livecellx.core.SingleCellStatic
- class livecellx.core.SingleCellStatic(timeframe=None, bbox=None, regionprops=None, img_dataset=None, mask_dataset=None, dataset_dict=None, feature_dict=None, contour=None, meta=None, uns=None, id=None, cache=None, update_mask_dataset_by_contour=False, empty_cell=False)[source]
Single cell at one time frame
_summary_
- Parameters
timeframe (int) – _description_
bbox (np.array, optional) – [x1, y1, x2, y2], by default None follwoing skimage convention: “Bounding box (min_row, min_col, max_row, max_col). Pixels belonging to the bounding box are in the half-open interval [min_row; max_row) and [min_col; max_col).”
regionprops (RegionProperties, optional) – _description_, by default None
img_dataset (_type_, optional) – _description_, by default None
feature_dict (dict, optional) – _description_, by default {}
contour (
Optional[array]) – an array of contour coordinates [(x1, y1), (x2, y2), …)], in a WHOLE image (not in a cropped image)empty_cell (bool) – use when intend to create an empty cell object. suppress the empty warning.
Methods
add_feature(name, features)compute_iou(other_cell[, bbox])compute_overlap_mask(other_cell[, bbox])compute_overlap_percent(other_cell[, bbox])compute overlap defined by: overlap = intersection / self's area.
compute_regionprops([crop])copy()gen_contour_mask(contour[, img, shape, ...])- rtype
array
gen_skimage_bbox_img_crop(bbox, img[, ...])get_bbox()- rtype
array
get_bbox_from_contour(contour[, dtype])get the bounding box of a contour
get_bbox_on_crop([bbox, padding])get_center([crop])- rtype
array
get_contour_coords_on_crop([bbox, padding])get_contour_coords_on_img_crop([padding])A utility function to calculate pixel coord in image crop's coordinate system to draw contours on an image crop.
get_contour_img([crop, bg_val])return a contour image with background set to background_val
get_contour_label_mask([padding, crop, ...])- rtype
array
get_contour_mask([padding, crop, bbox, dtype])- rtype
array
get_contour_mask_closed_form([padding, crop])If contour points are pixel-wise closed, use this function to fill the contour.
get_img()get_img_crop([padding, bbox])get_label_mask([dtype])get_label_mask_crop([bbox, dtype])get_mask([dtype])get_mask_crop([bbox, dtype])get_napari_shape_contour_vec([...])get_napari_shape_vec(coords)get_sc_img([crop, bg_val])return a contour image with background set to background_val
get_sc_label_mask([padding, crop, bbox, dtype])- rtype
array
get_sc_mask([padding, crop, bbox, dtype])- rtype
array
inflate_from_json_dict(json_dict[, ...])load from json dict
load_from_json_dict(json_dict[, ...])load from json dict
load_single_cells_json(path)load a json file containing a list of single cells
load_single_cells_jsons(paths)- rtype
show([crop, padding, ax])show_contour_img([padding, ax, crop])show_contour_mask([padding, ax, crop])show_label_mask([padding, ax, crop])show_mask([crop, padding, ax])show_panel([padding, figsize])show_whole_img([ax])show_whole_mask([ax])to_json_dict([include_dataset_json, ...])returns a dict that can be converted to json
update_bbox([bbox])update_contour(contour[, update_bbox, ...])update_sc_mask_by_crop(mask[, ...])Updates the single cell mask by cropping the input mask to the bounding box of the single cell and updating the contour.
write_json([path, dataset_json_dir])write_single_cells_json(single_cells, path, ...)write a json file containing a list of single cells
Attributes