AeroViz 0.1.12__py3-none-any.whl → 0.1.14__py3-none-any.whl

AeroViz/rawDataReader/script/APS.py

@@ -22,19 +22,23 @@ class Reader(AbstractReader):
     # QC data
     def _QC(self, _df):
         _df = _df.copy()
+        _index = _df.index.copy()
 
         # mask out the data size lower than 7
-        _df['total'] = _df.sum(axis=1, min_count=1) * (np.diff(np.log(_df.keys().to_numpy(float)))).mean()
-        _df_size = _df['total'].dropna().resample('1h').size().resample(_df.index.freq).ffill()
-        _df = _df.mask(_df_size < 7)
+        _df.loc[:, 'total'] = _df.sum(axis=1, min_count=1) * (np.diff(np.log(_df.keys().to_numpy(float)))).mean()
 
-        # remove total conc. lower than 700
-        _df = _df.mask(_df['total'] > 700)
+        hourly_counts = (_df['total']
+                         .dropna()
+                         .resample('h')
+                         .size()
+                         .resample('6min')
+                         .ffill()
+                         .reindex(_df.index, method='ffill', tolerance='6min'))
 
-        # not confirmed
-        # remove the bin over 4000 nm which num. conc. larger than 1
-        # _df_remv_ky = _df.keys()[:-2][_df.keys()[:-2]>=4.]
+        # Remove data with less than 6 data per hour
+        _df = _df.mask(hourly_counts < 6)
 
-        # _df_1hr[_df_remv_ky] = _df_1hr[_df_remv_ky].copy().mask(_df_1hr[_df_remv_ky]>1.)
+        # remove total conc. lower than 700 or lower than 1
+        _df = _df.mask((_df['total'] > 700) | (_df['total'] < 1))
 
         return _df[_df.keys()[:-1]]

AeroViz/rawDataReader/script/BAM1020.py

@@ -0,0 +1,35 @@
+from pandas import read_csv, to_numeric, NA
+
+from AeroViz.rawDataReader.core import AbstractReader
+
+
+class Reader(AbstractReader):
+    nam = 'BAM1020'
+
+    def _raw_reader(self, file):
+        PM = 'Conc'
+
+        _df = read_csv(file, parse_dates=True, index_col=0, usecols=range(0, 21))
+        _df.rename(columns={'Conc (mg/m3)': PM}, inplace=True)
+
+        # remove data when Conc = 1 or 0
+        _df[PM] = _df[PM].replace(1, NA)
+
+        _df = _df[[PM]].apply(to_numeric, errors='coerce')
+
+        # tranfer unit from mg/m3 to ug/m3
+        _df = _df * 1000
+
+        return _df.loc[~_df.index.duplicated() & _df.index.notna()]
+
+    def _QC(self, _df):
+        _index = _df.index.copy()
+
+        # remove negative value
+        _df = _df.mask((_df <= 0) | (_df > 500))
+
+        # use IQR_QC
+        _df = self.time_aware_IQR_QC(_df, time_window='1h')
+
+        # make sure all columns have values, otherwise set to nan
+        return _df.dropna(how='any').reindex(_index)

AeroViz/rawDataReader/script/NEPH.py

@@ -1,4 +1,4 @@
-from pandas import to_datetime, read_csv, DataFrame, to_numeric
+from pandas import to_datetime, read_csv, to_numeric
 
 from AeroViz.rawDataReader.core import AbstractReader
 
@@ -46,17 +46,13 @@ class Reader(AbstractReader):
 
                 return _df.loc[~_df.index.duplicated() & _df.index.notna()]
 
-            except ValueError:
-                # Define valid groups and find invalid indices
+            except ValueError:  # Define valid groups and find invalid indices
                 invalid_indices = _df[~_df[0].isin({'B', 'G', 'R', 'D', 'T', 'Y', 'Z'})].index
-                print("Invalid values and their indices:")
-                print("\n".join([f"Index: {idx}, Value: {_df.at[idx, 0]}" for idx in invalid_indices]))
+                self.logger.warning(
+                    f"\tInvalid values in {file.name}: {', '.join(f'{_}:{_df.at[_, 0]}' for _ in invalid_indices)}."
+                    f" Skipping file.")
 
