Merge pull request #184 from allen-cell-animated/feature/flip-volume

Feature/flip volume

agave_app/AppearanceSettingsWidget.cpp

@@ -134,32 +134,50 @@ QAppearanceSettingsWidget::QAppearanceSettingsWidget(QWidget* pParent,
   m_xscaleSpinner->setDecimals(6);
   m_xscaleSpinner->setValue(1.0);
   scaleSectionLayout->addWidget(m_xscaleSpinner, 0, 1);
+  m_xFlipCheckBox = new QCheckBox("Flip");
+  m_xFlipCheckBox->setStatusTip(tr("Invert volume in X dimension"));
+  m_xFlipCheckBox->setToolTip(tr("Invert volume in X dimension"));
+  scaleSectionLayout->addWidget(m_xFlipCheckBox, 0, 2);
   QObject::connect(m_xscaleSpinner,
                    QOverload<double>::of(&QDoubleSpinner::valueChanged),
                    this,
                    &QAppearanceSettingsWidget::OnSetScaleX);
+  QObject::connect(
+    m_xFlipCheckBox, &QCheckBox::clicked, [this](bool flipValue) { this->OnFlipAxis(Axis::X, flipValue); });
   scaleSectionLayout->addWidget(new QLabel("Y"), 1, 0);
   m_yscaleSpinner = new QDoubleSpinner();
   m_yscaleSpinner->setStatusTip(tr("Scale volume in Y dimension"));
   m_yscaleSpinner->setToolTip(tr("Scale volume in Y dimension"));
   m_yscaleSpinner->setDecimals(6);
   m_yscaleSpinner->setValue(1.0);
   scaleSectionLayout->addWidget(m_yscaleSpinner, 1, 1);
+  m_yFlipCheckBox = new QCheckBox("Flip");
+  m_yFlipCheckBox->setStatusTip(tr("Invert volume in Y dimension"));
+  m_yFlipCheckBox->setToolTip(tr("Invert volume in Y dimension"));
+  scaleSectionLayout->addWidget(m_yFlipCheckBox, 1, 2);
   QObject::connect(m_yscaleSpinner,
                    QOverload<double>::of(&QDoubleSpinner::valueChanged),
                    this,
                    &QAppearanceSettingsWidget::OnSetScaleY);
+  QObject::connect(
+    m_yFlipCheckBox, &QCheckBox::clicked, [this](bool flipValue) { this->OnFlipAxis(Axis::Y, flipValue); });
   scaleSectionLayout->addWidget(new QLabel("Z"), 2, 0);
   m_zscaleSpinner = new QDoubleSpinner();
   m_zscaleSpinner->setStatusTip(tr("Scale volume in Z dimension"));
   m_zscaleSpinner->setToolTip(tr("Scale volume in Z dimension"));
   m_zscaleSpinner->setDecimals(6);
   m_zscaleSpinner->setValue(1.0);
   scaleSectionLayout->addWidget(m_zscaleSpinner, 2, 1);
+  m_zFlipCheckBox = new QCheckBox("Flip");
+  m_zFlipCheckBox->setStatusTip(tr("Invert volume in Z dimension"));
+  m_zFlipCheckBox->setToolTip(tr("Invert volume in Z dimension"));
+  scaleSectionLayout->addWidget(m_zFlipCheckBox, 2, 2);
   QObject::connect(m_zscaleSpinner,
                    QOverload<double>::of(&QDoubleSpinner::valueChanged),
                    this,
                    &QAppearanceSettingsWidget::OnSetScaleZ);
+  QObject::connect(
+    m_zFlipCheckBox, &QCheckBox::clicked, [this](bool flipValue) { this->OnFlipAxis(Axis::Z, flipValue); });
 
   m_scaleSection->setContentLayout(*scaleSectionLayout);
   m_MainLayout.addRow(m_scaleSection);
@@ -369,6 +387,18 @@ QAppearanceSettingsWidget::createSkyLightingControls()
   return section;
 }
 
+void
+QAppearanceSettingsWidget::OnFlipAxis(Axis axis, bool value)
+{
+  if (!m_scene)
+    return;
+  int flipValue = value ? -1 : 1;
+  glm::ivec3 v = m_scene->m_volume->getVolumeAxesFlipped();
+  m_scene->m_volume->setVolumeAxesFlipped(
+    axis == Axis::X ? flipValue : v.x, axis == Axis::Y ? flipValue : v.y, axis == Axis::Z ? flipValue : v.z);
+  m_qrendersettings->renderSettings()->m_DirtyFlags.SetFlag(RenderParamsDirty);
+}
+
 void
 QAppearanceSettingsWidget::OnSetScaleX(double value)
 {
@@ -848,6 +878,10 @@ QAppearanceSettingsWidget::onNewImage(Scene* scene)
   m_xscaleSpinner->setValue(m_scene->m_volume->physicalSizeX());
   m_yscaleSpinner->setValue(m_scene->m_volume->physicalSizeY());
   m_zscaleSpinner->setValue(m_scene->m_volume->physicalSizeZ());
+  glm::ivec3 v = m_scene->m_volume->getVolumeAxesFlipped();
+  m_xFlipCheckBox->setChecked(v.x < 0);
+  m_yFlipCheckBox->setChecked(v.y < 0);
+  m_zFlipCheckBox->setChecked(v.z < 0);
 
