Merge pull request #1479 from AlexanderGetka-cbica/1.9.0.miscfixes

COLLAGE feature additions/warnings (also a DeepMedic model version fix)

3_HowToGuides.txt

@@ -440,7 +440,7 @@ Multi-institutional Performance Evaluation of Deep Learning Methods and Robust M
 <b>REQUIREMENTS:</b>
   -# An image or a set of co-registered images.
   -# An ROI file containing various labels, for which features will be extracted.
-	-# NOTE: CaPTk also extracts COLLAGE features [1] using the [Python implementation](https://github.com/radxtools/collageradiomics/).
+	-# NOTE: CaPTk can also extract COLLAGE features [1] using the [Python implementation](https://github.com/radxtools/collageradiomics/), but this functionality must be invoked from the separate "CollageFeatures" executable.
 
 <b>USAGE:</b>
   -# Once image(s) and an ROI file are loaded, go to the "Feature Extraction" panel.
@@ -1001,7 +1001,7 @@ This application is also available from the web on the [CBICA Image Processing P
 	-# If desired, enable registration of outputs and select a fixed image to register to.
 	-# Identify the diffusion measurements to be extracted, and the output directory.
 	-# Press the "Confirm" button.
-	-# The extracted measurements will be saved at the specified location (~5 minutes).
+	-# The extracted measurements will be saved at the specified location (~5 minutes). 
 \verbatim
 ${CaPTk_InstallDir}/bin/ DiffusionDerivatives.exe -i C:/inputDWI.nii.gz -m C:/mask.nii.gz -b C:/input.bval -g C:/input.bvec -a 1 -f 1 -r 1 -t 1 -z 1 -reg C:/template.nii.gz -o C:/output
 \endverbatim

data/cwlFiles/CollageFeatures.cwl

@@ -0,0 +1,73 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: CollageFeatures
+inputs:
+  input:
+    type: string
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -i
+    doc: Path to an input image from which features will be extracted..
+  mask:
+    type: string
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -m
+    doc: Path to a mask that will be considered as binary. The highest pixel value will be considered as information and all other values will be considered outside the mask..
+  outputfile:
+    type: string
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -o
+    doc: Path to the output CSV file..
+  runtest:
+    type: string?
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -rt
+    doc: Runs the tests.
+  cwl:
+    type: string?
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -cwl
+    doc: Generates a .cwl file for the software.
+  dimensions:
+    type: int?
+    label: 2-3
+    inputBinding:
+      position: 1
+      prefix: -d
+    doc: Optional number of dimensions upon which to run collage. Supported values are 2 and 3. If left out, we will default to the dimensionality of the image itself, which may not reflect expected behavior if the image has an alpha channel..
+  svdradius:
+    type: int?
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -s
+    doc: SVD radius is used for the dominant angle calculation pixel radius. DEFAULTS to 5 and is suggested to remain at the default..
+  binsize:
+    type: int?
+    label: none
+    inputBinding:
+      position: 1
+      prefix: -b
+    doc: Number of bins to use while calculating the grey level cooccurence matrix. DEFAULTS to 64..
+  Logger:
+    type: string?
+    label: log file which user has write access to
+    inputBinding:
+      position: 1
+      prefix: -L
+    doc: Full path to log file to store console outputs.By default, only console output is generated.
+hints:
+  SoftwareRequirement:
+    packages:
+      CollageFeatures:
+        version:
+          - 1.9.0.Alpha

data/deepMedic/saved_models/brainTumorSegmentation/VERSION.yaml

@@ -1,3 +1,3 @@
-Version: 1.8.2
-Minimum: 1.8.2
-Maximum: 1.8.2
+Version: 1.9.0
+Minimum: 1.9.0
+Maximum: 1.9.0

data/deepMedic/saved_models/skullStripping/VERSION.yaml

@@ -1,3 +1,3 @@
-Version: 1.7.0
-Minimum: 1.7.0
-Maximum: 1.8.2
+Version: 1.9.0
+Minimum: 1.9.0
+Maximum: 1.9.0

src/applications/CMakeLists.txt

@@ -42,6 +42,7 @@ SET( APPLICATIONS
   SBRT_LungField
   SBRT_Nodule
   SBRT_Analysis
+  CollageFeatures
 )
 SET( CAPTK_APP_LIST "" )
 
