CI TESTING

tests/python/utils.py

@@ -1,32 +1,58 @@
+from pathlib import Path
+from types import ModuleType
+from typing import Callable
 import importlib.util
 import inspect
-from pathlib import Path
 import shutil
-from types import ModuleType
 import urllib.request
 import zipfile
 
 from tomviz.executor import OperatorWrapper
 from tomviz.operators import Operator
+from tomviz._internal import add_transform_decorators
 
 OPERATOR_PATH = Path(__file__).parent.parent.parent / 'tomviz/python'
 
 
+def add_decorators(func: Callable, operator_name: str) -> Callable:
+    # Automatically add the decorators which would normally be
+    # automatically added by Tomviz.
+    json_path = OPERATOR_PATH / f'{operator_name}.json'
+    op_dict = {}
+    if json_path.exists():
+        with open(json_path, 'rb') as rf:
+            op_dict['description'] = rf.read()
+
+    func = add_transform_decorators(func, op_dict)
+    return func
+
+
 def load_operator_module(operator_name: str) -> ModuleType:
     module_path = OPERATOR_PATH / f'{operator_name}.py'
     spec = importlib.util.spec_from_file_location(operator_name, module_path)
     module = importlib.util.module_from_spec(spec)
     spec.loader.exec_module(module)
+
+    if hasattr(module, 'transform'):
+        # Add the decorators
+        module.transform = add_decorators(module.transform, operator_name)
+
     return module
 
 
 def load_operator_class(operator_module: ModuleType) -> Operator | None:
     # Locate the operator class
     for v in operator_module.__dict__.values():
         if inspect.isclass(v) and issubclass(v, Operator):
+            if hasattr(v, 'transform'):
+                # Decorate at the class level
+                name = operator_module.__name__
+                v.transform = add_decorators(v.transform, name)
+
             # Instantiate and set up wrapper
             operator = v()
             operator._operator_wrapper = OperatorWrapper()
+
             return operator
 
 

tomviz/ActiveObjects.h

@@ -49,6 +49,9 @@ class ActiveObjects : public QObject
   /// Returns the selected data source, nullptr if no data source is selected.
   DataSource* selectedDataSource() const { return m_selectedDataSource; }
 
+  /// Returns the active operator.
+  Operator* activeOperator() const { return m_activeOperator; }
+
   /// Returns the active data source.
   MoleculeSource* activeMoleculeSource() const
   {

tomviz/AddPythonTransformReaction.cxx

@@ -36,7 +36,6 @@
 #include <QVBoxLayout>
 #include <QtDebug>
 
-#include <cassert>
 
 namespace tomviz {
 
@@ -153,6 +152,9 @@ OperatorPython* AddPythonTransformReaction::addExpression(DataSource* source)
   } else if (scriptLabel == "Shift Volume") {
     auto t = source->producer();
     auto data = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
+    if (!data) {
+      return nullptr;
+    }
     int* extent = data->GetExtent();
 
     QDialog dialog(tomviz::mainWidget());
@@ -230,6 +232,9 @@ OperatorPython* AddPythonTransformReaction::addExpression(DataSource* source)
   } else if (scriptLabel == "Crop") {
     auto t = source->producer();
     auto data = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
+    if (!data) {
+      return nullptr;
+    }
     int* extent = data->GetExtent();
 
     QDialog dialog(tomviz::mainWidget());
@@ -301,6 +306,9 @@ OperatorPython* AddPythonTransformReaction::addExpression(DataSource* source)
     int extent[6];
     auto t = source->producer();
     vtkImageData* image = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
+    if (!image) {
+      return nullptr;
+    }
     image->GetOrigin(origin);
     image->GetSpacing(spacing);
     image->GetExtent(extent);
@@ -335,6 +343,9 @@ OperatorPython* AddPythonTransformReaction::addExpression(DataSource* source)
 
     auto t = source->producer();
     auto image = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
+    if (!image) {
+      return nullptr;
+    }
     image->GetOrigin(origin);
     image->GetSpacing(spacing);
     image->GetExtent(extent);
@@ -429,13 +440,18 @@ void AddPythonTransformReaction::addExpressionFromNonModalDialog()
       }
     }
 