   QColor cbbox = QColor::fromRgbF(m_scene->m_material.m_boundingBoxColor[0],
                                   m_scene->m_material.m_boundingBoxColor[1],

agave_app/AppearanceSettingsWidget.h

@@ -18,6 +18,13 @@ class RenderSettings;
 class Scene;
 class Section;
 
+enum Axis
+{
+  X = 0,
+  Y = 1,
+  Z = 2
+};
+
 class QAppearanceSettingsWidget : public QGroupBox
 {
   Q_OBJECT
@@ -73,6 +80,7 @@ public slots:
   void OnSetScaleX(double value);
   void OnSetScaleY(double value);
   void OnSetScaleZ(double value);
+  void OnFlipAxis(Axis axis, bool value);
 
 private:
   Scene* m_scene;
@@ -95,8 +103,11 @@ public slots:
 
   Section* m_scaleSection;
   QDoubleSpinner* m_xscaleSpinner;
+  QCheckBox* m_xFlipCheckBox;
   QDoubleSpinner* m_yscaleSpinner;
+  QCheckBox* m_yFlipCheckBox;
   QDoubleSpinner* m_zscaleSpinner;
+  QCheckBox* m_zFlipCheckBox;
   QCheckBox m_showBoundingBoxCheckBox;
   QColorPushButton m_boundingBoxColorButton;
   QCheckBox m_showScaleBarCheckBox;

agave_app/Serialize.h

@@ -82,7 +82,8 @@ struct ViewerState
   // [[xm, xM], [ym, yM], [zm, zM]]
   std::array<std::array<float, 2>, 3> clipRegion = { 0.0f, 1.0f, 0.0f, 1.0f, 0.0f, 1.0f };
 
-  std::array<float, 3> scale = { 1, 1, 1 }; // m_scaleX, m_scaleY, m_scaleZ
+  std::array<float, 3> scale = { 1, 1, 1 };  // m_scaleX, m_scaleY, m_scaleZ
+  std::array<int, 3> flipAxis = { 1, 1, 1 }; // 1 is unflipped, -1 is flipped
 
   CameraSettings_V1 camera;
 
@@ -106,28 +107,29 @@ struct ViewerState
   {
     return datasets == other.datasets && version == other.version && pathTracer == other.pathTracer &&
            timeline == other.timeline && clipRegion == other.clipRegion && scale == other.scale &&
-           camera == other.camera && backgroundColor == other.backgroundColor &&
+           flipAxis == other.flipAxis && camera == other.camera && backgroundColor == other.backgroundColor &&
            boundingBoxColor == other.boundingBoxColor && showBoundingBox == other.showBoundingBox &&
            showScaleBar == other.showScaleBar && channels == other.channels && density == other.density &&
            lights == other.lights && capture == other.capture;
   }
-  NLOHMANN_DEFINE_TYPE_INTRUSIVE(ViewerState,
-                                 datasets,
-                                 version,
-                                 rendererType,
-                                 pathTracer,
-                                 timeline,
-                                 clipRegion,
-                                 scale,
-                                 camera,
-                                 backgroundColor,
-                                 boundingBoxColor,
-                                 showBoundingBox,
-                                 channels,
-                                 density,
-                                 lights,
-                                 capture,
-                                 showScaleBar)
+  NLOHMANN_DEFINE_TYPE_INTRUSIVE_WITH_DEFAULT(ViewerState,
+                                              datasets,
+                                              version,
+                                              rendererType,
+                                              pathTracer,
+                                              timeline,
+                                              clipRegion,
+                                              scale,
+                                              flipAxis,
+                                              camera,
+                                              backgroundColor,
+                                              boundingBoxColor,
+                                              showBoundingBox,
+                                              channels,
+                                              density,
+                                              lights,
+                                              capture,
+                                              showScaleBar)
 };
 
