pyadps 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

pyadps/pages/01_Read_File.py

@@ -20,10 +20,10 @@ 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"
+    st.session_state.rawfilename = "RAW_DAT.nc"
 
 if "vleadfilename" not in st.session_state:
-    st.session_state.vleadfilename = "vlead.nc"
+    st.session_state.vleadfilename = "RAW_VAR.nc"
 
 
 ################ Functions #######################
@@ -132,6 +132,7 @@ if uploaded_file is not None:
     st.session_state.salinity = (
         ds.variableleader.salinity.data * ds.variableleader.salinity.scale
     )
+    st.session_state.filename = (ds.filename)
 
     # st.session_state.flead = flead
     # st.session_state.vlead = vlead

pyadps/pages/03_Download_Raw_File.py

@@ -18,13 +18,13 @@ 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"
+    st.session_state.rawfilename = "RAW_DAT.nc"
 
 if "fleadfilename" not in st.session_state:
-    st.session_state.fleadfilename = "flead.nc"
+    st.session_state.fleadfilename = "RAW_FIX.nc"
 
 if "vleadfilename" not in st.session_state:
-    st.session_state.vleadfilename = "vlead.nc"
+    st.session_state.vleadfilename = "RAW_VAR.nc"
 
 if "attributes" not in st.session_state:
     st.session_state.attributes = {}
@@ -32,6 +32,19 @@ if "attributes" not in st.session_state:
 if "add_attributes_DRW" not in st.session_state:
     st.session_state.add_attributes_DRW = "No"  # Default value
 
+if "file_prefix" not in st.session_state:
+    raw_basename = os.path.basename(st.session_state.fname)
+    st.session_state.filename = os.path.splitext(raw_basename)[0] 
+    st.session_state.file_prefix = st.session_state.filename
+
+
+if "prefix_saved" not in st.session_state:
+    st.session_state.prefix_saved = False
+
+if "filename" not in st.session_state:
+    st.session_state.filename = ""  # <-- Default file name if not passed
+
+
 
 ################ Functions #######################
 @st.cache_data()
@@ -50,11 +63,18 @@ def read_file(filepath):
         ds.fixensemble()
     st.session_state.ds = ds
 
+@st.cache_data
+def get_prefixed_filename(base_name):
+    """Generates the file name with the optional prefix."""
+    if st.session_state.file_prefix:
+        return f"{st.session_state.file_prefix}_{base_name}"
+    return base_name
+
 
 @st.cache_data
 def file_write(path, axis_option, add_attributes=True):
     tempdirname = tempfile.TemporaryDirectory(delete=False)
-    st.session_state.rawfilename = tempdirname.name + "/rawfile.nc"
+    st.session_state.rawfilename = os.path.join(tempdirname.name, get_prefixed_filename("RAW_DAT.nc"))
 
     if add_attributes:
         wr.rawnc(
@@ -72,7 +92,7 @@ def file_write(path, axis_option, add_attributes=True):
 @st.cache_data
 def file_write_flead(path, axis_option, add_attributes=True):
     tempvardirname = tempfile.TemporaryDirectory(delete=False)
-    st.session_state.fleadfilename = tempvardirname.name + "/flead.nc"
+    st.session_state.fleadfilename = os.path.join(tempvardirname.name, get_prefixed_filename("RAW_FIX.nc"))
 
     if add_attributes:
         wr.flead_nc(
@@ -90,7 +110,7 @@ def file_write_flead(path, axis_option, add_attributes=True):
 @st.cache_data
 def file_write_vlead(path, axis_option, add_attributes=True):
     tempvardirname = tempfile.TemporaryDirectory(delete=False)
-    st.session_state.vleadfilename = tempvardirname.name + "/vlead.nc"
+    st.session_state.vleadfilename = os.path.join(tempvardirname.name, get_prefixed_filename("RAW_VAR.nc"))
 
     if add_attributes:
         wr.vlead_nc(
@@ -106,6 +126,7 @@ def file_write_vlead(path, axis_option, add_attributes=True):
         )
 
 
+
 if "axis_option" not in st.session_state:
     st.session_state.axis_option = "ensemble"  # Default value
 
@@ -149,6 +170,32 @@ if st.session_state.add_attributes_DRW == "Yes":
 
     st.write("Attributes will be added to the NetCDF file once you submit.")
 
