pyadps 0.2.1b0__py3-none-any.whl → 0.3.0__py3-none-any.whl

pyadps/pages/07_Write_File.py

@@ -1,452 +0,0 @@
-import configparser
-import tempfile
-
-import numpy as np
-import pandas as pd
-import plotly.graph_objects as go
-import streamlit as st
-import utils.writenc as wr
-from plotly_resampler import FigureResampler
-
-if "flead" not in st.session_state:
-    st.write(":red[Please Select Data!]")
-    st.stop()
-
-if "fname" not in st.session_state:
-    st.session_state.fname = "No file selected"
-
-if "rawfilename" not in st.session_state:
-    st.session_state.rawfilename = "rawfile.nc"
-
-if "vleadfilename" not in st.session_state:
-    st.session_state.vleadfilename = "vlead.nc"
-
-
-# Check if attributes exist in session state
-if "attributes" not in st.session_state:
-    st.session_state.attributes = {}
-
-if st.session_state.isVelocityMask:
-    st.session_state.final_mask = st.session_state.velocity_mask
-    st.session_state.final_velocity = st.session_state.veltest_velocity
-    if st.session_state.isGridSave:
-        st.session_state.final_echo = st.session_state.echo_regrid
-        st.session_state.final_correlation = st.session_state.correlation_regrid
-        st.session_state.final_pgood = st.session_state.pgood_regrid
-    else:
-        st.session_state.final_echo = st.session_state.echo
-        st.session_state.final_correlation = st.session_state.correlation
-        st.session_state.final_pgood = st.session_state.pgood
-else:
-    if st.session_state.isGridSave:
-        st.session_state.final_mask = st.session_state.mask_regrid
-        st.session_state.final_velocity = st.session_state.velocity_regrid
-        st.session_state.final_echo = st.session_state.echo_regrid
-        st.session_state.final_correlation = st.session_state.correlation_regrid
-        st.session_state.final_pgood = st.session_state.pgood_regrid
-    else:
-        if st.session_state.isProfileMask:
-            st.session_state.final_mask = st.session_state.profile_mask
-        elif st.session_state.isQCMask:
-            st.session_state.final_mask = st.session_state.qc_mask
-        else:
-            st.session_state.final_mask = st.session_state.orig_mask
-        st.session_state.final_velocity = st.session_state.velocity
-        st.session_state.final_echo = st.session_state.echo
-        st.session_state.final_correlation = st.session_state.correlation
-        st.session_state.final_pgood = st.session_state.pgood
-
-
-if "depth" not in st.session_state:
-    st.session_state.isGrid = False
-
-
-@st.cache_data
-def file_write(filename="processed_file.nc"):
-    tempdirname = tempfile.TemporaryDirectory(delete=False)
-    outfilepath = tempdirname.name + "/" + filename
-    return outfilepath
-
-
-# If the data is not regrided based on pressure sensor. Use the mean depth
-if not st.session_state.isGrid:
-    st.write(":red[WARNING!]")
-    st.write(
-        "Data not regrided. Using the mean transducer depth to calculate the depth axis."