-                # Return an empty DataFrame with specified columns if there's a length mismatch
-                _df_out = DataFrame(index=_idx_tm, columns=['B', 'G', 'R', 'BB', 'BG', 'BR', 'RH'])
-                _df_out.index.name = 'Time'
-                print(f'\n\t\t\t Length mismatch in {file} data. Returning an empty DataFrame.')
-                return _df_out
+                return None
 
     def _QC(self, _df):
         MDL_sensitivity = {'B': .1, 'G': .1, 'R': .3}

AeroViz/rawDataReader/script/OCEC.py

@@ -9,12 +9,12 @@ class Reader(AbstractReader):
 
     def _raw_reader(self, file):
         with open(file, 'r', encoding='utf-8', errors='ignore') as f:
-            _df = read_csv(f, skiprows=3)
+            _df = read_csv(f, skiprows=3, on_bad_lines='skip')
 
             _df['Start Date/Time'] = _df['Start Date/Time'].str.strip()
             _df['time'] = to_datetime(_df['Start Date/Time'], format='%m/%d/%Y %I:%M:%S %p', errors='coerce')
 
-            if _df['time'].isna().any():
+            if _df['time'].isna().all():
                 _df['time'] = to_datetime(_df['Start Date/Time'], format='%m/%d/%Y %H:%M:%S', errors='coerce')
 
             _df = _df.set_index('time')

AeroViz/rawDataReader/script/SMPS.py

@@ -36,7 +36,7 @@ class Reader(AbstractReader):
             skip = find_header_row(f, delimiter)
             f.seek(0)
 
-            _df = read_csv(f, sep=delimiter, skiprows=skip)
+            _df = read_csv(f, sep=delimiter, skiprows=skip, low_memory=False)
 
             for date_format in date_formats:
                 _time_index = parse_date(_df, date_format)
@@ -56,30 +56,50 @@ class Reader(AbstractReader):
             _df_smps.columns = _df_smps.columns.astype(float)
             _df_smps = _df_smps.loc[_df_smps.index.dropna().copy()]
 
-            if _df_smps.columns[0] != self.size_range[0] or _df_smps.columns[-1] != self.size_range[1]:
-                self.logger.info(f'\tSMPS file: {file.name} is not match the default size range {self.size_range}, '
-                                 f'it is ({_df_smps.columns[0]}, {_df_smps.columns[-1]})')
+            size_range = self.kwargs.get('size_range') or (11.8, 593.5)
+
+            if _df_smps.columns[0] != size_range[0] or _df_smps.columns[-1] != size_range[1]:
+                self.logger.warning(f'\tSMPS file: {file.name} is not match the setting size range {size_range}, '
+                                    f'it is ({_df_smps.columns[0]}, {_df_smps.columns[-1]}). '
+                                    f'Please run by another RawDataReader instance, and set the correct size range')
+                return None
 
             return _df_smps.apply(to_numeric, errors='coerce')
 
     # QC data
     def _QC(self, _df):
-        df = _df.copy()
+        _df = _df.copy()
+        _index = _df.index.copy()
+
+        size_range = self.kwargs.get('size_range') or (11.8, 593.5)
 
-        size_range_mask = (df.columns.astype(float) >= self.size_range[0]) & (
-                df.columns.astype(float) <= self.size_range[1])
-        df = df.loc[:, size_range_mask]
+        size_range_mask = (_df.columns.astype(float) >= size_range[0]) & (
+                _df.columns.astype(float) <= size_range[1])
+        _df = _df.loc[:, size_range_mask]
 
         # mask out the data size lower than 7
-        df.loc[:, 'total'] = df.sum(axis=1, min_count=1) * (np.diff(np.log(df.columns[:-1].to_numpy(float)))).mean()
-        _df_size = df['total'].dropna().resample('1h').size().resample(df.index.freq).ffill()
-        df = df.mask(_df_size < 7)
+        _df.loc[:, 'total'] = _df.sum(axis=1, min_count=1) * (np.diff(np.log(_df.columns[:-1].to_numpy(float)))).mean()
+
+        hourly_counts = (_df['total']
+                         .dropna()
+                         .resample('h')
+                         .size()
+                         .resample('6min')
+                         .ffill()
+                         .reindex(_df.index, method='ffill', tolerance='6min'))
+
+        # Remove data with less than 6 data per hour
+        _df = _df.mask(hourly_counts < 6)
+
+        # remove total conc. (dN) lower than 2000
+        _df = _df.mask(_df['total'] < 2000)
+        _df = _df.drop('total', axis=1)
 
