Fix capitalization of parameters in

nbia_client.getPatients() and
nbia_client.getBodyPartCounts()

docs/example.ipynb

@@ -25,15 +25,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "23-12-02 13:19 | NBIAClient | DEBUG | Setting up OAuth2 client... with username nbia_guest\n"
+     ]
+    }
+   ],
    "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "\n",
     "from nbiatoolkit import NBIAClient\n",
     "from pprint import pprint\n",
     "\n",
     "# Instantiate the client. \n",
-    "client = NBIAClient()"
+    "client = NBIAClient(log_level='debug')"
    ]
   },
   {
@@ -63,9 +74,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "23-12-02 13:07 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getCollectionValues\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -93,9 +111,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "23-12-02 13:08 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/getCollectionValuesAndCounts\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -123,9 +148,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "23-12-02 13:08 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/getBodyPartValuesAndCounts\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -165,9 +197,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "23-12-02 13:28 | NBIAClient | DEBUG | Parsing params: {'self': <nbiatoolkit.nbia.NBIAClient object at 0x11100eba0>, 'Collection': '4D-Lung', 'Modality': 'CT'}\n",
+      "23-12-02 13:28 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getPatientByCollectionAndModality\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -177,7 +217,7 @@
     }
    ],
    "source": [
-    "patients = client.getPatients(collection=\"4D-Lung\", modality=\"CT\")\n",
+    "patients = client.getPatients(Collection=\"4D-Lung\", Modality=\"CT\")\n",
     "pprint(patients[0:5])"
    ]
   },
@@ -209,9 +249,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "23-12-02 13:34 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeries\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",

src/nbiatoolkit/nbia.py

@@ -18,15 +18,17 @@ class NBIAClient:
     """
 
     def __init__(self,
-                 username: str = "nbia_guest",
-                 password: str = "",
-                 log_level: str = "INFO"
-                 ) -> None:
+                    username: str = "nbia_guest",
+                    password: str = "",
+                    log_level: str = "INFO"
+                    ) -> None:
 
         # Setup logger
         self.logger = setup_logger(
-            name="NBIAClient", console_logging=True,
-            log_level=log_level, log_file=None)
+            name="NBIAClient",
+            log_level=log_level,
+            console_logging=True,
+            log_file=None)
 
         # Setup OAuth2 client
         self.logger.debug(
@@ -35,6 +37,31 @@ def __init__(self,
         self._oauth2_client = OAuth2(username=username, password=password)
         self.api_headers = self._oauth2_client.getToken()
 
+    # setter method to update logger with a new instance of setup_logger
+    def setLogger(
+        self,
+        log_level: str = "INFO",
+        console_logging: bool = False,
+        log_file: str = None,
+        log_dir: str = None,
+        log_format: str = '%(asctime)s | %(name)s | %(levelname)s | %(message)s',
+        datefmt: str = '%y-%m-%d %H:%M'
+    ) -> bool:
+        try:
+            self.logger = setup_logger(
+                name="NBIAClient",
+                log_level=log_level,
+                console_logging=console_logging,
+                log_file=log_file,
+                log_dir=log_dir,
+                log_format=log_format,
+                datefmt=datefmt
+            )
+            return True
+        except Exception as e:
+            self.logger.error("Error setting up logger: %s", e)
+            return False
+
     def query_api(self, endpoint: NBIA_ENDPOINTS, params: dict = {}) -> dict:
 
         query_url = NBIA_ENDPOINTS.BASE_URL.value + endpoint.value
@@ -81,13 +108,10 @@ def getCollectionPatientCount(self) -> list:
         return patientCount
 
     def getBodyPartCounts(
-        self, collection: str = "", modality: str = "") -> list:
+        self, Collection: str = "", Modality: str = "") -> list:
+
+        PARAMS = self.parsePARAMS(locals())
 
-        PARAMS = {}
-        if collection:
-            PARAMS["Collection"] = collection
-        if modality:
-            PARAMS["Modality"] = modality
         response = self.query_api(
             endpoint=NBIA_ENDPOINTS.GET_BODY_PART_PATIENT_COUNT,
             params=PARAMS)
@@ -99,11 +123,13 @@ def getBodyPartCounts(
                 "Count": bodypart["count"]})
         return bodyparts
 
-    def getPatients(self, collection: str, modality: str) -> list:
-        assert collection is not None
-        assert modality is not None
+    def getPatients(self, Collection: str, Modality: str) -> list:
+        assert Collection is not None
+        assert Modality is not None
+
+
+        PARAMS = self.parsePARAMS(locals())
 
-        PARAMS = {"Collection": collection, "Modality": modality}
         response = self.query_api(
             endpoint=NBIA_ENDPOINTS.GET_PATIENT_BY_COLLECTION_AND_MODALITY,
             params=PARAMS)
@@ -122,22 +148,24 @@ def getSeries(self,
         Manufacturer: str = "",
         ) -> list:
 
-        params = dict()
+        PARAMS = dict()
 
         for key, value in locals().items():
             if (value != "") and (key != "self"):
-                params[key] = value
+                PARAMS[key] = value
 
 
         response = self.query_api(
             endpoint = NBIA_ENDPOINTS.GET_SERIES,
-            params = params)
+            params = PARAMS)
 
         return response
 
 
     def downloadSeries(
-        self, SeriesInstanceUID: str, downloadDir: str,
+        self,
+        SeriesInstanceUID: str,
+        downloadDir: str = "./NBIA-Download",
         filePattern: str = '%PatientName/%StudyDescription-%StudyDate/%SeriesNumber-%SeriesDescription-%SeriesInstanceUID/%InstanceNumber.dcm',
         overwrite: bool = False
         ) -> bool:
@@ -175,9 +203,17 @@ def downloadSeries(
                 )
 
             sorter.sortDICOMFiles(option="move", overwrite=overwrite)
-
-        return True
 
+        return True
 
+    # parsePARAMS is a helper function that takes a locals() dict and returns
+    # a dict with only the non-empty values
+    def parsePARAMS(self, params: dict) -> dict:
+        self.logger.debug("Parsing params: %s", params)
+        PARAMS = dict()
+        for key, value in params.items():
+            if (value != "") and (key != "self"):
+                PARAMS[key] = value
+        return PARAMS
 
 

src/nbiatoolkit/utils/logger.py

@@ -4,61 +4,58 @@
 
 def setup_logger(
     name: str,
-    debug: bool = False,
-    console_logging: bool = False,
     log_level: str = 'INFO',
-    log_format: str = '%(asctime)s | %(name)s | %(levelname)s | %(message)s',
+    console_logging: bool = False,
     log_file: str = None,
-    log_dir: str = None
+    log_dir: str = None,
+    log_format: str = '%(asctime)s | %(name)s | %(levelname)s | %(message)s',
+    datefmt: str = '%y-%m-%d %H:%M'
 ) -> logging.Logger:
     """
     Set up a logger object that can be used to log messages to a file and/or console with daily log file rotation.
 
     Args:
-        name (str): The name of the logger. Defaults to 'root'.
-        debug (bool): Whether to enable debug logging. Defaults to False.
-        console_logging (bool): Whether to enable console logging. Defaults to False.
-        log_file (str): The name of the log file if logging to a file. 
-        log_level (str): The logging level for the logger. Defaults to 'INFO'.
-        log_format (str): The format of the log messages. Defaults to '%(asctime)s | %(name)s | %(levelname)s | %(message)s'.
-        log_dir (str): The directory where the log file will be saved.
+        name (str): The name of the logger.
+        log_level (str, optional): The log level. Defaults to 'INFO'.
+        console_logging (bool, optional): Whether to log to console. Defaults to False.
+        log_file (str, optional): The log file name. Defaults to None.
+        log_dir (str, optional): The log directory. Defaults to None.
+        log_format (str, optional): The log format. Defaults to '%(asctime)s | %(name)s | %(levelname)s | %(message)s'.
+        datefmt (str, optional): The date format. Defaults to '%y-%m-%d %H:%M'.
 
     Returns:
         logger (logging.Logger): The logger object.
     """
-    # Convert log_level string to logging level object
+    # Validate log level
     level = getattr(logging, log_level.upper(), None)
     if not isinstance(level, int):
         raise ValueError(f'Invalid log level: {log_level}')
 
+    # Create logger
     logger = logging.getLogger(name)
     logger.setLevel(level)
 
     # Formatters
-    formatter = logging.Formatter(log_format)
+    formatter = logging.Formatter(fmt=log_format, datefmt=datefmt)
 
-    # Adding file handler with TimedRotatingFileHandler for daily rotation
+# Set up file handler with TimedRotatingFileHandler for daily rotation
     if log_file:
-        if log_dir:
+        try:
             # Ensure log directory exists
-            try:
+            if log_dir:
                 os.makedirs(log_dir, exist_ok=True)
-            except Exception as e:
-                raise IOError(f"Error creating log directory: {log_dir}") from e
-
-            log_file = os.path.join(log_dir, log_file)
+                log_file = os.path.join(log_dir, log_file)
 
-        try:
             file_handler = TimedRotatingFileHandler(log_file, when='midnight', interval=1)
             file_handler.setFormatter(formatter)
             file_handler.setLevel(level)
             logger.addHandler(file_handler)
         except Exception as e:
             raise IOError(f"Error setting up file handler for logger: {e}") from e
 
+    # Set up console handler if console_logging is True
     if console_logging:
         try:
-            # Setup console handler with the same formatter and level
             console_handler = logging.StreamHandler()
             console_handler.setFormatter(formatter)
             console_handler.setLevel(level)

tests/test_nbia.py

@@ -22,7 +22,7 @@ def nbia_collections(nbia_client):
 @pytest.fixture(scope="session")
 def nbia_patients(nbia_client, nbia_collections):
     patients = nbia_client.getPatients(
-        collection=nbia_collections[0], modality = "CT")
+        Collection=nbia_collections[0], Modality = "CT")
     return patients
 
 def test_nbiaclient_access_token(nbia_client):
@@ -41,7 +41,7 @@ def test_getBodyPartCounts_all(nbia_client):
     assert int(bodyparts[0]["Count"]) > 0
 
 def test_getBodyPartCounts_4DLung(nbia_client):
-    bodyparts = nbia_client.getBodyPartCounts(collection="4D-Lung")
+    bodyparts = nbia_client.getBodyPartCounts(Collection="4D-Lung")
     assert isinstance(bodyparts, list)
     assert len(bodyparts) > 0
     assert isinstance(bodyparts[0], dict)