FIGSHARE_PROJECT_ID)
#print(articles)
for article in articles:
#print(article['title'])
newfiles = get_files_of_article(article['id'])
for i, f in enumerate(newfiles):
newfiles[i]['article_id'] = article['id']
newfiles[i]['article_name'] = article['title']
files += newfiles
fdf = pd.DataFrame(files)
#print("fdf",fdf)
fdf.sort_values(by=['article_id', 'article_name', 'name'])
fdfo = fdf[['article_id', 'article_name', 'name']]
fdfo = fdfo.merge(overleaf[['article_id', 'name', 'overleaf']],
on=['article_id', 'name'],
how='outer')
#print("fdfo", fdfo)
fdfo = fdfo.where(pd.notnull(fdfo), None)
for_download = overleaf.merge(fdf[['article_id', 'name', 'download_url']],
on=['article_id', 'name'])
#print("for_download",for_download)
# create individual files
for row in for_download.iterrows():
if len(row[1]['overleaf']) > 0:
download_url = row[1]['download_url']
file = raw_issue_request('GET', download_url, binary=True)
if '.pkl' in row[1]['name']:
with open(
'/mnt/labbook/output/untracked/tmp_overleaf-{}/{}'.
format(head, row[1]['name']), 'wb') as f:
f.write(file)
df = pd.read_pickle(
'/mnt/labbook/output/untracked/tmp_overleaf-{}/{}'.format(
head, row[1]['name']))
df.to_latex(
'/mnt/labbook/output/untracked/overleaf-{}/figshare/{}.tex'
.format(head, row[1]['overleaf']))
repo.git.add('figshare/{}.tex'.format(row[1]['overleaf']))
else:
extension = row[1]['name'].split('.')[-1]
with open(
'/mnt/labbook/output/untracked/overleaf-{}/figshare/{}.{}'
.format(head, row[1]['overleaf'],
extension), 'wb') as f:
f.write(file)
repo.git.add('figshare/{}.{}'.format(
row[1]['overleaf'], extension))
# create bibliography file
adf = pd.DataFrame(articles)
#print(adf)
bib_data = BibliographyData()
for row in for_download.iterrows():
if len(row[1]['overleaf']) > 0:
idx = adf[adf['id'] == row[1]['article_id']].index[0]
bib_data.add_entry(key=row[1]['overleaf'],
entry=Entry('article', [
('title', adf.at[idx, 'title']),
('journal', "figshare"),
('doi', adf.at[idx, 'doi']),
]))
bib_data.to_file(
'/mnt/labbook/output/untracked/overleaf-{}/figures_tables.bib'.format(
head))
repo.git.add('figures_tables.bib')
# write supplementary tex
geometry_options = {"tmargin": "1cm", "lmargin": "1cm"}
doc = ltx.Document(geometry_options=geometry_options)
doc.preamble.append(ltx.Package('biblatex', options=['sorting=none']))
doc.preamble.append(
ltx.Command('addbibresource',
arguments=[ltx.NoEscape("figures_tables.bib")]))
doc.preamble.append(ltx.Package('booktabs'))
doc.preamble.append(ltx.Package('longtable'))
with doc.create(ltx.Subsection('images and tables supplementary file')):
for row in for_download.iterrows():
if len(row[1]['overleaf']) > 0:
idx = adf[adf['id'] == row[1]['article_id']].index[0]
#print("The name is...",row[1]['name'])
if '.pkl' in row[1]['name']:
#print("I should be including something here")
with doc.create(ltx.Table(position='hbt')) as table_holder:
table_holder.append(
ltx.Command('input',
arguments=[
ltx.NoEscape(
"figshare/{}.tex".format(
row[1]['overleaf']))
]))
if row[1]['caption'] is not None:
table_holder.add_caption(row[1]['caption'])
with open(
"/mnt/labbook/output/untracked/overleaf-{}/figshare/{}_caption.tex"
.format(head, row[1]['overleaf']),
"w") as text_file:
text_file.write(row[1]['caption'])
else:
table_holder.add_caption(adf.at[idx, 'title'])
with open(
"/mnt/labbook/output/untracked/overleaf-{}/figshare/{}_caption.tex"
.format(head, row[1]['overleaf']),
"w") as text_file:
text_file.write(adf.at[idx, 'title'])
repo.git.add('figshare/{}_caption.tex'.format(
row[1]['overleaf']))
table_holder.append(
ltx.Command(
'cite',
arguments=[ltx.NoEscape(row[1]['overleaf'])]))
else:
with doc.create(
