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

disdrodb/l0/l0b_processing.py

@@ -91,7 +91,7 @@ def format_string_array(string: str, n_values: int) -> np.array:
 
         e.g. : format_string_array("2,44,22,33", 4) will return [ 2. 44. 22. 33.]
 
-    If empty string ("") --> Return an arrays of zeros
+    If empty string ("") or "" --> Return an arrays of zeros
     If the list length is not n_values -> Return an arrays of np.nan
 
     The function strip potential delimiters at start and end before splitting.
@@ -108,31 +108,38 @@ def format_string_array(string: str, n_values: int) -> np.array:
     np.array
         array of float
     """
-    split_str = infer_split_str(string)
-    values = np.array(string.strip(split_str).split(split_str))
-
-    # -------------------------------------------------------------------------.
-    ## Assumptions !!!
-    # If empty list --> Assume no precipitation recorded. Return an arrays of zeros
-    if len(values) == 0:
+    # Check for empty string or "0" case
+    # - Assume no precipitation recorded. Return an arrays of zeros
+    if string in {"", "0"}:
         values = np.zeros(n_values)
         return values
 
-    # -------------------------------------------------------------------------.
+    # Check for NaN case
+    # - Assume no data available. Return an arrays of NaN
+    if string == "NaN":
+        values = np.zeros(n_values) * np.nan
+        return values
+
+    # Retrieve list of values
+    split_str = infer_split_str(string)
+    values = np.array(string.strip(split_str).split(split_str))
+
     # If the length is not as expected --> Assume data corruption
     # --> Return an array with nan
     if len(values) != n_values:
         values = np.zeros(n_values) * np.nan
-    else:
-        # Ensure string type
-        values = values.astype("str")
-        # Replace '' with 0
-        values = replace_empty_strings_with_zeros(values)
-        # Replace "-9.999" with 0
-        values = np.char.replace(values, "-9.999", "0")
-        # Cast values to float type
-        # --> Note: the disk encoding is specified in the l0b_encodings.yml
-        values = values.astype(float)
+        return values
+
+    # Otherwise sanitize the list of value
+    # Ensure string type
+    values = values.astype("str")
+    # Replace '' with 0
+    values = replace_empty_strings_with_zeros(values)
+    # Replace "-9.999" with 0
+    values = np.char.replace(values, "-9.999", "0")
+    # Cast values to float type
+    # --> Note: the disk encoding is specified in the l0b_encodings.yml
+    values = values.astype(float)
     return values
 
 

disdrodb/l0/l0c_processing.py

@@ -117,7 +117,12 @@ def split_dataset_by_sampling_intervals(
 
     # If sample_interval is a dataset variable, use it to define dictionary of datasets
     if "sample_interval" in ds:
-        return {int(interval): ds.isel(time=ds["sample_interval"] == interval) for interval in measurement_intervals}
+        dict_ds = {}
+        for interval in measurement_intervals:
+            ds_subset = ds.isel(time=ds["sample_interval"] == interval)
+            if ds_subset.sizes["time"] > 2:
+                dict_ds[int(interval)] = ds_subset
+        return dict_ds
 
     # ---------------------------------------------------------------------------------------.
     # Otherwise exploit difference between timesteps to identify change point
@@ -460,9 +465,8 @@ def regularize_timesteps(ds, sample_interval, robust=False, add_quality_flag=Tru
         # if last_time == last_time_expected and qc_flag[-1] == flag_next_missing:
         #     qc_flag[-1] = 0
 
-        # Assign time quality flag coordinate
+        # Add time quality flag variable
         ds["time_qc"] = xr.DataArray(qc_flag, dims="time")
-        ds = ds.set_coords("time_qc")
 
         # Add CF attributes for time_qc
         ds["time_qc"].attrs = {
@@ -674,6 +678,16 @@ def create_l0c_datasets(
         log_info(logger=logger, msg=f"No data between {start_time} and {end_time}.", verbose=verbose)
         return {}
 
