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adding raman plot widget #12

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Nov 8, 2023
Merged

adding raman plot widget #12

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196 changes: 195 additions & 1 deletion aiidalab_qe_vibroscopy/utils/raman/result.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,12 @@
from widget_bandsplot import BandsPlotWidget

from aiidalab_qe.common.panel import ResultPanel

import ipywidgets as ipw
import numpy as np
from IPython.display import clear_output, display
import base64
import json


from aiida_vibroscopy.utils.broadenings import multilorentz
def plot_powder(
Expand Down Expand Up @@ -110,6 +114,196 @@ def _update_view(self):
g,
]

class SpectrumPlotWidget(ipw.VBox):
"""Widget that allows different options for plotting Raman Spectrum."""

description = ipw.HTML(
"""<div style="line-height: 140%; padding-top: 10px; padding-bottom: 10px">
Select the type of Raman spectrum to plot.
</div>"""
)
def __init__(self, node, **kwargs):
self.node = node
#VibriationalData
self.vibro = self.node.outputs.vibronic.iraman.vibrational_data.numerical_accuracy_4
self._plot_type = ipw.ToggleButtons(
options=[
("Powder", "powder"),
("Single Crystal", "single_crystal"),
],
value="powder",
description="Spectrum type:",
disabled=False,
style={"description_width": "initial"},
)
self.temperature = ipw.FloatText(
value=298.0,
description="Temperature (K):",
disabled=False,
style={"description_width": "initial"},
)
self.frequency_laser = ipw.FloatText(
value=532.0,
description="Laser frequency (nm):",
disabled=False,
style={"description_width": "initial"},
)
self.pol_incoming = ipw.Text(
value="0 0 1",
description="Incoming polarization:",
disabled=False,
style={"description_width": "initial"},
)
self.pol_outgoing = ipw.Text(
value="0 0 1",
description="Outgoing polarization:",
disabled=False,
style={"description_width": "initial"},
)
self.plot_button = ipw.Button(
description="Plot",
icon="pencil",
button_style="primary",
disabled=False,
layout=ipw.Layout(width="auto"),
)
self.download_button = ipw.Button(
description="Download Data",
icon="download",
button_style="primary",
disabled=False,
layout=ipw.Layout(width="auto", visibility="hidden"),
)
self.wrong_syntax = ipw.HTML(
value="""<i class="fa fa-times" style="color:red;font-size:2em;" ></i> wrong syntax""",
layout={"visibility": "hidden"},
)
self.spectrum_widget = ipw.Output()
self.frequencies = []
self.intensities = []
self.polarization_out = ipw.Output()

def download_data(_=None):
filename = "spectra.json"
my_dict = {"Frequencies cm-1": self.frequencies.tolist(), "Intensities": self.intensities.tolist()}
json_str = json.dumps(my_dict)
b64_str = base64.b64encode(json_str.encode()).decode()
self._download(payload=b64_str, filename=filename)


self._plot_type.observe(self._on_plot_type_change, names="value")
self.plot_button.on_click(self._on_plot_button_clicked)
self.download_button.on_click(download_data)
super().__init__(
children=[
self.description,
self._plot_type,
self.temperature,
self.frequency_laser,
self.polarization_out,
ipw.HBox([self.plot_button, self.download_button]),
self.wrong_syntax,
self.spectrum_widget,
]
)

