# -*- coding: utf-8 -*-
"""
***************************************************************************
    Processor_Inversion_core.py - LMU Agri Apps - Training of new ML-Models
    PROSAIL parameters - CORE
    -----------------------------------------------------------------------
    begin                : 09/2020
    copyright            : (C) 2024 Matthias Wocher, Martin Danner
    email                : m.wocher@iggf.geo.uni-muenchen.de

***************************************************************************
    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this software. If not, see <https://www.gnu.org/licenses/>.
***************************************************************************

This script handles the GUI for training new ML-models. There is no maximum flexibility as in the _core module,
because the user may not change the important hyperparameters on his own. There is only the possibility to create new
models on basis of individual Lookup-Tables.

"""
import sys
# import os
# import logging

# import numpy as np
# import pandas as pd

from qgis.gui import QgsMapLayerComboBox
from qgis.core import QgsMapLayerProxyModel
# from enmapbox.qgispluginsupport.qps.speclib.core.spectralprofile import decodeProfileValueDict
from qgis.core import QgsVectorLayer

# import LUT.CreateLUT_GUI
# ensure to call QGIS before PyQtGraph
from qgis.PyQt.QtWidgets import *
# from PyQt5.QtGui import QIntValidator
# from PyQt5.QtCore import QThread, pyqtSignal
# from PyQt5.QtCore import QTimer
import lmuvegetationapps.Processor.Processor_Inversion_core as processor
# import lmuvegetationapps.LUT.CreateLUT_GUI
from lmuvegetationapps import APP_DIR
from _classic.hubflow.core import *
import csv
import joblib
import json

from enmapbox.gui.utils import loadUi

from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
import matplotlib.pyplot as plt
from PyQt5.QtWidgets import QVBoxLayout

from sklearn.linear_model import LinearRegression
from sklearn.metrics import r2_score
from mpl_toolkits.axes_grid1 import make_axes_locatable

import warnings

warnings.filterwarnings('ignore', category=DeprecationWarning)
warnings.filterwarnings('ignore', category=UserWarning)

pathUI_train = os.path.join(APP_DIR, 'Resources/UserInterfaces/Processor_Train.ui')
pathUI_loadtxt = os.path.join(APP_DIR, 'Resources/UserInterfaces/LoadTxtFileInsitu.ui')
pathUI_wavelength = os.path.join(APP_DIR, 'Resources/UserInterfaces/Select_Wavelengths.ui')
pathUI_prgbar = os.path.join(APP_DIR, 'Resources/UserInterfaces/ProgressBar.ui')
pathUI_Performance = os.path.join(APP_DIR, 'Resources/UserInterfaces/Processor_Performance_View.ui')
pathUI_Printer = os.path.join(APP_DIR, 'Resources/UserInterfaces/Printer.ui')


class MLTrainingGUI(QDialog):
    def __init__(self, parent=None):
        mLayerSpeclib: QgsMapLayerComboBox
        super(MLTrainingGUI, self).__init__(parent)
        loadUi(pathUI_train, self)
        self.mLayerSpeclib.setFilters(QgsMapLayerProxyModel.PointLayer)


class LoadTxtFileGUI(QDialog):
    def __init__(self, parent=None):
        super(LoadTxtFileGUI, self).__init__(parent)
        loadUi(pathUI_loadtxt, self)


class SelectWavelengthsGUI(QDialog):
    def __init__(self, parent=None):
        super(SelectWavelengthsGUI, self).__init__(parent)
        loadUi(pathUI_wavelength, self)


class PRG_GUI(QDialog):
    def __init__(self, parent=None):
        super(PRG_GUI, self).__init__(parent)
        loadUi(pathUI_prgbar, self)
        self.allow_cancel = False

    def closeEvent(self, event):
        if self.allow_cancel:
            event.accept()
        else:
            event.ignore()


class Performance_GUI(QDialog):
    def __init__(self, parent=None):
        super(Performance_GUI, self).__init__(parent)
        loadUi(pathUI_Performance, self)


class PrinterGUI(QDialog):
    def __init__(self, parent=None):
        super(PrinterGUI, self).__init__(parent)
        loadUi(pathUI_Printer, self)


# MLTraining is a GUI handler for training new ML-models. For more information, go to Processor_Inversion_core.py
class ML_Training:
    def __init__(self, main):
        self.main = main
        self.gui = MLTrainingGUI()
        self.initial_values()
        self.params_dict_check()
        self.connections()

    def initial_values(self):
        # exclude_wavelengths: from ... to [nm]; these are default values for atmospheric water vapor absorption
        # self.exclude_wavelengths = [[1332, 1445], [1785, 1965], [2450, 2500]]
        self.exclude_wavelengths = [[1290, 1525], [1730, 1970], [2400, 2500]]
        self.lut_path = None  # file path to the LUT metafile
        self.model_process_dict = None  # file path to model proc file
        self.meta_dict = None  # intial empty dictionary for LUT meta
        self.wunit = "nanometers"
        self.wl, self.nbands, self.nbands_valid = (None, None, None)
        self.out_dir = None  # directory for output
        self.model_name = None  # name of the output model
        self.noisetype = 1
        self.noiselevel = 4
        self.use_al = False
        self.use_insitu = False
        self.split_method = 'train_test_split'
        self.kfolds = None
        self.test_size = None
        self.perf_eval = False
        self.n_initial = None
        self.algorithm = 'ANN'
        self.algorithm_dict = {0: 'ANN', 1: 'GPR', 2: 'RFR', 3: 'SVR', 4: 'KRR', 5: 'GBR'}
        self.all_labels = ["cab", "car", "anth", "cw", "cp", "cbc", "LAI", "AGBdry", "AGBfresh", "CWC", "Nitrogen",
                           "Carbon"]
        self.param_flags = [-1] * 12
        self.para_list = None
        self.hyperp_tuning = False
        self.hyperparas_dict = None
        self.val_data = None
        self.query_strat = 'PAL'
        self.saveALselection = False
        self.eval_on_insitu = False
        self.retrain_mode = False

        self.addItemSpeclib = []
        self.gui.mLayerSpeclib.setLayer(None)
        self.speclib = None
        self.soil_wavelengths = None
        self.soil_specs = None

    def connections(self):
        self.gui.cmdInputLUT.clicked.connect(lambda: self.open_lut())
        self.gui.pushCreateLUT.clicked.connect(lambda: self.start_GUI_LUT())
        self.gui.cmdModelDir.clicked.connect(lambda: self.get_folder())
        self.gui.cmdRun.clicked.connect(lambda: self.run_training())
        self.gui.cmdClose.clicked.connect(lambda: self.gui.close())

        self.gui.chkRetrain.toggled.connect(lambda: self.handle_retrain())
        self.gui.cmdInputModel.clicked.connect(lambda: self.open_model_proc())

        self.gui.cmdExcludeBands.clicked.connect(lambda: self.open_wavelength_selection())
        self.gui.cmbPCA.toggled.connect(lambda: self.handle_pca())
        # Art. Noise Radio Button Group
        self.gui.radNoiseOff.clicked.connect(lambda: self.select_noise(mode=0))  # off
        self.gui.radNoiseAdd.clicked.connect(lambda: self.select_noise(mode=1))  # additive
        self.gui.radNoiseGauss.clicked.connect(lambda: self.select_noise(mode=2))  # gaussian
        # ML Algorithms Radio Button Group
        self.gui.rbANN.clicked.connect(lambda: self.handle_algorithm(mode=0))  # 0: ANN
        self.gui.rbGPR.clicked.connect(lambda: self.handle_algorithm(mode=1))  # 1: GPR
        self.gui.rbRFR.clicked.connect(lambda: self.handle_algorithm(mode=2))  # 2: RFR
        self.gui.rbSVR.clicked.connect(lambda: self.handle_algorithm(mode=3))  # 3: SVR
        self.gui.rbKRR.clicked.connect(lambda: self.handle_algorithm(mode=4))  # 4: KRR
        self.gui.rbGBR.clicked.connect(lambda: self.handle_algorithm(mode=5))  # 5: GBR

