Merge pull request #12 from jjjermiah/development

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jjjermiah · Nov 25, 2023 · 931eb4a · 931eb4a
2 parents 0d638cb + b199a83
commit 931eb4a
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}  
     strategy:  
       matrix:  
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, macos-latest]
         python-version: ["3.12"]
 
     steps:  

diff --git a/docs/example.ipynb b/docs/example.ipynb
@@ -25,19 +25,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2023-11-20 16:49:13,681 | NBIAClient | INFO | Setting up OAuth2 client... with username nbia_guest\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from nbiatoolkit import NBIAClient\n",
+    "from pprint import pprint\n",
     "\n",
     "# Instantiate the client. \n",
     "client = NBIAClient()"
@@ -64,22 +57,75 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Counts of Patients grouped by Body Parts\n",
-    "`getBodyPartCounts(collection: str = \"\", modality: str = \"\")`"
+    "#### get list of collection (names)\n",
+    "`getCollections()`"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2023-11-20 16:49:13,981 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/getBodyPartValuesAndCounts\n"
+      "['4D-Lung',\n",
+      " 'A091105',\n",
+      " 'ACNS0332',\n",
+      " 'ACRIN-6698',\n",
+      " 'ACRIN-Contralateral-Breast-MR']\n"
      ]
-    },
+    }
+   ],
+   "source": [
+    "collections = client.getCollections()\n",
+    "pprint(collections[0:5])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### get Counts of Patients for each collection\n",
+    "`getCollectionPatientCount()`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[{'Collection': '4D-Lung', 'PatientCount': '20'},\n",
+      " {'Collection': 'A091105', 'PatientCount': '83'},\n",
+      " {'Collection': 'ACNS0332', 'PatientCount': '85'},\n",
+      " {'Collection': 'ACRIN-6698', 'PatientCount': '385'},\n",
+      " {'Collection': 'ACRIN-Contralateral-Breast-MR', 'PatientCount': '984'}]\n"
+     ]
+    }
+   ],
+   "source": [
+    "collectionsPatientCount = client.getCollectionPatientCount()\n",
+    "pprint(collectionsPatientCount[0:5])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### get Counts of Patients grouped by Body Parts\n",
+    "`getBodyPartCounts(collection: str = \"\", modality: str = \"\")`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
@@ -95,7 +141,6 @@
     }
    ],
    "source": [
-    "from pprint import pprint\n",
     "bodypart_count = client.getBodyPartCounts()\n",
     "print(\"Total Number of Collections:\" + str(len(bodypart_count)))\n",
     "\n",
@@ -107,7 +152,47 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Get Series Data\n",
+    "# Get Patient Methods"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### get Patient IDs by Collection and Modality\n",
+    "`getPatientData(collection: str = \"\", modality: str = \"\")`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['100_HM10395', '101_HM10395', '102_HM10395', '103_HM10395', '104_HM10395']\n"
+     ]
+    }
+   ],
+   "source": [
+    "patients = client.getPatients(collection=\"4D-Lung\", modality=\"CT\")\n",
+    "pprint(patients[0:5])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Get Series Data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### get Series Data queried by parameters\n",
     "\n",
     "``` python\n",
     "getSeries(\n",
@@ -124,75 +209,78 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2023-11-20 16:51:10,330 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeries\n"
+      "There are 6690 series in the 4D-Lung collection.\n",
+      "{'BodyPartExamined': 'LUNG',\n",
+      " 'Collection': '4D-Lung',\n",
+      " 'CollectionURI': 'https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE',\n",
+      " 'FileSize': 26405988,\n",
+      " 'ImageCount': 50,\n",
+      " 'LicenseName': 'Creative Commons Attribution 3.0 Unported License',\n",
+      " 'LicenseURI': 'http://creativecommons.org/licenses/by/3.0/',\n",
+      " 'Manufacturer': 'Varian Imaging Laboratories, Switzerland',\n",
+      " 'ManufacturerModelName': 'Trilogy Cone Beam CT',\n",
+      " 'Modality': 'CT',\n",
+      " 'PatientID': '100_HM10395',\n",
+      " 'ProtocolName': '5.1 4DCT & ITV FB + 4D + INSP/EXP',\n",
+      " 'SeriesDate': '1997-10-03 00:00:00.0',\n",
+      " 'SeriesDescription': 'P4^P100^S113^I0, Gated, 70.0%',\n",
