<reponame>PranavSudersan/Buggee<filename>app/_mainImportfile.py
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 19 12:10:12 2020

@author: adwait
"""
import pims
import numpy as np
import cv2
import matplotlib.pyplot as plt
# import openpyxl
import pandas as pd
import os.path
import logging
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import QFileDialog
from PyQt5.QtChart import QScatterSeries
# from source.analysis.forceanalysis import ForceAnal
from source.threads.countframethread import CountFrameThread

class MainImportFile:

    def load_image(self): #load image file
        self.videoPath, _ = QFileDialog.getOpenFileName(self, "Open Image File")
        if self.videoPath != "":
            self.cap = pims.open(self.videoPath)
            # self.frame = cv2.imread(self.videoPath)
            self.frame = self.cap[0]
            self.playStatus = False
            self.recordStatus = False
            self.frameCount = 1
            self.frameHeight, self.frameWidth = self.frame.shape[:2]
            roiCorners = np.array([[0, 0],[self.frameWidth, 0], 
                                        [self.frameWidth, self.frameHeight], 
                                        [0, self.frameHeight]],np.int32)
            self.roiBound = [0, 0, self.frameWidth, self.frameHeight]
            self.roiDict = {"Default": [roiCorners, self.roiBound, [], roiCorners, roiCorners]}
            self.frameBackground = 255 * np.ones((self.frameHeight,
                                                self.frameWidth, 3),dtype=np.uint8)
            self.renderVideo("Raw", self.frame)
            self.frame_current = self.frame.copy()
            #Frame no. ROI label, contour id, area, length, ecc, array
            self.contour_data = [[], [], [], [], [], [], [], []] 
            # contactArea = np.zeros(1, np.float64)
            # contactLength = np.zeros(1, np.float64)
            # contourNumber = np.zeros(1, np.uint64)
            # roiArea = np.zeros(1, np.float64)
            # roiLength = np.zeros(1, np.float64)
            # self.frameTime = np.zeros(1, np.float64)
            # eccAvg = np.zeros(1, np.float64)
            # contactAngle =  np.zeros(1, np.float64)
            # self.dataDict = {"Default" : {"Contact area": contactArea, 
            #                               "Contact length": contactLength,
            #                               "Contact number": contourNumber, 
            #                               "ROI area": roiArea,
            #                               "ROI length": roiLength, 
            #                               "Eccentricity": eccAvg,
            #                               "Ellipse fit": [(0,0),(0,0),0,1],
            #                               "Contact angle": contactAngle}
            #                  }
            self.dataDict = {}
            self.init_datadict("Default") #initialize self.dataDict
            self.effectChain = [True, False, False, False] #b/c, hist, bg sub, filter
##            self.roi_auto = self.threshROIGroupBox.isChecked()
            self.distinct_roi = self.distinctAutoROI.isChecked()
            self.roi_hull = self.applyHullROI.isChecked()
            self.combine_roi = self.combineROI.isChecked()
            self.roi_tresh_type = "Global"
            self.tresh_size_roi = self.threshROISpinBox1.value()
            self.tresh_cst_roi = self.threshROISpinBox2.value()
            self.blur_size_roi = self.blurROISpinBox.value()
            self.bg_roi_apply = self.applybgROI.isChecked()
            self.bg_blur_size_roi = self.bgblurROISpinBox.value()
            self.bg_blend_roi = self.bgblendROISpinBox.value()
            self.framePos = 0
            self.roi_min_area = self.roiMinSpinBox.value()
            self.epsilon_fraction = 10**(self.epsilonSpinBox.value())
            self.roi_morph = self.morphROI.isChecked()
            self.x_roi_morph = self.morphXSpinBox.value()
            self.y_roi_morph = self.morphYSpinBox.value()
            self.calibFactor = self.lengthValue.value()/self.pixelValue.value()
            
            self.definePaths()
            
            self.analyzeVideo.blockSignals(True)
            self.analyzeVideo.setChecked(False)
            self.analyzeVideo.blockSignals(False)
            
            self.dftGroupBox.blockSignals(True)
            self.dftGroupBox.setChecked(False)
            self.dftGroupBox.blockSignals(False)

            self.bgGroupBox.blockSignals(True)
            self.bgGroupBox.setChecked(False)
            self.bgGroupBox.blockSignals(False)

            # self.showContours.blockSignals(True)
            # self.showContours.setChecked(False)
            # self.showContours.blockSignals(False)
            self.rawViewTab.setTabEnabled(1,False)

            self.threshROIGroupBox.blockSignals(True)
            self.threshROIGroupBox.setChecked(False)
            self.threshROIGroupBox.blockSignals(False)

##            self.distinctAutoROI.setEnabled(False)
            self.roi_auto = False
            self.segment = self.segmentGroupBox.isChecked()
            self.show_segment = self.showSegment.isChecked()
            self.show_fg = self.segmentFGButton.isChecked()
            self.show_bg = self.segmentBGButton.isChecked()
##            self.distinct_roi = False
            
##            self.distinctAutoROI.blockSignals(True)
##            self.distinctAutoROI.setChecked(False)
##            self.distinctAutoROI.blockSignals(False)

            # self.correctZeroForce.blockSignals(True)
            # self.correctZeroForce.setChecked(False)
            # self.correctZeroForce.blockSignals(False)

            self.analyzeDataWindow.zero_subtract.setChecked(False)     
            self.analyzeDataWindow.zero_subtract.setEnabled(False)

