pyadps 0.1.0b0__py3-none-any.whl → 0.1.1__py3-none-any.whl

pyadps/pages/06_Velocity_Test.py

@@ -1,293 +0,0 @@
-import numpy as np
-import pandas as pd
-import plotly.express as px
-import plotly.graph_objects as go
-import streamlit as st
-from plotly.subplots import make_subplots
-from plotly_resampler import FigureResampler
-from streamlit.runtime.state import session_state
-from utils.profile_test import side_lobe_beam_angle
-from utils.signal_quality import default_mask
-from utils.velocity_test import (despike, flatline, magnetic_declination,
-                                 velocity_cutoff)
-
-if "flead" not in st.session_state:
-    st.write(":red[Please Select Data!]")
-    st.stop()
-
-flobj = st.session_state.flead
-vlobj = st.session_state.vlead
-fdata = flobj.fleader
-vdata = vlobj.vleader
-
-
-####### Initialize Mask File ##############
-# Is this the best way?
-if st.session_state.isProfileMask or st.session_state.isQCMask:
-    st.write(":grey[Working on a saved mask file ...]")
-    if st.session_state.isVelocityMask:
-        st.write(
-            ":orange[Warning: Velocity test already completed. Reset to change settings.]"
-        )
-        reset_selectbox = st.selectbox(
-            "Choose reset option",
-            ("Profile Test", "QC Test", "Default"),
-            index=None,
-            placeholder="Reset mask to ...",
-        )
-        if reset_selectbox == "Default":
-            st.write("Default mask file selected")
-            st.session_state.maskd = st.session_state.orig_mask
-            st.session_state.dummyvelocity = st.session_state.velocity
-        elif reset_selectbox == "QC Test":
-            st.write("QC Test mask file selected")
-            st.session_state.maskd = st.session_state.qc_mask
-            st.session_state.dummyvelocity = st.session_state.velocity
-        elif reset_selectbox == "Profile Test":
-            st.session_state.maskd = st.session_state.profile_mask
-            if st.session_state.isGridSave:
-                st.session_state.dummyvelocity = st.session_state.velocity_regrid
-            else:
-                st.session_state.dummyvelocity = st.session_state.velocity
-        else:
-            st.session_state.maskd = st.session_state.velocity_mask
-            st.session_state.dummyvelocity = st.session_state.velocity
-    else:
-        if st.session_state.isProfileMask:
-            st.session_state.maskd = st.session_state.profile_mask
-        elif st.session_state.isQCMask:
-            st.session_state.maskd = st.session_state.qc_mask
-        else:
-            st.session_state.maskd = st.session_state.orig_mask
-else:
-    st.write(":grey[Creating a new mask file ...]")
-
-
-if "isCutoff" not in st.session_state:
-    st.session_state.isMagnet = False
-    st.session_state.isCutoff = False
-    st.session_state.isDespike = False
-    st.session_state.isFlatline = False
-
-if "maskd" not in st.session_state:
-    if st.session_state.isProfileMask:
-        st.session_state.maskd = np.copy(st.session_state.profile_mask)
-    elif st.session_state.isQCMask:
-        st.session_state.maskd = np.copy(st.session_state.qc_mask)
-    else:
-        st.session_state.maskd = np.copy(st.session_state.orig_mask)
-
-# If data are not regrided use the default one
-if st.session_state.isGridSave:
-    st.session_state.dummyvelocity = np.copy(st.session_state.velocity_regrid)
-else:
-    st.session_state.dummyvelocity = np.copy(st.session_state.velocity)
-
-velocity = st.session_state.dummyvelocity
-
-ensembles = st.session_state.head.ensembles
-cells = flobj.field()["Cells"]
-x = np.arange(0, ensembles, 1)
-y = np.arange(0, cells, 1)
-
-
-########### Introduction ##########
-st.header("Velocity Test", divider="orange")
-
-st.write(
-    """
-The processing in this page apply only to the velocity data.
-"""
-)
-
-############ Magnetic Declination ##############
-st.header("Magnetic Declination", divider="blue")
-st.write(
-    """
-The magnetic declination is obtained from World Magnetic Model 2020 (WMM2020).
-The python wrapper module `wmm2020` is available from this [Link](https://github.com/space-physics/wmm2020). 
-If the magnetic declination is reset, re-run the remaining tests again.
