cellmap_flow.utils.data
Attributes
Classes
Configuration class for a CellmapModel. |
Functions
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Concatenate a list of arrays along the axis named channel_axis_name. |
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Reorder/remove axes so that the final array has axes in the desired order. |
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Reads a YAML file that defines a list of model configs. |
Module Contents
- cellmap_flow.utils.data.logger
- class cellmap_flow.utils.data.ModelConfig
- property config
- property output_dtype
Returns the output dtype of the model. If not defined, defaults to np.float32.
- class cellmap_flow.utils.data.ScriptModelConfig(script_path, name=None, scale=None)
- script_path
- name = None
- scale = None
- property command
- class cellmap_flow.utils.data.DaCapoModelConfig(run_name: str, iteration: int, name=None)
- run_name
- iteration
- name = None
- property command
- cellmap_flow.utils.data.load_eval_model(num_channels, checkpoint_path)
- class cellmap_flow.utils.data.FlyModelConfig(checkpoint_path: str, channels: [str], input_voxel_size: tuple, output_voxel_size: tuple, name: str = None, input_size=(178, 178, 178), output_size=(56, 56, 56))
- name = None
- checkpoint_path
- channels
- input_voxel_size
- output_voxel_size
- input_size = (178, 178, 178)
- output_size = (56, 56, 56)
- property command
- property model
- class cellmap_flow.utils.data.BioModelConfig(model_name: str, voxel_size, edge_length_to_process=None, name=None)
- model_name
- voxel_size
- name = None
- voxels_to_process = None
- property command
- load_input_information(model)
- load_output_information(model)
- get_axes_and_dims(sample)
- get_spatial_dims(axes, dims)
- get_input_slicer(input_axes)
- cellmap_flow.utils.data.check_config(config)
- class cellmap_flow.utils.data.Config
- cellmap_flow.utils.data.get_dacapo_channels(task)
- cellmap_flow.utils.data.get_dacapo_run_model(run_name, iteration)
- cellmap_flow.utils.data.concat_along_c(arrs, axes_list, channel_axis_name='c')
Concatenate a list of arrays along the axis named channel_axis_name.
- Parameters:
arrs (list of np.ndarray) – The list of arrays to concatenate.
axes_list (list of list of str) – The list of list-of-axis-names. axes_list[i] is the axis names corresponding to arrs[i].
channel_axis_name (str) – The name of the “channel” axis. Default is “c”.
- Returns:
out (np.ndarray) – The concatenated array.
out_axes (list of str) – The list of axis names for the output array.
- cellmap_flow.utils.data.reorder_axes(arr: numpy.ndarray, axes: list[str], desired_order: list[str] = ['z', 'y', 'x', 'c']) tuple[numpy.ndarray, list[str]]
Reorder/remove axes so that the final array has axes in the desired order.
Any axis not in desired_order is removed IF its size == 1,
otherwise a ValueError is raised. - If an axis from desired_order is missing, we insert a size-1 dimension in the correct position so the final shape has exactly 4 dimensions.
- Parameters:
arr (np.ndarray) – Input array.
axes (list of str) – Axis labels corresponding to arr.shape in order.
- Returns:
arr (np.ndarray) – The reshaped/reordered array with axes in desired_order.
out_axes (list of str) – The final axis labels, which should be exactly desired_order.
- cellmap_flow.utils.data.process_chunk_bioimage(self, idi: cellmap_flow.image_data_interface.ImageDataInterface, input_roi: funlib.geometry.Roi)
- cellmap_flow.utils.data.process_chunk_bioimage_test(self, idi: cellmap_flow.image_data_interface.ImageDataInterface, input_roi: funlib.geometry.Roi)
- cellmap_flow.utils.data.format_output_bioimage(self, output_sample, output_names=None, output_axes=None)
- cellmap_flow.utils.data.parse_model_configs(yaml_file_path: str) List[ModelConfig]
Reads a YAML file that defines a list of model configs. Validates them manually, then returns a list of constructed ModelConfig objects.
- class cellmap_flow.utils.data.CellMapModelConfig(folder_path, name, scale=None)
Configuration class for a CellmapModel. Similar to DaCapoModelConfig, but uses a CellmapModel object to populate the necessary metadata and define a prediction function.
- cellmap_model
- name
- scale = None
- property command: str
You can either return a placeholder command or remove this property if not needed. For consistency with your DaCapoModelConfig, we return something minimal here.