 ViewerState

agave_app/ViewerState.cpp

@@ -140,6 +140,10 @@ stateToPythonScript(const Serialize::ViewerState& s)
   ss << obj << SetPrimaryRayStepSizeCommand({ s.pathTracer.primaryStepSize }).toPythonString() << std::endl;
   ss << obj << SetSecondaryRayStepSizeCommand({ s.pathTracer.secondaryStepSize }).toPythonString() << std::endl;
   ss << obj << SetVoxelScaleCommand({ s.scale[0], s.scale[1], s.scale[2] }).toPythonString() << std::endl;
+  ss << obj
+     << SetFlipAxisCommand({ s.flipAxis[0] < 0 ? -1 : 1, s.flipAxis[1] < 0 ? -1 : 1, s.flipAxis[2] < 0 ? -1 : 1 })
+          .toPythonString()
+     << std::endl;
   ss << obj
      << SetClipRegionCommand({ s.clipRegion[0][0],
                                s.clipRegion[0][1],

agave_app/agaveGui.cpp

@@ -965,6 +965,7 @@ agaveGui::viewerStateToApp(const Serialize::ViewerState& v)
   m_currentScene = v.datasets[0].scene;
 
   m_appScene.m_volume->setPhysicalSize(v.scale[0], v.scale[1], v.scale[2]);
+  m_appScene.m_volume->setVolumeAxesFlipped(v.flipAxis[0], v.flipAxis[1], v.flipAxis[2]);
 
   m_appScene.m_material.m_backgroundColor[0] = v.backgroundColor[0];
   m_appScene.m_material.m_backgroundColor[1] = v.backgroundColor[1];
@@ -1039,6 +1040,10 @@ agaveGui::appToViewerState()
     v.scale[0] = m_appScene.m_volume->physicalSizeX();
     v.scale[1] = m_appScene.m_volume->physicalSizeY();
     v.scale[2] = m_appScene.m_volume->physicalSizeZ();
+    glm::ivec3 vflip = m_appScene.m_volume->getVolumeAxesFlipped();
+    v.flipAxis[0] = vflip.x > 0 ? 1 : -1;
+    v.flipAxis[1] = vflip.y > 0 ? 1 : -1;
+    v.flipAxis[2] = vflip.z > 0 ? 1 : -1;
   }
 
   v.backgroundColor = { m_appScene.m_material.m_backgroundColor[0],

agave_app/commandBuffer.cpp

@@ -124,6 +124,7 @@ commandBuffer::processBuffer()
           CMD_CASE(TrackballCameraCommand);
           CMD_CASE(LoadDataCommand);
           CMD_CASE(ShowScaleBarCommand);
+          CMD_CASE(SetFlipAxisCommand);
           default:
             // ERROR UNRECOGNIZED COMMAND SIGNATURE.
             // PRINT OUT PREVIOUS! BAIL OUT! OR DO SOMETHING CLEVER AND CORRECT!

agave_pyclient/agave_pyclient/agave.py

@@ -921,6 +921,22 @@ def show_scale_bar(self, on: int):
         # 45
         self.cb.add_command("SHOW_SCALE_BAR", on)
 
+    def set_flip_axis(self, x: int, y: int, z: int):
+        """
+        Flip the volume data on any axis
+
+        Parameters
+        ----------
+        x: int
+            -1 to flip, 1 to not flip
+        y: int
+            -1 to flip, 1 to not flip
+        z: int
+            -1 to flip, 1 to not flip
+        """
+        # 46
+        self.cb.add_command("SET_FLIP_AXIS", x, y, z)
+
     def batch_render_turntable(
         self, number_of_frames=90, direction=1, output_name="frame", first_frame=0
     ):

agave_pyclient/agave_pyclient/commandbuffer.py

@@ -75,6 +75,7 @@
     # path, scene, multiresolution level, t, channel indices, region
     "LOAD_DATA": [44, "S", "I32", "I32", "I32", "I32A", "I32A"],
     "SHOW_SCALE_BAR": [45, "I32"],
+    "SET_FLIP_AXIS": [46, "I32", "I32", "I32"],
 }
 
 

renderlib/ImageXYZC.cpp

@@ -26,6 +26,7 @@ ImageXYZC::ImageXYZC(uint32_t x,
   , m_scaleY(sy)
   , m_scaleZ(sz)
   , m_spatialUnits(spatialUnits)
+  , m_flipped(1, 1, 1)
 {
   for (uint32_t i = 0; i < m_c; ++i) {
     m_channels.push_back(new Channelu16(x, y, z, reinterpret_cast<uint16_t*>(ptr(i))));
@@ -79,9 +80,21 @@ ImageXYZC::maxPixelDimension() const
 void
 ImageXYZC::setPhysicalSize(float x, float y, float z)
 {
-  m_scaleX = x;
-  m_scaleY = y;
-  m_scaleZ = z;
+  m_scaleX = abs(x);
+  m_scaleY = abs(y);
+  m_scaleZ = abs(z);
+}
+
+void
+ImageXYZC::setVolumeAxesFlipped(int x, int y, int z)
+{
+  m_flipped = glm::ivec3(x < 0 ? -1 : 1, y < 0 ? -1 : 1, z < 0 ? -1 : 1);
+}
+
+glm::ivec3
+ImageXYZC::getVolumeAxesFlipped() const
+{
+  return m_flipped;
 }
 
 float

renderlib/ImageXYZC.h

@@ -85,19 +85,28 @@ class ImageXYZC
 
   void setPhysicalSize(float x, float y, float z);
 
