DiadFit 1.0.0__tar.gz → 1.0.1__tar.gz

{DiadFit-1.0.0 → DiadFit-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.0
+Version: 1.0.1
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser
@@ -17,5 +17,5 @@ Description: [![PyPI](https://badgen.net/pypi/v/DiadFit)](https://pypi.org/proje
 Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown

{DiadFit-1.0.0 → DiadFit-1.0.1}/setup.py

@@ -36,7 +36,7 @@ setup(
             'numpy<2',
             'matplotlib',
             'scikit-learn',
-            'scipy',
+            'scipy>1.6',
             'lmfit>=1.1.0',
             'tqdm',
             'python-docx'
@@ -47,5 +47,5 @@ setup(
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",
     ],
-    python_requires='>=3.7',
+    python_requires='>=3.8',
 )

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit/CO2_in_bubble_error.py

@@ -159,7 +159,7 @@ plot_figure=True, fig_i=0, neg_values=True):
 
         # This is the function doing the work to actually make the simulations for each variable.
         if error_vol_perc_bub is not None:
-            print('didnt get inside else loop')
+
 
             df_synthetic=propagate_CO2_in_bubble_ind(
     N_dup=N_dup,

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit/H2O_fitting.py

@@ -10,7 +10,7 @@ from dataclasses import dataclass
 from typing import Tuple, Optional
 from DiadFit.importing_data_files import *
 from numpy import trapz
-from scipy.integrate import simps
+from scipy.integrate import simpson
 ##
 def extract_xstal_MI_name(*, files, char_xstal, pos_xstal, char_MI, pos_MI,
                          prefix=True, str_prefix=" ", file_ext='.txt'):
@@ -872,30 +872,30 @@ fit_sil='poly', dpi=200):
     ydat_sil=y_corr_sil
 
     xspace_sil=xdat_sil[1]-xdat_sil[0]
-    area_trap = trapz(y_corr_sil, dx=xspace_sil)
-    area_simps = simps(y_corr_sil, dx=xspace_sil)
+    area_trap = trapezoid(y_corr_sil, dx=xspace_sil)
+    area_simps = simpson(y_corr_sil, dx=xspace_sil)
     # Just the LW area
     xsil_LW=xdat_sil[(xdat_sil>LW[0]) & (xdat_sil<LW[1])]
     y_corr_sil_LW=y_corr_sil[(xdat_sil>LW[0]) & (xdat_sil<LW[1])]
     xspace_sil_LW=xsil_LW[1]-xsil_LW[0]
-    area_trap_LW=trapz(y_corr_sil_LW, dx=xspace_sil_LW)
-    area_simp_LW=simps(y_corr_sil_LW, dx=xspace_sil_LW)
+    area_trap_LW=trapezoid(y_corr_sil_LW, dx=xspace_sil_LW)
+    area_simp_LW=simpson(y_corr_sil_LW, dx=xspace_sil_LW)
 
 
     # Just the HW area
     xsil_HW=xdat_sil[(xdat_sil>HW[0]) & (xdat_sil<HW[1])]
     y_corr_sil_HW=y_corr_sil[(xdat_sil>HW[0]) & (xdat_sil<HW[1])]
     xspace_sil_HW=xsil_HW[1]-xsil_HW[0]
-    area_trap_HW=trapz(y_corr_sil_HW, dx=xspace_sil_HW)
-    area_simp_HW=simps(y_corr_sil_HW, dx=xspace_sil_HW)
+    area_trap_HW=trapezoid(y_corr_sil_HW, dx=xspace_sil_HW)
+    area_simp_HW=simpson(y_corr_sil_HW, dx=xspace_sil_HW)
 
     # MW
     if MW is not None:
         xsil_MW=xdat_sil[(xdat_sil>MW[0]) & (xdat_sil<MW[1])]
         y_corr_sil_MW=y_corr_sil[(xdat_sil>MW[0]) & (xdat_sil<MW[1])]
         xspace_sil_MW=xsil_MW[1]-xsil_MW[0]
-        area_trap_MW=trapz(y_corr_sil_MW, dx=xspace_sil_MW)
-        area_simp_MW=simps(y_corr_sil_MW, dx=xspace_sil_MW)
+        area_trap_MW=trapezoid(y_corr_sil_MW, dx=xspace_sil_MW)
+        area_simp_MW=simpson(y_corr_sil_MW, dx=xspace_sil_MW)
 
