eclab.mpr: Further fixes (#182)

* mpr file fixes

* revert warning -> valueerror

* Fix appended/merged files.

* Add reference to paper.

* ruff

---------

Co-authored-by: Arnd Koeppe <[email protected]>

docs/source/citing.rst

@@ -2,18 +2,27 @@ Citing **yadg**
 ---------------
 **yadg** is currently being developed at the `ConCat Lab <https://tu.berlin/en/concat>`_ at Technische Universität Berlin, Berlin, Germany. It has been previously developed at `Materials for Energy Conversion lab <https://www.empa.ch/web/s501>`_ at Empa, Dübendorf, Switzerland. If you find **yadg** useful, please cite our recent paper [Kraus2022b]_, or our previous work where **yadg** was first introduced [Kraus2022a]_.
 
-Other works where **yadg** has been used include [Bernasconi2023a]_, [Kraus2024a]_ and [Senocrate2024a]_. If you found **yadg** useful, and would like your publication listed, let us know!
-
 We extend no warranty, neither express nor implied.
 
+.. [Kraus2022b]
+  Kraus, P.; Vetsch, N.; Battaglia, C. *yadg: yet another datagram*, Journal of Open Source Software **2022**, *7*, 4166, DOI: https://doi.org/10.21105/joss.04166
+
+.. [Kraus2022a]
+  Kraus, P.; Wolf, E.H.; Prinz, C.; Bellini, G.; Trunschke, A.; Schlögl, R. *Towards automation of operando experiments: a case study in contactless conductivity measurements*, Digital Discovery **2022**, *1*, 241, DOI: https://doi.org/10.1039/D1DD00029B
+
+
 Papers related to yadg
 ``````````````````````
-.. [Senocrate2024a] Senocrate, A.; Bernasconi, F.; Kraus, P.; Plainpan, N.; Trafkowski, J.; Tolle, F.; Weber, T.; Sauter, U.; Battaglia, C.; *Parallel experiments in electrochemical CO2 reduction enabled by standardized analytics*, Nature Catalysis **2024**, *7*, 742, DOI: https://doi.org/10.1038/s41929-024-01172-x
+If you found **yadg** useful, and would like your publication listed, let us know!
 
-.. [Kraus2024a] Kraus, P.; Bainglass, E.; Ramirez, F. F.; Svaluto-Ferro, E.; Ercole, L.; Kunz, B.; Huber, S. P.; Plainpan, N.; Marzari, N.; Battaglia, C.; Pizzi, G. *A bridge between trust and control: computational workflows meet automated battery cycling*, Journal of Materials Chemistry A **2024**, *12*, 10773, DOI: https://doi.org/10.1039/D3TA06889G
+.. [#]
+  Stüble, P.; Müller, C.; Bohn, N.; Müller, M.; Hofmann, A.; Akçay, T.; Klemens, J.; Koeppe, A.; Kolli, S.; Rajagopal, D.; Geßwein, H.; Schabel, W.; Scharfer, P.; Selzer, M.; Binder, J. R.; Smith, A.; *From Powder to Pouch Cell: Setting up a Sodium-Ion Battery Reference System Based on Na3V2(PO4)3/C and Hard Carbon*, Batteries & Supercaps **2024**, e202400406, DOI: https://doi.org/10.1002/batt.202400406
 
-.. [Bernasconi2023a] Bernasconi, F.; Senocrate, A.; Kraus, P.; Battaglia, C.; *Enhancing C≥2 product selectivity in electrochemical CO2 reduction by controlling the microstructure of gas diffusion electrodes*, EES Catalysis **2023**, *1*, 1009, DOI: https://doi.org/10.1039/D3EY00140G
+.. [#]
+  Senocrate, A.; Bernasconi, F.; Kraus, P.; Plainpan, N.; Trafkowski, J.; Tolle, F.; Weber, T.; Sauter, U.; Battaglia, C.; *Parallel experiments in electrochemical CO2 reduction enabled by standardized analytics*, Nature Catalysis **2024**, *7*, 742, DOI: https://doi.org/10.1038/s41929-024-01172-x
 
-.. [Kraus2022b] Kraus, P.; Vetsch, N.; Battaglia, C. *yadg: yet another datagram*, Journal of Open Source Software **2022**, *7*, 4166, DOI: https://doi.org/10.21105/joss.04166
+.. [#]
+  Kraus, P.; Bainglass, E.; Ramirez, F. F.; Svaluto-Ferro, E.; Ercole, L.; Kunz, B.; Huber, S. P.; Plainpan, N.; Marzari, N.; Battaglia, C.; Pizzi, G. *A bridge between trust and control: computational workflows meet automated battery cycling*, Journal of Materials Chemistry A **2024**, *12*, 10773, DOI: https://doi.org/10.1039/D3TA06889G
 
-.. [Kraus2022a] Kraus, P.; Wolf, E.H.; Prinz, C.; Bellini, G.; Trunschke, A.; Schlögl, R. *Towards automation of operando experiments: a case study in contactless conductivity measurements*, Digital Discovery **2022**, *1*, 241, DOI: https://doi.org/10.1039/D1DD00029B
