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Refactor plot generation and add parser functionality for *.xrd files
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@budschi
budschi committed Oct 3, 2024
1 parent 80c5bc9 commit fa6f699
Showing 1 changed file with 105 additions and 18 deletions.
123 changes: 105 additions & 18 deletions src/nomad_ikz_omega_theta_xrd/schema_packages/omegascan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,11 @@
import matplotlib.pyplot as plt
import numpy as np
import plotly.colors as pc
import plotly.figure_factory as ff
import plotly.graph_objects as go
from nomad.datamodel.data import ArchiveSection, EntryData
from nomad.datamodel.metainfo.basesections import (
CompositeSystemReference,
Instrument,
InstrumentReference,
Measurement,
Expand Down Expand Up @@ -184,6 +186,16 @@ class ParameterList(MeasurementResult, PlotSection, ArchiveSection):
section_def=ScanCurve,
repeats=True,
)
show_polar_plot = Quantity(
type=bool,
description='Generate polar plot',
a_eln={'component': 'BoolEditQuantity'},
)
show_scan_plot = Quantity(
type=bool,
description='Generate scan plot',
a_eln={'component': 'BoolEditQuantity'},
)

def generate_scan_plot(self):
fig = go.Figure()
Expand Down Expand Up @@ -249,7 +261,7 @@ def generate_stereographic_plot(self):
direction='clockwise',
),
radialaxis=dict(
range=[0, 0.5], # Maximalen Radius anpassen
range=[0, np.ceil(rho * 10) / 10], # Maximalen Radius anpassen
visible=True,
),
),
Expand Down Expand Up @@ -287,16 +299,24 @@ def generate_stereographic_plot(self):
label='Stereographic Projection', figure=fig_stereo.to_plotly_json()
)

# def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
# """
# The normalizer for the `ParameterList` class.
def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
"""
The normalizer for the `ParameterList` class.
Args:
archive (EntryArchive): The archive containing the section that is being
normalized.
logger (BoundLogger): A structlog logger.
"""
if self.show_polar_plot is True:
self.figures.append(self.generate_stereographic_plot())
if self.show_scan_plot is True:
self.figures.append(self.generate_scan_plot())
super().normalize(archive, logger)


# Args:
# archive (EntryArchive): The archive containing the section that is being
# normalized.
# logger (BoundLogger): A structlog logger.
# """
# super().normalize(archive, logger)
class Samples(CompositeSystemReference):
m_def = Section(label='Sample', a_eln=dict(overview=True))


class SampleSpecifications(ArchiveSection):
Expand Down Expand Up @@ -338,10 +358,11 @@ class OmegaThetaXRD(Measurement, PlotSection, EntryData, ArchiveSection):
description='Type of the measurement',
a_eln={'component': 'EnumEditQuantity'},
)

samples = SubSection(section_def=Samples, repeats=True)
sample_specifications = SubSection(
section_def=SampleSpecifications,
)

results = SubSection(
section_def=ParameterList,
repeats=True,
Expand All @@ -368,7 +389,7 @@ def generate_table_plot(self):
fig_table = go.Figure(
data=[
go.Table(
columnwidth=[1, 1, 1, 1.5, 1.5, 1.5, 1.5, 1.5],
columnwidth=[1, 1, 1, 1.5, 2, 2, 1.8, 1.8],
header=dict(
values=[
'X Pos.',
Expand Down Expand Up @@ -400,7 +421,7 @@ def generate_table_plot(self):
)
fig_table.update_layout(width=1000, height=200)
fig_table.update_layout(
margin=dict(l=10, r=10, t=10, b=10) # Set left, right, top, bottom margins
margin=dict(l=1, r=1, t=1, b=1) # Set left, right, top, bottom margins
)
return PlotlyFigure(label='Table', figure=fig_table.to_plotly_json())