            
            self.init_dict() #initialise dictionaries
                        
            # self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow,
            #                            self.analyzeDataWindow)
            # self.zeroForceData = ForceAnal() #initalise
            # self.correctZeroForce.setEnabled(False)
            self.clearData.setEnabled(True)
            # self.videoEffect.setCurrentIndex(0) CHECK TAB DISABLE!
            # self.videoEffect.model().item(5).setEnabled(False)
            # self.videoEffect.model().item(6).setEnabled(True)
            self.effectViewTab.setTabEnabled(4,False)
            # self.effectViewTab.setTabEnabled(6,True)
            
            self.videoFileNameLabel.setText("<b>Video file:</b>\n" + self.videoPath) #video path
            # self.forceFileNameLabel.setText("Select force data from file menu")
            # self.zeroForceFileNameLabel.setText("Select zero-force data from file menu")
            self.statusBar.showMessage("Frame number: " + str(int(self.framePos)))
            
            self.frame_bin_roi_full = None
            self.setWindowTitle(self.appVersion)
            self.msrmnt_num = None
            self.bgframeNumber = 0
           
    def load_video(self): #load video
        if self.msrListMode == False:
            self.videoPath, _ = QFileDialog.getOpenFileName(self, "Open Video File")
        if self.videoPath != "":
##            self.statusBar.showMessage("Loading...")
            # self.cap = cv2.VideoCapture(self.videoPath)
            self.cap = pims.Video(self.videoPath)
            self.playStatus = False
            self.frameAction = "Play"
            self.recordStatus = False
            # self.setVideoParam()
##            self.frameCount = self.cap.get(cv2.CAP_PROP_FRAME_COUNT)
            #BUG: frame number count calculation is dirty. fix it.
            self.countThread = CountFrameThread(cv2.VideoCapture(self.videoPath)) #count frames in separate thread
            self.countThread.output.connect(self.loading_indicate)
            self.countThread.finished.connect(self.setVideoParam)
            self.countThread.start()

    def setVideoParam(self): #set video parameters
##            self.count_frames() #count number of frames by loop
            # self.cap.set(cv2.CAP_PROP_POS_FRAMES, 0)
            self.frameCount = self.countThread.frameCount
            # self.frameWidth = int(self.cap.get(cv2.CAP_PROP_FRAME_WIDTH))
            # self.frameHeight = int(self.cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
   
            # self.frameCount = len(self.cap)
            self.frameHeight, self.frameWidth, _ = self.cap.frame_shape
            self.framePos = 1
            try:
                self.fpsSpinBox.setValue(self.cap.frame_rate)
            except Exception as e:
                logging.warning(f'{e}')   
            logging.debug('%s, %s, %s', self.frameCount, self.frameWidth, self.frameRate)
            
            roiCorners = np.array([[0, 0],[self.frameWidth, 0], 
                                        [self.frameWidth, self.frameHeight], 
                                        [0, self.frameHeight]],np.int32)
            self.roiBound = [0, 0, self.frameWidth, self.frameHeight]
            #roi dictionary: actual roi, bound, contours, adjusted roi, auto roi
            self.roiDict = {"Default": [roiCorners, self.roiBound,
                                        [], roiCorners, roiCorners]} 
            self.frameBackground = 255 * np.ones((self.frameHeight,
                                                self.frameWidth, 3),dtype=np.uint8)
            self.bgframeNumber = None
            
            # self.ret, self.frame = self.cap.read()
            # if self.ret == False: #reset video on error
            #         logging.debug("if")
            #         self.cap.release()
            #         self.cap = cv2.VideoCapture(self.videoPath)
            #         self.ret, self.frame = self.cap.read()
            self.frame = self.cap[0]
            self.renderVideo("Raw", self.frame)

            self.effectScene.removeItem(self.effectPixmapItem)
            self.effectPixmapItem = self.effectScene.addPixmap(self.blankPixmap)
            self.effectView.fitInView(self.effectPixmapItem, 1)
                
            # self.cap.set(cv2.CAP_PROP_POS_FRAMES, 0)
            self.frame_current = self.frame.copy()
            #Frame no. ROI label, contour id, area, length, ecc, array
            self.contour_data = [[], [], [], [], [], [], [], []]
            # contactArea = np.zeros(int(self.frameCount), np.float64)
            # contactLength = np.zeros(int(self.frameCount), np.float64)
            # contourNumber = np.zeros(int(self.frameCount), np.uint64)
            # roiArea = np.zeros(int(self.frameCount), np.float64)
            # roiLength = np.zeros(int(self.frameCount), np.float64)
            # eccAvg = np.zeros(int(self.frameCount), np.float64) #median eccentricity
            # contactAngle = np.zeros(int(self.frameCount), np.float64)
            # self.dataDict = {"Default" : {"Contact area": contactArea, 
            #                               "Contact length": contactLength,
            #                               "Contact number": contourNumber, 
            #                               "ROI area": roiArea,
            #                               "ROI length": roiLength, 
            #                               "Eccentricity": eccAvg,
            #                               "Ellipse fit": [[(0,0),(0,0),0,1]]*int(self.frameCount),
            #                               "Contact angle": contactAngle}
            #                  }
            self.dataDict = {}
            self.init_datadict("Default") #initialize self.dataDict
            self.frameTime = np.linspace(0,
                                         self.frameCount/self.frameRate,
                                         int(self.frameCount), dtype = np.float64)
            self.effectChain = [True, False, False, False] #b/c, hist, bg sub, filter
##            self.roi_auto = self.threshROIGroupBox.isChecked()
            self.distinct_roi = self.distinctAutoROI.isChecked()
            self.roi_hull = self.applyHullROI.isChecked()
            self.combine_roi = self.combineROI.isChecked()
            self.roi_tresh_type = "Global"
            self.tresh_size_roi = self.threshROISpinBox1.value()
            self.tresh_cst_roi = self.threshROISpinBox2.value()
            self.blur_size_roi = self.blurROISpinBox.value()
            self.bg_roi_apply = self.applybgROI.isChecked()
            self.bg_blur_size_roi = self.bgblurROISpinBox.value()
            self.bg_blend_roi = self.bgblendROISpinBox.value()
            # self.framePos = 0
            self.roi_min_area = self.roiMinSpinBox.value()
            self.epsilon_fraction = 10**(self.epsilonSpinBox.value())
            self.roi_morph = self.morphROI.isChecked()
            self.x_roi_morph = self.morphXSpinBox.value()
            self.y_roi_morph = self.morphYSpinBox.value()
            self.calibFactor = self.lengthValue.value()/self.pixelValue.value()

            self.definePaths()
            
            self.seekSlider.blockSignals(True)
            self.seekSlider.setValue(1)
            self.seekSlider.setTickInterval(int(0.2 *self.frameCount))
            self.seekSlider.setSingleStep(int(0.1 *self.frameCount))
            self.seekSlider.setMaximum(int(self.frameCount))
            self.seekSlider.blockSignals(False)
            
            self.analyzeVideo.blockSignals(True)
            self.analyzeVideo.setChecked(False)
            self.analyzeVideo.blockSignals(False)
            
            self.dftGroupBox.blockSignals(True)
            self.dftGroupBox.setChecked(False)
            self.dftGroupBox.blockSignals(False)

            self.bgGroupBox.blockSignals(True)
            self.bgGroupBox.setChecked(False)
            self.bgGroupBox.blockSignals(False)

            self.threshROIGroupBox.blockSignals(True)
            self.threshROIGroupBox.setChecked(False)
            self.threshROIGroupBox.blockSignals(False)

