From 6ab9571230916bb548d16973a4ea1c63b966742d Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Tue, 14 Feb 2023 15:35:01 +0100
Subject: [PATCH 01/11] Remove typesystem decorator from Table class

---
 ubermagtable/table.py | 38 ++++++++++++++++++++++++++++++++++----
 1 file changed, 34 insertions(+), 4 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index a1995e3..d801e99 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -2,15 +2,11 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import ubermagutil.typesystem as ts
 import ubermagutil.units
 
 import ubermagtable.util as uu
 
 
-@ts.typesystem(
-    data=ts.Typed(expected_type=pd.DataFrame), units=ts.Typed(expected_type=dict)
-)
 class Table:
     """Tabular data class.
 
@@ -111,6 +107,40 @@ def fromfile(cls, filename, /, x=None, rename=True):
             x=x,
         )
 
+    @property
+    def data(self):
+        """Scalar data of the drive.
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self._data
+
+    @data.setter
+    def data(self, data):
+        if not isinstance(data, pd.DataFrame):
+            raise TypeError(f"Invalid {type(data)=}; expected 'pandas.DataFrame'.")
+        self._data = data
+
+    @property
+    def units(self):
+        """Units of the scalar data.
+
+        Returns
+        -------
+        dict
+
+            Keys are the columns in the ``data`` property, values the respective units.
+        """
+        return self._units
+
+    @units.setter
+    def units(self, units):
+        if not isinstance(units, dict):
+            raise TypeError(f"Invalid {type(units)=}; 'expected dict'.")
+        self._units = units
+
     @property
     def x(self):
         """Independent variable.

From fe7cadc7a518783a7538216828f454a2c3385219 Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Thu, 16 Feb 2023 16:52:25 +0100
Subject: [PATCH 02/11] Re-write reading tabular data

---
 ubermagtable/table.py         | 229 +++++++++++++++++++++++-
 ubermagtable/util/__init__.py |   2 -
 ubermagtable/util/util.py     | 317 ----------------------------------
 3 files changed, 221 insertions(+), 327 deletions(-)
 delete mode 100644 ubermagtable/util/util.py

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index d801e99..a82e5f2 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -1,11 +1,11 @@
+import re
+
 import ipywidgets
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import ubermagutil.units
 
-import ubermagtable.util as uu
-
 
 class Table:
     """Tabular data class.
@@ -47,6 +47,139 @@ class Table:
 
     """
 
+    # The OOMMF columns are renamed according to this dictionary.
+    _OOMMF_DICT = {
+        "RungeKuttaEvolve:evolver:Total energy": "E",
+        "RungeKuttaEvolve:evolver:Energy calc count": "E_calc_count",
+        "RungeKuttaEvolve:evolver:Max dm/dt": "max_dm/dt",
+        "RungeKuttaEvolve:evolver:dE/dt": "dE/dt",
+        "RungeKuttaEvolve:evolver:Delta E": "delta_E",
+        "RungeKuttaEvolve::Total energy": "E",
+        "RungeKuttaEvolve::Energy calc count": "E_calc_count",
+        "RungeKuttaEvolve::Max dm/dt": "max_dm/dt",
+        "RungeKuttaEvolve::dE/dt": "dE/dt",
+        "RungeKuttaEvolve::Delta E": "delta_E",
+        "EulerEvolve:evolver:Total energy": "E",
+        "EulerEvolve:evolver:Energy calc count": "E_calc_count",
+        "EulerEvolve:evolver:Max dm/dt": "max_dmdt",
+        "EulerEvolve:evolver:dE/dt": "dE/dt",
+        "EulerEvolve:evolver:Delta E": "delta_E",
+        "TimeDriver::Iteration": "iteration",
+        "TimeDriver::Stage iteration": "stage_iteration",
+        "TimeDriver::Stage": "stage",
+        "TimeDriver::mx": "mx",
+        "TimeDriver::my": "my",
+        "TimeDriver::mz": "mz",
+        "TimeDriver::Last time step": "last_time_step",
+        "TimeDriver::Simulation time": "t",
+        "CGEvolve:evolver:Max mxHxm": "max_mxHxm",
+        "CGEvolve:evolver:Total energy": "E",
+        "CGEvolve:evolver:Delta E": "delta_E",
+        "CGEvolve:evolver:Bracket count": "bracket_count",
+        "CGEvolve:evolver:Line min count": "line_min_count",
+        "CGEvolve:evolver:Conjugate cycle count": "conjugate_cycle_count",
+        "CGEvolve:evolver:Cycle count": "cycle_count",
+        "CGEvolve:evolver:Cycle sub count": "cycle_sub_count",
+        "CGEvolve:evolver:Energy calc count": "energy_calc_count",
+        "CGEvolve::Max mxHxm": "max_mxHxm",
+        "CGEvolve::Total energy": "E",
+        "CGEvolve::Delta E": "delta_E",
+        "CGEvolve::Bracket count": "bracket_count",
+        "CGEvolve::Line min count": "line_min_count",
+        "CGEvolve::Conjugate cycle count": "conjugate_cycle_count",
+        "CGEvolve::Cycle count": "cycle_count",
+        "CGEvolve::Cycle sub count": "cycle_sub_count",
+        "CGEvolve::Energy calc count": "energy_calc_count",
+        "FixedMEL::Energy": "MEL_E",
+        "FixedMEL:magnetoelastic:Energy": "MEL_E",
+        "SpinTEvolve:evolver:Total energy": "E",
+        "SpinTEvolve:evolver:Energy calc count": "E_calc_count",
+        "SpinTEvolve:evolver:Max dm/dt": "max_dmdt",
+        "SpinTEvolve:evolver:dE/dt": "dE/dt",
+        "SpinTEvolve:evolver:Delta E": "delta_E",
+        "SpinTEvolve:evolver:average u": "average_u",
+        "SpinXferEvolve:evolver:Total energy": "E",
+        "SpinXferEvolve:evolver:Energy calc count": "E_calc_count",
+        "SpinXferEvolve:evolver:Max dm/dt": "max_dmdt",
+        "SpinXferEvolve:evolver:dE/dt": "dE/dt",
+        "SpinXferEvolve:evolver:Delta E": "delta_E",
+        "SpinXferEvolve:evolver:average u": "average_u",
+        "SpinXferEvolve:evolver:average J": "average_J",
+        "ThetaEvolve:evolver:Total energy": "E",
+        "ThetaEvolve:evolver:Energy calc count": "E_calc_count",
+        "ThetaEvolve:evolver:Max dm/dt": "max_dmdt",
+        "ThetaEvolve:evolver:dE/dt": "dE/dt",
+        "ThetaEvolve:evolver:Delta E": "delta_E",
+        "ThetaEvolve:evolver:Temperature": "T",
+        "ThermHeunEvolve:evolver:Total energy": "E",
+        "ThermHeunEvolve:evolver:Energy calc count": "E_calc_count",
+        "ThermHeunEvolve:evolver:Max dm/dt": "max_dmdt",
+        "ThermHeunEvolve:evolver:dE/dt": "dE/dt",
+        "ThermHeunEvolve:evolver:Delta E": "delta_E",
+        "ThermHeunEvolve:evolver:Temperature": "T",
+        "ThermSpinXferEvolve:evolver:Total energy": "E",
+        "ThermSpinXferEvolve:evolver:Energy calc count": "E_calc_count",
+        "ThermSpinXferEvolve:evolver:Max dm/dt": "max_dmdt",
+        "ThermSpinXferEvolve:evolver:dE/dt": "dE/dt",
+        "ThermSpinXferEvolve:evolver:Delta E": "delta_E",
+        "ThermSpinXferEvolve:evolver:Temperature": "T",
+        "MinDriver::Iteration": "iteration",
+        "MinDriver::Stage iteration": "stage_iteration",
+        "MinDriver::Stage": "stage",
+        "MinDriver::mx": "mx",
+        "MinDriver::my": "my",
+        "MinDriver::mz": "mz",
+        "UniformExchange::Max Spin Ang": "max_spin_ang",
+        "UniformExchange::Stage Max Spin Ang": "stage_max_spin_ang",
+        "UniformExchange::Run Max Spin Ang": "run_max_spin_ang",
+        "UniformExchange::Energy": "E_exchange",
+        "DMExchange6Ngbr::Energy": "E",
+        "DMI_Cnv::Energy": "E",
+        "DMI_T::Energy": "E",
+        "DMI_D2d::Energy": "E",
+        "Demag::Energy": "E",
+        "FixedZeeman::Energy": "E_zeeman",
+        "UZeeman::Energy": "E_zeeman",
+        "UZeeman::B": "B",
+        "UZeeman::Bx": "Bx",
+        "UZeeman::By": "By",
+        "UZeeman::Bz": "Bz",
+        "ScriptUZeeman::Energy": "E",
+        "ScriptUZeeman::B": "B",
+        "ScriptUZeeman::Bx": "Bx",
+        "ScriptUZeeman::By": "By",
+        "ScriptUZeeman::Bz": "Bz",
+        "TransformZeeman::Energy": "E",
+        "CubicAnisotropy::Energy": "E",
+        "UniaxialAnisotropy::Energy": "E",
+        "UniaxialAnisotropy4::Energy": "E",
+        "Southampton_UniaxialAnisotropy4::Energy": "E",
+        "Exchange6Ngbr::Energy": "E",
+        "Exchange6Ngbr::Max Spin Ang": "max_spin_ang",
+        "Exchange6Ngbr::Stage Max Spin Ang": "stage_max_spin_ang",
+        "Exchange6Ngbr::Run Max Spin Ang": "run_max_spin_ang",
+        "ExchangePtwise::Energy": "E",
+        "ExchangePtwise::Max Spin Ang": "max_spin_ang",
+        "ExchangePtwise::Stage Max Spin Ang": "stage_max_spin_ang",
+        "ExchangePtwise::Run Max Spin Ang": "run_max_spin_ang",
+        "TwoSurfaceExchange::Energy": "E",
+    }
+
+    # The mumax3 columns are renamed according to this dictionary.
+    _MUMAX3_DICT = {
+        "t": "t",
+        "mx": "mx",
+        "my": "my",
+        "mz": "mz",
+        "E_total": "E",
+        "E_exch": "E_totalexchange",
+        "E_demag": "E_demag",
+        "E_Zeeman": "E_zeeman",
+        "E_anis": "E_totalanisotropy",
+        "dt": "dt",
+        "maxTorque": "maxtorque",
+    }
+
     def __init__(self, data, units, x=None, attributes=None):
         self.data = data
         self.units = units
@@ -99,13 +232,93 @@ def fromfile(cls, filename, /, x=None, rename=True):
         >>> table = ut.Table.fromfile(odtfile, x='t')
 