@@ -195,6 +196,10 @@ FOREACH(application ${APPLICATIONS})
   IF ( (${application} STREQUAL GeodesicTraining))
     SET( CAPTK_APP_LIST "${CAPTK_APP_LIST} ${application}" )
   ENDIF()
+
+  IF ( (${application} STREQUAL CollageFeatures))
+   ADD_APPLICATION( ${application} )
+  ENDIF()
 
 ENDFOREACH()
 

src/applications/CollageFeatures.cxx

@@ -0,0 +1,60 @@
+#include "cbicaCmdParser.h"
+#include "cbicaLogging.h"
+
+
+// This application simply wraps the collageradiomics cli (included in bin as part of FeatureExtraction being built) and shows warnings.
+int main(int argc, char **argv)
+{
+  cbica::CmdParser parser = cbica::CmdParser(argc, argv, "CollageFeatures");
+
+  // Right now we add these parameters explicitly, perhaps we can just use the wrapped executable's text.
+  parser.addRequiredParameter("i", "input", cbica::Parameter::STRING, "", "Path to an input image from which features will be extracted.");
+  parser.addRequiredParameter("m", "mask", cbica::Parameter::STRING, "", "Path to a mask that will be considered as binary. The highest pixel value will be considered as information and all other values will be considered outside the mask.");
+  parser.addRequiredParameter("o", "outputfile", cbica::Parameter::STRING, "", "Path to the output CSV file.");
+  parser.addOptionalParameter("v", "verbose", cbica::Parameter::BOOLEAN, "", "Provides additional debug output.");
+  parser.addOptionalParameter("d", "dimensions", cbica::Parameter::INTEGER, "2-3", "Optional number of dimensions upon which to run collage. Supported values are 2 and 3. If left out, we will default to the dimensionality of the image itself, which may not reflect expected behavior if the image has an alpha channel.");
+  parser.addOptionalParameter("s", "svdradius", cbica::Parameter::INTEGER, "", "SVD radius is used for the dominant angle calculation pixel radius. DEFAULTS to 5 and is suggested to remain at the default.");
+  parser.addOptionalParameter("h", "haralickwindow", cbica::Parameter::INTEGER, "", "Number of pixels around each pixel used to calculate the haralick texture. DEFAULTS to svdradius * 2 - 1.");
+  parser.addOptionalParameter("b", "binsize", cbica::Parameter::INTEGER, "", "Number of bins to use while calculating the grey level cooccurence matrix. DEFAULTS to 64.");
+
+  parser.addOptionalParameter("L", "Logger", cbica::Parameter::STRING, "log file which user has write access to", "Full path to log file to store console outputs", "By default, only console output is generated");
+  parser.addExampleUsage("-i C:/inputImage.nii.gz -m C:/inputMask.nii.gz -o C:/output.csv", "Generates COLLAGE features with default parameters");
+  parser.addApplicationDescription("CoLlAGe captures subtle anisotropic differences in disease pathologies by measuring entropy of co-occurrences of voxel-level gradient orientations onn imaging computed within a local neighborhood. The CoLlAGe features were developed by BrIC Lab and the RadxTools team (https://doi.org/10.1038/srep37241, https://github.com/radxtools/collageradiomics). Feature requests, bug reports, and any other CoLlAGe related considerations, should be directed to https://github.com/radxtools/collageradiomics/issues .");
+
+  std::string outputFile;
+  parser.getParameterValue("o", outputFile);
+
+  std::string argv_complete;
+  for (int i = 1; i < argc; i++) // 1 to ignore the current executable name
+  {
+    argv_complete += " \"" + std::string(argv[i]) + "\""; // double quote for command tokenization
+  }
+
+  auto collage_cli = cbica::getExecutablePath() + "/collageradiomics"
+#ifdef _WIN32
+      + ".exe"
+#else
+
+#endif
+      ;
+
+  if (!cbica::isFile(collage_cli))
+  {
+      // If this happens, this is on our packaging and not on the RadxTools folks.
+      std::cerr << "Could not find the Collage CLI, so cannot extract collage features. Please report this bug to CBICA Software.\n";
+      return EXIT_FAILURE;
+  }
+
+
+  std::string commandToRun = collage_cli + argv_complete;
+  if(std::system(commandToRun.c_str()) > 0) 
+  {
+    std::cerr << "Errors occurred while running the collageradiomics application. See logs for more details." << std::endl;
+	return EXIT_FAILURE;
+  }
+  else 
+  {
+     std::cout << "Finished successfully.\n";
+  }
+  return EXIT_SUCCESS;
+}

src/applications/CollageFeatures.h

@@ -0,0 +1 @@
+// This is a blank header to ensure that CMake picks up the CollageFeatures wrapper for collageradiomics.

