263 telementry add tracking of code usage

.github/workflows/phantoms.yaml

@@ -67,12 +67,6 @@ jobs:
             brew install dcm2niix
           fi
 
-      - name: Debug
-        uses: mxschmitt/action-tmate@v3
-        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
-        timeout-minutes: 15
-        with:
-          limit-access-to-actor: true
 
       - name: Check dcm2niix is installed and on path
         if: runner.os != 'Windows'
@@ -106,10 +100,10 @@ jobs:
           dcm2niix4pet -h
 
       - name: Set Up Node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
 
       - name: Install BIDS Validator
-        run: npm install -g bids-validator
+        run: npm install -g bids-validator@1.14.6
 
       - name: Collect Phantoms
         if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }}
@@ -170,6 +164,13 @@ jobs:
         run: |
           bids-validator OpenNeuroPET-Phantoms/python
 
+      - name: Debug
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
       - name: Validate Matlab Conversion
         run: |
           bids-validator OpenNeuroPET-Phantoms/matlab

matlab/dcm2niix4pet.m

@@ -12,7 +12,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 %
 % :param FolderList: Cell array of char strings with filenames and paths
 % :param MetaList: Cell array of structures for metadata
-% :param options:
+% :param varargin:
 %   - *deletedcm*  to be 'on' or 'off'
 %   - *o*         the output directory or cell arrays of directories
 %                 IF the folder is BIDS sub-xx files are renamed automatically
@@ -30,6 +30,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 %   - *w*          = 2;      % write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix)
 %   - *x*          = 'n';    % crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquisitions)
 %   - *z*          = 'n';    % gz compress images (y/o/i/n/3, default y) [y=pigz, o=optimal pigz, i=internal:miniz, n=no, 3=no,3D]
+% - *notrack* Opt-out of sending tracking information of this run to the PET2BIDS developers. This information helps to improve PET2BIDS and provides an indicator of real world usage crucial for obtaining funding."
 %
 % .. code-block::
 %
@@ -50,7 +51,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 
 dcm2niixpath = 'D:\MRI\MRIcroGL12win\Resources\dcm2niix.exe'; % for windows machine indicate here, where is dcm2niix
 if ispc && ~exist(dcm2niixpath,'file')
-    error('for windows machine please edit the function line 42 and indicate the dcm2niix path')
+    error('for windows machine please edit the function line 51 and indicate the dcm2niix path')
 end
 
 if ~ispc % overwrite if not windowns (as it should be in the computer path)
@@ -63,9 +64,19 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 minimum_version = 'v1.0.20220720';
 minimum_version_date = datetime(minimum_version(6:end), 'InputFormat', 'yyyyMMdd');
 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');
 
+
+% initialize telemetry data fror later uploading
+telemetry_data = {};
+dcm2niix_data = {};
+dcm2niix_data.version = version(1);
+dcm2niix_data.returncode = 0;
+telemetry_data.dcm2niix = dcm2niix_data;
+telemetry_data.description = "Matlab_dcm2niix4pet.m"
+
 if length(version) >= 1
     version_date = version{1}(6:end);
     version_date = datetime(version_date, 'InputFormat', 'yyyyMMdd');
@@ -209,7 +220,12 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
         end
     elseif strcmpi(varargin{var},'o')
         outputdir = varargin{var+1};
+    elseif strcmpi(varargin{var},'notrack')
+        setenv('TELEMETRY_ENABLED', 'False')
+    else
+        error('unknown option %s',varargin{var})
     end
+
 end
 
 if isempty(outputdir)
@@ -225,6 +241,8 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     end
 end
 
+
+
 %% convert
 % ----------
 for folder = 1:size(FolderList,1)
@@ -249,10 +267,16 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     end
 
     out = system(command);
+    telemetry_data.dcm2niix.returncode = out;
+    % we still want to send telemetry even if this fails
     if out ~= 0
+        telemetry_data.returncode = 1;
+        telemetry(telemetry_data, folder);
         error('%s did not run properly',command)
+
     end
-
+
+
     % deal with dcm files
     dcmfiles = dir(fullfile(FolderList{folder},'*.dcm'));
     if isempty(dcmfiles) % since sometimes they have no ext :-(
@@ -318,4 +342,9 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
         jsonfilename = newmetadata;
     end
     updatejsonpetfile(jsonfilename,MetaList,dcminfo);
+
+    % if this all goes well update the telemetry data and send it with a positive return code of 0
+    telemetry_data.returncode = 0;
+    telemetry(telemetry_data, FolderList{folder})
+
 end

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
 % ------------
 
@@ -110,6 +114,8 @@
         gz = varargin{v+1};
     elseif strcmpi(varargin{v},'savemat')
         savemat = varargin{v+1};
+    elseif strcmpi(varargin{v},'notrack')
+        setenv('TELEMETRY_ENABLED', 'False')
     end
 end
 
@@ -131,14 +137,18 @@
 %% 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 +190,9 @@
             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 +219,6 @@
             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 +500,14 @@
         %     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
 

matlab/telemetry.m

@@ -0,0 +1,87 @@
+function telemetry(telemetry_data, input_path, output_path)
+    arguments
+        telemetry_data (1,:) struct
+        input_path (1,:) string = ''
+        output_path (1,:) string = ''
+    end
+
+    if telemetry_enabled
+        % do all the things
+
+        telemetry_data.description = "Matlab";
+
+        if strcmp(input_path, '')
+            % do nothing
+        else
+            input_file_count = count_input_files(input_path);
+            telemetry_data.TotalInputFiles = input_file_count.TotalInputFiles;
+            telemetry_data.TotalInputFileSize = input_file_count.TotalInputFileSize;
+        end
+
+        url = 'http://openneuropet.org/pet2bids/';
+        options = weboptions('MediaType', 'application/json');
+        response = webwrite(url, telemetry_data, options);
+
+    else
+        % don't do anything
+    end
+end
+
+function e = telemetry_enabled()
+    % checks to see if the telemetry is enabled or disabled 
+    environment = getenv();
+    % check environment too before loading the config file
+    if isfield(environment, 'TELEMETRY_ENABLED')
+        disable_telemetry_env = strcmpi(getenv("TELEMETRY_ENABLED"), 'false');
+    else
+        disable_telemetry_env = false;
+    end
+
+    home_dir = environment("HOME");
+    try
+        loadenv(fullfile(home_dir, '.pet2bidsconfig'), FileType='env');
+        % convert string to boolean/logical
+    catch ME
+        disable_telemetry = false;
+    end
+
+    disable_telemetry = strcmpi(getenv("TELEMETRY_ENABLED"), 'false');
+
+    if disable_telemetry | disable_telemetry_env
+        e = false;
+    else
+        e = true;
+    end 
+
+end
+
+
+function c = count_input_files(input_path)
+    % generate a list of all the files in the input directory
+    % count the number of files in the input directory
+    % count the total size of the files in the input directory
+    % return the count and the size
+
+    % if the input path is a file then return 1 and the size of the file
+    if isfile(input_path)
+        input_file = dir(input_path);
+        c.TotalInputFiles = 1;
+        c.TotalInputFileSize = input_file.bytes;
+        return
+    elseif isfolder(input_path)
+        % get the list of files in the input directory
+        input_files = dir(input_path);
+        % count the number of files in the input directory
+        file_count = length(input_files);
+        % count the total size of the files in the input directory
+        total_size = 0;
+        for i = 1:file_count
+            total_size = total_size + input_files(i).bytes;
+        end
+        c.TotalInputFiles = file_count;
+        c.TotalInputFileSize = total_size;
+        return
+    else
+        error('Input path is not a file or a directory');
+    end
+end

metadata/PET_Radionuclide.mkd

@@ -2,41 +2,41 @@
 
 Table taken from https://dicom.nema.org/medical/Dicom/2016b/output/chtml/part16/sect_CID_4020.html
 
-| Code Value |  Code Meaning   |
-|:----------:|:---------------:|
-| C-105A1    | ^11^Carbon      |
-| C-107A1    | ^13^Nitrogen    |  
-| C-1018C    | ^14^Oxygen      | 
-| C-B1038    | ^15^Oxygen      |
-| C-111A1    | ^18^Fluorine    |
-| C-155A1    | ^22^Sodium      |
-| C-135A4    | ^38^Potassium   |
-| 126605     | ^43^Scandium    |
-| 126600     | ^44^Scandium    |
-| C-166A2    | ^45^Titanium    |
-| 126601     | ^51^Manganese   |
-| C-130A1    | ^52^Iron        |
-| C-149A1    | ^52^Manganese   |
-| 126607     | ^52m^Manganese  |
-| C-127A4    | ^60^Copper      |
-| C-127A1    | ^61^Copper      |
-| C-127A5    | ^62^Copper      |
-| C-141A1    | ^62^Zinc        |
-| C-127A     | ^64^Copper      |
-| C-131A1    | ^66^Gallium     |
-| C-131A3    | ^68^Gallium     |
-| C-128A2    | ^68^Germanium   |
-| 126602     | ^70^Arsenic     |
-| C-115A2    | ^72^Arsenic     |
-| C-116A2    | ^73^Selenium    |
-| C-113A1    | ^75^Bromine     |
-| C-113A2    | ^76^Bromine     |
-| C-113A3    | ^77^Bromine     |
-| C-159A2    | ^82^Rubidium    |
-| C-162A3    | ^86^Yttrium     |
-| C-168A4    | ^89^Zirconium   |
-| 126603     | ^90^Niobium     |
-| C-162A7    | ^90^Yttrium     |
-| C-163AA    | ^94m^Technetium |
-| C-114A5    | ^124^Iodine     |
-| 126606     | ^152^Terbium    |
+| Code Value |  Code Meaning   | Isotope Abbreviation |
+|:----------:|:---------------:|:--------------------:|
+| C-105A1    | ^11^Carbon      | 11C                  |
+| C-107A1    | ^13^Nitrogen    | 13N                  |
+| C-1018C    | ^14^Oxygen      | 14O                  |
+| C-B1038    | ^15^Oxygen      | 150                  |
+| C-111A1    | ^18^Fluorine    | 18F                  |
+| C-155A1    | ^22^Sodium      | 22Na                 |
+| C-135A4    | ^38^Potassium   | 38K                  |
+| 126605     | ^43^Scandium    | 43Sc                 |
+| 126600     | ^44^Scandium    | 44Sc                 |
+| C-166A2    | ^45^Titanium    | 45Ti                 |
+| 126601     | ^51^Manganese   | 51Mn                 |
+| C-130A1    | ^52^Iron        | 52Fe                 |
+| C-149A1    | ^52^Manganese   | 52Mn                 |
+| 126607     | ^52m^Manganese  | 52mMn                |
+| C-127A4    | ^60^Copper      | 60Cu                 |
+| C-127A1    | ^61^Copper      | 61Cu                 |
+| C-127A5    | ^62^Copper      | 62Cu                 |
+| C-141A1    | ^62^Zinc        | 62Zn                 |
+| C-127A     | ^64^Copper      | 64Cu                 |
+| C-131A1    | ^66^Gallium     | 66Ga                 |
+| C-131A3    | ^68^Gallium     | 68Ga                 |
+| C-128A2    | ^68^Germanium   | 68Ge                 |
+| 126602     | ^70^Arsenic     | 70As                 |
+| C-115A2    | ^72^Arsenic     | 72As                 |
+| C-116A2    | ^73^Selenium    | 73Se                 |
+| C-113A1    | ^75^Bromine     | 75Br                 |
+| C-113A2    | ^76^Bromine     | 76Br                 |
+| C-113A3    | ^77^Bromine     | 77Br                 |
+| C-159A2    | ^82^Rubidium    | 82Rb                 |
+| C-162A3    | ^86^Yttrium     | 86Y                  |
+| C-168A4    | ^89^Zirconium   | 89Zr                 |
+| 126603     | ^90^Niobium     | 90Nb                 |
+| C-162A7    | ^90^Yttrium     | 90Y                  |
+| C-163AA    | ^94m^Technetium | 94mTc                |
+| C-114A5    | ^124^Iodine     | 124I                 |
+| 126606     | ^152^Terbium    | 152Tb                |