         """
-        cols = uu.columns(filename, rename=rename)
-
-        return cls(
-            data=pd.DataFrame(uu.data(filename), columns=cols),
-            units=uu.units(filename, rename=rename),
-            x=x,
+        quantities = cls._read_header(filename, rename=rename)
+        data = pd.read_csv(
+            filename,
+            sep=r"\s+",
+            comment="#",
+            header=None,
+            names=list(quantities.keys()),
         )
+        return cls(data=data, units=quantities, x=x)
+
+    @classmethod
+    def _read_header(cls, filename, rename=True):
+        """Extracts quantities for individual columns from a table file.
+
+        This method extracts both column names and units and returns a dictionary,
+        where keys are column names and values are the units.
+
+        Parameters
+        ----------
+        filename : str
+
+            OOMMF ``.odt`` or mumax3 ``.txt`` file.
+
+        rename : bool
+
+            If ``rename=True``, the column names are renamed with their shorter
+            versions. Defaults to ``True``.
+
+        Returns
+        -------
+        dict
+
+            Dictionary of column names and units.
+        """
+
+        with open(filename) as f:
+            if (header_line_1 := f.readline()).startswith("# ODT"):  # OOMMF odt file
+                cols_dict = cls._OOMMF_DICT
+                # COLUMN NAMES
+                while not (cline := f.readline()).startswith("# Columns"):
+                    pass
+                columns = cline.lstrip("# Columns:").rstrip()
+                cols = [
+                    re.sub(r"Oxs_|Anv_|Southampton_|My_|YY_|UHH_|Xf_", "", col)
+                    for col in re.findall(r"(?<={)[^}]+|[^ {}]+", columns)
+                ]
+                # UNITS
+                uline = f.readline()
+                assert uline.startswith("# Units:")
+                units = uline.split()[2:]  # [2:] to remove ["#", "Units:"]
+                units = [re.sub(r"[{}]", "", unit) for unit in units]
+            else:  # mumax3 txt file
+                cols_dict = cls._MUMAX3_DICT
+                header_line_1 = header_line_1[len("# ") :].rstrip().split("\t")
+                # COLUMN NAMES
+                cols = [elem.split()[0] for elem in header_line_1]
+                # UNITS
+                units = [re.sub(r"[()]", "", elem.split()[1]) for elem in header_line_1]
+
+        if rename:
+            cols = [cls._rename_column(col, cols_dict) for col in cols]
+        print(len(cols))
+        print(len(set(cols)))
+
+        return dict(zip(cols, units))
+
+    @staticmethod
+    def _rename_column(name, cols_dict):
+        """Rename columns to get shorter names without spaces.
+
+        Renaming is based on _OOMMF_DICT or _MUMAX3_DICT.
+        """
+        if name in cols_dict:
+            return cols_dict[name]
+
+        for key in cols_dict:
+            if len(key.split("::")) == 2:
+                start, end = key.split("::")
+                name_split = name.split(":")
+                if name_split[0] == start and name_split[-1] == end:
+                    term_name = name_split[1]
+                    type_name = cols_dict[key]
+                    # required for E_exchange in old and new OOMMF odt files
+                    if not type_name.endswith(term_name):
+                        type_name = f"{type_name}_{term_name}"
+                    return type_name
+        return name  # name cannot be found in dictionary
 
     @property
     def data(self):
diff --git a/ubermagtable/util/__init__.py b/ubermagtable/util/__init__.py
index 79f451e..e69de29 100644
--- a/ubermagtable/util/__init__.py
+++ b/ubermagtable/util/__init__.py
@@ -1,2 +0,0 @@
-"""Utility tools"""
-from .util import columns, data, units
diff --git a/ubermagtable/util/util.py b/ubermagtable/util/util.py
deleted file mode 100644
index 4a9cff4..0000000
--- a/ubermagtable/util/util.py
+++ /dev/null
@@ -1,317 +0,0 @@
-import re
-
-# The OOMMF columns are renamed according to this dictionary.
-oommf_dict = {
-    "RungeKuttaEvolve:evolver:Total energy": "E",
-    "RungeKuttaEvolve:evolver:Energy calc count": "E_calc_count",
-    "RungeKuttaEvolve:evolver:Max dm/dt": "max_dm/dt",
-    "RungeKuttaEvolve:evolver:dE/dt": "dE/dt",
-    "RungeKuttaEvolve:evolver:Delta E": "delta_E",
-    "RungeKuttaEvolve::Total energy": "E",
-    "RungeKuttaEvolve::Energy calc count": "E_calc_count",
-    "RungeKuttaEvolve::Max dm/dt": "max_dm/dt",
-    "RungeKuttaEvolve::dE/dt": "dE/dt",
-    "RungeKuttaEvolve::Delta E": "delta_E",
-    "EulerEvolve:evolver:Total energy": "E",
-    "EulerEvolve:evolver:Energy calc count": "E_calc_count",
-    "EulerEvolve:evolver:Max dm/dt": "max_dmdt",
-    "EulerEvolve:evolver:dE/dt": "dE/dt",
-    "EulerEvolve:evolver:Delta E": "delta_E",
-    "TimeDriver::Iteration": "iteration",
-    "TimeDriver::Stage iteration": "stage_iteration",
-    "TimeDriver::Stage": "stage",
-    "TimeDriver::mx": "mx",
-    "TimeDriver::my": "my",
-    "TimeDriver::mz": "mz",
-    "TimeDriver::Last time step": "last_time_step",
-    "TimeDriver::Simulation time": "t",
-    "CGEvolve:evolver:Max mxHxm": "max_mxHxm",
-    "CGEvolve:evolver:Total energy": "E",
-    "CGEvolve:evolver:Delta E": "delta_E",
-    "CGEvolve:evolver:Bracket count": "bracket_count",
-    "CGEvolve:evolver:Line min count": "line_min_count",
-    "CGEvolve:evolver:Conjugate cycle count": "conjugate_cycle_count",
-    "CGEvolve:evolver:Cycle count": "cycle_count",
-    "CGEvolve:evolver:Cycle sub count": "cycle_sub_count",
-    "CGEvolve:evolver:Energy calc count": "energy_calc_count",
-    "CGEvolve::Max mxHxm": "max_mxHxm",
-    "CGEvolve::Total energy": "E",
-    "CGEvolve::Delta E": "delta_E",
-    "CGEvolve::Bracket count": "bracket_count",
-    "CGEvolve::Line min count": "line_min_count",
-    "CGEvolve::Conjugate cycle count": "conjugate_cycle_count",
-    "CGEvolve::Cycle count": "cycle_count",
-    "CGEvolve::Cycle sub count": "cycle_sub_count",
-    "CGEvolve::Energy calc count": "energy_calc_count",
-    "FixedMEL::Energy": "MEL_E",
-    "FixedMEL:magnetoelastic:Energy": "MEL_E",
-    "SpinTEvolve:evolver:Total energy": "E",
-    "SpinTEvolve:evolver:Energy calc count": "E_calc_count",
-    "SpinTEvolve:evolver:Max dm/dt": "max_dmdt",
-    "SpinTEvolve:evolver:dE/dt": "dE/dt",
-    "SpinTEvolve:evolver:Delta E": "delta_E",
-    "SpinTEvolve:evolver:average u": "average_u",
-    "SpinXferEvolve:evolver:Total energy": "E",
-    "SpinXferEvolve:evolver:Energy calc count": "E_calc_count",
-    "SpinXferEvolve:evolver:Max dm/dt": "max_dmdt",
-    "SpinXferEvolve:evolver:dE/dt": "dE/dt",
-    "SpinXferEvolve:evolver:Delta E": "delta_E",
-    "SpinXferEvolve:evolver:average u": "average_u",
-    "SpinXferEvolve:evolver:average J": "average_J",
-    "ThetaEvolve:evolver:Total energy": "E",
-    "ThetaEvolve:evolver:Energy calc count": "E_calc_count",
-    "ThetaEvolve:evolver:Max dm/dt": "max_dmdt",
-    "ThetaEvolve:evolver:dE/dt": "dE/dt",
-    "ThetaEvolve:evolver:Delta E": "delta_E",
-    "ThetaEvolve:evolver:Temperature": "T",
-    "ThermHeunEvolve:evolver:Total energy": "E",
-    "ThermHeunEvolve:evolver:Energy calc count": "E_calc_count",
-    "ThermHeunEvolve:evolver:Max dm/dt": "max_dmdt",
-    "ThermHeunEvolve:evolver:dE/dt": "dE/dt",
-    "ThermHeunEvolve:evolver:Delta E": "delta_E",
-    "ThermHeunEvolve:evolver:Temperature": "T",
-    "ThermSpinXferEvolve:evolver:Total energy": "E",
-    "ThermSpinXferEvolve:evolver:Energy calc count": "E_calc_count",
-    "ThermSpinXferEvolve:evolver:Max dm/dt": "max_dmdt",
-    "ThermSpinXferEvolve:evolver:dE/dt": "dE/dt",
-    "ThermSpinXferEvolve:evolver:Delta E": "delta_E",
-    "ThermSpinXferEvolve:evolver:Temperature": "T",
-    "MinDriver::Iteration": "iteration",
-    "MinDriver::Stage iteration": "stage_iteration",
-    "MinDriver::Stage": "stage",
-    "MinDriver::mx": "mx",
-    "MinDriver::my": "my",
-    "MinDriver::mz": "mz",
-    "UniformExchange::Max Spin Ang": "max_spin_ang",
-    "UniformExchange::Stage Max Spin Ang": "stage_max_spin_ang",
-    "UniformExchange::Run Max Spin Ang": "run_max_spin_ang",
-    "UniformExchange::Energy": "E_exchange",
-    "DMExchange6Ngbr::Energy": "E",
-    "DMI_Cnv::Energy": "E",
-    "DMI_T::Energy": "E",
-    "DMI_D2d::Energy": "E",
-    "Demag::Energy": "E",
-    "FixedZeeman::Energy": "E_zeeman",
-    "UZeeman::Energy": "E_zeeman",
-    "UZeeman::B": "B",
-    "UZeeman::Bx": "Bx",
-    "UZeeman::By": "By",
-    "UZeeman::Bz": "Bz",
-    "ScriptUZeeman::Energy": "E",
-    "ScriptUZeeman::B": "B",
-    "ScriptUZeeman::Bx": "Bx",
-    "ScriptUZeeman::By": "By",
-    "ScriptUZeeman::Bz": "Bz",
-    "TransformZeeman::Energy": "E",
-    "CubicAnisotropy::Energy": "E",
-    "UniaxialAnisotropy::Energy": "E",
-    "UniaxialAnisotropy4::Energy": "E",
-    "Southampton_UniaxialAnisotropy4::Energy": "E",
-    "Exchange6Ngbr::Energy": "E",
-    "Exchange6Ngbr::Max Spin Ang": "max_spin_ang",
-    "Exchange6Ngbr::Stage Max Spin Ang": "stage_max_spin_ang",
-    "Exchange6Ngbr::Run Max Spin Ang": "run_max_spin_ang",
-    "ExchangePtwise::Energy": "E",
-    "ExchangePtwise::Max Spin Ang": "max_spin_ang",
-    "ExchangePtwise::Stage Max Spin Ang": "stage_max_spin_ang",
-    "ExchangePtwise::Run Max Spin Ang": "run_max_spin_ang",
-    "TwoSurfaceExchange::Energy": "E",
-}
-
-# The mumax3 columns are renamed according to this dictionary.
-mumax3_dict = {
-    "t": "t",
-    "mx": "mx",
-    "my": "my",
-    "mz": "mz",
-    "E_total": "E",
-    "E_exch": "E_totalexchange",
-    "E_demag": "E_demag",
-    "E_Zeeman": "E_zeeman",
-    "E_anis": "E_totalanisotropy",
-    "dt": "dt",
-    "maxTorque": "maxtorque",
-}
-
-
-def rename_column(name, cols_dict):
-    if name in cols_dict.keys():
-        return cols_dict[name]
-
-    for key in cols_dict.keys():
-        if len(key.split("::")) == 2:
-            start, end = key.split("::")
-            name_split = name.split(":")
-            if name_split[0] == start and name_split[-1] == end:
-                term_name = name.split(":")[1]
-                type_name = cols_dict[key]
-                # required for E_exchange in old and new OOMMF odt files
-                if not type_name.endswith(term_name):
-                    type_name = f"{type_name}_{term_name}"
-                return type_name
-    else:
-        return name  # name cannot be found in dictionary
-
-
-def columns(filename, rename=True):
-    """Extracts column names from a table file.
-
-    Parameters
-    ----------
-    filename : str
-
-        OOMMF ``.odt`` or mumax3 ``.txt`` file.
-
-    rename : bool
-
-        If ``rename=True``, the column names are renamed with their shorter
-        versions. Defaults to ``True``.
-
-    Returns
-    -------
-    list
-
-        List of column names.
-
-    Examples
-    --------
-    1. Extracting the column names from an OOMMF `.odt` file.
-
-    >>> import os
-    >>> import ubermagtable.util as uu
-    ...
-    >>> odtfile = os.path.join(os.path.dirname(__file__), '..',
-    ...                        'tests', 'test_sample', 'oommf-new-file1.odt')
-    >>> uu.columns(odtfile)
-    [...]
-
-    2. Extracting the names of columns from a mumax3 `.txt` file.
-
-    >>> odtfile = os.path.join(os.path.dirname(__file__), '..',
-    ...                        'tests', 'test_sample', 'mumax3-file1.txt')
-    >>> uu.columns(odtfile)
-    [...]
-
-    """
-    with open(filename) as f:
-        lines = f.readlines()
-
-    if lines[0].startswith("# ODT"):  # OOMMF odt file
-        cline = list(filter(lambda line: line.startswith("# Columns:"), lines))[0]
-        cline = re.split(r"Oxs_|Anv_|Southampton_|My_|YY_|UHH_|Xf_", cline)[1:]
-        cline = list(map(lambda col: re.sub(r"[{}]", "", col), cline))
-        cols = list(map(lambda s: s.strip(), cline))
-        cols_dict = oommf_dict
-    else:  # mumax3 txt file
-        cline = lines[0][2:].rstrip().split("\t")
-        cols = list(map(lambda s: s.split(" ")[0], cline))
-        cols_dict = mumax3_dict
-
-    if rename:
-        return [rename_column(col, cols_dict) for col in cols]
-    else:
-        return cols
-
-
-def units(filename, rename=True):
-    """Extracts units for individual columns from a table file.
-
-    This method extracts both column names and units and returns a dictionary,
-    where keys are column names and values are the units.
-
-    Parameters
-    ----------
-    filename : str
-
-        OOMMF ``.odt`` or mumax3 ``.txt`` file.
-
-    rename : bool
-
-        If ``rename=True``, the column names are renamed with their shorter
-        versions. Defaults to ``True``.
-
-    Returns
-    -------
-    dict
-
-        Dictionary of column names and units.
-
-    Examples
-    --------
-    1. Extracting units for individual columns from an OOMMF ``.odt`` file.
-
-    >>> import os
-    >>> import ubermagtable.util as uu
-    ...
-    >>> odtfile = os.path.join(os.path.dirname(__file__), '..',
-    ...                        'tests', 'test_sample', 'oommf-new-file2.odt')
-    >>> uu.units(odtfile)
-    {...}
-
-    2. Extracting units for individual columns from a mumax3 ``.txt`` file.
-
-    >>> odtfile = os.path.join(os.path.dirname(__file__), '..',
-    ...                        'tests', 'test_sample', 'mumax3-file1.txt')
-    >>> uu.units(odtfile)
-    {...}
-
-    """
-    with open(filename) as f:
-        lines = f.readlines()
-
-    if lines[0].startswith("# ODT"):  # OOMMF odt file
-        uline = list(filter(lambda line: line.startswith("# Units:"), lines))[0]
-        units = uline.split()[2:]
-        units = list(map(lambda s: re.sub(r"[{}]", "", s), units))
-    else:  # mumax3 txt file
-        uline = lines[0][2:].rstrip().split("\t")
-        units = list(map(lambda s: s.split()[1], uline))
-        units = list(map(lambda s: re.sub(r"[()]", "", s), units))
-
-    return dict(zip(columns(filename, rename=rename), units))
-
-
-def data(filename):
-    """Extracts numerical data from a table file.
-
-    Parameters
-    ----------
-    filename : str
-
-        OOMMF ``.odt`` or mumax3 ``.txt`` file.
-
-    Returns
-    -------
-    list
-
-        List of numerical data.
-
-    Examples
-    --------
-    1. Reading data from an OOMMF ``.odt`` file.
-
-    >>> import os
-    >>> import ubermagtable.util as uu
-    ...
-    >>> odtfile = os.path.join(os.path.dirname(__file__), '..',
-    ...                        'tests', 'test_sample', 'oommf-new-file3.odt')
-    >>> uu.data(odtfile)
-    [...]
-
-    2. Reading data from a mumax3 ``.txt`` file.
-
-    >>> odtfile = os.path.join(os.path.dirname(__file__), '..',
-    ...                        'tests', 'test_sample', 'mumax3-file1.txt')
-    >>> uu.data(odtfile)
-    [...]
-
-    """
-    with open(filename) as f:
-        lines = f.readlines()
-
-    values = []
-    for line in lines:
-        if not line.startswith("#"):
-            values.append(list(map(float, line.split())))
-
-    return values

