tsp 1.4.9__py3-none-any.whl → 1.5.3__py3-none-any.whl

tsp/physics.py

@@ -3,11 +3,11 @@ from typing import Optional
 
 
 def analytical_fourier(depths: "np.ndarray", times: "np.ndarray",
-              Q:"Optional[float]"=0.2, 
-              c:"Optional[float]"=1.6e6,
-              k:"Optional[float]"=2.5,
-              A:"Optional[float]"=6,
-              MAGST:"Optional[float]"=-0.5) -> "np.ndarray":
+              Q:float=0.2, 
+              c:float=1.6e6,
+              k:float=2.5,
+              A:float=6,
+              MAGST:float=-0.5) -> "np.ndarray":
     """Create sinusoidal synthetic data for examples and testing
 
     Parameters
@@ -32,13 +32,8 @@ def analytical_fourier(depths: "np.ndarray", times: "np.ndarray",
     TSP
         _description_
     """
-    Q = 0.2  # [W m-2]
-    c = 1.6e6  # J m-3 K-1
-    k = 2.5  # [W m-1 K-1]
     tau = 31536000  # [s]
     w = 2 * np.pi / tau  # []
-    A = 6  # [C]
-    MAGST = -0.5  # [C]
     alpha = k / c
 
     initial = initial_analytic(MAGST, Q, k, depths) 

tsp/readers.py

@@ -15,6 +15,8 @@ from typing import Union, Optional
 from tsp.dataloggers.Geoprecision import detect_geoprecision_type
 from tsp.dataloggers.HOBO import HOBO, HOBOProperties
 from tsp.dataloggers.logr import LogR, guessed_depths_ok
+from tsp.dataloggers.RBRXL800 import RBRXL800
+from tsp.dataloggers.RBRXR420 import RBRXR420
 
 from tsp.core import TSP, IndexedTSP
 from tsp.misc import _is_depth_column
@@ -161,7 +163,21 @@ def read_geotop(file: str) -> TSP:
     
     t._depths *= 0.001  # Convert to [m]
 
-    return t
+    # Only use last simulation period 
+    # TODO: this could be improved
+    raw = pd.read_csv(file)
+    last_run = np.logical_and(raw['Simulation_Period'] == max( raw['Simulation_Period'] ),
+               raw['Run'] == max( raw['Run'] ))
+    
+    last = TSP(times = t.times[last_run],
+               depths = t.depths,
+               values = t.values[last_run, :],
+               metadata={"Simulation_Period": max(raw['Simulation_Period']),
+                         "Run": max( raw['Run'] )
+                         }
+    )
+
+    return last
 
 
 def read_gtpem(file: str) -> "list[TSP]":
@@ -343,16 +359,17 @@ def read_geoprecision(filepath: str) -> IndexedTSP:
     IndexedTSP
         An IndexedTSP
     """
-    reader = detect_geoprecision_type(filepath)
+    Reader = detect_geoprecision_type(filepath)
     
-    if reader is None:
+    if Reader is None:
         raise RuntimeError("Could not detect type of geoprecision file (GP5W or FG2 missing from header")
-
-    data = reader().read(filepath)
-
+    reader = Reader()
+    
+    data = reader.read(filepath)
     t = IndexedTSP(times=data['TIME'].dt.to_pydatetime(),
                      values=data.drop("TIME", axis=1).values)
 
