disdrodb 0.1.5__py3-none-any.whl → 0.2.1__py3-none-any.whl

disdrodb/l0/readers/PARSIVEL/NCAR/VORTEX2_2010_UF.py

@@ -130,8 +130,8 @@ def reader(
         # "23": "station_number",
         "24": "rainfall_amount_absolute_32bit",
         # "25": "error_code",
-        # "30": "rainfall_rate_16_bit_30",
-        # "31": "rainfall_rate_16_bit_1200",
+        # "30": "rainfall_rate_16bit",
+        # "31": "rainfall_rate_12bit",
         "32": "rainfall_accumulated_16bit",
         # "90": "raw_drop_concentration",
         # "91": "raw_drop_average_velocity",
@@ -168,7 +168,7 @@ def reader(
     df = df.drop(columns=columns_to_drop)
 
     # Stations UF4-7 have NAN at the end of the raw drop number
-    df["raw_drop_number"] = df["raw_drop_number"].str.replace("NaN;", "").iloc[0]
+    df["raw_drop_number"] = df["raw_drop_number"].str.replace("NaN;", "")
 
     # Return the dataframe adhering to DISDRODB L0 standards
     return df

disdrodb/l0/readers/PARSIVEL2/BASQUECOUNTRY/EUSKALMET_OTT2.py

@@ -0,0 +1,232 @@
+# -----------------------------------------------------------------------------.
+# Copyright (c) 2021-2023 DISDRODB developers
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------.
+"""DISDRODB reader for EUSKALMET OTT Parsivel 2 raw data."""
+# import os
+# import tempfile
+# from disdrodb.utils.compression import unzip_file_on_terminal
+
+import numpy as np
+import pandas as pd
+
+from disdrodb.l0.l0_reader import is_documented_by, reader_generic_docstring
+from disdrodb.l0.l0a_processing import read_raw_text_file
+from disdrodb.utils.logger import log_error
+
+COLUMN_DICT = {
+    "01": "rainfall_rate_32bit",
+    "02": "rainfall_accumulated_32bit",
+    "03": "weather_code_synop_4680",
+    "04": "weather_code_synop_4677",
+    "05": "weather_code_metar_4678",  # empty
+    "06": "weather_code_nws",  # empty
+    "07": "reflectivity_32bit",
+    "08": "mor_visibility",
+    "09": "sample_interval",
+    "10": "laser_amplitude",
+    "11": "number_particles",
+    "12": "sensor_temperature",
+    # "13": "sensor_serial_number",
+    # "14": "firmware_iop",
+    # "15": "firmware_dsp",
+    "16": "sensor_heating_current",
+    "17": "sensor_battery_voltage",
+    "18": "sensor_status",
+    # "19": "start_time",
+    # "20": "sensor_time",
+    # "21": "sensor_date",
+    # "22": "station_name",
+    # "23": "station_number",
+    "24": "rainfall_amount_absolute_32bit",
+    "25": "error_code",
+    "26": "sensor_temperature_pcb",
+    "27": "sensor_temperature_receiver",
+    "28": "sensor_temperature_trasmitter",
+    "30": "rainfall_rate_16_bit_30",
+    "31": "rainfall_rate_16_bit_1200",
+    "32": "rainfall_accumulated_16bit",
+    "34": "rain_kinetic_energy",
+    "35": "snowfall_rate",
+    "90": "raw_drop_concentration",
+    "91": "raw_drop_average_velocity",
+    "93": "raw_drop_number",
+}
+
+
+def infill_missing_columns(df):
+    """Infill with NaN missing columns."""
+    columns = set(COLUMN_DICT.values())
+    for c in columns:
+        if c not in df.columns:
+            df[c] = "NaN"
+    return df
+
+
+def read_txt_file(file, filename, logger):
+    """Parse a single txt file within the daily zip file."""
+    ##------------------------------------------------------------------------.
+    #### Define column names
+    column_names = ["TO_PARSE"]
+
+    ##------------------------------------------------------------------------.
+    #### Define reader options
+    reader_kwargs = {}
+    # - Define delimiter
+    reader_kwargs["delimiter"] = "\\n"
+    # - Skip first row as columns names
+    # - Define encoding
+    reader_kwargs["encoding"] = "latin"  # "ISO-8859-1"
+    # - Avoid first column to become df index !!!
+    reader_kwargs["index_col"] = False
+    # - Define behaviour when encountering bad lines
+    reader_kwargs["on_bad_lines"] = "skip"
+    # - Define reader engine
+    #   - C engine is faster
+    #   - Python engine is more feature-complete
+    reader_kwargs["engine"] = "python"
+    # - Define on-the-fly decompression of on-disk data
+    #   - Available: gzip, bz2, zip
+    reader_kwargs["compression"] = "infer"
+    # - Strings to recognize as NA/NaN and replace with standard NA flags
+    #   - Already included: '#N/A', '#N/A N/A', '#NA', '-1.#IND', '-1.#QNAN',
+    #                       '-NaN', '-nan', '1.#IND', '1.#QNAN', '<NA>', 'N/A',
+    #                       'NA', 'NULL', 'NaN', 'n/a', 'nan', 'null'
+    reader_kwargs["na_values"] = ["na", "", "error"]
+
+    ##------------------------------------------------------------------------.
