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Change the model name in the Spleen seg example dataset to model.ts #222

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Dec 6, 2021
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Change the model name in the Spleen seg example dataset to model.ts #222

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10 changes: 5 additions & 5 deletions docs/source/getting_started/tutorials/03_segmentation_app.md
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Expand Up @@ -50,25 +50,25 @@ cd monai-deploy-app-sdk
# Install monai-deploy-app-sdk package
pip install monai-deploy-app-sdk

# Download/Extract ai_spleen_seg_data.zip from https://drive.google.com/file/d/1uTQsm8omwimBcp_kRXlduWBP2M6cspr1/view?usp=sharing
# Download/Extract ai_spleen_seg_data zip file from https://drive.google.com/file/d/1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n/view?usp=sharing

# Download ai_spleen_seg_data.zip
pip install gdown
gdown https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1
gdown https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n

# After downloading ai_spleen_seg_data.zip from the web browser or using gdown,
unzip -o ai_spleen_seg_data.zip
unzip -o ai_spleen_seg_data_updated_1203.zip

# Install necessary packages from the app
pip install monai pydicom SimpleITK Pillow nibabel

# Local execution of the app
python examples/apps/ai_spleen_seg_app/app.py -i dcm/ -o output -m model.pt
python examples/apps/ai_spleen_seg_app/app.py -i dcm/ -o output -m model.ts

# Package app (creating MAP docker image) using `-l DEBUG` option to see progress.
# This assumes that nvidia docker is installed in the local machine.
# Please see https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker to install nvidia-docker2.
monai-deploy package examples/apps/ai_spleen_seg_app --tag seg_app:latest --model model.pt -l DEBUG
monai-deploy package examples/apps/ai_spleen_seg_app --tag seg_app:latest --model model.ts -l DEBUG