-        # remove total conc. lower than 2000
-        df = df.mask(df['total'] < 2000)
+        # remove single bin conc. (dN/dlogdp) larger than 1e6
+        _df = _df.mask((_df > 1e6).any(axis=1))
 
         # remove the bin over 400 nm which num. conc. larger than 4000
-        _df_remv_ky = df.keys()[:-1][df.keys()[:-1] >= 400.]
-        df[_df_remv_ky] = df[_df_remv_ky].copy().mask(df[_df_remv_ky] > 4000.)
+        large_bins = _df.columns[_df.columns.astype(float) >= 400]
+        _df = _df.mask((_df[large_bins] > 4000).any(axis=1))
 
-        return df[df.keys()[:-1]]
+        return _df

AeroViz/rawDataReader/script/TEOM.py

@@ -1,3 +1,4 @@
+import pandas as pd
 from pandas import to_datetime, read_csv, Timedelta, to_numeric
 
 from AeroViz.rawDataReader.core import AbstractReader
@@ -7,9 +8,9 @@ class Reader(AbstractReader):
     nam = 'TEOM'
 
     def _raw_reader(self, file):
-        with open(file, 'r', encoding='utf-8', errors='ignore') as f:
-            _df = read_csv(f, skiprows=3, index_col=False)
+        _df = read_csv(file, skiprows=3, index_col=False)
 
+        if 'Time Stamp' in _df.columns:  # remote download
             _df = _df.rename(columns={'Time Stamp': 'time',
                                       'System status': 'status',
                                       'PM-2.5 base MC': 'PM_NV',
@@ -25,8 +26,19 @@ class Reader(AbstractReader):
 
             _df = _df.set_index(to_datetime(_tm_idx, errors='coerce', format='%d - %m - %Y %X'))
 
-            _df = _df.where(_df['status'] < 1)
+        elif 'tmoStatusCondition_0' in _df.columns:  # usb download
+            _df['time'] = pd.to_datetime(_df['Date'] + ' ' + _df['Time'], errors='coerce', format='%Y-%m-%d %H:%M:%S')
+            _df.drop(columns=['Date', 'Time'], inplace=True)
+            _df.set_index('time', inplace=True)
 
+            _df = _df.rename(columns={'tmoStatusCondition_0': 'status',
+                                      'tmoTEOMABaseMC_0': 'PM_NV',
+                                      'tmoTEOMAMC_0': 'PM_Total',
+                                      'tmoTEOMANoise_0': 'noise', })
+        else:
+            raise NotImplementedError
+
+        _df = _df.where(_df['status'] < 1)
         _df = _df[['PM_NV', 'PM_Total', 'noise']].apply(to_numeric, errors='coerce')
 
         return _df.loc[~_df.index.duplicated() & _df.index.notna()]

AeroViz/rawDataReader/script/__init__.py

@@ -8,6 +8,7 @@ __all__ = [
     'AE43',
     'BC1054',
     'MA350',
+    'BAM1020',
     'TEOM',
     'OCEC',
     'IGAC',

{AeroViz-0.1.12.dist-info → AeroViz-0.1.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: AeroViz
-Version: 0.1.12
+Version: 0.1.14
 Summary: Aerosol science
 Author-email: alex <alex870521@gmail.com>
 License: MIT
@@ -24,7 +24,7 @@ Requires-Dist: scikit-learn==1.5.1
 Requires-Dist: windrose==1.9.2
 Requires-Dist: cartopy==0.24.1
 Requires-Dist: tabulate==0.9.0
-Requires-Dist: rich~=13.7.1
+Requires-Dist: rich~=13.9.4
 Provides-Extra: test
 Requires-Dist: pytest>=7.0.0; extra == "test"
 Requires-Dist: pytest-cov>=4.1.0; extra == "test"
@@ -72,7 +72,8 @@ pip install AeroViz
 
