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finalize plots and add instrument ref
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@budschi
budschi committed Aug 13, 2024
1 parent 538f9df commit 0323917
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Showing 3 changed files with 262 additions and 29 deletions.
265 changes: 236 additions & 29 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 @@ -21,18 +21,25 @@

import matplotlib.pyplot as plt
import numpy as np
import plotly.colors as pc
import plotly.graph_objects as go
from nomad.datamodel.data import ArchiveSection, EntryData
from nomad.datamodel.metainfo.basesections import Measurement, MeasurementResult
from nomad.datamodel.metainfo.basesections import (
Instrument,
InstrumentReference,
Measurement,
MeasurementResult,
)
from nomad.datamodel.metainfo.plot import PlotlyFigure, PlotSection
from nomad.metainfo import Datetime, MEnum, Package, Quantity, Section, SubSection
from nomad.metainfo import MEnum, Package, Quantity, Section, SubSection

from nomad_ikz_omega_theta_xrd.schema_packages.omegathetaxrdreader import (
extract_data_and_metadata,
extract_general_info,
extract_parameter_list,
extract_scan_data,
)
from nomad_ikz_omega_theta_xrd.schema_packages.utils import create_archive

if TYPE_CHECKING:
from nomad.datamodel.datamodel import EntryArchive
Expand All @@ -41,6 +48,40 @@
m_package = Package(name='Omega Theta XRD')


class OmegaThetaXRDInstrument(Instrument, EntryData, ArchiveSection):
"""
Class autogenerated from yaml schema.
"""

m_def = Section()
instrument_name = Quantity(
type=str,
description='Name of the instrument used.',
default='Freiberger Omega Theta XRD',
)
lab_id = Quantity(
type=str,
description='Identifier for the instrument.',
default='26-0019',
label='serial_number',
)


class OmegaThetaXRDInstrumentReference(InstrumentReference):
"""
Class autogenerated from yaml schema.
"""

m_def = Section()
reference = Quantity(
type=OmegaThetaXRDInstrument,
a_eln={
'component': 'ReferenceEditQuantity',
'label': 'omega_theta_xrd_instrument',
},
)


class ScanCurve(PlotSection, ArchiveSection):
"""
Class autogenerated from yaml schema.
Expand Down Expand Up @@ -182,7 +223,7 @@ class ParameterList(MeasurementResult, PlotSection, ArchiveSection):


class SampleSpecifications(ArchiveSection):
m_def = Section()
m_def = Section(a_eln=dict(overview=True))
sample_preparation_status = Quantity(
type=str,
description='Status of the sample preparation',
Expand Down Expand Up @@ -211,21 +252,25 @@ class OmegaThetaXRD(Measurement, PlotSection, EntryData, ArchiveSection):
description='Data file *.xrd containing the XRD data.',
a_eln={'component': 'FileEditQuantity'},
)
time_stamp = Quantity(
type=Datetime,
a_eln={'component': 'DateTimeEditQuantity'},
)
# time_stamp = Quantity(
# type=Datetime,
# a_eln={'component': 'DateTimeEditQuantity'},
# )
measurement_type = Quantity(
type=MEnum(['single measurement', 'mapping']),
description='Type of the measurement',
a_eln={'component': 'EnumEditQuantity'},
)

sample_specifications = SubSection(
section_def=SampleSpecifications,
)
results = SubSection(
section_def=ParameterList,
repeats=True,
)
sample_specifications = SubSection(
section_def=SampleSpecifications,
instruments = SubSection(
section_def=OmegaThetaXRDInstrumentReference,
)

def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
Expand Down Expand Up @@ -261,8 +306,11 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
)
scan_dict = extract_scan_data(xrd_dict.get('Measurement', {}))

self.name = info_dict.get('name')
self.time_stamp = datetime.strptime(
self.name = info_dict.get('name').split('_')[
0
] # should be original_name
self.lab_id = self.name
self.datetime = datetime.strptime(
info_dict.get('time_stamp'), '%m/%d/%Y %H:%M:%S'
)
self.scan_recipe_name = info_dict.get('scan_recipe_name')
Expand Down Expand Up @@ -291,6 +339,22 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
# results.normalize(archive, logger)
self.results = [results]

xrdinstrumentref = OmegaThetaXRDInstrumentReference()
xrdinstrumentref.lab_id = info_dict.get('device_serial_no')
# xrdinstrumentref.normalize(archive, logger)
if xrdinstrumentref.reference is None:
xrdinstrument = OmegaThetaXRDInstrument(
lab_id=xrdinstrumentref.lab_id
)
# self.instruments = [ramanspectrometer]

xrdinstrumentref.reference = create_archive(
xrdinstrument,
archive,
f'Freiberger_Omega_Theta_XRD_{xrdinstrumentref.lab_id}.archive.json',
)
self.instruments = [xrdinstrumentref]

fig = go.Figure()
fig.add_trace(
go.Scatter(
Expand Down Expand Up @@ -329,8 +393,9 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
xrd_dict.get('MultiMeasurement', {})
)

self.name = info_dict.get('name')
self.time_stamp = datetime.strptime(
self.name = info_dict.get('name').split('_')[0]
self.lab_id = self.name
self.datetime = datetime.strptime(
info_dict.get('time_stamp'), '%m/%d/%Y %H:%M:%S'
)
self.scan_recipe_name = info_dict.get('scan_recipe_name')
Expand Down Expand Up @@ -369,6 +434,22 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
# results.normalize(archive, logger)
self.results.append(results)

xrdinstrumentref = OmegaThetaXRDInstrumentReference()
xrdinstrumentref.lab_id = info_dict.get('device_serial_no')
# xrdinstrumentref.normalize(archive, logger)
if xrdinstrumentref.reference is None:
xrdinstrument = OmegaThetaXRDInstrument(
lab_id=xrdinstrumentref.lab_id
)
# self.instruments = [ramanspectrometer]

xrdinstrumentref.reference = create_archive(
xrdinstrument,
archive,
f'Freiberger_Omega_Theta_XRD_{xrdinstrumentref.lab_id}.archive.json',
)
self.instruments = [xrdinstrumentref]

if self.results != None:
# Extracting data for the plots
x_coords = [int(point['x_pos']) for point in self.results]
Expand Down Expand Up @@ -399,29 +480,96 @@ def get_colors(values):
cmap = plt.cm.viridis
return [cmap(norm(value)) for value in values]