+      " 'SeriesInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',\n",
+      " 'SeriesNumber': 507,\n",
+      " 'SoftwareVersions': 'LightSpeedverrel',\n",
+      " 'StudyInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.552215730027211807644647167706',\n",
+      " 'TimeStamp': '2015-07-20 17:58:54.0'}\n"
      ]
     }
    ],
    "source": [
-    "seriesJSON = client.getSeries(Collection=\"4D-Lung\")"
+    "seriesJSON = client.getSeries(Collection=\"4D-Lung\")\n",
+    "print(f\"There are {len(seriesJSON)} series in the 4D-Lung collection.\")\n",
+    "pprint(seriesJSON[0])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[{'BodyPartExamined': 'LUNG',\n",
-      "  'Collection': '4D-Lung',\n",
-      "  'CollectionURI': 'https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE',\n",
-      "  'FileSize': 26405988,\n",
-      "  'ImageCount': 50,\n",
-      "  'LicenseName': 'Creative Commons Attribution 3.0 Unported License',\n",
-      "  'LicenseURI': 'http://creativecommons.org/licenses/by/3.0/',\n",
-      "  'Manufacturer': 'Varian Imaging Laboratories, Switzerland',\n",
-      "  'ManufacturerModelName': 'Trilogy Cone Beam CT',\n",
-      "  'Modality': 'CT',\n",
-      "  'PatientID': '100_HM10395',\n",
-      "  'ProtocolName': '5.1 4DCT & ITV FB + 4D + INSP/EXP',\n",
-      "  'SeriesDate': '1997-10-03 00:00:00.0',\n",
-      "  'SeriesDescription': 'P4^P100^S113^I0, Gated, 70.0%',\n",
-      "  'SeriesInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',\n",
-      "  'SeriesNumber': 507,\n",
-      "  'SoftwareVersions': 'LightSpeedverrel',\n",
-      "  'StudyInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.552215730027211807644647167706',\n",
-      "  'TimeStamp': '2015-07-20 17:58:54.0'},\n",
-      " {'BodyPartExamined': 'LUNG',\n",
-      "  'Collection': '4D-Lung',\n",
-      "  'CollectionURI': 'https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE',\n",
-      "  'FileSize': 26405988,\n",
-      "  'ImageCount': 50,\n",
-      "  'LicenseName': 'Creative Commons Attribution 3.0 Unported License',\n",
-      "  'LicenseURI': 'http://creativecommons.org/licenses/by/3.0/',\n",
-      "  'Manufacturer': 'Varian Imaging Laboratories, Switzerland',\n",
-      "  'ManufacturerModelName': 'Trilogy Cone Beam CT',\n",
-      "  'Modality': 'CT',\n",
-      "  'PatientID': '100_HM10395',\n",
-      "  'ProtocolName': '5.1 4DCT & ITV FB + 4D + INSP/EXP',\n",
-      "  'SeriesDate': '1997-10-07 00:00:00.0',\n",
-      "  'SeriesDescription': 'P4^P100^S116^I0, Gated, 70.0%',\n",
-      "  'SeriesInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884',\n",
-      "  'SeriesNumber': 507,\n",
-      "  'SoftwareVersions': 'LightSpeedverrel',\n",
-      "  'StudyInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.980344486630714096442107526343',\n",
-      "  'TimeStamp': '2015-07-20 17:40:07.0'}]\n"
+      "There are 350 series for patient 100_HM10395.\n",
+      "{'BodyPartExamined': 'LUNG',\n",
+      " 'Collection': '4D-Lung',\n",
+      " 'CollectionURI': 'https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE',\n",
+      " 'FileSize': 26405988,\n",
+      " 'ImageCount': 50,\n",
+      " 'LicenseName': 'Creative Commons Attribution 3.0 Unported License',\n",
+      " 'LicenseURI': 'http://creativecommons.org/licenses/by/3.0/',\n",
+      " 'Manufacturer': 'Varian Imaging Laboratories, Switzerland',\n",
+      " 'ManufacturerModelName': 'Trilogy Cone Beam CT',\n",
+      " 'Modality': 'CT',\n",
+      " 'PatientID': '100_HM10395',\n",
+      " 'ProtocolName': '5.1 4DCT & ITV FB + 4D + INSP/EXP',\n",
+      " 'SeriesDate': '1997-10-03 00:00:00.0',\n",
+      " 'SeriesDescription': 'P4^P100^S113^I0, Gated, 70.0%',\n",
+      " 'SeriesInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',\n",
+      " 'SeriesNumber': 507,\n",
+      " 'SoftwareVersions': 'LightSpeedverrel',\n",
+      " 'StudyInstanceUID': '1.3.6.1.4.1.14519.5.2.1.6834.5010.552215730027211807644647167706',\n",
+      " 'TimeStamp': '2015-07-20 17:58:54.0'}\n"
      ]
     }
    ],
    "source": [
-    "from pprint import pprint\n",
-    "\n",
-    "pprint(seriesJSON[0:2])"
+    "seriesbyPatientJSON = client.getSeries(PatientID=patients[0])\n",
+    "print(f\"There are {len(seriesbyPatientJSON)} series for patient {patients[0]}.\")\n",
+    "pprint(seriesbyPatientJSON[0])"
    ]
   },
   {

