From c6c6df5c4b857af3a10b1f03ef734a11ee25f903 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 18 Jul 2024 16:42:59 -0400
Subject: [PATCH 01/20] added telemetry call

---
 pypet2bids/pypet2bids/dcm2niix4pet.py | 32 +++++++++
 pypet2bids/pypet2bids/telemetry.py    | 94 +++++++++++++++++++++++++++
 2 files changed, 126 insertions(+)
 create mode 100644 pypet2bids/pypet2bids/telemetry.py

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index a05380d..e1a1f77 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -42,6 +42,7 @@
         metadata_dictionaries,
         get_metadata_from_spreadsheet,
     )
+    from telemetry import send_telemetry, count_input_files, enable_disable_telemetry, count_output_files
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
     import pypet2bids.is_pet as is_pet
@@ -54,6 +55,7 @@
         metadata_dictionaries,
         get_metadata_from_spreadsheet,
     )
+    from pypet2bids.telemetry import send_telemetry, count_input_files, enable_disable_telemetry, count_output_files
 
 logger = helper_functions.logger("pypet2bids")
 
@@ -319,6 +321,7 @@ def __init__(
                 # next we use the loaded python script to extract the information we need
                 self.load_spread_sheet_data()
         elif metadata_path and not metadata_translation_script or metadata_path == "":
+            self.metadata_path = Path(metadata_path)
             if not self.spreadsheet_metadata.get("nifti_json", None):
                 self.spreadsheet_metadata["nifti_json"] = {}
 
@@ -833,9 +836,38 @@ def post_dcm2niix(self):
                 json.dump(blood_json_data, outfile, indent=4)
 
     def convert(self):
+        # check the size of out the output folder
+        before_output_files = {}
+        if self.destination_path.exists():
+            before_output_files = count_output_files(self.destination_path)
         self.run_dcm2niix()
         self.post_dcm2niix()
 
+        # if telemetry isn't disabled we send a telemetry event to the pypet2bids server
+        if enable_disable_telemetry:
+            # count the number of files
+            data_out = count_input_files(self.image_folder)
+            # record if a blood tsv and json file were created
+            if self.spreadsheet_metadata.get("blood_tsv", {}):
+                data_out["blood_tsv"] = True
+            if self.spreadsheet_metadata.get("blood_json", {}):
+                data_out["blood_json"] = True
+            # record if a metadata spreadsheet was used
+            if self.metadata_path == "" or self.metadata_path is not None:
+                data_out["metadata_spreadsheet_used"] = True
+
+            # count the output files
+            after_output_files = count_output_files(self.destination_path)
+
+            if before_output_files != {}:
+                for key, value in after_output_files.items():
+                    data_out[key] = abs(after_output_files[key] - before_output_files[key])
+
+            send_telemetry(data_out)
+
+
+
+
     def match_dicom_header_to_file(self, destination_path=None):
         """
         Matches a dicom header to a nifti or json file produced by dcm2niix, this is run after dcm2niix converts the
diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
new file mode 100644
index 0000000..8d132a3
--- /dev/null
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -0,0 +1,94 @@
+import requests
+import os
+import pathlib
+from dotenv import load_dotenv
+from typing import Union
+
+
+# collect pet2bids version
+from pypet2bids.helper_functions import get_version
+
+
+def enable_disable_telemetry(config_path=None):
+    # load dcm2niix file
+    if not config_path:
+        config_file = pathlib.Path.home() / ".pet2bidsconfig"
+    else:
+        config_file = pathlib.Path(config_path)
+
+    if config_file.exists():
+        load_dotenv(dotenv_path=config_file)
+
+    # check to see if telemetry is disabled
+    if os.getenv("PET2BIDS_TELEMETRY_ENABLED") == "False".upper():
+        return False
+    else:
+        return True
+
+
+def send_telemetry(json_data: dict, url: str = "http://52.87.154.236/telemetry/"):
+    if enable_disable_telemetry():
+        # update data with version of pet2bids
+        json_data['pypet2bids_version'] = get_version()
+        # Send a POST request to the telemetry server
+        requests.post(url, json=json_data)
+    else:
+        pass
+
+
+def count_input_files(input_file_path: Union[str, pathlib.Path]):
+    # Count the number of input files in the input file path
+    if isinstance(input_file_path, str):
+        input_file_path = pathlib.Path(input_file_path)
+
+    if input_file_path.is_dir():
+        # collect all files in the input dir
+        all_files = [f for f in input_file_path.iterdir()]
+        # count the number of dicom files
+        num_dicom_files = 0
+        dicom_files_size = 0
+        total_files = 0
+        total_files_size = 0
+        for file in all_files:
+            if file.is_file():
+                total_files += 1
+                total_files_size += file.stat().st_size
+                if file.suffix == ".dcm" or file.suffix == ".ima" or file.suffix == ".img" or file.suffix == "":
+                    num_dicom_files += 1
+                    dicom_files_size += file.stat().st_size
+    return {
+        "TotalInputFiles": total_files,
+        "TotalInputFilesSize": total_files_size,
+        "DicomFiles": num_dicom_files,
+        "DicomFilesSize": dicom_files_size
+    }
+
+
+def count_output_files(output_file_path: Union[str, pathlib.Path]):
+    if isinstance(output_file_path, str):
+        output_file_path = pathlib.Path(output_file_path)
+
+    if output_file_path.is_file():
+        output_file_path = output_file_path.parent
+
+    if output_file_path.is_dir():
+        # collect all files in the output dir
+        all_files = [f for f in output_file_path.iterdir()]
+        # count the number nifti files
+        num_nifti_files = 0
+        nifti_files_size = 0
+        total_files = 0
+        total_files_size = 0
+        for file in all_files:
+            if file.is_file():
+                total_files += 1
+                total_files_size += file.stat().st_size
+                if file.suffix == ".nii" or file.suffix == ".nii.gz":
+                    num_nifti_files += 1
+                    nifti_files_size += file.stat().st_size
+    return {
+        "TotalOutputFiles": total_files,
+        "TotalOutputFilesSize": total_files_size,
+        "NiftiFiles": num_nifti_files,
+        "NiftiFilesSize": nifti_files_size
+    }
\ No newline at end of file

From 5a84ebbe5611ebaf07dd9e763f51703f76fa821e Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Fri, 19 Jul 2024 17:59:07 -0400
Subject: [PATCH 02/20] added file count to telemetery tracking for dcm2niix

---
 pypet2bids/pypet2bids/dcm2niix4pet.py | 25 +++++++++++--------------
 pypet2bids/pypet2bids/telemetry.py    | 15 +++++----------
 2 files changed, 16 insertions(+), 24 deletions(-)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index e1a1f77..7c43bc6 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -204,7 +204,7 @@ def __init__(
         # check to see if dcm2niix is installed
         self.blood_json = None
         self.blood_tsv = None
-
+        self.telemetry_data = {}
         self.dcm2niix_path = self.check_for_dcm2niix()
         if not self.dcm2niix_path:
             logger.error(
@@ -455,10 +455,15 @@ def run_dcm2niix(self):
             file_format_args = ""
         with TemporaryDirectory(dir=self.tempdir_location) as tempdir:
             tempdir_pathlike = Path(tempdir)
+            self.tempdir_location = tempdir_pathlike
             # people use screwy paths, we do this before running dcm2niix to account for that
             image_folder = helper_functions.sanitize_bad_path(self.image_folder)
             cmd = f"{self.dcm2niix_path} -b y -w 1 -z y {file_format_args} -o {tempdir_pathlike} {image_folder}"
             convert = subprocess.run(cmd, shell=True, capture_output=True)
+            self.telemetry_data['dcm2niix'] = {
+                "returncode": convert.returncode,
+            }
+            self.telemetry_data.update(count_output_files(self.tempdir_location))
 
             if convert.returncode != 0:
                 print(
@@ -838,32 +843,24 @@ def post_dcm2niix(self):
     def convert(self):
         # check the size of out the output folder
         before_output_files = {}
-        if self.destination_path.exists():
-            before_output_files = count_output_files(self.destination_path)
         self.run_dcm2niix()
         self.post_dcm2niix()
 
         # if telemetry isn't disabled we send a telemetry event to the pypet2bids server
         if enable_disable_telemetry:
             # count the number of files
-            data_out = count_input_files(self.image_folder)
+            self.telemetry_data.update(count_input_files(self.image_folder))
             # record if a blood tsv and json file were created
             if self.spreadsheet_metadata.get("blood_tsv", {}):
-                data_out["blood_tsv"] = True
+                self.telemetry_data["blood_tsv"] = True
             if self.spreadsheet_metadata.get("blood_json", {}):
-                data_out["blood_json"] = True
+                self.telemetry_data["blood_json"] = True
             # record if a metadata spreadsheet was used
             if self.metadata_path == "" or self.metadata_path is not None:
-                data_out["metadata_spreadsheet_used"] = True
-
-            # count the output files
-            after_output_files = count_output_files(self.destination_path)
+                self.telemetry_data["metadata_spreadsheet_used"] = True
 
-            if before_output_files != {}:
-                for key, value in after_output_files.items():
-                    data_out[key] = abs(after_output_files[key] - before_output_files[key])
 
-            send_telemetry(data_out)
+            send_telemetry(self.telemetry_data)
 
 
 
diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index 8d132a3..746a9b3 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -53,14 +53,9 @@ def count_input_files(input_file_path: Union[str, pathlib.Path]):
             if file.is_file():
                 total_files += 1
                 total_files_size += file.stat().st_size
-                if file.suffix == ".dcm" or file.suffix == ".ima" or file.suffix == ".img" or file.suffix == "":
-                    num_dicom_files += 1
-                    dicom_files_size += file.stat().st_size
     return {
         "TotalInputFiles": total_files,
         "TotalInputFilesSize": total_files_size,
-        "DicomFiles": num_dicom_files,
-        "DicomFilesSize": dicom_files_size
     }
 
 
@@ -79,13 +74,13 @@ def count_output_files(output_file_path: Union[str, pathlib.Path]):
         nifti_files_size = 0
         total_files = 0
         total_files_size = 0
-        for file in all_files:
-            if file.is_file():
+        for f in all_files:
+            if f.is_file():
                 total_files += 1
-                total_files_size += file.stat().st_size
-                if file.suffix == ".nii" or file.suffix == ".nii.gz":
+                total_files_size += f.stat().st_size
+                if str(f).endswith('.nii') or str(f).endswith('.nii.gz'):
                     num_nifti_files += 1
-                    nifti_files_size += file.stat().st_size
+                    nifti_files_size += f.stat().st_size
     return {
         "TotalOutputFiles": total_files,
         "TotalOutputFilesSize": total_files_size,

From 6b53ba4af4c14bb403322e9df2a39ebe0660423f Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 24 Jul 2024 19:13:00 -0400
Subject: [PATCH 03/20] added python functionality

---
 pypet2bids/pypet2bids/dcm2niix4pet.py     | 32 +++++++++++++++--------
 pypet2bids/pypet2bids/ecat.py             | 26 ++++++++++++++++++
 pypet2bids/pypet2bids/helper_functions.py | 10 +++----
 pypet2bids/pypet2bids/telemetry.py        | 24 ++++++++++++-----
 4 files changed, 69 insertions(+), 23 deletions(-)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index 7c43bc6..bb2b0e9 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -42,7 +42,12 @@
         metadata_dictionaries,
         get_metadata_from_spreadsheet,
     )
-    from telemetry import send_telemetry, count_input_files, enable_disable_telemetry, count_output_files
+    from telemetry import (
+        send_telemetry,
+        count_input_files,
+        telemetry_enabled,
+        count_output_files,
+    )
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
     import pypet2bids.is_pet as is_pet
@@ -55,7 +60,12 @@
         metadata_dictionaries,
         get_metadata_from_spreadsheet,
     )
-    from pypet2bids.telemetry import send_telemetry, count_input_files, enable_disable_telemetry, count_output_files
+    from pypet2bids.telemetry import (
+        send_telemetry,
+        count_input_files,
+        telemetry_enabled,
+        count_output_files,
+    )
 
 logger = helper_functions.logger("pypet2bids")
 
@@ -460,7 +470,7 @@ def run_dcm2niix(self):
             image_folder = helper_functions.sanitize_bad_path(self.image_folder)
             cmd = f"{self.dcm2niix_path} -b y -w 1 -z y {file_format_args} -o {tempdir_pathlike} {image_folder}"
             convert = subprocess.run(cmd, shell=True, capture_output=True)
-            self.telemetry_data['dcm2niix'] = {
+            self.telemetry_data["dcm2niix"] = {
                 "returncode": convert.returncode,
             }
             self.telemetry_data.update(count_output_files(self.tempdir_location))
@@ -847,24 +857,24 @@ def convert(self):
         self.post_dcm2niix()
 
         # if telemetry isn't disabled we send a telemetry event to the pypet2bids server
-        if enable_disable_telemetry:
+        if telemetry_enabled:
             # count the number of files
             self.telemetry_data.update(count_input_files(self.image_folder))
             # record if a blood tsv and json file were created
-            if self.spreadsheet_metadata.get("blood_tsv", {}):
+            if self.spreadsheet_metadata.get("blood_tsv", {}) != {}:
                 self.telemetry_data["blood_tsv"] = True
-            if self.spreadsheet_metadata.get("blood_json", {}):
-                self.telemetry_data["blood_json"] = True
+            else:
+                self.telemetry_data["blood_tsv"] = False
             # record if a metadata spreadsheet was used
-            if self.metadata_path == "" or self.metadata_path is not None:
+            if helper_functions.collect_spreadsheets(self.metadata_path):
                 self.telemetry_data["metadata_spreadsheet_used"] = True
+            else:
+                self.telemetry_data["metadata_spreadsheet_used"] = False
 
+            self.telemetry_data["InputType"] = "DICOM"
 
             send_telemetry(self.telemetry_data)
 
-
-
-
     def match_dicom_header_to_file(self, destination_path=None):
         """
         Matches a dicom header to a nifti or json file produced by dcm2niix, this is run after dcm2niix converts the
diff --git a/pypet2bids/pypet2bids/ecat.py b/pypet2bids/pypet2bids/ecat.py
index a900dbd..2b01c37 100644
--- a/pypet2bids/pypet2bids/ecat.py
+++ b/pypet2bids/pypet2bids/ecat.py
@@ -25,6 +25,7 @@
         get_metadata_from_spreadsheet,
         check_meta_radio_inputs,
     )
+    from telemetry import telemetry_enabled, send_telemetry
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
     import pypet2bids.sidecar as sidecar
@@ -35,6 +36,7 @@
         get_metadata_from_spreadsheet,
         check_meta_radio_inputs,
     )
+    from pypet2bids.telemetry import telemetry_enabled, send_telemetry
 
 from dateutil import parser
 
@@ -107,6 +109,8 @@ def __init__(
         self.output_path = None
         self.metadata_path = metadata_path
 
+        self.telemetry_data = {}
+
         # load config file
         default_json_path = helper_functions.check_pet2bids_config(
             "DEFAULT_METADATA_JSON"
@@ -169,6 +173,12 @@ def __init__(
         else:
             self.nifti_file = nifti_file
 
+        self.telemetry_data["InputType"] = "ECAT" + str(self.ecat_header["SV_VERSION"])
+        self.telemetry_data["TotalInputFiles"] = 1
+        self.telemetry_data["TotalInputFilesSize"] = (
+            pathlib.Path(self.ecat_file).stat().st_size
+        )
+
         # que up metadata path for spreadsheet loading later
         if self.metadata_path:
             if (
@@ -198,6 +208,16 @@ def __init__(
                 load_spreadsheet_data["blood_json"]
             )
 
+            if helper_functions.collect_spreadsheets(self.metadata_path):
+                self.telemetry_data.update({"metadata_spreadsheet_user": True})
+            else:
+                self.telemetry_data.update({"metadata_spreadsheet_user": False})
+
+            if self.spreadsheet_metadata.get("blood_tsv", None):
+                self.telemetry_data.update({"blood_tsv": True})
+            else:
+                self.telemetry_data.update({"blood_tsv": False})
+
     def make_nifti(self, output_path=None):
         """
         Outputs a nifti from the read in ECAT file.
@@ -221,6 +241,9 @@ def make_nifti(self, output_path=None):
             affine=self.affine,
         )
 
+        self.telemetry_data["NiftiFiles"] = 1
+        self.telemetry_data["NiftiFilesSize"] = pathlib.Path(output).stat().st_size
+
         if "nii.gz" not in output:
             output = helper_functions.compress(output)
 
@@ -653,3 +676,6 @@ def convert(self):
         self.prune_sidecar()
         self.show_sidecar(output_path=self.sidecar_path)
         self.write_out_blood_files()
+
+        if telemetry_enabled:
+            send_telemetry(self.telemetry_data)
diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index 2a28ec3..8a7d5c3 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -959,11 +959,11 @@ def ad_hoc_checks(
     if items_that_should_be_checked is None:
         items_that_should_be_checked = {}
     hardcoded_items = {
-        'InjectedRadioactivityUnits': ['MBq', 'mCi'],
-        'SpecificRadioactivityUnits': ['Bq/g', 'MBq/ug'],
-        'InjectedMassUnits': 'ug',
-        'MolarActivityUnits': 'GBq/umolug',
-        'MolecularWeightUnits': 'g/mol'
+        "InjectedRadioactivityUnits": ["MBq", "mCi"],
+        "SpecificRadioactivityUnits": ["Bq/g", "MBq/ug"],
+        "InjectedMassUnits": "ug",
+        "MolarActivityUnits": "GBq/umolug",
+        "MolecularWeightUnits": "g/mol",
     }
 
     # if none are
diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index 746a9b3..2913979 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -1,6 +1,7 @@
 import requests
 import os
 import pathlib
+import subprocess
 from dotenv import load_dotenv
 from typing import Union
 
@@ -9,7 +10,7 @@
 from pypet2bids.helper_functions import get_version
 
 
-def enable_disable_telemetry(config_path=None):
+def telemetry_enabled(config_path=None):
     # load dcm2niix file
     if not config_path:
         config_file = pathlib.Path.home() / ".pet2bidsconfig"
@@ -20,16 +21,25 @@ def enable_disable_telemetry(config_path=None):
         load_dotenv(dotenv_path=config_file)
 
     # check to see if telemetry is disabled
-    if os.getenv("PET2BIDS_TELEMETRY_ENABLED") == "False".upper():
+    if os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false":
         return False
     else:
         return True
 
 
 def send_telemetry(json_data: dict, url: str = "http://52.87.154.236/telemetry/"):
-    if enable_disable_telemetry():
+    if telemetry_enabled():
         # update data with version of pet2bids
-        json_data['pypet2bids_version'] = get_version()
+        json_data["pypet2bids_version"] = get_version()
+        # check if it's one of the dev's running this
+        running_from_cloned_repository = subprocess.run(
+            ["git", "status"], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL
+        )
+        if running_from_cloned_repository.returncode == 0:
+            json_data["running_from_cloned_repository"] = True
+
+        json_data["description"] = "pet2bids_python_telemetry"
+
         # Send a POST request to the telemetry server
         requests.post(url, json=json_data)
     else:
@@ -78,12 +88,12 @@ def count_output_files(output_file_path: Union[str, pathlib.Path]):
             if f.is_file():
                 total_files += 1
                 total_files_size += f.stat().st_size
-                if str(f).endswith('.nii') or str(f).endswith('.nii.gz'):
+                if str(f).endswith(".nii") or str(f).endswith(".nii.gz"):
                     num_nifti_files += 1
                     nifti_files_size += f.stat().st_size
     return {
         "TotalOutputFiles": total_files,
         "TotalOutputFilesSize": total_files_size,
         "NiftiFiles": num_nifti_files,
-        "NiftiFilesSize": nifti_files_size
-    }
\ No newline at end of file
+        "NiftiFilesSize": nifti_files_size,
+    }

From b3bf9af43bcc929229f8816d2df4a5dfa1d00854 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 1 Aug 2024 17:44:20 -0400
Subject: [PATCH 04/20] matlab is being weird and not finding dcm2niix on path

---
 matlab/dcm2niix4pet.m                 | 31 +++++++++--
 matlab/telemetry.m                    | 75 +++++++++++++++++++++++++++
 pypet2bids/pypet2bids/dcm2niix4pet.py |  2 +
 3 files changed, 103 insertions(+), 5 deletions(-)
 create mode 100644 matlab/telemetry.m

diff --git a/matlab/dcm2niix4pet.m b/matlab/dcm2niix4pet.m
index ebb7b9e..2baf951 100644
--- a/matlab/dcm2niix4pet.m
+++ b/matlab/dcm2niix4pet.m
@@ -50,11 +50,11 @@ 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)
-    dcm2niixpath = 'dcm2niix';
+    dcm2niixpath = '/usr/local/bin/dcm2niix';
 end
 
 % we rely on more recent version of dcm2niix, certain pet fields are unavailable in the sidecar jsons for versions
@@ -62,9 +62,19 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 
 minimum_version = 'v1.0.20220720';
 minimum_version_date = datetime(minimum_version(6:end), 'InputFormat', 'yyyyMMdd');
-version_cmd = ['dcm2niix', ' -v'];
+%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'];
+
 [status, version_output_string] = system(version_cmd);
-version = regexp(version_output_string, 'v[0-9].[0-9].{8}[0-9]', 'match');
+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
+
+% initalize telemetry data fror later uploading
+telemetry_data = {};
+dcm2niix_data = {};
+dcm2niix_data.version = version;
+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);
@@ -249,10 +259,16 @@ 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 +334,9 @@ 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
diff --git a/matlab/telemetry.m b/matlab/telemetry.m
new file mode 100644
index 0000000..dd61758
--- /dev/null
+++ b/matlab/telemetry.m
@@ -0,0 +1,75 @@
+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://52.87.154.236/telemetry/';
+        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();
+    home_dir = environment("HOME");
+    loadenv(fullfile(home_dir, '.pet2bidsconfig'), FileType='env');
+    % convert string to boolean/logical
+    disable_telemetry = strcmpi(getenv("PET2BIDS_TELEMETRY_ENABLED"), 'false');
+    
+    if disable_telemetry
+        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
diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index bb2b0e9..e31bda0 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -873,6 +873,8 @@ def convert(self):
 
             self.telemetry_data["InputType"] = "DICOM"
 
+            self.telemetry_data["returncode"] = 0
+
             send_telemetry(self.telemetry_data)
 
     def match_dicom_header_to_file(self, destination_path=None):

From 8550942db3bfe00641ed033e45c779a3c3b258e0 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Fri, 2 Aug 2024 15:13:57 -0400
Subject: [PATCH 05/20] added telemetry to matlab converters

---
 matlab/dcm2niix4pet.m | 10 +++++-----
 matlab/ecat2nii.m     | 25 ++++++++++++++++++++-----
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/matlab/dcm2niix4pet.m b/matlab/dcm2niix4pet.m
index 2baf951..08bad7f 100644
--- a/matlab/dcm2niix4pet.m
+++ b/matlab/dcm2niix4pet.m
@@ -54,7 +54,7 @@ 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
@@ -62,16 +62,16 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 
 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"
diff --git a/matlab/ecat2nii.m b/matlab/ecat2nii.m
index acfd52f..34222f7 100644
--- a/matlab/ecat2nii.m
+++ b/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
     

From 272780acb19681be7aae2cda7084d5865a094b80 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Fri, 2 Aug 2024 16:41:52 -0400
Subject: [PATCH 06/20] fixe typo, bump version

---
 pypet2bids/poetry.lock        | 109 +++++++++++++++++-----------------
 pypet2bids/pypet2bids/ecat.py |   2 +-
 pypet2bids/pyproject.toml     |   2 +-
 3 files changed, 56 insertions(+), 57 deletions(-)

diff --git a/pypet2bids/poetry.lock b/pypet2bids/poetry.lock
index f0e7fba..c644a2c 100644
--- a/pypet2bids/poetry.lock
+++ b/pypet2bids/poetry.lock
@@ -24,13 +24,13 @@ files = [
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.15.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
+    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
 ]
 
 [package.dependencies]
@@ -64,13 +64,13 @@ virtualenv = ["virtualenv (>=20.0.35)"]
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.7.4"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
-    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
+    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
 ]
 
 [[package]]
@@ -207,13 +207,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
 ]
 
 [package.extras]
@@ -243,22 +243,22 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.1.0"
+version = "8.2.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-7.1.0-py3-none-any.whl", hash = "sha256:30962b96c0c223483ed6cc7280e7f0199feb01a0e40cfae4d4450fc6fab1f570"},
-    {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
+    {file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"},
+    {file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"},
 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "importlib-resources"
@@ -291,13 +291,13 @@ files = [
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
-    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
+    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
+    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
 ]
 
 [package.dependencies]
@@ -308,13 +308,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "joblib"
-version = "1.4.0"
+version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "joblib-1.4.0-py3-none-any.whl", hash = "sha256:42942470d4062537be4d54c83511186da1fc14ba354961a2114da91efa9a4ed7"},
-    {file = "joblib-1.4.0.tar.gz", hash = "sha256:1eb0dc091919cd384490de890cb5dfd538410a6d4b3b54eef09fb8c50b409b1c"},
+    {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
+    {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
 ]
 
 [[package]]
@@ -480,13 +480,13 @@ files = [
 
 [[package]]
 name = "openpyxl"
-version = "3.1.2"
+version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "openpyxl-3.1.2-py2.py3-none-any.whl", hash = "sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5"},
-    {file = "openpyxl-3.1.2.tar.gz", hash = "sha256:a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184"},
+    {file = "openpyxl-3.1.5-py2.py3-none-any.whl", hash = "sha256:5282c12b107bffeef825f4617dc029afaf41d0ea60823bbb665ef3079dc79de2"},
+    {file = "openpyxl-3.1.5.tar.gz", hash = "sha256:cf0e3cf56142039133628b5acffe8ef0c12bc902d2aadd3e0fe5878dc08d1050"},
 ]
 
 [package.dependencies]
@@ -494,13 +494,13 @@ et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
-version = "24.0"
+version = "24.1"
 description = "Core utilities for Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
-    {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
+    {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
+    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
 ]
 
 [[package]]
@@ -607,17 +607,16 @@ docs = ["matplotlib", "numpy", "numpydoc", "pillow", "sphinx", "sphinx-copybutto
 
 [[package]]
 name = "pygments"
-version = "2.17.2"
+version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
-    {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
+    {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"},
+    {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"},
 ]
 
 [package.extras]
-plugins = ["importlib-metadata"]
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -655,13 +654,13 @@ hook-testing = ["execnet (>=1.5.0)", "psutil", "pytest (>=2.7.3)"]
 
 [[package]]
 name = "pyinstaller-hooks-contrib"
-version = "2024.5"
+version = "2024.7"
 description = "Community maintained hooks for PyInstaller"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pyinstaller_hooks_contrib-2024.5-py2.py3-none-any.whl", hash = "sha256:0852249b7fb1e9394f8f22af2c22fa5294c2c0366157969f98c96df62410c4c6"},
-    {file = "pyinstaller_hooks_contrib-2024.5.tar.gz", hash = "sha256:aa5dee25ea7ca317ad46fa16b5afc8dba3b0e43f2847e498930138885efd3cab"},
+    {file = "pyinstaller_hooks_contrib-2024.7-py2.py3-none-any.whl", hash = "sha256:8bf0775771fbaf96bcd2f4dfd6f7ae6c1dd1b1efe254c7e50477b3c08e7841d8"},
+    {file = "pyinstaller_hooks_contrib-2024.7.tar.gz", hash = "sha256:fd5f37dcf99bece184e40642af88be16a9b89613ecb958a8bd1136634fc9fac5"},
 ]
 
 [package.dependencies]
@@ -768,13 +767,13 @@ files = [
 
 [[package]]
 name = "requests"
-version = "2.31.0"
+version = "2.32.3"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
-    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+    {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
+    {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"},
 ]
 
 [package.dependencies]
@@ -827,19 +826,19 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "69.5.1"
+version = "72.1.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-69.5.1-py3-none-any.whl", hash = "sha256:c636ac361bc47580504644275c9ad802c50415c7522212252c033bd15f301f32"},
-    {file = "setuptools-69.5.1.tar.gz", hash = "sha256:6c1fccdac05a97e598fb0ae3bbed5904ccb317337a51139dcd51453611bbb987"},
+    {file = "setuptools-72.1.0-py3-none-any.whl", hash = "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1"},
+    {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -1059,13 +1058,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.2.2"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
+    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
 ]
 
 [package.extras]
@@ -1092,18 +1091,18 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.19.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
+    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
diff --git a/pypet2bids/pypet2bids/ecat.py b/pypet2bids/pypet2bids/ecat.py
index 2b01c37..efbc2ea 100644
--- a/pypet2bids/pypet2bids/ecat.py
+++ b/pypet2bids/pypet2bids/ecat.py
@@ -173,7 +173,7 @@ def __init__(
         else:
             self.nifti_file = nifti_file
 
-        self.telemetry_data["InputType"] = "ECAT" + str(self.ecat_header["SV_VERSION"])
+        self.telemetry_data["InputType"] = "ECAT" + str(self.ecat_header["SW_VERSION"])
         self.telemetry_data["TotalInputFiles"] = 1
         self.telemetry_data["TotalInputFilesSize"] = (
             pathlib.Path(self.ecat_file).stat().st_size
diff --git a/pypet2bids/pyproject.toml b/pypet2bids/pyproject.toml
index bc8e236..95760d0 100644
--- a/pypet2bids/pyproject.toml
+++ b/pypet2bids/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.12"
+version = "1.3.13dev"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"]
 license = "MIT"

From 62791ec61475b0722f35f1fac77c5ca193123c33 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 7 Aug 2024 19:40:20 -0400
Subject: [PATCH 07/20] added option to opt out of telemetry

---
 pypet2bids/pypet2bids/helper_functions.py |  3 +-
 pypet2bids/pypet2bids/telemetry.py        | 90 ++++++++++++++++++++++-
 2 files changed, 88 insertions(+), 5 deletions(-)

diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index 8a7d5c3..46afbf5 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -15,6 +15,7 @@
 | *Copyright OpenNeuroPET team*
 """
 
+
 import os
 import gzip
 import re
@@ -285,7 +286,7 @@ def decompress(file_like_object, output_path: str = None):
     return output_path
 
 
-def load_vars_from_config(path_to_config: str):
+def load_vars_from_config(path_to_config: str=pathlib.Path.home() / ".pet2bidsconfig"):
     """
     Loads values from a .env file given a path to said .env file.
 
diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index 2913979..6bdd1c6 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -2,15 +2,65 @@
 import os
 import pathlib
 import subprocess
+import time
+import sys
+import select
 from dotenv import load_dotenv
 from typing import Union
 
 
-# collect pet2bids version
-from pypet2bids.helper_functions import get_version
+try:
+    from helper_functions import get_version, load_vars_from_config, modify_config_file
+except ModuleNotFoundError:
+    # collect pet2bids version
+    from pypet2bids.helper_functions import get_version, load_vars_from_config, modify_config_file
+
+pet2bids_config = load_vars_from_config()
+telemetry_default_url = pet2bids_config.get("TELEMETRY_URL", "http://52.87.154.236/telemetry/")
+telemetry_enabled = pet2bids_config.get("TELEMETRY_ENABLED", True)
+telemetry_notify_user = pet2bids_config.get("NOTIFY_USER_OF_TELEMETRY", False)
+
+
+def ask_user_to_opt_out(timeout=10):
+    """Waits for user input for a specified number of seconds.
+
+    Args:
+        timeout: Number of seconds to wait for input.
+
+    Returns:
+        The user input if provided within the timeout, otherwise None.
+    """
+
+    print("Do you want to opt out of telemetry? (yes/no): ".format(timeout), end="", flush=True)
+    sys.stdout.flush()
+
+    ready, _, _ = select.select([sys.stdin], [], [], timeout)
+    if ready:
+        response = sys.stdin.readline().rstrip('\n')
+        if response.lower() == "yes":
+            return True
+    else:
+        return False
+
+
+if telemetry_notify_user is False:
+    opt_out = ask_user_to_opt_out()
+    if opt_out:
+        # update the config file
+        modify_config_file("TELEMETRY_ENABLED", False)
+
+    modify_config_file("NOTIFY_USER_OF_TELEMETRY", True)
 
 
 def telemetry_enabled(config_path=None):
+    """
+    Check if telemetry is enabled, if it isn't disabled in the .pet2bidsconfig file
+    it will be considered enabled. One must opt out of tracking usage manually.
+    :param config_path: The path to the config file
+    :type config_path: Union[str, pathlib.Path]
+    :return: Whether telemetry is enabled or not
+    :rtype: bool
+    """
     # load dcm2niix file
     if not config_path:
         config_file = pathlib.Path.home() / ".pet2bidsconfig"
@@ -27,7 +77,17 @@ def telemetry_enabled(config_path=None):
         return True
 
 
-def send_telemetry(json_data: dict, url: str = "http://52.87.154.236/telemetry/"):
+def send_telemetry(json_data: dict, url: str = telemetry_default_url):
+    """
+    Send telemetry data to the telemetry server, by default this will first try
+    to load the telemetry server url from the config file, if it's not found it will
+    default to the hardcoded value in this module. This will always send, unless a user
+    has disabled the pet2bids telemetry in the .pet2bidsconfig file.
+    :param json_data: The dat to be sent to the telemetry server
+    :type json_data: dict
+    :param url: The url of the telemetry server
+    :type url: str
+    """
     if telemetry_enabled():
         # update data with version of pet2bids
         json_data["pypet2bids_version"] = get_version()
@@ -47,7 +107,13 @@ def send_telemetry(json_data: dict, url: str = "http://52.87.154.236/telemetry/"
 
 
 def count_input_files(input_file_path: Union[str, pathlib.Path]):
-    # Count the number of input files in the input file path
+    """
+    Count the number of input files in the input file path
+    :param input_file_path: location of the input files
+    :type input_file_path: Union[str, pathlib.Path]
+    :return: The number of input files and their size
+    :rtype: dict
+    """
     if isinstance(input_file_path, str):
         input_file_path = pathlib.Path(input_file_path)
 
@@ -70,6 +136,20 @@ def count_input_files(input_file_path: Union[str, pathlib.Path]):
 
 
 def count_output_files(output_file_path: Union[str, pathlib.Path]):
+    """
+    Count the number of output files in the output file path. This can be usefull
+    in determining whether any additional files were created during the conversion process.
+    However, this is only useful if the conversion process initially takes place from within
+    a temporary directory.
+
+    # TODO check the last modified date of the files to determine if they were created during
+    # TODO the conversion process. That should make this usefull in all cases.
+    :param output_file_path: location of the output files
+    :type output_file_path: Union[str, pathlib.Path]
+    :return: The number of output files and their size and spefically the number of nifti files and
+    their size
+    :rtype: dict
+    """
     if isinstance(output_file_path, str):
         output_file_path = pathlib.Path(output_file_path)
 
@@ -97,3 +177,5 @@ def count_output_files(output_file_path: Union[str, pathlib.Path]):
         "NiftiFiles": num_nifti_files,
         "NiftiFilesSize": nifti_files_size,
     }
+
+

From e60aa57db36adf9b361550129e375bab3d23c201 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 12 Aug 2024 11:13:43 -0400
Subject: [PATCH 08/20] added cli flag and environment variable disabling of
 telemetry

---
 matlab/telemetry.m                        |  9 +++++++-
 pypet2bids/pypet2bids/dcm2niix4pet.py     | 11 ++++++++-
 pypet2bids/pypet2bids/ecat_cli.py         | 11 +++++++++
 pypet2bids/pypet2bids/helper_functions.py |  5 +++--
 pypet2bids/pypet2bids/telemetry.py        | 27 ++++++++++++++++++-----
 5 files changed, 53 insertions(+), 10 deletions(-)

diff --git a/matlab/telemetry.m b/matlab/telemetry.m
index dd61758..baebd18 100644
--- a/matlab/telemetry.m
+++ b/matlab/telemetry.m
@@ -30,12 +30,19 @@ function telemetry(telemetry_data, input_path, output_path)
 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, 'PET2BIDS_TELEMETRY_ENABLED')
+        disable_telemetry_env = strcmpi(getenv("PET2BIDS_TELEMETRY_ENABLED"), 'false');
+    else
+        disable_telemetry_env = false;
+    end
+
     home_dir = environment("HOME");
     loadenv(fullfile(home_dir, '.pet2bidsconfig'), FileType='env');
     % convert string to boolean/logical
     disable_telemetry = strcmpi(getenv("PET2BIDS_TELEMETRY_ENABLED"), 'false');
     
-    if disable_telemetry
+    if disable_telemetry | disable_telemetry_env
         e = false;
     else
         e = true;
diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index e31bda0..4d6761c 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -1109,7 +1109,14 @@ def cli():
         action="version",
         version=f"{helper_functions.get_version()}",
     )
-
+    parser.add_argument(
+        "--notrack",
+        action="store_true",
+        default=False,
+        help="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."
+    )
     return parser
 
 
@@ -1261,6 +1268,8 @@ def main():
             "DEFAULT_METADATA_JSON", cli_args.set_default_metadata_json
         )
         sys.exit(0)
+    if cli_args.notrack:
+        environ["PET2BIDS_TRACK"] = "False"
 
     elif cli_args.folder:
         # instantiate class
diff --git a/pypet2bids/pypet2bids/ecat_cli.py b/pypet2bids/pypet2bids/ecat_cli.py
index b1284f9..fa52584 100644
--- a/pypet2bids/pypet2bids/ecat_cli.py
+++ b/pypet2bids/pypet2bids/ecat_cli.py
@@ -190,6 +190,14 @@ def cli():
         action="version",
         version=f"{helper_functions.get_version()}",
     )
+    parser.add_argument(
+        "--notrack",
+        action="store_true",
+        default=False,
+        help="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."
+    )
 
     return parser
 
@@ -262,6 +270,9 @@ def main():
         print(example1)
         sys.exit(0)
 
+    if cli_args.notrack:
+        os.environ["PET2BIDS_TELEMETRY_ENABLED"] = "False"
+
     collect_pixel_data = False
     if cli_args.convert or cli_args.update:
         collect_pixel_data = True
diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index 46afbf5..e95856a 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -15,7 +15,6 @@
 | *Copyright OpenNeuroPET team*
 """
 
-
 import os
 import gzip
 import re
@@ -286,7 +285,9 @@ def decompress(file_like_object, output_path: str = None):
     return output_path
 
 
-def load_vars_from_config(path_to_config: str=pathlib.Path.home() / ".pet2bidsconfig"):
+def load_vars_from_config(
+    path_to_config: str = pathlib.Path.home() / ".pet2bidsconfig",
+):
     """
     Loads values from a .env file given a path to said .env file.
 
diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index 6bdd1c6..0ef9f19 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -13,11 +13,24 @@
     from helper_functions import get_version, load_vars_from_config, modify_config_file
 except ModuleNotFoundError:
     # collect pet2bids version
-    from pypet2bids.helper_functions import get_version, load_vars_from_config, modify_config_file
+    from pypet2bids.helper_functions import (
+        get_version,
+        load_vars_from_config,
+        modify_config_file,
+    )
 
 pet2bids_config = load_vars_from_config()
-telemetry_default_url = pet2bids_config.get("TELEMETRY_URL", "http://52.87.154.236/telemetry/")
+telemetry_default_url = pet2bids_config.get(
+    "TELEMETRY_URL", "http://52.87.154.236/telemetry/"
+)
+# check environment variables as well as the config file
+telemetry_enabled_env = os.getenv("PET2BIDS_TELEMETRY_ENABLED", True)
 telemetry_enabled = pet2bids_config.get("TELEMETRY_ENABLED", True)
+
+# if telemetry is disabled in the config file or the environment variable disable its use.
+if telemetry_enabled_env is False or telemetry_enabled is False:
+    telemetry_enabled = False
+
 telemetry_notify_user = pet2bids_config.get("NOTIFY_USER_OF_TELEMETRY", False)
 
 
@@ -31,12 +44,16 @@ def ask_user_to_opt_out(timeout=10):
         The user input if provided within the timeout, otherwise None.
     """
 
-    print("Do you want to opt out of telemetry? (yes/no): ".format(timeout), end="", flush=True)
+    print(
+        "Do you want to opt out of telemetry? (yes/no): ".format(timeout),
+        end="",
+        flush=True,
+    )
     sys.stdout.flush()
 
     ready, _, _ = select.select([sys.stdin], [], [], timeout)
     if ready:
-        response = sys.stdin.readline().rstrip('\n')
+        response = sys.stdin.readline().rstrip("\n")
         if response.lower() == "yes":
             return True
     else:
@@ -177,5 +194,3 @@ def count_output_files(output_file_path: Union[str, pathlib.Path]):
         "NiftiFiles": num_nifti_files,
         "NiftiFilesSize": nifti_files_size,
     }
-
-

From ff3645d8c7198f8c4e52aacd98e1332a38ceb282 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 12 Aug 2024 11:14:21 -0400
Subject: [PATCH 09/20] updating matlab to suit passing of --notrack to
 conversion functions

---
 matlab/dcm2niix4pet.m | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/matlab/dcm2niix4pet.m b/matlab/dcm2niix4pet.m
index 08bad7f..6dc6ac1 100644
--- a/matlab/dcm2niix4pet.m
+++ b/matlab/dcm2niix4pet.m
@@ -1,4 +1,4 @@
-function dcm2niix4pet(FolderList,MetaList,varargin)
+function dcm2niix4pet(FolderList,MetaList,varargin, notrack)
 
 % Converts dicom image file to nifti+json calling dcm2niix augmenting the
 % json file to be BIDS compliant. Note that you are always right when it
@@ -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 acquistions)
 %   - *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]
+% :param notrack: boolean to 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::
 %
@@ -220,6 +221,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     elseif strcmpi(varargin{var},'o')
         outputdir = varargin{var+1};
     end
+
 end
 
 if isempty(outputdir)
@@ -235,6 +237,26 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     end
 end
 
+% check to see if the user has disabled telemetry
+no_track_string = lower(string(notrack));
+if strcmp(no_track_string, 'true')
+    tracking = false;
+elseif strcmp(no_track_string, 'false')
+    tracking = true;
+else
+    try
+        numeric_notrack = str2num(no_track_string);
+        tracking = logical(numeric_notrack);
+    catch
+        % don't do anything
+    end
+end
+
+if ~tracking
+    setenv('PET2BIDS_TELEMETRY_ENABLED', 'false');
+end
+
+
 %% convert
 % ----------
 for folder = 1:size(FolderList,1)

From 400fec2649b4e951c2dae1a00aa615cddcd7f97b Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 12 Aug 2024 12:05:14 -0400
Subject: [PATCH 10/20] update tracking on matlab to set env to not track if
 provided via arguments

---
 matlab/dcm2niix4pet.m | 25 ++++++-------------------
 matlab/ecat2nii.m     |  3 +++
 2 files changed, 9 insertions(+), 19 deletions(-)

diff --git a/matlab/dcm2niix4pet.m b/matlab/dcm2niix4pet.m
index 6dc6ac1..e585a10 100644
--- a/matlab/dcm2niix4pet.m
+++ b/matlab/dcm2niix4pet.m
@@ -1,4 +1,4 @@
-function dcm2niix4pet(FolderList,MetaList,varargin, notrack)
+function dcm2niix4pet(FolderList,MetaList,varargin)
 
 % Converts dicom image file to nifti+json calling dcm2niix augmenting the
 % json file to be BIDS compliant. Note that you are always right when it
@@ -220,6 +220,11 @@ function dcm2niix4pet(FolderList,MetaList,varargin, notrack)
         end
     elseif strcmpi(varargin{var},'o')
         outputdir = varargin{var+1};
+    elseif strcmpi(varargin{var},'notrack')
+        notrack = varargin{var+1};
+        if notrack; setenv('TELEMETRY_ENABLED', 'False'); end
+    else
+        error('unknown option %s',varargin{var})
     end
 
 end
@@ -237,24 +242,6 @@ function dcm2niix4pet(FolderList,MetaList,varargin, notrack)
     end
 end
 
-% check to see if the user has disabled telemetry
-no_track_string = lower(string(notrack));
-if strcmp(no_track_string, 'true')
-    tracking = false;
-elseif strcmp(no_track_string, 'false')
-    tracking = true;
-else
-    try
-        numeric_notrack = str2num(no_track_string);
-        tracking = logical(numeric_notrack);
-    catch
-        % don't do anything
-    end
-end
-
-if ~tracking
-    setenv('PET2BIDS_TELEMETRY_ENABLED', 'false');
-end
 
 
 %% convert
diff --git a/matlab/ecat2nii.m b/matlab/ecat2nii.m
index 34222f7..c364010 100644
--- a/matlab/ecat2nii.m
+++ b/matlab/ecat2nii.m
@@ -114,6 +114,9 @@
         gz = varargin{v+1};
     elseif strcmpi(varargin{v},'savemat')
         savemat = varargin{v+1};
+    elseif strcmpi(varargin{v},'notrack')
+        notrack = varargin{v+1};
+        if notrack; setenv('TELEMETRY_ENABLED', 'False'); end
     end
 end
 

From 5903752ec9a444abd78ab292a1abd34f4a3cb702 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 12 Aug 2024 16:54:48 -0400
Subject: [PATCH 11/20] finished setting up matlab version

---
 matlab/dcm2niix4pet.m | 3 +--
 matlab/ecat2nii.m     | 3 +--
 matlab/telemetry.m    | 6 +++---
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/matlab/dcm2niix4pet.m b/matlab/dcm2niix4pet.m
index e585a10..da4399c 100644
--- a/matlab/dcm2niix4pet.m
+++ b/matlab/dcm2niix4pet.m
@@ -221,8 +221,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     elseif strcmpi(varargin{var},'o')
         outputdir = varargin{var+1};
     elseif strcmpi(varargin{var},'notrack')
-        notrack = varargin{var+1};
-        if notrack; setenv('TELEMETRY_ENABLED', 'False'); end
+        setenv('TELEMETRY_ENABLED', 'False')
     else
         error('unknown option %s',varargin{var})
     end
diff --git a/matlab/ecat2nii.m b/matlab/ecat2nii.m
index c364010..52b54e4 100644
--- a/matlab/ecat2nii.m
+++ b/matlab/ecat2nii.m
@@ -115,8 +115,7 @@
     elseif strcmpi(varargin{v},'savemat')
         savemat = varargin{v+1};
     elseif strcmpi(varargin{v},'notrack')
-        notrack = varargin{v+1};
-        if notrack; setenv('TELEMETRY_ENABLED', 'False'); end
+        setenv('TELEMETRY_ENABLED', 'False')
     end
 end
 
diff --git a/matlab/telemetry.m b/matlab/telemetry.m
index baebd18..06cd1e4 100644
--- a/matlab/telemetry.m
+++ b/matlab/telemetry.m
@@ -31,8 +31,8 @@ function telemetry(telemetry_data, input_path, output_path)
     % checks to see if the telemetry is enabled or disabled 
     environment = getenv();
     % check environment too before loading the config file
-    if isfield(environment, 'PET2BIDS_TELEMETRY_ENABLED')
-        disable_telemetry_env = strcmpi(getenv("PET2BIDS_TELEMETRY_ENABLED"), 'false');
+    if isfield(environment, 'TELEMETRY_ENABLED')
+        disable_telemetry_env = strcmpi(getenv("TELEMETRY_ENABLED"), 'false');
     else
         disable_telemetry_env = false;
     end
@@ -40,7 +40,7 @@ function telemetry(telemetry_data, input_path, output_path)
     home_dir = environment("HOME");
     loadenv(fullfile(home_dir, '.pet2bidsconfig'), FileType='env');
     % convert string to boolean/logical
-    disable_telemetry = strcmpi(getenv("PET2BIDS_TELEMETRY_ENABLED"), 'false');
+    disable_telemetry = strcmpi(getenv("TELEMETRY_ENABLED"), 'false');
     
     if disable_telemetry | disable_telemetry_env
         e = false;

From 4b4928a269fca0dd7e5d993f691cf94cf1fe72b9 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 14 Aug 2024 14:45:50 -0400
Subject: [PATCH 12/20] fix error with loading config

---
 pypet2bids/pypet2bids/helper_functions.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index e95856a..73ae19f 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -297,7 +297,10 @@ def load_vars_from_config(
     if os.path.isfile(path_to_config):
         parameters = dotenv.main.dotenv_values(path_to_config)
     else:
-        raise FileNotFoundError(path_to_config)
+        log = logger("pypet2bids")
+        log.warning(f"Unable to locate {path_to_config}, returning empty dictionary.")
+        parameters = {}
+        #raise FileNotFoundError(path_to_config)
 
     for parameter, value in parameters.items():
         try:

From 9bc9e56bf3a250560d4f1c846dd33aeee491e893 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 14 Aug 2024 15:08:36 -0400
Subject: [PATCH 13/20] automated message was more errofr that it's worth

---
 pypet2bids/pypet2bids/telemetry.py | 35 ------------------------------
 1 file changed, 35 deletions(-)

diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index 0ef9f19..bbc0683 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -34,41 +34,6 @@
 telemetry_notify_user = pet2bids_config.get("NOTIFY_USER_OF_TELEMETRY", False)
 
 
-def ask_user_to_opt_out(timeout=10):
-    """Waits for user input for a specified number of seconds.
-
-    Args:
-        timeout: Number of seconds to wait for input.
-
-    Returns:
-        The user input if provided within the timeout, otherwise None.
-    """
-
-    print(
-        "Do you want to opt out of telemetry? (yes/no): ".format(timeout),
-        end="",
-        flush=True,
-    )
-    sys.stdout.flush()
-
-    ready, _, _ = select.select([sys.stdin], [], [], timeout)
-    if ready:
-        response = sys.stdin.readline().rstrip("\n")
-        if response.lower() == "yes":
-            return True
-    else:
-        return False
-
-
-if telemetry_notify_user is False:
-    opt_out = ask_user_to_opt_out()
-    if opt_out:
-        # update the config file
-        modify_config_file("TELEMETRY_ENABLED", False)
-
-    modify_config_file("NOTIFY_USER_OF_TELEMETRY", True)
-
-
 def telemetry_enabled(config_path=None):
     """
     Check if telemetry is enabled, if it isn't disabled in the .pet2bidsconfig file

From b360317f3981b01b2f5dbf5748153b40a310e68d Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Wed, 14 Aug 2024 16:34:04 -0400
Subject: [PATCH 14/20] formatted files

---
 pypet2bids/pypet2bids/dcm2niix4pet.py     | 4 ++--
 pypet2bids/pypet2bids/ecat_cli.py         | 4 ++--
 pypet2bids/pypet2bids/helper_functions.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index 4d6761c..7d1bf3b 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -1114,8 +1114,8 @@ def cli():
         action="store_true",
         default=False,
         help="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."
+        "This information helps to improve PET2BIDS and provides an indicator of real world "
+        "usage crucial for obtaining funding.",
     )
     return parser
 
diff --git a/pypet2bids/pypet2bids/ecat_cli.py b/pypet2bids/pypet2bids/ecat_cli.py
index fa52584..d6a66f2 100644
--- a/pypet2bids/pypet2bids/ecat_cli.py
+++ b/pypet2bids/pypet2bids/ecat_cli.py
@@ -195,8 +195,8 @@ def cli():
         action="store_true",
         default=False,
         help="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."
+        "This information helps to improve PET2BIDS and provides an indicator of real world "
+        "usage crucial for obtaining funding.",
     )
 
     return parser
diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index 73ae19f..420da04 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -300,7 +300,7 @@ def load_vars_from_config(
         log = logger("pypet2bids")
         log.warning(f"Unable to locate {path_to_config}, returning empty dictionary.")
         parameters = {}
-        #raise FileNotFoundError(path_to_config)
+        # raise FileNotFoundError(path_to_config)
 
     for parameter, value in parameters.items():
         try:

From 878d4acfaed53a7746316d690f56f617fb321c9a Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 15 Aug 2024 14:33:17 -0400
Subject: [PATCH 15/20] add try catch for .env file check on telemetry.m

---
 matlab/telemetry.m | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/matlab/telemetry.m b/matlab/telemetry.m
index 06cd1e4..baab2d0 100644
--- a/matlab/telemetry.m
+++ b/matlab/telemetry.m
@@ -38,8 +38,13 @@ function telemetry(telemetry_data, input_path, output_path)
     end
 
     home_dir = environment("HOME");
-    loadenv(fullfile(home_dir, '.pet2bidsconfig'), FileType='env');
-    % convert string to boolean/logical
+    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

From 29e32a4cc9dd457231ff366e04c6b60051001966 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Fri, 16 Aug 2024 14:01:01 -0400
Subject: [PATCH 16/20] update poetry lock file

---
 pypet2bids/poetry.lock | 44 +++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/pypet2bids/poetry.lock b/pypet2bids/poetry.lock
index c644a2c..890a072 100644
--- a/pypet2bids/poetry.lock
+++ b/pypet2bids/poetry.lock
@@ -24,13 +24,13 @@ files = [
 
 [[package]]
 name = "babel"
-version = "2.15.0"
+version = "2.16.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
 [package.dependencies]
@@ -262,21 +262,21 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p
 
 [[package]]
 name = "importlib-resources"
-version = "6.4.0"
+version = "6.4.2"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.4.0-py3-none-any.whl", hash = "sha256:50d10f043df931902d4194ea07ec57960f66a80449ff867bfe782b4c486ba78c"},
-    {file = "importlib_resources-6.4.0.tar.gz", hash = "sha256:cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145"},
+    {file = "importlib_resources-6.4.2-py3-none-any.whl", hash = "sha256:8bba8c54a8a3afaa1419910845fa26ebd706dc716dd208d9b158b4b6966f5c5c"},
+    {file = "importlib_resources-6.4.2.tar.gz", hash = "sha256:6cbfbefc449cc6e2095dd184691b7a12a04f40bc75dd4c55d31c34f174cdf57a"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -654,13 +654,13 @@ hook-testing = ["execnet (>=1.5.0)", "psutil", "pytest (>=2.7.3)"]
 
 [[package]]
 name = "pyinstaller-hooks-contrib"
-version = "2024.7"
+version = "2024.8"
 description = "Community maintained hooks for PyInstaller"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pyinstaller_hooks_contrib-2024.7-py2.py3-none-any.whl", hash = "sha256:8bf0775771fbaf96bcd2f4dfd6f7ae6c1dd1b1efe254c7e50477b3c08e7841d8"},
-    {file = "pyinstaller_hooks_contrib-2024.7.tar.gz", hash = "sha256:fd5f37dcf99bece184e40642af88be16a9b89613ecb958a8bd1136634fc9fac5"},
+    {file = "pyinstaller_hooks_contrib-2024.8-py3-none-any.whl", hash = "sha256:0057fe9a5c398d3f580e73e58793a1d4a8315ca91c3df01efea1c14ed557825a"},
+    {file = "pyinstaller_hooks_contrib-2024.8.tar.gz", hash = "sha256:29b68d878ab739e967055b56a93eb9b58e529d5b054fbab7a2f2bacf80cef3e2"},
 ]
 
 [package.dependencies]
@@ -745,13 +745,13 @@ files = [
 
 [[package]]
 name = "pywin32-ctypes"
-version = "0.2.2"
+version = "0.2.3"
 description = "A (partial) reimplementation of pywin32 using ctypes/cffi"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "pywin32-ctypes-0.2.2.tar.gz", hash = "sha256:3426e063bdd5fd4df74a14fa3cf80a0b42845a87e1d1e81f6549f9daec593a60"},
-    {file = "pywin32_ctypes-0.2.2-py3-none-any.whl", hash = "sha256:bf490a1a709baf35d688fe0ecf980ed4de11d2b3e37b51e5442587a75d9957e7"},
+    {file = "pywin32-ctypes-0.2.3.tar.gz", hash = "sha256:d162dc04946d704503b2edc4d55f3dba5c1d539ead017afa00142c38b9885755"},
+    {file = "pywin32_ctypes-0.2.3-py3-none-any.whl", hash = "sha256:8a1513379d709975552d202d942d9837758905c8d01eb82b8bcc30918929e7b8"},
 ]
 
 [[package]]
@@ -826,18 +826,18 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "72.1.0"
+version = "72.2.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-72.1.0-py3-none-any.whl", hash = "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1"},
-    {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"},
+    {file = "setuptools-72.2.0-py3-none-any.whl", hash = "sha256:f11dd94b7bae3a156a95ec151f24e4637fb4fa19c878e4d191bfb8b2d82728c4"},
+    {file = "setuptools-72.2.0.tar.gz", hash = "sha256:80aacbf633704e9c8bfa1d99fa5dd4dc59573efcf9e4042c13d3bcef91ac2ef9"},
 ]
 
 [package.extras]
 core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
 test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -1091,13 +1091,13 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
+    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
 ]
 
 [package.extras]

From f312bbd18ba8aa06a76c401362b078359326f973 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Fri, 16 Aug 2024 17:55:31 -0400
Subject: [PATCH 17/20] added reordering for Isotope Number

---
 metadata/PET_Radionuclide.mkd             | 76 +++++++++++------------
 pypet2bids/pypet2bids/helper_functions.py | 34 ++++++++++
 pypet2bids/tests/test_helper_functions.py | 15 +++++
 3 files changed, 87 insertions(+), 38 deletions(-)

diff --git a/metadata/PET_Radionuclide.mkd b/metadata/PET_Radionuclide.mkd
index d0dfb4a..adda3d8 100644
--- a/metadata/PET_Radionuclide.mkd
+++ b/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                |
diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index 2a28ec3..a53e322 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -1149,3 +1149,37 @@ def first_middle_last_frames_to_text(
             delimiter="\t",
             fmt="%s",
         )
+
+def reorder_isotope(isotope: str) -> str:
+    """
+    Reorders the isotope string to be in the format of "isotope""element name"
+    :param isotope: isotope string
+    :type isotope: str
+    :return: reordered isotope string
+    :rtype: str
+    """
+    # remove all non-alphanumeric characters from isotope
+    isotope = re.findall(r"[a-zA-Z0-9]+", isotope)
+    # combine all elements in isotope into one string
+    isotope = "".join(isotope)
+    # collect the isotope number from the isotope string
+    isotope_num = re.findall(r"\d+", isotope)
+    # collect the element name from the isotope string
+    element_name = re.findall(r"[a-zA-Z]+", isotope)
+
+    # capitalize the first letter of the element name if the element name's length is <= 2
+    if 1 < len(element_name[0]) <= 2:
+        e = element_name[0][0].capitalize()
+        if len(element_name[0]) == 2:
+            e += element_name[0][1].lower()
+    elif len(element_name[0]) == 1:
+        e = element_name[0].capitalize()
+
+    # special case for 52mMn
+    if "".join(element_name).lower() == "mmn" or "".join(element_name).lower() == "mnm":
+        e = "mMn"
+
+    # reorder to put the number before the element name
+    isotope = f"{isotope_num[0]}{e}"
+
+    return isotope
diff --git a/pypet2bids/tests/test_helper_functions.py b/pypet2bids/tests/test_helper_functions.py
index 52ba136..5a2d39a 100644
--- a/pypet2bids/tests/test_helper_functions.py
+++ b/pypet2bids/tests/test_helper_functions.py
@@ -343,5 +343,20 @@ def test_collect_pet_spreadsheets():
     assert len(pet_spreadsheets) == 3
 
 
+def test_reorder_isotope():
+    # tests whether the isotope is reordered correctly with the numerical part appearing before the string part
+    # and if any non-alphanumeric characters are present
+    isotopes = {
+        "11C": ["C11", "^11^C", "C-11", "11-C", "11C", "c11", "c-11", "11c"],
+        "18F": ["F18", "^18^F", "F-18", "18-F", "18F"],
+        "68Ga": ["Ga68", "^68^Ga", "Ga-68", "68-Ga", "68Ga"],
+        "52mMn": ["Mn52m", "Mn-52m", "52m-Mn", "52mMn"]
+    }
+
+    for isotope, isotope_variants in isotopes.items():
+        for isotope_variant in isotope_variants:
+            assert helper_functions.reorder_isotope(isotope_variant) == isotope
+
+
 if __name__ == "__main__":
     unittest.main()

From 349ef31fa2560a612e0cead0b874a65220a60bdc Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Thu, 12 Sep 2024 11:06:55 -0400
Subject: [PATCH 18/20] bump version, update url for telemetry

---
 pypet2bids/pypet2bids/telemetry.py | 9 ++++++---
 pypet2bids/pyproject.toml          | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index bbc0683..2233088 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -21,7 +21,7 @@
 
 pet2bids_config = load_vars_from_config()
 telemetry_default_url = pet2bids_config.get(
-    "TELEMETRY_URL", "http://52.87.154.236/telemetry/"
+    "TELEMETRY_URL", "http://openneuropet.org/pet2bids/"
 )
 # check environment variables as well as the config file
 telemetry_enabled_env = os.getenv("PET2BIDS_TELEMETRY_ENABLED", True)
@@ -82,8 +82,11 @@ def send_telemetry(json_data: dict, url: str = telemetry_default_url):
 
         json_data["description"] = "pet2bids_python_telemetry"
 
-        # Send a POST request to the telemetry server
-        requests.post(url, json=json_data)
+        try:
+            # Send a POST request to the telemetry server
+            requests.post(url, json=json_data)
+        except requests.exceptions.RequestException as e:
+            pass
     else:
         pass
 
diff --git a/pypet2bids/pyproject.toml b/pypet2bids/pyproject.toml
index 95760d0..f7117d9 100644
--- a/pypet2bids/pyproject.toml
+++ b/pypet2bids/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.13dev"
+version = "1.3.13"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"]
 license = "MIT"

From 684e407faf8accf0dcf1fc1909036e61bbed2ecb Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 9 Dec 2024 17:50:47 -0500
Subject: [PATCH 19/20] set ModeOfAdministration to lower

---
 matlab/updatejsonpetfile.m                |  5 +++
 pypet2bids/poetry.lock                    | 54 ++++++++++++++++++-----
 pypet2bids/pypet2bids/dcm2niix4pet.py     | 10 +++++
 pypet2bids/pypet2bids/ecat.py             |  6 +++
 pypet2bids/pypet2bids/telemetry.py        |  5 ++-
 pypet2bids/tests/test_helper_functions.py |  2 +-
 6 files changed, 68 insertions(+), 14 deletions(-)

diff --git a/matlab/updatejsonpetfile.m b/matlab/updatejsonpetfile.m
index 3395d86..0aaaf8b 100644
--- a/matlab/updatejsonpetfile.m
+++ b/matlab/updatejsonpetfile.m
@@ -289,6 +289,11 @@
     end
     filemetadata = update_arrays(filemetadata);
 
+    % set ModeOfAdministration to lower case
+    if isfield(filemetadata,'ModeOfAdministration')
+        filemetadata.ModeOfAdministration = lower(filemetadata.ModeOfAdministration);
+    end
+
     % clean-up
     fn_check = fieldnames(filemetadata);
     for f=1:size(fn_check,1)
diff --git a/pypet2bids/poetry.lock b/pypet2bids/poetry.lock
index 9744b2d..ae2937f 100644
--- a/pypet2bids/poetry.lock
+++ b/pypet2bids/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -261,17 +261,17 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.2.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"},
-    {file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"},
+    {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"},
+    {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
 check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
@@ -891,13 +891,13 @@ type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.12
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
-    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+    {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
 [[package]]
@@ -1096,13 +1096,43 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.1.0"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.1.0-py3-none-any.whl", hash = "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"},
-    {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"},
+    {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"},
+    {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ece47d672db52ac607a3d9599a9d48dcb2f2f735c6c2d1f34130085bb12b112a"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6972ca9c9cc9f0acaa56a8ca1ff51e7af152a9f87fb64623e31d5c83700080ee"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c954d2250168d28797dd4e3ac5cf812a406cd5a92674ee4c8f123c889786aa8e"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:8dd28b3e155b80f4d54beb40a441d366adcfe740969820caf156c019fb5c7ec4"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_i686.whl", hash = "sha256:e59e304978767a54663af13c07b3d1af22ddee3bb2fb0618ca1593e4f593a106"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:33580bccab0338d00994d7f16f4c4ec25b776af3ffaac1ed74e0b3fc95e885a8"},
+    {file = "tomli-2.2.1-cp311-cp311-win32.whl", hash = "sha256:465af0e0875402f1d226519c9904f37254b3045fc5084697cefb9bdde1ff99ff"},
+    {file = "tomli-2.2.1-cp311-cp311-win_amd64.whl", hash = "sha256:2d0f2fdd22b02c6d81637a3c95f8cd77f995846af7414c5c4b8d0545afa1bc4b"},
+    {file = "tomli-2.2.1-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:4a8f6e44de52d5e6c657c9fe83b562f5f4256d8ebbfe4ff922c495620a7f6cea"},
+    {file = "tomli-2.2.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:8d57ca8095a641b8237d5b079147646153d22552f1c637fd3ba7f4b0b29167a8"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4e340144ad7ae1533cb897d406382b4b6fede8890a03738ff1683af800d54192"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:db2b95f9de79181805df90bedc5a5ab4c165e6ec3fe99f970d0e302f384ad222"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:40741994320b232529c802f8bc86da4e1aa9f413db394617b9a256ae0f9a7f77"},
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+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index 7d1bf3b..991484b 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -690,6 +690,16 @@ def run_dcm2niix(self):
                     sidecar_json.update(self.spreadsheet_metadata.get("nifti_json", {}))
                     sidecar_json.update(self.additional_arguments)
 
+                    # set ModeOfAdministration to lower case
+                    if sidecar_json.get("ModeOfAdministration"):
+                        sidecar_json.update(
+                            {
+                                "ModeOfAdministration": sidecar_json.get(
+                                    "ModeOfAdministration"
+                                ).lower()
+                            }
+                        )
+
                     # this is mostly for ezBIDS, but it helps us to make better use of the series description that
                     # dcm2niix generates by default for PET imaging
                     collect_these_fields = {
diff --git a/pypet2bids/pypet2bids/ecat.py b/pypet2bids/pypet2bids/ecat.py
index efbc2ea..a4f7988 100644
--- a/pypet2bids/pypet2bids/ecat.py
+++ b/pypet2bids/pypet2bids/ecat.py
@@ -453,6 +453,12 @@ def populate_sidecar(self, **kwargs):
         meta_radio_inputs = check_meta_radio_inputs(self.sidecar_template)
         self.sidecar_template.update(**meta_radio_inputs)
 
+        # set ModeOfAdministration to lower case
+        if self.sidecar_template.get("ModeOfAdministration", ""):
+            self.sidecar_template["ModeOfAdministration"] = self.sidecar_template[
+                "ModeOfAdministration"
+            ].lower()
+
     def prune_sidecar(self):
         """
         Eliminate unpopulated fields in sidecar while leaving in mandatory fields even if they are unpopulated.
diff --git a/pypet2bids/pypet2bids/telemetry.py b/pypet2bids/pypet2bids/telemetry.py
index 6ae54a9..b80d092 100644
--- a/pypet2bids/pypet2bids/telemetry.py
+++ b/pypet2bids/pypet2bids/telemetry.py
@@ -53,7 +53,10 @@ def telemetry_enabled(config_path=None):
         load_dotenv(dotenv_path=config_file)
 
     # check to see if telemetry is disabled
-    if os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false" or os.getenv("CI", "false") == "true":
+    if (
+        os.getenv("PET2BIDS_TELEMETRY_ENABLED", "").lower() == "false"
+        or os.getenv("CI", "false") == "true"
+    ):
         return False
     else:
         return True
diff --git a/pypet2bids/tests/test_helper_functions.py b/pypet2bids/tests/test_helper_functions.py
index 5a2d39a..8c9f177 100644
--- a/pypet2bids/tests/test_helper_functions.py
+++ b/pypet2bids/tests/test_helper_functions.py
@@ -350,7 +350,7 @@ def test_reorder_isotope():
         "11C": ["C11", "^11^C", "C-11", "11-C", "11C", "c11", "c-11", "11c"],
         "18F": ["F18", "^18^F", "F-18", "18-F", "18F"],
         "68Ga": ["Ga68", "^68^Ga", "Ga-68", "68-Ga", "68Ga"],
-        "52mMn": ["Mn52m", "Mn-52m", "52m-Mn", "52mMn"]
+        "52mMn": ["Mn52m", "Mn-52m", "52m-Mn", "52mMn"],
     }
 
     for isotope, isotope_variants in isotopes.items():

From 9d9e9873115dc1c9e83a98c3887e4b7ec290e4af Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 9 Dec 2024 17:56:06 -0500
Subject: [PATCH 20/20] bump version

---
 pypet2bids/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pypet2bids/pyproject.toml b/pypet2bids/pyproject.toml
index 1ddf2cd..ab015b0 100644
--- a/pypet2bids/pyproject.toml
+++ b/pypet2bids/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.14"
+version = "1.3.15"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"]
 license = "MIT"