import numpy as np
import pandas as pd
from ..tbl.table import Table, merge_different_index
from .. import setindex
[docs]class MaskArea(Table):
"""Calculate mask area by counting non-zero pixel number in an image.
Args:
reqs[0] (Image): Image stack to calculate area. Required param;
``length_unit``, ``pitch``.
param["split_depth"] (int): File split depth number.
Returns:
Table: Area Table
"""
[docs] def set_index(self):
"""Copy index from the required data index."""
setindex.from_req(self, 0)
[docs] def set_info(self, param={}):
"""Copy index information from reqs[0] and add area column."""
self.info.copy_req(0)
self.info.delete_column(keeps=self.info.get_column_name("index"))
length_unit = self.info.get_param_value("length_unit")
self.info.add_column(
0, "area", "float", length_unit + "^2", "Area size of mask image")
self.info.set_split_depth(param["split_depth"])
[docs] @staticmethod
def process(reqs, param):
"""Calculate mask area by counting non-zero pixel number in an image.
Args:
reqs[0] (numpy.ndarray): Image stack to calculate area.
param["pitch"] (int): Length per pixel in length_unit.
Returns:
pandas.DataFrame: Area table
"""
img = reqs[0].copy()
areas = []
for i in range(img.shape[0]):
areas.append(np.count_nonzero(img[i, :, :]))
return pd.DataFrame({"area": np.array(areas) * param["pitch"]**2})
[docs] def post_run(self):
"""Merge the index table to the split result data."""
merge_different_index(self, 0)