From 5cb42d98509c57ab4da21b30340cb71c7d0976d3 Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Thu, 16 Feb 2023 16:54:16 +0100
Subject: [PATCH 03/11] Explain problem in test

---
 ubermagtable/tests/test_table.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/ubermagtable/tests/test_table.py b/ubermagtable/tests/test_table.py
index d1d3e69..305a1a7 100644
--- a/ubermagtable/tests/test_table.py
+++ b/ubermagtable/tests/test_table.py
@@ -178,6 +178,11 @@ def test_oommf_mel(self):
         assert len(columns) == 16
 
     def test_oommf_issue1(self):
+        """The odt file contains columns ``Oxs_Exchange6Ngbr:...`` and
+        ``My_Exchange6Ngbr:...``. During processing we remove the ``Oxs_`` or ``My_``
+        prefix and subsequently loose the "duplicated" columns in the pandas dataframe.
+
+        """
         table = ut.Table.fromfile(self.odtfiles[-1])
         columns = table.data.columns.to_list()
         assert len(columns) == 30

From a8e4a063ca8c4069937f13995cc761037134c184 Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Fri, 17 Feb 2023 12:22:17 +0100
Subject: [PATCH 04/11] Detect and remove duplication in the data.

---
 ubermagtable/table.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index a82e5f2..1b252b8 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -186,6 +186,16 @@ def __init__(self, data, units, x=None, attributes=None):
         self.x = x
         self.attributes = attributes if attributes is not None else {}
         self.attributes.setdefault("fourierspace", False)
+        # Detect duplicated lines as a last step to make use of the checks when
+        # assigning 'x' as independent variable.
+        self._duplicated_lines = any(self.data.duplicated(subset=self.x, keep="last"))
+        if self._duplicated_lines:
+            self.data.drop_duplicates(
+                subset=self.x,
+                keep="last",
+                inplace=True,
+                ignore_index=True,  # reset the index to 0, 1, ..., n-1
+            )
 
     @classmethod
     def fromfile(cls, filename, /, x=None, rename=True):
@@ -442,6 +452,11 @@ def xmax(self):
         """
         return self.data[self.x].iloc[-1]
 
+    @property
+    def deduplicated(self):
+        """Indicate if the table on disk contains duplicated steps."""
+        return self._duplicated_lines
+
     def apply(self, func, columns=None, args=(), **kwargs):
         r"""Apply function.
 

From 62a687e2357f7922ef884ded45b1adc14bebbfbe Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Fri, 17 Feb 2023 12:29:04 +0100
Subject: [PATCH 05/11] Remove left-over print

---
 ubermagtable/table.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index 1b252b8..f96d7e4 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -303,8 +303,6 @@ def _read_header(cls, filename, rename=True):
 
         if rename:
             cols = [cls._rename_column(col, cols_dict) for col in cols]
-        print(len(cols))
-        print(len(set(cols)))
 
         return dict(zip(cols, units))
 

From cd9f7caf15896a126e2dbd9a529cf39f124e5f80 Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Mon, 20 Feb 2023 12:05:36 +0100
Subject: [PATCH 06/11] Update _OOMMF_DICT (add prefix)

---
 ubermagtable/table.py | 232 +++++++++++++++++++++---------------------
 1 file changed, 114 insertions(+), 118 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index f96d7e4..63fcaa3 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -49,120 +49,119 @@ class Table:
 
