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Merge pull request #191 from ArtesiaWater/dev
Update master for new release (0.11.0)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| import logging | ||
| import os | ||
| import zipfile | ||
|
|
||
| import numpy as np | ||
| import pandas as pd | ||
| from pyproj import Transformer | ||
|
|
||
| logger = logging.getLogger(__name__) | ||
|
|
||
|
|
||
| def read_solinst_file( | ||
| path, | ||
| transform_coords=True, | ||
| ): | ||
| """Read Solinst logger file (XLE) | ||
| Parameters | ||
| ---------- | ||
| path : str | ||
| path to Solinst file (.xle) | ||
| transform_coords : boolean | ||
| convert coordinates from WGS84 to RD | ||
| Returns | ||
| ------- | ||
| df : pandas.DataFrame | ||
| DataFrame containing file content | ||
| meta : dict, optional | ||
| dict containing meta | ||
| """ | ||
|
|
||
| # open file | ||
| path = str(path) | ||
| name = os.path.splitext(os.path.basename(path))[0] | ||
| if path.endswith(".xle"): | ||
| f = path | ||
| elif path.endswith(".zip"): | ||
| zf = zipfile.ZipFile(path) | ||
| f = zf.open("{}.xle".format(name)) | ||
| else: | ||
| raise NotImplementedError( | ||
| "File type '{}' not supported!".format(os.path.splitext(path)[-1]) | ||
| ) | ||
|
|
||
| logger.info("reading -> {}".format(f)) | ||
|
|
||
| # read channel 1 data header | ||
| df_ch1_data_header = pd.read_xml(path, xpath="/Body_xle/Ch1_data_header") | ||
| series_ch1_data_header = df_ch1_data_header.T.iloc[:, 0] | ||
| colname_ch1 = ( | ||
| series_ch1_data_header.Identification.lower() | ||
| + "_" | ||
| + series_ch1_data_header.Unit.lower() | ||
| ) | ||
|
|
||
| # read channel 2 data header | ||
| df_ch2_data_header = pd.read_xml(path, xpath="/Body_xle/Ch2_data_header") | ||
| series_ch2_data_header = df_ch2_data_header.T.iloc[:, 0] | ||
| colname_ch2 = ( | ||
| series_ch2_data_header.Identification.lower() | ||
| + "_" | ||
| + series_ch2_data_header.Unit.lower() | ||
| ) | ||
|
|
||
| # read observations | ||
| df = pd.read_xml( | ||
| path, | ||
| xpath="/Body_xle/Data/Log", | ||
| ) | ||
| df.rename(columns={"ch1": colname_ch1, "ch2": colname_ch2}, inplace=True) | ||
| if "ms" in df.columns: | ||
| df["date_time"] = pd.to_datetime( | ||
| df["Date"] + " " + df["Time"] | ||
| ) + pd.to_timedelta(df["ms"], unit="ms") | ||
| drop_cols = ["id", "Date", "Time", "ms"] | ||
| else: | ||
| df["date_time"] = pd.to_datetime(df["Date"] + " " + df["Time"]) | ||
| drop_cols = ["id", "Date", "Time"] | ||
| df.set_index("date_time", inplace=True) | ||
|
|
||
| df.drop(columns=drop_cols, inplace=True) | ||
|
|
||
| # parse meta into dict, per group in XLE file | ||
| meta = {} | ||
| # read file info | ||
| df_file_info = pd.read_xml(path, xpath="/Body_xle/File_info") | ||
| dict_file_info = df_file_info.T.iloc[:, 0].to_dict() | ||
|
|
||
| # read instrument info | ||
| df_instrument_info = pd.read_xml(path, xpath="/Body_xle/Instrument_info") | ||
| dict_instrument_info = df_instrument_info.T.iloc[:, 0].to_dict() | ||
|
|
||
| # read instrument info | ||
| df_instrument_info_data_header = pd.read_xml( | ||
| path, xpath="/Body_xle/Instrument_info_data_header" | ||
| ) | ||
| dict_instrument_info_data_header = df_instrument_info_data_header.T.iloc[ | ||
| :, 0 | ||
| ].to_dict() | ||
|
|
||
| meta = { | ||
| **dict_file_info, | ||
| **dict_instrument_info, | ||
| **dict_instrument_info_data_header, | ||
| } | ||
|
|
||
| if transform_coords: | ||
| # lat and lon has 0,000 when location is not supplied | ||
| # replace comma with point first | ||
| if isinstance(meta["Latitude"], str): | ||
| meta["Latitude"] = float(meta["Latitude"].replace(",", ".")) | ||
| if isinstance(meta["Longtitude"], str): | ||
| meta["Longtitude"] = float(meta["Longtitude"].replace(",", ".")) | ||
| if (meta["Latitude"] != 0) & (meta["Longtitude"] != 0): | ||
| # NOTE: check EPSG:28992 definition and whether location is showing up in | ||
| # the right spot. | ||
| transformer = Transformer.from_crs("epsg:4326", "epsg:28992") | ||
| x, y = transformer.transform(meta["Latitude"], meta["Longtitude"]) | ||
| x = np.round(x, 2) | ||
| y = np.round(y, 2) | ||
| else: | ||
| logger.warning("file has no location included") | ||
| x = None | ||
| y = None | ||
| else: | ||
| x = meta["Latitude"] | ||
| y = meta["Longtitude"] | ||
| meta["x"] = x | ||
| meta["y"] = y | ||
| meta["filename"] = f | ||
| meta["source"] = meta["Created_by"] | ||
| meta["name"] = name | ||
| meta["monitoring_well"] = name | ||
| meta["unit"] = series_ch1_data_header.Unit.lower() | ||
| meta["metadata_available"] = True | ||
|
|
||
| return df, meta |
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