diff --git a/# Subroutines that need to be modified.md b/# Subroutines that need to be modified.md
new file mode 100644
index 0000000..6e5e89f
--- /dev/null
+++ b/# Subroutines that need to be modified.md	
@@ -0,0 +1,37 @@
+# Subroutines that need to be modified
+
+# Done
+* DetermineYieldFunctionValue 
+DetermineYieldFunctionValue(IntGlo,SigC,c,phi,hyperbolic_a_constant, F)
+
+* CalculateDerivativesYieldFunctAndPlasticPotential
+ CalculateDerivativesYieldFunctAndPlasticPotential(Sig,p,J,Lode,S3TA,c,phi,psi, hyperbolic_a_constant, DFDSig,DPPDSig)
+
+* CalculateDerivativesYieldFunctSofteningParameters
+CalculateDerivativesYieldFunctSofteningParameters(p,J,Lode,S3TA,c,phi, hyperbolic_a_constant, DFDSP)
+
+* EndOfStepCorrection
+EndOfStepCorrection(IntGlo,D1,D2,GG,IPL,F,Sig,DSPDPEq,DEpsPEqDPS,EpsP,c,phi,psi, hyperbolic_a_constant)
+
+* DetermineElasticProportionPegasusMethod
+DetermineElasticProportionPegasusMethod(IntGlo,Sig,DSig,DEps,c,phi, hyperbolic_a_constant, YTOL,alpha)
+
+* DetermineDSigAndDEpsP
+DetermineDSigAndDEpsP(IntGlo,D1,D2,GG,c,phi,psi,Sig, hyperbolic_a_constant, DEpsPEqDPS,DSPDPEq,DEps,DSig,DEpsP)
+
+* MCSS_Ortiz_Simo_Integration(G, D1, D2, IntGlo, Sig, c, phi, psi, factor, dEps, EpsP, dEpsP, cr, phir, psir, cp, phip, &
+      psip, ctol, phitol, psitol, FTOL, max_iterations, hyperbolic_a_constant)
+
+dadc
+dadPhi
+
+# Need to be modified
+
+
+
+
+hyperbolic_a_constant
+
+C00P50
+
+# Need to check the derivatives
diff --git a/BlueDrop_TeamWork_v1.ipynb b/BlueDrop_TeamWork_v1.ipynb
index 98e2b09..b81fe60 100644
--- a/BlueDrop_TeamWork_v1.ipynb
+++ b/BlueDrop_TeamWork_v1.ipynb
@@ -2,20 +2,21 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 69,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy\n",
     "import numpy as np\n",
     "from numpy import trapz\n",
     "\n",
     "import pandas as pd\n",
+    "import os\n",
+    "import datetime\n",
     "\n",
     "import matplotlib\n",
     "\n",
     "# Uses tinker as the backend for matplotlib (Not really sure what this is doing)\n",
-    "matplotlib.use('TkAgg')\n",
+    "# matplotlib.use('TkAgg')\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from pathlib import Path\n",
@@ -34,200 +35,32 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 72,
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "SyntaxError",
-     "evalue": "non-default argument follows default argument (1948369725.py, line 88)",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[1;36m  Cell \u001b[1;32mIn[1], line 88\u001b[1;36m\u001b[0m\n\u001b[1;33m    areaCalcType, tipType):\u001b[0m\n\u001b[1;37m    ^\u001b[0m\n\u001b[1;31mSyntaxError\u001b[0m\u001b[1;31m:\u001b[0m non-default argument follows default argument\n"
-     ]
-    }
-   ],
+   "outputs": [],
+   "source": [
+    "# Local lib imports \n",
+    "# from lib.cone_area_funcs import calcFFPContactArea\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 73,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Define global values (use very selectively!)\n",
+    "PI = np.pi"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 74,
+   "metadata": {},
+   "outputs": [],
    "source": [
-    "def calcCylinderSurfaceArea(radius, height):\n",
-    "    # Calculates the Surface area of a cylinder\n",
-    "    # Inputs:\n",
-    "        # radius: Radius of the cylinder\n",
-    "        # height of the cylinder\n",
-    "\n",
-    "        baseArea = np.pi * radius**2 # Surface area of the base of the cylinder\n",
-    "        sideArea = 2 * np.pi * radius * height # Surface area on the side of the cylinder\n",
-    "        totalSurfaceArea = baseArea + sideArea\n",
-    "        return totalSurfaceArea\n",
-    "\n",
