From 6e70b6bf92a1d7911cac0a62c9de80871b33aff0 Mon Sep 17 00:00:00 2001
From: Loic Huder <loic.huder@esrf.fr>
Date: Thu, 18 Apr 2024 11:02:36 +0200
Subject: [PATCH] Remove spectra_url_dims and other little improvements in
XASObject
---
src/est/core/types/xasobject.py | 75 +++++++++------------------------
1 file changed, 21 insertions(+), 54 deletions(-)
diff --git a/src/est/core/types/xasobject.py b/src/est/core/types/xasobject.py
index 366914f0..c7ffbfb7 100644
--- a/src/est/core/types/xasobject.py
+++ b/src/est/core/types/xasobject.py
@@ -1,6 +1,6 @@
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):
--
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