private void analyze() {
if (WindowManager.getCurrentImage() != null) {
RConnection c = RServe.getConnection();
if (c != null) {
/* Special method to reuse the GUI method! */
IJTranserResultsTable.runParticleAnalysis(
c,
"run(\"Analyze Particles...\", \"size=0-Infinity circularity=0.00-1.00 show=Nothing display clear\")");
try {
c.eval("assign(paste0('Particles'," + count + ",sep=''),Particles)");
} catch (RserveException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
}
public void run() {
IPreferenceStore store = Bio7Plugin.getDefault().getPreferenceStore();
RConnection con = RServe.getConnection();
// boolean rPipe = store.getBoolean("r_pipe");
if (con == null) {
String selectionConsole = ConsolePageParticipant.getInterpreterSelection();
if (selectionConsole.equals("R")) {
String selected = null;
Shell s = new Shell();
FileDialog fd = new FileDialog(s, SWT.SAVE);
if (ApplicationWorkbenchWindowAdvisor.getOS().equals("Windows")) {
prefs = Preferences.userNodeForPackage(this.getClass());
String lastOutputDir = prefs.get("R_FILE_DIR", "");
fd.setFilterPath(lastOutputDir);
String[] filterExt = {"*.RData"};
fd.setFilterExtensions(filterExt);
fd.setOverwrite(true);
selected = fd.open();
prefs.put("R_FILE_DIR", fd.getFilterPath());
if (selected != null) {
selected = selected.replace("\\", "\\\\");
// selected = selected.replace("ä", "ae");
// selected = selected.replace("ü", "ue");
// selected = selected.replace("ö", "oe");
ConsolePageParticipant.pipeInputToConsole(
"save.image(file =\"" + selected + "\", version = NULL, ascii = FALSE)",
true,
true);
System.out.print(
"save.image(file =\"" + selected + "\", version = NULL, ascii = FALSE)");
System.out.println();
}
} else {
prefs = Preferences.userNodeForPackage(this.getClass());
String lastOutputDir = prefs.get("R_FILE_DIR", "");
fd.setFilterPath(lastOutputDir);
String[] filterExt = {"*.RData"};
fd.setFilterExtensions(filterExt);
fd.setOverwrite(true);
selected = fd.open();
prefs.put("R_FILE_DIR", fd.getFilterPath());
if (selected != null) {
ConsolePageParticipant.pipeInputToConsole(
"save.image(file =\"" + selected + "\", version = NULL, ascii = FALSE)",
true,
true);
System.out.print(
"save.image(file =\"" + selected + "\", version = NULL, ascii = FALSE)");
System.out.println();
}
}
ConsolePageParticipant.pipeInputToConsole("load(file = \"" + selected + "\")", true, true);
} else {
Bio7Dialog.message(
"Please start the \"Native R\" shell in the Bio7 console or the Rserve connection!");
}
} else {
saveRWorkspace();
}
}