DiadFit 0.0.78__py3-none-any.whl → 0.0.80__py3-none-any.whl

DiadFit/ne_lines.py

@@ -3,7 +3,7 @@ import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib import patches
 import lmfit
-from lmfit.models import GaussianModel, VoigtModel, LinearModel, ConstantModel, PseudoVoigtModel
+from lmfit.models import GaussianModel, VoigtModel, LinearModel, ConstantModel, PseudoVoigtModel, SkewedVoigtModel
 from scipy.signal import find_peaks
 import os
 import re
@@ -88,7 +88,8 @@ def calculate_Ne_splitting(wavelength=532.05, line1_shift=1117, line2_shift=1447
 def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
     """
     Calculates Raman shift for a given laser wavelength of Ne lines, using the datatable from NIST of Ne line
-    emissoin in air and the intensity of each line.
+    emissoin in air and the intensity of each line. 
+    Data from https://physics.nist.gov/PhysRefData/ASD/lines_form.html
 
     Parameters
     ---------------
@@ -106,6 +107,31 @@ def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
     """
 
     Ne_emission_line_air=np.array([
+    
+    
+541.85584,
+542.009,
+542.0155,
+543.36513,
+544.7120,
+
+544.85091,
+549.44158,
+550.73442,
+551.1176,
+551.1485,
+
+552.063,
+553.36788,
+553.86510,
+555.90978,
+556.24416,
+
+556.27662,
+556.30531,
+    
+    
+    
 556.244160,
 556.276620,
 556.305310,
@@ -142,7 +168,34 @@ def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
 
     ])
 
-    Intensity=np.array([1500.00,
+    Intensity=np.array([
+    
+1500,
+12	,
+500,
+2500,
+80,
+
+1500,
+500,
+250,
+30,
+150,
+
+30,
+750,
+500,
+350,
+1500,
+
+5000,
+750,
+
+    
+    
+    
+    
+    1500.00,
     5000.00,
     750.00,
     350.00,
@@ -689,6 +742,8 @@ const_params=True, spec_res=0.4) :
             model0 = PseudoVoigtModel(prefix='p0_')#+ ConstantModel(prefix='c0')
         if model_name=="VoigtModel":
             model0 = VoigtModel(prefix='p0_')#+ ConstantModel(prefix='c0')
+        if model_name=='SkewedVoigtModel':
+            model0=SkewedVoigtModel(prefix='p0_')
         
         pars0 = model0.make_params()
         pars0['p0_center'].set(Ne_center, min=Ne_center-2*spec_res, max=Ne_center+2*spec_res)
@@ -725,6 +780,10 @@ const_params=True, spec_res=0.4) :
             model1 = PseudoVoigtModel(prefix='p1_')#+ ConstantModel(prefix='c0')
         if model_name=="VoigtModel":
             model1 = VoigtModel(prefix='p1_')#+ ConstantModel(prefix='c0')
+            
+        if model_name=='SkewedVoigtModel':
+            model1=SkewedVoigtModel(prefix='p1_')
+            
         pars1 = model1.make_params()
         pars1['p1_'+ 'amplitude'].set(Amp_p0, min=min_off*Amp_p0, max=max_off*Amp_p0)
         pars1['p1_'+ 'center'].set(Center_p0, min=Center_p0-spec_res/2, max=Center_p0+spec_res/2)
@@ -737,6 +796,8 @@ const_params=True, spec_res=0.4) :
             peak = PseudoVoigtModel(prefix='p2_')#+ ConstantModel(prefix='c0')
         if model_name=="VoigtModel":
             peak = VoigtModel(prefix='p2_')#+ ConstantModel(prefix='c0')
+        if model_name=='SkewedVoigtModel':
+            peak=SkewedVoigtModel(prefix='p2_')
 
 
         pars = peak.make_params()
@@ -791,6 +852,8 @@ const_params=True, spec_res=0.4) :
             model_combo = PseudoVoigtModel(prefix='p1_')#+ ConstantModel(prefix='c0')
         if model_name=="VoigtModel":
             model_combo= VoigtModel(prefix='p1_')#+ ConstantModel(prefix='c0')
+        if model_name=='SkewedVoigtModel':
+            model_combo=SkewedVoigtModel(prefix='p1_')
 