@staticmethod
def _download(payload, filename):
from IPython.display import Javascript

javas = Javascript(
"""
var link = document.createElement('a');
link.href = 'data:text/json;charset=utf-8;base64,{payload}'
link.download = "{filename}"
document.body.appendChild(link);
link.click();
document.body.removeChild(link);
""".format(
payload=payload, filename=filename
)
)
display(javas)

def _on_plot_type_change(self, change):
if change["new"] == "single_crystal":
with self.polarization_out:
clear_output()
display(self.pol_incoming)
display(self.pol_outgoing)
else:
self.pol_incoming.value = "0 0 1"
self.pol_outgoing.value = "0 0 1"
self.wrong_syntax.layout.visibility = "hidden"
with self.polarization_out:
clear_output()

def _on_plot_button_clicked(self, change):
if self._plot_type.value == "powder":
# Powder spectrum
polarized_intensities, depolarized_intensities, frequencies, labels = self.vibro.run_powder_raman_intensities(frequencies=self.frequency_laser.value, temperature=self.temperature.value)
total_intensities = polarized_intensities + depolarized_intensities
self.frequencies , self.intensities = plot_powder(frequencies, total_intensities)
self._display_figure()


else:
# Single crystal spectrum
dir_incoming, correct_syntax_incoming = self._check_inputs_correct(self.pol_incoming)
dir_outgoing, correct_syntax_outgoing = self._check_inputs_correct(self.pol_outgoing)
if not correct_syntax_incoming or not correct_syntax_outgoing:
self.wrong_syntax.layout.visibility = "visible"
return
else:
self.wrong_syntax.layout.visibility = "hidden"
intensities, frequencies, labels = self.vibro.run_single_crystal_raman_intensities(pol_incoming=dir_incoming, pol_outgoing=dir_incoming, frequencies=self.frequency_laser.value, temperature=self.temperature.value)
self.frequencies , self.intensities = plot_powder(frequencies, intensities)
self._display_figure()

def _check_inputs_correct(self,polarization):
#Check if the polarization vectors are correct
input_text = polarization.value
input_values = input_text.split()
dir_values = []
if len(input_values) == 3:
try:
dir_values = [float(i) for i in input_values]
return dir_values, True
except:
return dir_values, False
else:
return dir_values, False

def _spectrum_widget(self):
import plotly.graph_objects as go

fig = go.FigureWidget(
layout=go.Layout(
title=dict(text="Raman spectrum"),
barmode="overlay",
)
)
fig.layout.xaxis.title = "Wavenumber (cm-1)"
fig.layout.yaxis.title = "Intensity (arb. units)"
fig.layout.xaxis.nticks = 0
fig.add_scatter(x=self.frequencies,y=self.intensities,name=f"")
fig.update_layout(
height=500,
width=700,
plot_bgcolor="white",


)
return fig

def _display_figure(self):
with self.spectrum_widget:
clear_output()
display(self._spectrum_widget())
self.download_button.layout.visibility = "visible"






Expand Down
21 changes: 4 additions & 17 deletions aiidalab_qe_vibroscopy/workflows/result.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from ..utils.raman.result import export_iramanworkchain_data
from ..utils.harmonic.result import export_phononworkchain_data
import ipywidgets as ipw

from ..utils.raman.result import SpectrumPlotWidget
class Result(ResultPanel):

title = "Vibrational Structure"
Expand Down Expand Up @@ -45,27 +45,14 @@ def _update_view(self):
table_html += "</table>"

active_modes = ipw.VBox([ipw.HTML(value="<b> Raman Active Modes </b>"),ipw.HTML(value=table_html)])

spectrum_widget = SpectrumPlotWidget(self.node)

if spectra_data[3] in ["Raman vibrational spectrum","Infrared vibrational spectrum"]:
import plotly.graph_objects as go

frequencies = spectra_data[1]
total_intensities = spectra_data[0]

g = go.FigureWidget(
layout=go.Layout(
title=dict(text=spectra_data[3]),
barmode="overlay",
)
)
g.layout.xaxis.title = "Wavenumber (cm-1)"
g.layout.yaxis.title = "Intensity (arb. units)"
g.layout.xaxis.nticks = 0
g.add_scatter(x=frequencies,y=total_intensities,name=f"")


self.children=[
ipw.HBox([active_modes, g])
ipw.HBox([spectrum_widget, active_modes ])
]

if phonon_data:
Expand Down