app.py

import cftime
import fsspec

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import panel as pn
import xarray as xr
from ipywidgets import (
    Checkbox,
#    FloatRangeSlider,
    FloatSlider,
    IntRangeSlider,
    IntSlider,
#    interactive,
)


import param

pn.extension("tabulator")

def greg_0h(jourjul):
    import math
    # Julian days start and end at noon.
    # Julian day 2440000 begins at 00 hours, May 23, 1968.

    # Round the input Julian day number to avoid precision errors
    fac = 10**9
    jourjul = np.round(fac * jourjul + 0.5) / fac

    # Calculate seconds in the day
    secs = (jourjul % 1) * 24 * 3600

    # Round seconds to avoid precision errors
    secs = np.round(fac * secs + 0.5) / fac

    # Gregorian calendar conversion
    j = math.floor(jourjul) - 1721119
    in_ = 4 * j - 1
    y = math.floor(in_ / 146097)
    j = in_ - 146097 * y
    in_ = math.floor(j / 4)
    in_ = 4 * in_ + 3
    j = math.floor(in_ / 1461)
    d = math.floor(((in_ - 1461 * j) + 4) / 4)
    in_ = 5 * d - 3
    m = math.floor(in_ / 153)
    d = math.floor(((in_ - 153 * m) + 5) / 5)
    y = y * 100 + j
    if m < 10:
        mo = m + 3
        yr = y
    else:
        mo = m - 9
        yr = y + 1

    hour = math.floor(secs / 3600)
    mins = math.floor((secs % 3600) / 60)
    sec = int(secs % 60)

    gtime = [yr, mo, d, hour, mins, sec]

    return gtime


def fix_time(ds):
    from datetime import datetime, timedelta

    time = ds["TIME"]
    time2 = time.dropna(dim="MAXT")
    time2 = time2.reindex_like(time, method="nearest")
    jourjul = [greg_0h(jourjul) for jourjul in time2.values]
    date = [
        datetime(jourjul[0], jourjul[1], jourjul[2], jourjul[3], jourjul[4], jourjul[5])
        for jourjul in jourjul
    ]
    date = xr.DataArray(date, dims="MAXT")
    return ds.assign(TIME=date)

@pn.cache(max_items=32,policy='LRU',per_session=True)
def load_csv():
    url="https://data-eurogoship.ifremer.fr/data/zarr_table.csv"
    fs = fsspec.filesystem("https")
    with fs.open(url) as f:
        df = pd.read_csv(f,index_col=None)
    df.sort_values(by="year") #inplace=True)
    return df

@pn.cache(max_items=4,policy='LRU',per_session=True)
def load_bathymetry():
    #url="https://data-eurogoship.ifremer.fr/bathymetrie/bathy6min.nc"
    #fs = fsspec.filesystem("https")
    return xr.open_dataset('/data/bathy6min.nc', decode_times=False, use_cftime=True)

@pn.cache(max_items=16,policy='LRU',per_session=True)
def load_zarr(selected_file):
    from datatree import open_datatree
    tree= open_datatree('/data/1H_file.zarr', engine='zarr')
    return tree[selected_file+"/"].ds

def filter_df(sorted_df,selected_file):
    dataframe = sorted_df[sorted_df["file_name"] == selected_file].drop(
                columns=[
                    "file_name",
                    "title",
                    "Conventions",
                    "featureType",
                    "date_update",
                    "ADCP_beam_angle",
                    "ADCP_ship_angle",
                    "middle_bin1_depth",
                    "heading_corr",
                    "pitch_corr",
                    "ampli_corr",
                    "pitch_roll_used",
                    "date_creation",
                    "ADCP_type",
                    "data_type",
                ]
            )
    dataframe2 = sorted_df[sorted_df["file_name"] == selected_file].drop(
                columns=[
                    "file_name",
                    "date_start",
                    "date_end",
                    "ADCP_frequency(kHz)",
                    "bin_length(meter)",
                    "year",
                ]
            )
    return dataframe.transpose(), dataframe2.transpose()

def quiver_depth_filterd(ax,ds_filtered, depth1, depth_range_slider, scale_factor_slider, color="blue"):
    import cartopy.crs as ccrs
    depth_filtered = ds_filtered.where(
        (depth1 > depth_range_slider.value[0])
        & (depth1 <= depth_range_slider.value[1])
    )

    lon = ds_filtered.coords["LONGITUDE"].values
    lat = ds_filtered.coords["LATITUDE"].values