-"""
-)
-
-if "isMagnetButton" not in st.session_state:
-    st.session_state.isMagnetButton = False
-
-
-def toggle_btns():
-    st.session_state.isMagnetButton = not st.session_state.isMagnetButton
-
-
-with st.form(key="magnet_form"):
-    lat = st.number_input("Latitude", -90.0, 90.0, 0.0, step=1.0)
-    lon = st.number_input("Longitude", 0.0, 360.0, 0.1, step=1.0, format="%.4f")
-    depth = st.number_input("Depth", 0, 1000, 0, step=1)
-    year = st.number_input("Year", 1950, 2100, 2024, 1)
-
-    if st.form_submit_button(
-        "Compute", on_click=toggle_btns, disabled=st.session_state.isMagnetButton
-    ):
-        st.session_state.dummyvelocity, mag = magnetic_declination(
-            velocity, lat, lon, depth, year
-        )
-        st.session_state.lat = lat
-        st.session_state.lon = lon
-        st.session_state.magnetic_dec_depth = depth
-        st.session_state.year = year
-        st.session_state.angle = np.trunc(mag[0][0])
-        st.session_state.isMagnet = True
-
-if st.session_state.isMagnet:
-    st.write(f"Magnetic declination: {st.session_state.angle}\u00b0")
-    st.write(":green[Magnetic declination correction applied to velocities]")
-
-if st.button(
-    "Reset Magnetic Declination",
-    on_click=toggle_btns,
-    disabled=not st.session_state.isMagnetButton,
-):
-    st.session_state.dummyvelocity = np.copy(velocity)
-    st.session_state.isMagnet = False
-
-############# Velocity Cutoffs #################
-st.header("Velocity Cutoffs", divider="blue")
-st.write(
-    """
-Drop velocities whose magnitude is larger than the threshold.
-"""
-)
-with st.form(key="cutbin_form"):
-    maxuvel = st.number_input("Maximum Zonal Velocity Cutoff (cm/s)", 0, 2000, 250, 1)
-    maxvvel = st.number_input(
-        "Maximum Meridional Velocity Cutoff (cm/s)", 0, 2000, 250, 1
-    )
-    maxwvel = st.number_input("Maximum Vertical Velocity Cutoff (cm/s)", 0, 2000, 15, 1)
-    submit_cutoff = st.form_submit_button(label="Submit")
-
-if submit_cutoff:
-
-    st.session_state.maxuvel = maxuvel
-    st.session_state.maxvvel = maxvvel
-    st.session_state.maxwvel = maxwvel
-
-
-    st.session_state.maskd = velocity_cutoff(
-        velocity[0, :, :], st.session_state.maskd, cutoff=maxuvel
-    )
-    st.session_state.maskd = velocity_cutoff(
-        velocity[1, :, :], st.session_state.maskd, cutoff=maxvvel
-    )
-    st.session_state.maskd = velocity_cutoff(
-        velocity[2, :, :], st.session_state.maskd, cutoff=maxwvel
-    )
-    st.session_state.isCutoff = True
-
-
-if st.session_state.isCutoff:
-    st.write("Cutoff Applied")
-    a = {
-        "Max. Zonal Velocity": maxuvel,
-        "Max. Meridional Velocity": maxvvel,
-        "Max. Vertical Velocity": maxwvel,
-    }
-    st.write(a)
-
-
-############## DESPIKE DATA #################
-st.header("Despike Data", divider="blue")
-despike_kernal = st.number_input(
-    "Enter Despike Kernal Size for Median Filter", 0, 1000, 5, 1
-)
-despike_cutoff = st.number_input("Enter Despike Cutoff (mm/s)", 0, 1000, 150, 1)
-despike_button = st.button("Despike")
-if despike_button:
-
-    st.session_state.despike_kernal = despike_kernal
-    st.session_state.despike_cutoff = despike_cutoff
-
-    st.session_state.maskd = despike(
-        velocity[0, :, :],
-        st.session_state.maskd,
-        kernal_size=despike_kernal,
-        cutoff=despike_cutoff,
-    )
-    st.session_state.maskd = despike(
-        velocity[1, :, :],
-        st.session_state.maskd,
-        kernal_size=despike_kernal,
-        cutoff=despike_cutoff,
-    )
-    st.session_state.isDespike = True
-
-if st.session_state.isDespike:
-    st.write("Data Despiked")
-    b = {
-        "Kernal Size": despike_kernal,
-        "Despike Cutoff": despike_cutoff,
-    }
-    st.write(b)
-
-st.header("Remove Flatline", divider="blue")
-flatline_kernal = st.number_input("Enter Flatline Kernal Size", 0, 100, 13, 1)
-flatline_cutoff = st.number_input("Enter Flatline deviation", 0, 100, 1, 1)
-
-flatline_button = st.button("Remove Flatline")
-
-if flatline_button:
-    st.session_state.flatline_kernal = flatline_kernal
-    st.session_state.flatline_cutoff = flatline_cutoff
-
-    st.session_state.maskd = flatline(
-        velocity[0, :, :],
-        st.session_state.maskd,
-        kernal_size=flatline_kernal,
-        cutoff=flatline_cutoff,
-    )
