v1.2

.gitignore

@@ -3,3 +3,4 @@ _site
 .jekyll-cache
 .jekyll-metadata
 vendor
+.Rhistory

.stylelintignore

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+info.R

global.R

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+# ######
+#
+# Welcome to the Battery Analyzer Utility!
+#
+# This script aims to make it quick and efficient to analyze data exported by an Arbin battery cycler
+#
+# ######
+
+# ######
+#
+# These are all the required packages to aid in several of the processes, ranging from data analysis to plotting
+#
+# ######
+
+# options(warn = 0)
+
+list.of.packages <- c("readxl", "dplyr", "shiny", "tcltk", "DT", "shinyjs", "shinyalert", "pracma", "purrr", "zoo", "plotrix", "tools", "shinyWidgets", "gifski")
+new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
+if (length(new.packages)) install.packages(new.packages)
+lapply(list.of.packages, require, character.only = TRUE)
+
+source("ui.R", local = TRUE)
+source("server.R")
+source("info.R")
+
+# This line tests if the current R environment is interactive, RStudio makes an interactive environment by default
+if (interactive()) {
+
+  # ######
+  #
+  # All the global variables within the script, aka variables that need to be accessed by more than one
+  # function or session
+  #
+  # "Reactive Values" are ones that need to be readily changed, such as user inputs and variables to be displayed
+  #
+  # ######
+  data <- reactiveValues(data = data.frame())
+  final <- data.frame()
+  dirLocation <- vector()
+  numCycles <- data.frame()
+  dQdVData <- data.frame()
+  total <- data.frame()
+  cycle_facts <- data.frame()
+  tmp_data <- data.frame()
+  dirName <<- ""
+  tmp_cycles <- vector()
+  titleLabel <- ""
+  xlabel <- ""
+  ylabel <- ""
+  addParams <- FALSE
+  arbinCM <- FALSE
+  catMetric <<- vector()
+  legTitle <<- ""
+  sheetName <<- ""
+  bounds <<- vector()
+  compCycleFacts <<- data.frame()
+}
+
+shinyApp(ui, server)

info.R

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+
+graphInfoTable <- HTML('
+              <style type="text/css">
+              .tg  {border-collapse: collapse;border-spacing: 0;}
+              .tg td{font-family: Arial, sans-serif;font-size: 14px;padding: 10px 5px;border-style: solid;border-width: 1px;overflow: hidden;word-break: normal;border-color: black;}
+              .tg th{font-family: Arial, sans-serif;font-size: 14px;font-weight: normal;padding: 10px 5px;border-style: solid;border-width: 1px;overflow: hidden;word-break: normal;border-color: black;}
+              .tg .tg-gfnm{background-color: #efefef;border-color: #000000;text-align: center;vertical-align: middle}
+              .tg .tg-i0p4{font-weight: bold;background-color: #ecf4ff;border-color: #000000;text-align: center;vertical-align: middle}
+              .tg .tg-3fas{background-color: #efefef;border-color: #000000;text-align: left;vertical-align: middle}
+              .tg .tg-o3hj{background-color: #ecf4ff;border-color: #000000;text-align: center;vertical-align: middle}
+              .tg .tg-xwyw{border-color: #000000;text-align: center;vertical-align: middle}
+              .tg .tg-0a7q{border-color: #000000;text-align: left;vertical-align: middle}
+              </style>
+              <table class="tg">
+                <tr>
+                  <th class="tg-i0p4">Graph</th>
+                  <th class="tg-i0p4">X Axis</th>
+                  <th class="tg-i0p4">Y Axis</th>
+                  <th class="tg-o3hj"><span style="font-weight: bold">Plot Frequency</span><br></th>
+                  <th class="tg-i0p4">Description</th>
+                </tr>
+                <tr>
+                  <td class="tg-xwyw">dQdV Graph</td>
+                  <td class="tg-xwyw">Voltage (V)</td>
+                  <td class="tg-xwyw">dQdV (Ah/V)</td>
+                  <td class="tg-xwyw">per cycle</td>
+                  <td class="tg-0a7q">The differential capacity plot for each cycle<br></td>
+                </tr>
+                <tr>
+                  <td class="tg-gfnm">Voltage Profile</td>
+                  <td class="tg-gfnm">Continuous Capacity (mAh/g or Ah)</td>
+                  <td class="tg-gfnm">Voltage (V)</td>
+                  <td class="tg-gfnm">per cycle</td>
+                  <td class="tg-3fas">Voltage vs. capacity plot for each cycle. Units depend if the masses are specified.</td>
+                </tr>
+                <tr>
+                  <td class="tg-xwyw">Voltage vs. Time</td>
+                  <td class="tg-xwyw">Time (min)</td>
+                  <td class="tg-xwyw">Voltage (V)</td>
+                  <td class="tg-xwyw">per cycle</td>
+                  <td class="tg-0a7q">The voltage as a function of time, including all steps</td>
+                </tr>
+                <tr>
+                  <td class="tg-gfnm">Discharge Capacity</td>
+                  <td class="tg-gfnm">Cycle</td>
+                  <td class="tg-gfnm">Discharge Capacity (mAh/g or Ah)</td>
+                  <td class="tg-gfnm">per cell</td>
+                  <td class="tg-3fas">Discharge capacity for each <span style="font-weight: bold">individual cell </span>per cycle. Coulombic efficiency is also plotted on a secondary axis. Units depend if the masses are specified.</td>
+                </tr>
+                <tr>
+                  <td class="tg-xwyw">Discharge Areal Capacity</td>
+                  <td class="tg-xwyw">Cycle</td>
+                  <td class="tg-xwyw">Discharge Capacity (Ah/cm<sup>2</sup>)</td>
+                  <td class="tg-xwyw">per cell</td>
+                  <td class="tg-0a7q">Discharge areal capacity for each <span style="font-weight: bold">individual cell </span>per cycle. Coulombic efficiency is also plotted on a secondary axis.</td>
+                </tr>
+                <tr>
+                  <td class="tg-gfnm">Total Discharge Capacity</td>
+                  <td class="tg-gfnm">Cycle</td>
+                  <td class="tg-gfnm">Discharge Capacity (mAh/g or Ah)</td>
+                  <td class="tg-gfnm">per analysis</td>
+                  <td class="tg-3fas">Discharge capacity summarized for <span style="font-weight: bold">all cells</span> in the analysis. Coulombic efficiency is also plotted on a secondary axis. Mean is plotted as a point with error bars presenting the standard error between the cells. Units depend if the masses are specified.</td>
+                </tr>
+                <tr>
+                  <td class="tg-xwyw">Average Voltage</td>
+                  <td class="tg-xwyw">Cycle</td>
+                  <td class="tg-xwyw">Voltage (V)</td>
+                  <td class="tg-xwyw">per cell</td>
+                  <td class="tg-0a7q">The average voltage vs capacity for each cycle. The charge voltage (V<sub>charge</sub>) and discharge voltage (V<sub>discharge</sub>) were calculated using the average value theorem. The average voltage is then (V<sub>charge</sub> + V<sub>discharge</sub>)/2. Charge and discharge voltages are plotted alongside the average.</td>
+                </tr>
+                <tr>
+                  <td class="tg-gfnm">Delta Voltage</td>
+                  <td class="tg-gfnm">Cycle</td>
+                  <td class="tg-gfnm">Voltage (V)</td>
+                  <td class="tg-gfnm">per cell</td>
+                  <td class="tg-3fas">The delta voltage vs capacity for each cycle. The charge voltage (V<sub>charge</sub>) and discharge voltage (V<sub>discharge</sub>) were calculated using the average value theorem. The delta voltage is then V<sub>charge</sub> - V<sub>discharge</sub>). Charge and discharge voltages are plotted alongside the average.</td>
+                </tr>
+                <tr>
+                  <td class="tg-xwyw">Capacity Loss</td>
+                  <td class="tg-xwyw">Cycle</td>
+                  <td class="tg-xwyw">Capacity (mAh/g or Ah)</td>
+                  <td class="tg-xwyw">per cell</td>
+                  <td class="tg-0a7q">The discharge capacity minus the charge capacity for each cycle. Units depend if the masses are specified.</td>
+                </tr>
+              </table>
+            ')

modal.R

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+# Defines the modal in which the cell masses can be exported from Excel
+graphModal <- modalDialog(
+  {
+    fluidPage(
+      style = "font-size:15pt;",
+      tags$head(tags$style(".modal-dialog{min-width:60%}")),
+      fluidRow(align = "center", graphInfoTable),
+    )
+  },
+  title = "Graph Types",
+  easyClose = TRUE
+)
+
+graphbuilder <- modalDialog(
+  {
+    fluidPage(
+      useShinyjs(),
+      useShinyalert(),
+      tags$head(tags$style(".modal-dialog{width:80%}")),
+      tags$head(tags$style(".modal-body{ min-height:1000px}")),
+      sidebarLayout(
+        sidebarPanel(
+          fluidRow(
+            headerPanel("Graph Options"),
+          ),
+          fluidRow(
+            style = "padding:5%; border: 1px solid black;",
+            strong("Basis for Plot Types"), tags$br(),
+            helpText("Between Analysis requires a second dataset to be imported"), tags$br(),
+            radioButtons("perType", NULL, choices = c("Within Analysis", "Between Analyses"), inline = TRUE),
+            hidden(fileInput("compAnalysis", "Data to Compare"))
+          ),
+          fluidRow(
+            style = "padding:5%; margin:5%;",
+            radioButtons("typeGraph", "Graph Type:", choices = c(
+              "dQdV Graphs", "Voltage Profiles", "Voltage vs. Time",
+              "Charge Voltage", "Discharge Voltage",
+              "Average Voltage", "Delta Voltage", "Discharge Capacity", "Charge Capacity"
+            ), inline = FALSE),
+            radioButtons("plotStyle", "Plot Style:", choiceNames = c("Point", "Line", "Both"), choiceValues = c("p", "l", "o"), inline = TRUE),
+            checkboxGroupInput("cells", "Cell to Analyze:", choices = 1, inline = FALSE),
+            selectInput("renderCycles", "Cycles of Interest:", choices = 1, multiple = TRUE),
+          ),
+          fluidRow(
+            strong("Click to show coordinates:"), tags$br(), tags$br(),
+            "X: ",
+            textOutput("hoverCoordx", inline = TRUE), tags$br(),
+            "Y: ",
+            textOutput("hoverCoordy", inline = TRUE),
+            style = "border: 1px solid black; padding: 5%; margin: 5%;"
+          ),
+          fluidRow(
+            textInput("fileName", "Name of graph file:"),
+            actionButton("saveGraph", "Save Graph", width = "100%", class = "btn-primary"),
+            style = "border: 4px double black; padding: 5%; margin: 5%;"
+          ),
+        ),
+        mainPanel(
+          fluidRow(
+            plotOutput("outputPlot", height = "800px", click = "plot_click"),
+            style = "padding: 5%;",
+          ),
+          fluidRow(
+            h3("Graph Formatting"),
+            helpText("*If left blank, they will be calculated using the min and max of the data to be plotted."),
+            column(
+              2,
+              numericInput("xMin", "X Min", value = NULL),
+              sliderInput("textSize", "Text Size", min = 0.1, max = 5, value = 1, ticks = FALSE),
+            ),
+            column(
+              2,
+              numericInput("xMax", "X Max", value = NULL),
+              sliderInput("pointSize", "Point/Line Size", min = 0.1, max = 5, value = 1, ticks = FALSE),
+            ),
+            column(
+              2,
+              numericInput("yMin", "Y Min", value = NULL),
+            ),
+            column(
+              2,
+              numericInput("yMax", "Y Max", value = NULL),
+            ),
+            column(
+              4,
+              textInput("originalData", "Original Data Name", value = "Original Data"),
+              textInput("compareData", "Comparison Data Name", value = "Comparison Data"),
+            ),
+            style = "border: 1px dashed black; padding: 2%;",
+          )
+        )
+      )
+    )
+  },
+  size = "l",
+  title = "Post-Processing Graph Builder"
+)