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docs: re-run with new adds
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@jjjermiah
jjjermiah committed Jan 7, 2024
1 parent 48174bd commit 36410f2
Showing 1 changed file with 19 additions and 90 deletions.
109 changes: 19 additions & 90 deletions docs/Tutorial.ipynb
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},
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{
"name": "stderr",
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"text": [
"24-01-07 11:57 | NBIAClient | DEBUG | Setting up OAuth2 client... with username nbia_guest\n"
]
}
],
"outputs": [],
"source": [
"from nbiatoolkit import NBIAClient\n",
"from pprint import pprint\n",
Expand All @@ -49,7 +41,7 @@
},
{
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"execution_count": null,
"execution_count": 2,
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Expand All @@ -74,16 +66,9 @@
},
{
"cell_type": "code",
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"text": [
"24-01-07 11:57 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getCollectionValues\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -111,16 +96,9 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
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{
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"text": [
"24-01-07 11:57 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/getCollectionValuesAndCounts\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -148,17 +126,9 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
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"text": [
"24-01-07 11:57 | NBIAClient | DEBUG | Parsing params: {'self': <nbiatoolkit.nbia.NBIAClient object at 0x116aff560>, 'Collection': '', 'Modality': ''}\n",
"24-01-07 11:57 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/getBodyPartValuesAndCounts\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -198,17 +168,9 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"metadata": {},
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{
"name": "stderr",
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"text": [
"24-01-07 11:58 | NBIAClient | DEBUG | Parsing params: {'self': <nbiatoolkit.nbia.NBIAClient object at 0x116aff560>, 'Collection': '4D-Lung', 'Modality': 'CT'}\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getPatientByCollectionAndModality\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -250,16 +212,9 @@
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{
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"execution_count": null,
"execution_count": 7,
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"text": [
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeries\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -295,16 +250,9 @@
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"execution_count": 8,
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"name": "stderr",
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"text": [
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeries\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -355,7 +303,7 @@
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{
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"outputs": [
{
Expand All @@ -381,37 +329,28 @@
},
{
"cell_type": "code",
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"execution_count": 10,
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{
"name": "stderr",
"name": "stdout",
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"text": [
"24-01-07 11:58 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n"
"Downloading to: /Users/bhklab/Documents/GitHub/NBIA-toolkit/docs/data\n"
]
},
{
"name": "stdout",
"name": "stderr",
"output_type": "stream",
"text": [
"Downloading to: /Users/bhklab/Documents/GitHub/NBIA-toolkit/docs/data\n"
"Downloading 5 series: 0%| | 0/5 [00:00<?, ?it/s]"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Downloading 5 series: 0%| | 0/5 [00:00<?, ?it/s]24-01-07 11:58 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825\n",
"Downloading 5 series: 20%|██ | 1/5 [00:02<00:10, 2.61s/it]24-01-07 11:58 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"Downloading 5 series: 100%|██████████| 5/5 [00:04<00:00, 1.05it/s]"
"Downloading 5 series: 100%|██████████| 5/5 [00:10<00:00, 2.10s/it]"
]
},
{
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},
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{
"name": "stderr",
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"text": [
"24-01-07 12:05 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921\n",
"Downloading 5 series: 0%| | 0/5 [00:00<?, ?it/s]24-01-07 12:05 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"24-01-07 12:05 | NBIAClient | DEBUG | Downloading series: 1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825\n",
"Downloading 5 series: 20%|██ | 1/5 [00:02<00:09, 2.29s/it]24-01-07 12:05 | NBIAClient | DEBUG | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/v2/getImageWithMD5Hash\n",
"Downloading 5 series: 100%|██████████| 5/5 [00:05<00:00, 1.04s/it]\n"
"Downloading 5 series: 100%|██████████| 5/5 [00:05<00:00, 1.13s/it]\n"
]
},
{
Expand All @@ -496,7 +425,7 @@
"True"
]
},
"execution_count": 19,
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
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