added telemetry to matlab converters

matlab/dcm2niix4pet.m

@@ -54,24 +54,24 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 end
 
 if ~ispc % overwrite if not windowns (as it should be in the computer path)
-    dcm2niixpath = '/usr/local/bin/dcm2niix';
+    dcm2niixpath = 'dcm2niix';
 end
 
 % we rely on more recent version of dcm2niix, certain pet fields are unavailable in the sidecar jsons for versions
 % before v1.0.20220720
 
 minimum_version = 'v1.0.20220720';
 minimum_version_date = datetime(minimum_version(6:end), 'InputFormat', 'yyyyMMdd');
-%version_cmd = ['dcm2niix', ' -v']; % TODO fix this as it's not detecting dcm2niix running matlab on osx as of matlab v2023b.
-version_cmd = ['/usr/local/bin/dcm2niix', ' -v'];
+version_cmd = ['dcm2niix', ' -v'];
 
 [status, version_output_string] = system(version_cmd);
-version = regexp(version_output_string, 'v[0-9].[0-9].{8}[0-9]', 'match'); % TODO this returns an array with two of the same versions
+version = regexp(version_output_string, 'v[0-9].[0-9].{8}[0-9]', 'match');
+
 
 % initalize telemetry data fror later uploading
 telemetry_data = {};
 dcm2niix_data = {};
-dcm2niix_data.version = version;
+dcm2niix_data.version = version(1);
 dcm2niix_data.returncode = 0;
 telemetry_data.dcm2niix = dcm2niix_data;
 telemetry_data.description = "Matlab_dcm2niix4pet.m"

matlab/ecat2nii.m

@@ -58,6 +58,10 @@
 parts = strsplit(ecat_save_steps_dir, filesep);
 ecat_save_steps_dir = strjoin([parts(1:end-2), 'ecat_testing', 'steps'], filesep);
 
+%% initialize telemetry variable for reporting
+telemetry_data = {};
+telemetry_data.description = "Matlab_ecat2nii";
+
 %% check inputs
 % ------------
 
@@ -131,14 +135,18 @@
 %% Read and write data
 % --------------------
 for j=1:length(FileListIn)
-    
+
     try
         fprintf('Conversion of file: %s\n',FileListIn{j});
-        
+
         % quickly ensure we have the TimeZero - key to all analyzes!
         info     = MetaList{1};
         if ~isfield(info,'TimeZero')
-            error('Metadata TimeZero is missing - set to ScanStart or empty to use the scanning time as injection time')
+            error_text = 'Metadata TimeZero is missing - set to ScanStart or empty to use the scanning time as injection time';
+            telemetry_data.returncode = 1;
+            telemetry_data.error = error_text;
+            telemetry(telemetry_data, FileListIn{j})
+            error(error_text)
         end
 
         % Read ECAT file headers
@@ -180,6 +188,9 @@
             end
         end
 
+        % capture ecat version
+        telemetry_data.InputType = append("ECAT", string(mh.sw_version));
+
         % save debugging steps 6 and 7
         if (ecat_save_steps == '1')
             first_middle_last_frames_to_text_cell(data,ecat_save_steps_dir, '6_ecat2nii_matlab');
@@ -206,8 +217,6 @@
             fclose(fid);
         end
 
-
-
         % save debugging step 8 - rescale to 16 bits
         if (ecat_save_steps == '1')
             first_middle_last_frames_to_text(img_temp,ecat_save_steps_dir, '8_rescale_to_16_ecat2nii_matlab');
@@ -489,8 +498,14 @@
         %     FileListOut{j} = [filenameout '_pet.nii'];
         %     niftiwrite(img_temp,FileListOut{j},info,'Endian','little','Compressed',false);
         % end
+
+        telemetry_data.returncode = 0;
+        telemetry(telemetry_data, FileListIn{j});
 
     catch conversionerr
+        telemetry_data.returncode = 1;
+        telemetry_data.error = conversionerr.message;
+        telemetry(telemetry_data, FileListIn{j});
         FileListOut{j} = sprintf('%s failed to convert:%s',FileListIn{j},conversionerr.message, conversionerr.stack.line);
     end