+    #### Read the data
+    df = read_raw_text_file(
+        filepath=file,
+        column_names=column_names,
+        reader_kwargs=reader_kwargs,
+        logger=logger,
+    )
+
+    ##--------------------------------\----------------------------------------.
+    #### Adapt the dataframe to adhere to DISDRODB L0 standards
+    # Empty file, raise error
+    if len(df) == 0:
+        raise ValueError(f"{filename} is empty.")
+
+    # Select rows with valid spectrum
+    # df = df[df["TO_PARSE"].str.count(";") == 1191]  # 1112
+
+    # Raise error if corrupted file
+    if len(df) == 4:
+        raise ValueError(f"{filename} is corrupted.")
+
+    # Extract string
+    string = df["TO_PARSE"].iloc[4]
+
+    # Split into lines
+    decoded_text = string.encode().decode("unicode_escape")
+    decoded_text = decoded_text.replace("'", "").replace('"', "")
+    lines = decoded_text.split()
+
+    # Extract time
+    time_str = lines[0].split(",")[1]
+
+    # Split each line at the first colon
+    data = [line.split(":", 1) for line in lines if ":" in line]
+
+    # Create the DataFrame
+    df = pd.DataFrame(data, columns=["ID", "Value"])
+
+    # Drop rows with invalid IDs
+    valid_id_str = np.char.rjust(np.arange(0, 94).astype(str), width=2, fillchar="0")
+    df = df[df["ID"].astype(str).isin(valid_id_str)]
+
+    # Select only rows with values
+    df = df[df["Value"].apply(lambda x: x is not None)]
+
+    # Reshape dataframe
+    df = df.set_index("ID").T
+
+    # Assign column names
+    df = df.rename(COLUMN_DICT, axis=1)
+
+    # Keep only columns defined in the dictionary
+    df = df.filter(items=list(COLUMN_DICT.values()))
+
+    # Infill missing columns
+    df = infill_missing_columns(df)
+
+    # Add time column ad datetime dtype
+    df["time"] = pd.to_datetime(time_str, format="%Y%m%d%H%M%S", errors="coerce")
+
+    # Preprocess the raw spectrum and raw_drop_average_velocity
+    # - Add 0 before every ; if ; not preceded by a digit
+    # - Example: ';;1;;' --> '0;0;1;0;'
+    df["raw_drop_number"] = df["raw_drop_number"].str.replace(r"(?<!\d);", "0;", regex=True)
+    df["raw_drop_average_velocity"] = df["raw_drop_average_velocity"].str.replace(r"(?<!\d);", "0;", regex=True)
+
+    # Return the dataframe adhering to DISDRODB L0 standards
+    return df
+
+
+@is_documented_by(reader_generic_docstring)
+def reader(
+    filepath,
+    logger=None,
+):
+    """Reader."""
+    import zipfile
+
+    # ---------------------------------------------------------------------.
+    #### Iterate over all files (aka timesteps) in the daily zip archive
+    # - Each file contain a single timestep !
+    # list_df = []
+    # with tempfile.TemporaryDirectory() as temp_dir:
+    #     # Extract all files
+    #     unzip_file_on_terminal(filepath, temp_dir)
+
+    #     # Walk through extracted files
+    #     for root, _, files in os.walk(temp_dir):
+    #         for filename in sorted(files):
+    #             if filename.endswith(".txt"):
+    #                 full_path = os.path.join(root, filename)
+    #                 try:
+    #                     df = read_txt_file(file=full_path, filename=filename, logger=logger)
+    #                     if df is not None:
+    #                         list_df.append(df)
+    #                 except Exception as e:
+    #                     msg = f"An error occurred while reading {filename}: {e}"
+    #                     log_error(logger=logger, msg=msg, verbose=True)
+
+    list_df = []
+    with zipfile.ZipFile(filepath, "r") as zip_ref:
+        filenames = sorted(zip_ref.namelist())
+        for filename in filenames:
+            if filename.endswith(".dat"):
+                # Open file
+                with zip_ref.open(filename) as file:
+                    try:
+                        df = read_txt_file(file=file, filename=filename, logger=logger)
+                        if df is not None:
+                            list_df.append(df)
+                    except Exception as e:
+                        msg = f"An error occurred while reading {filename}. The error is: {e}."
+                        log_error(logger=logger, msg=msg, verbose=True)
+
+    # Check the zip file contains at least some non.empty files
+    if len(list_df) == 0:
+        raise ValueError(f"{filepath} contains only empty files!")
+
+    # Concatenate all dataframes into a single one
+    df = pd.concat(list_df)
+
+    # ---------------------------------------------------------------------.
+    return df