 
 
@@ -934,6 +997,8 @@ model_name='PseudoVoigtModel', print_report=False, const_params=True, spec_res=0
         model = PseudoVoigtModel()#+ ConstantModel(prefix='c0')
     if model_name=="VoigtModel":
         model = VoigtModel()#+ ConstantModel(prefix='c0')
+    if model_name=="SkewedVoigtModel":
+        model = SkewedVoigtModel()#+ ConstantModel(prefix='c0')
 
 
 
@@ -1660,10 +1725,48 @@ def filter_Ne_Line_neighbours(*, df_combo=None, Corr_factor=None, number_av=6, o
 ## Lets make a plotting function for this notebook 
 
 def generate_Ne_corr_model(*, time, Ne_corr, N_poly=3, CI=0.67, bootstrap=False, std_error=True, N_bootstrap=500,save_fig=False, pkl_name='polyfit_data.pkl'):
+    """ This function takes time stamp and Ne correctoin data to make a predictive polynomial, which it then saves as a pkl file
+    
+    Parameters
+    ---------------
+    time: pd.Series
+        Time through the run
+        
+    Ne_corr: df or pd.Series
+        if dataframe, has to have the column 'Ne_corr'
+        Else, just Ne correction factor as a pd.Series itself
+        
+    CI: float. Default 0.67
+        Confidence interval to save as uncertainty on model. 
+        
+    Either:
+        
+    std_error: bool (True)
+        calculates uncertainty on model using CI
+        
+    Or:
+    boostrap: bool (False)
+        Used for testing of method, keep as False
+    
+    save_fig:bool
+        Saves figure. 
+        
+    pkl_name: str
+        Name of model that is saved. 
+        
+        
+    
+        
+    
+    """
 # Define the x and y values
     x_all   = np.array([time])
-    y_all = np.array([Ne_corr['Ne_Corr']])
-    y_err=Ne_corr['1σ_Ne_Corr']
+    if isinstance(Ne_corr, pd.DataFrame):
+        y_all = np.array([Ne_corr['Ne_Corr']])
+        y_err=Ne_corr['1σ_Ne_Corr']
+    else:
+        y_all=Ne_corr
+        y_err=0*Ne_corr
     non_nan_indices = ~np.isnan(x_all) & ~np.isnan(y_all)
 
     # Filter out NaN values

{DiadFit-0.0.78.dist-info → DiadFit-0.0.80.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 0.0.78
+Version: 0.0.80
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

