rpt_dosi.tmtv
=============

.. py:module:: rpt_dosi.tmtv


Classes
-------

.. autoapisummary::

   rpt_dosi.tmtv.TMTV


Functions
---------

.. autoapisummary::

   rpt_dosi.tmtv.dilate_mask
   rpt_dosi.tmtv.tmtv_mask_cut_the_head
   rpt_dosi.tmtv.tmtv_apply_mask
   rpt_dosi.tmtv.tmtv_mask_remove_rois
   rpt_dosi.tmtv.tmtv_mask_keep_rois
   rpt_dosi.tmtv.rois_to_remove_default
   rpt_dosi.tmtv.rois_to_keep_default
   rpt_dosi.tmtv.is_number
   rpt_dosi.tmtv.remove_small_areas
   rpt_dosi.tmtv.find_foci
   rpt_dosi.tmtv.get_label_centroids


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

.. py:function:: dilate_mask(itk_image, dilatation_mm)

.. py:function:: tmtv_mask_cut_the_head(itk_image, mask, skull_filename, margin_mm)

.. py:function:: tmtv_apply_mask(itk_image, np_mask)

.. py:function:: tmtv_mask_remove_rois(itk_image, np_mask, roi_list, roi_folder='', verbose=False)

.. py:function:: tmtv_mask_keep_rois(itk_image, np_mask, roi_list, roi_folder='', verbose=False)

.. py:function:: rois_to_remove_default()

.. py:function:: rois_to_keep_default()

.. py:class:: TMTV

   Compute TMTV Total Metabolic Tumor Volume
   Consider ITK images as input and output


   .. py:attribute:: verbose
      :value: True



   .. py:attribute:: intensity_threshold
      :value: 'auto'



   .. py:attribute:: population_mean_liver
      :value: None



   .. py:attribute:: cut_the_head
      :value: False



   .. py:attribute:: cut_the_head_margin_mm
      :value: 10



   .. py:attribute:: cut_the_head_roi_filename
      :value: 'rois/skull.nii.gz'



   .. py:attribute:: rois_to_remove


   .. py:attribute:: rois_to_remove_folder
      :value: 'rois'



   .. py:attribute:: removed_mask
      :value: None



   .. py:attribute:: rois_to_keep
      :value: []



   .. py:attribute:: rois_to_keep_folder
      :value: 'rois'



   .. py:attribute:: minimal_volume_cc
      :value: None



   .. py:attribute:: tmtv_mask_np
      :value: None



   .. py:method:: compute_mask(itk_image)


   .. py:method:: apply_threshold(itk_image, np_mask)


   .. py:method:: get_removed_rois_mean_value(np_image, removed_mask)


   .. py:method:: get_gafita2019_threshold(itk_image, population_mean_liver)


.. py:function:: is_number(n)

.. py:function:: remove_small_areas(itk_mask, minimal_volume_cc, keep_binary_mask=True)

.. py:function:: find_foci(tmtv, tmtv_mask, min_size_cm3=1, percentage_threshold=0.001)

.. py:function:: get_label_centroids(foci)