-    "def calcConeLateralSurfaceArea(radius, height):\n",
-    "    # Calculates the lateral surface of a cone (Doesn't calc the surface area of the base of the cone)\n",
-    "    # Inputs:\n",
-    "        # radius: radius of the base of the cone\n",
-    "        # height: height of the cone (measured normal to the base)\n",
-    "        # sideSlope: Side slope of the cone\n",
-    "\n",
-    "    return np.pi * radius * np.sqrt(height**2 + radius**2)\n",
-    "\n",
-    "def calcCircleArea(radius):\n",
-    "    # Calc the area of a circle\n",
-    "    # Input:\n",
-    "        # radius: radius of the circle\n",
-    "    return np.pi * radius**2\n",
-    "\n",
-    "def calcFFPConeContactArea(penetrationDepth, maxLength, baseRadius, coneTipRadius, coneTipHeight, areaCalcType):\n",
-    "    # Function calculates the contact area for the cone top of the FFP\n",
-    "\n",
-    "    # penetrationDepth: Array of penetration depth values\n",
-    "    # maxLength: Max length before the lateral area of the FFP is considered\n",
-    "    # baseRadius: Radius of the Cone at the base (Circular side)\n",
-    "    # coneTipRadius: Radius of the cone tip (is not zero)\n",
-    "    # coneTipHeight: Height of the cone when measured normal to the circular base\n",
-    "    # areaCalcType: Selection of mantle or projected\n",
-    "\n",
-    "    # Init array to store area\n",
-    "    area = np.ones(len(penetrationDepth))\n",
-    "\n",
-    "    # Calc cone side slope\n",
-    "    coneSideSlope = (baseRadius-coneTipRadius)/coneTipHeight\n",
-    "\n",
-    "    for i, depth in enumerate(penetrationDepth):\n",
-    "        \n",
-    "        # if the depth is greater than the maxLength of the cone\n",
-    "        if depth > maxLength:\n",
-    "            # decrease the depth used in the calculation to the maxLength\n",
-    "            depth = maxLength\n",
-    "        \n",
-    "        # Calc the radius\n",
-    "        radius = coneTipRadius + depth * coneSideSlope\n",
-    "\n",
-    "        # Check area selection\n",
-    "        if areaCalcType == \"mantle\":\n",
-    "            # if selected calc mantle area (Same as surface area without the base of cone)\n",
-    "            area[i] = calcConeLateralSurfaceArea(radius, depth)\n",
-    "\n",
-    "        elif areaCalcType == \"projected\":\n",
-    "            # if selected calc projected area\n",
-    "            area[i] = calcCircleArea(radius)\n",
-    "\n",
-    "        else: \n",
-    "            return ValueError(\"areaCalcType must be mantle or projected. Currently is: {}\".format(areaCalcType))\n",
-    "\n",
-    "    return area\n",
-    "\n",
-    "def calcFFPBluntContactArea(penetrationDepth, maxLength, baseRadius, areaCalcType):\n",
-    "\n",
-    "    # init array to store area calcs\n",
-    "    area = np.zeros(len(penetrationDepth))\n",
-    "\n",
-    "    for i, depth in enumerate(penetrationDepth):\n",
-    "        # if the depth is greater than the maxLength of the blunt cylinder\n",
-    "        if depth > maxLength:\n",
-    "            # decrease the depth used in the calculation to the maxLength\n",
-    "            depth = maxLength\n",
-    "        \n",
-    "        # radius is constant for cylinder\n",
-    "        radius = baseRadius\n",
-    "\n",
-    "        # Check area selection\n",
-    "        if areaCalcType == \"mantle\":\n",
-    "            # if selected calc mantle area (Surface Area of a cylinder)\n",
-    "            area[i] = calcCylinderSurfaceArea(radius, depth)\n",
-    "\n",
-    "        elif areaCalcType == \"projected\":\n",
-    "            # if selected calc projected area\n",
-    "            area[i] = calcCircleArea(radius)\n",