diff --git a/driver.py b/driver.py
@@ -9,13 +9,19 @@
 PASSWORD = "q6mJyLD8cPeGTwg!"
 
 
-client = NBIAClient(username=USERNAME, password=PASSWORD)
+client = NBIAClient(
+    username=USERNAME, 
+    password=PASSWORD,
+    log_level="DEBUG")
+
 series = client.getSeries(Collection="RADCURE")
 
 seriesList = [_["SeriesInstanceUID"] for _ in series]
 seriesList = seriesList[0:5]
 
 
+
+
 def download(series) -> bool:
     response = client.downloadSeries(
         SeriesInstanceUID = series,

diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py
@@ -21,7 +21,10 @@ def __init__(self,
 
         # Setup logger
         self.logger = setup_logger(
-            name = "NBIAClient", console_logging=True, log_level=log_level)
+            name = "NBIAClient", 
+            console_logging=True, 
+            log_level=log_level,
+            log_file = None)
 
         # Setup OAuth2 client
         self.logger.debug("Setting up OAuth2 client... with username %s", username)
@@ -33,7 +36,7 @@ def query_api(self, endpoint: NBIA_ENDPOINTS, params: dict = {}) -> dict:
         query_url = base_url + endpoint.value
 
         self.logger.debug("Querying API endpoint: %s", query_url)
-        self.logger.debug("API headers: %s", (self._createDebugURL(endpoint, params)))
+        # self.logger.debug("API headers: %s", (self._createDebugURL(endpoint, params)))
 
         try:
             response = requests.get(

diff --git a/src/nbiatoolkit/utils/__init__.py b/src/nbiatoolkit/utils/__init__.py
@@ -1,6 +1,8 @@
 from .logger import setup_logger
 from .nbia_endpoints import NBIA_ENDPOINTS
+from .md5 import validateMD5
 __all__ = [
     "setup_logger",
-    "NBIA_ENDPOINTS"
+    "NBIA_ENDPOINTS",
+    "validateMD5"
 ]
diff --git a/src/nbiatoolkit/utils/nbia_endpoints.py b/src/nbiatoolkit/utils/nbia_endpoints.py
@@ -14,12 +14,10 @@ class NBIA_ENDPOINTS(Enum):
 
     DOWNLOAD_SERIES = 'v2/getImageWithMD5Hash'
 
-    # TIMES OUT???
-    GET_SERIES_SIZE = 'v2/getSeriesSize'
-    GET_UPDATED_SERIES = 'v2/getUpdatedSeries'
-
-    # curl -H 'Authorization:Bearer eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJkZGFhMGY3YS1kZTBmLTRkYWQtYjM1ZS05MjljYjBiMTY3YjgifQ.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.YIrmcZcDT9w22diON2bFxDVcY1-BU59FwcklsnYHBT0' -k "https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeriesMetaData?SeriesInstanceUID=1.3.6.1.4.1.9590.100.1.2.374115997511889073021386151921807063992"
 
+    GET_SERIES_SIZE = 'v2/getSeriesSize'        # TIMES OUT???
+    GET_UPDATED_SERIES = 'v2/getUpdatedSeries'
+
     # https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeriesMetaData?SeriesInstanceUID=1.3.6.1.4.1.9590.100.1.2.374115997511889073021386151921807063992
 
     # https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeriesSize?SeriesInstanceUID=1.3.6.1.4.1.9590.100.1.2.374115997511889073021386151921807063992