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Add wafer diameter and grid size to general info extraction
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@budschi
budschi committed Nov 28, 2024
1 parent 2f9e43f commit baa44cf
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Showing 2 changed files with 163 additions and 38 deletions.
199 changes: 161 additions & 38 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 @@ -352,6 +352,19 @@ class OmegaThetaXRD(Measurement, PlotSection, EntryData, ArchiveSection):
description='Type of the measurement',
a_eln={'component': 'EnumEditQuantity'},
)
wafer_diameter = Quantity(
type=np.float64,
description='The diameter of the wafer that is measured',
a_eln={'component': 'NumberEditQuantity'},
# unit='cm', ?
)
grid_size = Quantity(
type=np.float64,
description='Grid size of the mapping',
a_eln={'component': 'NumberEditQuantity'},
# unit='cm', ?
)

samples = SubSection(section_def=Samples, repeats=True)
sample_specifications = SubSection(
section_def=SampleSpecifications,
Expand All @@ -367,8 +380,8 @@ class OmegaThetaXRD(Measurement, PlotSection, EntryData, ArchiveSection):

def generate_table_plot(self):
# Extract the values for each column from all self.results
x_pos_list = [result.x_pos for result in self.results]
y_pos_list = [result.y_pos for result in self.results]
x_pos_list = [f'{result.x_pos:.1f}' for result in self.results]
y_pos_list = [f'{result.y_pos:.1f}' for result in self.results]
tilt_list = [f'{result.tilt.magnitude:.3f}' for result in self.results]
tilt_direction_list = [
f'{result.tilt_direction.magnitude:.1f}' for result in self.results
Expand Down Expand Up @@ -461,6 +474,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
)
self.scan_recipe_name = info_dict.get('scan_recipe_name')
self.measurement_type = 'single measurement'
self.wafer_diameter = float(info_dict.get('wafer_diameter'))
self.samples = []
if '-MI_' or '-XY_' in self.data_file:
sampleid = self.data_file.split('_')[0][:-3]
Expand Down Expand Up @@ -558,6 +572,8 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
)
self.scan_recipe_name = info_dict.get('scan_recipe_name')
self.measurement_type = 'mapping'
self.wafer_diameter = float(info_dict.get('wafer_diameter'))
self.grid_size = float(info_dict.get('grid_size'))
self.samples = []
if '-MI_' or '-XY_' in self.data_file:
sampleid = self.data_file.split('_')[0][:-3]
Expand Down Expand Up @@ -721,14 +737,15 @@ def create_plot(x_coords, y_coords, values, title):
circle_center_y = 0 # 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
)
circle_radius = self.wafer_diameter/2
# (
# 1
# + max(
# max(x_coords) - min(x_coords),
# max(y_coords) - min(y_coords),
# )
# / 2
# )

# Add the circle to the plot
fig.add_shape(
Expand Down Expand Up @@ -756,12 +773,13 @@ def create_plot(x_coords, y_coords, values, title):
text_format = f'{float(value):.3f}'

# Adding box around the text with color gradient
grid_size=self.grid_size
fig.add_shape(
type='rect',
x0=x - 1.5,
y0=y - 1.5,
x1=x + 1.5,
y1=y + 1.5,
x0=x - grid_size/2,
y0=y - grid_size/2,
x1=x + grid_size/2,
y1=y + grid_size/2,
line=dict(color=color, width=2),
fillcolor=color,
opacity=1,
Expand Down Expand Up @@ -1304,15 +1322,135 @@ def create_stereographic_projection_quiver_plot(
component_0_values,
component_90_values,
title,
scaling_factor=1,
wafer_diameter=25, # Default wafer diameter
):
# Compute the u and v components
u = [-comp0 for comp0 in component_0_values] # Inverted x-component
v = [comp90 for comp90 in component_90_values] # y-component

# Create hover text
hovertext = [
f'X: {x}<br>Y: {y}<br>Tilt: {tilt:.3f}<br>Direction: {tilt_dir:.1f}°'
for x, y, tilt, tilt_dir in zip(
x_coords, y_coords, tilt_values, tilt_direction_values
)
]

