Merge pull request #29 from sarthakpati/master

0.0.3 ready

Author: sarthakpati

CMakeLists.txt

@@ -13,7 +13,7 @@ SET( ${PROJECT_NAME}_Variant "Full" ) # the particular variant of CaPTk (Full/Ne
 
 SET( PROJECT_VERSION_MAJOR 0 )
 SET( PROJECT_VERSION_MINOR 0 )
-SET( PROJECT_VERSION_PATCH 3-dev )
+SET( PROJECT_VERSION_PATCH 3 )
 SET( PROJECT_VERSION_TWEAK )
 
 # check for the string "nonRelease" in the PROJECT_VERSION_PATCH variable
@@ -596,18 +596,18 @@ IF( NOT BUILD_DOCUMENTATION_ONLY )
     ENDIF()
   ENDIF()
 
-  # SET( DOWNLOAD_LINK "ftp://www.nitrc.org/home/groups/captk/downloads/models/torch/pt_3dresunet_fets_phase1_brats20pretrained_init_1.pbuf" )
-  # SET( FILE_TO_EXTRACT "${PROJECT_SOURCE_DIR}/OpenFederatedLearning/bin/federations/weights/pt_3dresunet_fets_phase1_brats20pretrained_init_1.pbuf")
+  SET( DOWNLOAD_LINK "ftp://www.nitrc.org/home/groups/captk/downloads/models/torch/pt_3dresunet_fets_phase1_brats20pretrained_init_1.pbuf" )
+  SET( FILE_TO_EXTRACT "${PROJECT_SOURCE_DIR}/OpenFederatedLearning/bin/federations/weights/pt_3dresunet_fets_phase1_brats20pretrained_init_1.pbuf")
 
-  # IF( NOT EXISTS "${FILE_TO_EXTRACT}" )
+  IF( NOT EXISTS "${FILE_TO_EXTRACT}" )
 
-  #   # download exe from url
-  #   MESSAGE( STATUS "Downloading weights for BraTS evaluation model" )
-  #   FILE(DOWNLOAD "${DOWNLOAD_LINK}" "${FILE_TO_EXTRACT}" TIMEOUT 1000000 STATUS STATUS_CODE SHOW_PROGRESS)
-  #   IF(NOT STATUS_CODE EQUAL 0)
-  #     MESSAGE(FATAL_ERROR "Failed to download BraTS evaluation model weights. Status=${STATUS_CODE}")
-  #   ENDIF()
-  # ENDIF()
+    # download exe from url
+    MESSAGE( STATUS "Downloading weights for BraTS evaluation model" )
+    FILE(DOWNLOAD "${DOWNLOAD_LINK}" "${FILE_TO_EXTRACT}" TIMEOUT 1000000 STATUS STATUS_CODE SHOW_PROGRESS)
+    IF(NOT STATUS_CODE EQUAL 0)
+      MESSAGE(FATAL_ERROR "Failed to download BraTS evaluation model weights. Status=${STATUS_CODE}")
+    ENDIF()
+  ENDIF()
 
   # copy network information
   ## todo: change to a direct installation so that git doesn't get confused that submodule has changed

OpenFederatedLearning

@@ -30,6 +30,13 @@ inputs:
       position: 1
       prefix: -cwl
     doc: Generates a .cwl file for the software.
+  trainPlan:
+    type: boolean?
+    label: YAML file
+    inputBinding:
+      position: 1
+      prefix: -tp
+    doc: Training plan.Defaults to 'fets_phase1_1'.
   LoggingDir:
     type: Directory?
     label: Dir with write access

data/cwlFiles/FeTS_CLI.cwl

@@ -143,6 +143,19 @@ wget https://raw.githubusercontent.com/FETS-AI/Front-End/master/src/applications
 
 ## Training
 
+### Ensure Sanity Checking Is Done
+
+Proceed to training once [sanity check](#sanity-check) is successfully finished.
+### Transfer Certificates
+
+If you have a [signed certificate from a previous installation](https://fets-ai.github.io/Front-End/setup#set-up-the-collaborator), ensure they are copied **before** trying to train:
+```bash
+cd ${fets_root_dir}/bin/
+cp -r ${fets_root_dir_old}/bin/OpenFederatedLearning/bin/federations/pki/client ./OpenFederatedLearning/bin/federations/pki
+```
+
+### Start Training
+
 ```bash
 ${fets_root_dir}/bin/FeTS_CLI -d /path/to/output/DataForFeTS \ # input data, ensure "final_seg" is present for each subject
   -c ${collaborator_common_name} \ # common collaborator name created during setup

docs/runningApplication.md

@@ -60,7 +60,8 @@ int main(int argc, char** argv)
   }
   else
   {
-    loggingDir = dataDir + "/logs";
+    loggingDir = cbica::createTemporaryDirectory() + "/logs";
+    std::cout << "Using the following directory as logging directory: " << loggingDir << "\n";
     cbica::createDir(loggingDir);
   }
 
@@ -398,30 +399,38 @@ int main(int argc, char** argv)
   } // end of trainingRequested check
   else // for training
   {
-    std::string specialArgs, args, hardcodedModelName;
-    if (trainingRequested)
-    {
-      specialArgs = "-col " + colName;
-    }
-
+    std::string args = " -d " + dataDir + " -ld " + loggingDir + " -col " + colName + device_arg,
+      hardcodedModelName;
+    
     if (!cbica::isFile(hardcodedPythonPath))
     {
       std::cerr << "The python virtual environment was not found, please refer to documentation to initialize it.\n";
       return EXIT_FAILURE;
     }
+    
+    {
+      std::cout << "Starting model validation of 3DResUNet trained on BraTS20 training data...\n";
+
+      // brats20 model validation      
+      std::string fullCommandToRun = hardcodedPythonPath + " " + fetsApplicationPath;
+      fullCommandToRun += "/OpenFederatedLearning/bin/run_fets_validation.py";
+
+      auto temp_args = args + " -p fets_phase1_validate_full_brats_trained_model_1.yaml";
+
+      if (std::system((fullCommandToRun + " " + temp_args).c_str()) != 0)
+      {
+        std::cerr << "Couldn't complete the BraTS20 model validation task, please email [email protected]\n";
+      }
+    }
 
     std::string fullCommandToRun = hardcodedPythonPath + " " + fetsApplicationPath;
     fullCommandToRun += "/OpenFederatedLearning/bin/run_collaborator_from_flplan.py";
 
-    args += " -p " + hardcodedPlanName + ".yaml"
-      + " -d " + dataDir
-      + " -ld " + loggingDir;
-
-    args += device_arg;
+    auto temp_args = args + " -p " + hardcodedPlanName + ".yaml";
 
     std::cout << "Starting training...\n";
 
-    if (runCollaboratorTraining(fullCommandToRun + " " + args + " " + specialArgs) != 0)
+    if (runCollaboratorTraining(fullCommandToRun + " " + temp_args) != 0)
     {
       std::cerr << "Couldn't complete the training task, please email [email protected]\n";
       return EXIT_FAILURE;