diff extract_ipm_date_interval.R @ 0:4dccc60b3525 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_ipm_date_interval.R	Tue Jul 31 14:36:56 2018 -0400
@@ -0,0 +1,77 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("data.table"))
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("--input_dir"), action="store", dest="input_dir", help="Directory containing .csv outputs from insect_phenology_model"),
+    make_option(c("--start_date"), action="store", dest="start_date", default=NULL, help="Start date for custom date interval"),
+    make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory")
+)
+
+parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
+args <- parse_args(parser, positional_arguments=TRUE);
+opt <- args$options;
+
+get_new_temperature_data_frame = function(input_file) {
+    temperature_data_frame = read.csv(file=input_file, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
+    colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
+    return(temperature_data_frame);
+}
+
+# Import the shared utility functions.
+utils_path <- paste(opt$script_dir, "utils.R", sep="/");
+source(utils_path);
+
+# FIXME: currently custom date fields are free text, but
+# Galaxy should soon include support for a date selector
+# at which point this tool should be enhanced to use it.
+# Validate start_date.
+
+# Calaculate the number of days in the date interval.
+start_date = validate_date(opt$start_date);
+# Validate end_date.
+end_date = validate_date(opt$end_date);
+if (start_date >= end_date) {
+    stop_err("The start date must be between 1 and 50 days before the end date when setting date intervals for plots.");
+}
+# Calculate the number of days in the date interval.
+num_days = difftime(end_date, start_date, units=c("days"));
+# Add 1 to the number of days to make the dates inclusive.  For
+# example, if the user enters a date range of 2018-01-01 to
+# 2018-01-31, they likely expect the end date to be included.
+num_days = num_days + 1;
+if (num_days > 50) {
+    # We need to restrict date intervals since
+    # plots render tick marks for each day.
+    stop_err("Date intervals for plotting cannot exceed 50 days.");
+}
+# Display the total number of days in the Galaxy history item blurb.
+cat("Number of days in date interval: ", num_days, "\n");
+
+# Get the year from the start_date.
+year = get_year_from_date(start_date);
+# Get the DOY for start_date and end_date.
+start_date_doy = as.integer(strftime(start_date, format="%j"));
+end_date_doy = as.integer(strftime(end_date, format="%j"));
+# Get the ticks date labels for plots.
+ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, date_interval=TRUE);
+ticks = c(unlist(ticks_and_labels[1]));
+date_labels = c(unlist(ticks_and_labels[2]));
+# All latitude values are the same, so get the value
+# for plots from the first row.
+latitude = temperature_data_frame$LATITUDE[1];
+
+input_files = list.files(path=input_dir, full.names=TRUE);
+for(input_file in input_files) {
+    temperature_data_frame = get_new_temperature_data_frame(input_file);
+    start_date_row = which(temperature_data_frame$DATE==start_date);
+    end_date_row = which(temperature_data_frame$DATE==end_date);
+    # Extract the date interval.
+    temperature_data_frame = temperature_data_frame[start_date_row:end_date_row,];
+    # Save the date interval data into an output file
+    # named the same as the input.
+    file_path = paste("output_data_dir", input_file, sep="/");
+    write.csv(temperature_data_frame, file=file_path, row.names=F);
+    # TODO: Save the dat interval plots...
+}