diff --git a/applications/imaging_ai_segmentator/CMakeLists.txt b/applications/imaging_ai_segmentator/CMakeLists.txt index 83fbc00c..bea672b5 100644 --- a/applications/imaging_ai_segmentator/CMakeLists.txt +++ b/applications/imaging_ai_segmentator/CMakeLists.txt @@ -46,9 +46,6 @@ if(HOLOHUB_DOWNLOAD_DATASETS) add_custom_command( OUTPUT imaging_ai_segmentator_data COMMAND gdown -q https://drive.google.com/uc?id=1PHpFWboimEXmMSe2vBra6T8SaCMC2SHT -O ${DOWNLOAD_DATA_DIR}/models/model.pt - # uncomment the two commands below if URL accessible and automated download desired. - #COMMAND wget -q --no-parent -r -l 1 -nd -N "https://urm.nvidia.com/artifactory/sw-holoscan-generic/test_data/dicom/TCIA_CT_ABDOMEN/" - #WORKING_DIRECTORY ${DOWNLOAD_DATA_DIR}/dicom COMMENT "Downloading imaging_ai_segmentator model using gdown..." ) add_custom_target(run ALL diff --git a/applications/imaging_ai_segmentator/README.md b/applications/imaging_ai_segmentator/README.md index a704d6d5..12654958 100644 --- a/applications/imaging_ai_segmentator/README.md +++ b/applications/imaging_ai_segmentator/README.md @@ -33,10 +33,10 @@ This application uses the [MONAI whole-body segmentation model](https://github.c The input for this application is a folder of DICOM image files from a CT series. For testing, CT scan images can be downloaded from [The Cancer Imaging Archive](https://nbia.cancerimagingarchive.net/nbia-search/), subject to [Data Usage Policies and Restrictions](https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/) -One such data set, a CT Abdomen series described as `ABD/PANC_3.0_B31f`, is copied and made available [here](https://urm.nvidia.com/artifactory/sw-holoscan-generic/test_data/dicom/TCIA_CT_ABDOMEN/), though access is currently restricted to Nvidia internal use. +One such data set, a CT Abdomen series described as `ABD/PANC_3.0_B31f`, was used in testing the application. Other DICOM CT Abdomen series can be downloaded from TCIA as test inputs, and, of course, users' own DICOM seriese shall equally work. **_Note_**: -Before the test DICOM data is made publicly accessible, please download the DICOM files manually and save them in a folder, preferably named `data/imaging_ai_segmentator/dicom` under the project root, as this folder name is used in the examples in the following steps. Manual download scripts are shown in [`Run the Application in Dev Environment`](#run-the-application-in-dev-environment) +Please download, or otherwise make available, DICOM files of a CT Abdomen series and save them in a folder, preferably named `data/imaging_ai_segmentator/dicom` under the project root, as this folder name is used in the examples in the following steps. Manual download scripts are shown in [`Run the Application in Dev Environment`](#run-the-application-in-dev-environment) ### Data Citation @@ -49,7 +49,7 @@ There are a number of ways to build and run this application, as well as packagi ### Quick Start Using Holohub Container -This is the simplest and fastest way to see the application in action running as a container. As of now, the input DICOM files must be first downloaded and saved in the folder `$PWD/data/imaging_ai_segmentator/dicom`, whereas the PyTorch model is automatically downloaded when container image is built. +This is the simplest and fastest way to see the application in action running as a container. The input DICOM files must first be downloaded and saved in the folder `$PWD/data/imaging_ai_segmentator/dicom`, whereas the PyTorch model is automatically downloaded when container image is built. Use the following to build and run the application: @@ -91,15 +91,7 @@ Set the environment variables for the application source applications/imaging_ai_segmentator/env_settings.sh ``` -Download images of a CT series from [TCIA](https://nbia.cancerimagingarchive.net/nbia-search/) -(The following example shows downloading from the Holohub artifactory) - -```bash -wget --no-parent -r -l 1 "https://urm.nvidia.com/artifactory/sw-holoscan-generic/test_data/dicom/TCIA_CT_ABDOMEN/" -rm -f -r $HOLOSCAN_INPUT_PATH -mkdir -p $HOLOSCAN_INPUT_PATH -cp -r urm.nvidia.com/artifactory/sw-holoscan-generic/test_data/dicom/TCIA_CT_ABDOMEN/ $HOLOSCAN_INPUT_PATH -``` +If not already done, download images of a CT series from [TCIA](https://nbia.cancerimagingarchive.net/nbia-search/), unzip if necessary, and save the folder of DICOM files under the folder `$HOLOSCAN_INPUT_PATH`. Optionally download the AI model from [MONAI Model Zoo](https://github.com/Project-MONAI/model-zoo/tree/dev/models/wholeBody_ct_segmentation), or wait till the build step to have it downloaded automatically @@ -166,17 +158,9 @@ Set the environment variables for the application source applications/imaging_ai_segmentator/env_settings.sh ``` -Download images of a CT series from [TCIA](https://nbia.cancerimagingarchive.net/nbia-search/) -(The following example shows downloading from the Holohub artifactory) +If not already done, download images of a CT series from [TCIA](https://nbia.cancerimagingarchive.net/nbia-search/), unzip if necessary, and save the folder of DICOM files under the folder `$HOLOSCAN_INPUT_PATH`. -```bash -wget --no-parent -r -l 1 "https://urm.nvidia.com/artifactory/sw-holoscan-generic/test_data/dicom/TCIA_CT_ABDOMEN/" -rm -f -r $HOLOSCAN_INPUT_PATH -mkdir -p $HOLOSCAN_INPUT_PATH -cp -r urm.nvidia.com/artifactory/sw-holoscan-generic/test_data/dicom/TCIA_CT_ABDOMEN/ $HOLOSCAN_INPUT_PATH -``` - -Download the AI model from [MONAI Model Zoo](https://github.com/Project-MONAI/model-zoo/tree/dev/models/wholeBody_ct_segmentation), or wait till the build step to have it downloaded automatically +Optionally download the AI model from [MONAI Model Zoo](https://github.com/Project-MONAI/model-zoo/tree/dev/models/wholeBody_ct_segmentation), or wait till the build step to have it downloaded automatically ```bash mkdir -p $HOLOSCAN_MODEL_PATH