     # The OOMMF columns are renamed according to this dictionary.
     _OOMMF_DICT = {
-        "RungeKuttaEvolve:evolver:Total energy": "E",
-        "RungeKuttaEvolve:evolver:Energy calc count": "E_calc_count",
-        "RungeKuttaEvolve:evolver:Max dm/dt": "max_dm/dt",
-        "RungeKuttaEvolve:evolver:dE/dt": "dE/dt",
-        "RungeKuttaEvolve:evolver:Delta E": "delta_E",
-        "RungeKuttaEvolve::Total energy": "E",
-        "RungeKuttaEvolve::Energy calc count": "E_calc_count",
-        "RungeKuttaEvolve::Max dm/dt": "max_dm/dt",
-        "RungeKuttaEvolve::dE/dt": "dE/dt",
-        "RungeKuttaEvolve::Delta E": "delta_E",
-        "EulerEvolve:evolver:Total energy": "E",
-        "EulerEvolve:evolver:Energy calc count": "E_calc_count",
-        "EulerEvolve:evolver:Max dm/dt": "max_dmdt",
-        "EulerEvolve:evolver:dE/dt": "dE/dt",
-        "EulerEvolve:evolver:Delta E": "delta_E",
-        "TimeDriver::Iteration": "iteration",
-        "TimeDriver::Stage iteration": "stage_iteration",
-        "TimeDriver::Stage": "stage",
-        "TimeDriver::mx": "mx",
-        "TimeDriver::my": "my",
-        "TimeDriver::mz": "mz",
-        "TimeDriver::Last time step": "last_time_step",
-        "TimeDriver::Simulation time": "t",
-        "CGEvolve:evolver:Max mxHxm": "max_mxHxm",
-        "CGEvolve:evolver:Total energy": "E",
-        "CGEvolve:evolver:Delta E": "delta_E",
-        "CGEvolve:evolver:Bracket count": "bracket_count",
-        "CGEvolve:evolver:Line min count": "line_min_count",
-        "CGEvolve:evolver:Conjugate cycle count": "conjugate_cycle_count",
-        "CGEvolve:evolver:Cycle count": "cycle_count",
-        "CGEvolve:evolver:Cycle sub count": "cycle_sub_count",
-        "CGEvolve:evolver:Energy calc count": "energy_calc_count",
-        "CGEvolve::Max mxHxm": "max_mxHxm",
-        "CGEvolve::Total energy": "E",
-        "CGEvolve::Delta E": "delta_E",
-        "CGEvolve::Bracket count": "bracket_count",
-        "CGEvolve::Line min count": "line_min_count",
-        "CGEvolve::Conjugate cycle count": "conjugate_cycle_count",
-        "CGEvolve::Cycle count": "cycle_count",
-        "CGEvolve::Cycle sub count": "cycle_sub_count",
-        "CGEvolve::Energy calc count": "energy_calc_count",
-        "FixedMEL::Energy": "MEL_E",
-        "FixedMEL:magnetoelastic:Energy": "MEL_E",
-        "SpinTEvolve:evolver:Total energy": "E",
-        "SpinTEvolve:evolver:Energy calc count": "E_calc_count",
-        "SpinTEvolve:evolver:Max dm/dt": "max_dmdt",
-        "SpinTEvolve:evolver:dE/dt": "dE/dt",
-        "SpinTEvolve:evolver:Delta E": "delta_E",
-        "SpinTEvolve:evolver:average u": "average_u",
-        "SpinXferEvolve:evolver:Total energy": "E",
-        "SpinXferEvolve:evolver:Energy calc count": "E_calc_count",
-        "SpinXferEvolve:evolver:Max dm/dt": "max_dmdt",
-        "SpinXferEvolve:evolver:dE/dt": "dE/dt",
-        "SpinXferEvolve:evolver:Delta E": "delta_E",
-        "SpinXferEvolve:evolver:average u": "average_u",
-        "SpinXferEvolve:evolver:average J": "average_J",
-        "ThetaEvolve:evolver:Total energy": "E",
-        "ThetaEvolve:evolver:Energy calc count": "E_calc_count",
-        "ThetaEvolve:evolver:Max dm/dt": "max_dmdt",
-        "ThetaEvolve:evolver:dE/dt": "dE/dt",
-        "ThetaEvolve:evolver:Delta E": "delta_E",
-        "ThetaEvolve:evolver:Temperature": "T",
-        "ThermHeunEvolve:evolver:Total energy": "E",
-        "ThermHeunEvolve:evolver:Energy calc count": "E_calc_count",
-        "ThermHeunEvolve:evolver:Max dm/dt": "max_dmdt",
-        "ThermHeunEvolve:evolver:dE/dt": "dE/dt",
-        "ThermHeunEvolve:evolver:Delta E": "delta_E",
-        "ThermHeunEvolve:evolver:Temperature": "T",
-        "ThermSpinXferEvolve:evolver:Total energy": "E",
-        "ThermSpinXferEvolve:evolver:Energy calc count": "E_calc_count",
-        "ThermSpinXferEvolve:evolver:Max dm/dt": "max_dmdt",
-        "ThermSpinXferEvolve:evolver:dE/dt": "dE/dt",
-        "ThermSpinXferEvolve:evolver:Delta E": "delta_E",
-        "ThermSpinXferEvolve:evolver:Temperature": "T",
-        "MinDriver::Iteration": "iteration",
-        "MinDriver::Stage iteration": "stage_iteration",
-        "MinDriver::Stage": "stage",
-        "MinDriver::mx": "mx",
-        "MinDriver::my": "my",
-        "MinDriver::mz": "mz",
-        "UniformExchange::Max Spin Ang": "max_spin_ang",
-        "UniformExchange::Stage Max Spin Ang": "stage_max_spin_ang",
-        "UniformExchange::Run Max Spin Ang": "run_max_spin_ang",
-        "UniformExchange::Energy": "E_exchange",
-        "DMExchange6Ngbr::Energy": "E",
-        "DMI_Cnv::Energy": "E",
-        "DMI_T::Energy": "E",
-        "DMI_D2d::Energy": "E",
-        "Demag::Energy": "E",
-        "FixedZeeman::Energy": "E_zeeman",
-        "UZeeman::Energy": "E_zeeman",
-        "UZeeman::B": "B",
-        "UZeeman::Bx": "Bx",
-        "UZeeman::By": "By",
-        "UZeeman::Bz": "Bz",
-        "ScriptUZeeman::Energy": "E",
-        "ScriptUZeeman::B": "B",
-        "ScriptUZeeman::Bx": "Bx",
-        "ScriptUZeeman::By": "By",
-        "ScriptUZeeman::Bz": "Bz",
-        "TransformZeeman::Energy": "E",
-        "CubicAnisotropy::Energy": "E",
-        "UniaxialAnisotropy::Energy": "E",
-        "UniaxialAnisotropy4::Energy": "E",
-        "Southampton_UniaxialAnisotropy4::Energy": "E",
-        "Exchange6Ngbr::Energy": "E",
-        "Exchange6Ngbr::Max Spin Ang": "max_spin_ang",
-        "Exchange6Ngbr::Stage Max Spin Ang": "stage_max_spin_ang",
-        "Exchange6Ngbr::Run Max Spin Ang": "run_max_spin_ang",
-        "ExchangePtwise::Energy": "E",
-        "ExchangePtwise::Max Spin Ang": "max_spin_ang",
-        "ExchangePtwise::Stage Max Spin Ang": "stage_max_spin_ang",
-        "ExchangePtwise::Run Max Spin Ang": "run_max_spin_ang",
-        "TwoSurfaceExchange::Energy": "E",
+        "Oxs_RungeKuttaEvolve:evolver:Total energy": "E",
+        "Oxs_RungeKuttaEvolve:evolver:Energy calc count": "E_calc_count",
+        "Oxs_RungeKuttaEvolve:evolver:Max dm/dt": "max_dm/dt",
+        "Oxs_RungeKuttaEvolve:evolver:dE/dt": "dE/dt",
+        "Oxs_RungeKuttaEvolve:evolver:Delta E": "delta_E",
+        "Oxs_RungeKuttaEvolve::Total energy": "E",
+        "Oxs_RungeKuttaEvolve::Energy calc count": "E_calc_count",
+        "Oxs_RungeKuttaEvolve::Max dm/dt": "max_dm/dt",
+        "Oxs_RungeKuttaEvolve::dE/dt": "dE/dt",
+        "Oxs_RungeKuttaEvolve::Delta E": "delta_E",
+        "Oxs_EulerEvolve:evolver:Total energy": "E",
+        "Oxs_EulerEvolve:evolver:Energy calc count": "E_calc_count",
+        "Oxs_EulerEvolve:evolver:Max dm/dt": "max_dmdt",
+        "Oxs_EulerEvolve:evolver:dE/dt": "dE/dt",
+        "Oxs_EulerEvolve:evolver:Delta E": "delta_E",
+        "Oxs_TimeDriver::Iteration": "iteration",
+        "Oxs_TimeDriver::Stage iteration": "stage_iteration",
+        "Oxs_TimeDriver::Stage": "stage",
+        "Oxs_TimeDriver::mx": "mx",
+        "Oxs_TimeDriver::my": "my",
+        "Oxs_TimeDriver::mz": "mz",
+        "Oxs_TimeDriver::Last time step": "last_time_step",
+        "Oxs_TimeDriver::Simulation time": "t",
+        "Oxs_CGEvolve:evolver:Max mxHxm": "max_mxHxm",
+        "Oxs_CGEvolve:evolver:Total energy": "E",
+        "Oxs_CGEvolve:evolver:Delta E": "delta_E",
+        "Oxs_CGEvolve:evolver:Bracket count": "bracket_count",
+        "Oxs_CGEvolve:evolver:Line min count": "line_min_count",
+        "Oxs_CGEvolve:evolver:Conjugate cycle count": "conjugate_cycle_count",
+        "Oxs_CGEvolve:evolver:Cycle count": "cycle_count",
+        "Oxs_CGEvolve:evolver:Cycle sub count": "cycle_sub_count",
+        "Oxs_CGEvolve:evolver:Energy calc count": "energy_calc_count",
+        "Oxs_CGEvolve::Max mxHxm": "max_mxHxm",
+        "Oxs_CGEvolve::Total energy": "E",
+        "Oxs_CGEvolve::Delta E": "delta_E",
+        "Oxs_CGEvolve::Bracket count": "bracket_count",
+        "Oxs_CGEvolve::Line min count": "line_min_count",
+        "Oxs_CGEvolve::Conjugate cycle count": "conjugate_cycle_count",
+        "Oxs_CGEvolve::Cycle count": "cycle_count",
+        "Oxs_CGEvolve::Cycle sub count": "cycle_sub_count",
+        "Oxs_CGEvolve::Energy calc count": "energy_calc_count",
+        "YY_FixedMEL::Energy": "MEL_E",
+        "YY_FixedMEL:magnetoelastic:Energy": "MEL_E",  # NO SAMPLE, TODO DELETE?
+        "Anv_SpinTEvolve:evolver:Total energy": "E",
+        "Anv_SpinTEvolve:evolver:Energy calc count": "E_calc_count",
+        "Anv_SpinTEvolve:evolver:Max dm/dt": "max_dmdt",
+        "Anv_SpinTEvolve:evolver:dE/dt": "dE/dt",
+        "Anv_SpinTEvolve:evolver:Delta E": "delta_E",
+        "Anv_SpinTEvolve:evolver:average u": "average_u",
+        "Oxs_SpinXferEvolve:evolver:Total energy": "E",  # NO SAMPLE
+        "Oxs_SpinXferEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
+        "Oxs_SpinXferEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
+        "Oxs_SpinXferEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
+        "Oxs_SpinXferEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
+        "Oxs_SpinXferEvolve:evolver:average u": "average_u",  # NO SAMPLE
+        "Oxs_SpinXferEvolve:evolver:average J": "average_J",  # NO SAMPLE
+        "UHH_ThetaEvolve:evolver:Total energy": "E",  # NO SAMPLE
+        "UHH_ThetaEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
+        "UHH_ThetaEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
+        "UHH_ThetaEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
+        "UHH_ThetaEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
+        "UHH_ThetaEvolve:evolver:Temperature": "T",  # NO SAMPLE
+        "Xf_ThermHeunEvolve:evolver:Total energy": "E",  # NO SAMPLE
+        "Xf_ThermHeunEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
+        "Xf_ThermHeunEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
+        "Xf_ThermHeunEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
+        "Xf_ThermHeunEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
+        "Xf_ThermHeunEvolve:evolver:Temperature": "T",  # NO SAMPLE
+        "Xf_ThermSpinXferEvolve:evolver:Total energy": "E",  # NO SAMPLE
+        "Xf_ThermSpinXferEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
+        "Xf_ThermSpinXferEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
+        "Xf_ThermSpinXferEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
+        "Xf_ThermSpinXferEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
+        "Xf_ThermSpinXferEvolve:evolver:Temperature": "T",  # NO SAMPLE
+        "Oxs_MinDriver::Iteration": "iteration",
+        "Oxs_MinDriver::Stage iteration": "stage_iteration",
+        "Oxs_MinDriver::Stage": "stage",
+        "Oxs_MinDriver::mx": "mx",
+        "Oxs_MinDriver::my": "my",
+        "Oxs_MinDriver::mz": "mz",
+        "Oxs_UniformExchange::Max Spin Ang": "max_spin_ang",
+        "Oxs_UniformExchange::Stage Max Spin Ang": "stage_max_spin_ang",
+        "Oxs_UniformExchange::Run Max Spin Ang": "run_max_spin_ang",
+        "Oxs_UniformExchange::Energy": "E_exchange",
+        "Oxs_DMExchange6Ngbr::Energy": "E",  # NO SAMPLE
+        "Oxs_DMI_Cnv::Energy": "E",  # TODO: PREFIX
+        "Oxs_DMI_T::Energy": "E",  # NO SAMPLE,  TODO: PREFIX
+        "Oxs_DMI_D2d::Energy": "E",  # NO SAMPLE,  TODO: PREFIX
+        "Oxs_Demag::Energy": "E",
+        "Oxs_FixedZeeman::Energy": "E_zeeman",
+        "Oxs_UZeeman::Energy": "E_zeeman",
+        "Oxs_UZeeman::B": "B",
+        "Oxs_UZeeman::Bx": "Bx",
+        "Oxs_UZeeman::By": "By",
+        "Oxs_UZeeman::Bz": "Bz",
+        "Oxs_ScriptUZeeman::Energy": "E",  # NO SAMPLE
+        "Oxs_ScriptUZeeman::B": "B",  # NO SAMPLE
+        "Oxs_ScriptUZeeman::Bx": "Bx",  # NO SAMPLE
+        "Oxs_ScriptUZeeman::By": "By",  # NO SAMPLE
+        "Oxs_ScriptUZeeman::Bz": "Bz",  # NO SAMPLE
+        "Oxs_TransformZeeman::Energy": "E",  # NO SAMPLE
+        "Oxs_CubicAnisotropy::Energy": "E",
+        "Oxs_UniaxialAnisotropy::Energy": "E",
+        "Southampton_UniaxialAnisotropy4::Energy": "E",  # NO SAMPLE
+        "Oxs_Exchange6Ngbr::Energy": "E",
+        "Oxs_Exchange6Ngbr::Max Spin Ang": "max_spin_ang",
+        "Oxs_Exchange6Ngbr::Stage Max Spin Ang": "stage_max_spin_ang",
+        "Oxs_Exchange6Ngbr::Run Max Spin Ang": "run_max_spin_ang",
+        "Oxs_ExchangePtwise::Energy": "E",  # NO SAMPLE
+        "Oxs_ExchangePtwise::Max Spin Ang": "max_spin_ang",  # NO SAMPLE
+        "Oxs_ExchangePtwise::Stage Max Spin Ang": "stage_max_spin_ang",  # NO SAMPLE
+        "Oxs_ExchangePtwise::Run Max Spin Ang": "run_max_spin_ang",  # NO SAMPLE
+        "Oxs_TwoSurfaceExchange::Energy": "E",  # NO SAMPLE
     }
 
