added reordering for Isotope Number

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                |

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

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()