# Run the app with docker image and input file locally
monai-deploy run seg_app:latest dcm/ output
Expand Down
30 changes: 15 additions & 15 deletions notebooks/tutorials/03_segmentation_app.ipynb
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Expand Up @@ -137,10 +137,10 @@
"Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.26.6)\n",
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data.zip\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_update_1203.zip\n",
"104MB [00:10, 10.3MB/s] \n",
"Archive: ai_spleen_seg_data.zip\n",
"Archive: ai_spleen_seg_data_updated_1203.zip\n",
" creating: dcm/\n",
" inflating: dcm/IMG0001.dcm \n",
" inflating: dcm/IMG0002.dcm \n",
Expand Down Expand Up @@ -657,17 +657,17 @@
" inflating: dcm/IMG0513.dcm \n",
" inflating: dcm/IMG0514.dcm \n",
" inflating: dcm/IMG0515.dcm \n",
" inflating: model.pt \n"
" inflating: model.ts \n"
]
}
],
"source": [
"# Download ai_spleen_seg_data.zip\n",
"# Download ai_spleen_seg_data test data zip file\n",
"!pip install gdown \n",
"!gdown https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1\n",
"!gdown https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"\n",
"# After downloading ai_spleen_seg_data.zip from the web browser or using gdown,\n",
"!unzip -o \"ai_spleen_seg_data.zip\""
"# After downloading ai_spleen_seg_data zip file from the web browser or using gdown,\n",
"!unzip -o \"ai_spleen_seg_data_updated_1203.zip\""
]
},
{
Expand Down Expand Up @@ -873,7 +873,7 @@
"source": [
"## Executing app locally\n",
"\n",
"We can execute the app in the Jupyter notebook. Note that the DICOM files of the CT Abdomen series must be present in the `dcm` and the Torch Script model at `model.pt`. Please use the actual path in your environment.\n"
"We can execute the app in the Jupyter notebook. Note that the DICOM files of the CT Abdomen series must be present in the `dcm` and the Torch Script model at `model.ts`. Please use the actual path in your environment.\n"
]
},
{
Expand Down Expand Up @@ -988,7 +988,7 @@
"source": [
"app = AISpleenSegApp()\n",
"\n",
"app.run(input=\"dcm\", output=\"output\", model=\"model.pt\")"
"app.run(input=\"dcm\", output=\"output\", model=\"model.ts\")"
]
},
{
Expand Down Expand Up @@ -1221,7 +1221,7 @@
" # -o <output folder>, for the output folder, default $PWD/output\n",
" # -m <model file>, for model file path\n",
" # e.g.\n",
" # python3 app.py -i input -m model.pt\n",
" # python3 app.py -i input -m model.ts\n",
" #\n",
" AISpleenSegApp(do_run=True)"
]
Expand Down Expand Up @@ -1370,7 +1370,7 @@
}
],
"source": [
"!python my_app -i dcm -o output -m model.pt"
"!python my_app -i dcm -o output -m model.ts"
]
},
{
Expand Down Expand Up @@ -1465,7 +1465,7 @@
"source": [
"import os\n",
"os.environ['MKL_THREADING_LAYER'] = 'GNU'\n",
"!monai-deploy exec my_app -i dcm -o output -m model.pt"
"!monai-deploy exec my_app -i dcm -o output -m model.ts"
]
},
{
Expand Down Expand Up @@ -1514,7 +1514,7 @@
}
],
"source": [
"!monai-deploy package -b nvcr.io/nvidia/pytorch:21.11-py3 my_app --tag my_app:latest -m model.pt"
"!monai-deploy package -b nvcr.io/nvidia/pytorch:21.11-py3 my_app --tag my_app:latest -m model.ts"
]
},
{
Expand Down Expand Up @@ -1698,7 +1698,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.13"
"version": "3.7.5"
}
},
"nbformat": 4,
Expand Down
18 changes: 9 additions & 9 deletions notebooks/tutorials/04_mis_tutorial.ipynb
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Expand Up @@ -113,7 +113,7 @@
" \"models\": [\r\n",
" {\r\n",
" \"name\": \"model-54dd6cdaac290a0e800c0fa627cd60410bb2cea173ac8bb2f4816cc54ea88c90\",\r\n",
" \"path\": \"/opt/monai/models/model/model.pt\"\r\n",
" \"path\": \"/opt/monai/models/model/model.ts\"\r\n",
" }\r\n",
" ],\r\n",
" \"resources\": {\r\n",
Expand Down Expand Up @@ -270,7 +270,7 @@
"| `map.gpu` | Number of GPUs requested by application which can be obtained either from `pkg.json` OR from when we created app.py (check @resource decorator) |\n",
"| `map.inputPath` | Input volume path within MAP container, can be derived by appending the `input.path` with the `working-directory` in `app.json` |\n",
"| `map.outputPath` | Output volume path within MAP container, can be derived by appending the `output.path` with the `working-directory` in `app.json` |\n",
"| `map.modelPath` | Model volume path within MAP container, can be derived using a `path` of an entry under `models` in `pkg.json`, and taking the sub-path where the `/model` folder resides (ex: `path: \"/opt/monai/models/model/model.pt\"` -> `\"/opt/monai/models\"`) |"
"| `map.modelPath` | Model volume path within MAP container, can be derived using a `path` of an entry under `models` in `pkg.json`, and taking the sub-path where the `/model` folder resides (ex: `path: \"/opt/monai/models/model/model.ts\"` -> `\"/opt/monai/models\"`) |"
]
},
{
Expand Down Expand Up @@ -452,10 +452,10 @@
"Requirement already satisfied: soupsieve>1.2 in /home/gupta/miniconda3/envs/monairsna/lib/python3.6/site-packages (from beautifulsoup4->gdown) (2.3.1)\n",
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gupta/miniconda3/envs/monairsna/lib/python3.6/site-packages (from requests[socks]->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1\n",
"To: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data.zip\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