src/applications/FeatureExtraction/src/FeatureExtraction.cxx

@@ -211,6 +211,26 @@ void algorithmRunner(std::vector<typename TImageType::Pointer> inputImages, type
   features.SetValidMask();
   features.SetMaskImage(mask);
   features.SetRequestedFeatures(param_file);
+
+  // Interrupt here now that we have requested features if COLLAGE is present.
+  auto tmp_features = features.GetRequestedFeatures();
+  auto tmp_iterator = tmp_features.find(FeatureFamilyString[FeatureFamily::COLLAGE]);
+  // Below line checks if COLLAGE exists in the feature families at all, and if it does,
+  // then it checks if it's enabled in the struct
+  if (tmp_iterator != tmp_features.end() && (std::get<0>(tmp_iterator->second) == true))
+  {
+      std::string collageMessage = "COLLAGE features were requested for this computation, but are not available through this interface. Please note:\n\n";
+      collageMessage += "The COLLAGE features were developed by BrIC Lab and the RadxTools team \n (https://doi.org/10.1038/srep37241, https://github.com/radxtools/collageradiomics) \n\n";
+      collageMessage += "Based on published results indicating their importance, COLLAGE features are offered as part of the CaPTk platform to enable users to extract a more comprehensive and reproducible set of features, as shown in:\n[https://doi.org/10.1002/mp.14556] \n\n";
+      collageMessage += "Please note that extraction of COLLAGE features is a long running process (often >20 minutes) and might not produce results for all the input images.";
+      collageMessage += "In order to extract COLLAGE features, please use the separate COLLAGE command line executable (CollageFeatures) from the CaPTk install directory.";
+      collageMessage += "Future releases of CaPTk will include updated versions of COLLAGE when available.";
+      collageMessage += "\nTo continue with feature extraction, change parameters and try again. Exiting.";
+      std::cerr << collageMessage << std::endl;
+      exit(EXIT_FAILURE); // Using this to escape out, since no return code exists from this function... kind of hacky
+  }
+
+
   features.SetOutputFilename(outputFilename);
   features.SetVerticallyConcatenatedOutput(verticalConc);
   features.SetWriteFeatureMaps(featureMaps);

src/applications/FeatureExtraction/src/FeatureExtraction.h

@@ -234,6 +234,11 @@ class FeatureExtraction
   \brief Populates the feature structure from the GUI
   */
   void SetRequestedFeatures(std::map< std::string, std::vector< std::map<std::string, std::string> > >  featuresFromUI, std::map<std::string, bool> selected_features);
+
+  /** 
+  \brief Gets the requested features (as FeatureType)
+  */
+  FeatureType GetRequestedFeatures();
 
   /**
   \brief This function is used to populate the variables throughout the Update() step which are then used to write to a file

src/applications/FeatureExtraction/src/FeatureExtraction.hxx

@@ -1324,6 +1324,11 @@ void FeatureExtraction< TImage >::SetSelectedROIsAndLabels(std::vector< std::str
   m_algorithmDone = false;
 }
 
+template < class TImage > 
+FeatureType FeatureExtraction< TImage >::GetRequestedFeatures()
+{
+    return m_Features;
+}
 