##            self.distinctAutoROI.setEnabled(False)
            self.roi_auto = False
            self.segment = self.segmentGroupBox.isChecked()
            self.show_segment = self.showSegment.isChecked()
            self.show_fg = self.segmentFGButton.isChecked()
            self.show_bg = self.segmentBGButton.isChecked()
##            self.distinct_roi = False
            
##            self.distinctAutoROI.blockSignals(True)
##            self.distinctAutoROI.setChecked(False)
##            self.distinctAutoROI.blockSignals(False)

            # self.correctZeroForce.blockSignals(True)
            # self.correctZeroForce.setChecked(False)
            # self.correctZeroForce.blockSignals(False)
            
            self.analyzeDataWindow.zero_subtract.setChecked(False)     
            self.analyzeDataWindow.zero_subtract.setEnabled(False)
            

            self.rawViewTab.setTabEnabled(1,False)
            # self.showContours.setEnabled(False)
            # self.showEffect.setEnabled(False)
            
            
            # self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow,
            #                            self.analyzeDataWindow)
            # self.zeroForceData = ForceAnal() #initalise
            # self.correctZeroForce.setEnabled(False)
            self.clearData.setEnabled(True)
            # self.videoEffect.setCurrentIndex(0) CHECK TAB DISABLE!
            # self.videoEffect.model().item(5).setEnabled(False)
            # self.videoEffect.model().item(6).setEnabled(True)
            self.effectViewTab.setTabEnabled(4,False)
            # self.effectViewTab.setTabEnabled(6,True)

            self.videoFileNameLabel.setText("<b>Video file:</b>\n" + self.videoPath) #video path
            # self.forceFileNameLabel.setText("Select force data from file menu")
            # self.zeroForceFileNameLabel.setText("Select zero-force data from file menu")
##            self.statusBar.showMessage("Frame number: " + str(int(self.framePos)) + "\t("
##                                       + str(int((self.framePos)*100/self.frameCount)) +
##                                       "%)")
            self.statusBar.showMessage(str(int(self.frameCount)) + " frames loaded!")
            self.configRecWindow.videoTextbox.setText("")

            self.init_dict() #initialise dictionaries
            
            # self.framePos = 1 #avoid array indexing issue
            self.frame_bin_roi_full = None

            self.curve1 = QScatterSeries()#initialise live plot curves
            self.curve2 = QScatterSeries()
            self.initialise_live_plot(self.curve1, Qt.blue) #contact area plot
            self.initialise_live_plot(self.curve2, Qt.red) # roi area plot

            self.msrmnt_num = None
            self.setWindowTitle(self.appVersion)

            if self.msrListMode == True: #continue loading force data etc
                self.load_measurement_data()

    def import_file_list(self): #import file list
        fileListPath, _ = QFileDialog.getOpenFileName(self, "Open File List")

        if fileListPath != "":
            self.folderPath = os.path.dirname(fileListPath)
            # wb_obj = openpyxl.load_workbook(filename = fileListPath,
            #                                 read_only = True)# workbook object is created  
            # sheet_obj = wb_obj.active

            # m_row = sheet_obj.max_row

            # self.measurmntList = []
            # self.bottomviewList = []
            # self.sideviewList = []
            # self.forcedataList = []
             
            # for i in range(2, m_row + 1): #save filename lists
            #     self.measurmntList.append(sheet_obj.cell(row = i, column = 1).value)
            #     self.bottomviewList.append(sheet_obj.cell(row = i, column = 2).value)
            #     self.sideviewList.append(sheet_obj.cell(row = i, column = 3).value)
            #     self.forcedataList.append(sheet_obj.cell(row = i, column = 4).value)

            # wb_obj.close()
            self.fileListDf = pd.read_excel(fileListPath, index_col = 0, engine='openpyxl')
            #remove unecessary columns
            cols = self.fileListDf.columns
            for c in ['Data OK?', 'Comments']:
                if c in cols:
                    self.fileListDf.drop(columns = [c], inplace = True)
            self.chooseMsrmnt.setEnabled(True)
            self.statusBar.showMessage("Loaded file list from " + self.folderPath)
            logging.debug('%s', self.fileListDf)

    def import_force_data(self): #import force data
        # if self.msrListMode == False:
        #     self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow,
        #                                self.analyzeDataWindow)
        # self.zeroForceData = ForceAnal() #initalise
        # self.correctZeroForce.blockSignals(True)
        # self.correctZeroForce.setChecked(False)
        # self.correctZeroForce.blockSignals(False)        
        # self.correctZeroForce.setEnabled(False)
        self.analyzeDataWindow.zero_subtract.setChecked(False)     
        self.analyzeDataWindow.zero_subtract.setEnabled(False)
        self.zeroForceFileNameLabel.setText("Select zero-force data from file menu")
        
        self.forceData.importData(self.msrListMode)
        if self.forceData.force_filepath != "":
            logging.info('File loaded -> ' + self.forceData.force_filepath)
            self.forceData.calcData()
            # self.defl_vert1_raw = self.forceData.defl_vert1.copy() #copy of raw vert data
            # self.defl_vert1_actual = self.forceData.defl_vert1.copy() #copy of raw vert data
            self.configPlotWindow.plotDict['plot settings']['plot range']\
                .setText(str(0) + ',' + str(self.forceData.ptsnumber-1))
            # self.forceData.plot_slice = self.configPlotWindow.plotDict['plot settings']['plot range']
            self.openZeroForceFile.setEnabled(True)
            self.fpsSpinBox.blockSignals(True)
            self.fpsSpinBox.setValue(self.forceData.fps)
            self.fpsSpinBox.blockSignals(False)
            self.frameTime = self.forceData.time_video #recalculated time array
            self.frameRate = self.forceData.fps
            self.forceFileNameLabel.setText("<b>Force data:</b>\n" + self.forceData.force_filepath)
##            self.videoEffect.model().item(6).setEnabled(True)
            plt.close()
            self.plotSequence()
            # self.updateFitDict()
            # self.init_plotconfig()
            # self.forceData.dataClean()
            # self.forceData.calcData()
            logging.debug('%s', self.frameRate)