{DiadFit-0.0.78.dist-info → DiadFit-0.0.80.dist-info}/RECORD

@@ -1,33 +1,40 @@
-DiadFit/CO2_EOS.py,sha256=gkR8mp1zbXBmGlar7vBqJHVH-P7-hrqGJ8_Rijt1jtw,27460
-DiadFit/CO2_in_bubble_error.py,sha256=N-Ox8LcJV98ui_3B7n4oaSjiA4EapZiSnZDWw3EuZ60,14042
+DiadFit/CO2_EOS.py,sha256=AeiM_s0cIVip5i5q1Shy8QXTUWz4XHG0VnfuBH5qRDY,28034
+DiadFit/CO2_H2O_EOS.py,sha256=TLU2goWB6yGFbN4RBS0dRXG0oDQuuG0JftW32DZHmn4,37722
+DiadFit/CO2_in_bubble_error.py,sha256=Ga_hNA63m-OZg2hBOqM7VvpJhnvvTCg6L3Qixh1Bh7A,14196
 DiadFit/H2O_fitting.py,sha256=pbEa0JivZFAmWxEGY5VMetD95BGNCzkaatfXRVAV4fs,43889
 DiadFit/Highrho_polyfit_data.pkl,sha256=7t6uXxI-HdfsvreAWORzMa9dXxUsnXqKBSo1O3EgiBw,1213
+DiadFit/Highrho_polyfit_dataUCB_1117_1400.pkl,sha256=B7nX560JpBBBssSgr50oDDG-UKsNxAjp235eytquVaI,1213
 DiadFit/Highrho_polyfit_dataUCB_1220_1400.pkl,sha256=0_eZVQ3Byh9u5xW9TnvlUJg_-bTDSjG3EpVhCutZZkk,1213
 DiadFit/Highrho_polyfit_dataUCB_1220_1447.pkl,sha256=eQw3HIsZ7xRr9QKBKsxuZKyRdlMbnaFxtxlM72jcRjU,1213
+DiadFit/Highrho_polyfit_data_CCMR.pkl,sha256=8hgi0kFoEn6aWAHl0hX34ez3EDAndPXWX3wlBvqPQdA,909
 DiadFit/Highrho_polyfit_data_CMASS.pkl,sha256=g592Rk7HwM93_Ws8lg1RSun5GkqBZmdENQGf3rZv1Ig,829
 DiadFit/Lowrho_polyfit_data.pkl,sha256=LFg0C3D3FXzhp_LdwZ3xzdxDZzrA70xvFACCBwLmpF0,751
+DiadFit/Lowrho_polyfit_dataUCB_1117_1400.pkl,sha256=FttCfGvf9dKOXvFHeYLP3w1_N93N8_X4jwx9o5U_JOA,751
 DiadFit/Lowrho_polyfit_dataUCB_1220_1400.pkl,sha256=y_53yUG4lv_OIYVWs7BTJjqVh3w55EJ_7pkk8NWodOc,751
 DiadFit/Lowrho_polyfit_dataUCB_1220_1447.pkl,sha256=UNpo1WPgbqTApazne0DYbflrRr1kGbWXWA97XjNRQlg,751
+DiadFit/Lowrho_polyfit_data_CCMR.pkl,sha256=G58_l4TpdBmVdsR1z6FWTQ9qDsemNeZOJvbCl-36zKs,1141
 DiadFit/Lowrho_polyfit_data_CMASS.pkl,sha256=meT16KSMUAlxb0XC1T-vTa-X3ooJ2JjdWFJetHHCQfQ,997
 DiadFit/Mediumrho_polyfit_data.pkl,sha256=zfl3MuTE-Oyz0T9tsYS0uU43tL9zSqrdss9sGHldRb0,1301
+DiadFit/Mediumrho_polyfit_dataUCB_1117_1400.pkl,sha256=oGlsChnHyH4rWOg-HBsrW_oQKGoqe6-2zRodpHH9MSA,1301
 DiadFit/Mediumrho_polyfit_dataUCB_1220_1400.pkl,sha256=Qxj74-mcCFj8LmwgqdChqNlw4XMXlOuuL03SZNZz5R8,1301
 DiadFit/Mediumrho_polyfit_dataUCB_1220_1447.pkl,sha256=zdo1t0F8X6S8ovPldH9Hu2kYQGHU18w67TK48isp4NI,1301
+DiadFit/Mediumrho_polyfit_data_CCMR.pkl,sha256=U6ODSdurqS0-lynm1MG1zktg8NuhYRbrYCsx8KI4SQ4,1221
 DiadFit/Mediumrho_polyfit_data_CMASS.pkl,sha256=SBy1pIdqCAF9UtB9FLNTuD0-tFyD7swwJppdE2U_FsY,1557
 DiadFit/Psensor.py,sha256=C2xSlgxhUJIKIBDvUp02QaYRs5QsIqjGGRMP25ZLRZ0,10435
