WiP - UnityMol Database for lit spheres textures and more

Table of Contents

• Goals and objectives
• Roadmap
• Resources used
  • Key resources
  • Sphere repositories
  • Skybox repositories
  • Other resources
• Texture sets
  • To experiment
  • (Automatic) generation of lit sphere textures with povray
  • Manual generation of a texture set from an initial texture
    • Using Pixelmator method1
    • Using Pixelmator method2
• Data preparation
• Running a test PHP/MySQL environment
• PHP/MySQL implementation
  • Gitlab git repository
  • Fields to include in the tables
  • Implementation details
    • Images table
    • Generate SQL tables
  • Database features
    • Views
    • Troubleshooting
    • Inspiration

july-2016

Warning

This document is very much work in progress and not of any current use other than for its author. It started as a database specific for lit spheres textures, but evolved to a more general database that UnityMol can interact with.

Goals and objectives

Implement a database to handle the large number of customizable settings in UnityMol such as color palettes and collected sphere textures for lit sphere artistic lighting of scenes.

The settings we want to be able to retrieve from within UnityMol are:

• color palettes
• hballs lit spheres textures
• hballs lit spheres texture sets
• surface textures
• skyboxes

This is a generalization of an initial database version only for lit sphere textures. These settings are to be stored and managed within the database, for instance to rank them, sort according to criteria (e.g. hue for textures),..

Among the functionalities we want to be able to..

• rank the textures and select by several filters (eg ranking + image size + ??)
• generate the relevant data (scripts, raw asset resources etc) for UnityMol automatically

Roadmap

Todo:

umol: auto-generate snapshots for database

add table for color palettes

umol: retrieve color palettes from database

add table for surface textures

umol: retrieve surface textures from database

add table for skybox textures

umol: retrieve skybox textures from database

add table for hballs screenshot

add table for surface screenshot

add table for texture sets

umol: retrieve texture set from database

add table for comparisons and image similarity

add relationship between tables

generate custom database views with xataface

add thumbnails to database

cut out actual sphere for hue and gray determination so background doesn't factor in

move database to a publicly accessible server at the lab (eg ProxMox VM)

Emulate VMD, pymol, chimera, yasara looks and feel e.g, through color palettes and texture sets

Resources used

Key resources

• http://beaussier.developpez.com/articles/php/mysql/blob/ - tutorial on importing images in MySQL/PhP
• http://php.net/manual/en/function.basename.php - php docs on available functions etc.
• http://mkweb.bcgsc.ca/color-summarizer/?
• http://stackoverflow.com/questions/1518305/image-classification-detecting-an-image-is-cartoon-like/1518347#1518347
• http://cactuslab.com/imagemagick/
• http://xataface.com/
• http://hslpicker.com/

Sphere repositories

• Blender material repository :: http://matrep.parastudios.de/index.php
• Zbrush MatCap download library :: http://pixologic.com/zbrush/downloadcenter/library/

Skybox repositories

• https://www.assetstore.unity3d.com/en/#!/content/53752
• http://talesfromtherift.com/use-a-360-degree-panorama-as-a-skybox/
• https://www.reddit.com/r/Unity3D/comments/39vvup/3d_skybox_simple_but_very_effective_way_to_give_a/

Good search keywords (e.g. for Google image search) are: cylindrical projection / equirectangular panorama / skybox / cubemap

Other resources

• http://www.controlledvocabulary.com/imagedatabases/programs.html - about image cataloging tools
• http://www.phpform.org/formbuilder/index.php
• http://phpformgen.sourceforge.net/
• http://fpmgonline.com/

Texture sets

To experiment

This is a collection of sphere texture ideas:

• plankton
• shaded sphere
• charcoal !
• pastel
• aquarelle
• soap bubbles
• goutte / drop
• cross-hatch
• hatching
• 101 dalmatiens
• ink
• ballon gonflable
• gems
• comic
• Schakal 97 sphere

(Automatic) generation of lit sphere textures with povray

Generated a Makefile from examples on the net to render a color set, currently based on the pastel colors in UnityMol, with povray. Example usage:

make 4.png
make umol-inst

When textures/pigments/materials have many reflections, the scene ground, background and lights become very important.

Todo:

define relevant colors for palette, eg based on Pastel, Watercolor, etc. ; also relevant for Pixelmator method2

Todo:

find good sphere textures/pigments

Todo:

further tune Povray scene, in particular background, ground planes and lights

Manual generation of a texture set from an initial texture

Using Pixelmator method1

1. Image > Remplacer la couleur
2. Couleur > select dominant color from image with color picker
3. Etendue > extend the color selection to a maximum (200)
4. turn colored wheel until appropriate color is obtained
5. evtl. adjust Saturation and Luminosite

Using Pixelmator method2

1. Open texture
2. Evtl. treat the original image, such as desaturation of remaining color
3. Create new layer: Calque > Nouveau Calque
4. Fill layer with the desired color
5. Choose mixing option, e.g. Obscurcir, Lummiere tamisee, Couleur, ..
6. Save snapshot

Data preparation

• added textures currently within UnityMol
  (OK)
• find duplicate filenames (find_dupnmes.sh)
  (OK)
• check we have only image files left (find_non_image.sh)
  (OK)
• generate uniform filenames
  • remove spaces within filenames (replace_spaces.sh)
    (OK)
  • remove quotes within filenames
    (OK)
  • remove special characters (parenthesis) within filenames (replace_special.sh)
    (OK)
• detect non-square textures and manually adjust them to be of equal dimensions
• run UnityMol in batch mode and generate a snapshot for a hyperballs molecule textured with the given sphere and for a surface textured with it
• sort/store according to filenames/directory names
• tool(s) to modify/update existing entries through scripts (eg update ranking based on directory)

Running a test PHP/MySQL environment

• using MAMP to run a local environment from http://localhost:8888/MAMP/index.php?language=French
• administer through http://localhost:8888/MAMP/index.php?page=phpmyadmin&language=French
  • I had an issue with the plain MAMP installation and had to install a 4.x beta to get it work. Finally running MAMP Version 3.5.1 (3.5.1) seems to work now.
  • I had to switch to PHP 5.6.23 and activate the mysql module extension manually
• Apache root is in /Applications/MAMP/htdocs/

PHP/MySQL implementation

Check it out in the local environment from http://localhost:8888/lit-spheres-db/

I added a DB feature to UnityMol so that textures can be fetched by their ID number from this database through the apercu.php PHP page, from within the UnityMol application.

Gitlab git repository

• website is https://gitlab.galaxy.ibpc.fr/baaden/lit-spheres-db

Fields to include in the tables

• is_gray field!
• unique identifier/number
• user ranking (1 to 5 stars)
• image size
• lit sphere snapshot
• keywords (material, technique, ..)
• dominant color as in google image search
• Read support for EXIF (digital camera info) annotations
• Read support for IPTC annotations
• Read ICC color profiles?
• Color Histogram Viewable?
• Ability to set Highlight /Shadow Thresholds?
• toggles: hballs-proof, grayscale-proof, surface-proof, texture-series, in-unitymol

Make a separate table for small molecule snapshots

Make a separate table for surface snapshots

Make a separate scheme for inventorizing sphere series

Implementation details

Images table

Current fields:

Field	Type	Description
img_id	int	unique identifier, primary key
img_nom	varchar 50	(file)name of the image
img_dir	varchar 100	directory where image resides
img_taille	int	file size
img_type	varchar 25	what type of image? Eg JPG, PNG, ..
img_desc	varchar 100	short description of the image
img_blob	medium blob	the actual image data
img_pixels_x	int	image width in pixels
img_pixels_y	int	image height in pixels
img_rating	enum 1-5	One to five star rating of the image
img_avg_hue	int	Average hue of the image for sorting according to color
img_avg_gray	float	Average gray value (saturation) to filter grayscale images, which should have a value very close or equal to zero

Fields to add:

Field	Type	Description
umol_legacy	bool	present in UnityMol?
img_n_votes	int	number of votes received for this image
img_avg_vote	float	continuously updated average vote for this image
thumb_64	blob	small thumbnail picture for this image
thumb_256	blob	bigger thumbnail

Generate SQL tables

CREATE TABLE `images` (
    `img_id` INT NOT NULL AUTO_INCREMENT ,
    `img_nom` VARCHAR( 50 ) NOT NULL ,
    `img_dir` VARCHAR( 100 ) NOT NULL ,
    `img_taille` VARCHAR( 25 ) NOT NULL ,
    `img_type` VARCHAR( 25 ) NOT NULL ,
    `img_desc` VARCHAR( 100 ) NOT NULL ,
    `img_blob` MEDIUMBLOB NOT NULL ,
    PRIMARY KEY ( `img_id` )
)

CREATE TABLE `hball_snaps` (
    `img_id` INT NOT NULL AUTO_INCREMENT ,
    `litsph_ref` INT NOT NULL ,
    `img_nom` VARCHAR( 50 ) NOT NULL ,
    `img_dir` VARCHAR( 100 ) NOT NULL ,
    `img_desc` VARCHAR( 100 ) NOT NULL ,
    `img_blob` BLOB NOT NULL ,
    PRIMARY KEY ( `img_id` )
)

CREATE TABLE `surf_snaps` (
    `img_id` INT NOT NULL AUTO_INCREMENT ,
    `litsph_ref` INT NOT NULL ,
    `img_nom` VARCHAR( 50 ) NOT NULL ,
    `img_dir` VARCHAR( 100 ) NOT NULL ,
    `img_desc` VARCHAR( 100 ) NOT NULL ,
    `img_blob` BLOB NOT NULL ,
    PRIMARY KEY ( `img_id` )
)

Useful SQL snippets

$db = mysqli_connect("localhost","root","","DbName"); //keep your db name
$sql = "SELECT * FROM products WHERE id = $id";

Show DDL statement:

show create table litspheres.images;

Database features

• import textures through a command-line php script ()
• generate input files (eg txt) for UnityMol
• be able to identify duplicates (not only exact but also approximate ones)
• detect toon-style textures

Views

• generata an html page with a 4 column and infinte row view of
  1. gen image on the texture
  1. texture image
  1. hballs with texture screenshot
  1. surface with texture screenshot
• be able to filter the above webpage, eg on image pixel size, ranking, hue etc.

Troubleshooting

• issues with ImageMagick.. install recent version (6.9+)
• get hue -> shell/php script cascade
• get grayscale `convert '$image_path' -colorspace HSL -channel g -separate +channel -format '%[fx:mean]' info:`

Inspiration

• try imagemagick from php (http://stackoverflow.com/questions/23922654/detect-if-image-is-grayscale-or-color-using-imagick)

$imagick = new Imagick($image_path);
$imagick->transformImageColorspace(imagick::COLORSPACE_HSL);
$saturation_channel = $imagick->getImageChannelMean(imagick::CHANNEL_GREEN);
$saturation_level = $saturation_channel['mean']/65535;