Merge branch 'main' of https://github.com/lanl/MILK

MILK/MAUDText/spectraReader.py

@@ -42,4 +42,4 @@ def parse_spectra(file):
     return spectra
 
 def extract_spectra(files,poolsize=get_ncpus()):
-    return parallel_map(parse_spectra,poolsize,False,files)
+    return parallel_map(parse_spectra,poolsize,True,files)

MILK/data/prepareData.py

@@ -31,13 +31,14 @@ def remove_intensity(lines):
 
     return lines
 
-def swap_datasets(lines, datasets):
+def swap_datasets(lines, datasets, background=None):
     #Assume that all dataset files have the same extension
     ext = Path(datasets[0]).suffix
 
     # Find a list of datasets already in the template
     datasetsold = []
     datasetInd = []
+    datasetIsBk = []
     for ind in range(0, len(lines)):
         line = lines[ind]
         if ext in line:
@@ -46,10 +47,26 @@ def swap_datasets(lines, datasets):
             tmp = tmp.split(' ')[-1]
             tmp = tmp.replace("'", '')
             datasetsold.append(tmp.split(ext)[-2]+ext)
+        if "_riet_meas_datafile_as_background true" in line:
+            [datasetIsBk.append(True) for _ in range(0,3)]
+        elif "_riet_meas_datafile_as_background false" in line:
+            [datasetIsBk.append(False) for _ in range(0,3)]
+
+    datasetoldbk = []
+    datasetIndbk = []
+    for i, isBk in reversed(list(enumerate(datasetIsBk))):
+        if isBk:
+            datasetoldbk.append(datasetsold.pop(i))
+            datasetIndbk.append(datasetInd.pop(i))
 
     # Get the unique datasets make sure datasets make sense
     datasetsold = sorted(set(datasetsold))
+    datasetoldbk = sorted(set(datasetoldbk))
+    if datasetoldbk!=[]:
+        datasetsold = [datasetold for datasetold in datasetsold if datasetold not in datasetoldbk[0]]
+
     assert len(datasetsold) == len(datasets), 'The length of datasets were not the same!'
+    assert len(datasetoldbk) == 1 or datasetoldbk==[],'Only single backgrounds are supported'
 
     # Loop over the datasets and copy in the new file names
     for ind in datasetInd:
@@ -58,8 +75,17 @@ def swap_datasets(lines, datasets):
             if datasetsold[ind2] in line:
                 line = line.replace(datasetsold[ind2], datasets[ind2])
         lines[ind] = line
+
+    # Loop over the datasets and copy in the new file names
+    if background is not None: 
+        for ind in datasetIndbk:
+            line = lines[ind]
+            line = line.replace(datasetoldbk[0], background)
+            lines[ind] = line
     return lines
 
+
+
 def split_list_of_str(listofstr):
     tmp  = listofstr.replace('[','')
     tmp  = tmp.replace(']','')
@@ -71,15 +97,26 @@ def main(filename: str = "dataset.csv", work_dir: Path = Path.cwd(), keep_intens
     df = pd.read_csv(filename)
     db = df.to_dict(orient='list')
 
+    #Add backwards compatibility 
+    if 'background_files' not in db:
+        db['background_files']=[None]*len(db['run'])
+
     # Make directory specified by path (if doesn't exist) and copy in the data files
-    for data_files_tmp,data_dir,folder,ifile,ofile in zip(db["data_files"],db["data_dir"],db["folder"],db["ifile"],db["ofile"]):
+    for data_files_tmp,data_dir,folder,ifile,ofile,background_file in zip(db["data_files"],db["data_dir"],db["folder"],db["ifile"],db["ofile"],db["background_files"]):
         data_files = split_list_of_str(data_files_tmp)
 
         target_dir = work_dir / folder
         target_dir.mkdir(parents=True,exist_ok=True)
         for file in data_files:
             shutil.copyfile(Path(data_dir) / file, target_dir / Path(file).name)
 
+        if background_file is not None:
+            background_file_name = Path(background_file).name
+            shutil.copyfile(background_file, target_dir / background_file_name)
+        else:
+            background_file_name = None
+
+
         # Readin the template file
         linesTfile = read_file(ifile)
 
@@ -88,7 +125,7 @@ def main(filename: str = "dataset.csv", work_dir: Path = Path.cwd(), keep_intens
             linesTfile = remove_intensity(linesTfile)
 
         # detect the current dataset names and replace with new dataset names
-        linesTfile = swap_datasets(linesTfile, data_files)
+        linesTfile = swap_datasets(linesTfile, data_files, background_file_name)
 
         # Write the parameter file to the directory
         write_file(linesTfile, target_dir / ofile)