PartSegCore.mask.io_functions¶

class PartSegCore.mask.io_functions.LoadROI[source]¶

Bases: LoadBase

Load ROI segmentation data.

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Returns:: name of algorithm

classmethod load(load_locations, range_changed=None, step_changed=None, metadata=None)[source]¶

Function for load data

Parameters:

load_locations (List[Union[str, BytesIO, Path]]) – list of files to load
range_changed (Optional[Callable[[int, int], Any]]) – callback function for inform about number of steps to be done
step_changed (Optional[Callable[[int], Any]]) – callback function for report that single step has been done
metadata (Optional[dict]) – additional information needed by function. Like default spacing for load image

Return type:

MaskProjectTuple

Returns:

Project info or list of project info

classmethod partial()[source]¶: Inform that this class load complete data

class PartSegCore.mask.io_functions.LoadROIFromTIFF[source]¶

Bases: LoadBase

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Return type:: str
Returns:: name of algorithm

classmethod load(load_locations, range_changed=None, step_changed=None, metadata=None)[source]¶

Function for load data

Parameters:

load_locations (List[Union[str, BytesIO, Path]]) – list of files to load
range_changed (Optional[Callable[[int, int], Any]]) – callback function for inform about number of steps to be done
step_changed (Optional[Callable[[int], Any]]) – callback function for report that single step has been done
metadata (Optional[dict]) – additional information needed by function. Like default spacing for load image

Return type:

Union[ProjectInfoBase, List[ProjectInfoBase]]

Returns:

Project info or list of project info

class PartSegCore.mask.io_functions.LoadROIImage[source]¶

Bases: LoadBase

Load ROI segmentation and image which is pointed in.

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Returns:: name of algorithm

classmethod load(load_locations, range_changed=None, step_changed=None, metadata=None)[source]¶

Function for load data

Parameters:

load_locations (List[Union[str, BytesIO, Path]]) – list of files to load
range_changed (Optional[Callable[[int, int], Any]]) – callback function for inform about number of steps to be done
step_changed (Optional[Callable[[int], Any]]) – callback function for report that single step has been done
metadata (Optional[dict]) – additional information needed by function. Like default spacing for load image

Return type:

MaskProjectTuple

Returns:

Project info or list of project info

class PartSegCore.mask.io_functions.LoadROIParameters[source]¶

Bases: LoadBase

Load parameters of ROI segmentation. From segmentation file or from json

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Returns:: name of algorithm

classmethod load(load_locations, range_changed=None, step_changed=None, metadata=None)[source]¶

Function for load data

Parameters:

load_locations (List[Union[str, BytesIO, Path]]) – list of files to load
range_changed (Optional[Callable[[int, int], Any]]) – callback function for inform about number of steps to be done
step_changed (Optional[Callable[[int], Any]]) – callback function for report that single step has been done
metadata (Optional[dict]) – additional information needed by function. Like default spacing for load image

Return type:

MaskProjectTuple

Returns:

Project info or list of project info

class PartSegCore.mask.io_functions.LoadStackImage[source]¶

Bases: LoadBase

Load image from standard microscopy images

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Returns:: name of algorithm

classmethod load(load_locations, range_changed=None, step_changed=None, metadata=None)[source]¶

Function for load data

Parameters:

load_locations (List[Union[str, BytesIO, Path]]) – list of files to load
range_changed (Optional[Callable[[int, int], Any]]) – callback function for inform about number of steps to be done
step_changed (Optional[Callable[[int], Any]]) – callback function for report that single step has been done
metadata (Optional[dict]) – additional information needed by function. Like default spacing for load image

Return type:

MaskProjectTuple

Returns:

Project info or list of project info

class PartSegCore.mask.io_functions.LoadStackImageWithMask[source]¶

Bases: LoadBase

Load image, then mask from secondary file

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Return type:: str
Returns:: name of algorithm

classmethod load(load_locations, range_changed=None, step_changed=None, metadata=None)[source]¶

