Update docs and create new unit tests

.gitignore

@@ -37,3 +37,24 @@ Baseline_Comparison/nd70_statistics.csv
 Baseline_Comparison/ND70Spec.zip
 Baseline_Comparison/Comparison_Standards.csv
 Baseline_Comparison/CComparison_Standards.csv
+docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log
+docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log
+docs/examples/transmission_ftir/LOGFILES/RESULTS/STD_D1010_012821_256s_100x100_a.log
+docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a_statistics.txt
+docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/AC4_OL53_101220_256s_30x30_a_statistics.txt
+docs/examples/transmission_ftir/NPZTXTFILES/RESULTS/STD_D1010_012821_256s_100x100_a_statistics.txt
+docs/examples/transmission_ftir/PKLFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.pkl
+docs/examples/transmission_ftir/PKLFILES/RESULTS/STD_D1010_012821_256s_100x100_a.pkl
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/AC4_OL53_101220_256s_30x30_a_histogram.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/HISTOGRAM/STD_D1010_012821_256s_100x100_a_histogram.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/AC4_OL53_101220_256s_30x30_a_modelfit.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/MODELFIT/STD_D1010_012821_256s_100x100_a_modelfit.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/AC4_OL53_101220_256s_30x30_a_pairwise.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/PAIRWISE/STD_D1010_012821_256s_100x100_a_pairwise.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/AC4_OL53_101220_256s_30x30_a_trace.pdf
+docs/examples/transmission_ftir/PLOTFILES/RESULTS/TRACE/STD_D1010_012821_256s_100x100_a_trace.pdf
+docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log
+docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log
+docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL49_021920_30x30_H2O_a.log
+docs/examples/transmission_ftir/LOGFILES/RESULTS/AC4_OL53_101220_256s_30x30_a.log
+docs/examples/transmission_ftir/LOGFILES/RESULTS/STD_D1010_012821_256s_100x100_a.log

UnitTests/test_density_epsilon.py

@@ -49,15 +49,25 @@ def setUp(self):
 
     def test_density_calculation(self):
 
-        mol, density = pig.calculate_density(self.MI_Composition, self.T_room, self.P_room)
-        result = float(density.values)
-        expected = 2702.703558
+        _, density_ls = pig.calculate_density(self.MI_Composition, self.T_room, self.P_room, model='LS')
+        result_ls = float(density_ls.values)
+        expected_ls = 2702.703558
         self.assertAlmostEqual(
-            result,
-            expected,
+            result_ls,
+            expected_ls,
             self.decimalPlace,
             msg="Density test and expected values from the "
-            "calculate_density function do not agree")
+            "calculate_density function with LS do not agree")
+
+        _, density_it = pig.calculate_density(self.MI_Composition, self.T_room, self.P_room, model='IT')
+        result_it = float(density_it.values)
+        expected_it = 2750.959065
+        self.assertAlmostEqual(
+            result_it,
+            expected_it,
+            self.decimalPlace,
+            msg="Density test and expected values from the "
+            "calculate_density function with IT do not agree")
 
     def test_epsilon_calculation(self):
 

UnitTests/test_fittingfunc.py

@@ -74,6 +74,17 @@ def test_NIR(self):
             msg="H2Om5200 peak height test and expected values from the "
             "NearIR_Process function do not agree")
 
+    def test_NIR_invalid_peak_type(self):
+
+        valid_data = next(iter(self.dfs_dict.values()))
+        invalid_peak_type = "InvalidPeakType"  # Intentionally invalid peak type
+
+        with self.assertRaises(ValueError) as context:
+            pig.NIR_process(valid_data, 4875, 5400, invalid_peak_type)
+
+        self.assertTrue(f"Invalid peak type: {invalid_peak_type}" 
+                        in str(context.exception))
+
     def test_MIR(self):
 
         for _, data in self.dfs_dict.items():
@@ -112,21 +123,63 @@ def test_MCMC(self):
             expected_H2Om_5200,
             self.decimalPlace,
             msg="H2Om_5200 peak height test and expected values from the "
-            "Run_All_Spectra function do not agree")
+            "calculate_baselines function do not agree")
+
+        self.assertAlmostEqual(
+            result_H2Ot_3550,
+            expected_H2Ot_3550,
+            self.decimalPlace,
+            msg="H2Ot_3550 peak height test and expected values from the "
+            "calculate_baselines function do not agree")
+
+        self.assertAlmostEqual(
+            result_CO2_1515,
+            expected_CO2_1515,
+            self.decimalPlace - 3,
+            msg="CO2_1515 peak height test and expected values from the "
+            "calculate_baselines function do not agree")
+
+    def test_MCMC_interp(self):
+
+        first_index = self.df.index > 1000
+        if any(first_index):
+            first_index_position = np.argmax(first_index)
+            drop_indices = self.df.index[first_index_position + 1:first_index_position + 11] 
+            self.df_interp = self.df.drop(drop_indices)
+
+        self.dfs_dict_interp = {self.file: self.df_interp}
+
+        Volatiles_DF, _ = pig.calculate_baselines(self.dfs_dict_interp, None)
+
+        result_H2Om_5200 = float(Volatiles_DF['PH_5200_M'].iloc[0])
+        expected_H2Om_5200 = 0.00895907201720743
+
+        result_H2Ot_3550 = float(Volatiles_DF['PH_3550_M'].iloc[0])
+        expected_H2Ot_3550 = 1.52334293070956
+
+        result_CO2_1515 = float(Volatiles_DF['PH_1515_BP'].iloc[0])
+        expected_CO2_1515 = 0.057289618537916066
+
+        self.assertAlmostEqual(
+            result_H2Om_5200,
+            expected_H2Om_5200,
+            self.decimalPlace,
+            msg="H2Om_5200 peak height test and expected values from the "
+            "calculate_baselines function do not agree")
 
         self.assertAlmostEqual(
             result_H2Ot_3550,
             expected_H2Ot_3550,
             self.decimalPlace,
             msg="H2Ot_3550 peak height test and expected values from the "
-            "Run_All_Spectra function do not agree")
+            "calculate_baselines function do not agree")
 
         self.assertAlmostEqual(
             result_CO2_1515,
             expected_CO2_1515,
             self.decimalPlace - 3,
             msg="CO2_1515 peak height test and expected values from the "
-            "Run_All_Spectra function do not agree")
+            "calculate_baselines function do not agree")
 
     def test_MCMC_exportpath(self):
 

UnitTests/test_loading.py

@@ -76,6 +76,25 @@ def test_load_dir_chemthick(self):
         self.assertEqual(chemistry.shape, (9, 11))
         self.assertEqual(thickness.shape, (9, 2))
 
+    def test_spectrum_path_none(self):
+        with self.assertRaises(ValueError):
+            loader = pig.SampleDataLoader(spectrum_path=None)
+            loader.load_spectrum_directory()
+
+    def test_chemistry_thickness_path_none(self):
+        with self.assertRaises(ValueError):
+            loader = pig.SampleDataLoader(chemistry_thickness_path=None)
+            loader.load_chemistry_thickness()
+
+    def test_invalid_csv_format(self):
+        # Assuming you have an invalid CSV file for this test
+        invalid_csv_path = os.path.join(
+            os.path.dirname(os.path.realpath(__file__)),
+            'path/to/your/invalid_csv_file.csv'
+        )
+        with self.assertRaises(ValueError):
+            loader = pig.SampleDataLoader(spectrum_path=invalid_csv_path)
+            loader.load_spectrum_directory()
 
 if __name__ == '__main__':
     unittest.main()

docs/examples/transmission_ftir/FINALDATA/DF.csv

@@ -0,0 +1,4 @@
+,PH_3550_M,PH_3550_STD,H2Ot_3550_MAX,BL_H2Ot_3550_MAX,H2Ot_3550_SAT,PH_1635_BP,PH_1635_STD,PH_1515_BP,PH_1515_STD,P_1515_BP,P_1515_STD,STD_1515_BP,STD_1515_STD,PH_1430_BP,PH_1430_STD,P_1430_BP,P_1430_STD,STD_1430_BP,STD_1430_STD,PH_5200_M,PH_5200_STD,PH_4500_M,PH_4500_STD,STN_P5200,ERR_5200,STN_P4500,ERR_4500,AVG_BL_BP,AVG_BL_STD,PC1_BP,PC1_STD,PC2_BP,PC2_STD,PC3_BP,PC3_STD,PC4_BP,PC4_STD,m_BP,m_STD,b_BP,b_STD,PH_1635_PC1_BP,PH_1635_PC1_STD,PH_1635_PC2_BP,PH_1635_PC2_STD
+AC4_OL49_021920_30x30_H2O_a,2.1722500209939493,0.0022116149510955836,2.649837,0.4598586208562721,*,0.6583491880184121,0.0030749126402198697,0.10686432559386666,0.003617684246677255,1517.474274372431,1.5182396123926605,35.611038435771576,1.9426494612507434,0.10942913704159829,0.003998298365950207,1427.9922206706017,1.4193664333281357,28.85332005352919,1.2055094429028048,0.024909186694699683,0.0008013162213433842,0.014570093124893511,6.460708464050103e-05,12.195762674599015,-,8.157689580452923,-,1.1040470270583682,0.037503998964593735,-1.0504933455802845,0.3994585233071356,0.9376266092174402,0.019781423344117303,-0.09340636256800676,0.06045770843644922,0.29999999999999993,0.023016725028572844,-0.0003100922174198882,6.76489938725298e-05,1.2338252968133392,0.021301724598351394,0.11213209405817827,0.016193177122467085,0.044745957015674034,0.020451733221300252
+AC4_OL53_101220_256s_30x30_a,1.5233426827103218,0.0033092236185633846,1.631044,0.13554145039853702,-,0.29967506964819424,0.003062210614512881,0.05305994287064932,0.0036758392931568545,1519.2334635768602,2.8066057091459924,32.414304746275114,2.784238916959108,0.05024321853406153,0.004285715724583188,1427.2586532478908,3.1130943263832966,34.35120889642723,2.8233542411080745,0.008958906735709577,0.0004449140364037349,0.012517606386667756,0.00032036233298576015,6.90402676330999,-,5.527669572279575,-,0.511735256281459,0.043875233805488495,-2.963278565535986,0.4487172333197129,0.27570771325870513,0.020432535023846985,-0.5066370203992294,0.06132111604875771,0.22624896917334789,0.04227109362475997,-0.00044487318729776154,7.645869090603355e-05,0.7212552944882438,0.02301693318373148,-0.052546462541862994,0.01639656977793004,0.046798062360385494,0.017608365106921108
+STD_D1010_012821_256s_100x100_a,2.7108938068234614,0.0015870027387259998,2.915508,0.20664130261763228,*,0.17348651543140622,0.003056241542456818,0.07555997483046767,0.0033492756922561748,1522.9753584005089,2.39819240541948,35.370538256455376,2.4311378337852196,0.06757826142692784,0.004063170725884987,1431.4522834178945,2.293519583887849,31.066664742008154,2.4400999678819013,0.008596527707852878,0.00012849123724541835,0.018646773532606183,0.0003276983762892409,12.116667428210414,-,13.264652936348938,-,3.9999999999999996,0.006223452071132112,0.761701691291354,0.10161089931202222,-0.44300286478842543,0.019334750691436323,-0.37899896502503055,0.02716550018552502,0.17861839731787293,0.023738484937729454,-0.00023214668050949028,1.4671822466810936e-05,2.4623525441636516,0.006594444676255823,0.07665825504300086,0.01647606902504966,-0.027976898391759562,0.021748326300020524

docs/examples/transmission_ftir/FINALDATA/H2OCO2.csv

@@ -0,0 +1,4 @@
+,H2Ot_MEAN,H2Ot_STD,H2Ot_3550_M,H2Ot_3550_STD,H2Ot_3550_SAT,H2Om_1635_BP,H2Om_1635_STD,CO2_MEAN,CO2_STD,CO2_1515_BP,CO2_1515_STD,CO2_1430_BP,CO2_1430_STD,H2Om_5200_M,H2Om_5200_STD,OH_4500_M,OH_4500_STD,PH_5200_STN,ERR_5200,PH_4500_STN,ERR_4500,Density,Density_Sat,Tau,Eta,epsilon_H2Ot_3550,sigma_epsilon_H2Ot_3550,epsilon_H2Om_1635,sigma_epsilon_H2Om_1635,epsilon_CO2,sigma_epsilon_CO2,epsilon_H2Om_5200,sigma_epsilon_H2Om_5200,epsilon_OH_4500,sigma_epsilon_OH_4500
+AC4_OL49_021920_30x30_H2O_a,2.5439299152226322,0.16074153519987022,2.421720703313204,0.1898497089387326,*,1.3001072020452495,0.18973770039057375,748.7150728480483,36.86296041163745,740.746431155663,50.96691096280393,758.5248143152104,53.304705321880185,1.8186979013958553,0.3503436272858915,1.2469504909955509,0.25981952600301483,12.195762674599015,-,8.157689580452923,-,2681.9628385342203,2678.669397675602,0.7059903032671602,,66.11116080287024,7.524312502968801,37.32210817976659,8.645058408560972,259.75418947786505,19.25788234453022,1.0094574306540989,0.3008237891400822,0.8611962780779154,0.2795414046836688
+AC4_OL53_101220_256s_30x30_a,4.038926750147803,0.4329778857990654,4.038926750147803,0.4329778857990654,-,1.4866476286944408,0.25712304172380684,727.6581699782867,61.169513420349816,747.4989226544318,84.94476407660733,707.8174173021414,88.04103897784796,1.698555731286261,0.3927119226483464,2.744234853836663,0.6701353551484185,6.90402676330999,-,5.527669572279575,-,2702.703564503572,2702.703564503572,0.6828948534384355,,64.46286878053799,7.401239521051048,34.452486205577344,8.504267139737374,296.3770385011226,17.091250588327085,0.9014740083073014,0.295851133072247,0.7796110934580489,0.2748942822302944
+STD_D1010_012821_256s_100x100_a,0.9042708707728374,0.09700172482486706,1.2019858961960292,0.08831258244944437,*,0.15354829136765832,0.025439049432648915,154.4793817143202,7.22022065767248,162.57157814343182,9.763315053653848,145.39846834272782,10.569338351866723,0.3036153792808971,0.07283603511320189,0.7478287694979827,0.19139654049405352,12.116667428210414,-,13.264652936348938,-,2795.316980458168,2804.2911559980203,0.6585005613973197,,62.72188008969184,7.272084174154002,31.421482392916758,8.35434699872907,315.7646211973788,15.879741615329216,0.7874178128288873,0.29053392101418585,0.6934377201483826,0.2699749007943789