Js get cv

FrgTools/frgtools/Untitled2.ipynb

@@ -0,0 +1,212 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 108,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# getCV\n",
+    "\"\"\"\n",
+    "Loads CV data from a text file. Pulls the last curve out of the\n",
+    "repeats (red/ox cycle).\n",
+    "Returns structure. \n",
+    "\n",
+    "Example: mydata = getCV     (use UI to select file)\n",
+    "\n",
+    "         mydata = getCV ('C:\\Myname\\CV\\File.ras')   (directly offer filepath)\n",
+    "\n",
+    "Onset potential methods: \n",
+    "    1: Direct voltage at minimum cathodic peak\n",
+    "    2: Inflection point\n",
+    "    3: Intersection at baseline\n",
+    "    4: Fixed\n",
+    "\"\"\"\n",
+    "import os\n",
+    "import csv\n",
+    "import numpy as np\n",
+    "\n",
+    "# def getFileList(directory = os.path.dirname(file_name)):#os.path.realpath(__file__)))\n",
+    "#     return os.listdir(directory)\n",
+    "# getFileList(filepath)\n",
+    "\n",
+    "def getCV(fpath, area =1):\n",
+    "    cvdata = getcvdata(fpath)\n",
+    "    cvdata = getOnsetPotentials(cvdata)\n",
+    "    return cvdata\n",
+    "\n",
+    "def getcvdata(filepath, area = 1, nheaderlines = 53):\n",
+    "    area = float(area)\n",
+    "    rawCV = {'voltage' : [],\n",
+    "             'current' : [],\n",
+    "             'cycle' : [] }\n",
+    "\n",
+    "    with open(filepath,'r') as f:\n",
+    "        [next(f) for item in range(nheaderlines)] # Skips until the 54th line, where header line is. \n",
+    "        f_reader = csv.DictReader(f, delimiter = '\\t')    \n",
+    "        for row in f_reader:\n",
+    "            rawCV['voltage'].append(row['Ewe/V'])\n",
+    "            rawCV['current'].append(row['<I>/mA'])\n",
+    "            rawCV['cycle'].append(row['cycle number'])\n",
+    "\n",
+    "    num_of_scans = np.unique(rawCV['cycle'])\n",
+    "    fs = num_of_scans[-1]\n",
+    "    final_scan = {'voltage' : [],\n",
+    "                 'current' : [],\n",
+    "                 'currentdensity' : np.array([])}\n",
+    "\n",
+    "    j = 0  # This can probably be optimized. Final scan is the only important one.\n",
+    "    for n in rawCV['cycle']:\n",
+    "        if n == fs:\n",
+    "            final_scan['voltage'].append(rawCV['voltage'][j])\n",
+    "            final_scan['current'].append(rawCV['current'][j])\n",
+    "        j += 1\n",
+    "    \n",
+    "    final_scan['voltage'] = np.array(final_scan['voltage'], dtype = float)\n",
+    "    final_scan['current'] = np.array(final_scan['current'], dtype = float)\n",
+    "    final_scan['currentdensity'] = np.divide(final_scan['current'], area) # Gets current density\n",
+    "    return final_scan\n",
+    "\n",
+    "def smooth(a,WSZ=5):\n",
+    "    # a: NumPy 1-D array containing the data to be smoothed\n",
+    "    # WSZ: smoothing window size needs, which must be odd number,\n",
+    "    # as in the original MATLAB implementation\n",
+    "    out0 = np.convolve(a,np.ones(WSZ,dtype=int),'valid')/WSZ    \n",
+    "    r = np.arange(1,WSZ-1,2)\n",
+    "    start = np.cumsum(a[:WSZ-1])[::2]/r\n",
+    "    stop = (np.cumsum(a[:-WSZ:-1])[::2]/r)[::-1]\n",
+    "    return np.concatenate((  start , out0, stop  ))\n",
+    "\n",
+    "def getOnsetPotentials(cvdata,fitwidth = 40):\n",
+    "    #cvdata should be dict, output from getCV\n",
+    "    \n",
+    "    # Finding cathodic peak voltage\n",
+    "    X = cvdata['voltage']\n",
+    "    Y = cvdata['currentdensity']\n",
+    "    idx0 = np.argmin(Y)\n",
+    "    cvdata['cathodic_peak'] = X[idx0] \n",
+    "    \n",
+    "    # Finding anodic peak current at the end of the voltammogram\n",
+    "    idx1 = np.argmax(X)\n",
+    "    cvdata['anodic_peak'] = Y[idx1] \n",