+    t.metadata = reader.META
     return t
 
 
@@ -476,3 +493,44 @@ def read_classic(filepath: str, init_file: "Optional[str]"=None) -> TSP:
         t.set_depths(depths)
 
     return t
+
+
+def read_rbr(file_path: str) -> IndexedTSP:
+    """
+
+    Parameters
+    ----------
+    filepath
+
+    Returns
+    -------
+
+    """
+    file_extention = Path(file_path).suffix.lower()
+    if file_extention in [".dat", ".hex"]:
+        with open(file_path, "r") as f:
+            first_line = f.readline()
+            model = first_line.split()[1]
+            if model == "XL-800":
+                r = RBRXL800()
+            elif model in ["XR-420", "XR-420-T8"]:
+                r = RBRXR420()
+            else:
+                raise ValueError(f"logger model {model} unsupported")
+            data = r.read(file_path)
+    elif file_extention in [".xls", ".xlsx", ".rsk"]:
+        r = RBRXR420()
+        data = r.read(file_path)
+    else:
+        raise IOError("File is not .dat, .hex, .xls, .xlsx, or .rsk")
+
+    times = data['TIME'].dt.to_pydatetime()
+    channels = pd.Series(data.columns).str.match("^ch")
+    values = data.loc[:, channels.to_numpy()]
+
+    t = IndexedTSP(times=times, values=values.values)
+    if "utc offset" in list(r.META.keys()):
+        t.set_utc_offset(r.META["utc offset"])
+
+    return t
+

tsp/utils.py

@@ -85,7 +85,7 @@ def _strip_duplicate_time(t: TSP):
 def _average_duplicate_time(t: TSP):
     singleton = t.wide[~t.wide.index.duplicated(keep=False)]
     duplicated = t.wide[t.wide.index.duplicated(keep=False)].drop(['time'], axis=1).reset_index()
-    averaged = duplicated.groupby(duplicated['index']).apply(lambda x: x[~x.isna()].mean())  # TODO: replace with newer pandas .mean()
+    averaged = duplicated.groupby(duplicated['index']).apply(lambda x: x[~x.isna()].mean(numeric_only=True))  
     averaged.insert(0, 'time',averaged.index)
 
     df = pd.concat([singleton, averaged], ignore_index=False).sort_index()

{tsp-1.4.9.dist-info → tsp-1.5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tsp
-Version: 1.4.9
+Version: 1.5.3
 Summary: Making permafrost data effortless
 Home-page: https://gitlab.com/permafrostnet/teaspoon
 Author: Nick Brown
@@ -28,6 +28,9 @@ Requires-Dist: pfit (==0.2.1) ; extra == 'nc'
 Provides-Extra: plotting
 Requires-Dist: matplotlib ; extra == 'plotting'
 Requires-Dist: scipy ; extra == 'plotting'
+Provides-Extra: rbr
+Requires-Dist: pyrsktools ; extra == 'rbr'
+Requires-Dist: openpyxl ; extra == 'rbr'
 