        self.gui.chkHyptuning.toggled.connect(lambda: self.handle_hyp_tuning())
        self.gui.cmdLoadHyp.clicked.connect(lambda: self.load_hyperparas())
        self.gui.txtInputHyp.textChanged.connect(self.on_hypinput_text_deleted)

        self.gui.radAL.toggled.connect(lambda: self.handle_AL())
        self.gui.radNoAL.toggled.connect(lambda: self.handle_AL())

        self.gui.pushImportInsitu.clicked.connect(lambda: self.open_txt_file())  # load own in situ
        self.gui.pushImportValinsitu.clicked.connect(lambda: self.open_txt_file())

        self.gui.radInternal.toggled.connect(lambda: self.handle_AL_strat(mode='internal'))
        self.gui.radInsitu.toggled.connect(lambda: self.handle_AL_strat(mode='insitu'))
        self.gui.chkALsave.toggled.connect(lambda: self.handle_AL_selection_save())

        self.gui.radPerf.toggled.connect(lambda: self.handle_PerfEval())
        self.gui.radNoPerf.toggled.connect(lambda: self.handle_PerfEval())

        self.gui.radTrainTest.toggled.connect(lambda: self.handle_PerfEvalStrat())
        self.gui.radCrossVal.toggled.connect(lambda: self.handle_PerfEvalStrat())

        for para in self.paramsdict:
            self.paramsdict[para].stateChanged.connect(lambda group, pid=para:
                                                       self.set_params_flags(group="targets", para_id=pid))

        self.gui.mLayerSpeclib.layerChanged.connect(lambda: self.open_speclib(mode="libDropdown"))
        self.gui.cmdLibSelect.clicked.connect(lambda: self.open_speclib(mode='libSelect'))

    def start_GUI_LUT(self, *args):
        from lmuvegetationapps.LUT.CreateLUT_GUI import MainUiFunc
        lutapp = MainUiFunc()
        lutapp.show()

    def enable_all(self):
        self.gui.Exclusions_Box.setEnabled(True),
        self.gui.cmbPCA.setEnabled(True), self.gui.cmbPCA.setChecked(True), self.gui.Noise_Box.setEnabled(True),
        self.gui.Paras_Box.setEnabled(True), self.gui.AL_Box.setEnabled(True), self.gui.Perf_Box.setEnabled(True),
        self.gui.ML_Box.setEnabled(True), self.gui.rbANN.setEnabled(True), self.gui.rbGPR.setEnabled(True),
        self.gui.rbRFR.setEnabled(True), self.gui.rbSVR.setEnabled(True), self.gui.rbKRR.setEnabled(True),
        self.gui.rbGBR.setEnabled(True), self.gui.Hyp_frame.setEnabled(True)

    def disable_all_except_perfEval(self):
        self.gui.Exclusions_Box.setEnabled(False),
        self.gui.cmbPCA.setEnabled(False), self.gui.cmbPCA.setChecked(False), self.gui.Noise_Box.setEnabled(False),
        self.gui.Paras_Box.setEnabled(False), self.gui.AL_Box.setEnabled(False), self.gui.Perf_Box.setEnabled(True),
        self.gui.ML_Box.setEnabled(False), self.gui.rbANN.setEnabled(False), self.gui.rbGPR.setEnabled(False),
        self.gui.rbRFR.setEnabled(False), self.gui.rbSVR.setEnabled(False), self.gui.rbKRR.setEnabled(False),
        self.gui.rbGBR.setEnabled(False), self.gui.Hyp_frame.setEnabled(False)

    def handle_retrain(self):
        if not self.retrain_mode:
            self.retrain_mode = True
            self.gui.lblSelectModel.setEnabled(True), self.gui.lblInputModel.setEnabled(True), \
                self.gui.cmdInputModel.setEnabled(True)
        else:
            self.retrain_mode = False
            self.gui.lblSelectModel.setEnabled(False), self.gui.lblInputModel.setEnabled(False), \
                self.gui.cmdInputModel.setEnabled(False)
            self.gui.lblInputModel.setText("")
            self.model_process_dict = None
            self.gui.txtTrainSize.setText("")

    def handle_algorithm(self, mode):
        self.algorithm = self.algorithm_dict[mode]

    def handle_AL(self):
        if self.gui.radAL.isChecked():
            self.gui.AL_rbFrame.setEnabled(True), self.gui.lblInitSamples.setEnabled(True),
            self.gui.sbInitSamples.setEnabled(True),
            self.gui.chkALsave.setEnabled(True), self.gui.chkALsave.setChecked(True),
            self.gui.radPerf.setChecked(True), self.gui.radNoPerf.setEnabled(False),
            self.gui.radCrossVal.setEnabled(False), self.gui.radTrainTest.setChecked(True),
            self.gui.pushImportInsitu.setEnabled(False), self.gui.frameQueryStrat.setEnabled(True),
            self.gui.lblQueryStrat.setEnabled(True), self.gui.radEBD.setEnabled(True), self.gui.radPAL.setEnabled(True)
            self.gui.radValinsitu.setEnabled(False)
        if self.gui.radNoAL.isChecked():
            self.gui.AL_rbFrame.setEnabled(False), self.gui.lblInitSamples.setEnabled(False),
            self.gui.sbInitSamples.setEnabled(False), self.gui.chkALsave.setEnabled(
                False), self.gui.chkALsave.setChecked(False),
            self.gui.radNoPerf.setEnabled(True), self.gui.radInternal.setChecked(True),
            self.gui.radNoPerf.setChecked(True), self.gui.frameQueryStrat.setEnabled(False),
            self.gui.frameQueryStrat.setEnabled(False),
            self.gui.lblQueryStrat.setEnabled(False), self.gui.radEBD.setEnabled(False), self.gui.radPAL.setEnabled(
                False)

    def handle_AL_strat(self, mode):
        if mode == 'internal':
            self.gui.frame_PerfEvalOptions.setEnabled(True), self.gui.radTrainTest.setEnabled(True),
            self.gui.radCrossVal.setEnabled(False), self.gui.lblTrainSize.setEnabled(True),
            self.gui.txtTrainSize.setEnabled(True), self.gui.pushImportInsitu.setEnabled(False)
            self.gui.radValinsitu.setEnabled(False)
        if mode == 'insitu':
            self.gui.frame_PerfEvalOptions.setEnabled(False), self.gui.pushImportInsitu.setEnabled(True)
            self.gui.txtTrainSize.setPlaceholderText(""), self.gui.txtFolds.setPlaceholderText("")

    def handle_AL_selection_save(self):
        if self.gui.chkALsave.isChecked():
            self.saveALselection = True
        else:
            self.saveALselection = False

    def handle_PerfEval(self):
        if self.gui.radPerf.isChecked():
            if self.gui.radInsitu.isChecked():
                self.gui.frame_PerfEvalOptions.setEnabled(False)
            else:
                self.gui.frame_PerfEvalOptions.setEnabled(True),
                self.gui.radTrainTest.setEnabled(True), self.gui.radCrossVal.setEnabled(True),
                self.gui.lblTrainSize.setEnabled(True), self.gui.txtTrainSize.setEnabled(True),
                self.gui.txtTrainSize.setPlaceholderText("[0-99]"),
                self.gui.radValinsitu.setEnabled(True)

        if self.gui.radNoPerf.isChecked():
            self.gui.radTrainTest.setChecked(True),
            self.gui.radTrainTest.setEnabled(False), self.gui.radCrossVal.setEnabled(False),
            self.gui.lblTrainSize.setEnabled(False), self.gui.txtTrainSize.setEnabled(False),
            self.gui.lblFolds.setEnabled(False), self.gui.txtFolds.setEnabled(False),
            self.gui.txtTrainSize.setPlaceholderText(""), self.gui.txtFolds.setPlaceholderText(""),
            self.gui.radValinsitu.setEnabled(False), self.gui.pushImportValinsitu.setEnabled(False)
        if self.gui.radPerf.isChecked() and self.gui.chkRetrain.isChecked():
            self.gui.radCrossVal.setEnabled(False), self.gui.txtFolds.setEnabled(False),
            if self.gui.radTrainTest.isChecked():
                self.gui.txtTrainSize.setText("100"), self.gui.txtTrainSize.setEnabled(False)