-DiadFit/__init__.py,sha256=OePOoHHzXy3CbBtS7jHZWk9v91k0Hzc8yN_0TBfWaXU,1147
-DiadFit/_version.py,sha256=7PgzBnqkJyuXANSUrsXiuQCQ8oIU81lzmmbIMyDTwPI,296
+DiadFit/__init__.py,sha256=wXZHfLvkI9ye1TFrdykATP8Kn7I-UdNFBTmHZI1V9EQ,1181
+DiadFit/_version.py,sha256=SazyQZ1u3ZbLcm4V_X0Afuz2vYszLoDthUrzhh_eAB4,296
 DiadFit/argon_lines.py,sha256=vtzsuDdEgrAmEF9xwpejpFqKV9hKPS1JUYhIl4AfXZ0,7675
-DiadFit/cosmicray_filter.py,sha256=PvcI4jB58yZ9m-jrjt9BRjtANZzILA9gPgVq-Z5jQ50,23438
+DiadFit/cosmicray_filter.py,sha256=SqowmxChJG4Is6_K5E5OqJ1WaSWSaGKg-hSDBOJIVA0,23626
 DiadFit/densimeter_fitting.py,sha256=Uel9a4qUVz6r-my09uuHFRjD9oPFF-kd5ZBPYfYfOQM,8086
-DiadFit/densimeters.py,sha256=KKUEUcqqkIxdjPbpPjb99SdTU-MxgbjY7ZWmCoQa7Fo,45490
+DiadFit/densimeters.py,sha256=hcgcymwPf0POP5xT29mADM4L80arqW6ZKJ3Yq3EYJIE,48086
 DiadFit/density_depth_crustal_profiles.py,sha256=XPauKf62hMp-iw701XfphaVe3o6LRJSwuQXAcSDXv6s,16983
-DiadFit/diads.py,sha256=4nE-Y5y9i2gGbl_CjAjoCeL-Mfdk7gy0Bo6sfF0ip_g,169011
-DiadFit/error_propagation.py,sha256=G0RJ3zAiwdrWXC0rPk82NdSm8HQ_tuG5EACDnE6bT_A,34162
-DiadFit/importing_data_files.py,sha256=Gd9r8xvQxX3zr8aXCuSLdexKdz25sV0PgDvv0vd6K3A,37659
+DiadFit/diads.py,sha256=61B5qFSsTO81k6T9Qy3wLFOv7oR5tubIySrtXUmdCWM,173053
+DiadFit/error_propagation.py,sha256=_x82UIXz46-Qjvvz2tDAblyDkOe_51JI27wvSDkSOms,35080
+DiadFit/importing_data_files.py,sha256=zghBVGWLLQaG9dWKSIa7KaDmqUBmyhm7ZgBmV5f4SuI,38926
 DiadFit/molar_gas_proportions.py,sha256=_oEZn_vndHGDaXAjZ6UU8ycujBx_qB2KGCGqZSzotQU,3389
-DiadFit/ne_lines.py,sha256=EtNbaf1eqMWpnUd_Zk6o5DxqZZ_ZnToVEFOkC0tyHpw,65288
+DiadFit/ne_lines.py,sha256=-Xv62LJ2OOGSCeKsQjmXZ7yD3g2ZOG1okxvVp8PYzXM,67144
 DiadFit/relaxifi.py,sha256=hHzRsJPQIVohYi3liy9IQJpaomgsa2zbLQmhqkpdfrI,31549
-DiadFit-0.0.78.dist-info/METADATA,sha256=vtSJtJj12WiFBof6PitQi6gfsZIzzEeW-b8cOWLdQtc,1159
-DiadFit-0.0.78.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-DiadFit-0.0.78.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
-DiadFit-0.0.78.dist-info/RECORD,,
+DiadFit-0.0.80.dist-info/METADATA,sha256=EWYJK6FLJ5O1UaUS66QjXOPadAJQiJ41C1I8ZTR5riQ,1159
+DiadFit-0.0.80.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+DiadFit-0.0.80.dist-info/top_level.txt,sha256=yZC6OFLVznaFA5kcPlFPkvhKotcVd-YO4bKxZZw3LQE,8
+DiadFit-0.0.80.dist-info/RECORD,,

{DiadFit-0.0.78.dist-info → DiadFit-0.0.80.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any