BFDC.imjoy.html

<docs lang="markdown">
You need to install Python Engine first https://github.com/oeway/ImJoy-Python	
Then create a new plugin and paste this code to it.	
The plugin will configure Python automatically with all dependencies.	
Click on the BFDC to run the plugin.	
You'll see the file dialog to select zstack, roi and movie.	
Then the plugin will launch Python package to process the files and output the drift table.	
It will also show the drift plot in the separate window.
</docs>

<config lang="json">
{
  "name": "BFDC-test",
  "mode": "pyworker",
  "version": "0.1.0",
  "api_version": "0.1.1",
  "description": "A plugin for demonstrate python plugin.",
  "tags": null,
  "ui": "Ops for tracing, applying and batch processing bright field drift. Select your operation type and check the parameters.",
  "inputs": null,
  "outputs": null,
  "flags": [],
  "icon": null,
  "env": "conda create -n imjoy python=3.7",
  "requirements": ["git+https://github.com/imodpasteur/Brightfield-Drift-Correction-3D.git@v0.4.2"],
  "dependencies": []
}
</config>

<script lang="python">
#"git+https://github.com/imodpasteur/Brightfield-Drift-Correction-3D.git@v0.3.0"
import numpy as np
import sys
import os
#sys.path.insert(0,'/Volumes/Imod-grenier/Andrey/Phase retrieve/drift-correction/BFDC/')
from bfdc import drift
import base64
import asyncio
import json



class PythonPlugin():

  async def setup(self):
    print(f'Running BFDC in Python {sys.version}.')

    self.root = str(await api.getConfig('root'))
    
    self.config_root()

    self.config = {"trace":{'xypixel':110, 
                            'zstep':100,
                            'zdirection':['approach','retract'], 
                            'start':10, 
                            'nframes':0, 
                            'skip':10,
                            'minsignal':0,
                            'paths':['dictionary',
                                     'roi',
                                     'movie']},
                   "apply":{'smooth':0,
                            'zinvert':[0,1],
                            'maxbg':0,
                            'paths':['zola_table',
                                     'drift_table']},
                   "batch":{'xypixel':110, 
                            'zstep':100,
                            'zdirection':['approach','retract'], 
                            'start':10,  
                            'skip':10,
                            'fov_prefix': 'FOV',
                            'dict_folder_prefix': 'dict',
                            'dict_suffix': 'ome.tif',
                            'sr_folder_prefix': 'sr_',
                            'sr_movie_suffix': 'Pos0.ome.tif',
                            'zola_dc_filename':'ZOLA*BFDC*.csv',
                            'dc_table_filename': 'BFCC*.csv',
                            'zola_raw_filename': 'ZOLA_localization_table.csv',
                            'smooth': 50,
                            'filter_bg': 0,
                            'zinvert': 0,
                            'paths': ['batch_path']}
                   }
    
    await self.revoke_config()
    self.print_config()
    self.plot_menus()


  def plot_menus(self):
    ##bla
    for action in self.config:
        name = self.config[action]
        ui = []
        for param in self.config[action]:
            value = self.config[action][param]
            #print(f'{param}:{value}({type(value)})')
               
            if param is not 'paths':
                if isinstance(value,int):
                    line = {param: {"id": param, 
                                "type": "number", 
                                "min": 0, 
                                "placeholder":value}
                            }
                    #print(str(line))
                    ui.append(line)
                elif isinstance(value,str):
                    line = {param: {"id": param, 
                                "type": "string", 
                                "placeholder":value}
                            }
                    #print(str(line))
                    ui.append(line)
                elif isinstance(value,list):
                    line = {param: {"id": param, 
                                "type": "choose",
                                "options": value, 
                                "placeholder": value[0]}
                            }
                    #print(str(line))
                    ui.append(line)
                else:
                    raise('unknown entry, expected str, list or int')