    def import_zero_force(self): #import zero force line
        # self.zeroForceData = ForceAnal(analyzeDataWindow = self.analyzeDataWindow)
        # self.correctZeroForce.setEnabled(True)
        self.analyzeDataWindow.zero_subtract.setEnabled(True)
        self.analyzeDataWindow.zero_subtract.setChecked(False)             
        # self.zeroForceData.noiseSteps = ','.join(map(str,range(1,self.forceData.step_num + 1)))
        self.zeroForceData.importData(False)
        if self.zeroForceData.force_filepath != "":
            self.zeroForceData.dataClean()
            self.zeroForceData.evaluateForce()
            self.forceData.zeroDataDict = self.zeroForceData.fileDataDict.copy()
            self.zeroForceFileNameLabel.setText("<b>Zero force data:</b>\n" +
                                                self.zeroForceData.force_filepath)            
            # self.zero_force_calc()

#     def zero_force_calc(self): #calculate vertical force correction wrt zero
#         zero_shift = self.zeroForceData.defl_vert1[0] - self.forceData.defl_vert1[0]
#         self.zeroForceData.defl_vert1_corrected = [x-zero_shift for x in self.zeroForceData.defl_vert1]
# ##        self.defl_vert1_raw = self.forceData.defl_vert1.copy()
#         self.defl_vert1_actual = [self.forceData.defl_vert1[0] +
#                                  self.forceData.defl_vert1[i] -
#                                  self.zeroForceData.defl_vert1_corrected[i] \
#                                  for i in range(len(self.forceData.defl_vert1))]
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 19 12:10:12 2020

@author: adwait
"""
import pims
import numpy as np
import cv2
import matplotlib.pyplot as plt
# import openpyxl
import pandas as pd
import os.path
import logging
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import QFileDialog
from PyQt5.QtChart import QScatterSeries
# from source.analysis.forceanalysis import ForceAnal
from source.threads.countframethread import CountFrameThread

class MainImportFile:

    def load_image(self): #load image file
        self.videoPath, _ = QFileDialog.getOpenFileName(self, "Open Image File")
        if self.videoPath != "":
            self.cap = pims.open(self.videoPath)
            # self.frame = cv2.imread(self.videoPath)
            self.frame = self.cap[0]
            self.playStatus = False
            self.recordStatus = False
            self.frameCount = 1
            self.frameHeight, self.frameWidth = self.frame.shape[:2]
            roiCorners = np.array([[0, 0],[self.frameWidth, 0], 
                                        [self.frameWidth, self.frameHeight], 
                                        [0, self.frameHeight]],np.int32)
            self.roiBound = [0, 0, self.frameWidth, self.frameHeight]
            self.roiDict = {"Default": [roiCorners, self.roiBound, [], roiCorners, roiCorners]}
            self.frameBackground = 255 * np.ones((self.frameHeight,
                                                self.frameWidth, 3),dtype=np.uint8)
            self.renderVideo("Raw", self.frame)
            self.frame_current = self.frame.copy()
            #Frame no. ROI label, contour id, area, length, ecc, array
            self.contour_data = [[], [], [], [], [], [], [], []] 
            # contactArea = np.zeros(1, np.float64)
            # contactLength = np.zeros(1, np.float64)
            # contourNumber = np.zeros(1, np.uint64)
            # roiArea = np.zeros(1, np.float64)
            # roiLength = np.zeros(1, np.float64)
            # self.frameTime = np.zeros(1, np.float64)
            # eccAvg = np.zeros(1, np.float64)
            # contactAngle =  np.zeros(1, np.float64)
            # self.dataDict = {"Default" : {"Contact area": contactArea, 
            #                               "Contact length": contactLength,
            #                               "Contact number": contourNumber, 
            #                               "ROI area": roiArea,
            #                               "ROI length": roiLength, 
            #                               "Eccentricity": eccAvg,
            #                               "Ellipse fit": [(0,0),(0,0),0,1],
            #                               "Contact angle": contactAngle}
            #                  }
            self.dataDict = {}
            self.init_datadict("Default") #initialize self.dataDict
            self.effectChain = [True, False, False, False] #b/c, hist, bg sub, filter
##            self.roi_auto = self.threshROIGroupBox.isChecked()
            self.distinct_roi = self.distinctAutoROI.isChecked()
            self.roi_hull = self.applyHullROI.isChecked()
            self.combine_roi = self.combineROI.isChecked()
            self.roi_tresh_type = "Global"
            self.tresh_size_roi = self.threshROISpinBox1.value()
            self.tresh_cst_roi = self.threshROISpinBox2.value()
            self.blur_size_roi = self.blurROISpinBox.value()
            self.bg_roi_apply = self.applybgROI.isChecked()
            self.bg_blur_size_roi = self.bgblurROISpinBox.value()
            self.bg_blend_roi = self.bgblendROISpinBox.value()
            self.framePos = 0
            self.roi_min_area = self.roiMinSpinBox.value()
            self.epsilon_fraction = 10**(self.epsilonSpinBox.value())
            self.roi_morph = self.morphROI.isChecked()
            self.x_roi_morph = self.morphXSpinBox.value()
            self.y_roi_morph = self.morphYSpinBox.value()
            self.calibFactor = self.lengthValue.value()/self.pixelValue.value()
            
            self.definePaths()
            
            self.analyzeVideo.blockSignals(True)
            self.analyzeVideo.setChecked(False)
            self.analyzeVideo.blockSignals(False)
            
            self.dftGroupBox.blockSignals(True)
            self.dftGroupBox.setChecked(False)
            self.dftGroupBox.blockSignals(False)

            self.bgGroupBox.blockSignals(True)
            self.bgGroupBox.setChecked(False)
            self.bgGroupBox.blockSignals(False)

