Merge pull request #8 from IdahoLabResearch/HyPAT_v2.0

Updating HyPAT to v2.0. This primarily adds the "Absorption Plots" tab. It also fixes bug, performs smalls cosmetic changes, cleans up the code, improves error handling, and adds some small functionality in/on/to the other tabs.

HyPAT/backup_datafiles/brief_explanation_of_datafiles.txt → HyPAT/backup_data_files/brief_explanation_of_datafiles.txt

@@ -13,3 +13,5 @@ default_entry_vars and o-ring_data are used for some variables on the Permeation
 material_data and melting_tempK are used primarily in the Overview Plots tab, although they also provide the information used in the Permeation Estimates menu for sample material
 
 persistent_permeation_input_variables is used in the Permeation Plots tab
+
+persistent_absorption_input_variables is used in the Absorption Plots tab

HyPAT/main.py

@@ -1,10 +1,10 @@
-""" Hydrogen Permeation Analysis Tool (HyPAT)
+""" Hydrogen Permeation and Absorption Tool (HyPAT)
 
     Python Interpreter: 3.8, 3.9, or 3.10
 
-    Python Packages: matplotlib, pandas, numpy, tkmacosx, mplcursors, scipy, and openpyxl
+    Python Packages: Matplotlib, Pandas, NumPy, tkmacosx, mplcursors, SciPy, and openpyxl
 
-    compatible: macOS and Windows 10 """
+    compatible: macOS 12 and Windows 10 """
 from source_code.application import Application
 
 

HyPAT/source_code/application.py

@@ -7,23 +7,24 @@
 from . import permeation_estimates
 from . import overview_plots
 from . import permeation_plots
+from . import absorption_plots
 
 
 class Application(tk.Tk):
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         # Change the default font for text boxes to TkDefaultFont. This mostly affects
-        # the help window of the permeation_plot.py's settings, but may affect other places
+        # the help window of the permeation_plot.py's and absorption_plot.py's settings, but may affect other places
         default_font = font.nametofont("TkFixedFont")
         default_font.configure(family=font.nametofont("TkDefaultFont").cget("family"),
                                size=font.nametofont("TkDefaultFont").cget("size"))
 
-        self.title("Hydrogen Permeation Analysis Tool")
+        self.title("Hydrogen Permeation and Absorption Tool")
         self.resizable(width=None, height=None)
         self.minsize(900, 600)
 
-        # size of gui based of size of widgets
+        # size of gui based off size of widgets
         # this could be calculated later but would result in the gui appearing then moving to the center.
         width = 1429
         height = 750
@@ -34,7 +35,7 @@ def __init__(self, *args, **kwargs):
         self.geometry("{}x{}+{}+{}".format(width, height, pos_right, pos_down))
 
         # Ensure the program stops when the window is closed (counteracts a bug brought in from using
-        # constrained_layouts = True in the permeation_plots.py code)
+        # constrained_layouts = True in the permeation_plots.py and absorption_plots.py code)
         self.protocol("WM_DELETE_WINDOW", self.quit_me)
 
         self.storage = data_storage.Storage()
@@ -48,7 +49,7 @@ def __init__(self, *args, **kwargs):
 
     def quit_me(self):
         """ Ensure the program ends when window is closed """
-        # This counteracts a bug brought in by constrained_layout=True in the permeation_plots code
+        # This counteracts a bug brought in by constrained_layout=True in the permeation_plots and absorption_plots code
         # Function found at https://stackoverflow.com/a/55206851
         self.quit()
         self.destroy()
@@ -57,7 +58,9 @@ def load_pages(self):
         """ Load the GUI with the pages containing the calculations """
         front_page = permeation_estimates.InputForm(self.notebook, self.storage)  # Permeation estimates
         experiment_plots_page = permeation_plots.PermeationPlots(self.notebook, self.storage)  # Permeation plots
+        absorption_plots_page = absorption_plots.AbsorptionPlots(self.notebook, self.storage)  # Absorption plots
         overview_plots_page = overview_plots.Plots(self.notebook, self.storage)  # Theoretical plots (Overview)
         self.notebook.add(front_page, text="Permeation Estimates")
         self.notebook.add(experiment_plots_page, text="Permeation Plots")
+        self.notebook.add(absorption_plots_page, text="Absorption Plots")
         self.notebook.add(overview_plots_page, text="Overview Plots")

HyPAT/source_code/data_storage.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pandas as pd
 import os
-import platform  # allows for Mac vs Windows adaptions
+import platform  # allows for Mac vs. Windows adaptions
 
 
 class Storage:
@@ -16,21 +16,21 @@ def __init__(self):
 
         # Create dataframes to store values for updating source spreadsheets.
         # First the material_data spreadsheet
-        filename = os.path.join('datafiles', 'material_data.xlsx')
+        filename = os.path.join('data_files', 'material_data.xlsx')
         self.material_data = pd.read_excel(filename, header=[0, 1],
                                            engine="openpyxl")  # openpyxl supports .xlsx but not .xls
         # set up the index using material names
         self.material_data.set_index(('Unnamed: 0_level_0', "Material"), inplace=True)
         self.material_data.rename_axis("Material", axis="index", inplace=True)
         # Next for the melting_tempK file
-        melt_filename = os.path.join('datafiles', 'melting_tempK.xlsx')
+        melt_filename = os.path.join('data_files', 'melting_tempK.xlsx')
         self.melting_tempK = pd.read_excel(melt_filename, engine="openpyxl")
         self.melting_tempK.set_index("Material", inplace=True)
 
         # Read the o-ring data off an Excel sheet into a convenient dataframe.
         # (1/2, 1/4 VCR data comes from https://www.swagelok.com/downloads/webcatalogs/en/ms-01-24.pdf,
         # page 17 Silver Plated Nonretained)
-        self.oring_filename = os.path.join('datafiles', 'o-ring_data.xlsx')
+        self.oring_filename = os.path.join('data_files', 'o-ring_data.xlsx')
         self.oring_info = pd.read_excel(self.oring_filename, header=0, index_col=0)
         self.oring_info_4file = self.oring_info.copy()  # Duplicate used exclusively for saving to the o-ring file
 
@@ -67,7 +67,7 @@ def __init__(self):
         self.sample_material.trace_add("write", self.update_properties)
 
         # Read the file for some default values
-        self.defaults_filename = os.path.join('datafiles', 'default_entry_vals.xlsx')
+        self.defaults_filename = os.path.join('data_files', 'default_entry_vals.xlsx')
         self.defaults_info = pd.read_excel(self.defaults_filename, header=0)
 
         # Calibrated Leak Rate
@@ -91,8 +91,8 @@ def __init__(self):
         self.t_L = tk.DoubleVar(value=0)  # Estimated time lag
         self.Phi = tk.DoubleVar(value=0)  # Estimated permeability
         self.flux = tk.DoubleVar(value=0)  # Estimated molar flux
-        self.flux_atoms = tk.DoubleVar(value=0)  # Estimated atomic flux
-        self.Q = tk.DoubleVar(value=0)  # Estimated permeation rate
+        self.flux_atoms = tk.DoubleVar(value=0)  # Estimated  atomic flux
+        self.Q = tk.DoubleVar(value=0)  # Estimated molecular permeation rate
         self.del_sP = tk.DoubleVar(value=0)  # Estimated rate of pressure increase, Torr/s
         self.del_sP_Pa = tk.DoubleVar(value=0)  # /\, Pa/s
         self.sP_final = tk.DoubleVar(value=0)  # Estimated final secondary side pressure, Torr
@@ -104,13 +104,15 @@ def __init__(self):
 
         # tolerance used for finding steady state during permeation data analysis
         self.tol = tk.DoubleVar(value=1e-6)
-        # minimum number of seconds following t0 before finding a steady state
-        self.t_del = tk.DoubleVar(value=100) 
-        # default number of data points used in determining leak and/or steady state
+        # minimum number of seconds following t0 before finding a steady state or equilibrium
+        self.t_del = tk.DoubleVar(value=100)  # Note, as of 5/28/22, this isn't used in absorption_plots.py
+        # default number of data points used in determining leak, steady state, and/or equilibrium
         self.gen_dp_range = tk.IntVar(value=30)
 
-        # store the permeation calculations
-        self.PermeationParameters = pd.DataFrame()
+        # store the transport properties calculations
+        self.TransportParameters = pd.DataFrame()
+        self.PTransportParameters = pd.DataFrame()
+        self.ATransportParameters = pd.DataFrame()
 
     def connect_variables(self):
         """ Set up variables so that functions are triggered if they are changed"""
@@ -146,10 +148,10 @@ def load_data():
             diffusivity and solubility. Use that information to calculate those respective number for permeability.
             Read in the melting temp if available. Combine this all into a dataframe and return that dataframe """
         # read in diffusivity and solubility data
-        # todo It'd be nice to have the user select a file similar to "SaveFileExample.xlsx" in the datafiles folder
+        # todo It'd be nice to have the user select a file similar to "SaveFileExample.xlsx" in the data_files folder
         #      then if two of the three quantities (diffusivity, solubility, permeability) are present, the third
         #      will be calculated. This can be similar to how it is done in overview_plots.py - EditMaterials class.
-        filename = os.path.join('datafiles', 'material_data.xlsx')
+        filename = os.path.join('data_files', 'material_data.xlsx')
         df = pd.read_excel(filename, header=[0, 1], engine="openpyxl")  # openpyxl supports .xlsx file format, not .xls
         # set up the index using material names
         df.set_index(('Unnamed: 0_level_0', "Material"), inplace=True)
@@ -170,7 +172,7 @@ def round_to_13(df_col):
         df[("Permeability", "max. temp. [K]")] = [min((df[col[3]][i], df[col[7]][i])) for i in range(len(df))]
 
         # read in melting temp data
-        melt_filename = os.path.join('datafiles', 'melting_tempK.xlsx')
+        melt_filename = os.path.join('data_files', 'melting_tempK.xlsx')
         df2 = pd.read_excel(melt_filename, engine="openpyxl")
         df2.set_index("Material", inplace=True)