Function for load data

Parameters:

load_locations (List[Union[str, BytesIO, Path]]) – list of files to load
range_changed (Optional[Callable[[int, int], Any]]) – callback function for inform about number of steps to be done
step_changed (Optional[Callable[[int], Any]]) – callback function for report that single step has been done
metadata (Optional[dict]) – additional information needed by function. Like default spacing for load image

Return type:

Union[ProjectInfoBase, List[ProjectInfoBase]]

Returns:

Project info or list of project info

classmethod number_of_files()[source]¶: Number of files required for load method

class PartSegCore.mask.io_functions.MaskProjectTuple(file_path, image, mask=None, roi_info=<factory>, additional_layers=<factory>, selected_components=<factory>, roi_extraction_parameters=<factory>, history=<factory>, errors='', spacing=None, points=None, frame_thickness=2)[source]¶

Bases: ProjectInfoBase

Dataclass instance to describe segmentation state

Variables:

file_path (str) – path to current processed file
~.image (Union[Image,str,None]) – image which is proceeded in given segmentation. If str then it is path to image on drive
~.mask (Optional[np.ndarray]) – Mask limiting segmentation area.
~.roi_info (SegmentationInfo) – ROI information.
~.roi_info – ROI description
~.selected_components (List[int]) – list of selected components
~.segmentation_parameters (Dict[int,Optional[SegmentationProfile]]) – For each component description set of parameters used for segmentation
history (List[HistoryElement]) – list of operations needed to create mask
~.errors (str) – information about problems meet during calculation
~.spacing (Optional[List[float]]) – information about spacing when image is missed. For napari read plugin

get_raw_copy()[source]¶: Create copy with only image

class PartSegCore.mask.io_functions.SaveComponents[source]¶

Bases: SaveBase

Save selected components in separated files.

This algorithm has following parameters:

frame (int)- Frame, How many pixels around bounding box of ROI should be saved
mask_data (bool)- Keep data outside ROI, If not checked then data outside ROI will be replaced with zeros.

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Return type:: str
Returns:: name of algorithm

classmethod save(cls, save_location, project_info, parameters, range_changed=None, step_changed=None)[source]¶

Parameters:

save_location (Union[str, BytesIO, Path]) – location to save, can be buffer
project_info (MaskProjectTuple) – all project data
parameters (SaveComponentsOptions) – additional parameters for saving method
range_changed – report function for inform about steps num
step_changed – report function for progress

class PartSegCore.mask.io_functions.SaveComponentsImagej[source]¶

Bases: SaveBase

This algorithm has following parameters:

frame (int)- Frame, How many pixels around bounding box of ROI should be saved
mask_data (bool)- Keep data outside ROI, If not checked then data outside ROI will be replaced with zeros.

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Return type:: str
Returns:: name of algorithm

classmethod save(cls, save_location, project_info, parameters, range_changed=None, step_changed=None)[source]¶

Parameters:

save_location (Union[str, BytesIO, Path]) – location to save, can be buffer
project_info (MaskProjectTuple) – all project data
parameters (SaveComponentsOptions) – additional parameters for saving method
range_changed – report function for inform about steps num
step_changed – report function for progress

pydantic model PartSegCore.mask.io_functions.SaveComponentsOptions[source]¶

Bases: BaseModel

Show JSON schema

{
   "title": "SaveComponentsOptions",
   "type": "object",
   "properties": {
      "frame": {
         "default": 0,
         "description": "How many pixels around bounding box of ROI should be saved",
         "title": "Frame",
         "type": "integer"
      },
      "mask_data": {
         "default": false,
         "description": "If not checked then data outside ROI will be replaced with zeros.",
         "title": "Keep data outside ROI",
         "type": "boolean"
      }
   },
   "additionalProperties": false
}

