Test ci

.github/workflows/pyxrf_requirements.txt

@@ -7,3 +7,7 @@ scikit-beam
 tomopy
 # These are required for installing the pyxrf-utils environment
 hatchling
+# Pandas needs to be pinned to prevent a bug in xrf-tomo, until
+# it gets fixed and a new release comes out.
+# See: https://github.com/NSLS-II-SRX/xrf-tomo/pull/10
+pandas<3.0

tomviz/CMakeLists.txt

@@ -626,6 +626,7 @@ set(tomviz_python_modules
   __init__.py
   _internal.py
   dataset.py
+  executor.py
   external_dataset.py
   fix_pdb.py
   operators.py
@@ -635,7 +636,6 @@ set(tomviz_python_modules
   utils.py
   web.py
   modules.py
-  views.py
 )
 
 file(MAKE_DIRECTORY "${tomviz_python_binary_dir}/tomviz")

tomviz/DataPropertiesPanel.cxx

@@ -499,7 +499,7 @@ void DataPropertiesPanel::updateComponentsCombo()
   auto blocked = QSignalBlocker(combo);
 
   // Only make this editor visible if there is more than one component
-  bool visible = dsource->scalars()->GetNumberOfComponents() > 1;
+  bool visible = dsource->scalars() && dsource->scalars()->GetNumberOfComponents() > 1;
   label->setVisible(visible);
   combo->setVisible(visible);
 

tomviz/DataSource.h

@@ -171,6 +171,10 @@ class DataSource : public QObject
   /// Set/get the dark/white data, used in Data Exchange currently
   vtkImageData* whiteData() const;
 
+  // Used to track if a volume visualization module was added
+  bool volumeModuleAutoAdded() const;
+  void setVolumeModuleAutoAdded(bool b);
+
   /// Check to see if the data was subsampled while reading
   bool wasSubsampled() const;
 
@@ -458,6 +462,7 @@ protected slots:
   MetadataType m_metadata;
 
   bool m_changingTimeStep = false;
+  bool m_volumeModuleAutoAdded = false;
 };
 
 inline void DataSource::clearTiltAngles()
@@ -495,6 +500,16 @@ inline void DataSource::setSubsampleVolumeBounds(int bs[6])
   setSubsampleVolumeBounds(dataObject(), bs);
 }
 
+inline bool DataSource::volumeModuleAutoAdded() const
+{
+  return m_volumeModuleAutoAdded;
+}
+
+inline void DataSource::setVolumeModuleAutoAdded(bool b)
+{
+  m_volumeModuleAutoAdded = b;
+}
+
 } // namespace tomviz
 
 #endif

tomviz/ExternalPythonExecutor.cxx

@@ -84,7 +84,7 @@ Pipeline::Future* ExternalPythonExecutor::execute(vtkDataObject* data,
       } else if (exitCode != 0) {
         displayError(
           "External Python Error",
-          QString("The external python return a non-zero exist code: %1\n\n "
+          QString("The external python returned a non-zero exit code: %1\n\n "
                   "command: %2 \n\n stderr:\n%3 \n\n stdout:\n%4 \n")
             .arg(exitCode)
             .arg(commandLine(this->m_process.data()))

tomviz/Pipeline.cxx

@@ -361,6 +361,11 @@ void Pipeline::branchFinished()
   // doesn't already have an explicit child data source i.e.
   // hasChildDataSource is true.
   auto lastOp = start->operators().last();
+  if (!lastOp->isCompleted()) {
+    // Cannot continue
+    return;
+  }
+
   if (!lastOp->hasChildDataSource()) {
     DataSource* newChildDataSource = nullptr;
     if (lastOp->childDataSource() == nullptr) {

tomviz/PtychoDialog.cxx

@@ -15,8 +15,8 @@
 #include <QBrush>
 #include <QDebug>
 #include <QDir>
+#include <QFile>
 #include <QFileDialog>
-#include <QFileInfo>
 #include <QLabel>
 #include <QMessageBox>
 #include <QPointer>
@@ -83,6 +83,9 @@ class PtychoDialog::Internal : public QObject
 
     connect(ui.filterSIDsString, &QLineEdit::editingFinished,
             this, &Internal::updateFilteredSidList);
+    connect(ui.loadSidsFromTxt, &QPushButton::clicked, this,
+            &Internal::onLoadSidsFromTxtClicked);
+
     connect(ui.selectOutputDirectory, &QPushButton::clicked, this,
             &Internal::selectOutputDirectory);
 
@@ -535,6 +538,14 @@ class PtychoDialog::Internal : public QObject
       return;
     }
 
+    // If "recon_result" exists underneath the selected directory,
+    // it means the parent directory was selected.
+    // We should automatically select the child one.
+    auto possibleChildPath = QDir(file).filePath("recon_result");
+    if (QFile::exists(possibleChildPath)) {
+      file = possibleChildPath;
+    }
+
     setPtychoDirectory(file);
     ptychoDirEdited();
   }
@@ -677,6 +688,50 @@ class PtychoDialog::Internal : public QObject
     updateTable();
   }
 
+  void onLoadSidsFromTxtClicked()
+  {
+    QString caption = "Select txt file";
+    QString filter = "*.txt";
+    auto startPath = ptychoDirectory();
+    auto filePath =
+      QFileDialog::getOpenFileName(parent.data(), caption, startPath, filter);
+
+    if (filePath.isEmpty()) {
+      return;
+    }
+
+    QFile file(filePath);
+    if (!file.exists()) {
+      qCritical() << QString("Txt file does not exist: %1").arg(filePath);
+      return;
+    }
+
+    if (!file.open(QIODevice::ReadOnly)) {
+      qCritical()
+        << QString("Failed to open file \"%1\" with error: ").arg(filePath)
+        << file.errorString();
+      return;
+    }
+
+    QTextStream reader(&file);
+
+    // Now load the SIDs
+    QStringList sids;
+    while (!reader.atEnd()) {
+      auto line = reader.readLine().trimmed();
+      if (line.isEmpty() || line.startsWith('#')) {
+        // Skip over it
+        continue;
+      }
+
+      sids.append(line.split(' ')[0]);
+    }
+
+    ui.filterSIDsString->setText(sids.join(", "));
+
+    updateFilteredSidList();
+  }
+
   void selectLoadFromCSV()
   {
     QString caption = "Select CSV file to load Use and Version settings";