-    assert(volumeWidget);
+    if (!volumeWidget) {
+      return;
+    }
     int selection_extent[6];
     volumeWidget->getExtentOfSelection(selection_extent);
 
     int image_extent[6];
     auto t = source->producer();
     auto image = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
+    if (!image) {
+      return;
+    }
     image->GetExtent(image_extent);
 
     // The image extent is not necessarily zero-based.  The numpy array is.
@@ -466,13 +482,18 @@ void AddPythonTransformReaction::addExpressionFromNonModalDialog()
       }
     }
 
-    assert(volumeWidget);
+    if (!volumeWidget) {
+      return;
+    }
     int selection_extent[6];
     volumeWidget->getExtentOfSelection(selection_extent);
 
     int image_extent[6];
     auto t = source->producer();
     auto image = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
+    if (!image) {
+      return;
+    }
     image->GetExtent(image_extent);
     int indices[6];
     indices[0] = selection_extent[0] - image_extent[0];

tomviz/AddRenderViewContextMenuBehavior.cxx

@@ -78,7 +78,9 @@ void AddRenderViewContextMenuBehavior::onSetBackgroundColor()
 
   // Must set this to zero so that the render view will use its own
   // background color rather than the global palette.
-  vtkSMPropertyHelper(proxy, "UseColorPaletteForBackground").Set(0);
+  if (proxy->GetProperty("UseColorPaletteForBackground")) {
+    vtkSMPropertyHelper(proxy, "UseColorPaletteForBackground").Set(0);
+  }
 
   proxy->UpdateVTKObjects();
   view->render();

tomviz/Behaviors.cxx

@@ -5,7 +5,7 @@
 
 #include "ActiveObjects.h"
 #include "AddRenderViewContextMenuBehavior.h"
-#include "FxiWorkflowWidget.h"
+#include "ShiftRotationCenterWidget.h"
 #include "ManualManipulationWidget.h"
 #include "MoveActiveObject.h"
 #include "OperatorPython.h"
@@ -102,8 +102,8 @@ Behaviors::Behaviors(QMainWindow* mainWindow) : QObject(mainWindow)
 
 void Behaviors::registerCustomOperatorUIs()
 {
-  OperatorPython::registerCustomWidget("FxiWorkflowWidget", true,
-                                       FxiWorkflowWidget::New);
+  OperatorPython::registerCustomWidget("ShiftRotationCenterWidget", true,
+                                       ShiftRotationCenterWidget::New);
   OperatorPython::registerCustomWidget("RotationAlignWidget", true,
                                        RotateAlignWidget::New);
   OperatorPython::registerCustomWidget("ManualManipulationWidget", true,

tomviz/CMakeLists.txt

@@ -98,8 +98,8 @@ set(SOURCES
   FileFormatManager.h
   FxiFormat.cxx
   FxiFormat.h
-  FxiWorkflowWidget.cxx
-  FxiWorkflowWidget.h
+  ShiftRotationCenterWidget.cxx
+  ShiftRotationCenterWidget.h
   GenericHDF5Format.cxx
   GenericHDF5Format.h
   GradientOpacityWidget.h
@@ -308,6 +308,8 @@ list(APPEND SOURCES
   modules/ModuleMolecule.h
   modules/ModuleOutline.cxx
   modules/ModuleOutline.h
+  modules/ModulePlot.cxx
+  modules/ModulePlot.h
   modules/ModulePropertiesPanel.cxx
   modules/ModulePropertiesPanel.h
   modules/ModuleRuler.cxx
@@ -462,8 +464,8 @@ set(python_files
   Recon_ART.py
   Recon_SIRT.py
   Recon_TV_minimization.py
-  Recon_tomopy_gridrec.py
-  Recon_tomopy_fxi.py
+  Recon_tomopy.py
+  ShiftRotationCenter_tomopy.py
   FFT_AbsLog.py
   ManualManipulation.py
   Shift_Stack_Uniformly.py
@@ -508,13 +510,16 @@ set(python_files
   TV_Filter.py
   PoreSizeDistribution.py
   Tortuosity.py
+  PowerSpectrumDensity.py
+  FourierShellCorrelation.py
   Recon_real_time_tomography.py
   )
 