    # Moyenne des vecteurs de courant sur la plage de profondeur sélectionnée
    u_mean = depth_filtered.UCUR.mean(dim="MAXZ", skipna=True)
    v_mean = depth_filtered.VCUR.mean(dim="MAXZ", skipna=True)
    
    return ax.quiver(
        lon,
        lat,
        u_mean * scale_factor_slider.value,
        v_mean * scale_factor_slider.value,
        color=color,
        scale=2,
        width=0.001,
        headwidth=3,
        transform=ccrs.PlateCarree(),
    )

class SADCP_Viewer(param.Parameterized):
    df = load_csv()
    bathy = load_bathymetry()
    file_names = df["file_name"].tolist()
    years = sorted(df["year"].unique())

    year_slider = pn.widgets.IntRangeSlider(
        name="Year Range", start=df["year"].min(), end=df["year"].max()
    )
    file_dropdown = pn.widgets.Select(name="File Selector")
    data_table = pn.widgets.Tabulator(df, name="metadata", height=200, width=300)
    # data_table2 = pn.widgets.Tabulator(df2, name="metadata", height=900, width=400)

    longitude_slider = pn.widgets.RangeSlider(
        name="Longitude Range", start=-180, end=180, step=1
    )
    latitude_slider = pn.widgets.RangeSlider(
        name="Latitude Range", start=-90, end=90, step=1
    )

    depth_range_slider = pn.widgets.IntRangeSlider(
        start=100, end=300, value=(100, 300), step=1, name="Depth Range"
    )
    depth_2_checkbox = pn.widgets.Checkbox(value=False, name="Depth 2 Checkbox")
    depth_3_checkbox = pn.widgets.Checkbox(value=False, name="Depth 3 Checkbox")

    depth2_range_slider = pn.widgets.IntRangeSlider(
        start=100, end=300, value=(100, 300), step=1, name="Depth 2 Range"
    )
    depth3_range_slider = pn.widgets.IntRangeSlider(
        start=100, end=300, value=(100, 300), step=1, name="Depth 3 Range"
    )

    num_vectors_slider = pn.widgets.IntSlider(
        start=40, end=800, step=1, value=100, name="Number of Vectors"
    )
    scale_factor_slider = pn.widgets.FloatSlider(
        start=0.1, end=1, step=0.1, value=0.5, name="Scale Factor"
    )
    bathy_checkbox = pn.widgets.Checkbox(value=False, name="Bathy Checkbox")

    plot = pn.pane.HoloViews()
    plot_map = pn.pane.Matplotlib(width=800, height=600, sizing_mode="fixed")

    data_table = pn.widgets.Tabulator(width=400, height=200)

    metadata_table = pn.widgets.Tabulator(width=600, height=800)
    download_button = pn.widgets.Button(name="Download", button_type="primary")
    # plot = pn.Column()

    def __init__(self, **params):
        super(SADCP_Viewer, self).__init__(**params)
        self.file_dropdown.objects = self.get_file_list()
        self.file_dropdown.value = (
            self.file_dropdown.objects[0] if self.file_dropdown.objects else None
        )
        self.update_name_options()

    @param.depends("year_slider.value", "file_dropdown.value", watch=True)
    def update_name_options(self):
        start_year, end_year = self.year_slider.value
        mask = (self.df["year"] >= start_year) & (self.df["year"] <= end_year)
        sorted_df = self.df[mask].sort_values(by="year")
        files = sorted_df["file_name"].unique().tolist()

        self.file_dropdown.options = files
        if files:
            selected_file = self.file_dropdown.value
            if not selected_file or selected_file not in files:
                selected_file = files[0]
                self.file_dropdown.value = selected_file
            self.data_table.value, self.metadata_table.value  = filter_df(sorted_df,selected_file)

            self.ds=load_zarr(selected_file)

            lon_range = (
                int(self.ds["LONGITUDE"].min().round() - 1),
                int(self.ds["LONGITUDE"].max().round() + 1),
            )
            lat_range = (
                int(self.ds["LATITUDE"].min().round() - 1),
                int(self.ds["LATITUDE"].max().round() + 1),
            )
            self.depth1 = abs(self.ds.coords["PROFZ"])
            deph_range = (int(self.depth1.min()), int(self.depth1.max()))

            self.longitude_slider.start = lon_range[0]
            self.longitude_slider.end = lon_range[1]
            self.longitude_slider.value = lon_range

            self.latitude_slider.start = lat_range[0]
            self.latitude_slider.end = lat_range[1]
            self.latitude_slider.value = lat_range

            self.depth_range_slider.start = deph_range[0]
            self.depth_range_slider.end = deph_range[1]
            self.depth_range_slider.value = deph_range

            self.depth2_range_slider.start = deph_range[0]
            self.depth2_range_slider.end = deph_range[1]
            self.depth2_range_slider.value = deph_range

            self.depth3_range_slider.start = deph_range[0]
            self.depth3_range_slider.end = deph_range[1]
            self.depth3_range_slider.value = deph_range

            # self.update_plots()
            self.ds.close()

    @param.depends(
        "year_slider.value",
        "file_dropdown.value",
        "depth_range_slider.value",
        "depth_2_checkbox.value",
        "depth_3_checkbox.value",
        "depth2_range_slider.value",
        "depth3_range_slider.value",
        "longitude_slider.value",
        "latitude_slider.value",
        "num_vectors_slider.value",
        "scale_factor_slider.value",
        "bathy_checkbox.value",
        watch=False,
    )
    def update_plots(self):
        self.ds_filtered = self.filter_data()
        # vector_plot = self.vectors_plot()
        other_plots = self.hvplot_plots()

        # self.plot_map = pn.pane.Matplotlib(vector_plot, width=800, height=600, sizing_mode="fixed")
        self.plot = pn.Column(
            *(pn.pane.HoloViews(plot, width=400, height=200) for plot in other_plots),
            sizing_mode="stretch_width"
        )
        vector_plot = self.vectors_plot()  # Update vector plot
        self.plot_map.object = vector_plot
        # other_plots = self.plots()  # Update other plots
        # self.plot.objects = [*(pn.pane.HoloViews(p, width=400, height=200) for p in other_plots)]
        # self.plot.object=plot

        return pn.Row(self.plot_map, self.plot, sizing_mode="stretch_both")

    def filter_data(self):
        return self.ds.where(
            (self.ds.LONGITUDE >= self.longitude_slider.start)
            & (self.ds.LONGITUDE <= self.longitude_slider.end)
            & (self.ds.LATITUDE >= self.latitude_slider.start)
            & (self.ds.LATITUDE <= self.latitude_slider.end),
            drop=True,
        )

    def vectors_plot(self):
        import cartopy.crs as ccrs
        import cartopy.feature as cfeature

        self.ds_filtered = self.filter_data()

        # return self.ds_filtered['VSHIP'].hvplot(x='TIME',width=400, height=200) #if 'BATHY' in self.ds_filtered else hvplot.show(hvplot.text(0, 0, "No data available", fontsize=12))

        fig, ax = plt.subplots(
            figsize=(8, 7), subplot_kw={"projection": ccrs.Mercator()}
        )
        coords = ["LATITUDE", "LONGITUDE"]
        corsen = max(1, self.ds_filtered.MAXT.size // self.num_vectors_slider.value)
        self.ds_filtered = (
            self.ds_filtered.reset_coords(coords)
            .coarsen({"MAXT": corsen}, boundary="trim")
            .mean()
            .set_coords(coords)
        )

