diff --git a/pyleoclim/core/series.py b/pyleoclim/core/series.py index ef3bd0b1..d30860f8 100644 --- a/pyleoclim/core/series.py +++ b/pyleoclim/core/series.py @@ -2431,7 +2431,8 @@ def annualize(self, months=list(range(1, 13)), min_res=0.25, frac_req_months=2/3 Examples -------- - 1) Annual average + 1) Calendar average + .. jupyter-execute:: soi = pyleo.utils.load_dataset('SOI') @@ -2444,7 +2445,8 @@ def annualize(self, months=list(range(1, 13)), min_res=0.25, frac_req_months=2/3 fig, ax = soi.plot(title='Jan-Dec averaging') soi_a.plot(marker='o',ax=ax) - 2) JJA average : straightforward + 2) JJA average (straightforward) + .. jupyter-execute:: soi_jja = soi.annualize(months=[6, 7 , 8]) @@ -2452,6 +2454,7 @@ def annualize(self, months=list(range(1, 13)), min_res=0.25, frac_req_months=2/3 soi_jja.plot(marker='o',ax=ax, label='JJA average') 3) DJF average : straddles a year; handles it gracefully + .. jupyter-execute:: soi_djf = soi.annualize(months=[12, 1 , 2]) @@ -2459,17 +2462,18 @@ def annualize(self, months=list(range(1, 13)), min_res=0.25, frac_req_months=2/3 soi_djf.plot(marker='o',ax=ax, label='DJF average') 4) Varying the fraction of required months + .. jupyter-execute:: AprMar = [4,5,6,7,8,9,10,11,12,1,2,3] soi_am_default = soi.annualize(months=AprMar) - soi_am_stringent = soi.annualize(months=AprMar,frac_req_months=0.9) + soi_am_stringent = soi.annualize(months=AprMar,frac_req_months=1.0) - fig, ax = soi.plot(title='Apr-Mar averaging') + fig, ax = soi.plot(title='Apr-Mar averaging', xlim = [2000, 2026]) soi_am_default.plot(marker='o',ax=ax, label='Apr-Mar, $f=2/3$') - soi_am_stringent.plot(marker='o',ax=ax, label='Apr-Mar, $f=0.9$') + soi_am_stringent.plot(marker='o',ax=ax, label='Apr-Mar, $f=1.0$') - We see that insisting on a very high fraction of available months will result in dropped years + The last year is incomplete, so insisting on complete coverage results in dropping it Notes ----- @@ -3458,11 +3462,11 @@ def wavelet(self, method='cwt', settings=None, freq=None, freq_kwargs=None, verb Examples -------- - Wavelet analysis on the evenly-spaced SOI record. The CWT method will be applied by default. + Wavelet analysis on the evenly-spaced NINO3 record. The CWT method will be applied by default. .. jupyter-execute:: - ts = pyleo.utils.load_dataset('SOI') + ts = pyleo.utils.load_dataset('NINO3') scal1 = ts.wavelet() scal_signif = scal1.signif_test(number=20) # for research-grade work, use number=200 or larger fig, ax = scal_signif.plot() diff --git a/pyleoclim/data/metadata.yml b/pyleoclim/data/metadata.yml index 472f1f45..e5024013 100644 --- a/pyleoclim/data/metadata.yml +++ b/pyleoclim/data/metadata.yml @@ -1,9 +1,12 @@ SOI: - filename: 'soi_data' + filename: 'soi.long' file_extension: 'csv' pandas_kwargs: skiprows: 0 - header: 1 + header: 0 + parse_dates: [0] + index_col: 0 + skipfooter: 1 pyleo_kwargs: time_name: 'time' time_unit: 'year C.E.' @@ -11,8 +14,8 @@ SOI: value_unit: 'mb' label: 'Southern Oscillation Index' archiveType: 'Instrumental' - time_column: 1 - value_column: 2 + time_column: 0 + value_column: ' SOI from CRU missing value -99.99 https://psl.noaa.gov/data/timeseries/month/' NINO3: filename: 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b/pyleoclim/tests/test_core_Series.py index 4351e93e..7d10e1aa 100644 --- a/pyleoclim/tests/test_core_Series.py +++ b/pyleoclim/tests/test_core_Series.py @@ -585,13 +585,13 @@ def test_annualize_retrograde_series(self): def test_annualize_no_complete_years(self): """Test when no complete years exist with