PyIRoGlass v0.6.1!

sarahshi · Apr 4, 2024 · 90fd57d · 90fd57d
1 parent 0f79149
commit 90fd57d
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Showing 7 changed files with 17 additions and 11 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,8 @@ __pycache__
 /Baseline_Comparison/ND70Spec/
 /Baseline_Comparison/ND70_Merge.pdf
 /Baseline_Comparison/Comparison_Standards.csv
+/Baseline_Comparison/BLChem.pdf
+/Baseline_Comparison/BLChem_lim.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/STD_D1010_012821_256s_100x100_a.log
@@ -35,7 +37,7 @@ __pycache__
 /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
 /Epsilon_Inversion/OldEpsilonRegressions/
-/Inputs/TransmissionSpectra/Devolatilized
+/Inputs/TransmissionSpectra/BadSpectra/
 /Thickness/FuegoOlMicrometer.csv
 /Thickness/FuegoOlThickness.csv
 /Thickness/ND70_Micrometer.csv

diff --git a/Baseline_Comparison/BLChem_lim.png b/Baseline_Comparison/BLChem_lim.png
diff --git a/Baseline_PCA/BaselinePC_Vis.py b/Baseline_PCA/BaselinePC_Vis.py
@@ -159,7 +159,7 @@ def rescale_peak(abs, range):
 fig.supxlabel('Wavenumber ($\mathregular{cm^{-1}}$)', y=0.03)
 fig.supylabel('Absorbance', x = 0.05)
 plt.tight_layout()
-plt.savefig('AllBaselines1.pdf', bbox_inches='tight', pad_inches = 0.025)
+# plt.savefig('AllBaselines.pdf', bbox_inches='tight', pad_inches = 0.025)
 
 # %%
 

diff --git a/Baseline_PCA/H2OmPC_Generate.py b/Baseline_PCA/H2OmPC_Generate.py
@@ -63,7 +63,7 @@ def basic_scale_data(spectrum):
 
     Returns:
         spectrum_scale (numeric 2D array): The data after scaling to the range
-            of -0.5 to 0.5 and recentring by the mean spectrum.
+            of -0.5 to 0.5 and recentering by the mean spectrum.
         mean_baseline (numeric array): The mean baseline spectrum across all
             observations after scaling.
     """

diff --git a/Epsilon_Inversion/Epsilon_Comp_Regress.py b/Epsilon_Inversion/Epsilon_Comp_Regress.py
@@ -361,6 +361,6 @@
 
 fig.delaxes(ax[5])
 plt.tight_layout()
-plt.savefig('AllEpsilonRegress_SHI1.pdf', bbox_inches='tight', pad_inches=0.025)
+# plt.savefig('AllEpsilonRegress_SHI.pdf', bbox_inches='tight', pad_inches=0.025)
 
 # %%
diff --git a/PyIRoGlass_RUN.py b/PyIRoGlass_RUN.py
@@ -20,33 +20,37 @@
 # %% 
 
 # Get working paths 
-path_input = os.getcwd() + '/Inputs/'
+path_input = os.path.join(os.getcwd(), 'Inputs')
 
 # Change paths to direct to folder with SampleSpectra -- last bit should be whatever your folder with spectra is called. 
-PATHS = [path_input + 'TransmissionSpectra/' + string for string in ['Fuego/', 'Standards/', 'Fuego1974RH/']]
+PATHS = [os.path.join(path_input, 'TransmissionSpectra', directory) 
+         for directory in ['Fuego', 'Standards', 'Fuego1974RH']]
 
 # Put ChemThick file in Inputs. Direct to what your ChemThick file is called. 
-CHEMTHICK_PATHS = [path_input + string for string in ['FuegoChemThick.csv', 'StandardChemThick.csv', 'FuegoRHChemThick.csv']]
+CHEMTHICK_PATHS = [os.path.join(path_input, filename) 
+                   for filename in ['FuegoChemThick.csv', 'StandardChemThick.csv', 'FuegoRHChemThick.csv']]
 
 # Change last value in list to be what you want your output directory to be called. 
 OUTPUT_PATHS = ['FUEGO', 'STD', 'FRH']
 
 # %%
 # %% 
 
-ref_ol_loader = pig.SampleDataLoader(spectrum_path=path_input+'ReflectanceSpectra/FuegoOl/')
+ref_ol_loader = pig.SampleDataLoader(spectrum_path=os.path.join(path_input, 'ReflectanceSpectra/FuegoOl'))
 ref_ol_dfs_dict = ref_ol_loader.load_spectrum_directory(wn_high=2700, wn_low=2100)
 
 # Use DHZ parameterization of olivine reflectance index. 
 n_ol = pig.reflectance_index(0.72)
 ref_fuego = pig.calculate_mean_thickness(ref_ol_dfs_dict, n=n_ol, wn_high=2700, wn_low=2100, plotting=False, phaseol=True)
+display(ref_fuego)
 
-ref_gl_loader = pig.SampleDataLoader(spectrum_path=path_input+'ReflectanceSpectra/rf_ND70/')
+ref_gl_loader = pig.SampleDataLoader(spectrum_path=os.path.join(path_input, 'ReflectanceSpectra/rf_ND70'))
 ref_gl_dfs_dict = ref_gl_loader.load_spectrum_directory(wn_high=2850, wn_low=1700)
 
 # n=1.546 in the range of 2000-2700 cm^-1 following Nichols and Wysoczanski, 2007 for basaltic glass
 n_gl = 1.546
 ref_nd70 = pig.calculate_mean_thickness(ref_gl_dfs_dict, n=n_gl, wn_high=2850, wn_low=1700, plotting=False, phaseol=False)
+display(ref_nd70)
 
 # %% 
 # %%

diff --git a/docs/examples/reflectance_ftir/PyIRoGlass_Reflectance.ipynb b/docs/examples/reflectance_ftir/PyIRoGlass_Reflectance.ipynb
@@ -144,7 +144,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "FUEGO_THICK = pig.calculate_mean_thickness(REF_DFS_DICT_OL, n=n_ol, wn_high=2700, wn_low=2100, remove_baseline=True, plotting=True, phaseol=True)"
+    "FUEGO_THICK = pig.calculate_mean_thickness(REF_DFS_DICT_OL, n=n_ol, wn_high=2700, wn_low=2100, plotting=True, phaseol=True)"
    ]
   },
   {
@@ -195,7 +195,7 @@
     "\n",
     "n_gl = 1.546\n",
     "\n",
-    "REF_GLASS = pig.calculate_mean_thickness(REF_DFS_DICT_GL, n=n_gl, wn_high=2850, wn_low=1700, remove_baseline=True, plotting=True, phaseol=False)\n",
+    "REF_GLASS = pig.calculate_mean_thickness(REF_DFS_DICT_GL, n=n_gl, wn_high=2850, wn_low=1700, plotting=True, phaseol=False)\n",
     "\n",
     "REF_GLASS\n"
    ]