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#########################
# defs and imports
#########################

import logging
import os
import shutil
import json
import threading
import traceback

import numpy as np
from numpy.linalg import inv

from nis_util import *
from simple_detection import *

from skimage.transform import AffineTransform
from skimage.io import imread
from xmlrpc.client import ServerProxy

from annotation import manually_correct_rois
from automation import WidgetProgressIndicator


    

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###################
# set up the environment, nis, and image saving path
###################

import resources

# Wrapper for default values
class WingScannerSettings:
    def __init__(self):
        # value is (description, value)
        self.path_to_nis = ('Path to NIS .exe', 'C:\\Program Files\\NIS-Elements\\nis_ar.exe')
        self.save_base_path = ('Local Temp Folder', 'C:\\Users\\Nikon\\Documents\\automation_temp')
        self.save_server_path_local = ('Destination Folder on Server (Network Share)', 'Y:\\results')
        self.save_server_path_remote = ('Destination Folder on Server (On Server)', '/data/wing-scanner/results')

        # location of the calibration files
        self.calib_left = ('Calibration File (left)', resources.left_calib)
        self.calib_mid = ('Calibration File (mid)', resources.mid_calib)
        self.calib_right = ('Calibration File (right)', resources.right_calib)

        # detail images z settings
        self.z_drive= ('Z device for detail stacks', 'NIDAQ Piezo Z')
        self.z_range = ('Z range (um)', 50)
        self.z_step= ('Z steps (um)', 2)


# plot size
%matplotlib inline
plt.rcParams['figure.figsize'] = [10,10]


    

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#################
# do the scans
#################

style = {'description_width': 'initial'}

from ipywidgets import Layout, HBox, VBox, Box, Checkbox, Text, BoundedFloatText, Button, FloatProgress, Label, Dropdown, Tab, Layout
from IPython.display import display

import automation
from copy import copy

logging.basicConfig(format='%(asctime)s - %(levelname)s in %(funcName)s: %(message)s', level=logging.INFO)
logger = logging.getLogger(__name__)


settings = WingScannerSettings()

# this will fail on systems without nis -> use dummy values
try:
    pos = get_position(settings.path_to_nis[1])
    color = is_color_camera(settings.path_to_nis[1])
    ocs = get_optical_confs(settings.path_to_nis[1])
except FileNotFoundError as e:
    pos = (0, 0, 0, 0)
    color = False
    ocs = ['oc_1', 'oc_2']
    
if color:
    settings.calib_left = ('Calibration File (left)', resources.left_color_calib)
    settings.calib_mid = ('Calibration File (mid)', resources.mid_color_calib)
    settings.calib_right = ('Calibration File (right)', resources.right_color_calib)

# Tab 1: basic settings
selection_oc_ov = Dropdown(
    options=ocs,
    value=ocs[0],
    disabled=False,
    description='Overview OC:',
    style=style
)
selection_oc_det_dia = Dropdown(
    options=ocs,
    value=ocs[0],
    disabled=False,
    description='detailed DIA OC:',
    style=style
)
selection_oc_det_fluo_vb = Box(
    [Checkbox(description='',indent=False),
     Dropdown(
         options=ocs,
         value=ocs[0],
         description='Detail fluo OC :',
         disabled=False,
         style=style )])

manual_annot_check = Checkbox(description='Manually correct detections?')
detection_first_check = Checkbox(description='Do all overviews/detections first')
hbox_ocs_mendatory = VBox([selection_oc_ov, selection_oc_det_dia])
hbox_ocs_optionnal = VBox([selection_oc_det_fluo_vb, manual_annot_check, detection_first_check])
sub_folder = Text(description='subfolder name:', style=style)

left = HBox([Checkbox(description='left slide'), Text(description='prefix:'),
             Checkbox(description='manual focus position', value=True), BoundedFloatText(description='z', value=float(pos[2]), min=0, max=5000, step=10)])

mid = HBox([Checkbox(description='mid slide'), Text(description='prefix:'),
             Checkbox(description='manual focus position', value=True), BoundedFloatText(description='z', value=float(pos[2]), min=0, max=5000, step=10)])

