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Fixes for cli segment #73

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merged 4 commits into from
Aug 31, 2023
Merged

Fixes for cli segment #73

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2bb7b26
rename copied tmp files as expected
hasan7n Aug 28, 2023
45b3ee9
change inference script
hasan7n Aug 28, 2023
f61fb4d
fix model weights download path
hasan7n Aug 28, 2023
76d5a6f
misc fixes
hasan7n Aug 28, 2023
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ RUN echo "Installing separate environment for LabelFusion" && \
./venv/bin/pip install -e .

RUN echo "Downloading model weights" && \
cd bin/install/appdir/usr/data/fets && \
cd bin/install/appdir/usr/data && \
wget https://upenn.box.com/shared/static/f7zt19d08c545qt3tcaeg7b37z6qafum.zip -O nnunet.zip && \
unzip -qq nnunet.zip && rm -rf nnunet.zip && \
wget https://upenn.box.com/shared/static/hhvn8nb9xtz6nxcilmdl8kbx9n1afkdu.zip -O ./fets_consensus_models.zip && \
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28 changes: 14 additions & 14 deletions src/applications/FeTS_CLI_Segment.cxx
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Expand Up @@ -135,7 +135,7 @@ int main(int argc, char** argv)
hardcodedModelWeightPath = hardcodedOpenFLPath + "/bin/federations/weights/", // start with the common location
hardcodedPythonPath = hardcodedOpenFLPath + "/venv/bin/python", // this needs to change for Windows (wonder what happens for macOS?)
hardcodedPythonPath_fusion = fetsApplicationPath + "/LabelFusion/venv/bin/python", // this needs to change for Windows (wonder what happens for macOS?)
scriptToCall = hardcodedOpenFLPath + "/submodules/fets_ai/Algorithms/fets/bin/brainmage_validation_scores_to_disk.py"; // the script that does the inference and scoring
scriptToCall = hardcodedOpenFLPath + "/submodules/fets_ai/Algorithms/fets/bin/brainmage_validation_outputs_to_disk_newer.py"; // the script that does the inference and scoring
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auto fets_dataDir = getCaPTkDataDir();
auto hardcodedFinalModelsWeightsPath = fets_dataDir + "/fets_consensus";
auto hardcodedFinalModelsSeriesWeightsPath = fets_dataDir + "/fets_consensus_models/";
Expand Down Expand Up @@ -260,13 +260,13 @@ int main(int argc, char** argv)
std::string command_to_run;

auto current_temp_output = cbica::createTmpDir();
auto current_subject_temp_output = current_temp_output + "/subject";
auto current_subject_temp_output = current_temp_output + "/" + subjectDirs[s];
cbica::createDir(current_subject_temp_output);
// std::string file_t1gd, file_t1, file_t2, file_flair;
auto file_t1gd_temp = current_subject_temp_output + "/t1gd.nii.gz",
file_t1_temp = current_subject_temp_output + "/t1.nii.gz",
file_t2_temp = current_subject_temp_output + "/t2.nii.gz",
file_flair_temp = current_subject_temp_output + "/flair.nii.gz";
auto file_t1gd_temp = current_subject_temp_output + "/_t1gd.nii.gz",
file_t1_temp = current_subject_temp_output + "/_t1.nii.gz",
file_t2_temp = current_subject_temp_output + "/_t2.nii.gz",
file_flair_temp = current_subject_temp_output + "/_flair.nii.gz";
cbica::copyFile(file_t1gd, file_t1gd_temp);
cbica::copyFile(file_t1, file_t1_temp);
cbica::copyFile(file_t2, file_t2_temp);
Expand All @@ -277,9 +277,8 @@ int main(int argc, char** argv)
if (archs_split[a] == "fets_singlet")
{
std::cout << "== Starting inference using FeTS Singlet Consensus model...\n";
auto current_output_file = current_subject_temp_output + "/segmentation.nii.gz";
auto fileNameToCheck = subjectDirs[s] + "_fets_singlet_seg.nii.gz";
auto current_output_file_to_check = dataDir + "/" + subjectDirs[s] + "/" + fileNameToCheck;
auto fileNameToCheck = "fets_singlet.nii.gz";
auto current_output_file_to_check = currentSubjectOutputDir + fileNameToCheck;

if (!cbica::isFile(current_output_file_to_check))
{
Expand All @@ -290,13 +289,14 @@ int main(int argc, char** argv)
+ " -ET " + hardcodedFinalModelsSeriesWeightsPath + "52"
+ " -TC " + hardcodedFinalModelsSeriesWeightsPath + "52"
+ " -WT " + hardcodedFinalModelsSeriesWeightsPath + "52"
+ " -pp " + hardcodedOpenFLPlanPath + " -op " + current_outputDir + device_arg_for_second_script + " -dp " + current_temp_output + " -ptd";
+ " -pp " + hardcodedOpenFLPlanPath + " -mot _fets_singlet" + " -op " + current_outputDir + device_arg_for_second_script + " -dp " + current_temp_output;
if (std::system(command_to_run.c_str()) != 0)
{
std::cerr << "WARNING: The singlet model '52' did not run, please contact admin@fets.ai with this error.\n\n";
}
else
{
auto current_output_file = current_outputDir + "/" + subjectDirs[s] + "/" + subjectDirs[s] + "_fets_singlet_seg.nii.gz";
if (cbica::isFile(current_output_file))
{
cbica::copyFile(current_output_file, current_output_file_to_check);
Expand All @@ -308,9 +308,8 @@ int main(int argc, char** argv)
{
std::cout << "== Starting inference using FeTS Triplet Consensus model...\n";

auto current_output_file = current_subject_temp_output + "/segmentation.nii.gz";
auto fileNameToCheck = subjectDirs[s] + "_fets_triplet_seg.nii.gz";
auto current_output_file_to_check = dataDir + "/" + subjectDirs[s] + "/" + fileNameToCheck;
auto fileNameToCheck = "fets_triplet.nii.gz";
auto current_output_file_to_check = currentSubjectOutputDir + fileNameToCheck;

if (!cbica::isFile(current_output_file_to_check))
{
Expand All @@ -321,13 +320,14 @@ int main(int argc, char** argv)
+ " -ET " + hardcodedFinalModelsSeriesWeightsPath + "69"
+ " -TC " + hardcodedFinalModelsSeriesWeightsPath + "72"
+ " -WT " + hardcodedFinalModelsSeriesWeightsPath + "52"
+ " -pp " + hardcodedOpenFLPlanPath + " -op " + current_outputDir + device_arg_for_second_script + " -dp " + current_temp_output + " -ptd";
+ " -pp " + hardcodedOpenFLPlanPath + " -mot _fets_triplet" + " -op " + current_outputDir + device_arg_for_second_script + " -dp " + current_temp_output;
if (std::system(command_to_run.c_str()) != 0)
{
std::cerr << "WARNING: The triplet model '[69,72,52]' did not run, please contact admin@fets.ai with this error.\n\n";
}
else
{
auto current_output_file = current_outputDir + "/" + subjectDirs[s] + "/" + subjectDirs[s] + "_fets_triplet_seg.nii.gz";
if (cbica::isFile(current_output_file))
{
cbica::copyFile(current_output_file, current_output_file_to_check);
Expand Down