        # self.ds_filtered =self.ds_filtered.coarsen(MAXT = corsen,  side = "center", boundary = "trim").mean()[["LONGITUDE", "LONGITUDE", "TIME"]].isel(MAXZ=0)

        quiver_depth_filterd(ax,self.ds_filtered, self.depth1, self.depth_range_slider,self.scale_factor_slider,color="blue")

        if self.depth_2_checkbox.value:
            quiver_depth_filterd(ax,self.ds_filtered, self.depth1, self.depth2_range_slider,self.scale_factor_slider,color="green")

        if self.depth_3_checkbox.value:
            quiver_depth_filterd(ax,self.ds_filtered, self.depth1, self.depth3_range_slider,self.scale_factor_slider,color="red")

        ax.add_feature(cfeature.COASTLINE)
        ax.add_feature(cfeature.BORDERS, linestyle=":")
        ax.add_feature(cfeature.LAND, color="lightgray")

        if self.bathy_checkbox.value:
            contour_levels = [-1000]
            ax.contour(
                self.bathy.longitude,
                self.bathy.latitude,
                self.bathy.z,
                levels=contour_levels,
                colors="black",
                transform=ccrs.PlateCarree(),
            )

        ax.set_extent(
            [
                self.longitude_slider.value[0],
                self.longitude_slider.value[1],
                self.latitude_slider.value[0],
                self.latitude_slider.value[1],
            ]
        )
        ax.gridlines(draw_labels=True)
        plt.ylabel("Latitude", fontsize=15, labelpad=35)
        plt.xlabel("Longitude", fontsize=15, labelpad=20)
        plt.close()
        return fig

        # pn.pane.Matplotlib(fig,width=800, height=600, sizing_mode="fixed", name="Plot")

    # @param.depends( 'file_dropdown.value', 'longitude_slider.value', 'latitude_slider.value',  watch=True)
    def hvplot_plots(self):
        import hvplot.xarray
        return [
            self.ds_filtered["BATHY"].max(dim="MAXZ").hvplot(x="TIME", width=400, height=200),
            self.ds_filtered["USHIP"].max(dim="MAXZ").hvplot(x="TIME", width=400, height=200),
            self.ds_filtered["VSHIP"].max(dim="MAXZ").hvplot(x="TIME", width=400, height=200),
            self.ds_filtered["BOTTOM_DEPTH"].max(dim="MAXZ").hvplot(x="TIME", width=400, height=200),
          
        ]

    def get_file_list(self):
        return self.file_names


explorer = SADCP_Viewer()
# Instantiate the SADCP_Viewer class and create a template
tabs = pn.Tabs(
    ("Plots", pn.Column(explorer.update_plots)),
    (
        "Metadata",
        pn.Column(
            explorer.metadata_table, explorer.download_button, height=500, margin=10
        ),
    ),
)

sidebar = [
    """This application, developed in the frame of Euro Go Shop, helps to interactively visualise and download ship ADCP data.""",
    explorer.year_slider,
    explorer.file_dropdown,
    explorer.longitude_slider,
    explorer.latitude_slider,
    explorer.bathy_checkbox,
    explorer.depth_range_slider,
    explorer.depth_2_checkbox,
    explorer.depth_3_checkbox,
    explorer.depth2_range_slider,
    explorer.depth3_range_slider,
    explorer.num_vectors_slider,
    explorer.scale_factor_slider,
    explorer.data_table,
]
template = pn.template.FastListTemplate(
    title="SADCP data Viewer", sidebar=sidebar, main=[tabs]
)
template.servable()