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Class_Mod/DxReader.py

+from Packages import * 
+
+class DxReader:
+
+    '''This module is designed to help retrieve spectral data as well as metadata of smaples  from jcamp file'''
+    def __init__(self, path):
+        self.__path = path.replace('\\','/')
+        self.__dxfile = jc.jcamp_readfile(self.__path)
+        
+        # Access samples data
+        self.__nb = self.__dxfile['blocks'] # Get the total number of blocks = The total number of scanned samples
+        self.__list_of_blocks = self.__dxfile['children']  # Store all blocks within a a list
+        self.__wl = self.__list_of_blocks[0]["x"] # Wavelengths/frequencies/range 
+        
+
+
+        # Start retreiving the data
+        specs = np.zeros((self.__nb, len(self.__list_of_blocks[0]["y"])), dtype=float) # preallocate a np matrix for sotoring spectra
+        self.idx = np.arange(self.__nb) # This list is designed to store samples name
+        self.__met = {}
+
+
+        for i in range(self.__nb): # Loop over the blocks
+            specs[i] = self.__list_of_blocks[i]['y']
+            
+
+            block_met = {   'name':self.__list_of_blocks[i]['title'],
+                            'origin':self.__list_of_blocks[i]['origin'],
+                            'date':self.__list_of_blocks[i]['date'],
+                            'time':self.__list_of_blocks[i]['time'],
+                            'spectrometer/data system':self.__list_of_blocks[i]['spectrometer/data system'],
+                            'instrumental parameters':self.__list_of_blocks[i]['instrumental parameters'],
+                            'xunits':self.__list_of_blocks[i]['xunits'],
+                            'yunits':self.__list_of_blocks[i]['yunits'],
+                            'xfactor':self.__list_of_blocks[i]['xfactor'],
+                            'yfactor':self.__list_of_blocks[i]['yfactor'],
+                            'firstx':self.__list_of_blocks[i]['firstx'],
+                            'lastx':self.__list_of_blocks[i]['lastx'],
+                            'firsty':self.__list_of_blocks[i]['firsty'],
+                            'miny': self.__list_of_blocks[i]['miny'],
+                            'maxy': self.__list_of_blocks[i]['maxy'],
+                            'npoints':self.__list_of_blocks[i]['npoints'],
+                            'concentrations':self.__list_of_blocks[i]['concentrations'],
+                            'deltax':self.__list_of_blocks[i]['deltax'],
+                            }
+            self.__met[f'{i}'] = block_met
+        self.metadata_ = pd.DataFrame(self.__met).T
+            
+
+        self.spectra = pd.DataFrame(np.fliplr(specs), columns= self.__wl[::-1]) # Storing spectra in a pd.dataframe
+
+
+
+        #### Concentrarions
+        self.pattern = r"\(([^,]+),(\d+(\.\d+)?),([^)]+)"
+        aa = self.__list_of_blocks[0]['concentrations']
+        a = '\n'.join(line for line in aa.split('\n') if "NCU" not in line and "<<undef>>" not in line)
+        n_elements = a.count('(')
+
+        ## Get the name of analyzed chamical elements
+        elements_name = []
+        for match in re.findall(self.pattern, a):
+                elements_name.append(match[0])
+
+        ## Retrieve concentrationds
+        df = self.metadata_['concentrations']
+        cc = {}
+        for i in range(self.metadata_.shape[0]):
+            cc[df.index[i]] = self.conc(df[str(i)])
+
+        ### dataframe conntaining chemical data
+        self.chem_data = pd.DataFrame(cc, index=elements_name).T
+
+    ### Method for retrieving the concentration of a single sample
+    def conc(self,sample):
+        prep = '\n'.join(line for line in sample.split('\n') if "NCU" not in line and "<<undef>>" not in line)
+        c = []
+        for match in re.findall(self.pattern, prep):
+                c.append(match[1])
+        concentration = np.array(c)
+        return concentration
+
+    @property
+    def specs_df_(self):
+        return self.spectra
+    @property
+    def md_df_(self):
+        return self.metadata_
+    
+    @property
+    def chem_data_(self):
+         return self.chem_data
\ No newline at end of file

Packages.py

@@ -3,6 +3,8 @@
 import os
 import sys
 import csv
+import re
+import jcamp
 import random
 import numpy as np
 import pandas as pd