Commit 2e682f8f authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

refactor gp-sans app

parent 2e6e7265

trame/air-sans/air_sans/app/utilities/file_load.py

+1 −0
Original line number Diff line number Diff line
@@ -21,4 +21,5 @@ def load_mantid(file_path): 
    for col in range(count):

        y_data = ws.readY(col)

        array[:,col] = y_data

    array.tofile("heatmap_gpsans.np", sep='', format='%s')

    return array

trame/air-sans/air_sans/gpsans/core.py

+38 −20
Original line number Diff line number Diff line 
import os

import numpy



import logging

import time

import asyncio



from trame.app import get_server

from trame.decorators import TrameApp, change

from trame.decorators import TrameApp, change, controller

from trame.ui.vuetify import SinglePageWithDrawerLayout

from trame.widgets import vuetify, plotly



from .ui import (

    Directory,

    FileSelector,

    FigureControl,

)



from .visualization import Visualization

from .utilities import galaxy

from .visualization import Visualization





logger = logging.getLogger(__name__)
@@ -47,7 +42,7 @@ class GpSans: 
        self.state.staff_file = None

        self.server.state.ipts = None

        self.state.data = None

        self.ui = self._build_ui()

        self.ui = self.update_ui()



    @property

    def state(self):
@@ -57,26 +52,41 @@ class GpSans: 
    def ctrl(self):

        return self.server.controller



    async def run_in_backgorund(self,user_file,staff_file,ipts):

        data=None

        error=None

        await asyncio.sleep(1)

        try:

            data = galaxy.run_gpsans(user_file, staff_file, ipts)

        except Exception as e:

            error = f"Cannot execute Galaxy job: {e}"

        self.server.state.galaxy_running = False

        self.server.state.figure_ready = True

        with self.server.state:

            self._viz.create_gpsans_fig(data, error)



    def run(self):

        user_file = self.server.state.user_file

        staff_file = self.server.state.staff_file

        ipts = self.server.state.ipts

        data = galaxy.run_gpsans(user_file,staff_file,ipts)

        self._viz.create_gpsans_fig(data)

        self.server.state.figure_ready = True

        self.server.state.galaxy_running = True

        self.server.state.figure_ready = False

        asyncio.create_task(self.run_in_backgorund(user_file,staff_file,ipts))





    def _build_ui(self):

    def update_ui(self):

        self.state.trame__title = "gp-sans"

        with SinglePageWithDrawerLayout(self.server) as layout:

            with layout.icon:

                vuetify.VIcon("mdi-bullseye")



            with layout.title as title:

                title.set_text("GP-SANS")

                title.set_text("GP-SANS Data Reduction - Demo")

                title.classes = "font-weight-medium ml-0 pl-0"



            with layout.drawer as drawer:

                drawer.width = 350

                drawer.classes = "ml-0 pl-0"



                vuetify.VFileInput(

                    label="User Input File",

                    v_model=("user_file", None),
@@ -89,17 +99,25 @@ class GpSans: 
                    label="IPTS Number",

                    v_model=("ipts", None),

                )

                vuetify.VBtn("Run in Galaxy",icon=False, click=self.run)

                vuetify.VBtn("Run in Galaxy",

                             icon=False,

                             disabled = ("galaxy_running", False),

                             click=self.run)



            with layout.content:

                with vuetify.VContainer(

                    fluid=True,

                    classes="pa-0 fill-height",

                    classes="pa-0 fill-height text-center",

                ):

                    self.ctrl.update_d11 = plotly.Figure(

                        display_mode_bar=("false",),

                        v_show=("figure_ready", False),

                    ).update



                    with vuetify.VContainer(

                    ):

                        vuetify.VProgressCircular(

                            v_show=("galaxy_running", False),

                            indeterminate=True,

                        )

            return layout

trame/air-sans/air_sans/gpsans/visualization.py

+22 −9
Original line number Diff line number Diff line
@@ -15,24 +15,37 @@ class Visualization: 
    def __init__(self, server):

        self.server = server



    def create_gpsans_fig(self, data):

        data = BytesIO(data)

    def create_gpsans_fig(self, data, error):

        if error:

            fig = go.Figure(data=None)

            fig.add_annotation(

                text=error,

                showarrow=False,

                xref="paper",

                yref="paper",

                x=0.5,

                y=0.5,

                font=dict(size=16),

            )

            fig.update_xaxes(showgrid=False, zeroline=False, showticklabels=False)

            fig.update_yaxes(showgrid=False, zeroline=False, showticklabels=False)



        df = pd.read_csv(data, header=None, delim_whitespace=True, skiprows=4)

        values_df = df[[0, 1, 2]]

        values_df.replace('NAN', np.nan, inplace=True)

            self.server.controller.update_d11(fig)

            return fig



        x_values = values_df[0]

        y_values = values_df[1]

        z_values = values_df[2]

        data = BytesIO(data)



        # Replace 'NAN' values with NumPy NaN

        df = pd.read_csv(data, header=None, delim_whitespace=True, skiprows=4)

        x_values = df[0]

        y_values = df[1]

        z_values = df[2]



        # Create a heatmap using Plotly objects

        heatmap = go.Heatmap(

            x=x_values,

            y=y_values,

            z=z_values,

            zsmooth="best",

            colorscale='Viridis',  # You can choose another colorscale

            colorbar=dict(title='Value'),

        )