            # self.showContours.blockSignals(True)
            # self.showContours.setChecked(False)
            # self.showContours.blockSignals(False)
            self.rawViewTab.setTabEnabled(1,False)

            self.threshROIGroupBox.blockSignals(True)
            self.threshROIGroupBox.setChecked(False)
            self.threshROIGroupBox.blockSignals(False)

##            self.distinctAutoROI.setEnabled(False)
            self.roi_auto = False
            self.segment = self.segmentGroupBox.isChecked()
            self.show_segment = self.showSegment.isChecked()
            self.show_fg = self.segmentFGButton.isChecked()
            self.show_bg = self.segmentBGButton.isChecked()
##            self.distinct_roi = False
            
##            self.distinctAutoROI.blockSignals(True)
##            self.distinctAutoROI.setChecked(False)
##            self.distinctAutoROI.blockSignals(False)

            # self.correctZeroForce.blockSignals(True)
            # self.correctZeroForce.setChecked(False)
            # self.correctZeroForce.blockSignals(False)

            self.analyzeDataWindow.zero_subtract.setChecked(False)     
            self.analyzeDataWindow.zero_subtract.setEnabled(False)

            
            self.init_dict() #initialise dictionaries
                        
            # self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow,
            #                            self.analyzeDataWindow)
            # self.zeroForceData = ForceAnal() #initalise
            # self.correctZeroForce.setEnabled(False)
            self.clearData.setEnabled(True)
            # self.videoEffect.setCurrentIndex(0) CHECK TAB DISABLE!
            # self.videoEffect.model().item(5).setEnabled(False)
            # self.videoEffect.model().item(6).setEnabled(True)
            self.effectViewTab.setTabEnabled(4,False)
            # self.effectViewTab.setTabEnabled(6,True)
            
            self.videoFileNameLabel.setText("<b>Video file:</b>\n" + self.videoPath) #video path
            # self.forceFileNameLabel.setText("Select force data from file menu")
            # self.zeroForceFileNameLabel.setText("Select zero-force data from file menu")
            self.statusBar.showMessage("Frame number: " + str(int(self.framePos)))
            
            self.frame_bin_roi_full = None
            self.setWindowTitle(self.appVersion)
            self.msrmnt_num = None
            self.bgframeNumber = 0
           
    def load_video(self): #load video
        if self.msrListMode == False:
            self.videoPath, _ = QFileDialog.getOpenFileName(self, "Open Video File")
        if self.videoPath != "":
##            self.statusBar.showMessage("Loading...")
            # self.cap = cv2.VideoCapture(self.videoPath)
            self.cap = pims.Video(self.videoPath)
            self.playStatus = False
            self.frameAction = "Play"
            self.recordStatus = False
            # self.setVideoParam()
##            self.frameCount = self.cap.get(cv2.CAP_PROP_FRAME_COUNT)
            #BUG: frame number count calculation is dirty. fix it.
            self.countThread = CountFrameThread(cv2.VideoCapture(self.videoPath)) #count frames in separate thread
            self.countThread.output.connect(self.loading_indicate)
            self.countThread.finished.connect(self.setVideoParam)
            self.countThread.start()

    def setVideoParam(self): #set video parameters
##            self.count_frames() #count number of frames by loop
            # self.cap.set(cv2.CAP_PROP_POS_FRAMES, 0)
            self.frameCount = self.countThread.frameCount
            # self.frameWidth = int(self.cap.get(cv2.CAP_PROP_FRAME_WIDTH))
            # self.frameHeight = int(self.cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
   
            # self.frameCount = len(self.cap)
            self.frameHeight, self.frameWidth, _ = self.cap.frame_shape
            self.framePos = 1
            try:
                self.fpsSpinBox.setValue(self.cap.frame_rate)
            except Exception as e:
                logging.warning(f'{e}')   
            logging.debug('%s, %s, %s', self.frameCount, self.frameWidth, self.frameRate)
            
            roiCorners = np.array([[0, 0],[self.frameWidth, 0], 
                                        [self.frameWidth, self.frameHeight], 
                                        [0, self.frameHeight]],np.int32)
            self.roiBound = [0, 0, self.frameWidth, self.frameHeight]
            #roi dictionary: actual roi, bound, contours, adjusted roi, auto roi
            self.roiDict = {"Default": [roiCorners, self.roiBound,
                                        [], roiCorners, roiCorners]} 
            self.frameBackground = 255 * np.ones((self.frameHeight,
                                                self.frameWidth, 3),dtype=np.uint8)
            self.bgframeNumber = None
            
            # self.ret, self.frame = self.cap.read()
            # if self.ret == False: #reset video on error
            #         logging.debug("if")
            #         self.cap.release()
            #         self.cap = cv2.VideoCapture(self.videoPath)
            #         self.ret, self.frame = self.cap.read()
            self.frame = self.cap[0]
            self.renderVideo("Raw", self.frame)

            self.effectScene.removeItem(self.effectPixmapItem)
            self.effectPixmapItem = self.effectScene.addPixmap(self.blankPixmap)
            self.effectView.fitInView(self.effectPixmapItem, 1)
                
