Merge pull request #197 from h2020charisma/hdr_custom_meta

Custom meta names in hdr_from_multi_exposure

src/ramanchada2/spectrum/creators/from_local_file.py

@@ -1,7 +1,7 @@
 """Create spectrum from local files."""
 
 import os
-from typing import Literal, Union
+from typing import Literal, Union, Dict
 
 import spc_io
 from pydantic import validate_call
@@ -22,7 +22,8 @@ def from_local_file(
         filetype: Union[None, Literal['spc', 'sp', 'spa', '0', '1', '2',
                                       'wdf', 'ngs', 'jdx', 'dx',
                                       'txt', 'txtr', 'csv', 'prn', 'rruf', 'spe', 'cha']] = None,
-        backend: Union[None, Literal['native', 'rc1_parser']] = None):
+        backend: Union[None, Literal['native', 'rc1_parser']] = None,
+        custom_meta: Dict = {}):
     """
     Read experimental spectrum from a local file.
 
@@ -35,6 +36,8 @@ def from_local_file(
             `None` used to determine by extension of the file.
         backend:
             `native`, `rc1_parser` or `None`. `None` means both.
+        custom_meta: Dict
+            Add custom metadata fields in the created spectrum
 
     Raises:
         ValueError:
@@ -63,10 +66,10 @@ def load_native():
                 meta = spc.log_book.text
         elif ft in {'spe'}:
             x, y, meta = read_spe(in_file_name)
-            spe = Spectrum(x=x, y=y, metadata=meta)  # type: ignore
         else:
             raise ValueError(f'filetype {ft} not supported')
         meta["Original file"] = os.path.basename(in_file_name)
+        meta.update(custom_meta)
         spe = Spectrum(x=x, y=y, metadata=meta)  # type: ignore
         return spe
 

src/ramanchada2/spectrum/creators/hdr_from_multi_exposure.py

@@ -10,22 +10,33 @@
 
 @add_spectrum_constructor(set_applied_processing=True)
 @validate_call(config=dict(arbitrary_types_allowed=True))
-def hdr_from_multi_exposure(spes_in: List[Spectrum]):
-    """Create an HDR spectrum from several spectra with different exposures.
+def hdr_from_multi_exposure(spes_in: List[Spectrum],
+                            meta_exposure_time: str = 'intigration times(ms)',
+                            meta_ymax: str = 'yaxis_max'):
+    """
+    Create an HDR spectrum from several spectra with different exposures.
 
     The resulting spectrum will have the details in low-intensity peaks
     from long-exposure-time spectrum. As long-exposure-time
     spectrum might be sturated, the information for high-intensity
     peaks will be taken from short-exposure-time spectrum.
-    This function will work on a very limited number of spectra,
-    because we still do not have standardized metadata.
+
+    Args:
+        spes_in (List[Spectrum]): Set of spectra with different exposures
+        meta_exposure_time (str, optional): The name of the metadata parameter
+            having the exposure/integration time. The units should be the same
+            for all the spectra. Defaults to 'intigration times(ms)'.
+        meta_ymax (str, optional): The name fo the metadata parameter having
+            the maximum ADC value. This value will be used as a threshold. If
+            value in a spectrum is higher, the value will be taken from a
+            spectrum with shorter exposure. Defaults to 'yaxis_max'.
     """
 
-    spes = list(sorted(spes_in, key=lambda s: float(s.meta['intigration times(ms)'])))  # type: ignore
+    spes = list(sorted(spes_in, key=lambda s: float(s.meta[meta_exposure_time])))  # type: ignore
     if not np.all([spes[0].x == s.x for s in spes]):
         raise ValueError('x-axes of the spectra should be equal')
-    spes_cpms = np.array([s.y / float(s.meta['intigration times(ms)']) for s in spes])  # type: ignore
-    masks = np.array(list(map(lambda s: s.y > s.meta['yaxis_max'], spes)))  # type: ignore
+    spes_cpms = np.array([s.y / float(s.meta[meta_exposure_time]) for s in spes])  # type: ignore
+    masks = np.array(list(map(lambda s: s.y > s.meta[meta_ymax], spes)))  # type: ignore
     y = spes_cpms[0]
     for si in range(1, len(spes_cpms)):
         y[~masks[si]] = spes_cpms[si][~masks[si]]