    def handle_PerfEvalStrat(self):
        if self.gui.radTrainTest.isChecked():
            self.gui.lblTrainSize.setEnabled(True), self.gui.txtTrainSize.setEnabled(True)
            self.gui.lblFolds.setEnabled(False), self.gui.txtFolds.setEnabled(False)
            self.gui.txtTrainSize.setPlaceholderText("[1-99]")
            self.gui.txtFolds.setText("")
            self.gui.txtFolds.setPlaceholderText("")
            self.gui.pushImportValinsitu.setEnabled(False)
            if self.gui.chkRetrain.isChecked():
                self.gui.txtTrainSize.setText("100"), self.gui.txtTrainSize.setEnabled(False)
        if self.gui.radCrossVal.isChecked():
            self.gui.lblTrainSize.setEnabled(False), self.gui.txtTrainSize.setEnabled(False),
            self.gui.lblFolds.setEnabled(True), self.gui.txtFolds.setEnabled(True),
            self.gui.txtTrainSize.setText("")
            self.gui.txtTrainSize.setPlaceholderText("")
            self.gui.txtFolds.setPlaceholderText("[2-10]")
            self.gui.pushImportValinsitu.setEnabled(False)
        if self.gui.radValinsitu.isChecked():
            self.gui.pushImportValinsitu.setEnabled(True)
            self.gui.lblTrainSize.setEnabled(False), self.gui.txtTrainSize.setEnabled(False)
            self.gui.lblFolds.setEnabled(False), self.gui.txtFolds.setEnabled(False)
            self.gui.txtTrainSize.setText("")
            self.gui.txtTrainSize.setPlaceholderText("")
            self.gui.txtFolds.setText("")
            self.gui.txtFolds.setPlaceholderText("")

    def handle_hyp_tuning(self):
        if self.gui.chkHyptuning.isChecked():
            self.hyperp_tuning = True
            self.gui.AL_frame.setEnabled(False), self.gui.radNoAL.setChecked(True),
            self.gui.lblInitSamples.setEnabled(False),
            (self.gui.sbInitSamples.setEnabled(False), self.gui.chkALsave.setEnabled(False),
             self.gui.chkALsave.setChecked(False),)
            (self.gui.radInternal.setChecked(True), self.gui.radPerf.setChecked(True),
             self.gui.radNoPerf.setEnabled(False),)
            self.gui.radCrossVal.setChecked(False), self.gui.radCrossVal.setEnabled(False), \
                self.gui.radTrainTest.setEnabled(True),
            (self.gui.lblLoadHyp.setEnabled(False), self.gui.cmdLoadHyp.setEnabled(False),
             self.gui.txtInputHyp.setEnabled(False))
            self.handle_PerfEvalStrat()
        else:
            self.hyperp_tuning = False
            (self.gui.AL_frame.setEnabled(True), self.gui.chkALsave.setEnabled(True),
             self.gui.radNoPerf.setEnabled(True),)
            self.gui.radPerf.setChecked(False), self.gui.radTrainTest.setEnabled(True),
            (self.gui.lblLoadHyp.setEnabled(True), self.gui.cmdLoadHyp.setEnabled(True),
             self.gui.txtInputHyp.setEnabled(True))

    def load_hyperparas(self, **path):
        result = str(QFileDialog.getOpenFileName(
            caption='Select Hyperparameters file', filter="HYPER-file (*.hyper)")[0])
        if not result:
            self.gui.chkHyptuning.setEnabled(True)
            self.gui.MLRA_frame.setEnabled(True)
            return
        self.gui.txtInputHyp.setText(result)
        self.gui.chkHyptuning.setEnabled(False)
        try:
            self.hyperparas_dict = joblib.load(result)
        except ValueError:
            raise ValueError('Error reading hyperparameter file')

        algorithm_name = list(self.hyperparas_dict.keys())[0]
        paras = list(self.hyperparas_dict[algorithm_name].keys())
        self.set_algorithm_radiobutton(algorithm_name)
        self.set_checkboxes_from_paras(paras)

        self.gui.MLRA_frame.setEnabled(False)

    def set_algorithm_radiobutton(self, algorithm_name):
        # set the algorithm by loading a .hyper file
        # 1. Reverse the dictionary to map from name to index
        reverse_algorithm_dict = {v: k for k, v in self.algorithm_dict.items()}
        # 2. Map the indices to their respective radio buttons
        radio_buttons_map = {
            0: self.gui.rbANN,
            1: self.gui.rbGPR,
            2: self.gui.rbRFR,
            3: self.gui.rbSVR,
            4: self.gui.rbKRR,
            5: self.gui.rbGBR
        }
        # 3. Set the matched radio button to True
        if algorithm_name in reverse_algorithm_dict:
            idx = reverse_algorithm_dict[algorithm_name]
            radio_buttons_map[idx].setChecked(True)
            self.handle_algorithm(idx)

    def on_hypinput_text_deleted(self, text):
        # if a hyperparameter set is loaded, then deleted -> reactivate MLRA-Radio buttons
        if not text:
            self.gui.chkHyptuning.setEnabled(True)
            self.gui.MLRA_frame.setEnabled(True)
            self.hyperparas_dict = None

            for checkbox in self.paramsdict.values():
                checkbox.setChecked(False)

    def set_params_flags(self, para_id, group):
        if group == 'targets':
            # If checkbox checked, prepare param to be included for training
            self.param_flags[para_id] *= -1

    def set_params_from_checkboxes(self, param_flags):
        # sort out only the labels for the indices which should be calculated
        para_list = [self.all_labels[i] for i in range(len(self.all_labels)) if param_flags[i] == 1]
        return para_list

    def set_checkboxes_from_paras(self, paras):
        for idx, label in enumerate(self.all_labels):
            if label in paras:
                self.paramsdict[idx].setChecked(True)
            else:
                self.paramsdict[idx].setChecked(False)

    def open_lut(self, **path):  # open and read a lut-metafile
        if path:
            key, result = next(iter(path.items()))
            self.lut_path = result
        else:
            result = str(QFileDialog.getOpenFileName(caption='Select LUT meta-file', filter="LUT-file (*.lut)")[0])
            if not result:
                return
            self.lut_path = result
        self.gui.lblInputLUT.setText(result)
        with open(self.lut_path, 'r') as meta_file:
            content = meta_file.readlines()
            content = [item.rstrip("\n") for item in content]
        # This splits the keys and values in the meta file and extracts the values separated by ";"
        keys, values = list(), list()
        [[x.append(y) for x, y in zip([keys, values], line.split(sep="=", maxsplit=1))] for line in content]
        values = [value.split(';') if ';' in value else value for value in values]
        self.meta_dict = dict(zip(keys, values))  # file the metadata dictionary
        # wavelengths of the LUT are stored in the LUT-meta
        self.wl = np.asarray(self.meta_dict['wavelengths']).astype(np.float32)
        self.nbands = len(self.wl)
        # default wavelength ranges to be excluded are defined in __init__ and now with the metadata
        # of the spectral image, the respective "exclude bands" can be found
        self.exclude_bands = [i for i in range(len(self.wl)) if self.wl[i] < 400 or self.wl[i] > 2500
                              or self.exclude_wavelengths[0][0] <= self.wl[i] <= self.exclude_wavelengths[0][1]
                              or self.exclude_wavelengths[1][0] <= self.wl[i] <= self.exclude_wavelengths[1][1]
                              or self.exclude_wavelengths[2][0] <= self.wl[i] <= self.exclude_wavelengths[2][1]]
        self.gui.txtExclude.setText(" ".join(str(i) for i in self.exclude_bands))  # join to string for lineEdit
        self.gui.txtExclude.setCursorPosition(0)
        self.nbands_valid = self.nbands - len(self.exclude_bands)
        self.enable_all()
        self.handle_AL()