        #print(ui)
        api.register({"name" : action,
                         "ui": ui})
  
  async def run(self,my):
    print(my.config)
    arg_dict = my.config
    action = arg_dict.pop('type').split('/')[-1]
    if action in self.config:
        self.update_config(action,arg_dict)
        self.config_root()
        titles = self.config[action]['paths']
        print(titles)
        try:
            paths = await self.get_paths(titles)
        except:
            print('Canceled by user')
            return
        #paths = ['as','sdf']
        print(paths)
        
        args = [action]
        args += paths
        args += [f'--{key}={value}' for key,value in zip(arg_dict.keys(),arg_dict.values())]
        print(args)
        drift.main(argsv=args, callback=self.show_progress)
    else:
        #print("action")
        #print("not supported")
        api.alert('Select action from drop down menu BFDC')

  def update_config(self, action,new_dict):
    print('updating config')
    self.config[action].update(new_dict)
    self.dump_config()
    #print('New config: ')
    #print(json.dumps(self.config, indent=4))
  
  async def get_paths(self, title_list):
    if isinstance(title_list, list) or isinstance(title_list, tuple):
        path_list = []
        for title in title_list:
            print('request ' + title)
            
            path = await api.showFileDialog(title='Select ' + title, root=self.root)
            
            print('selected: ' + path)
            api.showSnackbar(f'Selected {path}')
            self.save_root(path)
            path_list.append(path)
        return path_list
    else:
        raise IndexError(f'Expected list/tuple, got {type(title_list)}')

  def show_config(self):
    print(f'Root directory is set to : {self.root}')
    api.showProgress(0)

  def config_root(self):
    print(f'found getConfig.root {self.root}')
    api.showStatus(f'Found root path: {self.root}')
    if self.root == "null" or not os.path.isdir(self.root):
        api.showDialog({"name": "Configure start folder",
                          "ui": "Please type in the path to start with: {id:'path', type:'string', placeholder: '%s'}."%self.root}).then(self.set_root)
    else:
        #self.root = root
        self.show_config()

  def set_root(self,path):
    api.showStatus(f'Received {path.path} from the dialog')
    path = path.path
    try:
        os.path.isdir(path)
    except:
        path = r'%s'%path

    if os.path.isdir(path):
        self.root = path
        api.setConfig('root', path)
        self.show_config()
    else:
        api.alert('Suggested path is wrong, try again')
        self.config_root()
    return

  def save_root(self,root):
    if os.path.isfile(root):
        root = os.path.dirname(root)
    self.root = root
    api.setConfig('root', root)
  
  async def revoke_config(self):
    conf = str(await api.getConfig('bfdc'))
    print(conf)
    print('Loaded conf from Imjoy bfdc key')
    try:
        print('Trying to serialize with json')
        config = json.loads(conf)
    except json.decoder.JSONDecodeError:
        print('No configuration found in Imjoy')
        return False
    print('Loaded configuration from Imjoy')
    if config.keys() == self.config.keys():
        print('Keys are the same')
        print('Updating current configuration from Imjoy')
        for it in self.config:
            for param in self.config[it]:
                try:
                    if isinstance(self.config[it][param], int) and isinstance(config[it][param], int):
                        self.config[it][param] = config[it][param]
                except KeyError:
                    pass
    else:
        print(f'Keys are different current vs remote: {self.config.keys()} vs {config.keys()}')
        print('Keep the curent configuration')
    return True

  def dump_config(self):
    print('Saving updated config to Imjoy')
    conf = json.dumps(self.config)
    api.setConfig('bfdc', conf)

  def print_config(self):
    print(json.dumps(self.config, sort_keys=False, indent=2))

  def show_drift_plot(self, plot_path):
    with open(plot_path, 'rb') as f:
        data = f.read()
        result = base64.b64encode(data).decode('ascii')
        imgurl = 'data:image/png;base64,' + result
        api.createWindow(name='Drift prediction', type = 'imjoy/image', w=5, h=5, data= {"src": imgurl})

  def show_progress(self, msg):
    assert isinstance(msg,dict)
    #print(json.dumps(msg, indent=4))
    if list(msg)[0] == 'Progress':
        current, total, found = msg['Progress'].values()
        api.showStatus(f'Processing {current}/{total}, found {found} BF frames')
        api.showProgress(int(current / total * 100))
    elif list(msg)[0] == 'Message':
        api.showStatus(msg['Message'])
    elif list(msg)[0] == 'Plot':
        print('plot ',msg['Plot'])
        self.show_drift_plot(msg['Plot'])

api.export(PythonPlugin())
</script>