+    # If 1 or 2 timesteps per time block, return empty dictionary
+    n_timesteps = len(ds["time"])
+    if n_timesteps < 3:
+        log_info(
+            logger=logger,
+            msg=f"Only {n_timesteps} timesteps between {start_time} and {end_time}.",
+            verbose=verbose,
+        )
+        return {}
+
     # ---------------------------------------------------------------------------------------.
     # If sample interval is a dataset variable, drop timesteps with unexpected measurement intervals !
     if "sample_interval" in ds:

disdrodb/l0/readers/LPM/ITALY/GID_LPM.py

@@ -31,7 +31,7 @@ def reader(
     """Reader."""
     ##------------------------------------------------------------------------.
     #### - Define raw data headers
-    column_names = ["TO_BE_SPLITTED"]
+    column_names = ["TO_PARSE"]
 
     ##------------------------------------------------------------------------.
     #### Define reader options
@@ -79,14 +79,22 @@ def reader(
 
     ##------------------------------------------------------------------------.
     #### Adapt the dataframe to adhere to DISDRODB L0 standards
-    # Count number of delimiters to identify valid rows
-    df = df[df["TO_BE_SPLITTED"].str.count(";") == 519]
+    # 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(";").isin([519, 520])]
+
+    # Check there are still valid rows
+    if len(df) == 0:
+        raise ValueError(f"No valid rows in {filepath}.")
 
     # Split by ; delimiter (before raw drop number)
-    df = df["TO_BE_SPLITTED"].str.split(";", expand=True, n=79)
+    df = df["TO_PARSE"].str.split(";", expand=True, n=79)
 
     # Assign column names
-    column_names = [
+    names = [
         "start_identifier",
         "device_address",
         "sensor_serial_number",
@@ -168,10 +176,10 @@ def reader(
         "number_particles_class_9_internal_data",
         "raw_drop_number",
     ]
-    df.columns = column_names
+    df.columns = names
 
     # Remove checksum from raw_drop_number
-    df["raw_drop_number"] = df["raw_drop_number"].str.rsplit(";", n=1, expand=True)[0]
+    df["raw_drop_number"] = df["raw_drop_number"].str.strip(";").str.rsplit(";", n=1, expand=True)[0]
 
