nanopyx.methods.drift_alignment.estimator_table

  1import os
  2import numpy as np
  3from importlib import metadata
  4from datetime import datetime
  5
  6
  7class DriftEstimatorTable(object):
  8    """
  9    Class used to store DriftAlignment parameters as a dictionary.
 10    Parameters can be changes individually by setting the corresponding params key value to desired parameter
 11    """
 12
 13    def __init__(self):
 14        self.params = {}
 15        self.params["lib_version"] = metadata.version("nanopyx")
 16        self.params["date"] = datetime.today()
 17        self.params["apply"] = False
 18        self.params["do_batch"] = False
 19        self.params["ref_option"] = 1  # 0 if it is to use first frame, 1 if uses the previous frame
 20        self.params["time_averaging"] = 1
 21        self.params["max_expected_drift"] = 0
 22        self.params["normalize"] = True
 23        self.params["shift_calc_method"] = "Max Fitting"
 24        self.params["use_roi"] = False
 25        self.params["roi"] = None
 26        self.params["show_ccm"] = True  # used for napari
 27        self.params["show_drift_plot"] = True  # used for napari
 28        self.params["show_drift_table"] = True  # used for napari
 29        self.params["comments"] = None
 30
 31        self.drift_table = None
 32
 33    def set_params(self, **kwargs):
 34        """
 35        Method used to set the parameters of drift alignment using keyword arguments.
 36        :param kwargs: same as self.params.keys()
 37        """
 38        for key, value in kwargs.items():
 39            self.params[key] = value
 40
 41    def set_comments(self, comment_string: str):
 42        """
 43        Method used to set comments for drift alignment operation
 44        :param comment_string: str, comment text to be added
 45        """
 46        self.params["comments"] = comment_string
 47
 48    def export_npy(self, path: str = None):
 49        """
 50        Method used to export drift table as a npy file.
 51        :param path: Path to export drift table as npy
 52        """
 53        tmp = []
 54        for key in self.params.keys():
 55            tmp.append((key, self.params[key]))
 56        tmp.append(self.drift_table)
 57        if path is None:
 58            path = input("Please provide a filepath to export drift table as npy") + "_drift_table.npy"
 59        else:
 60            path = os.path.join(path, "_drift_table.npy")
 61
 62        np.save(path, np.array(tmp, dtype=object))
 63
 64    def import_npy(self, path: str = None):
 65        """
 66        Method used to import drift table as a npy file.
 67        :param path: str, Path to drift table saved as a npy file
 68        """
 69        if path is None:
 70            path = input("Please provide a filepath to import drift table")
 71
 72        tmp = np.load(path, allow_pickle=True)
 73
 74        for i in range(tmp.shape[0] - 1):
 75            key, value = tmp[i]
 76            self.params[key] = value
 77        self.drift_table = tmp[tmp.shape[0] - 1]
 78
 79    def export_csv(self, path: str = None):
 80        """
 81        Method used to export drift table as a csv file.
 82        :param path: str, Path to export drift table as csv
 83        """
 84        if path is None:
 85            path = input("Please provide a filepath to export drift table as csv") + "_drift_table.csv"
 86        else:
 87            path = os.path.join(path, "_drift_table.csv")
 88
 89        txt = ""
 90        for key in self.params.keys():
 91            txt += key + ";" + str(self.params[key]) + "\n"
 92        txt += "Drift Table\n"
 93        txt += "XY;X;Y\n"
 94        for i in range(self.drift_table.shape[0]):
 95            txt += (
 96                str(self.drift_table[i][0])
 97                + ";"
 98                + str(self.drift_table[i][1])
 99                + ";"
100                + str(self.drift_table[i][2])
101                + "\n"
102            )
103
104        open(path, "w").writelines(txt)
105
106    def import_csv(self, path: str = None):
107        """
108        Method used to import drift table from a csv file
109        :param path: str, path to import drift table as csv
110        """
111        if path is None:
112            path = input("Please provide a filepath to import drift table")
113
114        tmp = open(path, "r").readlines()
115
116        count = 0
117        for line in tmp:
118            if line == "Drift Table\n":
119                break
120            else:
121                count += 1
122            param_split = line.split(";")
123            key = param_split[0]
124            value = param_split[1].split("\n")[0]
125            if value == "True":
126                value = True
127            elif value == "False":
128                value = False
129            elif value == "None":
130                value = None
131            self.params[key] = value
132
133        if self.params["roi"] is not None:
134            roi_str_list = self.params["roi"][1:-1].split(", ")
135            self.params["roi"] = tuple([int(coord) for coord in roi_str_list])
136
137        drift_table = []
138
139        for row in tmp[count + 2 :]:
140            row_split = row.split(";")
141            drift_xy = float(row_split[0])
142            drift_x = float(row_split[1])
143            drift_y = float(row_split[2])
144            drift_table.append([drift_xy, drift_x, drift_y])
145
146        self.drift_table = np.array(drift_table)