Merge pull request #187 from h2020charisma/ssl_csv_converter

ADD ssl_csv_converter as a standalone executable

setup.py

@@ -73,6 +73,7 @@
 
 CONSOLE_SCRIPTS = [
         'spg2csv = ramanchada2.standalone.spg2csv:spg2csv',
+        'ssl_csv_converter = ramanchada2.standalone.ssl_csv_converter:ssl_csv_converter',
 ]
 
 

src/ramanchada2/spectrum/creators/from_local_file.py

@@ -12,6 +12,7 @@
 from ramanchada2.misc.types import SpeMetadataModel
 
 from ..spectrum import Spectrum
+from .from_chada import from_chada
 
 
 @add_spectrum_constructor()
@@ -20,7 +21,7 @@ def from_local_file(
         in_file_name: str,
         filetype: Union[None, Literal['spc', 'sp', 'spa', '0', '1', '2',
                                       'wdf', 'ngs', 'jdx', 'dx',
-                                      'txt', 'txtr', 'csv', 'prn', 'rruf', 'spe']] = None,
+                                      'txt', 'txtr', 'csv', 'prn', 'rruf', 'spe', 'cha']] = None,
         backend: Union[None, Literal['native', 'rc1_parser']] = None):
     """
     Read experimental spectrum from a local file.
@@ -44,7 +45,9 @@ def load_native():
             ft = os.path.splitext(in_file_name)[1][1:]
         else:
             ft = filetype
-        if ft in {'txt', 'txtr', 'prn', 'rruf'}:
+        if ft in {'cha'}:
+            return from_chada(filename=in_file_name)
+        elif ft in {'txt', 'txtr', 'prn', 'rruf'}:
             with open(in_file_name) as fp:
                 x, y, meta = read_txt(fp)
         elif ft in {'csv'}:

src/ramanchada2/standalone/ssl_csv_converter.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+
+import numpy as np
+
+import ramanchada2 as rc2
+
+
+def ssl_csv_to_spectra(filename):
+    with open(filename) as f:
+        lines = [i.strip() for i in f.readlines()]
+        assert lines[0].startswith('ssl-SA')
+        head_sep = '***** X axis & Intensity *****'
+        assert head_sep in lines
+        global_meta = {'format': lines[0],
+                       'datetime': lines[1],
+                       }
+        header_sep_idx = lines.index(head_sep)
+
+        global_meta.update(dict([[j.strip() for j in i.split('=')] for i in lines[2:header_sep_idx] if '=' in i]))
+
+        k = 'Laser wavelength'
+        if k in global_meta.keys():
+            v = global_meta[k]
+            if v.endswith(' nm'):
+                v = int(v[:-3])
+                global_meta['laser wavelength [nm]'] = v
+
+        k = 'Integ time'
+        if k in global_meta.keys():
+            v = global_meta[k]
+            if v.endswith(' ms'):
+                v = int(v[:-3])
+                global_meta['integration time [ms]'] = v
+                global_meta['intigration times(ms)'] = v
+
+        basename = os.path.basename(filename)
+        global_meta['Original file'] = basename
+
+        ccc = np.loadtxt(lines[header_sep_idx+1:], delimiter=',')
+        ccc = ccc.T
+        x = ccc[0]
+        spectra = []
+        for y_i, y in enumerate(ccc[1:], 1):
+            meta = {'spectrum number': y_i, 'total spectra number': ccc.shape[1]}
+            meta.update(global_meta)
+            spectra.append(rc2.spectrum.Spectrum(x=x, y=y, metadata=meta))
+    return spectra
+
+
+def ssl_csv_converter():
+    parser = argparse.ArgumentParser(description='Convert ssl csv file format.')
+    parser.add_argument('-i', '--input', type=str, required=True, help='Path to ssl csv file')
+    parser.add_argument('-t', '--format-to', type=str, required=False,
+                        help='Output file format cha or csv', default='cha')
+    parser.add_argument('-o', '--output', type=str,
+                        help="Output file names in formated string "
+                        "Possible options are: {date} {succ_num} {all_spe_num} "
+                        "{laser_wavelength} {integration_time} "
+                        "{input_basename} {input_extension}"
+                        "(default: '{input_basename}--{laser_wavelength}nm"
+                        "-{integration_time}ms-{succ_num}-{all_spe_num}.cha')")
+    args = parser.parse_args()
+    out_fmt = args.format_to or 'cha'
+    out_file_format = (
+        args.output or
+        f'{args.input}-{{laser_wavelength}}nm-{{integration_time}}ms-{{succ_num}}-{{all_spe_num}}.{out_fmt}'
+    )
+
+    input_basename, input_extension = os.path.splitext(args.input)
+
+    spes = ssl_csv_to_spectra(args.input)
+
+    for spe_i, spe in enumerate(spes, 1):
+        dct = dict(input_basename=input_basename,
+                   input_extension=input_extension,
+                   date=spe.meta['datetime'].strftime('%F'),
+                   succ_num=spe_i,
+                   all_spe_num=len(spes),
+                   laser_wavelength=spe.meta['laser wavelength [nm]'],
+                   integration_time=spe.meta['integration time [ms]'],
+                   )
+
+        out_file_name = out_file_format.format(**dct)
+        if out_fmt == 'cha':
+            spe.write_cha(out_file_name, '/raw')
+        elif out_fmt == 'csv':
+            spe.write_csv(out_file_name)
+        else:
+            raise Exception('File format {out_fmt} is unknown')
+
+
+if __name__ == '__main__':
+    ssl_csv_converter()