ltx.Figure(position='hbt')) as image_holder:
image_holder.add_image('figshare/{}'.format(
row[1]['overleaf']))
#print("THE CAPTION IS:", row[1]['caption'])
if row[1]['caption'] is not None:
image_holder.add_caption(row[1]['caption'])
with open(
"/mnt/labbook/output/untracked/overleaf-{}/figshare/{}_caption.tex"
.format(head, row[1]['overleaf']),
"w") as text_file:
text_file.write(
ltx.utils.escape_latex(row[1]['caption']))
else:
image_holder.add_caption(
ltx.utils.escape_latex(adf.at[idx, 'title']))
with open(
"/mnt/labbook/output/untracked/overleaf-{}/figshare/{}_caption.tex"
.format(head, row[1]['overleaf']),
"w") as text_file:
text_file.write(
ltx.utils.escape_latex(adf.at[idx,
'title']))
repo.git.add('figshare/{}_caption.tex'.format(
row[1]['overleaf']))
image_holder.append(
ltx.Command(
'cite',
arguments=[ltx.NoEscape(row[1]['overleaf'])]))
doc.append(ltx.Command('printbibliography'))
doc.generate_tex(
'/mnt/labbook/output/untracked/overleaf-{}/supplementary'.format(head))
repo.git.add('supplementary.tex')
def _add_data(doc: pl.Document, dataset):
name = f'{dataset}_NR2_GBReg'
directory = dataset
aVp_graph = f'{name}.jpg'
angle_dist_graph = f'{name}_angledistribution.jpg'
error_dist_graph = f'{name}_errordistribution.jpg'
sqerror_graph = f'{name}_sqerror_vs_actual.jpg'
stats_csv_all = f'{name}_stats_all.csv'
stats_csv_out = f'{name}_stats_out.csv'
actualVpred_file = os.path.join(directory, aVp_graph)
ang_dist_file = os.path.join(directory, angle_dist_graph)
error_dist_file = os.path.join(directory, error_dist_graph)
sqerror_file = os.path.join(directory, sqerror_graph)
df_all = pd.read_csv(os.path.join(directory, stats_csv_all))
df_out = pd.read_csv(os.path.join(directory, stats_csv_out))
with doc.create(pl.Section(f'Results')):
with doc.create(pl.Subsection('Summary of method:')):
doc.append('Trained on PreAF2 dataset.')
doc.append('\n')
doc.append(f'Dataset tested: {dataset}')
doc.append('\n')
doc.append(f'GBR parameters: {gbr_params}.')
doc.append('\n')
with doc.create(pl.Subsection('Summary of the data:')):
with doc.create(pl.Figure(position='!htbp')) as actualVpred:
actualVpred.add_image(actualVpred_file, width='300px')
actualVpred.add_caption(
'Graph showing the predicted packing angle against the actual packing angle.'
)
with doc.create(pl.Table(position='!htbp')) as table:
table.add_caption('Summary of results for all data')
table.append(pl.Command('centering'))
table.append(pl.NoEscape(df_all.to_latex(escape=False)))
with doc.create(pl.Table(position='!htbp')) as table:
table.add_caption('Summary of results for outliers.')
table.append(pl.Command('centering'))
table.append(pl.NoEscape(df_out.to_latex(escape=False)))
with doc.create(pl.Figure(position='!htbp')) as graphs:
with doc.create(
pl.SubFigure(position='!htbp',
width=pl.NoEscape(
r'0.30\linewidth'))) as ang_dist_graph:
ang_dist_graph.add_image(ang_dist_file,
width=pl.NoEscape(r'\linewidth'))
ang_dist_graph.add_caption(
'Frequency distribution of the packing angle.')
with doc.create(
pl.SubFigure(position='!htbp',
width=pl.NoEscape(
r'0.33\linewidth'))) as error_dist_graph:
error_dist_graph.add_image(error_dist_file,
width=pl.NoEscape(r'\linewidth'))
error_dist_graph.add_caption(
'Distribution of errors calculated as the difference between the predicted and actual interface \
angle.')
with doc.create(
pl.SubFigure(position='!htbp',
width=pl.NoEscape(
r'0.33\linewidth'))) as sqerror_graph:
sqerror_graph.add_image(sqerror_file,
width=pl.NoEscape(r'\linewidth'))
sqerror_graph.add_caption(
'Squared error in predicted packing angle against actual packing angle.'
)
graphs.add_caption('Graphs for further metrics.')