    def open_model_proc(self, **path):
        if path:
            key, result = next(iter(path.items()))
        else:
            result = str(QFileDialog.getOpenFileName(caption='Select Machine Learning Model',
                                                     filter="Processor META File (*.proc)")[0])
            if not result:
                return
        self.gui.lblInputModel.setText(result)
        try:
            self.model_process_dict = joblib.load(result)
        except ValueError:
            raise ValueError('Error reading Modelspecs .proc-file')
        if 'pca' in self.model_process_dict:
            self.gui.PCA_Box.setEnabled(False)

    def params_dict_check(self):
        self.paramsdict = {0: self.gui.chkCab, 1: self.gui.chkCcx, 2: self.gui.chkCanth,
                           3: self.gui.chkCw, 4: self.gui.chkCp, 5: self.gui.chkCBC,
                           6: self.gui.chkLAI, 7: self.gui.chkAGBdry, 8: self.gui.chkAGBfresh,
                           9: self.gui.chkCWC, 10: self.gui.chkNitrogen, 11: self.gui.chkCarbon}

    def open_txt_file(self):
        self.main.loadtxtfile.open()

    def open_wavelength_selection(self):
        # Handle opening the GUI for adding/excluding wavelengths from the list
        try:
            self.invoke_selection()
        except ValueError as e:
            self.abort(message=str(e))

    def invoke_selection(self):
        # Open the GUI for adding/excluding wavelengths from the list
        if self.lut_path is None:
            raise ValueError('Specify Lookup-Table first')
        elif not os.path.isfile(self.lut_path):
            raise ValueError('Lookup-Table not found: {}'.format(self.lut_path))

        pass_exclude = list()  # list of bands that are passed to be excluded by default, empty at first
        if not self.gui.txtExclude.text() == "":  # lineEdit is NOT empty, so some information is already there
            try:
                pass_exclude = self.gui.txtExclude.text().split(" ")  # get whats in the field
                pass_exclude = [int(pass_exclude[i]) - 1 for i in range(len(pass_exclude))]  # convert the text to int
            except ValueError:  # lineEdit contains crap
                self.gui.txtExclude.setText("")
                pass_exclude = list()

        self.main.select_wavelengths.populate(default_exclude=pass_exclude)
        self.main.select_wavelengths.gui.setModal(True)
        self.main.select_wavelengths.gui.show()

    def handle_pca(self):
        # Fitting a PCA is optional; if the option is selected, the user also needs to provide the number of components
        if self.gui.cmbPCA.isChecked():
            self.gui.spnPCA.setEnabled(True)
            # Set the default value for PCA components: 1 component for less than 5 bands, 5 for l.t. 15 and so on
            if self.nbands_valid < 5:
                self.npca = 1
            elif 5 < self.nbands_valid <= 15:
                self.npca = 5
            elif 15 < self.nbands_valid <= 120:
                self.npca = 10
            else:
                self.npca = 20
            self.gui.spnPCA.setValue(self.npca)  # place the value in the spinBox of the GUI
        if not self.gui.cmbPCA.isChecked():
            self.gui.spnPCA.setDisabled(True)
            self.npca = 0

    def select_noise(self, mode):
        # Enables and disables lineEdit for noise level
        if mode == 0:
            self.gui.txtNoiseLevel.setDisabled(True)
        else:
            self.gui.txtNoiseLevel.setDisabled(False)
        self.noisetype = mode

    def get_folder(self, **path):
        # The model folder is important, as it contains all files needed
        if not __name__ == '__main__' or not path:
            path = str(QFileDialog.getExistingDirectory(caption='Select Output Directory for Model'))
            if not path:
                return
        else:  # test-case
            key, path = next(iter(path.items()))
            self.out_dir = path
            self.gui.txtModelName.setText("test")
            self.model_name = self.gui.txtModelName.text()
        if path:
            self.gui.txtModelDir.setText(path)
            self.out_dir = self.gui.txtModelDir.text().replace("\\", "/")
            if not self.out_dir[-1] == "/":  # last letter of the folder name needs to be a slash to add filenames
                self.out_dir += "/"

    def open_speclib(self, mode):
        if mode == "libSelect":
            if self.speclib is not None:
                self.speclib = None
            lib_input = QFileDialog.getOpenFileName(caption='Select Input Spectral Library',
                                                    filter="Spectral Library (*.gpkg *.sli)")[0]
            if not lib_input:
                return
            self.addItemSpeclib.append(lib_input)
            self.gui.mLayerSpeclib.setAdditionalItems(self.addItemSpeclib)
            self.gui.mLayerSpeclib.setCurrentText(lib_input)
            self.speclib = lib_input

        if mode == "libDropdown":
            if self.speclib is not None:
                self.speclib = None
            if self.gui.mLayerSpeclib.currentLayer() is not None:
                input = self.gui.mLayerSpeclib.currentLayer()
                lib_input = input.source()
            elif len(self.gui.mLayerSpeclib.currentText()) > 0:
                lib_input = self.gui.mLayerSpeclib.currentText()
            else:
                self.speclib = None
                return
            self.speclib = lib_input

        all_specs = []
        wl_values = []
        wl_extracted = False
        print(os.path.splitext(self.speclib))
        if os.path.splitext(self.speclib)[1] == ".gpkg":
            layer = QgsVectorLayer(self.speclib, "Soil spectra layer")  # <- works only for gpkg Geopackage
            # Loop through the features
            for feature in layer.getFeatures():
                # Assuming that the JSON string is in an attribute named 'json_data'
                data_dict = feature[2]
                # Parse the JSON string

                # Extract 'x' values only once
                if not wl_extracted:
                    wl_values = data_dict.get('x', [])
                    wl_extracted = True

                # Extract and store y_values
                y_values = data_dict.get('y', [])
                all_specs.append(y_values)

            self.soil_wavelengths = wl_values
            self.soil_specs = [list(row) for row in zip(*all_specs)]
        if os.path.splitext(self.speclib)[1] == ".sli":
            speclib = EnviSpectralLibrary(filename=self.speclib)
            raster = speclib.raster()
            self.soil_wavelengths = raster.dataset().metadataItem(key='wavelength', domain='ENVI', dtype=float)
            self.soil_specs = raster.dataset().array()[:, :, 0].tolist()

    def check_and_assign(self):
        if not self.lut_path:
            raise ValueError("A Lookup-Table metafile needs to be selected!")
        if self.retrain_mode and not self.model_process_dict:
            raise ValueError("Retrain Mode selected but .proc-file is missing")
        if not self.out_dir:
            raise ValueError("Output directory is missing")
        if not os.path.isdir(self.out_dir):
            raise ValueError("Output directory does not exist!")
        if self.gui.txtModelName.text() == "":
            raise ValueError("Please specify a name for the model")
        # if self.retrain_mode and self.gui.mLayerSpeclib.text() == "":
        #     raise ValueError("retrain")
        else:
            self.model_name = self.gui.txtModelName.text()
            self.model_meta = self.out_dir + self.model_name + '.meta'

        if self.gui.txtInputHyp.text() == "":
            self.hyperparas_path = None
        else:
            pass

        if not self.noisetype == 0:
            if self.gui.txtNoiseLevel.text() == "":
                raise ValueError('Please specify level for artificial noise')

            else:
                self.noiselevel = self.gui.txtNoiseLevel.text()
                try:
                    self.noiselevel = int(self.noiselevel)
                except ValueError:
                    raise ValueError('Cannot interpret noise level as decimal number')

        if self.gui.spnPCA.isEnabled():
            self.npca = self.gui.spnPCA.value()
            if self.npca > self.nbands_valid:
                raise ValueError("Model cannot be trained with {:d} components if LUT has only {:d} "
                                 "bands ({:d} minus {:d} excluded)".format(self.npca, self.nbands_valid, self.nbands,
                                                                           len(self.exclude_bands)))
        else:
            self.npca = 0

        if all(flag == -1 for flag in self.param_flags):
            raise ValueError("No target parameters selected")
        else:
            self.para_list = self.set_params_from_checkboxes(param_flags=self.param_flags)

        if self.gui.radAL.isChecked():
            self.use_al = True
            self.n_initial = self.gui.sbInitSamples.value()
        else:
            self.use_al = False
        if self.gui.radInsitu.isChecked():
            self.use_insitu = True
            if not self.val_data:
                raise ValueError("In situ data supported Active Learning is selected\nbut no data is loaded")
            else:
                # print(self.val_data)
                pass
        else:
            self.use_insitu = False