            # self.cap.set(cv2.CAP_PROP_POS_FRAMES, 0)
            self.frame_current = self.frame.copy()
            #Frame no. ROI label, contour id, area, length, ecc, array
            self.contour_data = [[], [], [], [], [], [], [], []]
            # contactArea = np.zeros(int(self.frameCount), np.float64)
            # contactLength = np.zeros(int(self.frameCount), np.float64)
            # contourNumber = np.zeros(int(self.frameCount), np.uint64)
            # roiArea = np.zeros(int(self.frameCount), np.float64)
            # roiLength = np.zeros(int(self.frameCount), np.float64)
            # eccAvg = np.zeros(int(self.frameCount), np.float64) #median eccentricity
            # contactAngle = np.zeros(int(self.frameCount), np.float64)
            # self.dataDict = {"Default" : {"Contact area": contactArea, 
            #                               "Contact length": contactLength,
            #                               "Contact number": contourNumber, 
            #                               "ROI area": roiArea,
            #                               "ROI length": roiLength, 
            #                               "Eccentricity": eccAvg,
            #                               "Ellipse fit": [[(0,0),(0,0),0,1]]*int(self.frameCount),
            #                               "Contact angle": contactAngle}
            #                  }
            self.dataDict = {}
            self.init_datadict("Default") #initialize self.dataDict
            self.frameTime = np.linspace(0,
                                         self.frameCount/self.frameRate,
                                         int(self.frameCount), dtype = np.float64)
            self.effectChain = [True, False, False, False] #b/c, hist, bg sub, filter
##            self.roi_auto = self.threshROIGroupBox.isChecked()
            self.distinct_roi = self.distinctAutoROI.isChecked()
            self.roi_hull = self.applyHullROI.isChecked()
            self.combine_roi = self.combineROI.isChecked()
            self.roi_tresh_type = "Global"
            self.tresh_size_roi = self.threshROISpinBox1.value()
            self.tresh_cst_roi = self.threshROISpinBox2.value()
            self.blur_size_roi = self.blurROISpinBox.value()
            self.bg_roi_apply = self.applybgROI.isChecked()
            self.bg_blur_size_roi = self.bgblurROISpinBox.value()
            self.bg_blend_roi = self.bgblendROISpinBox.value()
            # self.framePos = 0
            self.roi_min_area = self.roiMinSpinBox.value()
            self.epsilon_fraction = 10**(self.epsilonSpinBox.value())
            self.roi_morph = self.morphROI.isChecked()
            self.x_roi_morph = self.morphXSpinBox.value()
            self.y_roi_morph = self.morphYSpinBox.value()
            self.calibFactor = self.lengthValue.value()/self.pixelValue.value()

            self.definePaths()
            
            self.seekSlider.blockSignals(True)
            self.seekSlider.setValue(1)
            self.seekSlider.setTickInterval(int(0.2 *self.frameCount))
            self.seekSlider.setSingleStep(int(0.1 *self.frameCount))
            self.seekSlider.setMaximum(int(self.frameCount))
            self.seekSlider.blockSignals(False)
            
            self.analyzeVideo.blockSignals(True)
            self.analyzeVideo.setChecked(False)
            self.analyzeVideo.blockSignals(False)
            
            self.dftGroupBox.blockSignals(True)
            self.dftGroupBox.setChecked(False)
            self.dftGroupBox.blockSignals(False)

            self.bgGroupBox.blockSignals(True)
            self.bgGroupBox.setChecked(False)
            self.bgGroupBox.blockSignals(False)

            self.threshROIGroupBox.blockSignals(True)
            self.threshROIGroupBox.setChecked(False)
            self.threshROIGroupBox.blockSignals(False)

##            self.distinctAutoROI.setEnabled(False)
            self.roi_auto = False
            self.segment = self.segmentGroupBox.isChecked()
            self.show_segment = self.showSegment.isChecked()
            self.show_fg = self.segmentFGButton.isChecked()
            self.show_bg = self.segmentBGButton.isChecked()
##            self.distinct_roi = False
            
##            self.distinctAutoROI.blockSignals(True)
##            self.distinctAutoROI.setChecked(False)
##            self.distinctAutoROI.blockSignals(False)

            # self.correctZeroForce.blockSignals(True)
            # self.correctZeroForce.setChecked(False)
            # self.correctZeroForce.blockSignals(False)
            
            self.analyzeDataWindow.zero_subtract.setChecked(False)     
            self.analyzeDataWindow.zero_subtract.setEnabled(False)
            

            self.rawViewTab.setTabEnabled(1,False)
            # self.showContours.setEnabled(False)
            # self.showEffect.setEnabled(False)
            
            
            # self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow,
            #                            self.analyzeDataWindow)
            # self.zeroForceData = ForceAnal() #initalise
            # self.correctZeroForce.setEnabled(False)
            self.clearData.setEnabled(True)
            # self.videoEffect.setCurrentIndex(0) CHECK TAB DISABLE!
            # self.videoEffect.model().item(5).setEnabled(False)
            # self.videoEffect.model().item(6).setEnabled(True)
            self.effectViewTab.setTabEnabled(4,False)
            # self.effectViewTab.setTabEnabled(6,True)

            self.videoFileNameLabel.setText("<b>Video file:</b>\n" + self.videoPath) #video path
            # self.forceFileNameLabel.setText("Select force data from file menu")
            # self.zeroForceFileNameLabel.setText("Select zero-force data from file menu")
##            self.statusBar.showMessage("Frame number: " + str(int(self.framePos)) + "\t("
##                                       + str(int((self.framePos)*100/self.frameCount)) +
##                                       "%)")
            self.statusBar.showMessage(str(int(self.frameCount)) + " frames loaded!")
            self.configRecWindow.videoTextbox.setText("")

            self.init_dict() #initialise dictionaries
            
            # self.framePos = 1 #avoid array indexing issue
            self.frame_bin_roi_full = None

            self.curve1 = QScatterSeries()#initialise live plot curves
            self.curve2 = QScatterSeries()
            self.initialise_live_plot(self.curve1, Qt.blue) #contact area plot
            self.initialise_live_plot(self.curve2, Qt.red) # roi area plot

            self.msrmnt_num = None
            self.setWindowTitle(self.appVersion)

            if self.msrListMode == True: #continue loading force data etc
                self.load_measurement_data()

    def import_file_list(self): #import file list
        fileListPath, _ = QFileDialog.getOpenFileName(self, "Open File List")

        if fileListPath != "":
            self.folderPath = os.path.dirname(fileListPath)
            # wb_obj = openpyxl.load_workbook(filename = fileListPath,
            #                                 read_only = True)# workbook object is created  
            # sheet_obj = wb_obj.active

            # m_row = sheet_obj.max_row

            # self.measurmntList = []
            # self.bottomviewList = []
            # self.sideviewList = []
            # self.forcedataList = []
             
            # for i in range(2, m_row + 1): #save filename lists
            #     self.measurmntList.append(sheet_obj.cell(row = i, column = 1).value)
            #     self.bottomviewList.append(sheet_obj.cell(row = i, column = 2).value)
            #     self.sideviewList.append(sheet_obj.cell(row = i, column = 3).value)
            #     self.forcedataList.append(sheet_obj.cell(row = i, column = 4).value)