-    "\n",
-    "        else: \n",
-    "            return ValueError(\"areaCalcType must be mantle or projected. Currently is: {}\".format(areaCalcType))\n",
-    "        \n",
-    "    # Might need to convert this to m^2\n",
-    "    return area\n",
-    "\n",
-    "def calcFFPContactArea(penetrationDepth,  maxLength, areaCalcType, tipType, baseRadius = 4.375, coneTipRadius = 0.22, coneTipHeight = 7.55,):\n",
-    "    # Function calls the required functions to calculate the generated area for a cone\n",
-    "    # Inputs:\n",
-    "        # penetrationDepth: Array of depths the FFP has penetrated, [m]\n",
-    "        # maxLength: max length of penetration before radius become constant, [cm]\n",
-    "        # baseRadius: Base radius of the cone and blunt tip, [cm]\n",
-    "        # coneTipRadius: Tip radius of the cone??, [cm]\n",
-    "        # coneTipHeight: height of the cone, [cm]\n",
-    "        # areaCalcType: \"mantle or projected\"\n",
-    "        # tipType: blunt or cone tip type       \n",
-    "    \n",
-    "    # Convert penetration depth to centimeters [cm]\n",
-    "    penetrationDepth = penetrationDepth * 100 #[cm]\n",
-    "\n",
-    "    # Calc area for cone tip\n",
-    "    if tipType == \"cone\":\n",
-    "        area = calcFFPConeContactArea(penetrationDepth, maxLength, baseRadius, coneTipRadius, coneTipHeight, areaCalcType)\n",
-    "\n",
-    "     # Calc area for blunt tip\n",
-    "    elif tipType == \"blunt\":\n",
-    "        area = calcFFPBluntContactArea(penetrationDepth, maxLength, baseRadius, areaCalcType)\n",
-    "    \n",
-    "    # Convert to m^2\n",
-    "    return area/1e4 #[m^2]\n",
-    "    \n",
-    "def calcDynamicBearingCapacity(acceleration, massFFP, contactArea, rho_w = 1020, volumeFFP = 0.002473, waterDrop = True ):\n",
-    "    # Function calculates the dynamic bearing capacity of the soil\n",
-    "\n",
-    "    # Inputs\n",
-    "        # dropType (S: \"air\" or \"water\" drop\n",
-    "        # accleration: deaccleration array\n",
-    "        # massFFP: Mass of the Free Fall Penetrometer (FFP)\n",
-    "        # contactArea: Array of contact areas between the FFP and the soil\n",
-    "        # rho_w: Density of water\n",
-    "        # volumeFFP: Volume of the FFP\n",
-    "\n",
-    "    if waterDrop:\n",
-    "\n",
-    "        # Calc mass of water displaced by the FFP\n",
-    "        displacedWaterMass = rho_w * volumeFFP\n",
-    "\n",
-    "        # Calc Buoyant mass of the FFP\n",
-    "        buoyantMass = massFFP - displacedWaterMass\n",
-    "\n",
-    "        # Calc impact force\n",
-    "        force = buoyantMass * acceleration\n",
-    "\n",
-    "    # Check for air drop\n",
-    "    elif not waterDrop:\n",
-    "        force = massFFP * acceleration\n",
-    "\n",
-    "    # Dynamic bearing capacity\n",
-    "    qDyn = force/contactArea\n",
-    "\n",
-    "    return qDyn\n",
-    "\n",
-    "def calcQuasiStaticBearingCapacity(velocity, strainrateCorrectionType, qDyn, K_Factor = 0.1, refVelocity = 0.02, BrilliCoeff = 0.31):\n",
-    "    # Function calculates the quasi-static bearing capacity value\n",
-    "    # velocity: Array of FFP velocity values [m/s]\n",
-    "    # K_Factors: Array of K factors to be used\n",
-    "\n",
-    "    # Local Variables: \n",
-    "    # f_SR: Strain Rate factor\n",
-    "    # maxVelocity: Max velocity of the descent\n",
-    "\n",
-    "    maxVelocity = np.max(velocity)\n",
-    "\n",
-    "    if strainrateCorrectionType == \"log\":\n",
-    "        f_SR = 1 + K_Factor * np.log10(velocity/refVelocity)\n",
-    "\n",
-    "    elif strainrateCorrectionType == \"Brilli\":\n",
