BFDC-Imjoy plugin.

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",
  "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,
  "icon": null,
  "env": "conda create -n imjoy python=3.7",
  "requirements": [],
  "dependencies": []
}
</config>

<script lang="python">
#"git+https://github.com/imodpasteur/Brightfield-Drift-Correction-3D.git@dev"
import numpy as np
#from bfdc import drift
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}.')

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

    #api.getConfig('root').then(self.config_root).catch(print)
    
    self.config = {"trace":{'xypixel':100, 
                            'zstep':100, 
                            'start':0, 
                            'nframes':0, 
                            'skip':0,
                            'minsignal':0,
                            'paths':['dictionary',
                                     'roi',
                                     'movie']},
                   "apply":{'smooth':0,
                            'paths':['zola_table',
                                     'drift_table']},
                   "batch":{}
                   }
    
    self.revoke_config(await api.getConfig('bfdc'))
    self.print_config()
    self.plot_menus()


  def plot_menus(self):
    for action in self.config:
        name = self.config[action]
        ui = []
        for param in self.config[action]:
            if isinstance(self.config[action][param],int):
                line = {param: {"id": param, 
                              "type": "number", 
                               "min": 0, 
                               "placeholder":self.config[action][param]}
                }
                #print(str(line))
                ui.append(line)
        #print(ui)
        api.register({"name" : action,
                         "ui": ui})
  
  async def run(self,my):
    print(my.config)
    action = my.config.type
    arg_dict = my.config
    _ = arg_dict.pop('type')
    self.update_config(action,arg_dict)

    if action in self.config:
        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 = []
        args += [action]
        args += paths
        args += ['--%s=%d'%(key,value) for key,value in zip(arg_dict.keys(),arg_dict.values())]
        print(args)
        drift.main(argsv=args, callback=self.show_progress)
    else:
        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,args):
    print(f'Root directory is set to : {self.root}')
    api.showProgress(0)

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

  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(None)
    else:
        api.alert('Suggerted 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)
  
  def revoke_config(self, conf):
    print(f'Loaded {conf} from Imjoy bfdc key')
    if conf:
        print('Trying to serialize with json')
        config = json.loads(conf)
    else:
        print('No configuration found in Imjoy')
        return
    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:
            self.config[it].update(config[it])
    else:
        print(f'Keys are different current vs remote: {self.config.keys()} vs {config.keys()}')
        print('Keep the curent configuration')

  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))


  '''
    HIV_EDU_647_SR
        HIV_EDU_647_SR.Pos0.ome.tif
    HIV_EDU_647_WF
        HIV_EDU_647_WF.Pos0.ome.tif
        HIV_EDU_647_WF.Pos0_1.ome.tif
        HIV_EDU_647.roi
    HIV_EDU_647_BR
        HIV_EDU_647_BR.ome.tif
    HIV_EDU_647.roi
  '''

  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>