-    st.session_state.maskd = flatline(
-        velocity[1, :, :],
-        st.session_state.maskd,
-        kernal_size=flatline_kernal,
-        cutoff=flatline_cutoff,
-    )
-    st.session_state.maskd = flatline(
-        velocity[2, :, :],
-        st.session_state.maskd,
-        kernal_size=flatline_kernal,
-        cutoff=flatline_cutoff,
-    )
-    st.session_state.isFlatline = True
-
-if st.session_state.isFlatline:
-    st.write(":green[Flatline Removed]")
-    b = {
-        "Kernal Size": flatline_kernal,
-        "Flatline Cutoff": flatline_cutoff,
-    }
-    st.write(b)
-
-
-##################### SAVE DATA ###################
-st.header("Save & Reset Data", divider="blue")
-
-
-def reset_data():
-    st.session_state.dummyvelocity = np.copy(st.session_state.velocity_regrid)
-    st.session_state.isMagnet = False
-    st.session_state.isCutoff = False
-    st.session_state.isDespike = False
-    st.session_state.isFlatline = False
-
-
-col1, col2 = st.columns([1, 1])
-with col1:
-    save_button = st.button(label="Save Data")
-    if save_button:
-        st.session_state.veltest_velocity = np.copy(st.session_state.dummyvelocity)
-        st.session_state.velocity_mask = np.copy(st.session_state.maskd)
-        st.session_state.isVelocityMask = True
-        st.write(":green[Mask data saved]")
-    else:
-        st.write(":red[Data not saved]")
-
-with col2:
-    st.button(label="Reset Data", on_click=reset_data)

pyadps/pages/07_Write_File.py

@@ -1,367 +0,0 @@
-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
-import configparser
-
-
-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
-
-
-@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,
-    )
-    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,
-        )
-
-
-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)
-
-
-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",
-        )
-        
-        
-# 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["Main"] = {
-        "Input_FileName": st.session_state.fname
-    }
-
-    if st.session_state.isQCMask:
-        config["QC Test"] = {}
-
-        # 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["QC Test"][row["Threshold"].replace(" ", "_")] = row["Values"]
-
-
-    # Profile Test section
-    if st.session_state.isProfileMask:
-        config["Profile Test"] = {}
-
-        if st.session_state.update_mask:
-
-            config["Profile Test"]["Change_Range"] = str(st.session_state.ens_range)
-            config["Profile Test"]["Deployment_ensembles"] = str(st.session_state.start_ens)
-            config["Profile Test"]["Recovery_ensembles"] = str(st.session_state.end_ens)
-
-        if st.session_state.update_mask_cutbin:
-            config["Profile Test"]["Beam"] = str(st.session_state.beam + 1)  # Adding 1 since beams are 1-based
-            config["Profile Test"]["cell_to_delete"] = str(st.session_state.extra_cells)
-
-        if st.session_state.isGrid:
-            config["Profile Test"]["Regrid_Depth_cells"] = st.session_state.last_cell  # Bin or Surface
-
-
-    # Velocity Test Section
-    if st.session_state.isVelocityMask:
-        config["Velocity Test"] = {}
-
-        if st.session_state.isMagnet:
-            config["Velocity Test"]["Latitude"] = str(st.session_state.lat)
-            config["Velocity Test"]["Longitude"] = str(st.session_state.lon)
-            config["Velocity Test"]["Depth"] = str(st.session_state.magnetic_dec_depth)
-            config["Velocity Test"]["Year"] = str(st.session_state.year)
-
-        if st.session_state.isCutoff:
-            config["Velocity Test"]["Max_Zoank"] = str(st.session_state.maxuvel)
-            config["Velocity Test"]["Max_Meridional"] = str(st.session_state.maxvvel)
-            config["Velocity Test"]["Max_Vertical"] = str(st.session_state.maxwvel)
-
-        if st.session_state.isDespike:
-            config["Velocity Test"]["Despike_Kernal_Size"] = str(st.session_state.despike_kernal)
-            config["Velocity Test"]["Despike_Cutoff"] = str(st.session_state.despike_cutoff)
-
-        if st.session_state.isFlatline:
-            config["Velocity Test"]["Flatline_Kernal"] = str(st.session_state.flatline_kernal)
-            config["Velocity Test"]["Flatline_Deviation"] = str(st.session_state.flatline_cutoff)
-
-
-    # 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",
-        )