 set(json_files
   AddPoissonNoise.json
   AutoCenterOfMassTiltImageAlignment.json
   AutoCrossCorrelationTiltImageAlignment.json
+  AutoTiltAxisRotationAlignment.json
   AutoTiltAxisShiftAlignment.json
   PyStackRegImageAlignment.json
   BinaryThreshold.json
@@ -547,8 +552,8 @@ set(json_files
   Recon_DFT.json
   Recon_DFT_constraint.json
   Recon_TV_minimization.json
-  Recon_tomopy_gridrec.json
-  Recon_tomopy_fxi.json
+  Recon_tomopy.json
+  ShiftRotationCenter_tomopy.json
   Recon_SIRT.json
   Recon_WBP.json
   Shift3D.json
@@ -564,6 +569,8 @@ set(json_files
   TV_Filter.json
   PoreSizeDistribution.json
   Tortuosity.json
+  PowerSpectrumDensity.json
+  FourierShellCorrelation.json
   Recon_real_time_tomography.json
   )
 

tomviz/CentralWidget.cxx

@@ -235,7 +235,7 @@ void CentralWidget::setColorMapDataSource(DataSource* source)
   // Get the actual data source, build a histogram out of it.
   auto image = vtkImageData::SafeDownCast(source->dataObject());
 
-  if (image->GetPointData()->GetScalars() == nullptr) {
+  if (!image || image->GetPointData()->GetScalars() == nullptr) {
     return;
   }
 

