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

pyadps/pages/07_Write_File.py

@@ -0,0 +1,367 @@
+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",
+        )

pyadps/utils/__init__.py

@@ -1,12 +1,12 @@
 # pyadps/utils/__init__.py
 
+from pyadps.utils.cutbin import *
 from pyadps.utils.plotgen import *
 from pyadps.utils.profile_test import *
 from pyadps.utils.pyreadrdi import *
 from pyadps.utils.readrdi import *
-from pyadps.utils.sensor_health import *
+from pyadps.utils.regrid import *
 from pyadps.utils.signal_quality import *
 from pyadps.utils.velocity_test import *
 from pyadps.utils.writenc import *
-from pyadps.utils.autoprocess import *
-from pyadps.utils.script import *
+