-    )
-    mean_depth = np.mean(st.session_state.vlead.vleader["Depth of Transducer"]) / 10
-    mean_depth = np.trunc(mean_depth)
-    st.write(f"Mean depth of the transducer is `{mean_depth}`")
-    cells = st.session_state.flead.field()["Cells"]
-    cell_size = st.session_state.flead.field()["Depth Cell Len"] / 100
-    bin1dist = st.session_state.flead.field()["Bin 1 Dist"] / 100
-    max_depth = mean_depth - bin1dist
-    min_depth = max_depth - cells * cell_size
-    z = np.arange(-1 * max_depth, -1 * min_depth, cell_size)
-    st.session_state.final_depth = z
-else:
-    st.session_state.final_depth = st.session_state.depth
-
-
-# Functions for plotting
-@st.cache_data
-def fillplot_plotly(
-    x, y, data, maskdata, colorscale="balance", title="Data", mask=False
-):
-    fig = FigureResampler(go.Figure())
-    if mask:
-        data1 = np.where(maskdata == 1, np.nan, data)
-    else:
-        data1 = np.where(data == -32768, np.nan, data)
-
-    fig.add_trace(
-        go.Heatmap(
-            z=data1[:, 0:-1],
-            x=x,
-            y=y,
-            colorscale=colorscale,
-            hoverongaps=False,
-        )
-    )
-    fig.update_layout(
-        xaxis=dict(showline=True, mirror=True),
-        yaxis=dict(showline=True, mirror=True),
-        title_text=title,
-    )
-    fig.update_yaxes(autorange="reversed")
-    st.plotly_chart(fig)
-
-
-def call_plot(varname, beam, mask=False):
-    if varname == "Velocity":
-        fillplot_plotly(
-            st.session_state.date,
-            st.session_state.final_depth,
-            st.session_state.final_velocity[beam - 1, :, :],
-            st.session_state.final_mask,
-            title=varname,
-            mask=mask,
-        )
-    elif varname == "Echo":
-        fillplot_plotly(
-            st.session_state.date,
-            st.session_state.final_depth,
-            st.session_state.final_echo[beam - 1, :, :],
-            st.session_state.final_mask,
-            title=varname,
-            mask=mask,
-        )
-    elif varname == "Correlation":
-        fillplot_plotly(
-            st.session_state.date,
-            st.session_state.final_depth,
-            st.session_state.final_correlation[beam - 1, :, :],
-            st.session_state.final_mask,
-            title=varname,
-            mask=mask,
-        )
-    elif varname == "Percent Good":
-        fillplot_plotly(
-            st.session_state.date,
-            st.session_state.final_depth,
-            st.session_state.final_pgood[beam - 1, :, :],
-            st.session_state.final_mask,
-            title=varname,
-            mask=mask,
-        )
-
-
-# Option to View Processed Data
-st.header("View Processed Data", divider="blue")
-var_option = st.selectbox(
-    "Select a data type", ("Velocity", "Echo", "Correlation", "Percent Good")
-)
-beam = st.radio("Select beam", (1, 2, 3, 4), horizontal=True)
-
-mask_radio = st.radio("Apply Mask", ("Yes", "No"), horizontal=True)
-plot_button = st.button("Plot Processed Data")
-if plot_button:
-    if mask_radio == "Yes":
-        call_plot(var_option, beam, mask=True)
-    elif mask_radio == "No":
-        call_plot(var_option, beam, mask=False)
-
-
-# Option to Write Processed Data
-st.header("Write Data", divider="blue")
-
-mask_data_radio = st.radio("Do you want to mask the final data?", ("Yes", "No"))
-
-if mask_data_radio == "Yes":
-    mask = st.session_state.final_mask
-    st.session_state.write_velocity = np.copy(st.session_state.final_velocity)
-    st.session_state.write_velocity[:, mask == 1] = -32768
-else:
-    st.session_state.write_velocity = np.copy(st.session_state.final_velocity)
-
-
-file_type_radio = st.radio("Select output file format:", ("NetCDF", "CSV"))
-
-if file_type_radio == "NetCDF":
-    add_attr_button = st.checkbox("Add attributes to NetCDF file")
-
-    if add_attr_button:
-        st.write("### Modify Attributes")
-
-        # Create two-column layout for attributes
-        col1, col2 = st.columns(2)
-
-        with col1:
-            # Display attributes in the first column
-            for key in [
-                "Cruise_No.",
-                "Ship_Name",
-                "Project_No.",
-                "Water_Depth_m",
-                "Deployment_Depth_m",
-                "Deployment_Date",
-                "Recovery_Date",
-            ]:
-                if key in st.session_state.attributes:
-                    st.session_state.attributes[key] = st.text_input(
-                        key, value=st.session_state.attributes[key]
-                    )
-                else:
-                    st.session_state.attributes[key] = st.text_input(key)
-
-        with col2:
-            # Display attributes in the second column
-            for key in [
-                "Latitude",
-                "Longitude",
-                "Platform_Type",
-                "Participants",
-                "File_created_by",
-                "Contact",
-                "Comments",
-            ]:
-                if key in st.session_state.attributes:
-                    st.session_state.attributes[key] = st.text_input(
-                        key, value=st.session_state.attributes[key]
-                    )
-                else:
-                    st.session_state.attributes[key] = st.text_input(key)
-
-download_button = st.button("Generate Processed files")
-
-if download_button:
-    st.session_state.processed_filename = file_write()
-    st.write(":grey[Processed file created. Click the download button.]")
