Update Python integration to PsPM UI

src/pspm_cfg/pspm_cfg_pp_heart_data.m

@@ -1,8 +1,7 @@
 
 function pp_heart_data = pspm_cfg_pp_heart_data
 
-% $Id: pspm_cfg_pp_heart_data.m 784 2019-07-08 08:16:46Z esrefo $
-% $Rev: 784 $
+% Updated 27-Mar-2024 by Teddy
 
 % Initialise
 global settings
@@ -192,12 +191,29 @@
     'Heart beat conversion, or directly work on heart beat time stamps, ', ...
     'for example obtained by a pulse oxymeter.']};
 
+%% ppg2hb
+ppg2hb_heartpy      = pspm_cfg_python(1,'HeartPy');
+
+ppg2hb_classic      = cfg_const;
+ppg2hb_classic.name = 'Classic';
+ppg2hb_classic.tag  = 'classic';
+ppg2hb_classic.val  = {0};
+ppg2hb_classic.help = {'Analyse the data with the classic mode.'};
+
+ppg2hb_method       = cfg_choice;
+ppg2hb_method.name  = 'Select the method of converting the data';
+ppg2hb_method.tag   = 'method';
+ppg2hb_method.val   = {ppg2hb_classic};
+ppg2hb_method.values    = {ppg2hb_classic, ppg2hb_heartpy};
+ppg2hb_method.help  = {['Convert the PPG data into heart rate by using the ', ...
+                          'selected method.']};
+
 ppg2hb_chan         = pspm_cfg_channel_selector('peripheral pulse oxymetry');
 
 ppg2hb              = cfg_exbranch;
-ppg2hb.name         = 'Convert Peripheral pulse oximetry to Heart Beat';
+ppg2hb.name         = 'Convert peripheral pulse oximetry to Heart Beat';
 ppg2hb.tag          = 'ppg2hb';
-ppg2hb.val          = {ppg2hb_chan};
+ppg2hb.val          = {ppg2hb_chan, ppg2hb_method};
 ppg2hb.help          = {['Convert Peripheral pulse oximetry to ', ...
     'Heart Beat events.']};
 

src/pspm_cfg/pspm_cfg_python.m

@@ -0,0 +1,67 @@
+function out = pspm_cfg_python(varargin)
+% ● Description
+%   pspm_cfg_python is a GUI function that provides UI controls for
+%   python definition
+% ● Format
+%   out = pspm_cfg_python
+%   out = pspm_cfg_python(default_auto)
+%   out = pspm_cfg_python(python_package)
+%   out = pspm_cfg_python(default_auto, python_package)
+% ● Arguments
+%   default_auto:   [logical] The logical value that determines whether the 
+%                   to automatically detect python. If not determined, it 
+%                   will be set as 1. 
+%   python_package: [string] the python package PsPM wants to use.
+%   out:            [struct] The UI struct variable for python detection.
+% ● History
+%   Written on 08-04-2024 by Teddy
+
+%% Input checking
+switch length(varargin)
+  case 0
+    default_auto      = 1;
+    python_package    = 'Python';
+  case 1
+    switch class(varargin{1})
+      case 'double'
+        default_auto  = varargin{1};
+        python_package= 'Python';
+      case 'char'
+        default_auto  = 1;
+        python_package= varargin{1};
+    end
+  case 2
+    default_auto      = varargin{1};
+    python_package    = varargin{2};
+  otherwise
+    warning('ID:invalid_input', 'Up to one input variable is allowed');
+end
+%% Structs
+% automatically detect python
+ppg2hb_py_auto        = cfg_const;
+ppg2hb_py_auto.name   = 'Automatically detect Python';
+ppg2hb_py_auto.tag    = 'pypath_auto';
+ppg2hb_py_auto.val    = {0};
+ppg2hb_py_auto.help   = {['This only works if a Python environment ',...
+                          'already exists in Matlab, created by ',...
+                          'previous PsPM function calls or manually.']};
+% manually detect python
+pspm_py_path          = cfg_files;
+pspm_py_path.name     = 'Manually define Python';
+pspm_py_path.tag      = 'pypath';
+pspm_py_path.num      = [1 1];
+pspm_py_path.help     = {'Please specify python executable file on the computer.'};
+% the struct of python detection
+pspm_py_detect        = cfg_choice;
+if default_auto
+  pspm_py_detect.val  = {ppg2hb_py_auto};
+else
+  pspm_py_detect.val  = {pspm_py_path};
+end
+pspm_py_detect.values = {ppg2hb_py_auto, pspm_py_path};
+pspm_py_detect.name   = python_package;
+pspm_py_detect.tag    = python_package;
+pspm_py_detect.help   = {['Use ',python_package,' to analyse the input data. ',...
+                          'Please select how to detect Python in the following.']};
+%% Output
+out = pspm_py_detect;

src/pspm_cfg/pspm_cfg_run_pp_heart_data.m

@@ -1,5 +1,5 @@
 function out = pspm_cfg_run_pp_heart_data(job)
-% Updated on 08-01-2024 by Teddy
+% Updated on 26-03-2024 by Teddy
 fn = job.datafile{1};
 outputs = cell(size(job.pp_type));
 for i = 1:numel(job.pp_type)
@@ -64,6 +64,14 @@
         end
       case 'ppg2hb'
         options = struct();
+        if ~isfield(job.pp_type{i}.ppg2hb.method, 'HeartPy')
+          options.method = 'classic';
+        else
+          options.method = 'heartpy';
+          if isfield(job.pp_type{i}.ppg2hb.method.HeartPy, 'pypath')
+            options.python_path = job.pp_type{i}.ppg2hb.method.HeartPy.pypath{1};
+          end
+        end
         options.channel = chan;
         options = pspm_update_struct(options, job, {'channel_action'});
         [sts, winfo] = pspm_convert_ppg2hb(fn, options);
@@ -76,4 +84,4 @@
     end
   end
 end
-out = {fn};
+out = {fn};

src/pspm_check_python.m

@@ -1,18 +1,22 @@
 function sts = pspm_check_python(pythonPath)
-    % pspm_check_python Checks and sets the Python environment if path is provided.
+    % ● Description
+    %   pspm_check_python Checks and sets the Python environment if path is provided.
     %
-    % This function checks the current Python environment setup in MATLAB.
-    % If a specific Python executable path is provided, the function attempts
-    % to update the Python environment to use the provided path.
-    % It returns a status argument sts with values 0 or 1.
+    %   This function checks the current Python environment setup in MATLAB.
+    %   If a specific Python executable path is provided, the function attempts
+    %   to update the Python environment to use the provided path.
+    %   It returns a status argument sts with values 0 or 1.
     %
-    % Arguments:
+    % ● Arguments
     %   pythonPath - A string specifying the path to the Python executable.
     %                If this is empty or not provided, the function simply
     %                reports the current Python environment without making changes.
     %
-    % Returns:
+    % ● Returns
     %   sts - Status of the operation (1 for success, 0 for failure).
+    %
+    % ● History
+    %   Written in 2024 by Dominik R Bach (Uni Bonn)
 
     % Initialize the status to failure
     sts = 0;

src/pspm_check_python_modules.m

@@ -1,31 +1,48 @@
-function moduleNames = pspm_check_python_modules()
-    % pspm_check_python_modules Returns a list of currently imported Python modules in MATLAB.
+function [sts, moduleNames] = pspm_check_python_modules(module)
+    % ● Description
+    %   pspm_check_python_modules Returns a list of currently imported Python modules in MATLAB.
     %
-    % This function retrieves and returns the names of Python modules that have been imported
-    % into the current MATLAB session. 
+    %   This function retrieves and returns the names of Python modules that have been imported
+    %   into the current MATLAB session. If a module name is provided as
+    %   argument, will try to load this module of not already loaded
+    %
+    % ● History
+    %   Written in 2024 by Dominik R Bach (Uni Bonn)
 
-    % Initialize return variable
+    % Initialize return variables
+    sts = 0;
     moduleNames = {};
 
     try
         % Ensure Python is correctly set up in MATLAB
         pe = pyenv();
-        if strcmp(pe.Version, "")
-            fprintf('Python environment does not exist. Run ''pspm_check_python()'' to ensure that the environment is correctly set up.\n');
+         if strcmp(pe.Version, '')
+             warning('Python environment does not exist. Run ''pspm_check_python()'' to ensure that the environment is correctly set up.\n');
             return;
-        elseif ~strcmp(pe.Status, "Loaded")
+        elseif ~strcmp(pe.Status, 'Loaded')
             fprintf('No module is loaded yet.\n');
-            return;
         else
             % Get the dictionary of imported Python modules
             modulesDict = py.sys.modules;
             moduleNamesList = py.list(modulesDict.keys());
             moduleNames = cell(moduleNamesList);
+            moduleNames = cellfun(@(x) char(x), moduleNames, 'UniformOutput', false);
 
             % Print confirmation message
             fprintf('Python modules have been successfully retrieved. Total modules: %d\n', numel(moduleNames));
         end
     catch ME
         fprintf('An error occurred while retrieving Python modules: %s\n', ME.message);
+        return
+    end
+
+    if nargin > 0 && ischar(module) && ~ismember(module, moduleNames)
+        try
+            py.importlib.import_module(module);
+        catch ME
+            warning('An error occurred while loading Python modules: %s\n', ME.message);
+            return
+        end
     end
+    sts = 1;
 end