66This file takes the .pico spectrometer files and parses them to a numpy
77or pandas
88
9- @author: centos
9+ @author: Declan Valters
1010"""
1111
1212import json
1515
1616import unittest
1717
18- path = "/home/centos/Downloads/DATA/Spectra_dir/"
19- spectra_file_test = "QEP1USB1_b000000_s000002_light.pico"
20-
21- def read_json ():
22- """Simple JSON reader"""
23- with open (path + spectra_file_test , "r" ) as f :
24- data = json .load (f )
25- return data
26-
27- def pandas_read_json ():
28- """pandas read json to dataframe"""
29- with open (path + spectra_file_test , "r" ) as f :
30- data = json .load (f )
31- dataframe = pd .DataFrame (data )
32- return dataframe
33-
34- def pandas_read_json_spectra ():
35- """Normalise the results to get the spectra"""
36- with open (path + spectra_file_test , "r" ) as f :
37- data = json .load (f )
38- result = json_normalize (data ["Spectra" ])
39- return result
40-
41- def pandas_read_json_str ():
42- """Normalise the results to get the spectra"""
43- with open (path + spectra_file_test , "r" ) as f :
44- data = json .load (f )
45- return data
46-
47- def get_only_spectra_pixels ():
48- """Get just the spectra pixels"""
49- with open (path + spectra_file_test , "r" ) as f :
50- data = json .load (f )
51- result = json_normalize (data ["Spectra" ])
52- return result ["Pixels" ]
53-
54- def valid_spectra (spectra_num ):
55- """Checks the index provided is a valid range for the spectrometer data
56- """
57- return spectra_num in range (0 ,4 )
58-
59- def get_spectra_metadata (spectra_number ):
60- """Returns the dict represtning the metadata from the spectra file.
61- for ONE of the up/down pairs.
18+ class SpectraFile (object ):
19+ SPECTRAFILE = "None"
20+ SPECTRA_PATH = "None"
6221
63- Note the file layout is like this:
64-
65- Upwelling Spectra [0]
66- Upwelling Spectra [1]
67- Downwelling Spectra [2]
68- Downwelling Spectra [3]
22+ def set_spectra_file (self , spectra_filename , spectra_filepath ):
23+ self .SPECTRA_PATH = spectra_filepath
24+ self .SPECTRAFILE = spectra_filename
25+
26+ def read_json (self , path , spectra_file ):
27+ """Simple JSON reader"""
28+ with open (path + spectra_file , "r" ) as f :
29+ data = json .load (f )
30+ return data
6931
70- So to get the first upwelling spetra, 0 is used."""
71- if not valid_spectra (spectra_number ):
72- raise IndexError ("Not a valid spectra number for this spectrometer: [0-3]" )
73- whole_file = read_json ()
74- # File format has spectra which contains a list of dicts:
75- # Metadata [0] and Pixels [1]
76- return whole_file ['Spectra' ][spectra_number ]['Metadata' ]
77-
78- def get_spectra_pixels (spectra_number ):
79- """Returns the dict represtning the metadata from the spectra file.
80- for ONE of the up/down pairs.
32+ def pandas_read_json (self , path , spectra_file ):
33+ """pandas read json to dataframe"""
34+ with open (path + spectra_file , "r" ) as f :
35+ data = json .load (f )
36+ dataframe = pd .DataFrame (data )
37+ return dataframe
8138
82- Note the file layout is like this:
39+ def pandas_read_json_spectra (self , path , spectra_file ):
40+ """Normalise the results to get the spectra"""
41+ with open (path + spectra_file , "r" ) as f :
42+ data = json .load (f )
43+ result = json_normalize (data ["Spectra" ])
44+ return result
45+
46+ def pandas_read_json_str (self , path , spectra_file ):
47+ """Normalise the results to get the spectra"""
48+ with open (path + spectra_file , "r" ) as f :
49+ data = json .load (f )
50+ return data
51+
52+ def get_only_spectra_pixels (self , path , spectra_file ):
53+ """Get just the spectra pixels"""
54+ with open (path + spectra_file , "r" ) as f :
55+ data = json .load (f )
56+ result = json_normalize (data ["Spectra" ])
57+ return result ["Pixels" ]
58+
59+ def valid_spectra (self , spectra_num ):
60+ """Checks the index provided is a valid range for the spectrometer data
61+ """
62+ return spectra_num in range (0 ,4 )
63+
64+ def get_spectra_metadata (self , spectra_number ):
65+ """Returns the dict represtning the metadata from the spectra file.