        if self.gui.radPAL.isChecked():
            self.query_strat = 'PAL'
        elif self.gui.radEBD.isChecked():
            self.query_strat = 'EBD'

        if self.gui.radPerf.isChecked():
            self.perf_eval = True
            if self.gui.radInsitu.isChecked():
                self.test_size = 0.2  # just a dummy value but not used
            elif self.gui.radTrainTest.isChecked():
                self.split_method = 'train_test_split'
                if self.gui.txtTrainSize.text() == '':
                    raise ValueError('Please specify training set size')
                self.test_size = 1 - int(self.gui.txtTrainSize.text()) / 100
            elif self.gui.radCrossVal.isChecked():
                self.split_method = 'kfold'
                if self.gui.txtFolds.text() == '':
                    raise ValueError('Please specify number of folds for cross validation')
                self.kfolds = int(self.gui.txtFolds.text())
            elif self.gui.radValinsitu.isChecked():
                self.eval_on_insitu = True
                if not self.val_data:
                    raise ValueError("Performance evaluation on situ data is selected\nbut no data is loaded")
        else:
            self.perf_eval = False

        if self.soil_wavelengths:
            soil_nbands_valid = len(self.soil_wavelengths) - len(self.exclude_bands)
            if not soil_nbands_valid == self.nbands_valid:
                raise ValueError("LUT band number ({:d}) does not match band "
                                 "number of added soil spectra ({:d})".format(self.nbands_valid, soil_nbands_valid))

    def abort(self, message):
        QMessageBox.critical(self.gui, "Error", message)

    def run_training(self):
        # Starting the procedure of training the model
        try:
            self.check_and_assign()  # check which user definitions were made
        except ValueError as e:
            self.abort(message=str(e))
            return

        proc = processor.ProcessorMainFunction()  # instance of the Processor main class

        self.prg_widget = self.main.prg_widget
        if self.hyperp_tuning:
            self.prg_widget.gui.lblCaption_l.setText("Optimizing Hyperparameters... This may take some time...")
        elif self.use_al:
            self.prg_widget.gui.lblCaption_l.setText("Training Machine Learning Model with Active Learning...")
        else:
            self.prg_widget.gui.lblCaption_l.setText("Training Machine Learning Model...")
        self.prg_widget.gui.lblCaption_r.setText("Setting up training...")
        # self.prg_widget.gui.prgBar.setValue(5)
        self.prg_widget.gui.setModal(True)
        self.prg_widget.gui.show()

        self.main.qgis_app.processEvents()

        try:
            # Setup everything for training and jump over to Processor_Inversion_core.py
            proc.train_main.training_setup(lut_metafile=self.lut_path, exclude_bands=self.exclude_bands, npca=self.npca,
                                           model_meta=self.model_meta, para_list=self.para_list,
                                           noisetype=self.noisetype, noiselevel=self.noiselevel,
                                           algorithm=self.algorithm, model_proc_dict=self.model_process_dict,
                                           use_al=self.use_al, use_insitu=self.use_insitu,
                                           perf_eval=self.perf_eval,
                                           split_method=self.split_method, kfolds=self.kfolds,
                                           n_initial=self.n_initial, test_size=self.test_size,
                                           hyperp_tuning=self.hyperp_tuning, hyperparas_dict=self.hyperparas_dict,
                                           query_strat=self.query_strat, saveALselection=self.saveALselection,
                                           eval_on_insitu=self.eval_on_insitu, val_data=self.val_data,
                                           soil_wavelengths=self.soil_wavelengths, soil_specs=self.soil_specs)
        except ValueError as e:
            self.abort(message="Failed to setup model training: {}".format(str(e)))
            self.prg_widget.gui.lblCancel.setText("")
            self.prg_widget.gui.allow_cancel = True
            self.prg_widget.gui.close()
            return

        # if (self.use_insitu or self.eval_on_insitu) and self.val_data:
        #     proc.train_main.insitu_data_setup(self.val_data)

        # if new models are added, change the text of the ProgressBar accordingly
        self.prg_widget.gui.lblCaption_r.setText("Starting training of MLRA...")
        self.main.qgis_app.processEvents()

        # TODO: uncomment lines here
        # try:
        #     # Train model and dump it to memory
        proc.train_main.train_and_dump(prgbar_widget=self.prg_widget, qgis_app=self.main.qgis_app)

        # except ValueError as e:
        #     self.abort(message="Failed to train model: {}".format(str(e)))
        #     self.prg_widget.gui.lblCancel.setText("")
        #     self.prg_widget.gui.allow_cancel = True
        #     self.prg_widget.gui.close()
        #     return
        self.results_dict = proc.train_main.get_result_dict()
        self.best_hyperparams_dict = proc.train_main.get_hyperparams_dict()

        self.prg_widget.gui.lblCancel.setText("")
        self.prg_widget.gui.allow_cancel = True
        self.prg_widget.gui.close()
        self.prg_widget.gui.prgBar.setValue(0)

        QMessageBox.information(self.gui, "Finish", "Training finished")
        # ▬self.gui.close()
        if self.perf_eval:
            self.perfView_widget = self.main.performance_view
            self.perfView_widget.gui.modelComboBox.clear()
            self.perfView_widget.collect_results(self.results_dict)
            self.perfView_widget.gui.show()


class perfView:
    def __init__(self, main):
        self.main = main
        self.gui = Performance_GUI()
        self.connections()
        self.all_results_dict = None

        self.layout_perf = QVBoxLayout()
        self.gui.perfView.setLayout(self.layout_perf)

        self.figure_perf = Figure(figsize=(6, 6))
        self.canvas_perf = FigureCanvas(self.figure_perf)
        self.toolbar_perf = NavigationToolbar(self.canvas_perf, self.gui.scatterView)
        self.layout_perf.addWidget(self.canvas_perf)
        self.layout_perf.addWidget(self.toolbar_perf)

        self.layout_scatter = QVBoxLayout()
        self.gui.scatterView.setLayout(self.layout_scatter)

        self.figure_scatter = Figure(figsize=(6, 6))
        self.canvas_scatter = FigureCanvas(self.figure_scatter)
        self.toolbar_scatter = NavigationToolbar(self.canvas_scatter, self.gui.scatterView)
        self.layout_scatter.addWidget(self.canvas_scatter)
        self.layout_scatter.addWidget(self.toolbar_scatter)

    def connections(self):
        self.gui.cmdQuit.clicked.connect(lambda: self.gui.close())
        self.gui.modelComboBox.currentIndexChanged.connect(self.plot_results)
        self.gui.cmdExport.clicked.connect(self.export_data)

    def collect_results(self, dict):
        self.all_results_dict = dict
        for key in dict:
            self.gui.modelComboBox.addItem(str(key))

    def export_data(self, index):
        outpath = QFileDialog.getSaveFileName(caption='Specify Output File',
                                              filter="Text files (*.txt)")[0]
        key = self.gui.modelComboBox.itemText(index)
        data = self.all_results_dict.get(key, None)

        if outpath is None or data is None:
            return

        performances, y_val, predictions = data["performances"], data["y_val"], data["predictions"]
        if isinstance(performances, np.ndarray):
            performances = [performances]
        performances = np.asarray(performances).flatten()
        y_val = np.asarray(y_val).flatten()
        final_pred = np.asarray(predictions).flatten()
        try:
            pred_std = np.asarray(data["stds"]).flatten()
        except:
            pred_std = np.array([np.nan])

        max_length = max(len(y_val), len(final_pred), len(pred_std), len(performances))

        # Pad arrays with NaN values to match the maximum length
        x = np.pad(y_val, (0, max_length - len(y_val)), mode='constant', constant_values=np.nan)
        y = np.pad(final_pred, (0, max_length - len(final_pred)), mode='constant', constant_values=np.nan)
        std = np.pad(pred_std, (0, max_length - len(pred_std)), mode='constant', constant_values=np.nan)
        perf = np.pad(performances, (0, max_length - len(performances)), mode='constant', constant_values=np.nan)