+
+st.info(f"Current file name: **{st.session_state.filename}**")
+
+# Prefix editing option
+st.session_state.use_custom_filename = st.radio(
+    "Do you want to edit Output Filename?",
+    ["No", "Yes"],
+    horizontal=True,
+)
+
+if st.session_state.use_custom_filename == "Yes" and not st.session_state.prefix_saved:
+    st.session_state.file_prefix = st.text_input(
+        "Enter file name (e.g., GD10A000)",
+        value=st.session_state.file_prefix,
+    )
+
+    if st.button("Save Filename"):
+        if st.session_state.file_prefix.strip():
+            st.session_state.prefix_saved = True
+            st.rerun()
+        else:
+            st.warning("Please enter a valid filename before saving.")
+
+if st.session_state.prefix_saved:
+    st.success(f"Filename saved as: **{st.session_state.file_prefix}**")
+
 # Dropdown for axis_option
 st.session_state.axis_option_DRW = st.selectbox(
     "Select x-axis option:",
@@ -179,7 +226,7 @@ if st.session_state.rawnc_download_DRW:
         st.download_button(
             label="Download Raw File",
             data=file,
-            file_name="rawfile.nc",
+            file_name=get_prefixed_filename("RAW_DAT.nc"),
         )
 
 if st.session_state.fleadnc_download_DRW:
@@ -193,7 +240,7 @@ if st.session_state.fleadnc_download_DRW:
         st.download_button(
             label="Download Fixed Leader",
             data=file,
-            file_name="flead.nc",
+            file_name=get_prefixed_filename("RAW_FIX.nc"),
         )
 
 if st.session_state.vleadnc_download_DRW:
@@ -207,7 +254,7 @@ if st.session_state.vleadnc_download_DRW:
         st.download_button(
             label="Download Variable Leader",
             data=file,
-            file_name="vlead.nc",
+            file_name=get_prefixed_filename("RAW_VAR.nc"),
         )
 
 

pyadps/pages/06_Profile_Test.py

@@ -797,8 +797,8 @@ with tab4:
                 orientation=st.session_state.beam_direction_QCT,
                 method=st.session_state.interpolate_PT,
                 boundary_limit=boundary,
-                cells=cells,
-                cell_size=cell_size,
+                cells=fdata['Cells'],
+                cell_size=fdata['Depth Cell Len'],
                 bin1dist=bin1dist,
                 beams=beams,
             )
@@ -813,8 +813,8 @@ with tab4:
                 orientation=st.session_state.beam_direction_QCT,
                 method=st.session_state.interpolate_PT,
                 boundary_limit=boundary,
-                cells=cells,
-                cell_size=cell_size,
+                cells=fdata['Cells'],
+                cell_size=fdata['Depth Cell Len'],
                 bin1dist=bin1dist,
                 beams=beams,
             )
@@ -829,8 +829,8 @@ with tab4:
                 orientation=st.session_state.beam_direction_QCT,
                 method=st.session_state.interpolate_PT,
                 boundary_limit=boundary,
-                cells=cells,
-                cell_size=cell_size,
+                cells=fdata['Cells'],
+                cell_size=fdata['Depth Cell Len'],
                 bin1dist=bin1dist,
                 beams=beams,
             )
@@ -845,8 +845,8 @@ with tab4:
                 orientation=st.session_state.beam_direction_QCT,
                 method=st.session_state.interpolate_PT,
                 boundary_limit=boundary,
-                cells=cells,
-                cell_size=cell_size,
+                cells=fdata['Cells'],
+                cell_size=fdata['Depth Cell Len'],
                 bin1dist=bin1dist,
                 beams=beams,
             )
@@ -862,8 +862,8 @@ with tab4:
                 orientation=st.session_state.beam_direction_QCT,
                 method="nearest",
                 boundary_limit=boundary,
-                cells=cells,
-                cell_size=cell_size,
+                cells=fdata['Cells'],
+                cell_size=fdata['Depth Cell Len'],
                 bin1dist=bin1dist,
             )
 