right = HBox([Checkbox(description='right slide'), Text(description='sample name:'),
             Checkbox(description='manual focus position', value=True), BoundedFloatText(description='z', value=float(pos[2]), min=0, max=5000, step=10)])

status_main = HBox([FloatProgress(), Label()])
status_detail = HBox([FloatProgress(), Label()])


go = Button(description='GO')

tab1 = VBox([ hbox_ocs_mendatory, hbox_ocs_optionnal, sub_folder, left, mid, right, status_main, status_detail, go])

settings_textboxes = [Text(description=v[0], value=str(v[1]), layout=Layout(width='80%'), style=style) for _,v in vars(settings).items()]

tab2 = VBox([
    Label('Expert settings, only change if you know what you are doing')
] + settings_textboxes )

tabs = Tab(children=[tab1, tab2])
tabs.set_title(0, 'Wing Scanner')
tabs.set_title(1, 'Expert Settings')

display(tabs)


status = WidgetProgressIndicator(status_detail.children[0], status_detail.children[1])

def onclick_go(btn):
   
    btn.disabled = True
    
    # update settings object
    for i, k in enumerate(settings.__dict__):
        settings.__dict__[k] = (settings_textboxes[i].description, settings_textboxes[i].value)
        
     # NB: we change the calibration if we use the color cam
    # TODO: respect user choice for custom calibration
    try:
        set_optical_configuration(settings.path_to_nis[1], selection_oc_ov.value)
        color = is_color_camera(settings.path_to_nis[1])
        if color:
            settings.calib_left = ('Calibration File (left)', resources.left_color_calib)
            settings.calib_mid = ('Calibration File (mid)', resources.mid_color_calib)
            settings.calib_right = ('Calibration File (right)', resources.right_color_calib)
        else:
            settings.calib_left = ('Calibration File (left)', resources.left_calib)
            settings.calib_mid = ('Calibration File (mid)', resources.mid_calib)
            settings.calib_right = ('Calibration File (right)', resources.right_calib)
    except Exception as e:
        pass
    
    save_path_local = settings.save_server_path_local[1]
    save_path_remote = settings.save_server_path_remote[1]
    if sub_folder.value:
        save_path_local = os.path.join(save_path_local, sub_folder.value)
        save_path_remote = (os.path.join(save_path_remote, sub_folder.value)).replace(os.sep, '/')
    logger.info('Saving files to (local drive) %s '%(save_path_local))
    logger.info('Saving files to (server) %s '%(save_path_remote))
    
    oc_overview = selection_oc_ov.value
    ocs_detail = [selection_oc_det_dia.value]
    if selection_oc_det_fluo_vb.children[0].value:
        logger.info('Imaging also a second channel')
        ocs_detail.append(selection_oc_det_fluo_vb.children[1].value)
    
    slide_left = left.children[1].value if left.children[0].value else None 
    slide_mid = mid.children[1].value if mid.children[0].value else None
    slide_right = right.children[1].value if right.children[0].value else None

    z_left = float(left.children[3].value) if left.children[2].value else None 
    z_mid = float(mid.children[3].value) if mid.children[2].value else None
    z_right = float(right.children[3].value) if right.children[2].value else None

    status_main.children[0].value = 0
    status_main.children[1].value = 'scanning left'
    
    
    
    # TODO: set meaningful default in automation
    config = automation.CommonParameters()
    config.path_to_nis = settings.path_to_nis[1]
    config.prefix = 'experiment'
    config.progress_indicator = status
    config.save_base_path = settings.save_base_path[1]
    config.server_path_local = save_path_local
    config.server_path_remote = save_path_remote
    
    ov_param = automation.OverviewParameters()
    ov_param.export_as_tiff = True
    ov_param.field_def_file = None
    ov_param.manual_z = z_left
    ov_param.oc_overview = oc_overview
    ov_param.return_overview_img = True
    
    det_param = automation.DetectionParameters()
    # TODO: add to settings
    #det_param.detector_adress
    det_param.do_manual_annotation = manual_annot_check.value
    #det_param.object_filter = {}
    det_param.plot_detection = True
    