 Built-in `RawDataReader` supporting multiple aerosol instruments:
 - **Particle Sizers**: SMPS, APS, GRIMM, OPC
-- **Mass & Optical**: TEOM, NEPH, Aurora, AE33/43, BC1054
+- **Mass**: TEOM, BAM1020
+- **Optical**: NEPH, Aurora, AE33/43, BC1054
 - **Chemical Analysis**: OCEC, IGAC, XRF, VOC
 
 > Features include quality control, data filtering, flexible resampling, and CSV export. For detailed instrument support
@@ -82,7 +83,7 @@ Built-in `RawDataReader` supporting multiple aerosol instruments:
 
 Built-in `DataProcess` provides advanced aerosol analysis:
 - **Size Distribution**: Mode Fitting, Log-Normal Analysis
-- **Optical Properties**: Mie Theory, SOAP Calculation
+- **Optical Properties**: Mie Theory, IMPROVE
 - **Chemical**: Mass Closure, Source Apportionment
 - **VOC**: OFP, SOAP
 
@@ -104,8 +105,8 @@ from AeroViz import RawDataReader, DataProcess, plot
 
 # Read data from a supported instrument
 data = RawDataReader(
-    'NEPH',
-    Path('/path/to/data'),
+    instrument='Neph',
+    path=Path('/path/to/data'),
     start=datetime(2024, 2, 1),
     end=datetime(2024, 4, 30)
 )