# Define slider steps and frames
steps = []
frames = []
scales = np.linspace(1, 20, 20) # Range of scale values for the slider

for i, scale in enumerate(scales):
# Create quiver plot for each scale
quiver = ff.create_quiver(
x_coords,
y_coords,
u,
v,
scale=scale,
arrow_scale=0.2,
name="Tilt Direction",
hoverinfo="text",
text=hovertext,
)
# Add frame for the current scale
frames.append(dict(data=quiver.data, name=f"frame{i}"))

# Add a step to the slider
step = dict(
method="animate",
args=[
[f"frame{i}"], # The frame name to animate to
dict(frame=dict(duration=0, redraw=True), mode="immediate"),
],
label=f"Scale: {scale:.1f}",
)
steps.append(step)

# Create the initial quiver plot with the first scale
initial_scale = scales[0]
fig = ff.create_quiver(
x_coords,
y_coords,
u,
v,
scale=initial_scale,
arrow_scale=0.2,
name="Tilt Direction",
hoverinfo="text",
text=hovertext,
)

# Add the circle representing the wafer
circle_center_x = 0
circle_center_y = 0
circle_radius = wafer_diameter / 2

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,
)

# Add frames and slider to the figure
fig.frames = frames
sliders = [
dict(
steps=steps,
active=0,
currentvalue={"prefix": "Scale: "},
)
]

# Update the layout to include the slider
fig.update_layout(
sliders=sliders,
title=title,
xaxis_title="X Position",
yaxis_title="Y Position",
plot_bgcolor="white",
showlegend=False,
xaxis=dict(showgrid=True, zeroline=False, fixedrange=False),
yaxis=dict(
showgrid=True,
zeroline=False,
scaleanchor="x",
scaleratio=1,
fixedrange=False,
),
hovermode="closest",
dragmode="zoom",
)

return fig



def create_stereographic_projection_quiver_plot_alt(
x_coords,
y_coords,
tilt_values,
tilt_direction_values,
component_0_values,
component_90_values,
title,
#scaling_factor=1,
):
# Use quiver to plot arrows from the positions defined by x_coords and y_coords
# u (x-component) is component_0_values, v (y-component) is component_90_values
u = [
-comp0 * scaling_factor for comp0 in component_0_values
-comp0 for comp0 in component_0_values
] # Inverted x-component
v = [
comp90 * scaling_factor
comp90
for comp90 in component_90_values
] # y-component

Expand All @@ -1327,6 +1465,10 @@ def create_stereographic_projection_quiver_plot(
]

# Create quiver plot
# if self.wafer_diameter>=25:
# scaling=15
# elif self.wafer_diameter <=10:
# scaling=2
fig = ff.create_quiver(
x_coords,
y_coords,
Expand All @@ -1341,14 +1483,7 @@ def create_stereographic_projection_quiver_plot(
# Define the circle's center and radius
circle_center_x = 0
circle_center_y = 0
circle_radius = (
3
+ max(
max(x_coords) - min(x_coords),
max(y_coords) - min(y_coords),
)
/ 2
)
circle_radius = self.wafer_diameter/2

# Add the circle to the plot
fig.add_shape(
Expand All @@ -1363,18 +1498,6 @@ def create_stereographic_projection_quiver_plot(
fillcolor='grey',
opacity=0.3,
)
# for x, y, tilt, tilt_dir in zip(
# x_coords, y_coords, tilt_values, tilt_direction_values
# ):
# fig.add_annotation(
# x=x,
# y=y,
# text=f'{tilt:.3f}, {tilt_dir:.1f}°',
# showarrow=False,
# font=dict(color='black', size=10),
# xanchor='center',
# yanchor='middle',
# )

# Add layout settings
fig.update_layout(
Expand Down Expand Up @@ -1444,7 +1567,7 @@ def create_stereographic_projection_quiver_plot(
component_0_values,
component_90_values,
'Stereographic Projection',
scaling_factor=1,
wafer_diameter=self.wafer_diameter,
)
# Displaying the plots
# fig_tilt.show()
Expand Down
2 changes: 2 additions & 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 @@ -43,6 +43,8 @@ def extract_general_info(
'x_pos': xrd_dict.get('Info', {}).get('XPos'),
'y_pos': xrd_dict.get('Info', {}).get('YPos'),
'device_serial_no': xrd_dict.get('Info', {}).get('DeviceSerialNo'),
'wafer_diameter': xrd_dict.get('WaferInfo', {}).get('Diameter'),
'grid_size': xrd_dict.get('WaferInfo', {}).get('GridSize')
}
return general_info

Expand Down

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