 # Teaspoon
 

{tsp-1.4.9.dist-info → tsp-1.5.3.dist-info}/RECORD

@@ -1,23 +1,42 @@
-tsp/__init__.py,sha256=txeQiOv87P8Jsartlzx8o6yGhgLMzmLshJiqj-7m4BU,368
-tsp/__meta__.py,sha256=aJoYzKMTLxsj_ebew1nK76WJBzXRkt7Vr9-d6GBJABw,93
-tsp/core.py,sha256=zVITPQPYLeEh5_-DlqN9PzcJRkja0gADBvkrbFFm8IY,30354
+tsp/__init__.py,sha256=Ye8YN7QIbwkk6qMB_D0gB_F39JHY7WHsKKpNmE41g-U,380
+tsp/__meta__.py,sha256=YRWJbWvRef7F7Aeph-Cv-keq14LjWDj1ytAoDCkHp58,93
+tsp/core.py,sha256=zXIxGnQE8BIbGbAq672aFiIOOhp2RRx59Uf0R9fVefk,30720
 tsp/gtnp.py,sha256=kIxhLq_ve_cxU9v4_nDebc8jy6l7KQ87MOg8vK8lih4,3991
 tsp/misc.py,sha256=18w41G-umRi69lswXhpvJwrx4hqQ6r3bsvnmeKtpMU4,107
-tsp/physics.py,sha256=vUVsZdQOYaaWJ65VcHm1piuTem0I7xg4MtsJm8Uf33w,2877
-tsp/readers.py,sha256=2Z1tdvzgllbjSmqQtwFme6SNGmSrR3YFzu3R9kRtni8,16726
+tsp/physics.py,sha256=hgVOGU0Bj1g-gxBNhLEl7Gm3VXJKIHHu35uPvgVMOxE,2699
+tsp/readers.py,sha256=AR2__iJIDW4MGUd11B9RF3kPCEZAQ0xzNOHSrpgd-yM,18520
 tsp/time.py,sha256=82h7nxM-iXs2XwetF-alLtNvUm0qRtAA111gTMp5SY4,1379
-tsp/utils.py,sha256=ilJebXiiKcLhL7FQMJxU8TjnSpKoRtN_WrK1_peQfAQ,2956
+tsp/utils.py,sha256=sOJSZLmfv7sh4X971_gNgtZvXtS8ZwGmUdqnUybcVE4,2932
 tsp/data/2023-01-06_755-test-Dataset_2031-Constant_Over_Interval-Hourly-Ground_Temperature-Thermistor_Automated.timeserie.csv,sha256=Q3Ssnoo_kiSn9_orZHjtMxQ02YbrjCAEQKs5sHPFJCg,171
 tsp/data/2023-01-06_755-test.metadata.txt,sha256=Ux1YGqmAmRQmMIqqK8-OloQXflg4Y45FRwdT-WgCg8c,5686
 tsp/data/example_geotop.csv,sha256=rgVP7_tGEvUtn1K_KI98VVgm275D7qt8YegKMe3Vjw4,262289
 tsp/data/example_gtnp.csv,sha256=E5km06-cWlWMwzF-Qo7v0ZrlAvCTpyWIKY6hpzln4sc,191812
 tsp/dataloggers/AbstractReader.py,sha256=YsmESWrmH2jdL-Oli9pwjaFmPCEfJxjm4wx16FoRxpY,1777
-tsp/dataloggers/FG2.py,sha256=Qud2aAEEF8EBvUiluVJDk3REJUF2wJFVEfyxKmJCEY0,2947
-tsp/dataloggers/GP5W.py,sha256=q3yqxLtHCnW_SOIE40Vw-WIC2yuFwRdFiVJ1KvgrnNs,2975
+tsp/dataloggers/FG2.py,sha256=kvfjMQtoSs5ZzV7hc1lJ_SaDuSOOTONfI_nw2VaihO8,3281
+tsp/dataloggers/GP5W.py,sha256=dJ7I-P4_bIDDGb9zIdOf9vbxbxlcT3ZJ09HKLfRA6a0,3312
 tsp/dataloggers/Geoprecision.py,sha256=pDljZDasj7PNdiI5lOEpHZ9n7CZJ1aGlX96rN4cuPHI,916
 tsp/dataloggers/HOBO.py,sha256=xr5PvdMh_AO4CSsqdGLvtdVgfphc91Nl34Qs-AiP-wQ,33472
+tsp/dataloggers/RBRXL800.py,sha256=NjS6g_-grnC8BmLLW7qUppeOBYAOUJODNR-GwahnI7Y,8538
+tsp/dataloggers/RBRXR420.py,sha256=PIY46cjJnngul3OI4mZQ1TtlcFNTJmXmyxmex6TEEeI,13908
 tsp/dataloggers/__init__.py,sha256=4QcIctP5hoVfraU3PwhkTIca-4JIWH9u6-j4CQWoW1g,410
 tsp/dataloggers/logr.py,sha256=4IaqP6debop3QYnKWAyCzRxgve25txcr1itmtCciKkY,2665
+tsp/dataloggers/test_files/004448.DAT,sha256=1eJg5PtOrwlbzitp1XB5uE64ksqQHIIjTNgKIDn7zkI,201018
+tsp/dataloggers/test_files/004531.DAT,sha256=8Pag_PnR-3dK4rhr7os6kyQXVe8i1N5w1_ACefT9G4s,331292
+tsp/dataloggers/test_files/004531.HEX,sha256=0qJio9SvecR2MS4-nkjcZwqLh8h0sKdB6js_6yKqy5k,118535
+tsp/dataloggers/test_files/004534.HEX,sha256=cWMHCZ7JOu08RM2sjqay2aZiud35LY7NSsmBhjheGRI,118531
+tsp/dataloggers/test_files/010252.dat,sha256=_f9rvVq6U3ms3YQlN05doiy46PaNwqjeDlVCZK9NeU0,171935
+tsp/dataloggers/test_files/010252.hex,sha256=3o-A8c7v-KyQr0OR1CftJW1e7c6tyvY16MsZb_s0N74,84712
+tsp/dataloggers/test_files/010274.hex,sha256=4nB6jBzsP3XsraXZ_87IZZbZCqLQRtWcQ2mvR4R1c0I,62720
+tsp/dataloggers/test_files/010278.hex,sha256=8IOkmg1EC5mTj6vLECc9_t-Nb66Yp_dxcFCs6YzkCqo,173117
+tsp/dataloggers/test_files/012064.dat,sha256=LgwK9p0uzV0f7Gt1kIJWQSZWmG25i3vOJmTaG2jQ9gM,127062
+tsp/dataloggers/test_files/012064.hex,sha256=O2VReAh3xW-Rg-z8EJ0cR7aoVqvEfL6TpPkt5FXfagY,62921
+tsp/dataloggers/test_files/012081.hex,sha256=MwCQT5VLWiUVCmQGlzAMjZMwvdKolPAgtIIIvB2Z4sU,172576
+tsp/dataloggers/test_files/062834_20220904_2351.rsk,sha256=2DJa-wnrms1N_fJ9QmvcNFH5JMIBdBhcb-nXtUMp70k,1007616
+tsp/dataloggers/test_files/062834_20220904_2351.xlsx,sha256=z2sE1P--zcQJ1FoVJu43kXoxs1wIhwXGBukwzt1nIbc,308908
+tsp/dataloggers/test_files/07B1592.DAT,sha256=KalPKVVgzKTJrVQU8_3pmIJbEV1QJgXDUcJVwHnyYrY,107655
+tsp/dataloggers/test_files/07B1592.HEX,sha256=Eav6F_ExQ7qfg-mBMkZqrsASgWLM1RafNW43o8H4vEE,59683
+tsp/dataloggers/test_files/07B4450.DAT,sha256=1CpQviX4xhtkXL6wHENMmNvmJNarOAm6UcGL2G4AMZ8,162502
+tsp/dataloggers/test_files/07B4450.HEX,sha256=MyjYMf9EwWi7c91JwrNd4n0cPyAYZT1w719MygMQWO4,84576
 tsp/dataloggers/test_files/FG2_399.csv,sha256=Uonw_fFY3TUZ1O-XFtjRrV1yLr2iqUyBOlJM_wdZQGA,648322
 tsp/dataloggers/test_files/GP5W.csv,sha256=2mQl3YfzFVtvi3pdkEfyw9Cam3TzeHqAMnY06JSU6co,36948
 tsp/dataloggers/test_files/GP5W_260.csv,sha256=AbLBA12XLQLlNXpvht7Jy_DrvCUqhC1cQdFGnNYVXg0,68696
@@ -46,10 +65,22 @@ tsp/dataloggers/test_files/hobo_1_AB_var3.csv,sha256=xwtPv3llA-LReippxcOUE20cBb_
 tsp/dataloggers/test_files/logR_ULogC16-32_1.csv,sha256=0HcCjf_jEBDpgpyTqiJC1oIoJsnt5Qdk4qV_s_KfuTQ,21966