{AeroViz-0.1.12.dist-info → AeroViz-0.1.14.dist-info}/RECORD

@@ -1,5 +1,5 @@
 AeroViz/__init__.py,sha256=4ICXg4UATkGXIUziaXcPX2Yaqj6OK5SL0ilU1JKeGFw,341
-AeroViz/__pycache__/__init__.cpython-312.pyc,sha256=rFyv4c4j1wZFxgjgaelbYczxY_f23IRZy8MmUe6HJF4,428
+AeroViz/__pycache__/__init__.cpython-312.pyc,sha256=Y13IWcTa8td9cc-YYgsLO6zeIsG3VBgqTvS38opGtF8,428
 AeroViz/data/DEFAULT_DATA.csv,sha256=eeeyeh8vSLKkE5tAF0TYnUNOyQIH98VA41bJaAP204Y,2248526
 AeroViz/data/DEFAULT_PNSD_DATA.csv,sha256=imLvLA80oYwo_jzXZtlQn5hZ76d47HUIlK2jp0tZPrg,2636511
 AeroViz/data/hysplit_example_data.txt,sha256=DWfY83EW3fOcv9dW-Y4pudq8-M7BJlXD-tlMSYrAk2w,8946
@@ -13,10 +13,10 @@ AeroViz/dataProcess/Chemistry/_partition.py,sha256=tKhb6BJns46UiUlEq6Zq7ahYnvUJ_
 AeroViz/dataProcess/Chemistry/_teom.py,sha256=IiM-TrifWpQLTbKllG-4k4c3mvQulfcmjswWu6muCXA,486
 AeroViz/dataProcess/Chemistry/isrpia.cnf,sha256=iWXTqsOZFmNrJxAI9nYuilZ9h6ru1icdPFVim7YKc_k,566
 AeroViz/dataProcess/Chemistry/isrpia2.exe,sha256=xFYPTXHSjl_-atmVcTmqqOkTZgUn1p8h-kFMcoGMIQw,1560032
-AeroViz/dataProcess/Chemistry/__pycache__/__init__.cpython-312.pyc,sha256=-QZKV4EnCIk6T63GVXVvd1_BabdLXgyDxOhUMMISgPM,2712
+AeroViz/dataProcess/Chemistry/__pycache__/__init__.cpython-312.pyc,sha256=wh_P_F75cgzp99Y_aBs-su2_Mbva-t9eOERhy_lO7cQ,2712
 AeroViz/dataProcess/Optical/Angstrom_exponent.py,sha256=KSGM_hf2oUPsLoLuhYSRDK5zdekwce9KgqhzRnf2Y4g,706
 AeroViz/dataProcess/Optical/PyMieScatt_update.py,sha256=3W2nqo9sQLqj9dqWh5Eqx2XUdu44bGWDLTa3QnjiUvM,20943
-AeroViz/dataProcess/Optical/_IMPROVE.py,sha256=n3uHUQTivckIrNlbE8rP7lPZGcMWZUAnS_qX8pXd55Q,1670
+AeroViz/dataProcess/Optical/_IMPROVE.py,sha256=deS94SmoW9H3YyFyzCZ6mWLYoY2f2M-UWLr4qN6RwbI,1662
 AeroViz/dataProcess/Optical/__init__.py,sha256=h_IYhaum0DhK7Qw6lWFvjAEv7uAqLVVPEwU0V4hJnX4,1371
 AeroViz/dataProcess/Optical/_absorption.py,sha256=pYHIoj_R23wKvxR4acUqqU9JXKY40wgsFvZH78rETrY,1234
 AeroViz/dataProcess/Optical/_extinction.py,sha256=anUemSXmLvJi2CSxqTYgQCgUW4pSUqgZ0q0xZ4zs0zY,1189
@@ -25,9 +25,9 @@ AeroViz/dataProcess/Optical/_mie_sd.py,sha256=cbWSorfG-l92csaXsZJ7005f8ij2H_VZop
 AeroViz/dataProcess/Optical/_scattering.py,sha256=w5xXXOfafV9a_dXY60YqTyzFDZppjBJeLcKl5PeCQe4,961
 AeroViz/dataProcess/Optical/fRH.pkl,sha256=PhJ-BYTaUDjl2Lp5Wz0zeiLQCzrsNdq8nP7Jd1BXyXE,4528
 AeroViz/dataProcess/Optical/mie_theory.py,sha256=EC3SsUaq5G3SdQyPMQxcosbEokqAgJw-4Gz6moJiOsk,8666
-AeroViz/dataProcess/Optical/__pycache__/PyMieScatt_update.cpython-312.pyc,sha256=W5tzeZnoJ8IF0mWMImZNv7wqTGhny-KkoMxHMgE-R14,32602
-AeroViz/dataProcess/Optical/__pycache__/__init__.cpython-312.pyc,sha256=kLT99igZ1AIE5MLY_pGl3L5AwTvbcHEN5FmFbNciOro,2114
-AeroViz/dataProcess/Optical/__pycache__/mie_theory.cpython-312.pyc,sha256=6pnzZmtCgElE2NAzdUiZ8NwKB2hwhcmxZSO-hAls49s,10662
+AeroViz/dataProcess/Optical/__pycache__/PyMieScatt_update.cpython-312.pyc,sha256=4JslxM_9_B4rkxvbqVbCGMc51a8EeJ-sfuTXcxrQVJw,32602
+AeroViz/dataProcess/Optical/__pycache__/__init__.cpython-312.pyc,sha256=x7t1wgKRTRNaux19n3JnMywUVfaihHj5BMzT_7fxaLM,2114