pyadps/pages/08_Write_File.py

@@ -16,10 +16,23 @@ 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"
+    st.session_state.rawfilename = "RAW_DAT.nc"
 
 if "vleadfilename" not in st.session_state:
-    st.session_state.vleadfilename = "vlead.nc"
+    st.session_state.vleadfilename = "RAW_VAR.nc"
+
+if "file_prefix" not in st.session_state:
+    raw_basename = os.path.basename(st.session_state.fname)
+    st.session_state.filename = os.path.splitext(raw_basename)[0] 
+    st.session_state.file_prefix = st.session_state.filename
+
+
+if "prefix_saved" not in st.session_state:
+    st.session_state.prefix_saved = False
+
+if "filename" not in st.session_state:
+    st.session_state.filename = ""  # <-- Default file name if not passed
+
 
 
 # Check if attributes exist in session state
@@ -72,9 +85,15 @@ else:
 if "depth_axis" not in st.session_state:
     st.session_state.isRegridCheck_PT = False
 
+@st.cache_data
+def get_prefixed_filename(base_name):
+    """Generates the file name with the optional prefix."""
+    if st.session_state.file_prefix:
+        return f"{st.session_state.file_prefix}_{base_name}"
+    return base_name
 
 @st.cache_data
-def file_write(filename="processed_file.nc"):
+def file_write(filename=get_prefixed_filename("PRO_DAT.nc")):
     tempdirname = tempfile.TemporaryDirectory(delete=False)
     outfilepath = tempdirname.name + "/" + filename
     return outfilepath
@@ -297,7 +316,7 @@ if download_button:
             st.download_button(
                 label="Download NetCDF File",
                 data=file,
-                file_name="processed_file.nc",
+                file_name=get_prefixed_filename("PRO_DAT.nc"),
             )
 
     if st.session_state.file_type_WF == "CSV":

pyadps/utils/profile_test.py

@@ -1,6 +1,6 @@
 import numpy as np
 import scipy as sp
-from pyadps.utils.readrdi import ReadFile
+from pyadps.utils.readrdi import ReadFile, check_equal
 from .plotgen import PlotEnds
 
 
@@ -214,6 +214,217 @@ def manual_cut_bins(mask, min_cell, max_cell, min_ensemble, max_ensemble):
     return mask
 
