update docs

jjjermiah · Nov 20, 2023 · 65ba441 · 65ba441
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,4 +1,4 @@
-name: Unit Testsfrom nbiatoolkit import NBIAClient 
+name: Unit Tests
 
 on: [push]  
 

diff --git a/.gitignore b/.gitignore
@@ -137,3 +137,4 @@ old_src
 resources/*
 dicomsort.py
 NBIA-toolkit.code-workspace
+docs/data/*
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,4 +1,4 @@
-# Required
+https://github.com/jjjermiah/NBIA-toolkit/tree/main# Required
 version: 2
 
 # Image to use

diff --git a/docs/example.ipynb b/docs/example.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Example Usage: python3 examples.ipynb\n",
+    "# Example Usage: \n",
     "### Description: \n",
     "This is a simple example of how to use the `nbiatoolkit` package."
    ]
@@ -13,7 +13,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Setup \n",
+    "# Setup \n",
     "\n",
     "By default the client will use the Public API with the Guest Login credentials.\n",
     "from the nbia which has access to all public data. \n",
@@ -25,9 +25,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "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"
+     ]
+    }
+   ],
    "source": [
     "from nbiatoolkit import NBIAClient\n",
     "\n",
@@ -37,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,7 +57,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Get Collection Methods"
+    "# Get Collection Methods"
    ]
   },
   {
@@ -62,9 +70,30 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "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"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Total Number of Collections:98\n",
+      "First 5 body parts:\n",
+      "[{'BodyPartExamined': 'NOT SPECIFIED', 'Count': '8490'},\n",
+      " {'BodyPartExamined': 'ABDOMEN', 'Count': '2968'},\n",
+      " {'BodyPartExamined': 'ABDOMEN CAVIT', 'Count': '2'},\n",
+      " {'BodyPartExamined': 'ABDOMENPELVIC', 'Count': '2'},\n",
+      " {'BodyPartExamined': 'ABDOMENPELVIS', 'Count': '51'}]\n"
+     ]
+    }
+   ],
    "source": [
     "from pprint import pprint\n",
     "bodypart_count = client.getBodyPartCounts()\n",
@@ -74,94 +103,184 @@
     "pprint(bodypart_count[0:5])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Get Series Data\n",
+    "\n",
+    "``` python\n",
+    "getSeries(\n",
+    "        Collection: str = \"\", \n",
+    "        PatientID: str = \"\",\n",
+    "        StudyInstanceUID: str = \"\",\n",
+    "        Modality: str = \"\",\n",
+    "        SeriesInstanceUID: str = \"\",\n",
+    "        BodyPartExamined: str = \"\",\n",
+    "        ManufacturerModelName: str = \"\",\n",
+    "        Manufacturer: str = \"\") \n",
+    "```"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "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"
+     ]
+    }
+   ],
    "source": [
-    "# add /home/bioinf/bhklab/jermiah/projects/NBIA-toolkit/src to path\n",
-    "import sys, os\n",
-    "import requests\n",
-    "sys.path.append(os.path.abspath(\"/home/bioinf/bhklab/jermiah/projects/NBIA-toolkit/src\"))\n",
+    "seriesJSON = client.getSeries(Collection=\"4D-Lung\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "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"
+     ]
+    }
+   ],
+   "source": [
+    "from pprint import pprint\n",
     "\n",
-    "from nbiatoolkit.utils import NBIA_ENDPOINTS\n",
-    "import pandas as pd\n",
-    "from pprint import pprint"
+    "pprint(seriesJSON[0:2])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# download Series Data\n",
+    "``` python\n",
+    "downloadSeries(\n",
+    "    SeriesInstanceUID: str,\n",
+    "    downloadDir: str)\n",
+    "```"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',\n",
+       " '1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884',\n",
+       " '1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921',\n",
+       " '1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963',\n",
+       " '1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825']"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "response = client.getSeries(Collection=\"4D-Lung\")\n",
-    "pprint(response[0:5])\n",
-    "# df = pd.DataFrame(response)\n",
-    "# df.head()"
+    "# first get a list of the SeriesInstanceUIDs\n",
+    "seriesUIDS = [series['SeriesInstanceUID'] for series in seriesJSON]\n",
+    "seriesUIDS[0:5]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2023-11-20 16:08:28,847 | NBIAClient | INFO | Setting up OAuth2 client... with username nbia_guest\n",
-      "2023-11-20 16:08:29,136 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeries\n",
-      "2023-11-20 16:08:29,136 | NBIAClient | DEBUG | API headers: 'Authorization:Bearer eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJkZGFhMGY3YS1kZTBmLTRkYWQtYjM1ZS05MjljYjBiMTY3YjgifQ.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.7nI2jqCgAu646UGEp0uQWG5vxu_K_9dGGHHEcrgGMnE' -k 'https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeries?Collection=4D-Lung&params={'Collection': '4D-Lung', 'params': {...}}'\n"
+      "2023-11-20 16:55:28,455 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloading to: /home/bioinf/bhklab/jermiah/projects/NBIA-toolkit/docs/data\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2023-11-20 16:55:33,722 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
+      "2023-11-20 16:55:39,813 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
+      "2023-11-20 16:55:44,858 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
+      "2023-11-20 16:55:49,399 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n"
      ]
     },
     {
      "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",
-      "<class 'dict'>\n",
-      "\n",
-      "v2/getImageWithMD5Hash\n",
-      "<Response [200]>\n"
+      "['1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921', '1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884', '1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695', '1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963', '1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825']\n"
      ]
     }
    ],
    "source": [
-    "from nbiatoolkit import NBIAClient\n",
-    "import requests\n",
-    "from pprint import pprint\n",
-    "import io, zipfile\n",
-    "\n",
-    "client = NBIAClient(log_level=\"DEBUG\")\n",
-    "series = client.getSeries(Collection=\"4D-Lung\")\n",
-    "pprint(series[0])\n",
-    "print(type(series[0]))\n",
-    "print()\n",
-    "response = client.downloadSeries(series[0][\"SeriesInstanceUID\"])\n",
-    "pprint(response)\n",
-    "\n",
-    "file = zipfile.ZipFile(io.BytesIO(response.content))\n",
-    "file.extractall(path = \".\")"
+    "# call client.downloadSeries() on each SeriesInstanceUID\n",
+    "import os\n",
+    "downloadDir = \"./data\"\n",
+    "os.makedirs(downloadDir, exist_ok=True)\n",
+    "print(\"Downloading to: \" + os.path.abspath(downloadDir))\n",
+    "for seriesUID in seriesUIDS[0:5]:\n",
+    "    client.downloadSeries(seriesUID, downloadDir)\n",
+    "    \n",
+    "pprint(os.listdir(downloadDir))\n",
+    "    "
    ]
   },
   {

diff --git a/docs/index.md b/docs/index.md
@@ -2,7 +2,7 @@
 ```
 
 ```{toctree}
-:maxdepth: 1
+:maxdepth: 2
 :hidden:
 
 example.ipynb

diff --git a/requirements.txt b/requirements.txt
@@ -3,4 +3,4 @@ pytest==7.2.2
 pytest-cov==4.0.0
 ruff==v0.0.260
 coverage-badge~=1.1.0
-requests==2.31.0
+requests==2.31.0