• Created by Unknown User (oconnort), last modified on Feb 16, 2010

Autogeneration of cycles is one of the more advanced and, consequently, more powerful features of Ephus. It is relatively straightforward to write a function to generate a cycle. There are essentially only two tasks that need to be done. First is to create a series of pulses and second is to map those pulses into a cycle. A new autogenerated cycle can be created using the following steps, including some finishing touches to make the function especially user-friendly:

  • Gather the necessary variables; these often include the pulseJacker handle and the required sampleRate.
mapperObj = getGlobal(progmanager, 'hObject', 'mapper', 'mapper');
sampleRate = getLocalBatch(progmanager, mapperObj, 'sampleRate');
pj = getGlobal(progmanager, 'hObject', 'pulseJacker', 'pulseJacker');
  • Identify the full path to the target pulseSet (the location in which the new pulses will be stored).
destDir = getDefaultCacheDirectory(progmanager, 'myCustomPulses');%Use a cached value, to reduce the need to prompt the user.
if strcmpi(destDir, pwd)
     destDir = getDefaultCacheDirectory(progmanager, 'pulseDir'); %Use the pulseEditor's cached directory if this function's cached value is just Matlab's current directory (the default).
end
destDir = uigetdir(destDir, 'Choose a pulseSet for the destination of new pulses.'); %Prompt the user to choose a directory, defaulting to the cached value.
if length(destDir) == 1
     if destDir == 0
          return; %The user has cancelled the directory selection, take that as a queue to quit the function completely.
     end
end

%Test that the directory is valid before proceeding.
if exist(destDir, 'dir')
     error('pulseDest must be a valid directory: ''%s'' does not exist.', destDir);
end
setDefaultCacheValue(progmanager, 'myCustomPulses', destDir); %Update the cached value, for the subsequent calls to this function.
[pulseDir, pulseSetName] = fileparts(destDir); %Hold on to these values for later use.
  • Create pulses, which will get re-used within a loop.
channel1Pulse = signalobject('Name', 'myCustomCycleChan1', 'repeatable', 0, 'sampleRate', sampleRate);
channel2Pulse = signalobject('Name', 'myCustomCycleChan2', 'repeatable', 0, 'sampleRate', sampleRate);
  • Configure the pulses, within a loop, and save them to the selected directory.
for i = 1 : 10
     set(channel1Pulse , 'Name', ['myCustomCycleChan1' num2str(i)]); %Update the pulse's name/number.
     set(channel2Pulse , 'Name', ['myCustomCycleChan2' num2str(i)]); %Update the pulse's name/number.
     %Set the pulse's values.
     dc(channel1Pulse , i);
     sin(channel1Pulse, i, 0, 1000, 0);
     %Now save the pulses.
     for signal = [channel1Pulse, channel2Pulse]
          fprintf(1, 'Writing pulse to disk - ''%s''...\n', get(signal, 'Name'));%Print an informative message for the user.
          saveCompatible(fullfile(destDir, [get(signal, 'Name') '.signal']), 'signal', '-mat');
     end
end
  • Pulse objects are pass-by-reference objects, and thus they represent a potential memory leak in Matlab. It is good practice to delete them when they are no longer needed.
delete(channel1Pulse);
delete(channel2Pulse);
  • Create a new cycle in the pulseJacker.
%This will prompt the user to name the cycle, and potentially overwrite an existing one.
if ~pj_new(pj)
     %The pj_new command was cancelled or failed. Don't go overwriting an existing cycle if someone cancelled.
     return;
end

%Make sure the pulse path matches where we just made new pulses.
pj_setPulsePath(pj, pulseDir);
fprintf(1, 'Creating associated cycle ''%s''...\n', getLocal(progmanager, pj, 'cycleName'));%Print a message for the user.

%Get the list of channels that are in the pulseJacker.
channels = getLocalGh(progmanager, pj, 'currentChannel', 'String');
  • Populate the new cycle, mapping the created pulses to the correct channels and cycle positions.
for i = 1 : 10
fprintf(1, 'Creating cycle position %s...\n', num2str(i) ); %Print a message for the user.

pj_newPosition(pj);%Create a new cycle position.
%Iterate over the channels, there may be configured channels that will not be used during this cycle.
for j = 1 : length(channels)
     fprintf(1, 'Configuring pulse for channel ''%s''...\n', channels{j});
          %Select the channel we want to edit.
          pj_currentChannel(pj, channels{j});
          %Set the pulseSet for this channel.
          pj_setPulseSetName(pj, pulseSetName);%pulseSetName was defined earlier, when selecting the pulse destination.
          %Depending on which channel we currently have selected, choose the appropriate pulse.
          %Only operate on the channels of interest.
          if endsWithIgnoreCase(channels{j}, ':myChannel1')
               pj_setPulseName(pj, ['myCustomCycleChan1', num2str(i)]);
          elseif endsWithIgnoreCase(channels{j}, ':myChannel2')
               pj_setPulseName(pj, ['myCustomCycleChan2', num2str(i)]);
          end
     end
end

%Make things nice for the user, so it's ready to go immediately.
pj_currentPosition(pj, 1);%Set the new cycle to the first position.
pj_currentChannel(pj, channels{1});%Set the new cycle to the first channel.
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