Merge pull request #13 from psavery/sphinx-docs

Sphinx documentation updates

Author: celiafish

pixi.toml

@@ -7,8 +7,7 @@ platforms = ["linux-64"]
 
 [dependencies]
 python = "==3.12"
-tomviz = ">=2.1.3"
-h5py = "*"
+tomviz = ">=2.2.1"
 tomopy = "*"
 
 [tasks]

tomviz/CMakeLists.txt

@@ -625,9 +625,12 @@ endforeach()
 set(tomviz_python_modules
   __init__.py
   _internal.py
+  dataset.py
+  external_dataset.py
   fix_pdb.py
   operators.py
   internal_dataset.py
+  internal_utils.py
   itkutils.py
   utils.py
   web.py

tomviz/PtychoDialog.cxx

@@ -5,6 +5,7 @@
 #include "ui_PtychoDialog.h"
 
 #include "PythonUtilities.h"
+#include "Utilities.h"
 
 #include <pqApplicationCore.h>
 #include <pqSettings.h>
@@ -87,6 +88,8 @@ class PtychoDialog::Internal : public QObject
 
     connect(ui.buttonBox, &QDialogButtonBox::accepted, this,
             &Internal::accepted);
+    connect(ui.buttonBox, &QDialogButtonBox::helpRequested, this,
+            [](){ openHelpUrl("https://tomviz.readthedocs.io/en/latest/workflows_ptycho.html"); });
   }
 
   void setupTable()

tomviz/PtychoDialog.ui

@@ -100,7 +100,7 @@
       <enum>Qt::Horizontal</enum>
      </property>
      <property name="standardButtons">
-      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
+      <set>QDialogButtonBox::Close|QDialogButtonBox::Help|QDialogButtonBox::Ok</set>
      </property>
     </widget>
    </item>

tomviz/PyXRFMakeHDF5Dialog.cxx

@@ -4,6 +4,8 @@
 #include "PyXRFMakeHDF5Dialog.h"
 #include "ui_PyXRFMakeHDF5Dialog.h"
 
+#include "Utilities.h"
+
 #include <pqApplicationCore.h>
 #include <pqSettings.h>
 
@@ -43,6 +45,8 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
 
     connect(ui.buttonBox, &QDialogButtonBox::accepted, this,
             &Internal::accepted);
+    connect(ui.buttonBox, &QDialogButtonBox::helpRequested, this,
+            [](){ openHelpUrl("https://tomviz.readthedocs.io/en/latest/workflows_pyxrf.html"); });
   }
 
   QString command() const

tomviz/PyXRFMakeHDF5Dialog.ui

@@ -32,7 +32,7 @@
       <enum>Qt::Horizontal</enum>
      </property>
      <property name="standardButtons">
-      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
+      <set>QDialogButtonBox::Close|QDialogButtonBox::Help|QDialogButtonBox::Ok</set>
      </property>
     </widget>
    </item>

tomviz/PyXRFProcessDialog.cxx

@@ -5,6 +5,7 @@
 #include "ui_PyXRFProcessDialog.h"
 
 #include "PythonUtilities.h"
+#include "Utilities.h"
 
 #include <pqApplicationCore.h>
 #include <pqSettings.h>
@@ -80,6 +81,8 @@ class PyXRFProcessDialog::Internal : public QObject
 
     connect(ui.buttonBox, &QDialogButtonBox::accepted, this,
             &Internal::accepted);
+    connect(ui.buttonBox, &QDialogButtonBox::helpRequested, this,
+            [](){ openHelpUrl("https://tomviz.readthedocs.io/en/latest/workflows_pyxrf.html#process-projections"); });
   }
 
   void setupTableColumns()

tomviz/PyXRFProcessDialog.ui

@@ -52,7 +52,7 @@
       <enum>Qt::Horizontal</enum>
      </property>
      <property name="standardButtons">
-      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
+      <set>QDialogButtonBox::Close|QDialogButtonBox::Help|QDialogButtonBox::Ok</set>
      </property>
     </widget>
    </item>

tomviz/Utilities.cxx

@@ -1214,10 +1214,17 @@ void openUrl(const QUrl& url)
 
 void openHelpUrl(const QString& path)
 {
-  QString webPath = "https://tomviz.readthedocs.io/en/latest/";
+  QString basePath = "https://tomviz.readthedocs.io/en/latest/";
+
+  QString fullUrl;
+  if (!path.startsWith("http")) {
+    // Assume this is a relative path that needs toe base added.
+    fullUrl = basePath;
+  }
+  fullUrl += path;
 
   // For now, no local paths have been added. Just use the web path.
-  openUrl(webPath + path);
+  openUrl(fullUrl);
 }
 
 double offWhite[3] = { 204.0 / 255, 204.0 / 255, 204.0 / 255 };

tomviz/python/AutoCenterOfMassTiltImageAlignment.py

@@ -5,11 +5,11 @@
 
 class CenterOfMassAlignmentOperator(tomviz.operators.CancelableOperator):
 
-    def transform_scalars(self, dataset):
+    def transform(self, dataset):
         """Automatically align tilt images by center of mass method"""
         self.progress.maximum = 1
 
-        tiltSeries = utils.get_array(dataset).astype(float)
+        tiltSeries = dataset.active_scalars.astype(float)
 
         self.progress.maximum = tiltSeries.shape[2]
         step = 1
@@ -29,7 +29,7 @@ def transform_scalars(self, dataset):
             step += 1
             self.progress.value = step
 
-        utils.set_array(dataset, tiltSeries)
+        dataset.active_scalars = tiltSeries
 
         # Create a spreadsheet data set from table data
         column_names = ["X Offset", "Y Offset"]