work on plotting functions

SFB-ELAINE · Aug 8, 2023 · 0fd64d2 · 0fd64d2
1 parent 946d0c5
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Showing 7 changed files with 173 additions and 44 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
+# Directories
+output/
+
 # History files
 .Rhistory
 .Rapp.history

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,4 +11,4 @@ License: LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports: tidyverse, yaml, scattermore
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/R/getWaveforms.R b/R/getWaveforms.R
@@ -80,6 +80,8 @@ getWaveforms <- function(input_file = NULL, input_directory = NULL) {
     return(NULL)
   }
 
+  first_non_zero_data <- FALSE
+
   for(i in 1:length(yaml_files)){
     # Read data
     if(zip_container){
@@ -90,20 +92,29 @@ getWaveforms <- function(input_file = NULL, input_directory = NULL) {
       df_data_list <- yaml::read_yaml(file = file.path(input_directory, yaml_files[i]))
     }
 
-    # Convert list to tibble
-    df_data_dummy <- dplyr::as_tibble(df_data_list)
+    if(length(df_data_list[[1]]) > 0){
+
+      # Convert list to tibble
+      df_data_dummy <- dplyr::as_tibble(df_data_list)
+
+      # Get date and time of measurement
+      df_data_dummy$date_time <- gsub(pattern = "-wave\\.yml",
+                                      replacement = "",
+                                      x = basename(yaml_files[i]))
 
-    # Get date and time of measurement
-    df_data_dummy$date_time <- gsub(pattern = "-wave\\.yml",
-                                    replacement = "",
-                                    x = basename(yaml_files[i]))
+      df_data_dummy$ID <- i
 
-    df_data_dummy$ID <- i
+      if(i == 1 || first_non_zero_data){
+        df_data <- df_data_dummy
+        first_non_zero_data <- FALSE
+      }else{
+        df_data <- dplyr::bind_rows(df_data, df_data_dummy)
+      }
 
-    if(i == 1){
-      df_data <- df_data_dummy
     }else{
-      df_data <- dplyr::bind_rows(df_data, df_data_dummy)
+      if(i == 1){
+        first_non_zero_data <- TRUE
+      }
     }
 
   }

diff --git a/R/plotMeasurements.R b/R/plotMeasurements.R
@@ -17,9 +17,12 @@
 # Created: 2022/04/20
 # Last changed: 2023/02/21
 
-plotMeasurements <- function(input_data = NULL, output_dir = NULL,
-                             vavg_min = NULL, vavg_max = NULL,
-                             vpp_min = NULL, vpp_max = NULL,
+plotMeasurements <- function(input_data = NULL,
+                             output_dir = NULL,
+                             vavg_min = NULL,
+                             vavg_max = NULL,
+                             vpp_min = NULL,
+                             vpp_max = NULL,
                              plot_title = NULL) {
 
   # Some function parameters
@@ -56,18 +59,26 @@ plotMeasurements <- function(input_data = NULL, output_dir = NULL,
 
   # Determine Vavg minimum and maximum if not given
   if(is.null(vavg_min)){
-    vavg_min <- as.numeric(quantile(df_data$VAVG, 0.01, na.rm = TRUE))*factor_for_min_max_scaling
+    vavg_min <- round(
+      as.numeric(quantile(df_data$VAVG, 0.01, na.rm = TRUE)) *
+        factor_for_min_max_scaling, digits = 0)
   }
   if(is.null(vavg_max)){
-    vavg_max <- as.numeric(quantile(df_data$VAVG, 0.99, na.rm = TRUE))*factor_for_min_max_scaling
+    vavg_max <- round(
+      as.numeric(quantile(df_data$VAVG, 0.99, na.rm = TRUE)) *
+        factor_for_min_max_scaling, digits = 0)
   }
 
   # Determine Vpp minimum and maximum if not given
   if(is.null(vpp_min)){
-    vpp_min <- as.numeric(quantile(df_data$VPP, 0.01, na.rm = TRUE))*factor_for_min_max_scaling
+    vpp_min <- round(
+      as.numeric(quantile(df_data$VPP, 0.01, na.rm = TRUE)) *
+        factor_for_min_max_scaling, digits = 0)
   }
   if(is.null(vpp_max)){
-    vpp_max <- as.numeric(quantile(df_data$VPP, 0.99, na.rm = TRUE))*factor_for_min_max_scaling
+    vpp_max <- round(
+      as.numeric(quantile(df_data$VPP, 0.99, na.rm = TRUE)) *
+        factor_for_min_max_scaling, digits = 0)
   }
 
   # # Set time breaks

diff --git a/R/plotWaveforms.R b/R/plotWaveforms.R
@@ -23,7 +23,7 @@
 #' @return 0
 
 # Created: 2022/04/21
-# Last changed: 2023/02/21
+# Last changed: 2023/08/01
 
 plotWaveforms <- function(input_data = NULL,
                           output_dir = NULL,
@@ -57,7 +57,7 @@ plotWaveforms <- function(input_data = NULL,
   # Set plot title
   if(is.null(plot_title)){
     plot_title <- ""
-    plot_title_without_date <- ""
+    # plot_title_without_date <- ""
 
     # Get date of experiment
     date_of_experiment <- unique(as.Date(input_data$date_time))[1]
@@ -156,7 +156,7 @@ plotWaveforms <- function(input_data = NULL,
     waveforms <- NA
   }
 
-  if(!is.na(waveforms)){
+  if(length(waveforms) > 1 || !is.na(waveforms)){
     for(i in waveforms){
 
       input_data_filtered <- input_data %>%
@@ -179,9 +179,12 @@ plotWaveforms <- function(input_data = NULL,
       if(is.na(p2p_value)){
         p2p_value <- 0
       }
-      p2p_value <- format(round(p2p_value, digits = 2), nsmall = 2)
+      p2p_value <- format(round(p2p_value, digits = 1), nsmall = 1)
       p2p_value <- paste("V_p2p=", p2p_value, "V", sep="")
 
+      max_value_text <- paste("V_max=", format(round(max_value, digits = 1), nsmall = 1), "V", sep="")
+      min_value_text <- paste("V_min=", format(round(min_value, digits = 1), nsmall = 1), "V", sep="")
+
       # Calculate mean value of stimulation pulses ###########################
 
       if(start_point_function_generator_pulse == end_point_function_generator_pulse){
@@ -198,9 +201,12 @@ plotWaveforms <- function(input_data = NULL,
         mean_value <- mean(df_dummy$U)
       }
 
+      mean_value_value_text <- paste("V_mean=", format(round(mean_value, digits = 1), nsmall = 1), "V", sep="")
+
 
       # Plot complete data from YAML file ####################################
-      plot_annotation_x <- 0.05*max(input_data_filtered$time)
+      plot_annotation_x <- 0.5*max(input_data_filtered$time)
+      plot_annotation_x_minmax <- 0.1*max(input_data_filtered$time)
       xaxis_lab <- ifelse(test = show_time_in_us,yes = "time/\U00B5s", no = "time/s")
 
       plot_waveform <- ggplot2::ggplot(data = input_data_filtered,
@@ -209,9 +215,14 @@ plotWaveforms <- function(input_data = NULL,
         geom_hline(yintercept=max_value, linetype="dashed", color = "darkgray", size=1) +
         geom_hline(yintercept=min_value, linetype="dashed", color = "darkgray", size=1) +
         geom_hline(yintercept=mean_value, linetype="dotdash", color = "darkgray", size=1) +
-        annotate("text", x=plot_annotation_x, y=(voltage_limits_of_plot-2), label=p2p_value) +
+        annotate("text", x=plot_annotation_x, y=(voltage_limits_of_plot-1), label=p2p_value) +
+        annotate("text", x=plot_annotation_x_minmax, y=(max_value-1), label=max_value_text) +
+        annotate("text", x=plot_annotation_x_minmax, y=(min_value+1), label=min_value_text) +
+        annotate("text", x=plot_annotation_x, y=-0.5, label=mean_value_value_text) +
         coord_cartesian(ylim = c(-voltage_limits_of_plot, voltage_limits_of_plot)) +
-        labs(title=paste(plot_title_without_date, input_data_filtered$date_time[1], sep=" "),
+        # labs(title=paste(plot_title_without_date, input_data_filtered$date_time[1], sep=" "),
+        #      x = xaxis_lab, y = "U/V") +
+        labs(title=paste(plot_title, format(as.POSIXct(input_data_filtered$date_time[1]), format = "%H:%M:%S"), sep=" "),
              x = xaxis_lab, y = "U/V") +
         theme_bw() +
         theme(axis.text.x = element_text(angle=90, vjust = 0.5),
@@ -251,9 +262,13 @@ plotWaveforms <- function(input_data = NULL,
   if(is.na(p2p_value)){
     p2p_value <- 0
   }
-  p2p_value <- format(round(p2p_value, digits = 2), nsmall = 2)
+  p2p_value <- format(round(p2p_value, digits = 1), nsmall = 1)
   p2p_value <- paste("V_p2p=", p2p_value, "V", sep="")
 
+  max_value_text <- paste("V_max=", format(round(max_value, digits = 1), nsmall = 1), "V", sep="")
+  min_value_text <- paste("V_min=", format(round(min_value, digits = 1), nsmall = 1), "V", sep="")
+
+
   # Calculate mean
   if(start_point_function_generator_pulse == end_point_function_generator_pulse){
     df_dummy <- input_data %>%
@@ -269,12 +284,14 @@ plotWaveforms <- function(input_data = NULL,
     mean_value <- mean(df_dummy$U)
   }
 
+  mean_value_value_text <- paste("V_mean=", format(round(mean_value, digits = 1), nsmall = 1), "V", sep="")
 
 
 
 
-  # Plot complete data from YAML file ####################################
-  plot_annotation_x <- 0.05*max(input_data$time)
+  # Plot complete data from YAML file ######################################
+  plot_annotation_x <- 0.5*max(input_data$time)
+  plot_annotation_x_minmax <- 0.1*max(input_data$time)
 
   plot_waveform <- ggplot2::ggplot(data = input_data,
                                    aes(x = time, y = U, color=Channel)) +
@@ -283,9 +300,12 @@ plotWaveforms <- function(input_data = NULL,
     geom_hline(yintercept=max_value, linetype="dashed", color = "darkgray") +
     geom_hline(yintercept=min_value, linetype="dashed", color = "darkgray") +
     geom_hline(yintercept=mean_value, linetype="dotdash", color = "darkgray", size=1) +
-    annotate("text", x=plot_annotation_x, y=(voltage_limits_of_plot-2), label=p2p_value) +
+    annotate("text", x=plot_annotation_x, y=(voltage_limits_of_plot-1), label=p2p_value) +
+    annotate("text", x=plot_annotation_x_minmax, y=(max_value-1), label=max_value_text) +
+    annotate("text", x=plot_annotation_x_minmax, y=(min_value+1), label=min_value_text) +
+    annotate("text", x=plot_annotation_x, y=-0.5, label=mean_value_value_text) +
     coord_cartesian(ylim = c(-voltage_limits_of_plot, voltage_limits_of_plot)) +
-    labs(title=paste(plot_title, sep=" "),
+    labs(title=plot_title,
          x = xaxis_lab, y = "U/V") +
     theme_bw() +
     theme(axis.text.x = element_text(angle=90, vjust = 0.5),

diff --git a/inst/testscriptDevelop.R b/inst/testscriptDevelop.R
@@ -1,7 +1,7 @@
 # Testscript for using the R package oscilloscopeR for development  ++++++++++++++
 # Author: Kai Budde
 # Created: 2022/04/19
-# Last changed: 2022/04/21
+# Last changed: 2023/08/01
 
 # Delete everything in the environment
 rm(list = ls())
@@ -11,18 +11,18 @@ graphics.off()
 # Load packages ############################################################
 
 # Set groundhog day for reproducibility (see https://groundhogr.com)
-groundhog.day <- "2022-03-01"
+groundhog.day <- "2023-01-01"
 
 if(!any(grepl(pattern = "groundhog", x = installed.packages(), ignore.case = TRUE))){
   install.packages("groundhog")
 }
 
+# Load packages
 # Load packages
 library(groundhog)
-pkgs <- c("tidyverse", "yaml", "ggplot2", "devtools", "scattermore")
+pkgs <- c("tidyverse", "yaml", "scattermore", "devtools")
 groundhog.library(pkgs, groundhog.day)
 
-
 # Package development ######################################################
 
 # Check package
@@ -36,18 +36,48 @@ devtools::load_all()
 
 # Please adapt the following parameters ####################################
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-# YAML File
-input_file <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/IonOptixMeasurements/1_GateOut/20211203-110117-measurement.yml"
-input_file <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/IonOptixMeasurements/1_GateOut/20211203-110117-wave.yml"
-
 # ZIP File (containing yaml files)
-input_file <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/CellBioShortStimI.zip"
-
-# Directory (containing yaml files)
-input_directory <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/01_hotMedium_hotElectrodes"
+input_zip_file <- file.path("inst", "testdata","recorded_stimulation.zip")
+
+# # YAML File
+# # input_file <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/IonOptixMeasurements/1_GateOut/20211203-110117-measurement.yml"
+# # input_file <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/IonOptixMeasurements/1_GateOut/20211203-110117-wave.yml"
+#
+# # ZIP File (containing yaml files)
+# input_file <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/CellBioShortStimI.zip"
+#
+# # Directory (containing yaml files)
+# input_directory <- "C:/Users/Kai/Documents/git/gitHub/OscilloscopeRecordings/data/01_hotMedium_hotElectrodes"
 
 # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# Measurement data ---------------------------------------------------------
+# Zip file
+df_data <- getMeasurements(input_file = input_zip_file)
+# Plot measurement data
+plotMeasurements(input_data = df_data)
+
+
+# Waveform data ------------------------------------------------------------
+df_data <- getWaveforms(input_file = input_zip_file)
+
+# Plot wave form data
+plotWaveforms(input_data = df_data,
+              plot_waveforms = "one")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 ### Test small functions ---------------------------------------------------
 
 # Get Vavg (average voltage) and Vpp (peak-to-peak voltage) and plot the data
@@ -60,3 +90,51 @@ df_data <- getWaveforms(input_file = input_file)
 df_data <- getWaveforms(input_directory = input_directory)
 plotWaveforms(input_data = df_data, channel_function_generator = "CHAN2",
               channel_stimulation_pulse = "CHAN1")
+
+
+### Plotting IonOptix Measurements ---------------------------------------------------
+
+# Version of R package oscilloscopeR: 0.1.0
+input_directory <- "C:/Users/Kai/Documents/git/gitHub/SI_IonOptix_Measurements/IonOptixMeasurements/1_GateOut"
+df_data <- getMeasurements(input_directory = input_directory)
+plotMeasurements(input_data = df_data)
+
+df_data <- getWaveforms(input_directory = input_directory)
+plotWaveforms(input_data = df_data, epsilon = 0.01, channel_stimulation_pulse = "CHAN1",
+              channel_function_generator = "CHAN2")
+
+
+input_directory <- "C:/Users/Kai/Documents/git/gitHub/SI_IonOptix_Measurements/IonOptixMeasurements/2_GateAndAux"
+df_data <- getMeasurements(input_directory = input_directory)
+plotMeasurements(input_data = df_data)
+
+df_data <- getWaveforms(input_directory = input_directory)
+plotWaveforms(input_data = df_data, epsilon = 0.01, channel_stimulation_pulse = "CHAN1",
+              channel_function_generator = "CHAN2")
+
+
+input_directory <- "C:/Users/Kai/Documents/git/gitHub/SI_IonOptix_Measurements/IonOptixMeasurements/3_Reihenmessung"
+df_data <- getMeasurements(input_directory = input_directory)
+plotMeasurements(input_data = df_data)
+
+df_data <- getWaveforms(input_directory = input_directory)
+plotWaveforms(input_data = df_data, epsilon = 0.01, channel_stimulation_pulse = "CHAN1",
+              channel_function_generator = "CHAN2")
+
+
+input_directory <- "C:/Users/Kai/Documents/git/gitHub/SI_IonOptix_Measurements/IonOptixMeasurements/4_Breakoutbox_trocken/a1c1"
+df_data <- getMeasurements(input_directory = input_directory)
+plotMeasurements(input_data = df_data)
+
+df_data <- getWaveforms(input_directory = input_directory)
+plotWaveforms(input_data = df_data, epsilon = 0.01, channel_stimulation_pulse = "CHAN3",
+              channel_function_generator = "CHAN2")
+
+plot_waveform <- ggplot2::ggplot(data = df_data,
+                                 aes(x = time, y = U, color=Channel)) +
+  geom_line() +
+  theme_bw() +
+  theme(axis.text.x = element_text(angle=90, vjust = 0.5),
+        plot.title = element_text(hjust = 0.5))
+
+
diff --git a/man/plotWaveforms.Rd b/man/plotWaveforms.Rd