-    st.write(st.session_state.processed_filename)
-    depth = np.trunc(st.session_state.final_depth)
-
-    if file_type_radio == "NetCDF":
-        if add_attr_button and st.session_state.attributes:
-            # Generate file with attributes
-            wr.finalnc(
-                st.session_state.processed_filename,
-                depth,
-                st.session_state.date,
-                st.session_state.write_velocity,
-                attributes=st.session_state.attributes,  # Pass edited attributes
-            )
-        else:
-            # Generate file without attributes
-            wr.finalnc(
-                st.session_state.processed_filename,
-                depth,
-                st.session_state.date,
-                st.session_state.write_velocity,
-            )
-
-    with open(st.session_state.processed_filename, "rb") as file:
-        st.download_button(
-            label="Download NetCDF File",
-            data=file,
-            file_name="processed_file.nc",
-        )
-
-    if file_type_radio == "CSV":
-        udf = pd.DataFrame(
-            st.session_state.write_velocity[0, :, :].T,
-            index=st.session_state.date,
-            columns=-1 * depth,
-        )
-        vdf = pd.DataFrame(
-            st.session_state.write_velocity[1, :, :].T,
-            index=st.session_state.date,
-            columns=-1 * depth,
-        )
-        wdf = pd.DataFrame(
-            st.session_state.write_velocity[2, :, :].T,
-            index=st.session_state.date,
-            columns=-1 * depth,
-        )
-        ucsv = udf.to_csv().encode("utf-8")
-        vcsv = vdf.to_csv().encode("utf-8")
-        wcsv = wdf.to_csv().encode("utf-8")
-        st.download_button(
-            label="Download Zonal Velocity File",
-            data=ucsv,
-            file_name="zonal_velocity.csv",
-            mime="text/csf",
-        )
-        st.download_button(
-            label="Download Meridional Velocity File",
-            data=vcsv,
-            file_name="meridional_velocity.csv",
-            mime="text/csf",
-        )
-        st.download_button(
-            label="Download Vertical Velocity File",
-            data=vcsv,
-            file_name="vertical_velocity.csv",
-            mime="text/csf",
-        )
-
-
-# Option to Download Config file
-# ------------------------------
-
-# Header for the Config.ini File Generator
-st.header("Config.ini File Generator", divider="blue")
-
-# Radio button to decide whether to generate the config.ini file
-generate_config_radio = st.radio(
-    "Do you want to generate a config.ini file?", ("No", "Yes")
-)
-
-
-if generate_config_radio == "Yes":
-    # Create a config parser object
-    config = configparser.ConfigParser()
-
-    # Main section
-    config["FileSettings"] = {}
-    config["DownloadOptions"] = {}
-    config["QCTest"] = {"qc_test": "False"}
-    config["ProfileTest"] = {"profile_test": "False"}
-    config["VelocityTest"] = {"velocity_test": "False"}
-    config["Optional"] = {"attributes": "False"}
-
-    config["FileSettings"]["input_file_path"] = ""
-    config["FileSettings"]["input_file_name"] = st.session_state.fname
-    config["FileSettings"]["output_file_path"] = ""
-    config["FileSettings"]["output_file_name_raw"] = ""
-    config["FileSettings"]["output_file_name_processed"] = ""
-    config["FileSettings"]["output_format_raw"] = str(file_type_radio).lower()
-    config["FileSettings"]["output_format_processed"] = str(file_type_radio).lower()
-
-    config["DownloadOptions"]["download_raw"] = "True"
-    config["DownloadOptions"]["download_processed"] = "True"
-    config["DownloadOptions"]["apply_mask"] = "True"
-    config["DownloadOptions"]["download_mask"] = "True"
-
-    # QC Test Options
-    if st.session_state.isQCMask:
-        config["QCTest"]["qc_test"] = "True"
-
-        # Add the contents of the current QC Mask thresholds
-        if "newthresh" in st.session_state:
-            for idx, row in st.session_state.newthresh.iterrows():
