Extract
- class celltk.extract.Extract(images=[], masks=[], channels=[], regions=[], lineages=[], time=None, condition='condition', position_id=0, min_trace_length=0, remove_parent=True, output='data_frame', save=True, force_rerun=True, skip_frames=(), _output_id=None, **kwargs)
- Parameters
images (
Collection
[str
], default:[]
) –masks (
Collection
[str
], default:[]
) –channels (
Collection
[str
], default:[]
) –regions (
Collection
[str
], default:[]
) –lineages (
Collection
[ndarray
], default:[]
) –time (
Optional
[float
], default:None
) –condition (
str
, default:'condition'
) –position_id (
int
, default:0
) –min_trace_length (
int
, default:0
) –remove_parent (
bool
, default:True
) –output (
str
, default:'data_frame'
) –save (
bool
, default:True
) –force_rerun (
bool
, default:True
) –skip_frames (
Tuple
[int
], default:()
) –_output_id (
Optional
[Tuple
[str
]], default:None
) –
- add_derived_metric(metric_name, keys, func='sum', inverse=False, propagate=False, frame_rng=None, *args, **kwargs)
Calculate additional metrics based on information already in array
- Parameters
metric_name (
str
) – Key to save the metric underkeys (
Collection
[Tuple
[str
]]) – One or multiple keys to calculate with. Each key will be used to index an array, ConditionArray[key]. Each key should produce a 2D array when indexed.func (
str
, default:'sum'
) – Name of numpy function to apply, e.g. ‘sum’inverse (
bool
, default:False
) – If True, repeats the calculation as if the keys were passed in the opposite order and saves in the other keys.propagate ((
str
,bool
), default:False
) – If True, propagates the results of the calculation to the other keys in the array.frame_rng (
Union
[int
,Tuple
[int
],None
], default:None
) – Frames to use in calculation. If int, takes that many frames from start of trace. If tuple, uses passed frames.
- Return type
None
- add_extra_metric(name, func=None)
Add custom metrics or metrics from regionprops to array. If function is none, value will just be nan.
- Parameters
name (
str
) – key for the metric in the ConditionArrayfunc (
Optional
[Callable
], default:None
) – If str, name of the metric from skiamge.regionprops. if Callable, function that calculates the metric. Cannot be used if Operation must be saved as YAML before running.
- Return type
None
- add_filter(filter_name, metric, region=0, channel=0, frame_rng=None, *args, **kwargs)
Remove cells from array that do not match the filter.
- Parameters
filter_name (
str
) – Options are ‘outside’, ‘inside’, ‘outside_percentile’, ‘inside_percentile’.metric (
str
) – Name of metric to use. Can be any key in the array.region (
Union
[str
,int
], default:0
) – Name of region to calculate the filter in.channel (
Union
[str
,int
], default:0
) – Name of channel to calculate filter in.frame_rng (
Union
[int
,Tuple
[int
],None
], default:None
) – Frames to use in calculation. If int, takes that many frames from start of trace. If tuple, uses passed frames.
- Return type
None
- extract_data_from_image(images, masks, channels=[], regions=[], lineages=[], time=None, condition='default', position_id=None, min_trace_length=0, skip_frames=(), remove_parent=True, parent_track=0)
Extracts data from stacks of images and constructs a ConditionArray.
- Parameters
images (
Image
) – Images to extract data from.masks (
Mask
) – Masks to segment images with.channels (
Collection
[str
], default:[]
) – Names of channels corresponding toregions (
Collection
[str
], default:[]
) – Names of segmented regions corresponding, tracks and masks, in that order.lineages (
Collection
[ndarray
], default:[]
) – Lineage files corresponding to masks if provided.time (
Union
[float
,ndarray
,None
], default:None
) – If int or float, designates time between frames. If array, marks the frame time points.condition (
str
, default:'default'
) – Name of the conditionposition_id (
Optional
[int
], default:None
) – Unique identifier if multiple ConditionArrays will share the same conditionmin_trace_length (
int
, default:0
) – All cells with shorter traces will be deleted from the final array.skip_frames (
Tuple
[int
], default:()
) – Use to specify frames to be skipped. If provided to Pipeline, does not need to be provided again, but must match.remove_parent (
bool
, default:True
) – If true, parents of cells are not kept in the final ConditionArray.parent_track (
int
, default:0
) – If multiple tracks are provided, designates the one to use for lineage tracking
- Returns
ConditionArray with data from the images.
- Return type
The following axes dimensions are used: ax 0 - cell locations (nuc, cyto, population, etc.) ax 1 - channels (TRITC, FITC, etc.) ax 2 - metrics (median_int, etc.) ax 3 - cells ax 4 - frames
- set_metric_list(metrics)
Sets the list of metrics to get. For a possible list, see skimage.regionprops or Extract._possible_metrics.
- Parameters
metrics (
Collection
[str
]) – List of metrics to measure from images- Return type
None
- Returns
None
Note
CellTK can only use the scalar metrics in regionprops.