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readme.md

Cinema::Explorer, a general viewer for Cinema

This is a general viewer for all Cinema Databases following the current Cinema specification.

Usage

The viewer consists of a main html file, accompanying javascript, css and json files, and several external dependencies. There are two ways to use this viewer:

  • If you are using it on a system connected to the internet, the external dependencies will be loaded automatically, through the browser.
  • If you are using it on a system without connection to the internet, you will need to install the external dependencies locally, per the instrucgtions below.

A Note on Browser Security

To use Cinema:Explorer, you must allow local file access. Do this in the following way, but be sure to reset these options when you are done:

  • Firefox (preferred)
    • type about:config in the navigaion bar
      • set privacy.file_unique_origin to false
      • set security.fileuri.strict_origin_policy to false
  • Safari
    • Safari->Preferences->Advanced->Show Develop menu in menu bar
    • Safari->Develop->Disable Local File Restrictions (on)
  • Chrome
    • open chrome with the option --disable-web-security
    • Mac example:
      • open -na "Google Chrome" cinema_explorer.html --args --user-data-dir="YOUR_PATH_TO_REPO" --disable-web-security

Installation

To install Cinema:Explorer, copy the cinema_explorer.html and cinema/ directory to the same directory as your data. In a simple example, the installed files might look like this:

   cinema_explorer.html
   cinema/
       database_01.cdb
       database_02.cdb
       database_03.cdb

The cinema/ directory is the general directory for all cinema applications, each of which has an application and version directory. This is designed to allow cinema applications to reside next to data, with a minimum of clutter from Cinema. For example:

    cinema/
    	explorer/
        	1.9/
        		css/
        		js/
        		lib/
        		license.md
        		databases.json

The cinema databases can be anywhere below the directory that contains the cinema.html and cinema/ directory. So, you could also have this:

   cinema.html
   cinema/
   data/
       database_01.cdb
       database_02.cdb
       database_03.cdb

Loading your databases into the viewer

To add your data to the viewer, edit cinema/explorer/<version>/databases.json to include references to your data. This is the default file that is loaded by the viewer.

You may override the default location and name of the databases.json by passing arguments in the URL. The databases attribute name may be used in the following ways:

  • provide a properly formatted json file with one or more database paths:
    file:///Users/me/data/cinema.html?databases=somedirectory/somename.json
  • provide the path to one or more cinema databases:
    file:///Users/me/data/cinema.html?databases=somedirectory/database.cdb
    file:///Users/me/data/cinema.html?databases=somedirectory/database.cdb,somdirectory/another.cdb

Dependencies

The viewer has several dependencies, which are loaded in the normal way, through URLS. The top section of the cinema_explorer.html file contains <script src=...> clauses in the <head> section that link to the dependencies.

If you are installing this viewer on a system that does not have access to the internet, you can download and install these dependencies in the cinema/ directory, and change the ``src``` links to point to the internal location. Your directory structure might look something like this (the exact structure is up to you):

    cinema/
        libs/
            d3.v5.min.js
            vtk.js
            ...

The databases.json file

  • databases.json is a list of objects where each object must contain at least a 'name' field and 'directory' field. 'name' is the name of the databases that will be shown in the viewer. 'directory' is the path to the '.cdb' directory for your database.
  • Due to browser security features, most browsers will not read files if they are not in the same directory or in a subdirectory with cinema_explorer.html
  • Optionally, each object in databases.json may contain a 'filter' field. This field is a regular expression to filter out dimensions in the database from being displayed on the chart in the viewer. Any dimension whose name matches with the regex will be filtered out.
  • By default, any dimension beginning with FILE will be filtered, but this can be overridden with the 'filter' field.

Viewing Data

  • Start the viewer by opening cinema_explorer.html in a web browser.
  • By default, the first database listed in databases.json will be loaded. To load a different database, select it in the "Database Select" drop-down at the top of the page and press "Load." (For large databases (300+ rows) a warning will be displayed).
  • The viewer is split into two sections, the top section contains the Parallel Coordinates chart (called the pcoord area for brevity) and the bottom section contains a component for viewing the data, either a spread of images, a scatter plot or a line chart depending on the selected tab (this is called the view area). The two sections can be resized by click-and-dragging on the black bar between them.

Using the Paralell Coordinates Chart

  • Each vertical axis on the chart represents one dimension in the database. Each horizontal (gray) line represents a row/data point. It crosses through each axis at the row's value for that dimension.
  • If a data point contains a NaN value, then the line will pass through the red area below the axis marked 'NaN.' If a data point has an undefined value, then the line will not be drawn through that axis.
  • Moving the mouse over a line will display a readout of that data point in the corner of the screen.
  • The axes can be re-arranged by click-and-dragging on their titles. If the database you loaded contains a valid axis_order.csv file, the top of the page will include drop-downs to select from preset orderings of the axes.
  • You can filter data by click-and-dragging vertically along an axis. This will create a selection and the chart will only show data that passes through the selected region on the axis. You can filter the selection further by creating selections on other axes. Remove a selection by clicking on the axis outside of the selected area.
  • The component in the view area will automatically update to show only the selected data on the chart.