-                config["QCTest"][row["Threshold"].replace(" ", "_")] = row["Values"]
-
-    # Profile Test Options
-    if st.session_state.isProfileMask:
-        config["ProfileTest"]["profile_test"] = "True"
-
-        if st.session_state.isTrimEnds:
-            config["ProfileTest"]["trim_ends"] = "True"
-            config["ProfileTest"]["trim_ends_start_index"] = str(
-                st.session_state.start_ens
-            )
-            config["ProfileTest"]["trim_ends_end_index"] = str(st.session_state.end_ens)
-        else:
-            config["ProfileTest"]["trim_ends"] = "False"
-
-        if st.session_state.isCutBins:
-            config["ProfileTest"]["cut_bins"] = "True"
-            config["ProfileTest"]["cut_bins_add_cells"] = str(
-                st.session_state.extra_cells
-            )
-        else:
-            config["ProfileTest"]["cut_bins"] = "False"
-
-        if st.session_state.isGrid:
-            config["ProfileTest"]["regrid"] = "True"
-            config["ProfileTest"][
-                "Regrid_Option"
-            ] = st.session_state.end_bin_option
-        else:
-            config["ProfileTest"]["regrid"] = "False"
-
-    # Velocity Test Section
-    if st.session_state.isVelocityMask:
-        config["VelocityTest"]["velocity_test"] = "True"
-
-        if st.session_state.isMagnet:
-            config["VelocityTest"]["magnetic_declination"] = str(True)
-            config["VelocityTest"]["latitude"] = str(st.session_state.lat)
-            config["VelocityTest"]["longitude"] = str(st.session_state.lon)
-            config["VelocityTest"]["depth"] = str(st.session_state.magnetic_dec_depth)
-            config["VelocityTest"]["year"] = str(st.session_state.year)
-        else:
-            config["VelocityTest"]["magnetic_declination"] = str(False)
-
-        if st.session_state.isCutoff:
-            config["VelocityTest"]["cutoff"] = str(True)
-            config["VelocityTest"]["max_zonal_velocity"] = str(st.session_state.maxuvel)
-            config["VelocityTest"]["max_meridional_velocity"] = str(
-                st.session_state.maxvvel
-            )
-            config["VelocityTest"]["max_vertical_velocity"] = str(
-                st.session_state.maxwvel
-            )
-        else:
-            config["VelocityTest"]["cutoff"] = str(False)
-
-        if st.session_state.isDespike:
-            config["VelocityTest"]["despike"] = str(True)
-            config["VelocityTest"]["despike_Kernal_Size"] = str(
-                st.session_state.despike_kernal
-            )
-            config["VelocityTest"]["despike_Cutoff"] = str(
-                st.session_state.despike_cutoff
-            )
-        else:
-            config["VelocityTest"]["Despike"] = str(False)
-
-        if st.session_state.isFlatline:
-            config["VelocityTest"]["flatline"] = str(True)
-            config["VelocityTest"]["flatline_kernal_size"] = str(
-                st.session_state.flatline_kernal
-            )
-            config["VelocityTest"]["flatline_deviation"] = str(
-                st.session_state.flatline_cutoff
-            )
-        else:
-            config["VelocityTest"]["flatline"] = str(False)
-
-    # Optional section (attributes)
-    config["Optional"] = {}
-    for key, value in st.session_state.attributes.items():
-        config["Optional"][key] = str(value)  # Ensure all values are strings
-
-    # Write config.ini to a temporary file
-    config_filepath = "config.ini"
-    with open(config_filepath, "w") as configfile:
-        config.write(configfile)
-
-    # Allow the user to download the generated config.ini file
-    with open(config_filepath, "rb") as file:
-        st.download_button(
-            label="Download config.ini File",
-            data=file,
-            file_name="config.ini",
-        )
-
-    display_config_radio = st.radio(
-        "Do you want to display config.ini file?", ("No", "Yes")
-    )
-    if display_config_radio == "Yes":
-        st.write({section: dict(config[section]) for section in config.sections()})