"100%|████████████████████████████████████████| 104M/104M [00:20<00:00, 4.97MB/s]\n",
"Archive: ai_spleen_seg_data.zip\n",
"Archive: ai_spleen_seg_data_updated_1203.zip\n",
" inflating: dcm/IMG0001.dcm \n",
" inflating: dcm/IMG0002.dcm \n",
" inflating: dcm/IMG0003.dcm \n",
Expand Down Expand Up @@ -983,16 +983,16 @@
" inflating: dcm/IMG0513.dcm \n",
" inflating: dcm/IMG0514.dcm \n",
" inflating: dcm/IMG0515.dcm \n",
" inflating: model.pt \n",
" inflating: model.ts \n",
"input.zip\n"
]
}
],
"source": [
"# Download ai_spleen_seg_data.zip if not done so already\n",
"# Download ai_spleen_seg_data if not done so already\n",
"!pip install gdown \n",
"!gdown https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1\n",
"!unzip -o \"ai_spleen_seg_data.zip\"\n",
"!gdown https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"!unzip -o \"ai_spleen_seg_data_updated_1203.zip\"\n",
"\n",
"!cd dcm; zip -rq ../input.zip *\n",
"!ls input.zip"
Expand Down
32 changes: 16 additions & 16 deletions notebooks/tutorials/05_full_tutorial.ipynb
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Expand Up @@ -128,10 +128,10 @@
"Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.26.6)\n",
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data.zip\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
"104MB [00:10, 10.3MB/s] \n",
"Archive: ai_spleen_seg_data.zip\n",
"Archive: ai_spleen_seg_data_update_1203.zip\n",
" creating: dcm/\n",
" inflating: dcm/IMG0001.dcm \n",
" inflating: dcm/IMG0002.dcm \n",
Expand Down Expand Up @@ -648,17 +648,17 @@
" inflating: dcm/IMG0513.dcm \n",
" inflating: dcm/IMG0514.dcm \n",
" inflating: dcm/IMG0515.dcm \n",
" inflating: model.pt \n"
" inflating: model.ts \n"
]
}
],
"source": [
"# Download ai_spleen_seg_data.zip\n",
"# Download ai_spleen_seg_data test data zip file\n",
"!pip install gdown \n",
"!gdown https://drive.google.com/uc?id=1uTQsm8omwimBcp_kRXlduWBP2M6cspr1\n",
"!gdown https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"\n",
"# After downloading ai_spleen_seg_data.zip from the web browser or using gdown,\n",
"!unzip -o \"ai_spleen_seg_data.zip\""
"# After downloading ai_spleen_seg_data zip file from the web browser or using gdown,\n",
"!unzip -o \"ai_spleen_seg_data_updated_1203.zip\""
]
},
{
Expand Down Expand Up @@ -864,7 +864,7 @@
"source": [
"## Executing app locally\n",
"\n",
"We can execute the app in the Jupyter notebook. Note that the DICOM files of the CT Abdomen series must be present in the `dcm` and the Torch Script model at `model.pt`. Please use the actual path in your environment.\n"
"We can execute the app in the Jupyter notebook. Note that the DICOM files of the CT Abdomen series must be present in the `dcm` and the Torch Script model at `model.ts`. Please use the actual path in your environment.\n"
]
},
{
Expand Down Expand Up @@ -935,7 +935,7 @@
"source": [
"app = AISpleenSegApp()\n",
"\n",
"app.run(input=\"dcm\", output=\"output\", model=\"model.pt\")"
"app.run(input=\"dcm\", output=\"output\", model=\"model.ts\")"
]
},
{
Expand Down Expand Up @@ -1168,7 +1168,7 @@
" # -o <output folder>, for the output folder, default $PWD/output\n",
" # -m <model file>, for model file path\n",
" # e.g.\n",
" # python3 app.py -i input -m model.pt\n",
" # python3 app.py -i input -m model.ts\n",
" #\n",
" AISpleenSegApp(do_run=True)"
]
Expand Down Expand Up @@ -1276,7 +1276,7 @@
}
],
"source": [
"!python my_app -i dcm -o output -m model.pt"
"!python my_app -i dcm -o output -m model.ts"
]
},
{
Expand Down Expand Up @@ -1328,7 +1328,7 @@
}
],
"source": [
"!monai-deploy exec my_app -i dcm -o output -m model.pt"
"!monai-deploy exec my_app -i dcm -o output -m model.ts"
]
},
{
Expand Down Expand Up @@ -1377,7 +1377,7 @@
}
],
"source": [
"!monai-deploy package my_app --tag my_app:latest -m model.pt"
"!monai-deploy package my_app --tag my_app:latest -m model.ts"
]
},
{
Expand Down Expand Up @@ -1634,7 +1634,7 @@
" \"models\": [\n",
" {\n",
" \"name\": \"model-54dd6cdaac290a0e800c0fa627cd60410bb2cea173ac8bb2f4816cc54ea88c90\",\n",
" \"path\": \"/opt/monai/models/model/model.pt\"\n",
" \"path\": \"/opt/monai/models/model/model.ts\"\n",
" }\n",
" ],\n",
" \"resources\": {\n",
Expand Down Expand Up @@ -1791,7 +1791,7 @@
"| `map.gpu` | Number of GPUs requested by application which can be obtained either from `pkg.json` OR from when we created app.py (check @resource decorator) |\n",
"| `map.inputPath` | Input volume path within MAP container, can be derived by appending the `input.path` with the `working-directory` in `app.json` |\n",
"| `map.outputPath` | Output volume path within MAP container, can be derived by appending the `output.path` with the `working-directory` in `app.json` |\n",
"| `map.modelPath` | Model volume path within MAP container, can be derived using a `path` of an entry under `models` in `pkg.json`, and taking the sub-path where the `/model` folder resides (ex: `path: \"/opt/monai/models/model/model.pt\"` -> `\"/opt/monai/models\"`) |"
"| `map.modelPath` | Model volume path within MAP container, can be derived using a `path` of an entry under `models` in `pkg.json`, and taking the sub-path where the `/model` folder resides (ex: `path: \"/opt/monai/models/model/model.ts\"` -> `\"/opt/monai/models\"`) |"
]
},
{
Expand Down