more tests written

README.md

@@ -1,27 +1,18 @@
 # jws2txt
-JASCO file to text file converter
 
-jws2txt converts JASCO spectrophotometer *.jws files to *.txt files.
+A program to convert binary JASCO SpectraManager (JWS and JWB) files to text files.
 
-
-Introduction
+## Introduction
 ------------
-jws2txt is a simple command line tool allowing conversion
-JWS and JWB files from Jasco SpectraManager software. jws2txt converts JWS and JWB files to
-text files that can be used in any data analysis workflows and software.
+jws2txt is a simple command line tool that allows for the conversion of JWS and JWB files from JASCO SpectraManager software to text files. These text files can be used in any data analysis workflows and software.
 
-Contrary to Jasco SpectraManager software jws2txt allows for batch conversion
-of JWS/JWB files.
+Unlike JASCO SpectraManager software, jws2txt enables batch conversion of JWS/JWB files.
 
-Data unpack is based on Víctor M. Hernández-Rocamora's jwsProcessor
-(https://github.com/vhernandez/jwsProcessor).
+Data unpacking is based on Víctor M. Hernández-Rocamora's jwsProcessor (https://github.com/vhernandez/jwsProcessor).
 
-Installation and usage
+## Installation and Usage
 ------------
-1. Download python, preferentially in Anaconda distribution.
-2. Download this repository, unzip it.
-3. Run the 'pip install -r requirements.txt' command in the command line.
-4. To convert the files run the 'python jws2txt.py path_to_folder' command, where path_to_folder
-is a folder containing JWS or JWB files.
-5. Input the number of channels the files have.
-6. Converted files will be in the folder containing source JWS or JWB files
+1. Download Python.
+2. Run the 'pip install jws2txt' command in the command line.
+3. To convert the files, run the 'jws2txt --in-path path_to_folder --out-dir output_folder_path' command, where path_to_folder is the folder containing the JWS or JWB files.
+4. The converted files will be located in the folder containing the source JWS or JWB files.

jws2txt/helpers/helpers.py

@@ -1,7 +1,7 @@
 from struct import unpack
 import csv
 import olefile as ofio
-
+from typing import Iterator
 
 DATAINFO_FMT = '<LLLLLLdddLLLLdddd'
 
@@ -16,7 +16,7 @@
 
 
 
-def frange(start: float, stop: float = 0, step: float = 1.0):
+def frange(start: float, stop: float = 0, step: float = 1.0) -> Iterator[float]:
     """Return evenly spaced number over specified range.
 
     Args:
@@ -96,6 +96,8 @@ def __init__(self, path: str) -> None:
             self.sample_name = ''
             self.comment = ''
 
+        file.close()
+
     def __unpack_y_data(self, y_data: bytes, format: str, num_chanels: int) -> None:
         """Unpacks the Y-Data from the JWS file.
         """

jws2txt/jws2txt.py

@@ -3,7 +3,7 @@
 from .helpers.helpers import JWSFile
 
 
-def str2bool(v) -> bool:
+def str2bool(v: str) -> bool:
     """Converts string to bool."""
     if isinstance(v, bool):
         return v

temp/test.py

@@ -1,12 +1,21 @@
 #%%
 import jws2txt
 import matplotlib.pyplot as plt
-
+from io import StringIO
 test_file = jws2txt.JWSFile(r'001Hg.jws')
 
 
+
+
 x, cd, ht, abs = test_file.unpacked_data
 
+outfile = StringIO()
+test_file.write_data(outfile)
+outfile.seek(0)
+content = outfile.read()
+print(content)
+
+
 #%%
 # %%
 
@@ -22,7 +31,15 @@
 
 test_file.decode_sample_info()
 # %%
-test_file.unpacked_data[0][2]
-test_file.unpacked_data[1][2]
-test_file.unpacked_data[2][2]
-test_file.unpacked_data[3][2]
+test_file = jws2txt.JWSFile(r'../tests/files/sample_fluorescence.jws')
+test_file = jws2txt.JWSFile(r'../tests/files/2022_05_14-1.jwb')
+
+
+# %%
+
+
+from jws2txt.helpers.helpers import frange
+
+
+tuple(frange(2, 0.9, -0.1))
+# %%

tests/test_helpers.py

@@ -1,12 +1,19 @@
 import unittest
 import jws2txt
+from jws2txt.helpers.helpers import frange
+import csv
+import os
+
+
+test_file = 'test.txt'
 
 class JWSFileTest(unittest.TestCase):
 
     def setUp(self) -> None:
         self.three_channels = jws2txt.JWSFile(r'tests/files/001Hg.jws')
-
-
+        self.single_channel = jws2txt.JWSFile(r'tests/files/sample_fluorescence.jws')
+        self.jwb_file = jws2txt.JWSFile(r'tests/files/2022_05_14-1.jwb')
+
     def test_three_channels_creation(self):
         # Test file creation and initialization
 
