ENH: Allow editing and saving of registration presets

Built-in elastix registration presets can be copied into the scene, edited, and saved in the scene. When registration is launched then the in-scene configuration data is written to files and passed to Elastix.

In-scene presets can also be saved as user presets, into the user profile folder (each preset in a separate subfolder, containing all necessary information, so that presets can be easily shared with other just by copying the complete folder content).

see #50

Elastix/CMakeLists.txt

@@ -5,8 +5,11 @@ set(MODULE_NAME Elastix)
 set(MODULE_PYTHON_SCRIPTS
   ${MODULE_NAME}.py
   ElastixLib/__init__
-  ElastixLib/constants.py
+  ElastixLib/utils.py
+  ElastixLib/database.py
+  ElastixLib/preset.py
   ElastixLib/manager.py
+  ElastixLib/ElastixPresetSubjectHierarchyPlugin.py
   )
 
 set(MODULE_PYTHON_RESOURCES

Elastix/ElastixLib/ElastixPresetSubjectHierarchyPlugin.py

@@ -0,0 +1,44 @@
+import qt, ctk, slicer
+from AbstractScriptedSubjectHierarchyPlugin import *
+
+
+class ElastixPresetSubjectHierarchyPlugin(AbstractScriptedSubjectHierarchyPlugin):
+
+  # Necessary static member to be able to set python source to scripted subject hierarchy plugin
+  filePath = __file__
+
+  def __init__(self, scriptedPlugin):
+    scriptedPlugin.name = 'Elastix'
+    AbstractScriptedSubjectHierarchyPlugin.__init__(self, scriptedPlugin)
+
+  def canAddNodeToSubjectHierarchy(self, node, parentItemID = None):
+    if node is not None and node.IsA("vtkMRMLScriptedModuleNode"):
+      if node.GetAttribute("Type") == "ElastixPreset":
+        return 0.9
+    return 0.0
+
+  def canOwnSubjectHierarchyItem(self, itemID):
+    pluginHandlerSingleton = slicer.qSlicerSubjectHierarchyPluginHandler.instance()
+    shNode = pluginHandlerSingleton.subjectHierarchyNode()
+    associatedNode = shNode.GetItemDataNode(itemID)
+    return self.canAddNodeToSubjectHierarchy(associatedNode)
+
+  def roleForPlugin(self):
+    return "ElastixPreset"
+
+  def icon(self, itemID):
+    import os
+    iconPath = None
+    pluginHandlerSingleton = slicer.qSlicerSubjectHierarchyPluginHandler.instance()
+    shNode = pluginHandlerSingleton.subjectHierarchyNode()
+    associatedNode = shNode.GetItemDataNode(itemID)
+    if associatedNode is not None and associatedNode.IsA("vtkMRMLScriptedModuleNode"):
+      if associatedNode.GetAttribute("Type") == "ElastixPreset":
+        iconPath = os.path.join(os.path.dirname(__file__), '../Resources/Icons/Elastix.png')
+    if iconPath and os.path.exists(iconPath):
+      return qt.QIcon(iconPath)
+    # Item unknown by plugin
+    return qt.QIcon()
+
+  def tooltip(self, itemID):
+    return "Elastix preset"