-    "        # Strain rate correction factor following Brilli et al. (20??) Commonly used for air drops\n",
-    "        f_SR = 1 + BrilliCoeff * maxVelocity * np.log10(velocity/refVelocity)\n",
-    "\n",
-    "    elif strainrateCorrectionType == \"invHyperSin\":\n",
-    "        # Inv hyperbolic sin correction factor following Stephan (2015) and Randolph (2004)\n",
-    "        f_SR = 1 + K_Factor/np.log(10) * np.arcsinh(velocity/refVelocity)\n",
-    "\n",
-    "    else:\n",
-    "        ValueError(\"strainrateCorrectionType must be one of the folliwng: log, Brilli, invHyperSin.\")\n",
-    "\n",
-    "    # calc Quasi Static Bearing capacity value\n",
-    "    qsbc = qDyn/f_SR\n",
-    "    return qsbc\n",
     "\n",
-    "FFP_Properties =\n",
+    "# FFP_Properties =\n",
     "    \n",
     "def integrateFunc(x, func, order = 1):\n",
     "    # x: Dependent Variable that the derivative should be taken with respect to\n",
@@ -244,6 +77,51 @@
     "\n",
     "    pass\n",
     "\n",
+    "# def tipProperties(tipType):\n",
+    "#     if tipType == \"cone\":\n",
+    "#         mass = 7.71 # [kg]\n",
+    "#         length = 8.48 - 0.93 #[cm], originally 7.87, 7.57 fors perfect 60 deg, 8.48 measured - .93 measured 90 deg\n",
+    "#     if tipType == \"\"\n",
+    "\n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 75,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# SETUP VARIABLES - USER INPUTS\n",
+    "BD = 3 #Bluedrop file is from \n",
+    "fileNum = '01F3' # write the bin file number you want to analyze (do not include 'bLog' or '.bin')\n",
+    "soiltype = \"c\" #s = sand, c=clay, m=mixed, u=unknown\n",
+    "tiptype = 'c'  # c = cone, p = parabolic, b = blunt\n",
+    "truncate_at_cone = \"n\" #\"y\" to end analysis at a penetration depth equal to the cone length, \"n\" to consider full cone length\n",
+    "droptype = \"w\" #w = water, #a = air\n",
+    "unit_wt = \"uk\" #enter an effective unit weight value in kg/m^3 or \"uk\" if unknown \n",
+    "Nkt = 10 #default value for cone factor used in su calculations\n",
+    "drop_finding = \"m\" #\"m\" for manual drop picking, \"a\" for automatic drop picking\n",
+    "\n",
+    "# paste the filepath to the folder where the BD data is stored\n",
+    "binFilepath = Path(\"C:/Users/elise/Desktop/bd_manual/sample_drops\")\n",
+    "\n",
+    "# paste the filepath to an excel file that the analysis results will be printed in\n",
+    "outputPath = Path(\"C:/Users/elise/Desktop/bd_manual/sample_drops/Figures/Summary_Excel.xlsx\")\n",
+    "\n",
+    "# paste the filepath to the folder where the output figures will be saved\n",
+    "plotPath = Path(\"C:/Users/elise/Desktop/bd_manual/sample_drops/Figures\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 105,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lib.BinaryFile import BinaryFile\n",
+    "\n",
+    "\n",
     "\n",
     "\n",
     "    "
@@ -251,23 +129,108 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 107,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Get directories of all binary files in the specified directory\n",
+    "dir = r\"C:\\Geotech_Research\\Field_Analysis\\Bluedrop_data\\Mouth 1\"\n",
+    "\n",
+    "import glob\n",
+    "\n",
+    "\n",
+    "column_names = [\"Count\", 'Unknown', \"2g_accel\", \"18g_accel\", \"50g_accel\", \"pore_pressure\", \"200g_accel\", \n",
+    "                                                                \"55g_x_tilt\",\"55g_y_tilt\", \"250g_accel\"]\n",
+    "\n",
+    "binary_file_dirs  = get_binary_file_dirs(dir)\n",
+    "\n",
+    "# Add a function to sort the binary files by date\n",
+    "\n",
+    "# init list to store the data files\n",
+    "data_files = [None] * len(binary_file_dirs)\n",
