Merge pull request #38 from PlasmaFAIR/latex-variable-name-processing

Latex variable name processing

src/sdf_xarray/__init__.py

@@ -1,6 +1,8 @@
 import os
 import pathlib
+import re
 from collections import Counter, defaultdict
+from itertools import product
 from typing import Iterable
 
 import numpy as np
@@ -21,6 +23,29 @@ def _rename_with_underscore(name: str) -> str:
     return name.replace("/", "_").replace(" ", "_").replace("-", "_")
 
 
+def _process_latex_name(variable_name: str) -> str:
+    """Converts variable names to LaTeX format where possible
+    using the following rules:
+    - E -> $E_x$
+    - E -> $E_y$
+    - E -> $E_z$
+
+    This repeats for B, J and P. It only changes the variable
+    name if there are spaces around the affix (prefix + suffix)
+    or if there is no trailing space. This is to avoid changing variable
+    names that may contain these affixes as part of the variable name itself.
+    """
+    prefixes = ["E", "B", "J", "P"]
+    suffixes = ["x", "y", "z"]
+    for prefix, suffix in product(prefixes, suffixes):
+        # Match affix with preceding space and trailing space or end of string
+        affix_pattern = rf"\b{prefix}{suffix}\b"
+        # Insert LaTeX format while preserving spaces
+        replacement = rf"${prefix}_{suffix}$"
+        variable_name = re.sub(affix_pattern, replacement, variable_name)
+    return variable_name
+
+
 def combine_datasets(path_glob: Iterable | str, **kwargs) -> xr.Dataset:
     """Combine all datasets using a single time dimension"""
 
@@ -271,7 +296,7 @@ def _process_grid_name(grid_name: str, transform_func) -> str:
                     dim_name,
                     coord,
                     {
-                        "long_name": label,
+                        "long_name": label.replace("_", " "),
                         "units": unit,
                         "point_data": value.is_point_data,
                         "full_name": value.name,
@@ -290,11 +315,6 @@ def _process_grid_name(grid_name: str, transform_func) -> str:
                 continue
 
             if isinstance(value, Constant) or value.grid is None:
-                data_attrs = {}
-                data_attrs["full_name"] = key
-                if value.units is not None:
-                    data_attrs["units"] = value.units
-
                 # We don't have a grid, either because it's just a
                 # scalar, or because it's an array over something
                 # else. We have no more information, so just make up
@@ -303,6 +323,12 @@ def _process_grid_name(grid_name: str, transform_func) -> str:
                 dims = [f"dim_{key}_{n}" for n, _ in enumerate(shape)]
                 base_name = _rename_with_underscore(key)
 
+                data_attrs = {}
+                data_attrs["full_name"] = key
+                data_attrs["long_name"] = base_name.replace("_", " ")
+                if value.units is not None:
+                    data_attrs["units"] = value.units
+
                 data_vars[base_name] = Variable(dims, value.data, attrs=data_attrs)
                 continue
 
@@ -341,13 +367,15 @@ def _process_grid_name(grid_name: str, transform_func) -> str:
                 ]
 
             # TODO: error handling here? other attributes?
+            base_name = _rename_with_underscore(key)
+            long_name = _process_latex_name(base_name.replace("_", " "))
             data_attrs = {
                 "units": value.units,
                 "point_data": value.is_point_data,
                 "full_name": key,
+                "long_name": long_name,
             }
             lazy_data = indexing.LazilyIndexedArray(SDFBackendArray(key, self))
-            base_name = _rename_with_underscore(key)
             data_vars[base_name] = Variable(var_coords, lazy_data, data_attrs)
 
         # TODO: might need to decode if mult is set?

tests/test_basic.py

@@ -3,7 +3,7 @@
 import pytest
 import xarray as xr
 
-from sdf_xarray import SDFPreprocess, open_mfdataset
+from sdf_xarray import SDFPreprocess, _process_latex_name, open_mfdataset
 
 EXAMPLE_FILES_DIR = pathlib.Path(__file__).parent / "example_files"
 EXAMPLE_MISMATCHED_FILES_DIR = (
@@ -115,6 +115,38 @@ def test_time_dim_units():
     assert df["time"].full_name == "time"
 
 
+def test_latex_rename_variables():
+    df = xr.open_mfdataset(
+        EXAMPLE_ARRAYS_DIR.glob("*.sdf"),
+        preprocess=SDFPreprocess(),
+        keep_particles=True,
+    )
+    assert df["Electric_Field_Ex"].attrs["long_name"] == "Electric Field $E_x$"
+    assert df["Electric_Field_Ey"].attrs["long_name"] == "Electric Field $E_y$"
+    assert df["Electric_Field_Ez"].attrs["long_name"] == "Electric Field $E_z$"
+    assert df["Magnetic_Field_Bx"].attrs["long_name"] == "Magnetic Field $B_x$"
+    assert df["Magnetic_Field_By"].attrs["long_name"] == "Magnetic Field $B_y$"
+    assert df["Magnetic_Field_Bz"].attrs["long_name"] == "Magnetic Field $B_z$"
+    assert df["Current_Jx"].attrs["long_name"] == "Current $J_x$"
+    assert df["Current_Jy"].attrs["long_name"] == "Current $J_y$"
+    assert df["Current_Jz"].attrs["long_name"] == "Current $J_z$"
+    assert df["Particles_Px_Electron"].attrs["long_name"] == "Particles $P_x$ Electron"
+    assert df["Particles_Py_Electron"].attrs["long_name"] == "Particles $P_y$ Electron"
+    assert df["Particles_Pz_Electron"].attrs["long_name"] == "Particles $P_z$ Electron"
+
+    assert _process_latex_name("Example") == "Example"
+    assert _process_latex_name("PxTest") == "PxTest"
+
+    assert (
+        df["Absorption_Fraction_of_Laser_Energy_Absorbed"].attrs["long_name"]
+        == "Absorption Fraction of Laser Energy Absorbed"
+    )
+    assert (
+        df["Derived_Average_Particle_Energy"].attrs["long_name"]
+        == "Derived Average Particle Energy"
+    )
+
+
 def test_arrays_with_no_grids():
     with xr.open_dataset(EXAMPLE_ARRAYS_DIR / "0001.sdf") as df:
         laser_phase = "laser_x_min_phase"