From 5966d662f2e1cf8bb3c280fd6520a3a477dd4426 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 4 Mar 2024 11:17:11 -0500
Subject: [PATCH 1/3] update error messages

---
 pypet2bids/pypet2bids/dcm2niix4pet.py | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index e65a01e1..2ac275df 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -173,7 +173,8 @@ def __init__(self, image_folder, destination_path=None, metadata_path=None,
 
         self.dcm2niix_path = self.check_for_dcm2niix()
         if not self.dcm2niix_path:
-            raise FileNotFoundError("dcm2niix not found, this module depends on it for conversions, exiting.")
+            logger.error("dcm2niix not found, this module depends on it for conversions, exiting.")
+            sys.exit(1)
 
         # check for the version of dcm2niix
         minimum_version = 'v1.0.20220720'
@@ -263,7 +264,7 @@ def __init__(self, image_folder, destination_path=None, metadata_path=None,
             load_spreadsheet_data = get_metadata_from_spreadsheet(metadata_path=metadata_path,
                                                                   image_folder=self.image_folder,
                                                                   image_header_dict=self.dicom_headers[
-                                                                    next(iter(self.dicom_headers))],
+                                                                      next(iter(self.dicom_headers))],
                                                                   **self.additional_arguments)
 
             self.spreadsheet_metadata['nifti_json'].update(load_spreadsheet_data['nifti_json'])
@@ -286,11 +287,25 @@ def check_posix():
             dcm2niix_path = subprocess.run('which dcm2niix',
                                            shell=True,
                                            capture_output=True).stdout.decode('utf-8').strip()
+            # check to see if dcm2niix is set in the config file, default to that if it's the case and alert user
+            set_in_config = helper_functions.check_pet2bids_config()
+            if set_in_config:
+                logger.warning(f"dcm2niix found on system path, but dcm2niix path is also set in ~/.pet2bidsconfig."
+                               f" Defaulting to dcm2niix path set in config at {set_in_config}")
+
         else:
+            dcm2niix_path = helper_functions.check_pet2bids_config()
+
+        if not dcm2niix_path:
             pkged = "https://github.com/rordenlab/dcm2niix/releases"
             instructions = "https://github.com/rordenlab/dcm2niix#install"
-            no_dcm2niix = f"""Dcm2niix does not appear to be installed. Installation instructions can be found here 
-                       {instructions} and packaged versions can be found at {pkged}"""
+            no_dcm2niix = f"""Unable to locate Dcm2niix on your system $PATH or using the path specified in 
+                        $HOME/.pypet2bidsconfig. Installation instructions for dcm2niix can be found here 
+                        {instructions} 
+                        and packaged versions can be found at 
+                        {pkged}
+                        Alternatively, you can set the path to dcm2niix in the config file at $HOME/.pet2bidsconfig
+                        using the command dcm2niix4pet --set-dcm2niix-path."""
             logger.error(no_dcm2niix)
             dcm2niix_path = None
 

From 1f71e90285c9aa807ecabc7ccfe76f9d97804ff2 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:06:38 -0500
Subject: [PATCH 2/3] Update pypet2bids/pypet2bids/dcm2niix4pet.py

remove spaces
---
 pypet2bids/pypet2bids/dcm2niix4pet.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index 2ac275df..596d735d 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -264,7 +264,7 @@ def __init__(self, image_folder, destination_path=None, metadata_path=None,
             load_spreadsheet_data = get_metadata_from_spreadsheet(metadata_path=metadata_path,
                                                                   image_folder=self.image_folder,
                                                                   image_header_dict=self.dicom_headers[
-                                                                      next(iter(self.dicom_headers))],
+                                                                    next(iter(self.dicom_headers))],
                                                                   **self.additional_arguments)
 
             self.spreadsheet_metadata['nifti_json'].update(load_spreadsheet_data['nifti_json'])

From 4f6f4ba1508ece8a82d6e76d452ca4502d1b1e4d Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:10:48 -0500
Subject: [PATCH 3/3] actually using the one in the config if it's present

---
 pypet2bids/pypet2bids/dcm2niix4pet.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index 2ac275df..0d35f24b 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -292,6 +292,7 @@ def check_posix():
             if set_in_config:
                 logger.warning(f"dcm2niix found on system path, but dcm2niix path is also set in ~/.pet2bidsconfig."
                                f" Defaulting to dcm2niix path set in config at {set_in_config}")
+                dcm2niix_path = set_in_config
 
         else:
             dcm2niix_path = helper_functions.check_pet2bids_config()