+    "\n",
+    "for i, file_dir in enumerate(binary_file_dirs):\n",
+    "    data_files[i] = PFFP_File(file_dir)\n",
+    "    data_files[i] = PFFP_File.binary_file_2_df(file_dir, column_names)    "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Things to do\n",
+    "\n",
+    "* Convert the df data to SI units\n",
+    "* Make a way to plot the data\n",
+    "* Make a way to try to get the number of drops\n",
+    "* Convert data to bearing capacity\n",
+    "* Create function to assign PPFP properties\n",
+    "  * I don't want to do this on init because there might be surveys were you use more than one tip or bluedrop \n",
+    "* Assume that each folder only contains data from one PFFP"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 117,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import glob\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 119,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# from lib.pffpDataFolder import pffpDataFolder\n",
+    "calib_dir = r\"C:\"\n",
+    "\n",
+    "folder = pffpDataFolder(dir, pffp_id=1, calibration_factor_dir=calib_dir)\n",
+    "folder.store_binary_files()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<built-in function dir>\n",
+      "[]\n"
+     ]
+    }
+   ],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "10000.0"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<lib.BinaryFile.BinaryFile object at 0x00000141882DAE10>\n"
+     ]
     }
    ],
    "source": [
-    "100**2\n",
-    "1e4"
+    "print(file)"
    ]
   },
   {
@@ -275,13 +238,7 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "def tipProperties(tipType):\n",
-    "    if tipType == \"cone\":\n",
-    "        mass = 7.71 # [kg]\n",
-    "        length = 8.48 - 0.93 #[cm], originally 7.87, 7.57 fors perfect 60 deg, 8.48 measured - .93 measured 90 deg\n",
-    "    if tipType == \"\""
-   ]
+   "source": []
   }
  ],
  "metadata": {
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diff --git a/test.ipynb b/test.ipynb
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--- /dev/null
+++ b/test.ipynb
@@ -0,0 +1,68 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'lib.BinaryFile'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[1], line 2\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mglob\u001b[39;00m\n\u001b[1;32m----> 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mBinaryFile\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m BinaryFile\n\u001b[0;32m      4\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget_binary_file_dirs\u001b[39m(folder_dir):\n\u001b[0;32m      5\u001b[0m     \u001b[38;5;66;03m# Purpose: Get all of the binary file directories from a folder\u001b[39;00m\n\u001b[0;32m      6\u001b[0m     binary_file_dirs \u001b[38;5;241m=\u001b[39m []\n",
+      "\u001b[1;31mModuleNotFoundError\u001b[0m: No module named 'lib.BinaryFile'"
+     ]
+    }
+   ],
+   "source": [
+    "import glob\n",
+    "from lib.BinaryFile import BinaryFile\n",
+    "\n",
+    "def get_binary_file_dirs(folder_dir):\n",
+    "    # Purpose: Get all of the binary file directories from a folder\n",
+    "    binary_file_dirs = []\n",
+    "\n",
+    "    print(folder_dir)\n",
+    "    # for file in glob.glob(folder_dir + '**/*.bin', recursive = True):\n",
+    "    #     file_path = os.path.join(folder_dir, file)\n",
+    "    #     binary_file_dirs.append(file_path)\n",
+    "\n",
+    "    return binary_file_dirs\n",
+    "file_dir = get_binary_file_dirs(dir)\n",
+    "print(file_dir)\n",
+    "file = BinaryFile(file_dir)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "PFFP_FieldWork",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}