tomviz/DataPropertiesPanel.cxx

@@ -38,6 +38,7 @@
 #include <QClipboard>
 #include <QDebug>
 #include <QDoubleValidator>
+#include <QFileDialog>
 #include <QKeyEvent>
 #include <QMainWindow>
 #include <QMessageBox>
@@ -98,6 +99,7 @@ DataPropertiesPanel::DataPropertiesPanel(QWidget* parentObject)
   connect(&ActiveObjects::instance(), SIGNAL(viewChanged(vtkSMViewProxy*)),
           SLOT(updateAxesGridLabels()));
   connect(m_ui->SetTiltAnglesButton, SIGNAL(clicked()), SLOT(setTiltAngles()));
+  connect(m_ui->saveTiltAngles, SIGNAL(clicked()), SLOT(saveTiltAngles()));
   connect(m_ui->unitBox, SIGNAL(editingFinished()), SLOT(updateUnits()));
   connect(m_ui->xLengthBox, &QLineEdit::editingFinished,
           [this]() { this->updateLength(m_ui->xLengthBox, 0); });
@@ -402,18 +404,38 @@ void DataPropertiesPanel::updateData()
     m_tiltAnglesSeparator->show();
     m_ui->SetTiltAnglesButton->show();
     m_ui->TiltAnglesTable->show();
+    m_ui->saveTiltAngles->show();
     QVector<double> tiltAngles = dsource->getTiltAngles();
+    QVector<int> scanIDs = dsource->getScanIDs();
+    m_hasScanIDs = scanIDs.size() == tiltAngles.size() && !scanIDs.isEmpty();
     m_ui->TiltAnglesTable->setRowCount(tiltAngles.size());
-    m_ui->TiltAnglesTable->setColumnCount(1);
+    int numCols = m_hasScanIDs ? 2 : 1;
+    m_ui->TiltAnglesTable->setColumnCount(numCols);
+    int tiltCol = m_hasScanIDs ? 1 : 0;
     for (int i = 0; i < tiltAngles.size(); ++i) {
+      if (m_hasScanIDs) {
+        QTableWidgetItem* scanItem = new QTableWidgetItem();
+        scanItem->setData(Qt::DisplayRole, QString::number(scanIDs[i]));
+        scanItem->setFlags(scanItem->flags() & ~Qt::ItemIsEditable);
+        m_ui->TiltAnglesTable->setItem(i, 0, scanItem);
+      }
       QTableWidgetItem* item = new QTableWidgetItem();
       item->setData(Qt::DisplayRole, QString::number(tiltAngles[i]));
-      m_ui->TiltAnglesTable->setItem(i, 0, item);
+      m_ui->TiltAnglesTable->setItem(i, tiltCol, item);
+    }
+    // Set column headers
+    QStringList headers;
+    if (m_hasScanIDs) {
+      headers << "Scan ID";
     }
+    headers << "Tilt Angle";
+    m_ui->TiltAnglesTable->setHorizontalHeaderLabels(headers);
+    m_ui->TiltAnglesTable->horizontalHeader()->setStretchLastSection(true);
   } else {
     m_tiltAnglesSeparator->hide();
     m_ui->SetTiltAnglesButton->hide();
     m_ui->TiltAnglesTable->hide();
+    m_ui->saveTiltAngles->show();
   }
   connect(m_ui->TiltAnglesTable, SIGNAL(cellChanged(int, int)),
           SLOT(onTiltAnglesModified(int, int)));
@@ -515,6 +537,11 @@ void DataPropertiesPanel::onTiltAnglesModified(int row, int column)
   // The table shouldn't be shown if this is not true, so this slot shouldn't be
   // called
   Q_ASSERT(dsource->type() == DataSource::TiltSeries);
+  // Tilt angles are in column 1 when scan IDs are present, column 0 otherwise
+  int tiltCol = m_hasScanIDs ? 1 : 0;
+  if (column != tiltCol) {
+    return;
+  }
   QTableWidgetItem* item = m_ui->TiltAnglesTable->item(row, column);
   auto ok = false;
   auto value = item->data(Qt::DisplayRole).toDouble(&ok);
@@ -627,6 +654,49 @@ void DataPropertiesPanel::setTiltAngles()
   SetTiltAnglesReaction::showSetTiltAnglesUI(mainWindow, dsource);
 }
 
+void DataPropertiesPanel::saveTiltAngles()
+{
+  DataSource* dsource = m_currentDataSource;
+  if (!dsource) {
+    return;
+  }
+
+  // Prompt user to select a file for saving
+  QString fileName = QFileDialog::getSaveFileName(
+    nullptr,
+    "Save Tilt Angles",
+    QString(),  // Default directory (or you can specify a path)
+    "TXT Files (*.txt);;All Files (*)"
+  );
+
+  // Check if user cancelled
+  if (fileName.isEmpty()) {
+      return;
+  }
+
+  auto tiltAngles = dsource->getTiltAngles();
+  auto scanIDs = dsource->getScanIDs();
+
+  // Open file for writing
+  QFile file(fileName);
+  if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
+    QMessageBox::warning(nullptr, "Error",
+      "Could not open file for writing: " + file.errorString());
+    return;
+  }
+
+  // Write scan IDs (if available) and tilt angles, one per line
+  QTextStream out(&file);
+  for (int i = 0; i < tiltAngles.size(); ++i) {
+    if (m_hasScanIDs) {
+      out << scanIDs[i] << " ";
+    }
+    out << tiltAngles[i] << "\n";
+  }
+
+  file.close();
+}
+
 void DataPropertiesPanel::scheduleUpdate()
 {
   m_updateNeeded = true;
@@ -811,6 +881,7 @@ void DataPropertiesPanel::clear()
   m_ui->TiltAnglesTable->clear();
   m_ui->TiltAnglesTable->setRowCount(0);
   m_ui->TiltAnglesTable->hide();
+  m_ui->saveTiltAngles->hide();
 }
 
 void DataPropertiesPanel::updateSpacing(int axis, double newLength)