 tsp/dataloggers/test_files/logR_ULogC16-32_2.csv,sha256=MU58RvTSwFrhJIbaKPSSKf51tPyZC9_ZXgPCCfk9p4M,19066
 tsp/dataloggers/test_files/mon_3_Ta_2010-08-18_2013-02-08.txt,sha256=Sqv23n-r1KLLdSsjjVeDvS-sX061Ivklhv5sDwRMwpA,734009
+tsp/dataloggers/test_files/rbr_001.dat,sha256=pS1QV_he33ccbfUpZMWm54AYDekez5us4MxS917wh0g,111570
+tsp/dataloggers/test_files/rbr_001.hex,sha256=HNrSlP05Y2LUqtvlzX_5O7rQrTGItUlZpMswra-dJpc,55293
+tsp/dataloggers/test_files/rbr_001_no_comment.dat,sha256=s_-tc-ShQfYqc4ObMh35xr8tQBHDxwjuBLDftX6Pc9U,111547
+tsp/dataloggers/test_files/rbr_001_no_comment.hex,sha256=HKG-sl7kw1A_Z3melKKT2xgVEAayv2fvCKzCFNM4LXA,55270
+tsp/dataloggers/test_files/rbr_002.dat,sha256=tUIX8InqQHObWzDVZrv1vTmY02zpIeepbKDpv4p5cpA,93525
+tsp/dataloggers/test_files/rbr_002.hex,sha256=W29e__jot7deVVC2XDtXwAgqfmvHzU7qi-7yQb4_mz0,57536
+tsp/dataloggers/test_files/rbr_003.hex,sha256=cjUaYWGm39WthiPvdzQKaOQ5FEKj3U9rCIe_0my7v2M,62703
+tsp/dataloggers/test_files/rbr_003.xls,sha256=PRxsKD88dTQEYOqz5z1FrkPox1jCkYyiBBZK0Kg-7tQ,263680
+tsp/dataloggers/test_files/rbr_xl_001.DAT,sha256=yZXKaClXMtYWDCs1cD2xTVdGj6LBMLKSjKnTgB4qPio,80057
+tsp/dataloggers/test_files/rbr_xl_002.DAT,sha256=JQNHL6X9z4Rp6IDqDBYx8vWsUU6oigl8nC23rMa3Enk,81601
+tsp/dataloggers/test_files/rbr_xl_003.DAT,sha256=ZEKheCvB1CiubY2kMngigY0NNhWTYAiC_hmQhzODPYw,221656
+tsp/dataloggers/test_files/rbr_xl_003.HEX,sha256=sunCD5C1t8l5y4p1b9iiHNsZUznYIuBLz4uwoGkZh3E,118459
 tsp/plots/__init__.py,sha256=i5AhpNwyuT6il7uk2Vtc4YBjVnZ0ifvHNXw19rvDtsM,71
 tsp/plots/static.py,sha256=hH-FkazPMKgqI74NtGUn_D_avo6ts9ZmzWgov2GLmEU,9448
-tsp-1.4.9.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-tsp-1.4.9.dist-info/METADATA,sha256=_iyP8WbiCvHDWsbxi1F7AJrqE5f328G1F_qXLJo-JZg,2731
-tsp-1.4.9.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-tsp-1.4.9.dist-info/top_level.txt,sha256=7tOR6y7BarphfWD2D7QFi_3F1jxagUZpHG8zwJIw4ck,30
-tsp-1.4.9.dist-info/RECORD,,
+tsp-1.5.3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+tsp-1.5.3.dist-info/METADATA,sha256=nObnySvS_vS3145_sZ9CBKEB5gSMeaxx72A5y2amAeU,2835
+tsp-1.5.3.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+tsp-1.5.3.dist-info/top_level.txt,sha256=7tOR6y7BarphfWD2D7QFi_3F1jxagUZpHG8zwJIw4ck,30
+tsp-1.5.3.dist-info/RECORD,,

{tsp-1.4.9.dist-info → tsp-1.5.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: bdist_wheel (0.40.0)
 Root-Is-Purelib: true
 Tag: py3-none-any