@@ -42,6 +49,97 @@ def test_three_channels_creation(self):
         self.assertEqual(self.three_channels.unpacked_data[2][2], 206.2129669189453)
         self.assertEqual(self.three_channels.unpacked_data[3][2], 0.11851496249437332)
 
+        # todo test for 1 ch file
+        # todo test for saving
+
+    def test_single_channel(self):
+        # Test file creation and initialization
+
+        self.assertEqual(self.single_channel.numchanels, 1)
+        self.assertEqual(self.single_channel.npoints, 301)
+        self.assertEqual(self.single_channel.x_for_first_point, 400.0)
+        self.assertEqual(self.single_channel.x_for_last_point, 700.0)
+        self.assertEqual(self.single_channel.x_increment, 1)
+        self.assertEqual(self.single_channel.header_codes, (268435715, 14))
+        self.assertEqual(self.single_channel.header_names, ['WAVELENGTH',
+                                                            'FLUORESCENCE'])
+        self.assertEqual(self.single_channel.data_list, [3,
+                                                        1,
+                                                        0,
+                                                        1,
+                                                        1,
+                                                        301,
+                                                        400.0,
+                                                        700.0,
+                                                        1.0,
+                                                        268435715,
+                                                        14,
+                                                        268435715,
+                                                        14,
+                                                        400.0,
+                                                        700.0,
+                                                        700.0,
+                                                        0.0])
+        self.assertEqual(self.single_channel.sample_name, 'photonic wire')
+        self.assertEqual(self.single_channel.comment, '')
+        #test x-axis and 3 channels
+        self.assertEqual(self.single_channel.unpacked_data[0][2], 402.0)
+        self.assertEqual(self.single_channel.unpacked_data[1][2], 24.556852340698242)
+
+    def test_jwb_file_creation(self):
+        self.assertEqual(self.jwb_file.numchanels, 8)
+        self.assertEqual(self.jwb_file.npoints, 1001)
+        self.assertEqual(self.jwb_file.x_for_first_point, 900.0)
+        self.assertEqual(self.jwb_file.x_for_last_point, 400.0)
+        self.assertEqual(self.jwb_file.x_increment, -0.5)
+        self.assertEqual(self.jwb_file.header_codes, (268435715, 3, 0, 8))
+        self.assertEqual(self.jwb_file.header_names, ['WAVELENGTH', 'ABSORBANCE',
+                                                       'undefined', 'undefined'])
+        self.assertEqual(self.jwb_file.data_list, [3,
+                                                    8,
+                                                    1,
+                                                    1,
+                                                    1,
+                                                    1001,
+                                                    900.0,
+                                                    400.0,
+                                                    -0.5,
+                                                    268435715,
+                                                    3,
+                                                    0,
+                                                    8,
+                                                    24.979999542236328,
+                                                    60.0099983215332,
+                                                    0.0,
+                                                    2.00000035762821])
+        self.assertEqual(self.jwb_file.sample_name, '')
+        self.assertEqual(self.jwb_file.comment, '')
+        # test x-axis and 3 channels
+        self.assertEqual(self.jwb_file.unpacked_data[0][2], 899.0)
+        # test 7th channel
+        self.assertEqual(self.jwb_file.unpacked_data[7][2], 0.07367147505283356)
+
+    def test_writing(self):
+        self.three_channels.write_data(test_file)
+        with open(test_file, 'r') as file:
+             reader = csv.reader(file, dialect='excel')
+             self.assertEqual(next(reader), ['HK14_CN'])
+        os.remove(test_file)
+
+
+
+class FrangeTest(unittest.TestCase):
+
+    def test_frange(self):
+        self.assertEqual(tuple(frange(1, 2, 0.2)), (1.0, 1.2, 1.4, 1.6, 1.8))
+        self.assertEqual(tuple(frange(2, 0.9, -0.1)), (2.0, 1.9, 1.8, 1.7, 1.6, 1.5,
+                                                        1.4, 1.2999999999999998, 1.2,
+                                                        1.1, 1.0))
+
+
+
+
+
 
 if __name__=='__main__':
 	unittest.main()

tests/test_main.py

@@ -0,0 +1,19 @@
+import unittest
+from jws2txt.jws2txt import str2bool
+from argparse import ArgumentTypeError
+
+
+class TestStr2Bool(unittest.TestCase):
+
+     def test_str2bool(self):
+          self.assertTrue(str2bool('y'))
+          self.assertTrue(str2bool('true'))
+          self.assertFalse(str2bool('n'))
+          self.assertFalse(str2bool('f'))
+          with self.assertRaises(ArgumentTypeError):
+               str2bool('blurb')
+
+
+
+if __name__=='__main__':
+	unittest.main()