feat: read mw, mp, d, mn values for sec (#192)

chem_spectra/lib/composer/ni.py

@@ -130,6 +130,16 @@ def __gen_header_cyclic_voltammetry(self):
             '$$ === CHEMSPECTRA CYCLIC VOLTAMMETRY ===\n',
         ]
 
+    def __gen_header_sec(self):
+        core_dic = self.core.dic
+        sec_data_key = ['MN', 'MW', 'MP', 'D']
+        result = []
+        for key in sec_data_key:
+            dic_value = core_dic.get(key, [])
+            key_str = f"##{key}={dic_value[0]}\n" if len(dic_value) > 0 else f'##{key}=\n'
+            result.append(key_str)
+        return result
+
     def __get_xy_of_peak(self, peak):
         if peak is None:
             return '', ''
@@ -201,6 +211,8 @@ def __compose(self):
         meta.extend(self.gen_headers_root())
 
         meta.extend(self.__gen_headers_spectrum_orig())
+        if self.core.is_sec:
+            meta.extend(self.__gen_header_sec())
         meta.extend(self.gen_spectrum_orig())
         meta.extend(self.__gen_headers_im())
         meta.extend(self.__gen_headers_integration())
@@ -509,6 +521,9 @@ def tf_img(self):
             plt.ylabel("Y ({})".format(self.core.label['y']), fontsize=18)
         plt.locator_params(nbins=self.__plt_nbins())
         plt.grid(False)
+
+        self.__generate_info_box(plt)
+
         # Save
         tf_img = tempfile.NamedTemporaryFile(suffix='.png')
         plt.savefig(tf_img, format='png')
@@ -517,6 +532,25 @@ def tf_img(self):
         plt.cla()
         return tf_img
 
+
+    def __generate_info_box(self, plotlib):
+        if not self.core.is_sec:
+            return
+        core_dic = self.core.dic
+        sec_data_key = ['MN', 'MW', 'MP', 'D']
+        result = []
+        for key in sec_data_key:
+            dic_value = core_dic.get(key, [])
+            key_str = f"{key}={dic_value[0]}" if len(dic_value) > 0 else None
+            if key_str is not None:
+                result.append(key_str)
+
+        info_str = '\n'.join(result)
+        props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
+        ax = plotlib.gca()
+        ax.text(0.05, 0.95, info_str, fontsize=14, verticalalignment='top', bbox=props, transform=ax.transAxes)
+
+
     def __prepare_metadata_info_for_csv(self, csv_writer: csv.DictWriter):
         csv_writer.writerow({
             'Anodic E(V)': 'Measurement type',

tests/lib/composer/test_ni_composer.py

@@ -1,15 +1,19 @@
 import json
 import pytest
 import numpy as np
+import tempfile
+import zipfile
 from chem_spectra.lib.converter.jcamp.base import JcampBaseConverter
 from chem_spectra.lib.converter.jcamp.ni import JcampNIConverter
 from chem_spectra.lib.composer.ni import NIComposer
 from chem_spectra.controller.helper.file_container import FileContainer
+from chem_spectra.lib.converter.bagit.base import BagItBaseConverter as BagItConveter
 
 source_nmr = './tests/fixtures/source/1H.dx'
 source_nmr_edit = './tests/fixtures/source/1H.edit.jdx'
 source_ir = './tests/fixtures/source/IR.dx'
 source_dir_molfile = './tests/fixtures/source/molfile/c60h57fn4.mol'
+source_sec =  './tests/fixtures/source/sec/SEC-ExFile.zip'
 
 @pytest.fixture
 def data_schema():
@@ -37,6 +41,10 @@ def molfile_data():
     molfile_str = molfile.read()
     return molfile_str
 
+@pytest.fixture
+def bagit_file_sec():
+    return source_sec
+
 def test_init_ni_composer_failed():
     with pytest.raises(Exception) as error:
         _ = NIComposer(None)
@@ -250,3 +258,19 @@ def test_ni_composer_generate_nmrium_with_molfile(jcamp_file_1h, molfile_data):
         assert 'id' in molecule_data.keys()
         assert molecule_data['label'] == 'P1'
         assert molecule_data['molfile'] == molfile_data
+
+def test_ni_composer_generate_jcamp(bagit_file_sec):
+    with tempfile.TemporaryDirectory() as td:
+        with zipfile.ZipFile(bagit_file_sec, 'r') as z:
+            z.extractall(td)
+
+        converter = BagItConveter(td)
+        for jcamp_file in converter.data:
+            base_converter = JcampBaseConverter(jcamp_file.name)
+            ni_converter = JcampNIConverter(base=base_converter)
+            ni_composer = NIComposer(core=ni_converter)
+            headers = ni_composer._NIComposer__gen_header_sec()
+            assert headers in [
+                ['##MN=1.287E+3\n', '##MW=1.465E+3\n', '##MP=1.345E+3\n', '##D=1.139E+0\n'],
+                ['##MN=\n', '##MW=\n', '##MP=\n', '##D=\n']
+            ]