Merge pull request #2019 from SCIInstitute/2017-windows-python

2017 windows python
SCIInstitute · Mar 22, 2023 · f7a5020 · f7a5020
2 parents 6858231 + 04fb943
commit f7a5020
Show file tree

Hide file tree

Showing 19 changed files with 40 additions and 34 deletions.
diff --git a/Examples/Python/deep_ssm.py b/Examples/Python/deep_ssm.py
@@ -249,7 +249,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimizeCmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimizeCmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimizeCmd)
 
     print("To analyze train shape model, call:")
@@ -533,7 +533,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     print("To analyze validation shape model, call:")
@@ -690,4 +690,4 @@ def check_results(args, mean_dist):
         print("Done with test, verification succeeded.")
         exit(0)
     else:
-        return
+        return
diff --git a/Examples/Python/ellipsoid.py b/Examples/Python/ellipsoid.py
@@ -206,7 +206,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/ellipsoid_cut.py b/Examples/Python/ellipsoid_cut.py
@@ -169,7 +169,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/ellipsoid_fd.py b/Examples/Python/ellipsoid_fd.py
@@ -185,7 +185,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/ellipsoid_mesh.py b/Examples/Python/ellipsoid_mesh.py
@@ -173,7 +173,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/ellipsoid_multiple_domain.py b/Examples/Python/ellipsoid_multiple_domain.py
@@ -271,7 +271,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/ellipsoid_multiple_domain_mesh.py b/Examples/Python/ellipsoid_multiple_domain_mesh.py
@@ -204,7 +204,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/femur_cut.py b/Examples/Python/femur_cut.py
@@ -225,7 +225,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimizeCmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimizeCmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimizeCmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/hip_multiple_domain.py b/Examples/Python/hip_multiple_domain.py
@@ -248,7 +248,7 @@ def Run_Pipeline(args):
 
 
 	# Run optimization
-	optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+	optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
 	subprocess.check_call(optimize_cmd)
 
 	# # If tiny test or verify, check results and exit

diff --git a/Examples/Python/incremental_supershapes.py b/Examples/Python/incremental_supershapes.py
@@ -198,7 +198,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     print(optimize_cmd)
     subprocess.check_call(optimize_cmd)
 
@@ -284,7 +284,7 @@ def Run_Pipeline(args):
         project.save(spreadsheet_file)
 
         # Run optimization
-        optimize_cmd = ('shapeworks optimize --name ' +
+        optimize_cmd = ('shapeworks optimize --progress --name ' +
                         spreadsheet_file).split()
         subprocess.check_call(optimize_cmd)
 

diff --git a/Examples/Python/left_atrium.py b/Examples/Python/left_atrium.py
@@ -208,7 +208,7 @@ def Run_Pipeline(args):
         parameter_dictionary["multiscale"] = 1
         parameter_dictionary["multiscale_particles"] = 128
 
-    print('Generating project sheet')
+    print('Generating project file')
     # Add param dictionary to spreadsheet
     for key in parameter_dictionary:
         parameters.set(key, sw.Variant([parameter_dictionary[key]]))
@@ -217,7 +217,8 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    print('Running optimization')
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/lumps.py b/Examples/Python/lumps.py
@@ -127,7 +127,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/peanut_shared_boundary.py b/Examples/Python/peanut_shared_boundary.py
@@ -218,7 +218,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/supershapes_1mode_contour.py b/Examples/Python/supershapes_1mode_contour.py
@@ -99,7 +99,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Examples/Python/thin_cavity_bean.py b/Examples/Python/thin_cavity_bean.py
@@ -123,7 +123,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

diff --git a/Installation/install_python_module.bat b/Installation/install_python_module.bat
@@ -2,7 +2,7 @@ REM Installs the shapeworks python module.
 REM  NOTE: assumes all library dependencies are in this directory\bin
 
 REM install pip module
-call pip install Python\shapeworks
+call pip install Python\shapeworks.tar.gz
 
 set CONDA_INSTALL_DIR=%CONDA_PREFIX%\lib\site-packages\shapeworks
 

diff --git a/Libs/Optimize/Optimize.cpp b/Libs/Optimize/Optimize.cpp
@@ -2204,7 +2204,9 @@ void Optimize::ComputeTotalIterations() {
 void Optimize::UpdateProgress() {
   auto now = std::chrono::system_clock::now();
 
-  if ((now - m_last_update_time) > std::chrono::milliseconds(100)) {
+  bool final = current_particle_iterations_ == total_particle_iterations_;
+
+  if (final || (now - m_last_update_time) > std::chrono::milliseconds(100)) {
     m_last_update_time = now;
     std::chrono::duration<double> elapsed_seconds =
         std::chrono::duration_cast<std::chrono::seconds>(now - m_start_time);

diff --git a/Support/package_windows.sh b/Support/package_windows.sh
@@ -43,13 +43,12 @@ cp -r $BUILD/bin/Release bin
 rm bin/*Tests.pdb bin/Recon*.pdb bin/Mesh*.pdb
 rm -rf Post
 
-# Run auto-documentation
-cd $ROOT
-PATH=$BUILD/bin/Release/bin:$PATH
-
-# add $PATH to $PYTHONPATH
-PYTHONPATH=$PYTHONPATH:$PATH
-
+# Build python packages
+for package in DataAugmentationUtilsPackage DatasetUtilsPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do
+    cd Python
+    tar czvf ${package}.tar.gz $package
+    cd ..
+done
 
 # Remove tests, they won't work for users anyway
 rm bin/*Tests.exe

diff --git a/install_shapeworks.bat b/install_shapeworks.bat
@@ -11,7 +11,7 @@ call conda config --add channels anaconda
 call conda config --add channels conda-forge
 
 REM install shapeworks deps
-call conda create --yes --name %CONDAENV% python=3.9.13 openblas=0.3.20 'vtk=9.1.0=qt*' scikit-learn=1.1.1 pip=22.1.2
+call conda create --yes --name %CONDAENV% python=3.9.13 'vtk=9.1.0=qt*' pip=22.1.2
 call conda activate %CONDAENV%
 
 REM reactivate shapeworks environment
@@ -38,12 +38,16 @@ call pip install itk-elastix==0.13.0
 call pip install SimpleITK==2.1.1.2
 call pip install bokeh==2.4.3
 call pip install seaborn==0.11.2
+call pip install scikit-learn==1.1.1
+call pip install pyvista==0.34.1
 
-call pip install Python/DatasetUtilsPackage
-call pip install Python/DocumentationUtilsPackage
-call pip install Python/DataAugmentationUtilsPackage
-call pip install Python/DeepSSMUtilsPackage
-call pip install Python/ShapeCohortGenPackage
+call pip install swcc==1.0.3
+
+call pip install Python/DatasetUtilsPackage.tar.gz
+call pip install Python/DocumentationUtilsPackage.tar.gz
+call pip install Python/DataAugmentationUtilsPackage.tar.gz
+call pip install Python/DeepSSMUtilsPackage.tar.gz
+call pip install Python/ShapeCohortGenPackage.tar.gz
 
 REM install the shapeworks python module and conda [de]activate scripts
 call .\Installation\install_python_module.bat