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import json
from typing import List, Union
import numpy as np
class BaseReport:
"""The Abstract base class for all reports
"""
def __init__(self, imgstack_files: str, coord_infos: str):
self.imgstack = self._read_imgstack(imgstack_files)
if isinstance(coord_infos, list):
merged_json = dict()
for coord_info in coord_infos:
a_file = open(coord_info, "r")
_contents = json.load(a_file)
for k, v in _contents.items():
# print(v)
if not (k in merged_json):
# if the key isnt in the merged dictionary, then add and initialise it. This is python 3.6+ behaviour
merged_json[k] = v
continue
if not isinstance(merged_json[k], list) or isinstance(
merged_json[k], str
):
# If there is unique data and the value at k in merged dict is not a list already, make it one
merged_json[k] = [merged_json[k]]
_test_dict = merged_json[k].copy()
_base_set = set(_test_dict)
if isinstance(v, list):
_test_dict.extend(v)
else:
_test_dict.append(v)
_test_set = set(_test_dict)
# print(_test_set)
# print(_base_set)
if len(_test_set) == len(_base_set):
# If there is nothing unique when making the set of the new content at that key and the old content, then skip
continue
if isinstance(v, list):
merged_json[k].extend(v)
else:
merged_json[k].append(v)
self.coords = merged_json
# print(self.coords)
else:
a_file = open(coord_infos, "r")
self.coords = json.load(a_file)
self.pdf = None
# PDF controls--------------------------------------------
def set_pdf(self, pdf) -> None:
"""Takes a PdfPages object and sets that as the internal variable
Args:
pdf : the pdf pages object
"""
self.pdf = pdf
def get_pdf(self):
"""Return the pdfpages object
Returns:
_type_: _description_
"""
return self.pdf
def isPdf(self) -> bool:
"""Checks if the pdf has been set
Returns:
bool: _description_
"""
if self.pdf is None:
return False
return True
def closePdf(self) -> None:
"""Closes the pdf
"""
if self.isPdf():
self.pdf.close()
self.pdf = None
def _read_imgstack(self, imgstack_files: Union[List[str], str]):
"""Read in an image stack created by utils.fileIO function
Args:
imgstack_files (str): The
Returns:
_type_: Loaded Image stack
"""
if isinstance(imgstack_files, list):
# If there is a list of images, then extend the image stack along the last dimension
_imgstack = np.array(
[np.load(image_stack) for image_stack in imgstack_files]
)
imgstack = np.stack(_imgstack, axis=-1)
else:
imgstack = np.load(imgstack_files)
return imgstack
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