+    "\n",
+    "    # Inflection point onset\n",
+    "    idx2 = np.argmin(X)\n",
+    "    XX = X[idx1+500 : idx2 - 20]\n",
+    "    YY = Y[idx1+500 : idx2 - 20]\n",
+    "    \n",
+    "    dydx = np.gradient(YY)/np.gradient(XX) # Finds first derivative, delta y/ delta x\n",
+    "    dydx = smooth(dydx)\n",
+    "    \n",
+    "    idx3 = np.argmax(dydx) # Inflection point on the cathodic curve\n",
+    "    idx4 = np.argmin(abs(YY)) # Getting closest to the baseline center as possible\n",
+    "    cvdata['inflection_onset'] = XX[idx3]\n",
+    "    \n",
+    "    X_ = XX[idx3 - fitwidth//2: idx3 + fitwidth//2]\n",
+    "    Y_ = YY[idx3 - fitwidth//2: idx3 + fitwidth//2]\n",
+    "    linfit_3 = np.polyfit(X_,Y_,1)\n",
+    "    \n",
+    "    X_ = XX[idx4 - fitwidth//2: idx4 + fitwidth//2]\n",
+    "    Y_ = YY[idx4 - fitwidth//2: idx4 + fitwidth//2]\n",
+    "    linfit_4 = np.polyfit(X_,Y_,1)\n",
+    "    \n",
+    "    intersect_x = (linfit_4[1] - linfit_3[1]) / (linfit_3[0] - linfit_4[1])\n",
+    "    intersect_y = linfit_3[0] * intersect_x + linfit_3[1]\n",
+    "    cvdata['intersect_onset'] = [intersect_x, intersect_y]\n",
+    "    return cvdata\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 99,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'voltage': array([0.19229576, 0.19345422, 0.19439143, ..., 0.19039437, 0.19128586,\n",
+      "       0.19239724]), 'current': array([0.00034713, 0.00034614, 0.00034744, ..., 0.00037424, 0.00037562,\n",
+      "       0.00040446]), 'currentdensity': array([0.00069426, 0.00069228, 0.00069488, ..., 0.00074847, 0.00075123,\n",
+      "       0.00080892])}\n"
+     ]
+    }
+   ],
+   "source": [
+    "cvdata = getcvdata(filepath, area = .5)\n",
+    "print(cvdata)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 111,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'voltage': array([0.19229576, 0.19345422, 0.19439143, ..., 0.19039437, 0.19128586,\n",
+       "        0.19239724]),\n",
+       " 'current': array([0.00034713, 0.00034614, 0.00034744, ..., 0.00037424, 0.00037562,\n",
+       "        0.00040446]),\n",
+       " 'currentdensity': array([0.00034713, 0.00034614, 0.00034744, ..., 0.00037424, 0.00037562,\n",
+       "        0.00040446]),\n",
+       " 'cathodic_peak': -0.444778711,\n",
+       " 'anodic_peak': 0.010884792647427984,\n",
+       " 'inflection_onset': -0.309950382,\n",
+       " 'intersect_onset': [-0.18963104576730827, -0.00028764459757954497]}"
+      ]
+     },
+     "execution_count": 111,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "filepath = r\"C:\\Users\\Skaggs\\Desktop\\Perovskites\\2019_08_09 CV SnOx\\10nm\\180_11.4_FTO_02_CV_C02.txt\"\n",
+    "getCV(filepath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 112,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "4199"
+      ]
+     },
+     "execution_count": 112,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(_['voltage'])"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

FrgTools/frgtools/cyclicvolt.py

@@ -0,0 +1,28 @@
+# getCV
+"""
+Loads CV data from a text file. Pulls the last curve out of the
+repeats (red/ox cycle).
+Returns structure. 
+
+Example: mydata = getCV     (use UI to select file)
+
+         mydata = getCV ('C:\Myname\CV\File.ras')   (directly offer filepath)
+
+Onset potential methods: 
+    1: Direct minimum
+    2: Inflection point
+    3: Intersection at baseline
+    4: Fixed
+"""
+import os
+
+def getFileList(directory = os.path.dirname(file_name)):#os.path.realpath(__file__)))
+	return os.listdir(directory)
+
+def getCV(filepath, area=1):
+	#getFileList(filepath)
+	txt = open(filepath,'r')
+	if area == 1: 
+		#Make title say Current (mA)
+
+print(getCV("C:\Users\Skaggs\Desktop\Perovskites\2019_08_09 CV SnOx\10nm\180_11.4_FTO_02_CV_C02"))