# def get_colors_pl(values):
# norm = plt.Normalize(min(values), max(values))
# colorscale = pc.get_colorscale('balance')
# return [
# pc.find_intermediate_color(
# colorscale, intermed=norm(value), colortype='rgb'
# )
# for value in values
# ]
def get_colors_pl(values):
norm = plt.Normalize(min(values), max(values))
colorscale = pc.get_colorscale('Picnic')

def get_interpolated_color(value):
scaled_value = norm(value)

for i in range(1, len(colorscale)):
low_pos, low_color = colorscale[i - 1]
high_pos, high_color = colorscale[i]

# Ensure positions are treated as floats
low_pos = float(low_pos)
high_pos = float(high_pos)

if low_pos <= scaled_value <= high_pos:
return pc.find_intermediate_color(
lowcolor=low_color,
highcolor=high_color,
intermed=(scaled_value - low_pos)
/ (high_pos - low_pos),
colortype='rgb',
)

# Return the last color if value exceeds the colorscale range
return colorscale[-1][1]

return [get_interpolated_color(value) for value in values]

# Function to convert RGBA to hex
def rgba_to_hex(rgba):
return f'#{int(rgba[0]*255):02x}{int(rgba[1]*255):02x}{int(rgba[2]*255):02x}'

# Function to create a scatter plot with text annotations and color gradient boxes
def create_plot(x_coords, y_coords, values, title):
colors = get_colors(values)
hex_colors = [rgba_to_hex(color) for color in colors]
colors = get_colors_pl(values)
# hex_colors = [rgba_to_hex(color) for color in colors]

fig = go.Figure()

# Define the circle's center and radius
circle_center_x = sum(x_coords) / len(
x_coords
) # Center of x_coords
circle_center_y = sum(y_coords) / len(
y_coords
) # Center of y_coords
circle_radius = (
3
+ max(
max(x_coords) - min(x_coords),
max(y_coords) - min(y_coords),
)
/ 2
)

# Add the circle to the plot
fig.add_shape(
type='circle',
xref='x',
yref='y',
x0=circle_center_x - circle_radius,
y0=circle_center_y - circle_radius,
x1=circle_center_x + circle_radius,
y1=circle_center_y + circle_radius,
line=dict(color='darkgrey', width=2),
fillcolor='grey',
opacity=0.3,
)

for x, y, value, color in zip(
x_coords, y_coords, values, hex_colors
x_coords,
y_coords,
values,
colors, # hex_colors
):
fig.add_trace(
go.Scatter(
x=[x],
y=[y],
mode='text',
text=[f'{float(value):.3f}'],
textposition='middle center',
showlegend=False,
)
)
if title == 'Tilt Direction':
text_format = f'{float(value):.1f}'
else:
text_format = f'{float(value):.3f}'

# Adding box around the text with color gradient
fig.add_shape(
type='rect',
Expand All @@ -431,15 +579,74 @@ def create_plot(x_coords, y_coords, values, title):
y1=y + 1.5,
line=dict(color=color, width=2),
fillcolor=color,
opacity=0.5,
opacity=1,
)
# fig.add_trace(
# go.Scatter(
# x=[x],
# y=[y],
# mode='text',
# # marker=dict(
# # size=0,
# # ),
# text=text_format, # [f'{float(value):.3f}'],
# textfont=dict(
# size=12, # Font size
# color='black', # Font color
# family='Arial', # Font family
# weight='bold', # Font weight for bold text
# ),
# textposition='middle center',
# showlegend=False,
# )
# )
# Add text annotation on top of the colored box
fig.add_annotation(
x=x,
y=y,
text=text_format,
showarrow=False,
font=dict(color='black', size=12),
xanchor='center',
yanchor='middle',
)

# Add color bar
fig.add_trace(
go.Scatter(
x=x_coords,
y=y_coords,
mode='markers',
opacity=0,
marker=dict(
size=0, # Hide the markers
color=values,
colorscale='Picnic', # Choose a colorscale
colorbar=dict(
title='',
titleside='right',
),
),
showlegend=False,
)
)
fig.update_layout(
title=title,
xaxis_title='X Position',
yaxis_title='Y Position',
plot_bgcolor='white',
xaxis=dict(showgrid=True, zeroline=False),
yaxis=dict(showgrid=True, zeroline=False),
xaxis=dict(
showgrid=True,
zeroline=False,
# scaleanchor='y',
# scaleratio=1,
),
yaxis=dict(
showgrid=True,
zeroline=False,
scaleanchor='x',
scaleratio=1,
),
)
return fig

Expand Down
1 change: 1 addition & 0 deletions src/nomad_ikz_omega_theta_xrd/schema_packages/omegathetaxrdreader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ def extract_general_info(
"""Extract general information from the XRD data."""
general_info = {
'name': xrd_dict.get('Info', {}).get('Name'),
'original_name': xrd_dict.get('Info', {}).get('OriginalName'),
'time_stamp': xrd_dict.get('Info', {}).get('TimeStamp'),
'user': xrd_dict.get('Info', {}).get('User'),
'description': xrd_dict.get('Info', {}).get('Comment'),
Expand Down
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