            # wb_obj.close()
            self.fileListDf = pd.read_excel(fileListPath, index_col = 0, engine='openpyxl')
            #remove unecessary columns
            cols = self.fileListDf.columns
            for c in ['Data OK?', 'Comments']:
                if c in cols:
                    self.fileListDf.drop(columns = [c], inplace = True)
            self.chooseMsrmnt.setEnabled(True)
            self.statusBar.showMessage("Loaded file list from " + self.folderPath)
            logging.debug('%s', self.fileListDf)

    def import_force_data(self): #import force data
        # if self.msrListMode == False:
        #     self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow,
        #                                self.analyzeDataWindow)
        # self.zeroForceData = ForceAnal() #initalise
        # self.correctZeroForce.blockSignals(True)
        # self.correctZeroForce.setChecked(False)
        # self.correctZeroForce.blockSignals(False)        
        # self.correctZeroForce.setEnabled(False)
        self.analyzeDataWindow.zero_subtract.setChecked(False)     
        self.analyzeDataWindow.zero_subtract.setEnabled(False)
        self.zeroForceFileNameLabel.setText("Select zero-force data from file menu")
        
        self.forceData.importData(self.msrListMode)
        if self.forceData.force_filepath != "":
            logging.info('File loaded -> ' + self.forceData.force_filepath)
            self.forceData.calcData()
            # self.defl_vert1_raw = self.forceData.defl_vert1.copy() #copy of raw vert data
            # self.defl_vert1_actual = self.forceData.defl_vert1.copy() #copy of raw vert data
            self.configPlotWindow.plotDict['plot settings']['plot range']\
                .setText(str(0) + ',' + str(self.forceData.ptsnumber-1))
            # self.forceData.plot_slice = self.configPlotWindow.plotDict['plot settings']['plot range']
            self.openZeroForceFile.setEnabled(True)
            self.fpsSpinBox.blockSignals(True)
            self.fpsSpinBox.setValue(self.forceData.fps)
            self.fpsSpinBox.blockSignals(False)
            self.frameTime = self.forceData.time_video #recalculated time array
            self.frameRate = self.forceData.fps
            self.forceFileNameLabel.setText("<b>Force data:</b>\n" + self.forceData.force_filepath)
##            self.videoEffect.model().item(6).setEnabled(True)
            plt.close()
            self.plotSequence()
            # self.updateFitDict()
            # self.init_plotconfig()
            # self.forceData.dataClean()
            # self.forceData.calcData()
            logging.debug('%s', self.frameRate)

    def import_zero_force(self): #import zero force line
        # self.zeroForceData = ForceAnal(analyzeDataWindow = self.analyzeDataWindow)
        # self.correctZeroForce.setEnabled(True)
        self.analyzeDataWindow.zero_subtract.setEnabled(True)
        self.analyzeDataWindow.zero_subtract.setChecked(False)             
        # self.zeroForceData.noiseSteps = ','.join(map(str,range(1,self.forceData.step_num + 1)))
        self.zeroForceData.importData(False)
        if self.zeroForceData.force_filepath != "":
            self.zeroForceData.dataClean()
            self.zeroForceData.evaluateForce()
            self.forceData.zeroDataDict = self.zeroForceData.fileDataDict.copy()
            self.zeroForceFileNameLabel.setText("<b>Zero force data:</b>\n" +
                                                self.zeroForceData.force_filepath)            
            # self.zero_force_calc()

#     def zero_force_calc(self): #calculate vertical force correction wrt zero
#         zero_shift = self.zeroForceData.defl_vert1[0] - self.forceData.defl_vert1[0]
#         self.zeroForceData.defl_vert1_corrected = [x-zero_shift for x in self.zeroForceData.defl_vert1]
# ##        self.defl_vert1_raw = self.forceData.defl_vert1.copy()
#         self.defl_vert1_actual = [self.forceData.defl_vert1[0] +
#                                  self.forceData.defl_vert1[i] -
#                                  self.zeroForceData.defl_vert1_corrected[i] \
#                                  for i in range(len(self.forceData.defl_vert1))]
# -*- coding: utf-8 -*- Created on Fri Jun 19 12:10:12 2020
 