+AeroViz/dataProcess/Optical/__pycache__/mie_theory.cpython-312.pyc,sha256=Xmm2DCS4Jnwpwoorxu5LNwrsIjTDSeOWEHCOHbqVvWo,10662
 AeroViz/dataProcess/SizeDistr/__init__.py,sha256=fka1IJW4wZzYWE9HjWi8i03ab0JLFXOUdaHWYs4VHEQ,2172
 AeroViz/dataProcess/SizeDistr/__merge.py,sha256=A-ZmduUA9a0nVM8szhG1AWhsfUPu2UhGIaqFLcmg7Lk,9422
 AeroViz/dataProcess/SizeDistr/_merge.py,sha256=CyZwUc2M4lL-OE74e8mXq41nC6X0LJTAV8TwpO3fS2o,9176
@@ -37,14 +37,14 @@ AeroViz/dataProcess/SizeDistr/_merge_v3.py,sha256=HN2ARFmeWOawOWRPPv_pHEGBBZNgXV
 AeroViz/dataProcess/SizeDistr/_merge_v4.py,sha256=b8RVAievGIOLrmJHJXRsKXQ1tkMkm6rx43S7XAfeXE4,16228
 AeroViz/dataProcess/SizeDistr/_size_distr.py,sha256=ULhGKlxE9QmbDO_PS3HOSKzepeMfJZWabJvGXqsDEvE,3259
 AeroViz/dataProcess/SizeDistr/prop.py,sha256=7f18SOkkLgDiY_g1c1We8g-3WDJJIFcxkfR4F99jUgc,1845
-AeroViz/dataProcess/SizeDistr/__pycache__/__init__.cpython-312.pyc,sha256=vobgdfNHncQnFALFjqHXbtjVbxRgTA-NIVYpb38NOuM,2552
+AeroViz/dataProcess/SizeDistr/__pycache__/__init__.cpython-312.pyc,sha256=GZMB4pFrbNYFFbrl1YK6Ls1WZZj4tSwDLZWD7vZR7qI,2552
 AeroViz/dataProcess/VOC/__init__.py,sha256=8GNP0RMymTkJXK18pSgfLHqrKPWboN-3x1_Ke4UrI44,259
 AeroViz/dataProcess/VOC/_potential_par.py,sha256=h3rVdvtBvC6xHa_ZG4Oq5eXezeSZtHNy6T6I40maIcM,3863
 AeroViz/dataProcess/VOC/support_voc.json,sha256=tMYp_NERqhSriVRE2NavXh33CQ5CnsbJHtmMFlE5q_E,6804
-AeroViz/dataProcess/VOC/__pycache__/__init__.cpython-312.pyc,sha256=vZ0R_PqF1Vg1AHsk9F28VCdDeNYcu0vJhgs6Ff6H89g,716
-AeroViz/dataProcess/__pycache__/__init__.cpython-312.pyc,sha256=LuAWC7ehbPJv5ZPlYLfkkSkIlN3lCwYT97OOGoHsnNk,1067
+AeroViz/dataProcess/VOC/__pycache__/__init__.cpython-312.pyc,sha256=PGySgMDbLbtV7Aq6eYozqmLOKGT18D_4TdLsGPaFn9c,716
+AeroViz/dataProcess/__pycache__/__init__.cpython-312.pyc,sha256=khm0ATrZsMsICtRedGEurvdD3ZJu03BAyPYEXBcuX58,1067
 AeroViz/dataProcess/core/__init__.py,sha256=FhGwqlP8ZwXZQS0LjH0YOz2g1Q2yJniUUhRZ_jDOQ6k,2707
-AeroViz/dataProcess/core/__pycache__/__init__.cpython-312.pyc,sha256=uK4tH5hPSgqBUEF2j8I0fPgBvjiOX2CbKOdH9c3c8X8,4430
+AeroViz/dataProcess/core/__pycache__/__init__.cpython-312.pyc,sha256=iDbt-y6LWk8oTpo1ba3cJBDNaROhOVH1sI64JEFbBWs,4430
 AeroViz/plot/__init__.py,sha256=Cy42d1t58zeutxLYDkm8bFbRNGE0G1T8VpqGj1li1Cw,419
 AeroViz/plot/bar.py,sha256=cSPKJLWGifCzICCZVPcbZtrDrea_AStlwSli9-b-lsA,4246
 AeroViz/plot/box.py,sha256=8zDd8jYndSv5f0P1lFeX0m7VWYh9okYgJTClh2Lj7Dg,2115
@@ -53,50 +53,50 @@ AeroViz/plot/radar.py,sha256=QHXkLQlAZZQDWHcqVGJBeRsGiu45GYmy3lN6gwlh6xY,6965
 AeroViz/plot/regression.py,sha256=mTCNrCAYvH7QjIb_5WlltCR1Kqwer1anpGEsxmO2S3o,7292
 AeroViz/plot/scatter.py,sha256=sxk5QxgC1Jk9PuY18q9aRgR_Ipvg5dM1RkwYQxRkn1c,6787
 AeroViz/plot/violin.py,sha256=pU2Z2yTWocEtImmCAmbtn0WvXtUOrnCGOdDOrLxjooU,2689
-AeroViz/plot/__pycache__/__init__.cpython-312.pyc,sha256=-UYqvtOwl4R9EM-lCBETEFNzqtAbctoHZgUdrironkU,684
-AeroViz/plot/__pycache__/bar.cpython-312.pyc,sha256=dES5kB3XgvSNwNGjlOjzviJadz6weDEewAdmc8m1Wi8,5954
-AeroViz/plot/__pycache__/box.cpython-312.pyc,sha256=MGKi1tcGbP_GjdKo15zEDOJpQIC5XjjdnvpB-yIblh8,4043
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