cellmap_flow.models.models_config
=================================

.. py:module:: cellmap_flow.models.models_config


Attributes
----------

.. autoapisummary::

   cellmap_flow.models.models_config.logger


Classes
-------

.. autoapisummary::

   cellmap_flow.models.models_config.ModelConfig
   cellmap_flow.models.models_config.ScriptModelConfig
   cellmap_flow.models.models_config.DaCapoModelConfig
   cellmap_flow.models.models_config.FlyModelConfig
   cellmap_flow.models.models_config.BioModelConfig
   cellmap_flow.models.models_config.CellMapModelConfig


Functions
---------

.. autoapisummary::

   cellmap_flow.models.models_config.concat_along_c
   cellmap_flow.models.models_config.reorder_axes
   cellmap_flow.models.models_config.process_chunk_bioimage
   cellmap_flow.models.models_config.format_output_bioimage


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

.. py:data:: logger

.. py:class:: ModelConfig

   .. py:property:: config


   .. py:property:: output_dtype

      Returns the output dtype of the model. Defaults to np.float32.


   .. py:method:: to_dict()
      :abstractmethod:


      Export model configuration as a dict that can be used with build_model_from_entry.

      :returns: Dictionary containing model type and all init parameters.



.. py:class:: ScriptModelConfig(script_path, name=None, scale=None)



   .. py:attribute:: script_path


   .. py:attribute:: name
      :value: None



   .. py:attribute:: scale
      :value: None



   .. py:property:: command


   .. py:method:: to_dict()

      Export configuration for use with build_model_from_entry.



.. py:class:: DaCapoModelConfig(run_name: str, iteration: int, name=None, scale=None)



   .. py:attribute:: run_name


   .. py:attribute:: iteration


   .. py:attribute:: name
      :value: None



   .. py:attribute:: scale
      :value: None



   .. py:property:: command


   .. py:method:: to_dict()

      Export configuration for use with build_model_from_entry.



.. py:class:: FlyModelConfig(checkpoint_path: str, channels: list[str], input_voxel_size: tuple, output_voxel_size: tuple, name: str = None, input_size=None, output_size=None, scale=None)



   .. py:attribute:: name
      :value: None



   .. py:attribute:: checkpoint_path


   .. py:attribute:: channels


   .. py:attribute:: input_voxel_size


   .. py:attribute:: output_voxel_size


   .. py:attribute:: scale
      :value: None



   .. py:attribute:: input_size
      :value: None



   .. py:attribute:: output_size
      :value: None



   .. py:property:: command


   .. py:method:: load_eval_model(num_channels, checkpoint_path)

      Load evaluation model from checkpoint (TorchScript or PyTorch).



   .. py:property:: model


   .. py:method:: to_dict()

      Export configuration for use with build_model_from_entry.



.. py:class:: BioModelConfig(model_name: str, voxel_size, edge_length_to_process=None, name=None, scale=None)



   .. py:attribute:: model_name


   .. py:attribute:: voxel_size


   .. py:attribute:: name
      :value: None



   .. py:attribute:: scale
      :value: None



   .. py:attribute:: voxels_to_process
      :value: None



   .. py:property:: command


   .. py:method:: load_input_information(model)


   .. py:method:: load_output_information(model)


   .. py:method:: get_axes_and_dims(sample)


   .. py:method:: get_spatial_dims(axes, dims)


   .. py:method:: get_input_slicer(input_axes)


   .. py:method:: to_dict()

      Export configuration for use with build_model_from_entry.



.. py:function:: concat_along_c(arrs, axes_list, channel_axis_name='c')

   Concatenate arrays along the channel axis, adding channel dim if missing.


.. py:function:: reorder_axes(arr: numpy.ndarray, axes: list[str], desired_order: list[str] = ['z', 'y', 'x', 'c']) -> tuple[numpy.ndarray, list[str]]

   Reorder/remove axes to match desired_order, removing size-1 unwanted axes.


.. py:function:: process_chunk_bioimage(self, idi: cellmap_flow.image_data_interface.ImageDataInterface, input_roi: funlib.geometry.Roi)

.. py:function:: format_output_bioimage(self, output_sample, output_names=None, output_axes=None)

.. py:class:: CellMapModelConfig(folder_path, name, scale=None)



   Configuration class for a CellmapModel.


   .. py:attribute:: cellmap_model


   .. py:attribute:: name


   .. py:attribute:: scale
      :value: None



   .. py:property:: command
      :type: str



   .. py:method:: to_dict()

      Export configuration for use with build_model_from_entry.