    detail_param = automation.DetailParameters()
    detail_param.auto_focus_detail = True
    detail_param.channel_for_autofocus = 0
    detail_param.channel_for_stitch = 0
    detail_param.dry_run_details = False
    detail_param.ocs_detail = ocs_detail
    detail_param.projection_params = True
    #detail_param.stitcher_adress
    detail_param.tiff_export_details = True
    detail_param.z_drive = settings.z_drive[1]
    detail_param.z_range = int(settings.z_range[1])
    detail_param.z_step = int(settings.z_step[1])
    
    # TODO: add callback to set 
    
    configs = []
    ov_params = []
    det_params = []
    detail_params = []
    
    do_scan_left  = slide_left != None
    if do_scan_left:
        logger.info('Scanning left scan.')
        
        config_l = copy(config)
        config_l.prefix = slide_left
        ov_param_l = copy(ov_param)
        ov_param_l.field_def_file = settings.calib_left[1]
        
        configs.append(config_l)
        ov_params.append(ov_param_l)
        det_params.append(det_param)
        detail_params.append(detail_param)
        
        '''
        do_scan(settings.calib_left[1], oc_overview, ocs_detail, settings.path_to_nis[1], settings.save_base_path[1],
                slide_left, save_path_local, save_path_remote,
                manual_z_overview=z_left, z_drive=settings.z_drive[1],
                z_range=int(settings.z_range[1]), z_step=int(settings.z_step[1]), progress_indicator=status,
                manual_annotation_check = manual_annot_check.value )
        '''
    else:
        logger.info('Skipping left slide.')

    # mid slide
    
    status_main.children[0].value = 33
    status_main.children[1].value = 'scanning mid'
    
    do_scan_mid  = slide_mid != None
    if do_scan_mid:
        logger.info('Scanning mid scan.')
        
        config_m = copy(config)
        config_m.prefix = slide_mid
        ov_param_m = copy(ov_param)
        ov_param_m.field_def_file = settings.calib_mid[1]
        
        configs.append(config_m)
        ov_params.append(ov_param_m)
        det_params.append(det_param)
        detail_params.append(detail_param)
        
        '''
        do_scan(settings.calib_mid[1], oc_overview, ocs_detail, settings.path_to_nis[1], settings.save_base_path[1],
                slide_mid, save_path_local, save_path_remote,
                manual_z_overview=z_mid, z_drive=settings.z_drive[1],
                z_range=int(settings.z_range[1]), z_step=int(settings.z_step[1]), progress_indicator=status,
               manual_annotation_check = manual_annot_check.value)
        '''
    else:
        logger.info('Skipping middle slide.')

    status_main.children[0].value = 66
    status_main.children[1].value = 'scanning right'
    
    # right slide
    do_scan_right  = slide_right != None
    if do_scan_right:
        logger.info('Scanning right scan.')
        
        config_r = copy(config)
        config_r.prefix = slide_right
        ov_param_r = copy(ov_param)
        ov_param_r.field_def_file = settings.calib_right[1]
        
        configs.append(config_r)
        ov_params.append(ov_param_r)
        det_params.append(det_param)
        detail_params.append(detail_param)
        
        '''
        do_scan(settings.calib_right[1], oc_overview, ocs_detail, settings.path_to_nis[1], settings.save_base_path[1],
                slide_right, save_path_local, save_path_remote,
                manual_z_overview=z_right, z_drive=settings.z_drive[1],
                z_range=int(settings.z_range[1]), z_step=int(settings.z_step[1]), progress_indicator=status,
               manual_annotation_check = manual_annot_check.value)
        '''
    else:
        logger.info('Skipping right slide.')
    
    status_main.children[0].value = 100
    status_main.children[1].value = 'Done'
    
    
    if not detection_first_check.value:
        automation.do_scan(configs, ov_params, det_params, detail_params)
    else:
        automation.do_scan_detection_first(configs, ov_params, det_params, detail_params)
    
    btn.disabled = False
    
go.on_click(onclick_go)