Querying the Parallel Coordinates Chart

  • Click the '>' button on the left-side of the page by the chart to open the query panel. Click the '<' button to close it again.
  • The query panel contains a slider for every numeric (Integer or Float) dimension in the database. They can be used to select an arbitrary value along that dimension.
  • The checkbox next to each slider indicates whether or not to include that dimension in your query.
  • When you define an arbitrary data point using the sliders and checkboxes, a red dotted line will be drawn on the chart to represent the data you defined. Two light pink lines on either side of the red line give a rough approximation of the range of results that your query will return.
  • The threshold for the query (how close a data point has to be to one you defined to be included) can be changed with the "Threshold" input at the top of the panel. Notice that the two pink lines on the chart move closer to or further away from the red line as you change the threshold.
  • A query can be performed by pressing the "Find Similar" button at the top of the panel. If any data was found within the threshold, the selections on the chart will be automatically changed to encapsulate all the data found.

Using the Image Spread View

  • With the "Image Spread" tab selected, the view area contains the images for all the currently selected data.
  • Each box represents a selected data point and contains an image for every 'FILE' dimension in the database. If the dimension's filetype is a valid image (GIF,PNG or JPEG), then the image will be displayed. Otherwise, a warning will be shown saying that the file could not be displayed.
  • Moving the mouse over a box will display a readout of that data point in the corner of the screen as well as highlight the corresponding data point in the Parallel Coordinates Chart.
  • You can click on an image to view the full-size version. With the full-size version open, click anywhere on the screen to close it again.
  • The thumbnail size of the images can be changed with the "Image Size" slider in the top-right corner of the panel.
  • You can re-arrange the order of the data displayed in the view by using the "Sort By" drop-down to select a dimension to sort the data by. By default, data is sorted in ascending order, but it can be changed to descending by checking the "Reverse Sort Order" checkbox.
  • If the data shown extends beyond the screen, you can scroll to view the rest of the page of data.
  • If there is too much data to display on a single page, a window will appear at the bottom of the panel to allow you to browse through the different pages. The number of data points shown on each page can be changed with the "Results Per Page" drop-down menu.

Using the Scatter Plot View

  • With the "Scatter Plot" tab selected, the view area contains a 2D Scatter Plot with points for all the currently selected data.
  • Moving the mouse over a dot will display a readout of that data point in the corner of the screen as well as highlight the corresponding data point in the Parallel Coordinates Chart (and vice versa).
  • The two dimensions used as the x and y axes in the chart can be changed with the drop-down menus on the left-side and bottom of the panel.
  • If data contains NaN or undefined values in at least one of the two dimensions selected, the data will not be plotted and a warning will be displayed in the lower-right corner of the panel.

Using the Line chart

  • Add "image_measures" : ["prefix1", ...] to the databases.json entry of your dataset to set the used image measures.
  • Add "exclude_dimension" : ["prefix1", ...] to the databases.json entry of your dataset to exclude image measures.
  • Show/hide image measures using the checkboxes. The checkboxes with bold text are grouped image measures and can be used to select or hide a group of image measures.
  • Select an x-axis by the using the dropdown menu.
  • Select a range on the x-axis by holding down the left mouse button and dragging it.
  • The line chart can only be used if the dataset has a selected image measure. One uncertainty example is included (Example Uncertainty Bubbles), where the uncertainty is used as an image measure. The u_avg_local_contrast measure is the most meaningful measure here and should be explored by hiding other measures, showing a zoomed in version of that measure.

Changelog

V1.9.1

  • Update to v2.7.1 of Cinema Components Library
  • Embedded the Line Chart component as a tab

V1.9

  • Update to v2.6.1 of Cinema Components Library
  • Can specify 'query' and 'selection' parameters in Databases.json
  • Alternative json to Databases.json can be specified with HTTP paramters

V1.8

  • Now using v2.4 of Cinema Components library
  • Scatter Plot will remember which two dimensions you were viewing when changing tabs

V1.7

  • Now using v2.3 of Cinema Components library
  • Added Scatter Plot viewing mode

V1.6

  • Now using v2.2 of Cinema Components library
  • Added support for axis_order.csv files in databases

V1.5

  • Significant refactoring. Now used v2.0 of Cinema Components library
  • ImageSpread and Query Panel have be re-implemented as components in library

V1.4.3

  • Page selection widget changes to a more compact form when there are many pages of results
  • Added "Reverse Sort Order" option
  • Fixed results not being sorted correctly when changing the database being viewed

V1.4.2

  • Update to use v1.4.02 of Parallel Coordinates Component

V1.4.1

  • Now displays all FILE fields for each result
  • Fixed sorting not working properly when undefined or NaN values were involved
  • Update to use v1.4.01 of Parallel Coordinates Component

V1.4

  • Compatible with v1.1 of Cinema SpecD and v1.4 of Parallel Coordinates Component

V1.3.1

  • Added toggle for smoothing lines on chart

V1.3

  • Up to Spec with Cinema Spec-D V1.0. (Can read both Type I and Type II)

V1.2

  • Updated to use version 1.3.1 of Parallel Coordinates Component
  • Added feature to allow user to define a custom result, and query for results similiar to it.
  • Filetype and dimension filter are defined in databases.json

V1.1

  • Updated to use version 1.2 of Parallel Cooridinates Component

V1.0

  • Initial