 @author: adwait # import openpyxl # from source.analysis.forceanalysis import ForceAnal #load image file # self.frame = cv2.imread(self.videoPath) #Frame no. ROI label, contour id, area, length, ecc, array # contactArea = np.zeros(1, np.float64) # contactLength = np.zeros(1, np.float64) # contourNumber = np.zeros(1, np.uint64) # roiArea = np.zeros(1, np.float64) # roiLength = np.zeros(1, np.float64) # self.frameTime = np.zeros(1, np.float64) # eccAvg = np.zeros(1, np.float64) # contactAngle =  np.zeros(1, np.float64) # self.dataDict = {"Default" : {"Contact area": contactArea, #                               "Contact length": contactLength, #                               "Contact number": contourNumber, #                               "ROI area": roiArea, #                               "ROI length": roiLength, #                               "Eccentricity": eccAvg, #                               "Ellipse fit": [(0,0),(0,0),0,1], #                               "Contact angle": contactAngle} #                  } #initialize self.dataDict #b/c, hist, bg sub, filter ##            self.roi_auto = self.threshROIGroupBox.isChecked() # self.showContours.blockSignals(True) # self.showContours.setChecked(False) # self.showContours.blockSignals(False) ##            self.distinctAutoROI.setEnabled(False) ##            self.distinct_roi = False ##            self.distinctAutoROI.blockSignals(True) ##            self.distinctAutoROI.setChecked(False) ##            self.distinctAutoROI.blockSignals(False) # self.correctZeroForce.blockSignals(True) # self.correctZeroForce.setChecked(False) # self.correctZeroForce.blockSignals(False) #initialise dictionaries # self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow, #                            self.analyzeDataWindow) # self.zeroForceData = ForceAnal() #initalise # self.correctZeroForce.setEnabled(False) # self.videoEffect.setCurrentIndex(0) CHECK TAB DISABLE! # self.videoEffect.model().item(5).setEnabled(False) # self.videoEffect.model().item(6).setEnabled(True) # self.effectViewTab.setTabEnabled(6,True) #video path # self.forceFileNameLabel.setText("Select force data from file menu") # self.zeroForceFileNameLabel.setText("Select zero-force data from file menu") #load video ##            self.statusBar.showMessage("Loading...") # self.cap = cv2.VideoCapture(self.videoPath) # self.setVideoParam() ##            self.frameCount = self.cap.get(cv2.CAP_PROP_FRAME_COUNT) #BUG: frame number count calculation is dirty. fix it. #count frames in separate thread #set video parameters ##            self.count_frames() #count number of frames by loop # self.cap.set(cv2.CAP_PROP_POS_FRAMES, 0) # self.frameWidth = int(self.cap.get(cv2.CAP_PROP_FRAME_WIDTH)) # self.frameHeight = int(self.cap.get(cv2.CAP_PROP_FRAME_HEIGHT)) # self.frameCount = len(self.cap) #roi dictionary: actual roi, bound, contours, adjusted roi, auto roi # self.ret, self.frame = self.cap.read() # if self.ret == False: #reset video on error #         logging.debug("if") #         self.cap.release() #         self.cap = cv2.VideoCapture(self.videoPath) #         self.ret, self.frame = self.cap.read() # self.cap.set(cv2.CAP_PROP_POS_FRAMES, 0) #Frame no. ROI label, contour id, area, length, ecc, array # contactArea = np.zeros(int(self.frameCount), np.float64) # contactLength = np.zeros(int(self.frameCount), np.float64) # contourNumber = np.zeros(int(self.frameCount), np.uint64) # roiArea = np.zeros(int(self.frameCount), np.float64) # roiLength = np.zeros(int(self.frameCount), np.float64) # eccAvg = np.zeros(int(self.frameCount), np.float64) #median eccentricity # contactAngle = np.zeros(int(self.frameCount), np.float64) # self.dataDict = {"Default" : {"Contact area": contactArea, #                               "Contact length": contactLength, #                               "Contact number": contourNumber, #                               "ROI area": roiArea, #                               "ROI length": roiLength, #                               "Eccentricity": eccAvg, #                               "Ellipse fit": [[(0,0),(0,0),0,1]]*int(self.frameCount), #                               "Contact angle": contactAngle} #                  } #initialize self.dataDict #b/c, hist, bg sub, filter ##            self.roi_auto = self.threshROIGroupBox.isChecked() # self.framePos = 0 ##            self.distinctAutoROI.setEnabled(False) ##            self.distinct_roi = False ##            self.distinctAutoROI.blockSignals(True) ##            self.distinctAutoROI.setChecked(False) ##            self.distinctAutoROI.blockSignals(False) # self.correctZeroForce.blockSignals(True) # self.correctZeroForce.setChecked(False) # self.correctZeroForce.blockSignals(False) # self.showContours.setEnabled(False) # self.showEffect.setEnabled(False) # self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow, #                            self.analyzeDataWindow) # self.zeroForceData = ForceAnal() #initalise # self.correctZeroForce.setEnabled(False) # self.videoEffect.setCurrentIndex(0) CHECK TAB DISABLE! # self.videoEffect.model().item(5).setEnabled(False) # self.videoEffect.model().item(6).setEnabled(True) # self.effectViewTab.setTabEnabled(6,True) #video path # self.forceFileNameLabel.setText("Select force data from file menu") # self.zeroForceFileNameLabel.setText("Select zero-force data from file menu") ##            self.statusBar.showMessage("Frame number: " + str(int(self.framePos)) + "\t(" ##                                       + str(int((self.framePos)*100/self.frameCount)) + ##                                       "%)") #initialise dictionaries # self.framePos = 1 #avoid array indexing issue #initialise live plot curves #contact area plot # roi area plot #continue loading force data etc #import file list # wb_obj = openpyxl.load_workbook(filename = fileListPath, #                                 read_only = True)# workbook object is created # sheet_obj = wb_obj.active # m_row = sheet_obj.max_row # self.measurmntList = [] # self.bottomviewList = [] # self.sideviewList = [] # self.forcedataList = [] # for i in range(2, m_row + 1): #save filename lists #     self.measurmntList.append(sheet_obj.cell(row = i, column = 1).value) #     self.bottomviewList.append(sheet_obj.cell(row = i, column = 2).value) #     self.sideviewList.append(sheet_obj.cell(row = i, column = 3).value) #     self.forcedataList.append(sheet_obj.cell(row = i, column = 4).value) # wb_obj.close() #remove unecessary columns #import force data # if self.msrListMode == False: #     self.forceData = ForceAnal(self.fitWindow, self.configPlotWindow, #                                self.analyzeDataWindow) # self.zeroForceData = ForceAnal() #initalise # self.correctZeroForce.blockSignals(True) # self.correctZeroForce.setChecked(False) # self.correctZeroForce.blockSignals(False) # self.correctZeroForce.setEnabled(False) # self.defl_vert1_raw = self.forceData.defl_vert1.copy() #copy of raw vert data # self.defl_vert1_actual = self.forceData.defl_vert1.copy() #copy of raw vert data # self.forceData.plot_slice = self.configPlotWindow.plotDict['plot settings']['plot range'] #recalculated time array ##            self.videoEffect.model().item(6).setEnabled(True) # self.updateFitDict() # self.init_plotconfig() # self.forceData.dataClean() # self.forceData.calcData() #import zero force line # self.zeroForceData = ForceAnal(analyzeDataWindow = self.analyzeDataWindow) # self.correctZeroForce.setEnabled(True) # self.zeroForceData.noiseSteps = ','.join(map(str,range(1,self.forceData.step_num + 1))) # self.zero_force_calc() #     def zero_force_calc(self): #calculate vertical force correction wrt zero #         zero_shift = self.zeroForceData.defl_vert1[0] - self.forceData.defl_vert1[0] #         self.zeroForceData.defl_vert1_corrected = [x-zero_shift for x in self.zeroForceData.defl_vert1] # ##        self.defl_vert1_raw = self.forceData.defl_vert1.copy() #         self.defl_vert1_actual = [self.forceData.defl_vert1[0] + #                                  self.forceData.defl_vert1[i] - #                                  self.zeroForceData.defl_vert1_corrected[i] \ #                                  for i in range(len(self.forceData.defl_vert1))]