 
+def modifiedRegrid2d(
+    ds,
+    data,
+    fill_value,
+    end_cell_option="cell",
+    trimends=None,
+    method="nearest",
+    orientation="default",
+    boundary_limit=0,
+    cells=None,
+    cell_size=None,
+    bin1dist=None,
+):
+    """
+    Modified Regrids 2D data onto a new grid based on specified parameters.
+    The function is capable of handling data with non-uniform number of cells
+    and Depth cell length.
+
+    Parameters:
+    -----------
+    ds : pyadps.dataset or numpy.ndarray
+        If pyadps dataframe is loaded, the data from the fixed and variable leader
+        is automatically obtained. This includes the depth of the transducer and other relevant information
+        for trimming the data.
+
+        If numpy.ndarray is loaded, the value should contain the transducer_depth.
+        In such cases provide cells, cell_size, and bin 1 distance.
+        Orientiation should be either 'up' or 'down' and not 'default'.
+
+
+    data : array-like
+        The 2D data array to be regridded.
+
+    fill_value : scalar
+        The value used to fill missing or undefined grid points.
+
+    end_cell_option : str or float, optional, default="cell"
+        The depth of the last bin or boundary for the grid.
+        Options include:
+        - "cell" : Calculates the depth of the default last bin for the grid.
+                   Truncates to surface for upward ADCP.
+        - "surface": The data is gridded till the surface
+        - "manual": User-defined depth for the grid.
+                      Use boundary_limit option to provide the value.
+        otherwise, a specific numerical depth value can be provided.
+
+    trimends : tuple of floats, optional, default=None
+        If provided, defines the ensemble range (start, end) for
+        calculating the maximum/minimum transducer depth.
+        Helps avoiding the deployment or retrieval data.
+        E.g. (10, 3000)
+
+    method : str, optional, default="nearest"
+        The interpolation method to use for regridding based
+        on scipy.interpolate.interp1d.
+        Options include:
+        - "nearest" : Nearest neighbor interpolation.
+        - "linear" : Linear interpolation.
+        - "cubic" : Cubic interpolation.
+
+    orientation : str, optional, default="up"
+        Defines the direction of the regridding for an upward/downward looking ADCP. Options include:
+        - "up" : Regrid upwards (for upward-looking ADCP).
+        - "down" : Regrid downwards (for downward-looking ADCP).
+
+    boundary_limit : float, optional, default=0
+        The limit for the boundary depth. This restricts the grid regridding to depths beyond the specified limit.
+
+    cells: int, optional
+        Number of cells
+
+    cell_size: int, optional
+        Cell size or depth cell length in cm
+
+    bin1dist: int, optional
+        Distance from the first bin in cm
+
+
+    Returns:
+    --------
+    z: regridded depth
+    regridded_data : array-like
+        The regridded 2D data array, based on the specified method,
+        orientation, and other parameters.
+
+    Notes:
+    ------
+    - If `end_cell_option == boundary`, then `boundary_limit` is used to regrid the data.
+    - This function allows for flexible regridding of 2D data to fit a new grid, supporting different interpolation methods.
+    - The `boundary_limit` parameter helps restrict regridding to depths above or below a certain threshold.
+    """
+
+    if isinstance(ds, ReadFile) or ds.__class__.__name__ == "ReadFile":
+        flobj = ds.fixedleader
+        vlobj = ds.variableleader
+        # Get values and convert to 'm'
+        bin1dist = flobj.field()["Bin 1 Dist"] / 100
+        transdepth = vlobj.vleader["Depth of Transducer"] / 10
+        cell_size = flobj.field()["Depth Cell Len"] / 100
+        cells = flobj.field()["Cells"]
+        ensembles = flobj.ensembles
+        if orientation.lower() == "default":
+            orientation = flobj.system_configuration()["Beam Direction"]
+
+    elif isinstance(ds, np.ndarray) and np.squeeze(ds).ndim == 1:
+        transdepth = ds / 10
+        ensembles = np.size(ds)
+
+        if cells is None:
+            raise ValueError("Input must include number of cells.")
+
+        if cell_size is None:
+            raise ValueError("Input must include cell size.")
+        else:
+            cell_size = cell_size / 100
+
+        if bin1dist is None:
+            raise ValueError("Input must include bin 1 distance.")
+        else:
+            bin1dist = bin1dist / 100
+
+        if orientation.lower() != "up" and orientation.lower() != "down":
+            raise ValueError("Orientation must be `up` or `down`.")
+    else:
+        raise ValueError("Input must be a 1-D numpy array or a PyADPS instance")
+
+    if orientation.lower() == "up":
+        sgn = -1
+    else:
+        sgn = 1
+
+    # Create a regular grid
+
+    # Find depth of first cell
+    depth = transdepth + sgn * bin1dist
+    # print("depth: ", depth)
+
+    # Find the maximum and minimum depth for first cell for upward
+    # looking ADCP (minimum and maximum for downward looking)
+    if trimends is not None:
+        max_depth = abs(np.min(sgn * depth[trimends[0] : trimends[1]]))
+        min_depth = abs(np.max(sgn * depth[trimends[0] : trimends[1]]))
+    else:
+        max_depth = abs(np.min(sgn * depth))
+        min_depth = abs(np.max(sgn * depth))
+
+    # FIRST CELL
+    # Convert the first cell depth to the first regular grid depth
+    depthfirstcell = max_depth - max_depth % min(cell_size)
+    # print("depthfirstcell: ", depthfirstcell)
+
+    # LAST CELL
+    # Convert the last cell depth to last regular grid depth
+    if end_cell_option.lower() == "surface":
+        # Added one additional negative cell to accomodate 0 m.
+        depthlastcell = sgn * min(cell_size)
+        # print("depthlastcell: ", depthlastcell)
+    elif end_cell_option.lower() == "cell":
+        min_depth_regrid = min_depth - sgn * min_depth % min(cell_size)
+        depthlastcell = min_depth_regrid + sgn * (max(cells) + 1) * min(cell_size)
+        # print("depthlastcell: ", depthlastcell)
+        # Check if this is required. Use 'surface' option
+        if depthlastcell < 0:
+            depthlastcell = sgn * min(cell_size)
+    elif end_cell_option.lower() == "manual":
+        if sgn < 0 and boundary_limit > depthfirstcell:
+            print(
+                "ERROR: For upward looking ADCP, boundary limit should be less than transducer depth"
+            )
+            return
+        if sgn > 0 and boundary_limit < depthfirstcell:
+            print(
+                "ERROR: For downward looking ADCP, boundary limit should be greater than transducer depth"
+            )
+            return
+        # Set the last grid cell depth
+        depthlastcell = boundary_limit
+    else:
+        print("ERROR: `end_cell_option` not recognized.")
+        return
+
+    # Negative used for upward and positive for downward.
+    z = np.arange(sgn * depthfirstcell, sgn * depthlastcell, min(cell_size))
+    regbins = len(z)
+
+    regridded_data = np.zeros((regbins, ensembles))
+
+    # Create original depth array
+    for i, d in enumerate(depth):
+        n = d + sgn * cell_size[i] * cells[i]
+        # np.arange may include unexpected elements due to floating-point
+        # precision issues at the stopping point. Changed to np.linspace.
+        #
+        # depth_bins = np.arange(sgn*d, sgn*n, cell_size)
+        depth_bins = np.linspace(sgn * d, sgn * n, max(cells))
+        # print("depth_bins: ", depth_bins, "len: ", len(depth_bins))
+        # print("data:", data, "len:", len(data))
+        # print("i: ", i)
+        f = sp.interpolate.interp1d(
+            depth_bins,
+            data[:, i],
+            kind=method,
+            fill_value=fill_value,
+            bounds_error=False,
+        )
+        gridz = f(z)
+
+        regridded_data[:, i] = gridz
+
+    return abs(z), regridded_data
+
 def regrid2d(
     ds,
     data,
@@ -305,6 +516,11 @@ def regrid2d(
     """
 