 
      # Plotting what its doing
@@ -1155,8 +1155,8 @@ def fit_area_for_water_region(*, path, filename, Spectra=None, config1: water_bc
 
 
     xspace_water=xdat_water[1]-xdat_water[0]
-    area_trap = trapz(y_corr_water, dx=xspace_water)
-    area_simps = simps(y_corr_water, dx=xspace_water)
+    area_trap = trapezoid(y_corr_water, dx=xspace_water)
+    area_simps = simpson(y_corr_water, dx=xspace_water)
 
 
      # Plotting what its doing

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit/_version.py

@@ -5,4 +5,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module
-__version__ = '1.0.0'
+__version__ = '1.0.1'

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit/densimeters.py

@@ -944,20 +944,29 @@ def merge_fit_files(path):
 
     if os.path.exists(os.path.join(path, 'Weak_Diads.xlsx')):
         grp1 = pd.read_excel(os.path.join(path, 'Weak_Diads.xlsx'))
+        grp1['Standard']='No'
     else:
         grp1 = None
 
     if os.path.exists(os.path.join(path, 'Medium_Diads.xlsx')):
         grp2 = pd.read_excel(os.path.join(path, 'Medium_Diads.xlsx'))
+        grp2['Standard']='No'
     else:
         grp2 = None
 
     if os.path.exists(os.path.join(path, 'Strong_Diads.xlsx')):
         grp3 = pd.read_excel(os.path.join(path, 'Strong_Diads.xlsx'))
+        grp3['Standard']='No'
     else:
         grp3 = None
+        
+    if os.path.exists(os.path.join(path, 'Std_Diads.xlsx')):
+        grp4 = pd.read_excel(os.path.join(path, 'Std_Diads.xlsx'))
+        grp4['Standard']='Yes'
+    else:
+        grp4 = None
 
-    df2 = pd.concat([grp1, grp2, grp3], axis=0).reset_index(drop=True)
+    df2 = pd.concat([grp1, grp2, grp3, grp4], axis=0).reset_index(drop=True)
 
     if discard is not None:
         discard_cols=discard[discard.columns.intersection(df2.columns)]

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit/diads.py

@@ -18,7 +18,7 @@ import matplotlib.patches as patches
 import warnings as w
 from tqdm import tqdm
 from numpy import trapz
-from scipy.integrate import simps
+from scipy.integrate import simpson
 from scipy.interpolate import interp1d
 
 # Allowed models
@@ -725,7 +725,7 @@ def plot_peak_params(fit_params,
 def filter_splitting_prominence(*, fit_params, data_y_all,
                                 x_cord,
                                 splitting_limits=[100, 107],
-                                lower_diad1_prom=10, exclude_str):
+                                lower_diad1_prom=10, exclude_str=None, str_filt=None):
     """ Filters Spectra based on approximate splitting, draws a plot showing spectra to discard and those to keep
 
     Parameters
@@ -746,6 +746,12 @@ def filter_splitting_prominence(*, fit_params, data_y_all,
         Only keeps spectra that meet the splitting parameter, and have an absolute
         diad1 prominence greater than this value (helps filter out other weird spectra)
 
+    exclude_str: str
+        Excludes files with this string.
+
+    str_filt: str
+        Filters just based on string in filename
+
     Returns
     --------------
     fit_params_filt: pd.DataFrame
@@ -759,21 +765,30 @@ def filter_splitting_prominence(*, fit_params, data_y_all,
 
 
     """
+    if str_filt is not None:
+        filt=fit_params['filename'].str.contains(str_filt)
 
-    reas_split=(fit_params['approx_split'].between(splitting_limits[0], splitting_limits[1]))
-    reas_heigh=fit_params['Diad1_abs_prom']>lower_diad1_prom
-    if exclude_str is not None:
-        name_in_file=~fit_params['filename'].str.contains(exclude_str)
     else:
-        name_in_file=reas_heigh
 