66+ for ONE of the up/down pairs.
8367
84- Upwelling Spectra [0] len = 1044
85- Upwelling Spectra [1] len = 2048
86- Downwelling Spectra [2] len = 1044
87- Downwelling Spectra [3] len = 2048
68+ Note the file layout is like this:
69+
70+ Upwelling Spectra [0]
71+ Upwelling Spectra [1]
72+ Downwelling Spectra [2]
73+ Downwelling Spectra [3]
74+
75+ So to get the first upwelling spetra, 0 is used."""
76+ if not self .valid_spectra (spectra_number ):
77+ raise IndexError ("Not a valid spectra number for this spectrometer: [0-3]" )
78+ whole_file = self .read_json ()
79+ # File format has spectra which contains a list of dicts:
80+ # Metadata [0] and Pixels [1]
81+ return whole_file ['Spectra' ][spectra_number ]['Metadata' ]
8882
89- So to get the first upwelling spetra, 0 is used."""
90- if not valid_spectra (spectra_number ):
91- raise IndexError ("Not a valid spectra number for this spectrometer: [0-3]" )
92- whole_file = read_json ()
93- # File format has spectra which contains a list of dicts:
94- # Metadata [0] and Pixels [1]
95- return whole_file ['Spectra' ][spectra_number ]['Pixels' ]
83+ def get_spectra_pixels (self , spectra_number , path , filename ):
84+ """Returns the dict represtning the metadata from the spectra file.
85+ for ONE of the up/down pairs.
86+
87+ Note the file layout is like this:
88+
89+ Upwelling Spectra [0] len = 1044
90+ Upwelling Spectra [1] len = 2048
91+ Downwelling Spectra [2] len = 1044
92+ Downwelling Spectra [3] len = 2048
93+
94+ So to get the first upwelling spetra, 0 is used."""
95+ if not self .valid_spectra (spectra_number ):
96+ raise IndexError ("Not a valid spectra number for this spectrometer: [0-3]" )
97+ whole_file = self .read_json (path , filename )
98+ # File format has spectra which contains a list of dicts:
99+ # Metadata [0] and Pixels [1]
100+ return whole_file ['Spectra' ][spectra_number ]['Pixels' ]
96101
97102
98103class spectra_metadata ():
@@ -103,21 +108,28 @@ def __init__(self):
103108class TestSpectraParser (unittest .TestCase ):
104109
105110 def test_valid_sepctra (self ):
111+ sf = SpectraFile ()
106112 for x in range (0 ,4 ):
107- self .assertTrue (valid_spectra (x ))
113+ self .assertTrue (sf . valid_spectra (x ))
108114
109115 def test_invalid_spectra (self ):
116+ sf = SpectraFile ()
110117 for item in [1.5 , "foobar" , 7 , - 2 ]:
111- self .assertFalse (valid_spectra (item ))
118+ self .assertFalse (sf . valid_spectra (item ))
112119
113120if __name__ == "__main__" :
114121 unittest .main ()
115122
116- data1 = read_json ()
117- df = pandas_read_json ()
118- df1 = pandas_read_json_str ()
119- df2 = pandas_read_json_spectra () # This is getting all four spectra pairs (UP/DOWN)
120- pixels = get_only_spectra_pixels ()
121- metadata_upwell_zero = get_spectra_metadata (0 )
123+ sf = SpectraFile ()
124+
125+ path = '/home/centos/Downloads/'
126+ filename = 'spectra.csv'
127+
128+ data1 = sf .read_json (path , filename )
129+ df = sf .pandas_read_json (path , filename )
130+ df1 = sf .pandas_read_json_str (path , filename )
131+ df2 = sf .pandas_read_json_spectra (path , filename ) # This is getting all four spectra pairs (UP/DOWN)
132+ pixels = sf .get_only_spectra_pixels (path , filename )
133+ metadata_upwell_zero = sf .get_spectra_metadata (0 )
122134
123135
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