     if isinstance(ds, ReadFile) or ds.__class__.__name__ == "ReadFile":
+        if not (check_equal(ds.fleader['Cells']) or check_equal(ds.fleader['Depth Cell Len'])):
+            print("\033[93m Warning: The number of cells or depth cell length are not equal. Using the modifiedRegrid2d function, which may take some time.\033[0m")
+            return modifiedRegrid2d(ds, data, fill_value, end_cell_option, trimends, method, orientation,
+            boundary_limit, cells, cell_size, bin1dist)
+
         flobj = ds.fixedleader
         vlobj = ds.variableleader
         # Get values and convert to 'm'
@@ -322,11 +538,21 @@ def regrid2d(
 
         if cells is None:
             raise ValueError("Input must include number of cells.")
+        else:
+            if not check_equal(cells):
+                print("\033[93m Warning: The number of cells or depth cell length are not equal. Using the modifiedRegrid2d function, which may take some time.\033[0m")
+                return modifiedRegrid2d(ds, data, fill_value, end_cell_option, trimends, method, orientation,
+                boundary_limit, cells, cell_size, bin1dist)
+            cells = cells[0]
 
         if cell_size is None:
             raise ValueError("Input must include cell size.")
         else:
-            cell_size = cell_size / 100
+            if not check_equal(cell_size):
+                # print("\033[93m Warning: The number of cells or depth cell length are not equal. Using the modifiedRegrid2d function, which may take some time.\033[0m")
+                return modifiedRegrid2d(ds, data, fill_value, end_cell_option, trimends, method, orientation,
+                boundary_limit, cells, cell_size, bin1dist)
+            cell_size = cell_size[0] / 100
 
         if bin1dist is None:
             raise ValueError("Input must include bin 1 distance.")

{pyadps-0.1.1.dist-info → pyadps-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pyadps
-Version: 0.1.1
+Version: 0.1.2
 Summary: A Python package for ADCP data processing
 Home-page: https://pyadps.readthedocs.io/en/latest/index.html
 License: MIT

pyadps-0.1.2.dist-info/RECORD

@@ -0,0 +1,33 @@
+pyadps/Home_Page.py,sha256=j_-3fsp1hkhpNEl5jE-CEQvClDGpMi1H3ZQPXfuKWBg,1782
+pyadps/__init__.py,sha256=bNCm6_WIhiwvaUeOZhRkyLZyzzUKfSH80Fslg0JPJyk,232
+pyadps/__main__.py,sha256=cIFUayxPnKl00oIR99L6IUEvc8trW7dijtfBQCAen5c,356
+pyadps/pages/01_Read_File.py,sha256=swujYGZvQX30zcccWhn5MiFVY_MBUYXuZ9_8GtvpQI4,14421
+pyadps/pages/02_View_Raw_Data.py,sha256=AhT7gvDbcMRPf-WIBzTQ0o-nn9_q7NH6plTlpMtgzaY,6170
+pyadps/pages/03_Download_Raw_File.py,sha256=XF25xog8bkdsm3s1MFA10ZxbvqgDmvxBDOo6OPBHQwQ,12382
+pyadps/pages/04_Sensor_Health.py,sha256=2Qnwl7D46H-f8LmXLVZj5X36h8MjRwmVRK6Bs_wuB_k,33905
+pyadps/pages/05_QC_Test.py,sha256=8wt7h-RHLOf3GZ8-B_kXA0IqzHTBwW_H7YQFEk5EM6E,15904
+pyadps/pages/06_Profile_Test.py,sha256=Vir91oRIWApbO2elBm4I59rdf83NtspUmtzAyWdsIiY,34891
+pyadps/pages/07_Velocity_Test.py,sha256=K4vEiLPMXrU4JMLj-mIA1G4H5ORozMbHMiMov3ZZXP0,23008
+pyadps/pages/08_Write_File.py,sha256=SUHGvOTN2hnwhxGucmTtclU6BhaJKWO2qGV4zS-JsPU,22954
+pyadps/pages/09_Auto_process.py,sha256=SRtQVD9_kodlSvYdF9-02ur6EaWG2zMvN6-BcWdzYV8,1874
+pyadps/pages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyadps/utils/__init__.py,sha256=nCqRp-OT_1BC7RnL3ARUIldlw9sWyr1XqQvQid-B4ts,407
+pyadps/utils/autoprocess.py,sha256=8KAg5-7uC7dsMHrCPfvM5icPzle3MU1gpFNcC-eZrkM,20086
+pyadps/utils/metadata/config.ini,sha256=TC7htzGwUukIXt_u3JR5ycyvOoDj_JxWgGY6khjNeck,2154
+pyadps/utils/metadata/demo.000,sha256=qxB3sgjABrpv4DNXkwjpbSxk5sc4UwAI8kgQX0--PM8,234468
+pyadps/utils/metadata/flmeta.json,sha256=diIB9nht_0uw9YJNSFGdZYGzeVbR-07zIZS9Nf4VPSE,14245
+pyadps/utils/metadata/vlmeta.json,sha256=_dkQlGkkUvpAIM7S6kEUenSaiCpOrwXg8n1aU3dDF3s,22535
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