specified months""" soi = pyleo.utils.load_dataset("SOI") - inc = soi.sel(time=slice(1951, 1953)) + inc = soi.sel(time=slice(2025, 2026)) # Create a scenario where no complete years exist # Use a very restrictive month selection that's unlikely to have complete coverage with pytest.raises(ValueError, match="No years found with sufficient data coverage"): # This should fail for some edge case datasets - tsa = inc.annualize(months=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], frac_req_months=1.0) + inc.annualize(months=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], frac_req_months=1.0) @pytest.mark.parametrize("ds_name", ["SOI", "NINO3"]) def test_annualize_preserve_metadata(self, ds_name): @@ -1556,7 +1556,7 @@ def test_ssa_t3(self): """Test Series.ssa() with Knee truncation""" ts = pyleo.utils.load_dataset("SOI") ssa = ts.ssa(trunc="knee") - knee = 12 + knee = 32 assert_array_equal(ssa.mode_idx, np.arange(knee + 1)) def test_ssa_t4(self): @@ -1569,7 +1569,7 @@ def test_ssa_t4(self): soi_m.value[missing] = np.nan # put NaNs at the randomly chosen locations miss_ssa = soi_m.ssa() assert all(miss_ssa.eigvals >= 0) - assert np.square(miss_ssa.RCseries.value - soi.value).mean() < 0.3 + assert np.square(miss_ssa.RCseries.value - soi.value).mean() < 0.35 class TestUISeriesPlot: diff --git a/pyleoclim/utils/datasets.py b/pyleoclim/utils/datasets.py index 804d731f..29395811 100644 --- a/pyleoclim/utils/datasets.py +++ b/pyleoclim/utils/datasets.py @@ -97,14 +97,15 @@ def load_dataset(name): Returns ------- - pyleoclim_util.Series of the dataset + Series object Examples -------- .. jupyter-execute:: - from pyleoclim.utils.datasets import load_dataset - pyleo_series = load_dataset('LR04') + + LR04 = pyleo.utils.load_dataset('LR04') + LR04.view() """ # load the metadata for this dataset @@ -123,46 +124,87 @@ def load_dataset(name): # load into pandas df = pd.read_csv(path, **pandas_kwargs) - # use iloc if we're given an int - if isinstance(time_column, int): - time=df.iloc[:, time_column] - # use column name otherwise + # Check if the index is a DatetimeIndex - if so, use from_pandas() + if isinstance(df.index, pd.DatetimeIndex): + # Filter out rows with NaT (Not a Time) values and missing data + valid_mask = df.index.notna() + if isinstance(value_column, int): + value_series = df.iloc[:, value_column] + else: + value_series = df[value_column] + + # Also filter out rows where values are NaN + valid_mask = valid_mask & value_series.notna() + + # Apply the mask to get clean data + clean_index = df.index[valid_mask] + clean_values = value_series[valid_mask] + + # Create a pandas Series with the clean DatetimeIndex + pandas_series = pd.Series(clean_values.values, index=clean_index) + + # Use from_pandas() method which handles DatetimeIndex properly + if 'lat' in pyleo_kwargs.keys() and 'lon' in pyleo_kwargs.keys(): + if pyleo_kwargs['lat'] is not None and pyleo_kwargs['lon'] is not None: + ts = pyleo.GeoSeries.from_pandas( + pandas_series, + metadata=pyleo_kwargs, + verbose=False + ) + else: + ts = pyleo.Series.from_pandas( + pandas_series, + metadata=pyleo_kwargs, + verbose=False + ) + else: + ts = pyleo.Series.from_pandas( + pandas_series, + metadata=pyleo_kwargs, + verbose=False + ) else: - # if its a column - if time_column in df.columns: - time = df[time_column] + # Original logic for non-DatetimeIndex data + # use iloc if we're given an int + if isinstance(time_column, int): + time=df.iloc[:, time_column] + # use column name otherwise + else: + # if its a column + if