Config:

extra: str = forbid

Fields:

frame (int)
mask_data (bool)

field frame: int = 0¶: How many pixels around bounding box of ROI should be saved

field mask_data: bool = False¶: If not checked then data outside ROI will be replaced with zeros.

class PartSegCore.mask.io_functions.SaveParametersJSON[source]¶

Bases: SaveBase

Save parameters of roi mask segmentation

classmethod get_fields()[source]¶

This function return list of parameters needed by algorithm. It is used for generate form in User Interface

Return type:: List[Union[AlgorithmProperty, str]]
Returns:: list of algorithm parameters and comments

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Return type:: str
Returns:: name of algorithm

classmethod save(save_location, project_info, parameters=None, range_changed=None, step_changed=None)[source]¶

Parameters:

save_location (Union[str, BytesIO, Path]) – path to save
project_info (Union[ROIExtractionProfile, MaskProjectTuple]) – data to save in json file
parameters (Optional[dict]) – Not used, keep for satisfy interface
range_changed – Not used, keep for satisfy interface
step_changed – Not used, keep for satisfy interface

Returns:

class PartSegCore.mask.io_functions.SaveROI[source]¶

Bases: SaveBase

Save current ROI as a project

This algorithm has following parameters:

relative_path (bool)- Relative Path in segmentation, Use relative path to image in segmentation file
mask_data (bool)- Keep data outside ROI, When loading data in ROI analysis, if not checked then data outside ROI will be replaced with zeros.
frame_thickness (int)- Frame thickness, Thickness of frame around ROI

classmethod get_name()[source]¶

Algorithm name. It will be used during interface generating and in registering to proper PartSeg.PartSegCore.algorithm_describe_base.Register.

Returns:: name of algorithm

classmethod save(cls, save_location, project_info, parameters, range_changed=None, step_changed=None)[source]¶

Parameters:

save_location (Union[str, BytesIO, Path]) – location to save, can be buffer
project_info (MaskProjectTuple) – all project data
parameters (SaveROIOptions) – additional parameters for saving method
range_changed – report function for inform about steps num
step_changed – report function for progress

pydantic model PartSegCore.mask.io_functions.SaveROIOptions[source]¶

Bases: BaseModel

Show JSON schema

{
   "title": "SaveROIOptions",
   "type": "object",
   "properties": {
      "relative_path": {
         "default": true,
         "description": "Use relative path to image in segmentation file",
         "title": "Relative Path\nin segmentation",
         "type": "boolean"
      },
      "mask_data": {
         "default": false,
         "description": "When loading data in ROI analysis, if not checked then data outside ROI will be replaced with zeros.",
         "title": "Keep data outside ROI",
         "type": "boolean"
      },
      "frame_thickness": {
         "default": 2,
         "description": "Thickness of frame around ROI",
         "title": "Frame thickness",
         "type": "integer"
      },
      "spacing": {
         "default": [
            1e-06,
            1e-06,
            1e-06
         ],
         "hidden": true,
         "items": {
            "type": "number"
         },
         "title": "Spacing",
         "type": "array"
      }
   },
   "additionalProperties": false
}

Config:

extra: str = forbid

Fields:

frame_thickness (int)
mask_data (bool)
relative_path (bool)
spacing (List[float])

field frame_thickness: int = 2¶: Thickness of frame around ROI

field mask_data: bool = False¶: When loading data in ROI analysis, if not checked then data outside ROI will be replaced with zeros.

field relative_path: bool = True¶: Use relative path to image in segmentation file

field spacing: List[float] = [1e-06, 1e-06, 1e-06]¶

PartSegCore.mask.io_functions.empty_fun(_a0=None, _a1=None)[source]¶: This is empty fun to pass as callback to for report.

PartSegCore.mask.io_functions.load_metadata(data)[source]¶: Load metadata saved in json format for segmentation mask :type data: Union[str, Path, TextIO] :param data: path to json file, string with json, or opened file :return: restored structures

PartSegCore.mask.io_functions¶

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