-    fit_params_filt=fit_params.loc[(reas_split&reas_heigh&name_in_file)].reset_index(drop=True)
-    fit_params_disc=fit_params.loc[~(reas_split&reas_heigh&name_in_file)].reset_index(drop=True)
+        reas_split=(fit_params['approx_split'].between(splitting_limits[0], splitting_limits[1]))
+        reas_heigh=fit_params['Diad1_abs_prom']>lower_diad1_prom
+
+        if exclude_str is not None:
+            name_in_file=~fit_params['filename'].str.contains(exclude_str)
+        else:
+            name_in_file=reas_heigh
+
+        filt=reas_split&reas_heigh&name_in_file
+
+    fit_params_filt=fit_params.loc[filt].reset_index(drop=True)
+    fit_params_disc=fit_params.loc[~(filt)].reset_index(drop=True)
 
     print('Keeping N='+str(len(fit_params_filt)))
     print('Discarding N='+str(len(fit_params_disc)))
 
-    filt=reas_split&reas_heigh&name_in_file
+
+
+    # Then apply to get data
     data_y_filt=data_y_all[:, (filt)]
     data_y_disc=data_y_all[:, ~(filt)]
 
@@ -804,17 +819,21 @@ def filter_splitting_prominence(*, fit_params, data_y_all,
             Diff=np.nanmax(data_y_filt[:, i])-np.nanmin(data_y_filt[:, i])
             av_prom_Keep=fit_params_filt['Diad1_abs_prom'].iloc[i]
             prom_filt=prom_filt+av_prom_Keep
+            file=fit_params_filt['filename'].iloc[i]
             ax2.plot(x_cord+i*5, (data_y_filt[:, i]-np.nanmin(data_y_filt[:, i]))/Diff+i/3, '-b', lw=0.5)
+            yplot=np.quantile((data_y_filt[:, i]-np.nanmin(data_y_filt[:, i]))/Diff+i/3, 0.65)
+            ax2.annotate(str(file), xy=(1450+i*5, yplot),
+                    xycoords="data", fontsize=8, bbox=dict(facecolor='white', edgecolor='none', pad=2))
 
 
         ax2.set_xlim([1250, 1450+i*5])
         ax2.set_xticks([])
         ax2.set_yticks([])
 
-    return fit_params_filt, data_y_filt, fit_params_disc, data_y_disc
+    return fit_params_filt.reset_index(drop=True), data_y_filt, fit_params_disc.reset_index(drop=True), data_y_disc
 
 
-def identify_diad_group(*, fit_params, data_y,  x_cord, filter_bool,y_fig_scale=0.1, grp_filter='Weak'):
+def identify_diad_group(*, fit_params, data_y,  x_cord, filter_bool,y_fig_scale=0.1, grp_filter='Weak', str_filt=None):
 
     """Sorts diads into two groups. Those meeting the 'filter_bool' criteria, and those not
      meeting this criteria. Ones meeting the criteria are shown on the left hand plot,
@@ -853,6 +872,9 @@ def identify_diad_group(*, fit_params, data_y,  x_cord, filter_bool,y_fig_scale=
 
 
     """
+    if str_filt is not None:
+        filt_name=~fit_params['filename'].str.contains(str_filt)
+        filt_bool=filt_name&filt_bool
 
     if np.shape(data_y)[1]==0:
         Group1_df=pd.DataFrame().reindex_like(fit_params)
@@ -3835,8 +3857,8 @@ path=None, filename=None, filetype=None,
 
 
                 xspace_sil=x_new[1]-x_new[0]
-                area_trap = trapz(Baseline_ysub_sil, dx=xspace_sil)
-                area_simps = simps(Baseline_ysub_sil, dx=xspace_sil)
+                area_trap = trapezoid(Baseline_ysub_sil, dx=xspace_sil)
+                area_simps = simpson(Baseline_ysub_sil, dx=xspace_sil)
 
 
 

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 1.0.0
+Version: 1.0.1
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser
@@ -17,5 +17,5 @@ Description: [![PyPI](https://badgen.net/pypi/v/DiadFit)](https://pypi.org/proje
 Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown

{DiadFit-1.0.0 → DiadFit-1.0.1}/src/DiadFit.egg-info/requires.txt

@@ -2,7 +2,7 @@ pandas
 numpy<2
 matplotlib
 scikit-learn
-scipy
+scipy>1.6
 lmfit>=1.1.0
 tqdm
 python-docx