DataBrowser View Plug-in Tutorial

You can download the complete script here: databrowser_example.py

ScopeFoundry provides a DataBrowserApp that makes it easy for a user to explore a set of experiemental results on their computer. It is a plug-in based application, where data-type plug-ins (a DataBrowserView) can show relevant data within the file. The FoundryDataBrowser project is an example of the ScopeFoundry DataBrowser with a number of Views used to browse common experiemental data the Molecular Foundry.

Setup

Note: We recommend the Anaconda python distribution, which contains many easy to install scientific python packages.

• Download and Install Anaconda. Recommended python version is 3.5.

• Create an conda environment includes ScopeFoundry and its dependencies. Open an Anaconda prompt and run the following commands:

$ conda create -n scopefoundry python=3.6 anaconda
$ source activate scopefoundry 
(scopefoundry) $ conda install pyqtgraph
(scopefoundry) $ pip install ScopeFoundry

Note: On Windows source activate scopefoundry should be replaced by activate scopefoundry

Defining a DataBrowserView

Lets define a custom view. We do this by subclassing the DataBrowserView class. Three methods should be defined setup(), is_file_supported(), and on_change_data_filename().

Here is an example of a simple dataviewer that uses a PyQtGraph ImageView to display an image loaded via scipy (this file is called viewers/images.py in FoundryDataBrowser):

from ScopeFoundry.data_browser import DataBrowserView
import pyqtgraph as pg
import numpy as np
from scipy.misc import imread
import os

#scipy imread uses the Python Imaging Library (PIL) to read an image

class ScipyImreadView(DataBrowserView):

    # This name is used in the GUI for the DataBrowser
    name = 'scipy_imread_view'
    
    def setup(self):
        # create the GUI and viewer settings, runs once at program start up
        # self.ui should be a QWidget of some sort, here we use a pyqtgraph ImageView
        self.ui = self.imview = pg.ImageView()

    def is_file_supported(self, fname):
    	 # Tells the DataBrowser whether this plug-in would likely be able
    	 # to read the given file name
    	 # here we are using the file extension to make a guess
        _, ext = os.path.splitext(fname)
        return ext.lower() in ['.png', '.tif', '.tiff', '.jpg']

        
    def on_change_data_filename(self, fname):
        #  A new file has been selected by the user, load and display it
        try:
            self.data = imread(fname)
            self.imview.setImage(self.data.swapaxes(0,1))
        except Exception as err:
        	  # When a failure to load occurs, zero out image
        	  # and show error message
            self.imview.setImage(np.zeros((10,10)))
            self.databrowser.ui.statusbar.showMessage(
            	"failed to load %s:\n%s" %(fname, err))
            raise(err)

Running your DataBrowser

To use this view you can create a DataBrowser script like this:

from ScopeFoundry.data_browser import DataBrowser
import sys

app = DataBrowser(sys.argv)

# views are loaded in order of more generic to more specific.
## ie the last loaded views are checked first for compatibility


app.load_view(ScipyImreadView(app))
    
# More views here

sys.exit(app.exec_())

You can download the complete script here: databrowser_example.py

Here is a resulting screen shot of running this data browser script and navigating to a folder with TIFF images.

Where to Find More

This example is part of the FoundryDataBrowser repository. There are many more examples of DataBrowserViews available for download there.

For questions about this tutorial or ScopeFoundry in general, please visit and post on the ScopeFoundry project mailing list / forum

For Source Code of all ScopeFoundry sub-projects visit our GitHub page