     # The mumax3 columns are renamed according to this dictionary.
@@ -284,10 +283,7 @@ def _read_header(cls, filename, rename=True):
                 while not (cline := f.readline()).startswith("# Columns"):
                     pass
                 columns = cline.lstrip("# Columns:").rstrip()
-                cols = [
-                    re.sub(r"Oxs_|Anv_|Southampton_|My_|YY_|UHH_|Xf_", "", col)
-                    for col in re.findall(r"(?<={)[^}]+|[^ {}]+", columns)
-                ]
+                cols = re.findall(r"(?<={)[^}]+|[^ {}]+", columns)
                 # UNITS
                 uline = f.readline()
                 assert uline.startswith("# Units:")

From 19348349665619d6ba4b7576d1541612924cc34d Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Mon, 20 Feb 2023 12:45:54 +0100
Subject: [PATCH 07/11] Re-write renaming functionality

---
 ubermagtable/table.py | 270 ++++++++++++++++++++++--------------------
 1 file changed, 142 insertions(+), 128 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index 63fcaa3..b212408 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -49,119 +49,134 @@ class Table:
 
     # The OOMMF columns are renamed according to this dictionary.
     _OOMMF_DICT = {
-        "Oxs_RungeKuttaEvolve:evolver:Total energy": "E",
-        "Oxs_RungeKuttaEvolve:evolver:Energy calc count": "E_calc_count",
-        "Oxs_RungeKuttaEvolve:evolver:Max dm/dt": "max_dm/dt",
-        "Oxs_RungeKuttaEvolve:evolver:dE/dt": "dE/dt",
-        "Oxs_RungeKuttaEvolve:evolver:Delta E": "delta_E",
-        "Oxs_RungeKuttaEvolve::Total energy": "E",
-        "Oxs_RungeKuttaEvolve::Energy calc count": "E_calc_count",
-        "Oxs_RungeKuttaEvolve::Max dm/dt": "max_dm/dt",
-        "Oxs_RungeKuttaEvolve::dE/dt": "dE/dt",
-        "Oxs_RungeKuttaEvolve::Delta E": "delta_E",
-        "Oxs_EulerEvolve:evolver:Total energy": "E",
-        "Oxs_EulerEvolve:evolver:Energy calc count": "E_calc_count",
-        "Oxs_EulerEvolve:evolver:Max dm/dt": "max_dmdt",
-        "Oxs_EulerEvolve:evolver:dE/dt": "dE/dt",
-        "Oxs_EulerEvolve:evolver:Delta E": "delta_E",
-        "Oxs_TimeDriver::Iteration": "iteration",
-        "Oxs_TimeDriver::Stage iteration": "stage_iteration",
-        "Oxs_TimeDriver::Stage": "stage",
-        "Oxs_TimeDriver::mx": "mx",
-        "Oxs_TimeDriver::my": "my",
-        "Oxs_TimeDriver::mz": "mz",
-        "Oxs_TimeDriver::Last time step": "last_time_step",
-        "Oxs_TimeDriver::Simulation time": "t",
-        "Oxs_CGEvolve:evolver:Max mxHxm": "max_mxHxm",
-        "Oxs_CGEvolve:evolver:Total energy": "E",
-        "Oxs_CGEvolve:evolver:Delta E": "delta_E",
-        "Oxs_CGEvolve:evolver:Bracket count": "bracket_count",
-        "Oxs_CGEvolve:evolver:Line min count": "line_min_count",
-        "Oxs_CGEvolve:evolver:Conjugate cycle count": "conjugate_cycle_count",
-        "Oxs_CGEvolve:evolver:Cycle count": "cycle_count",
-        "Oxs_CGEvolve:evolver:Cycle sub count": "cycle_sub_count",
-        "Oxs_CGEvolve:evolver:Energy calc count": "energy_calc_count",
-        "Oxs_CGEvolve::Max mxHxm": "max_mxHxm",
-        "Oxs_CGEvolve::Total energy": "E",
-        "Oxs_CGEvolve::Delta E": "delta_E",
-        "Oxs_CGEvolve::Bracket count": "bracket_count",
-        "Oxs_CGEvolve::Line min count": "line_min_count",
-        "Oxs_CGEvolve::Conjugate cycle count": "conjugate_cycle_count",
-        "Oxs_CGEvolve::Cycle count": "cycle_count",
-        "Oxs_CGEvolve::Cycle sub count": "cycle_sub_count",
-        "Oxs_CGEvolve::Energy calc count": "energy_calc_count",
-        "YY_FixedMEL::Energy": "MEL_E",
-        "YY_FixedMEL:magnetoelastic:Energy": "MEL_E",  # NO SAMPLE, TODO DELETE?
-        "Anv_SpinTEvolve:evolver:Total energy": "E",
-        "Anv_SpinTEvolve:evolver:Energy calc count": "E_calc_count",
-        "Anv_SpinTEvolve:evolver:Max dm/dt": "max_dmdt",
-        "Anv_SpinTEvolve:evolver:dE/dt": "dE/dt",
-        "Anv_SpinTEvolve:evolver:Delta E": "delta_E",
-        "Anv_SpinTEvolve:evolver:average u": "average_u",
-        "Oxs_SpinXferEvolve:evolver:Total energy": "E",  # NO SAMPLE
-        "Oxs_SpinXferEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
-        "Oxs_SpinXferEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
-        "Oxs_SpinXferEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
-        "Oxs_SpinXferEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
-        "Oxs_SpinXferEvolve:evolver:average u": "average_u",  # NO SAMPLE
-        "Oxs_SpinXferEvolve:evolver:average J": "average_J",  # NO SAMPLE
-        "UHH_ThetaEvolve:evolver:Total energy": "E",  # NO SAMPLE
-        "UHH_ThetaEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
-        "UHH_ThetaEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
-        "UHH_ThetaEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
-        "UHH_ThetaEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
-        "UHH_ThetaEvolve:evolver:Temperature": "T",  # NO SAMPLE
-        "Xf_ThermHeunEvolve:evolver:Total energy": "E",  # NO SAMPLE
-        "Xf_ThermHeunEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
-        "Xf_ThermHeunEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
-        "Xf_ThermHeunEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
-        "Xf_ThermHeunEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
-        "Xf_ThermHeunEvolve:evolver:Temperature": "T",  # NO SAMPLE
-        "Xf_ThermSpinXferEvolve:evolver:Total energy": "E",  # NO SAMPLE
-        "Xf_ThermSpinXferEvolve:evolver:Energy calc count": "E_calc_count",  # NO SAMPLE
-        "Xf_ThermSpinXferEvolve:evolver:Max dm/dt": "max_dmdt",  # NO SAMPLE
-        "Xf_ThermSpinXferEvolve:evolver:dE/dt": "dE/dt",  # NO SAMPLE
-        "Xf_ThermSpinXferEvolve:evolver:Delta E": "delta_E",  # NO SAMPLE
-        "Xf_ThermSpinXferEvolve:evolver:Temperature": "T",  # NO SAMPLE
-        "Oxs_MinDriver::Iteration": "iteration",
-        "Oxs_MinDriver::Stage iteration": "stage_iteration",
-        "Oxs_MinDriver::Stage": "stage",
-        "Oxs_MinDriver::mx": "mx",
-        "Oxs_MinDriver::my": "my",
-        "Oxs_MinDriver::mz": "mz",
-        "Oxs_UniformExchange::Max Spin Ang": "max_spin_ang",
-        "Oxs_UniformExchange::Stage Max Spin Ang": "stage_max_spin_ang",
-        "Oxs_UniformExchange::Run Max Spin Ang": "run_max_spin_ang",
-        "Oxs_UniformExchange::Energy": "E_exchange",
-        "Oxs_DMExchange6Ngbr::Energy": "E",  # NO SAMPLE
-        "Oxs_DMI_Cnv::Energy": "E",  # TODO: PREFIX
-        "Oxs_DMI_T::Energy": "E",  # NO SAMPLE,  TODO: PREFIX
-        "Oxs_DMI_D2d::Energy": "E",  # NO SAMPLE,  TODO: PREFIX
-        "Oxs_Demag::Energy": "E",
-        "Oxs_FixedZeeman::Energy": "E_zeeman",
-        "Oxs_UZeeman::Energy": "E_zeeman",
-        "Oxs_UZeeman::B": "B",
-        "Oxs_UZeeman::Bx": "Bx",
-        "Oxs_UZeeman::By": "By",
-        "Oxs_UZeeman::Bz": "Bz",
-        "Oxs_ScriptUZeeman::Energy": "E",  # NO SAMPLE
-        "Oxs_ScriptUZeeman::B": "B",  # NO SAMPLE
-        "Oxs_ScriptUZeeman::Bx": "Bx",  # NO SAMPLE
-        "Oxs_ScriptUZeeman::By": "By",  # NO SAMPLE
-        "Oxs_ScriptUZeeman::Bz": "Bz",  # NO SAMPLE
-        "Oxs_TransformZeeman::Energy": "E",  # NO SAMPLE
-        "Oxs_CubicAnisotropy::Energy": "E",
-        "Oxs_UniaxialAnisotropy::Energy": "E",
-        "Southampton_UniaxialAnisotropy4::Energy": "E",  # NO SAMPLE
-        "Oxs_Exchange6Ngbr::Energy": "E",
-        "Oxs_Exchange6Ngbr::Max Spin Ang": "max_spin_ang",
-        "Oxs_Exchange6Ngbr::Stage Max Spin Ang": "stage_max_spin_ang",
-        "Oxs_Exchange6Ngbr::Run Max Spin Ang": "run_max_spin_ang",
-        "Oxs_ExchangePtwise::Energy": "E",  # NO SAMPLE
-        "Oxs_ExchangePtwise::Max Spin Ang": "max_spin_ang",  # NO SAMPLE
-        "Oxs_ExchangePtwise::Stage Max Spin Ang": "stage_max_spin_ang",  # NO SAMPLE
-        "Oxs_ExchangePtwise::Run Max Spin Ang": "run_max_spin_ang",  # NO SAMPLE
-        "Oxs_TwoSurfaceExchange::Energy": "E",  # NO SAMPLE
+        "Oxs_RungeKuttaEvolve": {
+            "Total energy": "E",
+            "Energy calc count": "E_calc_count",
+            "Max dm/dt": "max_dm/dt",
+            "dE/dt": "dE/dt",
+            "Delta E": "delta_E",
+        },
+        "Oxs_EulerEvolve": {
+            "Total energy": "E",
+            "Energy calc count": "E_calc_count",
+            "Max dm/dt": "max_dmdt",
+            "dE/dt": "dE/dt",
+            "Delta E": "delta_E",
+        },
+        "Oxs_TimeDriver": {
+            "Iteration": "iteration",
+            "Stage iteration": "stage_iteration",
+            "Stage": "stage",
+            "mx": "mx",
+            "my": "my",
+            "mz": "mz",
+            "Last time step": "last_time_step",
+            "Simulation time": "t",
+        },
+        "Oxs_CGEvolve": {
+            "Max mxHxm": "max_mxHxm",
+            "Total energy": "E",
+            "Delta E": "delta_E",
+            "Bracket count": "bracket_count",
+            "Line min count": "line_min_count",
+            "Conjugate cycle count": "conjugate_cycle_count",
+            "Cycle count": "cycle_count",
+            "Cycle sub count": "cycle_sub_count",
+            "Energy calc count": "energy_calc_count",
+        },
+        "YY_FixedMEL": {"Energy": "MEL_E"},
+        "Anv_SpinTEvolve": {
+            "Total energy": "E",
+            "Energy calc count": "E_calc_count",
+            "Max dm/dt": "max_dmdt",
+            "dE/dt": "dE/dt",
+            "Delta E": "delta_E",
+            "average u": "average_u",
+        },
+        "Oxs_SpinXferEvolve": {
+            "Total energy": "E",  # NO SAMPLE
+            "Energy calc count": "E_calc_count",  # NO SAMPLE
+            "Max dm/dt": "max_dmdt",  # NO SAMPLE
+            "dE/dt": "dE/dt",  # NO SAMPLE
+            "Delta E": "delta_E",  # NO SAMPLE
+            "average u": "average_u",  # NO SAMPLE
+            "average J": "average_J",  # NO SAMPLE
+        },
+        "UHH_ThetaEvolve": {
+            "Total energy": "E",  # NO SAMPLE
+            "Energy calc count": "E_calc_count",  # NO SAMPLE
+            "Max dm/dt": "max_dmdt",  # NO SAMPLE
+            "dE/dt": "dE/dt",  # NO SAMPLE
+            "Delta E": "delta_E",  # NO SAMPLE
+            "Temperature": "T",  # NO SAMPLE
+        },
+        "Xf_ThermHeunEvolve": {
+            "Total energy": "E",  # NO SAMPLE
+            "Energy calc count": "E_calc_count",  # NO SAMPLE
+            "Max dm/dt": "max_dmdt",  # NO SAMPLE
+            "dE/dt": "dE/dt",  # NO SAMPLE
+            "Delta E": "delta_E",  # NO SAMPLE
+            "Temperature": "T",  # NO SAMPLE
+        },
+        "Xf_ThermSpinXferEvolve": {
+            "Total energy": "E",  # NO SAMPLE
+            "Energy calc count": "E_calc_count",  # NO SAMPLE
+            "Max dm/dt": "max_dmdt",  # NO SAMPLE
+            "dE/dt": "dE/dt",  # NO SAMPLE
+            "Delta E": "delta_E",  # NO SAMPLE
+            "Temperature": "T",  # NO SAMPLE
+        },
+        "Oxs_MinDriver": {
+            "Iteration": "iteration",
+            "Stage iteration": "stage_iteration",
+            "Stage": "stage",
+            "mx": "mx",
+            "my": "my",
+            "mz": "mz",
+        },
+        "Oxs_UniformExchange": {
+            "Max Spin Ang": "max_spin_ang",
+            "Stage Max Spin Ang": "stage_max_spin_ang",
+            "Run Max Spin Ang": "run_max_spin_ang",
+            "Energy": "E_exchange",
+        },
+        "Oxs_DMExchange6Ngbr": {"Energy": "E_DM_exchange6ngbr"},  # NO SAMPLE
+        "Oxs_DMI_Cnv": {"Energy": "E_DMI_Cnv"},  # TODO: PREFIX
+        "Oxs_DMI_T": {"Energy": "E_DMI_T"},  # NO SAMPLE,  TODO: PREFIX
+        "Oxs_DMI_D2d": {"Energy": "E_DMI_Dd"},  # NO SAMPLE,  TODO: PREFIX
+        "Oxs_Demag": {"Energy": "E_demag"},
+        "Oxs_FixedZeeman": {"Energy": "E_zeeman"},
+        "Oxs_UZeeman": {
+            "Energy": "E_zeeman",
+            "B": "B",
+            "Bx": "Bx",
+            "By": "By",
+            "Bz": "Bz",
+        },
+        "Oxs_ScriptUZeeman": {
+            "Energy": "E_zeeman",  # NO SAMPLE
+            "B": "B",  # NO SAMPLE
+            "Bx": "Bx",  # NO SAMPLE
+            "By": "By",  # NO SAMPLE
+            "Bz": "Bz",  # NO SAMPLE
+        },
+        "Oxs_TransformZeeman": {"Energy": "E_zeeman"},  # NO SAMPLE
+        "Oxs_CubicAnisotropy": {"Energy": "E_zeeman"},
+        "Oxs_UniaxialAnisotropy": {"Energy": "E_zeeman"},
+        "Southampton_UniaxialAnisotropy4": {"Energy": "E_zeeman"},  # NO SAMPLE
+        "Oxs_Exchange6Ngbr": {
+            "Energy": "E_exchange6ngbr",
+            "Max Spin Ang": "max_spin_ang",
+            "Stage Max Spin Ang": "stage_max_spin_ang",
+            "Run Max Spin Ang": "run_max_spin_ang",
+        },
+        "Oxs_ExchangePtwise": {
+            "Energy": "E_exchange_ptwise",  # NO SAMPLE
+            "Max Spin Ang": "max_spin_ang",  # NO SAMPLE
+            "Stage Max Spin Ang": "stage_max_spin_ang",  # NO SAMPLE
+            "Run Max Spin Ang": "run_max_spin_ang",  # NO SAMPLE
+        },
+        "Oxs_TwoSurfaceExchange": {"Energy": "E_two_surface_exchange"},  # NO SAMPLE
     }
 
     # The mumax3 columns are renamed according to this dictionary.
@@ -308,21 +323,20 @@ def _rename_column(name, cols_dict):
 
         Renaming is based on _OOMMF_DICT or _MUMAX3_DICT.
         """
-        if name in cols_dict:
-            return cols_dict[name]
-
-        for key in cols_dict:
-            if len(key.split("::")) == 2:
-                start, end = key.split("::")
-                name_split = name.split(":")
-                if name_split[0] == start and name_split[-1] == end:
-                    term_name = name_split[1]
-                    type_name = cols_dict[key]
-                    # required for E_exchange in old and new OOMMF odt files
-                    if not type_name.endswith(term_name):
-                        type_name = f"{type_name}_{term_name}"
-                    return type_name
-        return name  # name cannot be found in dictionary
+        name_split = name.split(":")
+        try:
+            group = cols_dict[name_split[0]]
+            if isinstance(group, str):  # Mumax3 keys
+                return group
+            quantity = group[name_split[-1]]
+            term_name = name_split[1]
+            if not quantity.endswith(term_name):
+                # unique names if the same quantity is present multiple times
+                # e.g. multiple Zeeman fields
+                quantity = f"{quantity}_{term_name}"
+            return quantity
+        except KeyError:
+            return name
 
     @property
     def data(self):

From 154a47163a2ffd87f49fc327cbcd682d04403f5c Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Mon, 20 Feb 2023 12:48:05 +0100
Subject: [PATCH 08/11] Re-order _OOMMF_DICT

