Merge pull request #12 from mikibonacci/raman_spectrum_widget

adding raman plot widget

aiidalab_qe_vibroscopy/utils/raman/result.py

@@ -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(
@@ -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"
+
+
+
 
 
 

aiidalab_qe_vibroscopy/workflows/result.py

@@ -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"
@@ -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: