From d22b66968a8e306de04e360d446fde37592fd1b2 Mon Sep 17 00:00:00 2001
From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>
Date: Fri, 20 Dec 2024 13:26:46 -0600
Subject: [PATCH] added feature to ignore non-pet files

---
 pypet2bids/pypet2bids/dcm2niix4pet.py     | 35 +++++++++++++++++++++++
 pypet2bids/pypet2bids/helper_functions.py | 29 ++++++++++---------
 pypet2bids/pyproject.toml                 |  3 +-
 3 files changed, 53 insertions(+), 14 deletions(-)

diff --git a/pypet2bids/pypet2bids/dcm2niix4pet.py b/pypet2bids/pypet2bids/dcm2niix4pet.py
index 991484b..f0cbbd4 100644
--- a/pypet2bids/pypet2bids/dcm2niix4pet.py
+++ b/pypet2bids/pypet2bids/dcm2niix4pet.py
@@ -301,6 +301,15 @@ def __init__(
         # we consider values stored in a default JSON file to be additional arguments, we load those
         # values first and then overwrite them with any user supplied values
 
+        # check to make sure the dicom is a PET dicom
+        modalities = [dicom.Modality for dicom in self.dicom_headers.values()]
+        non_pet_dicom = [modality for modality in modalities if modality != "PT"]
+
+        if len(non_pet_dicom) > 0:
+            logger.warning(
+                f"Non PET dicoms found in {self.image_folder}. Modalities f{non_pet_dicom} detected"
+            )
+
         # load config file
         default_json_path = helper_functions.check_pet2bids_config(
             "DEFAULT_METADATA_JSON"
@@ -500,6 +509,32 @@ def run_dcm2niix(self):
                 join(tempdir_pathlike, file) for file in listdir(tempdir_pathlike)
             ]
 
+            # check to see if there are any modalities present that aren't PET
+            remove_these_non_pet_files = []
+            for json_file in [f for f in files_created_by_dcm2niix if ".json" in f]:
+                with open(json_file, "r") as infile:
+                    json_data = json.load(infile)
+                    if json_data.get("Modality") != "PT":
+                        logger.warning(
+                            f"Non PET modality found in {json_file}, skipping. Files relating to this json and it's"
+                            f"nifti will not be included at the destination folder {self.destination_folder}"
+                        )
+                        remove_these_non_pet_files.append(json_file)
+                        remove_these_non_pet_files.append(
+                            json_file.replace(".json", ".nii.gz")
+                        )
+                        remove_these_non_pet_files.append(
+                            json_file.replace(".json", ".nii")
+                        )
+
+            # if there are non PET files remove them from files_created_by_dcm2niix
+            if remove_these_non_pet_files:
+                for file in remove_these_non_pet_files:
+                    try:
+                        files_created_by_dcm2niix.remove(file)
+                    except ValueError:
+                        pass
+
             # make sure destination path exists if not try creating it.
             try:
                 if self.destination_path.exists():
diff --git a/pypet2bids/pypet2bids/helper_functions.py b/pypet2bids/pypet2bids/helper_functions.py
index 4edb0a3..f8f28f8 100644
--- a/pypet2bids/pypet2bids/helper_functions.py
+++ b/pypet2bids/pypet2bids/helper_functions.py
@@ -125,19 +125,22 @@ def flatten_series(series):
 
 def collect_spreadsheets(folder_path: pathlib.Path):
     spreadsheet_files = []
-    all_files = [
-        folder_path / pathlib.Path(file)
-        for file in os.listdir(folder_path)
-        if os.path.isfile(os.path.join(folder_path, file))
-    ]
-    for file in all_files:
-        if (
-            file.suffix == ".xlsx"
-            or file.suffix == ".csv"
-            or file.suffix == ".xls"
-            or file.suffix == ".tsv"
-        ):
-            spreadsheet_files.append(file)
+    if folder_path.is_file():
+        spreadsheet_files.append(folder_path)
+    else:
+        all_files = [
+            folder_path / pathlib.Path(file)
+            for file in os.listdir(folder_path)
+            if os.path.isfile(os.path.join(folder_path, file))
+        ]
+        for file in all_files:
+            if (
+                file.suffix == ".xlsx"
+                or file.suffix == ".csv"
+                or file.suffix == ".xls"
+                or file.suffix == ".tsv"
+            ):
+                spreadsheet_files.append(file)
     return spreadsheet_files
 
 
diff --git a/pypet2bids/pyproject.toml b/pypet2bids/pyproject.toml
index ab015b0..a8211dd 100644
--- a/pypet2bids/pyproject.toml
+++ b/pypet2bids/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.15"
+version = "1.3.16"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"]
 license = "MIT"
@@ -30,6 +30,7 @@ pandas = ">=1.4.4"
 pyxlsb = "^1.0.9"
 joblib = "^1.2.0"
 toml = ">=0.10.2"
+requests = "^2.32.3"
 
 
 [tool.poetry.dev-dependencies]