+  // +1 means do not flip, -1 means flip
+  void setVolumeAxesFlipped(int x, int y, int z);
+
   uint32_t sizeX() const;
   uint32_t sizeY() const;
   uint32_t sizeZ() const;
   uint32_t maxPixelDimension() const;
+
+  // should always return positive values
   float physicalSizeX() const;
   float physicalSizeY() const;
   float physicalSizeZ() const;
+
   std::string spatialUnits() const;
 
   glm::vec3 getNormalizedDimensions() const;
 
   glm::vec3 getPhysicalDimensions() const;
 
+  // +1 means do not flip, -1 means flip
+  glm::ivec3 getVolumeAxesFlipped() const;
+
   uint32_t sizeC() const;
 
   uint32_t sizeOfElement() const;
@@ -114,6 +123,7 @@ class ImageXYZC
   uint32_t m_x, m_y, m_z, m_c, m_bpp;
   uint8_t* m_data;
   float m_scaleX, m_scaleY, m_scaleZ;
+  glm::ivec3 m_flipped;
   std::string m_spatialUnits;
   std::vector<Channelu16*> m_channels;
 };

renderlib/command.cpp

@@ -550,8 +550,7 @@ LoadVolumeFromFileCommand::execute(ExecutionContext* c)
 void
 SetTimeCommand::execute(ExecutionContext* c)
 {
-  LOG_DEBUG << "SetTime command: "
-            << " T=" << m_data.m_time;
+  LOG_DEBUG << "SetTime command: " << " T=" << m_data.m_time;
 
   // setting same time is a no-op.
   if (m_data.m_time == c->m_appScene->m_timeLine.currentTime()) {
@@ -733,13 +732,22 @@ ShowScaleBarCommand::execute(ExecutionContext* c)
   c->m_appScene->m_showScaleBar = m_data.m_on ? true : false;
 }
 
+void
+SetFlipAxisCommand::execute(ExecutionContext* c)
+{
+  LOG_DEBUG << "SetFlipAxis " << m_data.m_x << " " << m_data.m_y << " " << m_data.m_z;
+  c->m_appScene->m_volume->setVolumeAxesFlipped(m_data.m_x, m_data.m_y, m_data.m_z);
+  c->m_renderSettings->m_DirtyFlags.SetFlag(RenderParamsDirty);
+}
+
 SessionCommand*
 SessionCommand::parse(ParseableStream* c)
 {
   SessionCommandD data;
   data.m_name = c->parseString();
   return new SessionCommand(data);
 }
+
 size_t
 SessionCommand::write(WriteableStream* o) const
 {
@@ -1630,6 +1638,27 @@ ShowScaleBarCommand::write(WriteableStream* o) const
   return bytesWritten;
 }
 
+SetFlipAxisCommand*
+SetFlipAxisCommand::parse(ParseableStream* c)
+{
+  SetFlipAxisCommandD data;
+  data.m_x = c->parseInt32();
+  data.m_y = c->parseInt32();
+  data.m_z = c->parseInt32();
+  return new SetFlipAxisCommand(data);
+}
+
+size_t
+SetFlipAxisCommand::write(WriteableStream* o) const
+{
+  size_t bytesWritten = 0;
+  bytesWritten += o->writeInt32(m_ID);
+  bytesWritten += o->writeInt32(m_data.m_x);
+  bytesWritten += o->writeInt32(m_data.m_y);
+  bytesWritten += o->writeInt32(m_data.m_z);
+  return bytesWritten;
+}
+
 std::string
 SessionCommand::toPythonString() const
 {
@@ -2082,3 +2111,15 @@ ShowScaleBarCommand::toPythonString() const
   ss << ")";
   return ss.str();
 }
+
+std::string
+SetFlipAxisCommand::toPythonString() const
+{
+  std::ostringstream ss;
+  ss << PythonName() << "(";
+  ss << m_data.m_x << ", ";
+  ss << m_data.m_y << ", ";
+  ss << m_data.m_z;
+  ss << ")";
+  return ss.str();
+}