Remove spectra_url_dims and other little improvements in XASObject

src/est/core/types/xasobject.py

 from __future__ import annotations
 import copy
-from typing import Any, Optional, Tuple, Union
+from typing import Any, Sequence
 
 import pint
 import numpy
@@ -9,7 +9,7 @@ from silx.io.url import DataUrl
 from est.io.utils import get_data_from_url
 from est.units import ur
 from est.settings import DEFAULT_READ_TIMEOUT
-from est.core.types import dimensions as dimensions_mod
+from est.core.types.dimensions import STANDARD_DIMENSIONS
 from .spectra import Spectra
 from .spectrum import Spectrum
 
@@ -20,43 +20,33 @@ class XASObject:
     :param spectra: absorbed beam as a list of :class:`.Spectrum` or a
                     numpy.ndarray. If is a numpy array, the axes should
                     have the `STANDARD_DIMENSIONS` order.
-    :type: Union[numpy.ndarray, list]
     :param energy: beam energy
-    :type: numpy.ndarray of one dimension
-    :param dict configuration: configuration of the different process
-    :param int dim1: first dimension of the spectra
-    :param int dim2: second dimension of the spectra
-    :param str name: name of the object. Will be used for the hdf5 entry
+    :param configuration: configuration of the different process
+    :param dim1: first dimension of the spectra
+    :param dim2: second dimension of the spectra
+    :param name: name of the object. Will be used for the hdf5 entry
     :param spectra_url: path to the spectra data if any. Used when serializing
                         the XASObject. Won't read it from it.
-    :type: Union[None,str]
-    :param spectra_url_dims: dimensions of the stored spectra. WARNING:
-                                   this is different of the spectra dimension
-                                   which should be given in the
-                                   `STANDARD_DIMENSIONS` order
-    :type: Union[tuple,None]
     :param energy_url: path to the energy / channel  data if any. Used when
                        serializing the XASObject. Won't read it from it.
-    :type: Union[None,str]
     """
 
     def __init__(
         self,
-        spectra=None,
-        energy=None,
-        configuration: Union[dict, None] = None,
-        dim1: Union[int, None] = None,
-        dim2: Union[int, None] = None,
+        spectra: numpy.ndarray | Sequence[Any] | None = None,
+        energy: numpy.ndarray | None = None,
+        configuration: dict | None = None,
+        dim1: int | None = None,
+        dim2: int | None = None,
         name: str = "scan1",
-        spectra_url: Union[DataUrl, None] = None,
-        spectra_url_dims: Optional[dimensions_mod.DimensionsType] = None,
-        energy_url: Union[DataUrl, None] = None,
-        check_energy: bool = True,
+        spectra_url: DataUrl | None = None,
+        energy_url: DataUrl | None = None,
     ):
         if isinstance(energy, numpy.ndarray) and not isinstance(energy, pint.Quantity):
             # automatic energy unit guess. convert energy provided in keV to eV
             # works because EXAFS data are never longer than 2 keV and a low
-            # energy XANES is never shorter than 3 eV. See issue 30
+            # energy XANES is never shorter than 3 eV.
+            # See https://gitlab.esrf.fr/workflow/ewoksapps/est/-/issues/30
             if (energy.max() - energy.min()) < 3.0:
                 energy = energy * ur.keV
             else:
@@ -65,13 +55,8 @@ class XASObject:
         if energy is not None:
             energy = energy.m_as(ur.eV)
 
-        self.__channels = None
-        self.__spectra = Spectra(energy=energy)
-        self.__dim1 = None
-        self.__dim2 = None
         self.__entry_name = name
         self.__spectra_url = spectra_url
-        self.__spectra_url_dims = spectra_url_dims
         self.__energy_url = energy_url
         self.spectra = (energy, spectra, dim1, dim2)
         self.configuration = configuration
@@ -106,7 +91,7 @@ class XASObject:
         return self.__spectra
 
     @property
-    def spectra_url(self) -> Union[None, DataUrl]:
+    def spectra_url(self) -> DataUrl | None:
         """Url from where the spectra is available.
         Used for object serialization"""
         return self.__spectra_url
@@ -116,18 +101,7 @@ class XASObject:
         self.__spectra_url = url
 
     @property
-    def spectra_url_dims(
-        self,
-    ) -> dimensions_mod.DimensionsType | Tuple[int, ...] | None:
-        """used to interpret the spectra_url if any"""
-        return self.__spectra_url_dims
-
-    @spectra_url_dims.setter
-    def spectra_url_dims(self, dims: Tuple[int, ...]):
-        self.__spectra_url_dims = dims
-
-    @property
-    def energy_url(self) -> Union[DataUrl, None]:
+    def energy_url(self) -> DataUrl | None:
         """Url from where the energy is available.
         Used for object serialization"""
         return self.__energy_url
@@ -185,13 +159,6 @@ class XASObject:
         """convert the XAS object to a dict
 
         By default made to simply import raw data.
-
-        :param with_process_details: used to embed a list of spectrum with
-                                     intermediary result instead of only raw mu.
-                                     This is needed especially for the
-                                     pushworkflow actors to keep a trace of the
-                                     processes.
-        :type: bool
         """
 
         res = {
@@ -200,6 +167,7 @@ class XASObject:
             "dim2": self.spectra.shape[1],
             "energy": self.spectra.energy,
             "spectra": [spectrum.to_dict() for spectrum in self.spectra],
+            "dimensions": STANDARD_DIMENSIONS,  # spectra dimensions are always changed to STANDARD on load
         }
         return res
 
@@ -210,10 +178,8 @@ class XASObject:
         """load XAS values from a dict"""
         if not isinstance(ddict, dict):
             raise TypeError(f"ddict is expected to be a dict. Not {type(ddict)}")
-        # TODO: is this correct? Shouldn't this be `self.spectra_url_dims`?
-        #       We don't have a test for this.
-        dimensions = dimensions_mod.STANDARD_DIMENSIONS
-        # default yay of storing data
+        dimensions = ddict.get("dimensions", STANDARD_DIMENSIONS)
+        # default way of storing data
         from est.io import load_data  # avoid cyclic import
 
         """The dict can be on the scheme of the to_dict function, containing
@@ -282,6 +248,7 @@ class XASObject:
             channel_url=energy_url,
             config_url=config_url,
             dimensions=dimensions,
+            timeout=timeout,
         )
 
     def dump(self, h5_file: str):