disdrodb/l0/readers/PARSIVEL2/DENMARK/EROSION_raw.py

@@ -184,7 +184,7 @@ def read_par_format(filepath, logger):
     # Retrieve raw array
     df_split = df["TO_SPLIT"].str.split(",", expand=True)
     df["raw_drop_concentration"] = df_split.iloc[:, :32].agg(",".join, axis=1)
-    df["raw_drop_average_velocity"] = df_split.iloc[:, 32:].agg(",".join, axis=1)
+    df["raw_drop_average_velocity"] = df_split.iloc[:, 32:64].agg(",".join, axis=1)
     df["raw_drop_number"] = df_split.iloc[:, 64:].agg(",".join, axis=1)
     df["raw_drop_number"] = df["raw_drop_number"].str.replace("-9", "0")
     del df_split

disdrodb/l0/readers/PARSIVEL2/JAPAN/PRECIP.py

@@ -0,0 +1,155 @@
+# -----------------------------------------------------------------------------.
+# Copyright (c) 2021-2023 DISDRODB developers
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------.
+"""DISDRODB reader for Colorado State University PRECIP OTT Parsivel 2 raw data."""
+
+import pandas as pd
+
+from disdrodb.l0.l0_reader import is_documented_by, reader_generic_docstring
+from disdrodb.l0.l0a_processing import read_raw_text_file
+
+
+@is_documented_by(reader_generic_docstring)
+def reader(
+    filepath,
+    logger=None,
+):
+    """Reader."""
+    ##------------------------------------------------------------------------.
+    #### Define column names
+    column_names = ["TO_PARSE"]
+
+    ##------------------------------------------------------------------------.
+    #### Define reader options
+    reader_kwargs = {}
+
+    # - Define delimiter
+    reader_kwargs["delimiter"] = "\\n"
+
+    # - Skip first row as columns names
+    reader_kwargs["header"] = None
+
+    # - Skip header
+    reader_kwargs["skiprows"] = 0
+
+    # - Define encoding
+    reader_kwargs["encoding"] = "ISO-8859-1"
+
+    # - Avoid first column to become df index !!!
+    reader_kwargs["index_col"] = False
+
+    # - Define behaviour when encountering bad lines
+    reader_kwargs["on_bad_lines"] = "skip"
+
+    # - Define reader engine
+    #   - C engine is faster
+    #   - Python engine is more feature-complete
+    reader_kwargs["engine"] = "python"
+
+    # - Define on-the-fly decompression of on-disk data
+    #   - Available: gzip, bz2, zip
+    # reader_kwargs['compression'] = 'xz'
+
+    # - Strings to recognize as NA/NaN and replace with standard NA flags
+    #   - Already included: '#N/A', '#N/A N/A', '#NA', '-1.#IND', '-1.#QNAN',
+    #                       '-NaN', '-nan', '1.#IND', '1.#QNAN', '<NA>', 'N/A',
+    #                       'NA', 'NULL', 'NaN', 'n/a', 'nan', 'null'
+    reader_kwargs["na_values"] = ["na", "error", "-.-", " NA"]
+
+    ##------------------------------------------------------------------------.
+    #### Read the data
+    df = read_raw_text_file(
+        filepath=filepath,
+        column_names=column_names,
+        reader_kwargs=reader_kwargs,
+        logger=logger,
+    )
+
+    ##------------------------------------------------------------------------.
+    #### Adapt the dataframe to adhere to DISDRODB L0 standards
+    # Raise error if empty file
+    if len(df) == 0:
+        raise ValueError(f"{filepath} is empty.")
+
+    # Select only rows with expected number of delimiters
+    df = df[df["TO_PARSE"].str.count(",") == 1041]
+