Expand All @@ -413,7 +434,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
normalized.
logger (BoundLogger): A structlog logger.
"""
super().normalize(archive, logger)
# super().normalize(archive, logger)

if self.data_file is not None:
# read_function = extract_data_and_metadata
Expand Down Expand Up @@ -446,6 +467,34 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
)
self.scan_recipe_name = info_dict.get('scan_recipe_name')
self.measurement_type = 'single measurement'
self.samples = []
if '-MI_' or '-XY_' in self.data_file:
sampleid = self.data_file.split('_')[0][:-3]
else:
sampleid = self.data_file
sample = Samples(lab_id=sampleid)
self.samples.append(sample)
samplespecs = SampleSpecifications()
if '-NU' in self.data_file:
samplespecs.sample_side_facing_down = 'N unten'
elif '-AU' in self.data_file:
samplespecs.sample_side_facing_down = 'Al unten'
sampleprep = ''
if '-AL' in self.data_file:
sampleprep += 'Al polar lapped, '
elif '-AP' in self.data_file:
sampleprep += 'Al polar polished, '
elif '-AS' in self.data_file:
sampleprep += 'Al polar sawed, '
if '-NL' in self.data_file:
sampleprep += 'N polar lapped'
elif '-NP' in self.data_file:
sampleprep += 'N polar polished'
elif '-NS' in self.data_file:
sampleprep += 'N polar sawed'
samplespecs.sample_preparation_status = sampleprep
self.sample_specifications = samplespecs

results = ParameterList()
results.name = info_dict.get('name')
results.x_pos = float(paramter_dict.get('xpos'))
Expand Down Expand Up @@ -515,6 +564,33 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
)
self.scan_recipe_name = info_dict.get('scan_recipe_name')
self.measurement_type = 'mapping'
self.samples = []
if '-MI_' or '-XY_' in self.data_file:
sampleid = self.data_file.split('_')[0][:-3]
else:
sampleid = self.data_file
sample = Samples(lab_id=sampleid)
self.samples.append(sample)
samplespecs = SampleSpecifications()
if '-NU' in self.data_file:
samplespecs.sample_side_facing_down = 'N unten'
elif '-AU' in self.data_file:
samplespecs.sample_side_facing_down = 'Al unten'
sampleprep = ''
if '-AL' in self.data_file:
sampleprep += 'Al polar lapped, '
elif '-AP' in self.data_file:
sampleprep += 'Al polar polished, '
elif '-AS' in self.data_file:
sampleprep += 'Al polar sawed, '
if '-NL' in self.data_file:
sampleprep += 'N polar lapped'
elif '-NP' in self.data_file:
sampleprep += 'N polar polished'
elif '-NS' in self.data_file:
sampleprep += 'N polar sawed'
samplespecs.sample_preparation_status = sampleprep
self.sample_specifications = samplespecs
for measurement in (
xrd_dict.get('MultiMeasurement', {})
.get('Measurements', {})
Expand Down Expand Up @@ -1224,9 +1300,6 @@ def create_stereographic_projection_plot_cartesian2(
)
return fig

import plotly.figure_factory as ff
import plotly.graph_objects as go

def create_stereographic_projection_quiver_plot(
x_coords,
y_coords,
Expand All @@ -1247,15 +1320,24 @@ def create_stereographic_projection_quiver_plot(
for comp90 in component_90_values
] # y-component

hovertext = [
f'Tilt: {tilt:.3f}<br>Direction: {tilt_dir:.1f}°'
for tilt, tilt_dir in zip(
tilt_values, tilt_direction_values
)
]

# Create quiver plot
fig = ff.create_quiver(
x_coords,
y_coords,
u,
v,
scale=20,
scale=15,
arrow_scale=0.2,
name='Tilt Direction',
hoverinfo='text',
text=hovertext, # Add hover text for each arrow
)
# Define the circle's center and radius
circle_center_x = 0
Expand Down Expand Up @@ -1305,13 +1387,17 @@ def create_stereographic_projection_quiver_plot(
xaxis=dict(
showgrid=True,
zeroline=False,
fixedrange=False,
),
yaxis=dict(
showgrid=True,
zeroline=False,
scaleanchor='x', # Make sure x and y are on the same scale
scaleratio=1,
fixedrange=False,
),
hovermode='closest',
dragmode='zoom',
)

return fig
Expand Down Expand Up @@ -1438,6 +1524,7 @@ def create_stereographic_projection_quiver_plot(
# self.figures.append(
# PlotlyFigure(label='figure 1', index=1, figure=figure1.to_plotly_json())
# )
super().normalize(archive, logger)


m_package.__init_metainfo__()

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