time_column in df.columns: + time = df[time_column] + else: + time = df.Index + + if isinstance(value_column, int): + value=df.iloc[:, value_column] else: - time = df.Index + value = df[value_column] + + if 'lat' in pyleo_kwargs.keys() and 'lon' in pyleo_kwargs.keys(): + if pyleo_kwargs['lat'] is not None and pyleo_kwargs['lon'] is not None: + ts=pyleo.GeoSeries( + time=time, + value=value, + **pyleo_kwargs, + verbose=False + ) + else: + ts=pyleo.Series( + time=time, + value=value, + **pyleo_kwargs, + verbose=False + ) - if isinstance(value_column, int): - value=df.iloc[:, value_column] - else: - value = df[value_column] - - if 'lat' in pyleo_kwargs.keys() and 'lon' in pyleo_kwargs.keys(): - if pyleo_kwargs['lat'] is not None and pyleo_kwargs['lon'] is not None: - ts=pyleo.GeoSeries( + else: + # convert to pyleo.Series + ts=pyleo.Series( time=time, value=value, **pyleo_kwargs, verbose=False ) - else: - ts=pyleo.Series( - time=time, - value=value, - **pyleo_kwargs, - verbose=False - ) - - else: - # convert to pyleo.Series - ts=pyleo.Series( - time=time, - value=value, - **pyleo_kwargs, - verbose=False - ) # if this is a json elif metadata['file_extension'] == 'json': ts=jsonutils.json_to_PyleoObj(str(path), 'Series') diff --git a/pyleoclim/utils/tsutils.py b/pyleoclim/utils/tsutils.py index 28831df2..740dcbb8 100644 --- a/pyleoclim/utils/tsutils.py +++ b/pyleoclim/utils/tsutils.py @@ -2067,6 +2067,7 @@ def custom_year_averages( import pandas as pd import numpy as np + import pyleoclim.utils.tsutils as ut # Create sample monthly data dates = pd.date_range('2020-01-01', '2023-12-31', freq='M') @@ -2075,35 +2076,35 @@ def custom_year_averages( # Example 1: Single year (int) # Compute Jan-Mar average for 2021 only - avg_single = custom_year_averages(ts, 1, 3, years=2021) + avg_single = ut.custom_year_averages(ts, 1, 3, years=2021) print("Single year (2021):") print(avg_single) print() # Example 2: List of specific years # Compute Apr-Mar averages for selected years - avg_list = custom_year_averages(ts, 4, 3, years=[2021, 2023]) + avg_list = ut.custom_year_averages(ts, 4, 3, years=[2021, 2023]) print("Specific years [2021, 2023]:") print(avg_list) print() # Example 3: Range of years # Compute Oct-Sep averages for consecutive years - avg_range = custom_year_averages(ts, 10, 9, years=range(2021, 2024)) + avg_range = ut.custom_year_averages(ts, 10, 9, years=range(2021, 2024)) print("Range of years (2021-2023):") print(avg_range) print() # Example 4: All available years (None - default) # Compute Jan-Dec averages for all years in data - avg_all = custom_year_averages(ts, 1, 12, years=None) + avg_all = ut.custom_year_averages(ts, 1, 12, years=None) print("All available years (None):") print(avg_all) print() # Example 5: Straddling periods with different year specifications # Apr-Mar periods: year refers to the March year - avg_straddle = custom_year_averages(ts, 4, 3, years=range(2021, 2024)) + avg_straddle = ut.custom_year_averages(ts, 4, 3, years=range(2021, 2024)) print("Straddling periods (Apr-Mar), years 2021-2023:") print(avg_straddle) @@ -2119,7 +2120,7 @@ def custom_year_averages( daily_ts = pd.Series(daily_values, index=daily_dates, name='daily_data') # Compute weighted average (accounts for uneven spacing) - daily_avg = custom_year_averages(daily_ts, 1, 3, years=2021) + daily_avg = ut.custom_year_averages(daily_ts, 1, 3, years=2021) print("Daily data with uneven spacing (Jan-Mar 2021):") print(f"Weighted average: {daily_avg.iloc[0]:.2f}") print(f"Simple mean: {daily_ts.mean():.2f}")