+.. [#]
+  Bernasconi, F.; Senocrate, A.; Kraus, P.; Battaglia, C.; *Enhancing C≥2 product selectivity in electrochemical CO2 reduction by controlling the microstructure of gas diffusion electrodes*, EES Catalysis **2023**, *1*, 1009, DOI: https://doi.org/10.1039/D3EY00140G

docs/source/conf.py

@@ -88,3 +88,5 @@
     "datatree": ("https://xarray-datatree.readthedocs.io/en/latest/", None),
     "babel": ("https://babel.pocoo.org/en/latest/", None),
 }
+
+suppress_warnings = ["ref.footnote"]

src/yadg/extractors/eclab/common/techniques.py

@@ -1030,6 +1030,7 @@
     0x32: ("ZIR", _zir_params_dtypes),
     0x33: ("CVA", _cva_params_dtypes),
     0x6C: ("LSV", _lsv_params_dtype),
+    0x77: ("GCPL", _gcpl_params_dtypes),
     0x7F: ("MB", _mb_params_dtypes),
 }
 

src/yadg/extractors/eclab/mpr.py

@@ -410,6 +410,7 @@ def process_data(
     values = np.frombuffer(data, offset=offset, dtype=data_dtype, count=n_datapoints)
     values = [dict(zip(value.dtype.names, value.item())) for value in values]
     warn_I_range = False
+    warn_Ns = False
     for vi, vals in enumerate(values):
         # Lets split this into two loops: get the indices first, then the data
         for (name, value), unit in list(zip(vals.items(), unitlist)):
@@ -431,6 +432,10 @@ def process_data(
                 vals[name] = (flag_bits & bitmask) >> shift
 
         Ns = vals.get("Ns", 0)
+        # Manually merged/appended mpr files have a mysteriously larger Ns
+        if Ns >= len(Eranges):
+            warn_Ns = True
+            Ns = len(Eranges) - 1
         Erange = Eranges[Ns]
         Irstr = Iranges[Ns]
         if "I Range" in vals:
@@ -444,13 +449,15 @@ def process_data(
 
         if "control_V_I" in vals:
             icv = controls[Ns]
-            name = f"control_{icv}"
+            name = "control_I" if icv in {"I", "C"} else "control_V"  # f"control_{icv}"
             vals[name] = vals.pop("control_V_I")
             units[name] = "mA" if icv in {"I", "C"} else "V"
         devs = get_devs(vals=vals, units=units, Erange=Erange, Irange=Irange)
         dgutils.append_dicts(vals, devs, allvals, allmeta, li=vi)
     if warn_I_range:
         logger.warning("I Range could not be understood, defaulting to 1 A.")
+    if warn_Ns:
+        logger.warning("Ns found in data exceeds Ns in header, using last defined Ns.")
 
     ds = dgutils.dicts_to_dataset(allvals, allmeta, units, fulldate=False)
     return ds

src/yadg/extractors/eclab/mpt.py

@@ -210,7 +210,7 @@ def process_data(
     units = dict()
     columns = list()
     for n in names:
-        c, u = column_units[n]
+        c, u = column_units[n.strip()]
         if c in columns:
             logger.warning("Duplicate column '%s' with unit '%s'.", c, u)
             c = f"duplicate {c}"

tests/test_x_eclab.py

@@ -100,3 +100,30 @@ def test_eclab_consistency_partial(afile, bfile, locale, _datadir):
         except AssertionError as e:
             e.args = (e.args[0] + f"Error happened on key: {key!r}\n",)
             raise e
+
+
+@pytest.mark.parametrize(
+    "afile, bfile, locale",
+    [
+        ("gcpl.pr_182.1.mpr", "gcpl.pr_182.1.mpt", "en_US"),
+        ("gcpl.pr_182.2.mpr", "gcpl.pr_182.2.mpt", "en_US"),
+    ],
+)
+def test_eclab_consistency_partial_2(afile, bfile, locale, _datadir):
+    os.chdir(_datadir)
+    aret = extract_mpr(fn=afile, timezone="Europe/Berlin")
+    bret = extract_mpt(
+        fn=bfile, timezone="Europe/Berlin", encoding="windows-1252", locale=locale
+    )
+    print(f"{aret.data_vars=}")
+    print(f"{bret.data_vars=}")
+    for key in aret.variables:
+        if key.endswith("std_err"):
+            continue
+        elif key in {"control_I"}:
+            continue
+        try:
+            xr.testing.assert_allclose(aret[key], bret[key])
+        except AssertionError as e:
+            e.args = (e.args[0] + f"Error happened on key: {key!r}\n",)
+            raise e