     # Define datetime "time" column
     df["time"] = df["sensor_date"] + "-" + df["sensor_time"]

disdrodb/l0/readers/LPM/ITALY/GID_LPM_PI.py

@@ -0,0 +1,279 @@
+# -----------------------------------------------------------------------------.
+# 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 GID LPM sensor TC-PI with incorrect reported time."""
+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
+
+
+def read_txt_file(file, filename, logger):
+    """Parse for TC-PI LPM file."""
+    #### - Define raw data headers
+    column_names = ["TO_PARSE"]
+
+    ##------------------------------------------------------------------------.
+    #### Define reader options
+    # - For more info: https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html
+    reader_kwargs = {}
+
+    # - Define delimiter
+    reader_kwargs["delimiter"] = "\\n"
+
+    # - Avoid first column to become df index !!!
+    reader_kwargs["index_col"] = False
+
+    # Since column names are expected to be passed explicitly, header is set to None
+    reader_kwargs["header"] = None
+
+    # - Number of rows to be skipped at the beginning of the file
+    reader_kwargs["skiprows"] = 1
+
+    # - 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
+    # Raise error if empty file
+    if len(df) == 0:
+        raise ValueError(f"{filename} is empty.")
+
+    # Select only rows with expected number of delimiters
+    df = df[df["TO_PARSE"].str.count(" ") == 526]
+
+    # Check there are still valid rows
+    if len(df) == 0:
+        raise ValueError(f"No valid rows in {filename}.")
+
+    # Split by ; delimiter (before raw drop number)
+    df = df["TO_PARSE"].str.split(" ", expand=True, n=82)
+
+    # Assign column names
+    names = [
+        "date",
+        "time",
+        "unknown",
+        "start_identifier",
+        "device_address",
+        "sensor_serial_number",
+        "sensor_date",
+        "sensor_time",
+        "weather_code_synop_4677_5min",
+        "weather_code_synop_4680_5min",
+        "weather_code_metar_4678_5min",
+        "precipitation_rate_5min",
+        "weather_code_synop_4677",
+        "weather_code_synop_4680",
+        "weather_code_metar_4678",
+        "precipitation_rate",
+        "rainfall_rate",
+        "snowfall_rate",
+        "precipitation_accumulated",
+        "mor_visibility",
+        "reflectivity",
+        "quality_index",
+        "max_hail_diameter",
+        "laser_status",
+        "static_signal_status",
+        "laser_temperature_analog_status",
+        "laser_temperature_digital_status",
+        "laser_current_analog_status",
+        "laser_current_digital_status",
+        "sensor_voltage_supply_status",
+        "current_heating_pane_transmitter_head_status",
+        "current_heating_pane_receiver_head_status",
+        "temperature_sensor_status",
+        "current_heating_voltage_supply_status",
+        "current_heating_house_status",
+        "current_heating_heads_status",
+        "current_heating_carriers_status",
+        "control_output_laser_power_status",
+        "reserved_status",
+        "temperature_interior",
+        "laser_temperature",
+        "laser_current_average",
+        "control_voltage",
+        "optical_control_voltage_output",
+        "sensor_voltage_supply",
+        "current_heating_pane_transmitter_head",
+        "current_heating_pane_receiver_head",
+        "temperature_ambient",
+        "current_heating_voltage_supply",
+        "current_heating_house",
+        "current_heating_heads",
+        "current_heating_carriers",
+        "number_particles",
+        "number_particles_internal_data",
+        "number_particles_min_speed",
+        "number_particles_min_speed_internal_data",
+        "number_particles_max_speed",
+        "number_particles_max_speed_internal_data",
+        "number_particles_min_diameter",
+        "number_particles_min_diameter_internal_data",
+        "number_particles_no_hydrometeor",
+        "number_particles_no_hydrometeor_internal_data",
+        "number_particles_unknown_classification",
+        "number_particles_unknown_classification_internal_data",
+        "number_particles_class_1",
+        "number_particles_class_1_internal_data",
+        "number_particles_class_2",
+        "number_particles_class_2_internal_data",
+        "number_particles_class_3",
+        "number_particles_class_3_internal_data",
+        "number_particles_class_4",
+        "number_particles_class_4_internal_data",
+        "number_particles_class_5",
+        "number_particles_class_5_internal_data",
+        "number_particles_class_6",
+        "number_particles_class_6_internal_data",
+        "number_particles_class_7",
+        "number_particles_class_7_internal_data",
+        "number_particles_class_8",
+        "number_particles_class_8_internal_data",
+        "number_particles_class_9",
+        "number_particles_class_9_internal_data",
+        "TO_BE_FURTHER_PROCESSED",
+    ]
+    df.columns = names
+
+    # Define datetime "time" column
+    df["time"] = df["date"] + " " + df["time"]
+    df["time"] = pd.to_datetime(df["time"], format="%Y-%m-%d %H:%M:%S", errors="coerce")
+
+    # Drop row if start_identifier different than 00
+    df = df[df["start_identifier"].astype(str) == "00"]
+
+    # Extract the last variables remained in raw_drop_number
+    df_parsed = df["TO_BE_FURTHER_PROCESSED"].str.rsplit(" ", n=5, expand=True)
+    df_parsed.columns = [
+        "raw_drop_number",
+        "air_temperature",
+        "relative_humidity",
+        "wind_speed",
+        "wind_direction",
+        "checksum",
+    ]
+
+    # Assign columns to the original dataframe
+    df[df_parsed.columns] = df_parsed
+
+    # Drop rows with invalid raw_drop_number
+    # --> 440 value # 22x20
+    df = df[df["raw_drop_number"].astype(str).str.len() == 1759]
+
+    # Drop columns not agreeing with DISDRODB L0 standards
+    columns_to_drop = [
+        "start_identifier",
+        "device_address",
+        "sensor_serial_number",
+        "sensor_date",
+        "sensor_time",
+        "date",
+        "unknown",
+        "TO_BE_FURTHER_PROCESSED",
+        "air_temperature",
+        "relative_humidity",
+        "wind_speed",
+        "wind_direction",
+        "checksum",
+    ]
+    df = df.drop(columns=columns_to_drop)
+    return df
+
+
+@is_documented_by(reader_generic_docstring)
+def reader(
+    filepath,
+    logger=None,
+):
+    """Reader."""
+    import zipfile
+
+    ##------------------------------------------------------------------------.
+    # filename = os.path.basename(filepath)
+    # return read_txt_file(file=filepath, filename=filename, logger=logger)
+
+    # ---------------------------------------------------------------------.
+    #### 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(".txt"):
+                # 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