---
 ubermagtable/table.py | 50 +++++++++++++++++++++----------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index b212408..1011bd9 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -63,16 +63,6 @@ class Table:
             "dE/dt": "dE/dt",
             "Delta E": "delta_E",
         },
-        "Oxs_TimeDriver": {
-            "Iteration": "iteration",
-            "Stage iteration": "stage_iteration",
-            "Stage": "stage",
-            "mx": "mx",
-            "my": "my",
-            "mz": "mz",
-            "Last time step": "last_time_step",
-            "Simulation time": "t",
-        },
         "Oxs_CGEvolve": {
             "Max mxHxm": "max_mxHxm",
             "Total energy": "E",
@@ -84,7 +74,6 @@ class Table:
             "Cycle sub count": "cycle_sub_count",
             "Energy calc count": "energy_calc_count",
         },
-        "YY_FixedMEL": {"Energy": "MEL_E"},
         "Anv_SpinTEvolve": {
             "Total energy": "E",
             "Energy calc count": "E_calc_count",
@@ -134,17 +123,40 @@ class Table:
             "my": "my",
             "mz": "mz",
         },
+        "Oxs_TimeDriver": {
+            "Iteration": "iteration",
+            "Stage iteration": "stage_iteration",
+            "Stage": "stage",
+            "mx": "mx",
+            "my": "my",
+            "mz": "mz",
+            "Last time step": "last_time_step",
+            "Simulation time": "t",
+        },
         "Oxs_UniformExchange": {
             "Max Spin Ang": "max_spin_ang",
             "Stage Max Spin Ang": "stage_max_spin_ang",
             "Run Max Spin Ang": "run_max_spin_ang",
             "Energy": "E_exchange",
         },
+        "Oxs_Exchange6Ngbr": {
+            "Energy": "E_exchange6ngbr",
+            "Max Spin Ang": "max_spin_ang",
+            "Stage Max Spin Ang": "stage_max_spin_ang",
+            "Run Max Spin Ang": "run_max_spin_ang",
+        },
+        "Oxs_ExchangePtwise": {
+            "Energy": "E_exchange_ptwise",  # NO SAMPLE
+            "Max Spin Ang": "max_spin_ang",  # NO SAMPLE
+            "Stage Max Spin Ang": "stage_max_spin_ang",  # NO SAMPLE
+            "Run Max Spin Ang": "run_max_spin_ang",  # NO SAMPLE
+        },
+        "Oxs_TwoSurfaceExchange": {"Energy": "E_two_surface_exchange"},  # NO SAMPLE
+        "Oxs_Demag": {"Energy": "E_demag"},
         "Oxs_DMExchange6Ngbr": {"Energy": "E_DM_exchange6ngbr"},  # NO SAMPLE
         "Oxs_DMI_Cnv": {"Energy": "E_DMI_Cnv"},  # TODO: PREFIX
         "Oxs_DMI_T": {"Energy": "E_DMI_T"},  # NO SAMPLE,  TODO: PREFIX
         "Oxs_DMI_D2d": {"Energy": "E_DMI_Dd"},  # NO SAMPLE,  TODO: PREFIX
-        "Oxs_Demag": {"Energy": "E_demag"},
         "Oxs_FixedZeeman": {"Energy": "E_zeeman"},
         "Oxs_UZeeman": {
             "Energy": "E_zeeman",
@@ -164,19 +176,7 @@ class Table:
         "Oxs_CubicAnisotropy": {"Energy": "E_zeeman"},
         "Oxs_UniaxialAnisotropy": {"Energy": "E_zeeman"},
         "Southampton_UniaxialAnisotropy4": {"Energy": "E_zeeman"},  # NO SAMPLE
-        "Oxs_Exchange6Ngbr": {
-            "Energy": "E_exchange6ngbr",
-            "Max Spin Ang": "max_spin_ang",
-            "Stage Max Spin Ang": "stage_max_spin_ang",
-            "Run Max Spin Ang": "run_max_spin_ang",
-        },
-        "Oxs_ExchangePtwise": {
-            "Energy": "E_exchange_ptwise",  # NO SAMPLE
-            "Max Spin Ang": "max_spin_ang",  # NO SAMPLE
-            "Stage Max Spin Ang": "stage_max_spin_ang",  # NO SAMPLE
-            "Run Max Spin Ang": "run_max_spin_ang",  # NO SAMPLE
-        },
-        "Oxs_TwoSurfaceExchange": {"Energy": "E_two_surface_exchange"},  # NO SAMPLE
+        "YY_FixedMEL": {"Energy": "MEL_E"},
     }
 
     # The mumax3 columns are renamed according to this dictionary.

From d205f9bbbf5309167980f468581251421b110b4b Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Mon, 20 Feb 2023 12:57:24 +0100
Subject: [PATCH 09/11] Move tests for columns and units to Table class

---
 ubermagtable/tests/test_table.py | 28 ++++++++++++++--
 ubermagtable/tests/test_util.py  | 55 --------------------------------
 2 files changed, 26 insertions(+), 57 deletions(-)
 delete mode 100644 ubermagtable/tests/test_util.py

diff --git a/ubermagtable/tests/test_table.py b/ubermagtable/tests/test_table.py
index 305a1a7..5bae337 100644
--- a/ubermagtable/tests/test_table.py
+++ b/ubermagtable/tests/test_table.py
@@ -68,10 +68,34 @@ def test_init(self):
         assert isinstance(table.data, pd.DataFrame)
 
     def test_fromfile(self):
+        for odtfile in self.odtfiles:
+            table = ut.Table.fromfile(odtfile, rename=False)
+            check_table(table)
+
+            table_short_names = ut.Table.fromfile(odtfile, rename=True)
+            check_table(table_short_names)
+
+            assert len(table.data) == len(table_short_names.data)
+            assert len(table.data.columns) == len(table_short_names.data.columns)
+
+    def test_columns(self):
+        for odtfile in self.odtfiles:
+            for rename in [True, False]:
+                table = ut.Table.fromfile(odtfile, rename=rename)
+                columns = table.data.columns
+                assert all(isinstance(column, str) for column in columns)
+                assert len(columns) == len(set(columns))  # unique column names
+
+    def test_units(self):
         for odtfile in self.odtfiles:
             for rename in [True, False]:
-                table = ut.Table.fromfile(odtfile)
-                check_table(table)
+                table = ut.Table.fromfile(odtfile, rename=rename)
+                units = table.units
+                assert isinstance(units, dict)
+                assert all(isinstance(unit, str) for unit in units.keys())
+                assert all(isinstance(unit, str) for unit in units.values())
+                assert "J" in units.values()  # Energy is always in
+                assert "" in units.values()  # Columns with no units are always in
 
     def test_xy(self):
         table = ut.Table.fromfile(self.odtfiles[0], x="t")
diff --git a/ubermagtable/tests/test_util.py b/ubermagtable/tests/test_util.py
deleted file mode 100644
index 0d45ebe..0000000
--- a/ubermagtable/tests/test_util.py
+++ /dev/null
@@ -1,55 +0,0 @@
-import itertools
-import numbers
-import os
-
-import ubermagtable.util as uu
-
-dirname = os.path.join(os.path.dirname(__file__), "test_sample/")
-filenames = [
-    "oommf-old-file1.odt",
-    "oommf-old-file2.odt",
-    "oommf-old-file3.odt",
-    "oommf-old-file4.odt",
-    "oommf-old-file5.odt",
-    "oommf-old-file6.odt",
-    "oommf-old-file7.odt",
-    "oommf-old-file8.odt",
-    "oommf-new-file1.odt",
-    "oommf-new-file2.odt",
-    "oommf-new-file3.odt",
-    "oommf-new-file4.odt",
-    "oommf-new-file5.odt",
-    "mumax3-file1.txt",
-    "oommf-mel-file.odt",
-]
-odtfiles = [os.path.join(dirname, f) for f in filenames]
-
-
-def test_columns():
-    for odtfile in odtfiles:
-        for rename in [True, False]:
-            columns = uu.columns(odtfile, rename=rename)
-
-            assert isinstance(columns, list)
-            assert all(isinstance(column, str) for column in columns)
-            assert len(columns) == len(set(columns))  # unique column names
-
-
-def test_units():
-    for odtfile in odtfiles:
-        for rename in [True, False]:
-            units = uu.units(odtfile, rename=rename)
-
-            assert isinstance(units, dict)
-            assert all(isinstance(unit, str) for unit in units.keys())
-            assert all(isinstance(unit, str) for unit in units.values())
-            assert "J" in units.values()  # Energy is always in
-            assert "" in units.values()  # Columns with no units are always in
-
-
-def test_data():
-    for odtfile in odtfiles:
-        data = uu.data(odtfile)
-
-        assert isinstance(data, list)
-        assert all(isinstance(i, numbers.Real) for i in itertools.chain(*data))

From 0ef000e7b63aeeeb2d8ccfedb8bb0c3a9f26355b Mon Sep 17 00:00:00 2001
From: Martin Lang <m.lang@soton.ac.uk>
Date: Mon, 20 Feb 2023 13:39:29 +0100
Subject: [PATCH 10/11] Change variable names in _rename_column

---
 ubermagtable/table.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index 1011bd9..f28effb 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -328,13 +328,15 @@ def _rename_column(name, cols_dict):
             group = cols_dict[name_split[0]]
             if isinstance(group, str):  # Mumax3 keys
                 return group
-            quantity = group[name_split[-1]]
+            attribute = group[name_split[-1]]
             term_name = name_split[1]
-            if not quantity.endswith(term_name):
-                # unique names if the same quantity is present multiple times
-                # e.g. multiple Zeeman fields
-                quantity = f"{quantity}_{term_name}"
-            return quantity
+            if not attribute.endswith(term_name):
+                # - unique names if the same quantity is present multiple times
+                #   e.g. multiple Zeeman fields
+                # - also required for changes in the exchange field in "old" and "new"
+                #   OOMMF odt files
+                attribute = f"{attribute}_{term_name}"
+            return attribute
         except KeyError:
             return name
 

From 86bc155e703f913292dde9c115901c695e7419f5 Mon Sep 17 00:00:00 2001
From: Martin Lang <martin.lang@mpsd.mpg.de>
Date: Wed, 29 Nov 2023 16:17:28 +0100
Subject: [PATCH 11/11] Remove all functionality to read table data from file

This functionality is calculator-specific and is moved to the individual adapter packages
---
 ubermagtable/table.py | 278 ------------------------------------------
 1 file changed, 278 deletions(-)

diff --git a/ubermagtable/table.py b/ubermagtable/table.py
index f28effb..7b8af0c 100644
--- a/ubermagtable/table.py
+++ b/ubermagtable/table.py
@@ -1,5 +1,3 @@
-import re
-
 import ipywidgets
 import matplotlib.pyplot as plt
 import numpy as np
@@ -47,153 +45,6 @@ class Table:
 
     """
 
-    # The OOMMF columns are renamed according to this dictionary.
-    _OOMMF_DICT = {
-        "Oxs_RungeKuttaEvolve": {
-            "Total energy": "E",
-            "Energy calc count": "E_calc_count",
-            "Max dm/dt": "max_dm/dt",
-            "dE/dt": "dE/dt",
-            "Delta E": "delta_E",
-        },
-        "Oxs_EulerEvolve": {
-            "Total energy": "E",
-            "Energy calc count": "E_calc_count",
-            "Max dm/dt": "max_dmdt",
-            "dE/dt": "dE/dt",
-            "Delta E": "delta_E",
-        },
-        "Oxs_CGEvolve": {
-            "Max mxHxm": "max_mxHxm",
-            "Total energy": "E",
-            "Delta E": "delta_E",
-            "Bracket count": "bracket_count",
-            "Line min count": "line_min_count",
-            "Conjugate cycle count": "conjugate_cycle_count",
-            "Cycle count": "cycle_count",
-            "Cycle sub count": "cycle_sub_count",
-            "Energy calc count": "energy_calc_count",
-        },
-        "Anv_SpinTEvolve": {
-            "Total energy": "E",
-            "Energy calc count": "E_calc_count",
-            "Max dm/dt": "max_dmdt",
-            "dE/dt": "dE/dt",
-            "Delta E": "delta_E",
-            "average u": "average_u",
-        },
-        "Oxs_SpinXferEvolve": {
-            "Total energy": "E",  # NO SAMPLE
-            "Energy calc count": "E_calc_count",  # NO SAMPLE
-            "Max dm/dt": "max_dmdt",  # NO SAMPLE
-            "dE/dt": "dE/dt",  # NO SAMPLE
-            "Delta E": "delta_E",  # NO SAMPLE
-            "average u": "average_u",  # NO SAMPLE
-            "average J": "average_J",  # NO SAMPLE
-        },
-        "UHH_ThetaEvolve": {
-            "Total energy": "E",  # NO SAMPLE
-            "Energy calc count": "E_calc_count",  # NO SAMPLE
-            "Max dm/dt": "max_dmdt",  # NO SAMPLE
-            "dE/dt": "dE/dt",  # NO SAMPLE
-            "Delta E": "delta_E",  # NO SAMPLE
-            "Temperature": "T",  # NO SAMPLE
-        },
-        "Xf_ThermHeunEvolve": {
-            "Total energy": "E",  # NO SAMPLE
-            "Energy calc count": "E_calc_count",  # NO SAMPLE
-            "Max dm/dt": "max_dmdt",  # NO SAMPLE
-            "dE/dt": "dE/dt",  # NO SAMPLE
-            "Delta E": "delta_E",  # NO SAMPLE
-            "Temperature": "T",  # NO SAMPLE
-        },
-        "Xf_ThermSpinXferEvolve": {
-            "Total energy": "E",  # NO SAMPLE
-            "Energy calc count": "E_calc_count",  # NO SAMPLE
-            "Max dm/dt": "max_dmdt",  # NO SAMPLE
-            "dE/dt": "dE/dt",  # NO SAMPLE
-            "Delta E": "delta_E",  # NO SAMPLE
-            "Temperature": "T",  # NO SAMPLE
-        },
-        "Oxs_MinDriver": {
-            "Iteration": "iteration",
-            "Stage iteration": "stage_iteration",
-            "Stage": "stage",
-            "mx": "mx",
-            "my": "my",
-            "mz": "mz",
-        },
-        "Oxs_TimeDriver": {
-            "Iteration": "iteration",
-            "Stage iteration": "stage_iteration",
-            "Stage": "stage",
-            "mx": "mx",
-            "my": "my",
-            "mz": "mz",
-            "Last time step": "last_time_step",
-            "Simulation time": "t",
-        },
-        "Oxs_UniformExchange": {
-            "Max Spin Ang": "max_spin_ang",
-            "Stage Max Spin Ang": "stage_max_spin_ang",
-            "Run Max Spin Ang": "run_max_spin_ang",
-            "Energy": "E_exchange",
-        },
-        "Oxs_Exchange6Ngbr": {
-            "Energy": "E_exchange6ngbr",
-            "Max Spin Ang": "max_spin_ang",
-            "Stage Max Spin Ang": "stage_max_spin_ang",
-            "Run Max Spin Ang": "run_max_spin_ang",
-        },
-        "Oxs_ExchangePtwise": {
-            "Energy": "E_exchange_ptwise",  # NO SAMPLE
-            "Max Spin Ang": "max_spin_ang",  # NO SAMPLE
-            "Stage Max Spin Ang": "stage_max_spin_ang",  # NO SAMPLE
-            "Run Max Spin Ang": "run_max_spin_ang",  # NO SAMPLE
-        },
-        "Oxs_TwoSurfaceExchange": {"Energy": "E_two_surface_exchange"},  # NO SAMPLE
-        "Oxs_Demag": {"Energy": "E_demag"},
-        "Oxs_DMExchange6Ngbr": {"Energy": "E_DM_exchange6ngbr"},  # NO SAMPLE
-        "Oxs_DMI_Cnv": {"Energy": "E_DMI_Cnv"},  # TODO: PREFIX
-        "Oxs_DMI_T": {"Energy": "E_DMI_T"},  # NO SAMPLE,  TODO: PREFIX
-        "Oxs_DMI_D2d": {"Energy": "E_DMI_Dd"},  # NO SAMPLE,  TODO: PREFIX
-        "Oxs_FixedZeeman": {"Energy": "E_zeeman"},
-        "Oxs_UZeeman": {
-            "Energy": "E_zeeman",
-            "B": "B",
-            "Bx": "Bx",
-            "By": "By",
-            "Bz": "Bz",
-        },
-        "Oxs_ScriptUZeeman": {
-            "Energy": "E_zeeman",  # NO SAMPLE
-            "B": "B",  # NO SAMPLE
-            "Bx": "Bx",  # NO SAMPLE
-            "By": "By",  # NO SAMPLE
-            "Bz": "Bz",  # NO SAMPLE
-        },
-        "Oxs_TransformZeeman": {"Energy": "E_zeeman"},  # NO SAMPLE
-        "Oxs_CubicAnisotropy": {"Energy": "E_zeeman"},
-        "Oxs_UniaxialAnisotropy": {"Energy": "E_zeeman"},
-        "Southampton_UniaxialAnisotropy4": {"Energy": "E_zeeman"},  # NO SAMPLE
-        "YY_FixedMEL": {"Energy": "MEL_E"},
-    }
-
-    # The mumax3 columns are renamed according to this dictionary.
-    _MUMAX3_DICT = {
-        "t": "t",
-        "mx": "mx",
-        "my": "my",
-        "mz": "mz",
-        "E_total": "E",
-        "E_exch": "E_totalexchange",
-        "E_demag": "E_demag",
-        "E_Zeeman": "E_zeeman",
-        "E_anis": "E_totalanisotropy",
-        "dt": "dt",
-        "maxTorque": "maxtorque",
-    }
-
     def __init__(self, data, units, x=None, attributes=None):
         self.data = data
         self.units = units
@@ -211,135 +62,6 @@ def __init__(self, data, units, x=None, attributes=None):
                 ignore_index=True,  # reset the index to 0, 1, ..., n-1
             )
 
-    @classmethod
-    def fromfile(cls, filename, /, x=None, rename=True):
-        """Reads an OOMMF ``.odt`` or mumax3 ``.txt`` scalar data file and
-        returns a ``ubermagtable.Table`` object.
-
-        Parameters
-        ----------
-        filename : str
-
-            OOMMF ``.odt`` or mumax3 ``.txt`` file.
-
-        x : str, optional
-
-            Independent variable name. Defaults to ``None``.
-
-        rename : bool, optional
-
-            If ``rename=True``, the column names are renamed with their shorter
-            versions. Defaults to ``True``.
-
-        Returns
-        -------
-        ubermagtable.Table
-
-            Table object.
-
-        Examples
-        --------
-        1. Defining ``ubermagtable.Table`` by reading an OOMMF ``.odt`` file.
-
-        >>> import os
-        >>> import ubermagtable as ut
-        ...
-        >>> odtfile = os.path.join(os.path.dirname(__file__),
-        ...                        'tests', 'test_sample',
-        ...                        'oommf-hysteresis1.odt')
-        >>> table = ut.Table.fromfile(odtfile, x='B_hysteresis')
-
-        2. Defining ``ubermagtable.Table`` by reading a mumax3 ``.txt`` file.
-
-        >>> odtfile = os.path.join(os.path.dirname(__file__),
-        ...                        'tests', 'test_sample', 'mumax3-file1.txt')
-        >>> table = ut.Table.fromfile(odtfile, x='t')
-
-        """
-        quantities = cls._read_header(filename, rename=rename)
-        data = pd.read_csv(
-            filename,
-            sep=r"\s+",
-            comment="#",
-            header=None,
-            names=list(quantities.keys()),
-        )
-        return cls(data=data, units=quantities, x=x)
-
-    @classmethod
-    def _read_header(cls, filename, rename=True):
-        """Extracts quantities for individual columns from a table file.
-
-        This method extracts both column names and units and returns a dictionary,
-        where keys are column names and values are the units.
-
-        Parameters
-        ----------
-        filename : str
-
-            OOMMF ``.odt`` or mumax3 ``.txt`` file.
-
-        rename : bool
-
-            If ``rename=True``, the column names are renamed with their shorter
-            versions. Defaults to ``True``.
-
-        Returns
-        -------
-        dict
-
-            Dictionary of column names and units.
-        """
-
-        with open(filename) as f:
-            if (header_line_1 := f.readline()).startswith("# ODT"):  # OOMMF odt file
-                cols_dict = cls._OOMMF_DICT
-                # COLUMN NAMES
-                while not (cline := f.readline()).startswith("# Columns"):
-                    pass
-                columns = cline.lstrip("# Columns:").rstrip()
-                cols = re.findall(r"(?<={)[^}]+|[^ {}]+", columns)
-                # UNITS
-                uline = f.readline()
-                assert uline.startswith("# Units:")
-                units = uline.split()[2:]  # [2:] to remove ["#", "Units:"]
-                units = [re.sub(r"[{}]", "", unit) for unit in units]
-            else:  # mumax3 txt file
-                cols_dict = cls._MUMAX3_DICT
-                header_line_1 = header_line_1[len("# ") :].rstrip().split("\t")
-                # COLUMN NAMES
-                cols = [elem.split()[0] for elem in header_line_1]
-                # UNITS
-                units = [re.sub(r"[()]", "", elem.split()[1]) for elem in header_line_1]
-
-        if rename:
-            cols = [cls._rename_column(col, cols_dict) for col in cols]
-
-        return dict(zip(cols, units))
-
-    @staticmethod
-    def _rename_column(name, cols_dict):
-        """Rename columns to get shorter names without spaces.
-
-        Renaming is based on _OOMMF_DICT or _MUMAX3_DICT.
-        """
-        name_split = name.split(":")
-        try:
-            group = cols_dict[name_split[0]]
-            if isinstance(group, str):  # Mumax3 keys
-                return group
-            attribute = group[name_split[-1]]
-            term_name = name_split[1]
-            if not attribute.endswith(term_name):
-                # - unique names if the same quantity is present multiple times
-                #   e.g. multiple Zeeman fields
-                # - also required for changes in the exchange field in "old" and "new"
-                #   OOMMF odt files
-                attribute = f"{attribute}_{term_name}"
-            return attribute
-        except KeyError:
-            return name
-
     @property
     def data(self):
         """Scalar data of the drive.