        # Create structured array using dtype to define the columns
        structured_array = np.array(list(zip(x, y, std, perf)))

        # Save the structured array to a text file
        np.savetxt(outpath, structured_array, delimiter='\t', header=r'measured\testimated\test_std\tRMSE', comments='')

    def plot_results(self, index):

        plt.rcParams["savefig.dpi"] = 300
        key = self.gui.modelComboBox.itemText(index)  # Get the text of the selected item
        data = self.all_results_dict.get(key, None)  # Retrieve the data from the dictionary

        def format_float_by_scale(value):
            if value >= 100:
                formatted_value = "{:.0f}".format(value)
            elif value >= 10:
                formatted_value = "{:.1f}".format(value)
            elif value >= 1:
                formatted_value = "{:.2f}".format(value)
            elif value >= 0.1:
                formatted_value = "{:.3f}".format(value)
            else:
                formatted_value = "{:.4f}".format(value)
            return formatted_value

        if data is None:
            return
        try:
            performances, y_val, predictions, al_training_indices = \
                data["performances"], data["y_val"], data["predictions"], data['al_training_indices'][0]
        except:
            performances, y_val, predictions, al_training_indices = \
                data["performances"], data["y_val"], data["predictions"], data['al_training_indices']
        if isinstance(performances, np.ndarray):
            performances = [performances]
        performances = np.asarray(performances).flatten()
        y_val = np.asarray(y_val).flatten()
        final_pred = np.asarray(predictions).flatten()

        try:
            pred_std = np.asarray(data["stds"]).flatten()
        except:
            pred_std = np.empty((0,))

        r2 = r2_score(y_val, final_pred)
        rmse = performances[-1]
        rmse_float = format_float_by_scale(rmse)

        self.figure_perf.clf()
        self.figure_scatter.clf()
        # Create a new subplot
        ax = self.figure_perf.add_subplot(111)
        if isinstance(performances, np.ndarray) and len(performances) > 1:
            # Plot the data
            ax.plot(range(len(performances)), performances, 'k-')
            ax.set_xlabel('Number of added samples')
            ax.set_ylabel('RMSE {}'.format(key))
            ax.tick_params("both")
            # Redraw the canvas
        else:
            performance = [format_float_by_scale(i) for i in performances]
            ax.text(0.5, 0.5,
                    'No Active Learning applied\nFull test set RMSE = ' + str(np.array(performance[0], dtype=float)),
                    ha='center', va='center', transform=ax.transAxes)
            ax.set_xticks([])
            ax.set_yticks([])
        self.canvas_perf.draw()

        # Create a new subplot
        ax0 = self.figure_scatter.add_subplot(111, aspect='equal')
        # Scatter plot
        if not isinstance(pred_std, np.ndarray):
            pred_std = np.array(pred_std)
        if pred_std.size > 0:
            scatter = ax0.scatter(y_val, final_pred, s=10, c=pred_std, cmap='plasma', )
        else:
            scatter = ax0.scatter(y_val, final_pred, s=10, c='k')
        # 1:1 line
        ax_max = max(y_val.max(), final_pred.max())
        ax_min = min(y_val.min(), final_pred.min())
        ax0.plot([0, ax_max], [0, ax_max], 'k-')
        # Regression line
        lr = LinearRegression()
        lr.fit(y_val.reshape(-1, 1), final_pred)
        nice_offest = 3 * ax_max / 100
        x_fit = np.linspace(0, ax_max + nice_offest, 100)
        y_fit = lr.predict(x_fit.reshape(-1, 1))
        ax0.plot(x_fit, y_fit, 'r-')
        if ax_min > 0:
            ax0.set_xlim(0, ax_max + nice_offest)
            ax0.set_ylim(0, ax_max + nice_offest)
        else:
            ax0.set_xlim(ax_min, ax_max + nice_offest)
            ax0.set_ylim(ax_min, ax_max + nice_offest)

        ax0.text(0.05, 0.90, 'R² = {:.2f}'.format(r2) + '\nRMSE = ' + str(rmse_float), transform=ax0.transAxes)
        ax0.set_xlabel('{} - measured'.format(key))
        ax0.set_ylabel('{} - estimated'.format(key))
        ax0.tick_params("both")

        # Colorbar.
        if pred_std.size > 0:
            the_divider = make_axes_locatable(ax0)
            color_axis = the_divider.append_axes("right", size="5%", pad=0.1)
            # scatter = ax0.scatter(y_val, final_pred, c=pred_std, cmap='plasma')
            cbar = plt.colorbar(scatter, cax=color_axis)
            cbar.set_label(label='SD', labelpad=0)

        # Redraw the canvas
        self.canvas_scatter.draw()


# LoadTxtFile is a class to open a new GUI in which a text file is opened which needs to meet certain criteria
# In this case, it's the background spectrum which needs to be a two column text file with wavelengths and
# reflectance values.
class LoadTxtFile:
    def __init__(self, main):
        self.main = main
        self.gui = LoadTxtFileGUI()
        self.initial_values()
        self.connections()

    def connections(self):
        self.gui.cmdOK.clicked.connect(lambda: self.ok())
        self.gui.cmdCancel.clicked.connect(lambda: self.gui.close())
        self.gui.cmdInputFile.clicked.connect(lambda: self.open_file())
        self.gui.radioHeader.toggled.connect(lambda: self.change_radioHeader())
        self.gui.cmbDelimiter.activated.connect(
            lambda: self.change_cmbDelimiter())  # "activated" signal is only called for user activity, not code call
        self.gui.spinDivisionFactor.valueChanged.connect(lambda: self.change_division())

    def initial_values(self):
        self.header_bool = None
        self.filenameIn = None
        self.delimiter_str = ["Tab", "Space", ",", ";"]
        self.gui.cmbDelimiter.clear()
        self.gui.cmbDelimiter.addItems(self.delimiter_str)
        self.gui.tablePreview.setRowCount(0)
        self.gui.tablePreview.setColumnCount(0)
        self.gui.radioHeader.setDisabled(True)
        self.gui.radioHeader.setChecked(False)
        self.gui.cmbDelimiter.setDisabled(True)
        self.gui.spinDivisionFactor.setDisabled(True)
        self.gui.spinDivisionFactor.setValue(1.0)
        self.gui.cmdOK.setDisabled(True)
        self.gui.label.setStyleSheet("color: rgb(170, 0, 0);")
        self.gui.label.setText("No File selected")
        self.gui.lblInputFile.setText("")
        self.divide_by = 1.0
        self.open_type = None
        self.wl_open, self.data_mean, self.nbands = (None, None, None)
        self.para_list = None
        self.data_array = None
        self.spinboxes, self.ref_spinbox = [], None

    def open(self):
        self.initial_values()
        self.populate_paras()
        if self.para_list:
            self.gui.show()
        else:
            return

    def populate_paras(self):
        if all(flag == -1 for flag in self.main.mlra_training.param_flags):
            QMessageBox.critical(self.gui, 'No targets',
                                 "select target RTM parameters for training first.")
            return
        else:
            self.para_list = self.main.mlra_training.set_params_from_checkboxes(
                param_flags=self.main.mlra_training.param_flags)

            if self.para_list:
                self.clear_dynamic_layout()
                self.setup_dynamic_layout()

    def open_file(self):
        file_choice, _filter = QFileDialog.getOpenFileName(None, 'Select In-Situ Data File',
                                                           APP_DIR + "/Resources/Example_Files", "(*.txt *.csv)")
        if not file_choice:  # Cancel clicked
            if not self.filenameIn:
                self.houston(message="No File selected")  # plus: no file in memory
            return
        self.filenameIn = file_choice
        self.gui.lblInputFile.setText(self.filenameIn)
        self.gui.radioHeader.setEnabled(True)
        self.gui.cmbDelimiter.setEnabled(True)
        self.gui.spinDivisionFactor.setEnabled(True)
        self.header_bool = False
        self.inspect_file()

    def inspect_file(self):
        # Look into the file and detect the delimiter and if it has a header
        sniffer = csv.Sniffer()  # the csv.Sniffer detects the "dialect" of the text file
        with open(self.filenameIn, 'r') as raw_file:
            self.dialect = sniffer.sniff(raw_file.readline())
            if self.dialect.delimiter == "\t":
                self.gui.cmbDelimiter.setCurrentIndex(0)
            elif self.dialect.delimiter == " ":
                self.gui.cmbDelimiter.setCurrentIndex(1)
            elif self.dialect.delimiter == ",":
                self.gui.cmbDelimiter.setCurrentIndex(2)
            elif self.dialect.delimiter == ";":
                self.gui.cmbDelimiter.setCurrentIndex(3)
            raw_file.seek(0)
            raw = csv.reader(raw_file, self.dialect)
            try:
                # if the first row can be converted to int, it most likely does not contain a header
                _ = int(next(raw)[0])
                self.header_bool = False
            except:
                self.header_bool = True
            self.gui.radioHeader.setChecked(self.header_bool)
            self.read_file()  # now read the file for good with the information you have

    def change_radioHeader(self):
        self.header_bool = self.gui.radioHeader.isChecked()
        self.read_file()

    def change_cmbDelimiter(self):
        index = self.gui.cmbDelimiter.currentIndex()
        if index == 0:
            self.dialect.delimiter = "\t"
        elif index == 1:
            self.dialect.delimiter = " "
        elif index == 2:
            self.dialect.delimiter = ","
        elif index == 3:
            self.dialect.delimiter = ";"
        self.read_file()

    def change_division(self):
        self.read_file()
        self.divide_by = self.gui.spinDivisionFactor.value()
        self.apply_division_factor_to_reflectance_rows(self.divide_by)

    def read_file(self):
        if not self.filenameIn:
            return

        header_offset = 0

        with open(self.filenameIn, 'r') as raw_file:
            raw_file.seek(0)
            raw = csv.reader(raw_file, self.dialect)
            data = list()
            for content in raw:
                data.append(content)  # write the content of the file to "data"

        n_entries = len(data)
        if self.header_bool:
            header = data[0]  # if file has a header, first row is taken as header
            if not len(header) == len(data[1]):  # header needs to have as many columns as the rest of the data
                self.houston(
                    message="Error: Data has %i columns, but header has %i columns" % (len(data[1]), len(header)))
                return
            header_offset += 1
            n_entries -= 1
        n_cols = len(data[0 + header_offset])
        try:
            first_col = [float(data[i + header_offset][0]) for i in range(n_entries)]  # read row_labels
        except ValueError:
            self.houston(message="Error: Cannot read file. Please check delimiter and header!")
            return

        # row labels of the QTableWidget are the actual data
        row_labels = [str(first_col[i]) for i in range(n_entries)]

        self.data_array = np.zeros(shape=(n_entries, n_cols - 1))  # prepare for reading the data into numpy array
        for data_list in range(n_entries):
            self.data_array[data_list, :] = np.asarray(data[data_list + header_offset][1:]).astype(dtype=np.float16)

        # Populate QTableWidget:
        self.gui.tablePreview.setRowCount(n_entries)
        self.gui.tablePreview.setColumnCount(n_cols)

        if self.header_bool:
            headers = ['Row Labels'] + header[1:]
            self.gui.tablePreview.setHorizontalHeaderLabels(headers)
        else:
            headers = ['Row Labels'] + [str(i) for i in range(1, n_cols)]
            self.gui.tablePreview.setHorizontalHeaderLabels(headers)

        self.gui.tablePreview.setVerticalHeaderLabels([str(i) for i in range(1, n_entries + 1)])
        # self.gui.tablePreview.setVerticalHeaderLabels(row_labels)

        # Place the data of the text file into the QTableWidget
        for row in range(n_entries):
            item = QTableWidgetItem(row_labels[row])  # This line is for the new column
            self.gui.tablePreview.setItem(row, 0, item)
            for col in range(1, n_cols):
                item = QTableWidgetItem(str(self.data_array[row, col - 1]))
                self.gui.tablePreview.setItem(row, col, item)
                self.gui.tablePreview.setColumnWidth(col, 100)

        self.gui.tablePreview.resizeColumnToContents(0)

        # Prepare for Statistics
        # wl_offset = 400 - int(self.wl_open[0])  # PROSAIL wavelengths start at 400, consider an offset if necessary)
        # if wl_offset > 0:
        #     data_array = data_array[wl_offset:]  # cut off first Bands to start at appropriate band
        #     self.wl_open = self.wl_open[wl_offset:]

        self.gui.label.setStyleSheet("color: rgb(0, 170, 0);")
        self.gui.label.setText("Ok. No Errors")
        self.gui.cmdOK.setEnabled(True)

    def apply_division_factor_to_reflectance_rows(self, factor):
        # Get the row index of the start of reflectance values from the spinbox
        # Subtract 1 to account for 0-based indexing
        if self.ref_spinbox:
            ref_start_row_idx = self.ref_spinbox.value() - 1

            # The maximum row index to loop up to should be the smaller of tablePreview.rowCount()
            # and the number of rows in self.data_array
            max_row_idx = min(self.gui.tablePreview.rowCount(), len(self.data_array))

            # Iterate from the reflectance start row to the last row
            for row in range(ref_start_row_idx, max_row_idx):
                for col in range(1, self.gui.tablePreview.columnCount()):  # Starting from 1 to skip the label column
                    item = self.gui.tablePreview.item(row, col)
                    if item:  # Check if the item exists (in case of blank cells)
                        original_value = self.data_array[row][col - 1]
                        adjusted_value = original_value / factor
                        item.setText(str(adjusted_value))

    def clear_dynamic_layout(self):
        # Get current layout
        layout = self.gui.dynamicLayoutWidget.layout()

        # If the layout exists, clear it and delete
        if layout:
            while layout.count():
                child = layout.takeAt(0)
                if child.widget():
                    child.widget().deleteLater()

    def setup_dynamic_layout(self):
        # Set up the dynamic layout below the QTableWidget
        dynamic_layout = self.gui.dynamicLayoutWidget.layout()

        if dynamic_layout is None:
            dynamic_layout = QGridLayout(self.gui.dynamicLayoutWidget)
            self.gui.dynamicLayoutWidget.setLayout(dynamic_layout)

        # Number of max possible columns in the grid
        num_cols = 8
        col_counter = 0
        row_counter = 0

        for param in self.para_list:
            label = QLabel(f"Row for {param}:")
            spinbox = QSpinBox()
            spinbox.setRange(0, 99)
            spinbox.setButtonSymbols(QAbstractSpinBox.NoButtons)
            self.spinboxes.append(spinbox)

            # Add to the grid layout
            dynamic_layout.addWidget(label, row_counter, col_counter)
            col_counter += 1  # Move to next column for the QLineEdit
            dynamic_layout.addWidget(spinbox, row_counter, col_counter)

            # Adjust row and column counters for next iteration
            row_counter += (col_counter + 1) // num_cols
            col_counter = (col_counter + 1) % num_cols

        # LineEdit for the starting row of reflectance values
        reflectance_label = QLabel("Reflectance start row:")
        reflectance_spinbox = QSpinBox()
        reflectance_spinbox.setRange(0, 99)
        reflectance_spinbox.setButtonSymbols(QAbstractSpinBox.NoButtons)
        self.ref_spinbox = reflectance_spinbox

        dynamic_layout.addWidget(reflectance_label, row_counter, col_counter)
        col_counter += 1  # Move to next column for the QLineEdit
        dynamic_layout.addWidget(reflectance_spinbox, row_counter, col_counter)

        # Setting the dynamic layout to the QWidget you've placed in QtDesigner
        # self.gui.dynamicLayoutWidget.setLayout(dynamic_layout)
        self.gui.dynamicLayoutWidget.update()
        self.gui.dynamicLayoutWidget.show()
        # self.ref_spinbox.valueChanged.connect(self.apply_division_factor_to_reflectance_rows(self.divide_by))

    def extract_data_from_table(self):
        extracted_data = {}

        # Assuming your data is stored in a 2D list called "data_array"
        # If you use another structure or variable name, adjust the below code accordingly

        for i, para_name in enumerate(self.para_list):
            # Get row index from spinbox (remember to subtract 1 due to label)
            row_idx = self.spinboxes[i].value() - 1

            # Extract the data from that row
            extracted_row = [self.gui.tablePreview.item(row_idx, col).text() for col in
                             range(1, self.gui.tablePreview.columnCount())]

            # Convert to float for processing (if needed)
            extracted_row = [float(val) for val in extracted_row]

            # Assign to dictionary
            extracted_data[para_name] = extracted_row

        # Extract reflectance start row (always last added spinbox)
        ref_start_row_idx = self.ref_spinbox.value() - 1
        max_row_idx = min(self.gui.tablePreview.rowCount(), len(self.data_array))
        reflectance_data = []
        wavelengths = []
        for row in range(ref_start_row_idx, max_row_idx):
            # Extract data for this row
            row_data = [self.gui.tablePreview.item(row, col).text() for col in
                        range(1, self.gui.tablePreview.columnCount())]
            # Convert to float
            row_data = [float(val) for val in row_data]
            # Append this row data to reflectance_data
            reflectance_data.append(row_data)
            # Extract and store wavelength
            wavelength_value = self.gui.tablePreview.item(row, 0).text()
            wavelengths.append(float(wavelength_value))
        extracted_data["Reflectance"] = reflectance_data
        extracted_data["Wavelengths"] = wavelengths

        # Now, "extracted_data" contains your extracted data, indexed by parameter name
        return extracted_data

    def houston(self, message):
        # Houston, we have a problem
        self.gui.label.setStyleSheet("color: rgb(170, 0, 0);")
        self.gui.label.setText(message)
        self.gui.tablePreview.setRowCount(0)
        self.gui.tablePreview.setColumnCount(0)
        self.gui.cmdOK.setDisabled(True)

    def ok(self):
        self.main.mlra_training.val_data = self.extract_data_from_table()
        # self.main.gui.
        self.gui.close()


# The SelectWavelengths class allows to add/remove wavelengths from the inversion
class SelectWavelengths:
    def __init__(self, main):
        self.main = main
        self.gui = SelectWavelengthsGUI()
        self.connections()

    def connections(self):
        self.gui.cmdSendExclude.clicked.connect(lambda: self.send(direction="in_to_ex"))
        self.gui.cmdSendInclude.clicked.connect(lambda: self.send(direction="ex_to_in"))
        self.gui.cmdAll.clicked.connect(lambda: self.select(select="all"))
        self.gui.cmdNone.clicked.connect(lambda: self.select(select="none"))
        self.gui.cmdCancel.clicked.connect(lambda: self.gui.close())
        self.gui.cmdOK.clicked.connect(lambda: self.ok())

    def populate(self, default_exclude):
        if self.main.mlra_training.nbands < 10:
            width = 1
        elif self.main.mlra_training.nbands < 100:
            width = 2
        elif self.main.mlra_training.nbands < 1000:
            width = 3
        else:
            width = 4

        # Any bands with central wavelengths in the specified domain are excluded by default,
        # i.e. the GUI is prepared to add these to the exclude list;
        for i in range(self.main.mlra_training.nbands):
            if i in default_exclude:
                str_band_no = '{num:0{width}}'.format(num=i + 1, width=width)
                label = "band %s: %6.2f %s" % (
                str_band_no, self.main.mlra_training.wl[i], self.main.mlra_training.wunit)
                self.gui.lstExcluded.addItem(label)
            else:
                str_band_no = '{num:0{width}}'.format(num=i + 1, width=width)
                label = "band %s: %6.2f %s" % (
                str_band_no, self.main.mlra_training.wl[i], self.main.mlra_training.wunit)
                self.gui.lstIncluded.addItem(label)

    def send(self, direction):
        # Send wavelengths to the include or the exclude list (the function handles both, the direction is passed)
        if direction == "in_to_ex":
            origin = self.gui.lstIncluded
            destination = self.gui.lstExcluded
        elif direction == "ex_to_in":
            origin = self.gui.lstExcluded
            destination = self.gui.lstIncluded
        else:
            return

        for item in origin.selectedItems():
            # move the selected Items from the origin list to the destination list
            index = origin.indexFromItem(item).row()
            destination.addItem(origin.takeItem(index))

        # re-sort the items in both lists (items were added at the bottom)
        origin.sortItems()
        destination.sortItems()
        self.gui.setDisabled(False)

    def select(self, select):
        self.gui.setDisabled(True)
        if select == "all":
            self.gui.lstIncluded.selectAll()
            self.gui.lstExcluded.clearSelection()
            self.send(direction="in_to_ex")
        elif select == "none":
            self.gui.lstExcluded.selectAll()
            self.gui.lstIncluded.clearSelection()
            self.send(direction="ex_to_in")
        else:
            return

    def ok(self):
        list_object = self.gui.lstExcluded
        raw_list = []
        for i in range(list_object.count()):  # read from the QtObect "list" all items as text
            item = list_object.item(i).text()
            raw_list.append(item)

        # convert the text-string of the list object into a python list of integers (bands to be excluded)
        self.main.mlra_training.exclude_bands = [int(raw_list[i].split(" ")[1][:-1]) - 1 for i in range(len(raw_list))]
        self.main.mlra_training.nbands_valid = self.main.mlra_training.nbands - len(
            self.main.mlra_training.exclude_bands)

        # Join the list to a string and set it to the txtExclude lineEdit
        exclude_string = " ".join(str(x + 1) for x in self.main.mlra_training.exclude_bands)
        self.main.mlra_training.gui.txtExclude.setText(exclude_string)

        # clean up
        for list_object in [self.gui.lstIncluded, self.gui.lstExcluded]:
            list_object.clear()

        self.gui.close()


class PRG:
    # class PRG handles the GUI of the ProgressBar
    def __init__(self, main):
        self.main = main
        self.gui = PRG_GUI()
        self.gui.lblCancel.setVisible(False)
        self.connections()

    def connections(self):
        self.gui.cmdCancel.clicked.connect(lambda: self.cancel())

    def cancel(self):
        self.gui.allow_cancel = True
        self.gui.cmdCancel.setDisabled(True)
        self.gui.lblCancel.setText("-1")
        self.gui.close()
        self.gui.lblCancel.setText("1")


# class Printer:
#     def __init__(self, main):
#         self.main = main
#         self.gui = PrinterGUI()
#
#         # Set up custom logging handler
#         logger = logging.getLogger('sklearn')
#         logger.setLevel(logging.INFO)
#         handler = TextEditLogger(self.gui.printCanvas)
#         formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
#         handler.setFormatter(formatter)
#         logger.addHandler(handler)
#
#     def updateTextEdit(self):
#         self.gui.printCanvas.append(captured_output)
#         sys.stdout.truncate(0)
#         sys.stdout.seek(0)

# class TextEditLogger(logging.Handler):
#     def __init__(self, widget):
#         super().__init__()
#         self.widget = widget
#
#     def emit(self, record):
#         msg = self.format(record)
#         self.widget.append(msg)


# class MainUiFunc is the interface between all sub-GUIs, so they can communicate between each other
class MainUiFunc:
    def __init__(self):
        self.qgis_app = QApplication.instance()
        self.mlra_training = ML_Training(self)
        self.loadtxtfile = LoadTxtFile(self)
        self.select_wavelengths = SelectWavelengths(self)
        self.prg_widget = PRG(self)
        self.performance_view = perfView(self)
        # self.printer = Printer(self)

    def show(self):
        self.mlra_training.gui.show()


if __name__ == '__main__':
    from enmapbox.testing import start_app

    app = start_app()
    m = MainUiFunc()
    m.show()
    #lut_path = r"C:\Data\Daten\Testdaten\LUT\testLUT_1000_CpCBCcheck_00meta.lut"
    #m.mlra_training.open_lut(lutpath=lut_path)
    #out_folder = r"C:\Data\Daten\Testdaten\Model_TEST/"
    #m.mlra_training.get_folder(path=out_folder)
    sys.exit(app.exec_())