utils.segmentation_utils
========================

.. py:module:: utils.segmentation_utils


Classes
-------

.. autoapisummary::

   utils.segmentation_utils.SegmentationMixin


Module Contents
---------------

.. py:class:: SegmentationMixin

   Mixin class for the segmentation functionality of the RANO module.
   This class handles the segmentation of the input volumes and the loading of the results into Slicer.
   It also handles the progress bar and the cancellation of the segmentation process.


   .. py:attribute:: start_time_t1
      :value: None


      Start time for the first segmentation process


   .. py:attribute:: start_time_t2
      :value: None


      Start time for the second segmentation process


   .. py:method:: onCalcSegmentationsButton()

      Run processing when user clicks the "Calculate Segmentations" button.



   .. py:method:: onCliNodeStatusUpdate(cliNode, event, progressBar, task_dir, tmp_path_out, output_segmentation, input_volume_list, timepoint, original_log_level=32)

      Callback function to handle the status update of the CLI node.

      :param cliNode: The CLI node that is being observed.
      :param event: The event that triggered the callback.
      :param progressBar: The progress bar to update.
      :param task_dir: The task directory for the segmentation.
      :param tmp_path_out: The temporary output path for the segmentation.
      :param output_segmentation: The output segmentation node.
      :param input_volume_list: The list of input volume nodes.
      :param timepoint: The timepoint for the segmentation ('timepoint1' or 'timepoint2').
      :param original_log_level: The original log level for the Slicer application.



   .. py:method:: onSegmentationCliNodeSuccess(input_volume_list, output_segmentation, task_dir, timepoint, tmp_path_out)

      Callback function to handle the success of the CLI node.
      This function loads the output segmentation into Slicer and applies the transformation if required.

      :param input_volume_list: The list of input volume nodes.
      :param output_segmentation: The output segmentation node.
      :param task_dir: The task directory for the segmentation.
      :param timepoint: The timepoint for the segmentation ('timepoint1' or 'timepoint2').
      :param tmp_path_out: The temporary output path for the segmentation.



   .. py:method:: onCancel(cliNode, progressBar)


   .. py:method:: ImportLabelmapToSegmentationNodeWithBackgroundSegment(loadedLabelVolumeNode, output_segmentation)
      :staticmethod:


      Import the labelVolumeNode into the segmentation node. The labels in the labelVolumeNode are increased by 1
      temporarily to include the background label (0) and then decreased by 1 again to have the original labels.
      (This is because slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode ignores the background label)
      Finally, the segmentIDs are reduced by 1 to have the correct segmentIDs in the segmentation node.

      Args:
      loadedLabelVolumeNode: The label volume node to import.
      output_segmentation: The output segmentation node to import the label volume into.



   .. py:method:: setDefaultSegmentFor2DMeasurements(defaultSegmentName='ETC')

      Set the default segment for 2D measurements in the segment selector widget.
      This function checks if the default segment exists in either of the segmentations
      and sets it as the current segment in the segment selector widget.

      :param defaultSegmentName: The name of the default segment to set.



   .. py:method:: get_task_dir(model_key, parameterNode)
      :staticmethod:


      Get the task directory for the given model key.

      :param model_key: The key of the model to get the task directory for.
      :param parameterNode: The parameter node for the RANO module.

      :returns: The task directory for the given model key.