Merge pull request #169 from h2020charisma/spg_spa_converter

Add convertion script for Thermo Nicolet spa and spg files

setup.py

@@ -71,6 +71,10 @@
     'Topic :: Software Development :: Libraries',
 ]
 
+CONSOLE_SCRIPTS = [
+        'spg2csv = ramanchada2.standalone.spg2csv:spg2csv',
+]
+
 
 def setup_package():
     setup(
@@ -91,6 +95,7 @@ def setup_package():
         packages=PACKAGES,
         python_requires=PYTHON_REQUIRES,
         url=URL,
+        entry_points=dict(console_scripts=CONSOLE_SCRIPTS),
         version=VERSION,
     )
 

src/ramanchada2/standalone/spg2csv.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+
+import argparse
+import csv
+import os
+
+try:
+    from tqdm import trange as range
+except ModuleNotFoundError:
+    pass
+
+from spectrochempy.core.readers.read_omnic import read_spg
+
+
+def spg2csv():
+    parser = argparse.ArgumentParser(description='Convert SPA/SPG file format.')
+    parser.add_argument('-i', '--input', type=str, required=True, help='Path to SPA or SPG file')
+    parser.add_argument('-o', '--output', type=str,
+                        help="Output file names in formated string like "
+                        "'/path/to/file-{y_label_name}.csv'. "
+                        "Possible options are: {y_label_date} {y_label_name} {y_coordinate} "
+                        "{input_basename} {input_extension}"
+                        "(default: '{input_basename}-{y_label_name}.csv')")
+    args = parser.parse_args()
+    out_file_format = args.output or f'{args.input}-{{y_label_name}}.csv'
+
+    input_basename, input_extension = os.path.splitext(args.input)
+
+    spe = read_spg(args.input)
+
+    x = spe.coordset['x'].data
+    for i in range(spe.coordset['y'].size):
+        (y_label_date, y_label_name), y_coordinate = spe.coordset['y'].labels[i], spe.coordset['y'].data[i]
+        y_label_name = str(y_label_name).replace('/', '_')
+        out_file_name = out_file_format.format(basename=input_basename,
+                                               y_label_date=y_label_date,
+                                               y_label_name=y_label_name,
+                                               y_coordinate=y_coordinate)
+        y = spe.data[i]
+        print(out_file_name)
+        with open(out_file_name, 'w') as fp:
+            csv_writer = csv.writer(fp)
+            csv_writer.writerows(zip(x, y))
+
+
+if __name__ == '__main__':
+    spg2csv()