Elastix/ElastixLib/database.py

@@ -0,0 +1,139 @@
+import logging
+import shutil
+
+import qt
+import vtk
+
+import abc
+import os
+
+from typing import Callable
+
+import slicer
+from pathlib import Path
+from ElastixLib.preset import Preset, UserPreset, createPreset
+
+
+class ElastixDatabase(abc.ABC):
+
+  @property
+  def logCallback(self):
+    return self._logCallback
+
+  @logCallback.setter
+  def logCallback(self, cb: Callable = None):
+    self._logCallback = cb
+
+  def getRegistrationPresetsFromXML(self, elastixParameterSetDatabasePath, presetClass):
+    if not os.path.isfile(elastixParameterSetDatabasePath):
+      raise ValueError("Failed to open parameter set database: " + elastixParameterSetDatabasePath)
+    elastixParameterSetDatabaseXml = vtk.vtkXMLUtilities.ReadElementFromFile(elastixParameterSetDatabasePath)
+
+    # Create python list from XML for convenience
+    registrationPresets = []
+    if elastixParameterSetDatabaseXml is not None:
+      for parameterSetIndex in range(elastixParameterSetDatabaseXml.GetNumberOfNestedElements()):
+        parameterSetXml = elastixParameterSetDatabaseXml.GetNestedElement(parameterSetIndex)
+        parameterFilesXml = parameterSetXml.FindNestedElementWithName('ParameterFiles')
+        parameterFiles = []
+        for parameterFileIndex in range(parameterFilesXml.GetNumberOfNestedElements()):
+          parameterFiles.append(os.path.join(
+            str(Path(elastixParameterSetDatabasePath).parent),
+            parameterFilesXml.GetNestedElement(parameterFileIndex).GetAttribute('Name'))
+          )
+        parameterSetAttributes = \
+          [parameterSetXml.GetAttribute(attr) if parameterSetXml.GetAttribute(attr) is not None else "" for attr in ['id', 'modality', 'content', 'description', 'publications']]
+        try:
+          registrationPresets.append(
+            createPreset(*parameterSetAttributes, parameterFiles=parameterFiles, presetClass=presetClass)
+          )
+        except FileNotFoundError as exc:
+          msg = f"Cannot load preset. Loading failed with error: {exc}"
+          logging.error(msg)
+          if self.logCallback:
+            self.logCallback(msg)
+          continue
+    return registrationPresets
+
+  def __init__(self):
+    self._logCallback = None
+    self.registrationPresets = None
+
+  def getRegistrationPresets(self, force_refresh=False):
+    if self.registrationPresets and not force_refresh:
+      return self.registrationPresets
+
+    self.registrationPresets = self._getRegistrationPresets()
+
+    return self.registrationPresets
+
+  @abc.abstractmethod
+  def _getRegistrationPresets(self):
+    pass
+
+
+class BuiltinElastixDatabase(ElastixDatabase):
+
+  # load txt files into slicer scene
+  DATABASE_FILE = os.path.abspath(
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', 'Resources', 'RegistrationParameters',
+                 'ElastixParameterSetDatabase.xml'))
+
+  def getPresetsDir(self):
+    return str(Path(self.DATABASE_FILE).parent)
+
+  def _getRegistrationPresets(self):
+    return self.getRegistrationPresetsFromXML(self.DATABASE_FILE, presetClass=Preset)
+
+
+class UserElastixDataBase(ElastixDatabase):
+
+  DATABASE_LOCATION = Path(slicer.app.slicerUserSettingsFilePath).parent / "Elastix"
+
+  @staticmethod
+  def getAllXMLFiles(directory):
+    import fnmatch
+    files = []
+    for root, dirnames, filenames in os.walk(directory):
+      for filename in fnmatch.filter(filenames, '*{}'.format(".xml")):
+        files.append(os.path.join(root, filename))
+    return files
+
+  def __init__(self):
+    self.DATABASE_LOCATION.mkdir(exist_ok=True)
+    self._presetLocations = {}
+    super().__init__()
+
+  def getPresetsDir(self):
+    return str(self.DATABASE_LOCATION)
+
+  def _getRegistrationPresets(self):
+    xml_files = self.getAllXMLFiles(self.DATABASE_LOCATION)
+    registrationPresets = []
+    for xml_file in xml_files:
+      presets = self.getRegistrationPresetsFromXML(xml_file, presetClass=UserPreset)
+      if len(presets) > 1:
+        raise RuntimeError("The User presets are intended to have one preset per .xml file only.")
+      for preset in presets:
+        self._presetLocations[preset] = str(Path(xml_file).parent)
+      registrationPresets.extend(presets)
+    return registrationPresets
+
+  def deletePreset(self, preset: UserPreset):
+    path = self._presetLocations.pop(preset)
+    shutil.rmtree(path)
+
+
+class InSceneElastixDatabase(ElastixDatabase):
+
+  def _getRegistrationPresets(self):
+    registrationPresets = []
+
+    nodes = filter(lambda n: n.GetAttribute('Type') == 'ElastixPreset',
+           slicer.util.getNodesByClass('vtkMRMLTextNode'))
+
+    from ElastixLib.preset import getInScenePreset
+    for node in nodes:
+      registrationPresets.append(getInScenePreset(node))
+
+    return registrationPresets