+    # Raise error if no data left
+    if len(df) == 0:
+        raise ValueError(f"No valid data in {filepath}.")
+
+    # Split into columns
+    df = df["TO_PARSE"].str.split(",", expand=True, n=17)
+
+    # Assign columns names
+    names = [
+        "date",
+        "time",
+        "rainfall_rate_32bit",
+        "rainfall_accumulated_32bit",
+        "weather_code_synop_4680",
+        "weather_code_metar_4678",
+        "weather_code_nws",
+        "reflectivity_32bit",
+        "mor_visibility",
+        "laser_amplitude",
+        "number_particles",
+        "sensor_temperature",
+        "sensor_heating_current",
+        "sensor_battery_voltage",
+        "sensor_status",
+        "rain_kinetic_energy",
+        "snowfall_rate",
+        "raw_drop_number",
+    ]
+    df.columns = names
+
+    # Add datetime time column
+    time_str = df["date"] + "-" + df["time"]
+    df["time"] = pd.to_datetime(time_str, format="%d.%m.%Y-%H:%M:%S", errors="coerce")
+
+    # Derive the raw spectrum
+    # Remove <SPECTRUM> and </SPECTRUM> prefix and suffix from the raw_drop_number field
+    df["raw_drop_number"] = df["raw_drop_number"].astype("string")
+    df["raw_drop_number"] = df["raw_drop_number"].str.replace("<SPECTRUM>", "")
+    df["raw_drop_number"] = df["raw_drop_number"].str.replace("</SPECTRUM>", "")
+
+    # Preprocess the raw spectrum and raw_drop_average_velocity
+    # - Add 0 before every ; if ; not preceded by a digit
+    # - Example: ';;1;;' --> '0;0;1;0;'
+    df["raw_drop_number"] = df["raw_drop_number"].str.replace(r"(?<!\d),", "0,", regex=True)
+
+    # Infill missing timesteps with raw_drop_number = 0 spectrum
+    # - Define the full time range with 30-second frequency
+    full_time_index = pd.date_range(start=df["time"].iloc[0], end=df["time"].iloc[-1], freq="30s")
+
+    # - Reindex the DataFrame to include all 30-second timesteps
+    df = df.set_index("time").reindex(full_time_index)
+
+    # - Fill missing raw_drop_number with 0
+    df["raw_drop_number"] = df["raw_drop_number"].fillna(0)
+
+    # - Restore 'time' as a column
+    df = df.rename_axis("time").reset_index()
+
+    # Drop columns not agreeing with DISDRODB L0 standards
+    columns_to_drop = [
+        "date",
+    ]
+    df = df.drop(columns=columns_to_drop)
+
+    # Return the dataframe adhering to DISDRODB L0 standards
+    return df

disdrodb/l0/readers/PARSIVEL2/MPI/BCO_PARSIVEL2.py

@@ -38,11 +38,14 @@ def reader(
     # - Define delimiter
     reader_kwargs["delimiter"] = "/\n"
 
-    # Skip first row as columns names
+    # - Skip first row as columns names
     reader_kwargs["header"] = None
 
-    # Skip first 2 rows
-    reader_kwargs["skiprows"] = 1
+    # - Skip first 2 rows
+    reader_kwargs["skiprows"] = 0
+
+    # - Define encoding
+    reader_kwargs["encoding"] = "ISO-8859-1"
 
     # - Avoid first column to become df index !!!
     reader_kwargs["index_col"] = False
@@ -76,12 +79,17 @@ def reader(
 
     ##------------------------------------------------------------------------.
     #### Adapt the dataframe to adhere to DISDRODB L0 standards
-    # Remove rows with invalid length
-    # df = df[df["TO_BE_PARSED"].str.len().isin([4664])]
+    # Raise error if empty file
+    if len(df) == 0:
+        raise ValueError(f"{filepath} is empty.")
 
-    # Count number of delimiters to select valid rows
+    # Select only rows with expected number of delimiters
     df = df[df["TO_BE_PARSED"].str.count(";") == 1107]
 
+    # Raise error if no data left
+    if len(df) == 0:
+        raise ValueError(f"No valid data in {filepath}.")
+
     # Split by ; delimiter
     df = df["TO_BE_PARSED"].str.split(";", expand=True, n=19)
 
@@ -132,5 +140,4 @@ def reader(
         "sample_interval",
     ]
     df = df.drop(columns=columns_to_drop)
-
     return df

disdrodb/l0/readers/PARSIVEL2/MPI/BOWTIE.py

@@ -157,12 +157,17 @@ def reader(
 
     ##------------------------------------------------------------------------.
     #### Adapt the dataframe to adhere to DISDRODB L0 standards
-    # Remove rows with invalid length
-    # df = df[df["TO_BE_PARSED"].str.len().isin([4664])]
+    # Raise error if empty file
+    if len(df) == 0:
+        raise ValueError(f"{filepath} is empty.")
 
-    # Count number of delimiters to select valid rows
+    # Select only rows with expected number of delimiters
     df = df[df["TO_BE_PARSED"].str.count(";") == 1107]
 
+    # Raise error if no data left
+    if len(df) == 0:
+        raise ValueError(f"No valid data in {filepath}.")
+
     # Split by ; delimiter
     df = df["TO_BE_PARSED"].str.split(";", expand=True, n=19)
 

disdrodb/l0/readers/PARSIVEL2/NASA/APU.py

@@ -44,13 +44,13 @@ def reader(
     """Reader."""
     ##------------------------------------------------------------------------.
     #### Define column names
-    column_names = ["time", "TO_BE_SPLITTED"]
+    column_names = ["TO_PARSE"]
 
     ##------------------------------------------------------------------------.
     #### Define reader options
     reader_kwargs = {}
     # - Define delimiter
-    reader_kwargs["delimiter"] = ";"
+    reader_kwargs["delimiter"] = "//n"
     # - Skip first row as columns names
     reader_kwargs["header"] = None
     reader_kwargs["skiprows"] = 0
@@ -84,6 +84,20 @@ def reader(
 
     ##------------------------------------------------------------------------.
     #### Adapt the dataframe to adhere to DISDRODB L0 standards
+    # Remove rows with invalid number of separators
+    df = df[df["TO_PARSE"].str.count(";") == 1]
+    if len(df) == 0:
+        raise ValueError(f"No valid data in {filepath}")
+
+    # Retrieve time and telegram field
+    df = df["TO_PARSE"].str.split(";", expand=True)
+    df.columns = ["time", "TO_BE_SPLITTED"]
+
+    # Remove rows with invalid number of separators
+    df = df[df["TO_BE_SPLITTED"].str.count(",") == 1033]
+    if len(df) == 0:
+        raise ValueError(f"No valid data in {filepath}")
+
     # Convert time column to datetime
     df_time = pd.to_datetime(df["time"], format="%Y%m%d%H%M%S", errors="coerce")
 
@@ -91,7 +105,7 @@ def reader(
     df = df["TO_BE_SPLITTED"].str.split(",", n=9, expand=True)
 
     # Assign column names
-    names = [
+    columns_names = [
         "station_name",
         "sensor_status",
         "sensor_temperature",
@@ -103,7 +117,7 @@ def reader(
         "weather_code_synop_4677",
         "raw_drop_number",
     ]
-    df.columns = names
+    df.columns = columns_names
 
     # Add the time column
     df["time"] = df_time
@@ -111,10 +125,19 @@ def reader(
     # Drop columns not agreeing with DISDRODB L0 standards
     df = df.drop(columns=["station_name"])
 
+    # Remove rows with invalid raw drop number
+    # --> Occurs e.g. in UCONN apu28
+    # def mask_invalid_raw_drop_number(df)
+    #     df_split = df["raw_drop_number"].str.split(",", expand=True)
+    #     idx = np.where(np.any(df_split.astype(float) > 998, axis=1))[0]
+    #     df.loc[idx, "raw_drop_number"] = "NaN"
+    #     return df
+    df = df[df["raw_drop_number"].str.len() == 4096]
+
     # Drop rows with invalid values
     # --> Ensure that weather_code_synop_4677 has length 2
     # --> If a previous column is missing it will have 000
-    df = df[df["weather_code_synop_4677"].str.len() == 2]
+    # df = df[df["weather_code_synop_4677"].str.len() == 2]
 
     # Return the dataframe adhering to DISDRODB L0 standards
     return df

disdrodb/l0/readers/PARSIVEL2/NCAR/RELAMPAGO_PARSIVEL2.py

@@ -42,7 +42,7 @@ def reader(
     # - Define encoding
     reader_kwargs["encoding"] = "ISO-8859-1"
 
-    # Skip first row as columns names
+    # - Skip first row as columns names
     reader_kwargs["header"] = None
 
     # - Avoid first column to become df index !!!