 template< class TImage >
 void FeatureExtraction< TImage >::SetRequestedFeatures(std::string filename, std::string selected_features)
@@ -2857,6 +2862,15 @@ void FeatureExtraction< TImage >::Update()
             }
             case COLLAGE:
             {
+                std::string collageMessage = "COLLAGE features were requested for this computation, but are not available through this interface. Please note:\n\n";
+                collageMessage += "The COLLAGE features were developed by BrIC Lab and the RadxTools team (https://doi.org/10.1038/srep37241, https://github.com/radxtools/collageradiomics) \n\n";
+                collageMessage += "Based on published results indicating their importance, COLLAGE features are offered as part of the CaPTk platform to enable users to extract a more comprehensive and reproducible set of features, as shown in : [https://doi.org/10.1002/mp.14556] \n\n";
+                collageMessage += "Please note that extraction of COLLAGE features is a long running process (often >20 minutes) and might not produce results for all the input images.\n";
+                collageMessage += "In order to extract COLLAGE features, please use the separate COLLAGE command line executable from the CaPTk install directory.\n";
+                collageMessage += "Future releases of CaPTk will include updated versions of COLLAGE when available.\n";
+              m_logger.Write(collageMessage);
+              break; // Display message and break out of these features if it gets here (this *should* be caught by CLI/GUI, but just in case)
+
               // this is a special case, where a pre-compiled python binary is called for every image/mask
               if (!allROIs[j].latticeGridPoint) // this is not currently working for lattice patches - https://github.com/radxtools/collageradiomics/issues/89
               { // start lattice check

src/view/gui/fFeaturePanel.cpp

@@ -33,12 +33,17 @@ fFeaturePanel::fFeaturePanel(QWidget * parent) : QWidget(parent)
   connect(m_btnBrowseSaveFile, SIGNAL(clicked()), this, SLOT(browseOutputFileName()));
   connect(m_cmbFeatureType, SIGNAL(currentIndexChanged(int)), this, SLOT(featureTypeChanged(int)));
   connect(HelpButton, SIGNAL(clicked()), this, SLOT(helpClicked()));
+
   //csv_format->setChecked(true);
   m_verticalConcat->setChecked(true);
   radio1->setChecked(true);
   loadFeatureFiles();
   featureTypeChanged(0);
 
+  // Disable collage by default on GUI, so that users must be prompted with RadXTools info
+  m_Collage->setChecked(false);
+  connect(m_Collage, SIGNAL(toggled(bool)), this, SLOT(onCollageToggled(bool)));
+
 }
 
 void fFeaturePanel::helpClicked()
@@ -389,4 +394,25 @@ void fFeaturePanel::advancedButtonClicked()
   m_featureDialog->exec();
   m_FeatureMaps[selectedFeatureType] = m_featureDialog->getFeatureMap();
 
+}
+
+void fFeaturePanel::onCollageToggled(bool checked)
+{
+    if (checked)
+    {
+        std::string collageMessage = "COLLAGE features were requested for this computation, but are not available through this interface. Please note:\n\n";
+        collageMessage += "The COLLAGE features were developed by BrIC Lab and the RadxTools team (https://doi.org/10.1038/srep37241, https://github.com/radxtools/collageradiomics) \n\n";
+        collageMessage += "Based on published results indicating their importance, COLLAGE features are offered as part of the CaPTk platform to enable users to extract a more comprehensive and reproducible set of features, as shown in : [https://doi.org/10.1002/mp.14556] \n\n";
+        collageMessage += "Please note that extraction of COLLAGE features is a long running process (often >20 minutes) and might not produce results for all the input images.\n";
+        collageMessage += "In order to extract COLLAGE features, please use the separate COLLAGE command line executable from the CaPTk install directory.\n";
+        collageMessage += "Future releases of CaPTk will include updated versions of COLLAGE when available.\n";
+        collageMessage += "Feature requests, bug reports, and any other COLLAGE related considerations, should be directed to https://github.com/radxtools/collageradiomics/issues.";
+        QMessageBox msgbox;
+        msgbox.setText(QString::fromStdString(collageMessage));
+        msgbox.setWindowTitle("COLLAGE Warning");
+        msgbox.setStandardButtons(QMessageBox::Ok);
+        msgbox.setDefaultButton(QMessageBox::Ok);
+        m_Collage->setChecked(false);
+        msgbox.exec();
+    }
 }

src/view/gui/fFeaturePanel.h

@@ -69,6 +69,7 @@ class fFeaturePanel : public QWidget, private Ui::fFeaturePanel
   void featureTypeChanged(int type);
   void advancedButtonClicked();
   void helpClicked();
+  void onCollageToggled(bool checked);
   std::map< std::string, bool > getEnabledFeatures();
 
 private: