ShapeWORKS - Project documentation (software) –

- 10, September, 2013

CERENA

This project is free and open-source software under GNU General Public License v3.*

It was developed using Python programming language with base libraries numpy,

wxpyhton and matplotlib**. All art was gathered from Icon Archive and is free for

non-commercial purposes***.

* See GNU_GPL_license.txt for more information.

** Respectively: http://www.python.org/ , http://www.numpy.org/ , http://www.wxpython.org/ , http://matplotlib.org/ .

*** See ICO\Art_License.txt for more information.

PURPOSE

ShapeWorks is a tool for complex shape interpretation and characterization in

geosciences. It’s main purpose was to facilitate the use of Sequential Indicator Block

Simulation created within research center CERENA* (using as base Liu and Journel

idea of block simulation)**.

** Procedure based on the idea published by Liu and Journel, 2008 - A package for geostatistical integration of coarse and fine scale data , Computer and

Geosciences

* http://cerena.ist.utl.pt/

Multiple algorithms were necessary to allow an easy man-machine interface (since

the interpretation is mostly done by “hand” or mouse pick on screen), therefore a

software was developed.

Mouse picked interpretation

of a channel in an acoustic

impedance map.

Binary mesh of the

interpreted channel. Most likely image from a

characterization with

sequential indicator block

simulation.

Probability map of the

simulations.

P10 and P90 uncertainty

evaluation over the

simulations.

MOVING AROUND THE SOFTWARE

Object manager (where you

chose most of the stuff).

Object viewer (updated

automatically by object

selection on object

manager).

First buttons on the toolbar. You use them to

import your data (there are four types of data

recognized by ShapeWORKS).

Context menus in the object

manager (called by right click button

on the object). You use them to call

for all sort of operations menus

(some specific to each object type).

1

2

3

4 version 1

version 1

MOVING AROUND THE SOFTWARE

Every time you pick an operation from the context menu you get a new frame (there are exceptions

such as export or delete).

4

5

From that new frame you can perform the operation you’ve called for (and sometimes even change the

object it was destined for).

So from these steps you can

pretty much access the great

majority of the things you can

do within the software. All you

need more is to know what

actually can be done within

the software.

ShapeWORKS objects

Symbol for point data (hard-data, scenario markers)

Symbol for mesh data (grid, and associated objects)

Symbol for block data (viewable by its centroids)

Symbol for web data (for block generation, viewable

as a mesh)

version 1

ShapeWORKS objects

13.0 7.0 2.0 21.0 35.0 1.0 25.0 69.0 1.0 36.0 109.0 1.0 … … …

X Y Value

Point appear as colored

dots in ShapeWORKS.

0.1552 0.1569 0.1578 0.1578 …

Value

Given number of blocks

in x and y, mesh appears

as a colored image.

BLOCK_FILE 99 block #0 0.94;0.00;0.00;0.05 0.3 55.0 0.0 55.0 1.0 55.0 2.0 … …

Probability for each bin

Error

Points in block

Block appear as colored

big dots in ShapeWORKS

(centroids).

Web appear as an image

with lines delimiting blocks.

55.000 110.000 0.000 110.000 0.000 27.500 55.000 110.000 0.000 27.500 110.000 165.000 0.000 27.500 165.000 220.000 27.500 55.000 0.000 55.000 … … … …

X0 X1 Y0 Y1

version 1

version 1 version 1

IMPORTING DATA

From the toolbar you can import your data from

the buttons above. When you push them you’ll

have a dialog to chose a file and than (right figure)

an import frame will appear where you have to

insert the details of the object.

In this case we’re importing a mesh (grid) and we

have to give the number of blocks in X and Y.

ShapeWORKS only accepts bi-dimensional data

with blocks size 1 and first coordinate 0.

CREATING DATA

Since some operators

need some kind of spatial

reference which is

automatically retrieved

from an object we must

have a reference (mesh)

in the first place. For this

reason there is a button

specific to create an

empty mesh.

You give the number of

cells in each direction and

than you click import

(actually it should be

create since nothing is

actually imported) to

create a new object

which will appear in

object manager.

CALLING FOR OPERATIONS

Each object has its own symbol which appears in the object

manager after import, facilitating identification. There are

operations specific for mesh (grid), points, web or blocks.

Most of these operators will create new objects of the same

or different kind which the user can choose the name or

use the default.

MESH OPERATIONS - ATTRIBUTES

We have a mesh in the object manager. Pressing right click mouse button will open the mesh context

menu from which we chose “Calculate attribute” operation.

This opens a new frame from which we can calculate a new attribute (shown right) from the chosen mesh

(shown left). Pressing preview will only show the result. Pressing calculate will actually create a new object in the

object manager with the name given in the “New name” field.

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2

There are several attributes. The one shown on in this

image is called equalization. The attribute, as well as its

specifics, must be chosen in the “X;Y size”, “Attribute”, and “Order; Rank; Percentile” fields.

Each attribute has its own parameters.

3

MESH OPERATIONS - BINARIZE

Binarize transforms a continues variable into an indicator or discrete

one by giving the same value to intervals of values in the range of the

mesh variable to be binarized.

1

In this particular variable binarizing is not really a fundamental step but it does clean our image a bit.

Notice you’ll have to use the sliders to select the percentile intervals to be binarized and, although its

called binarize, you can actually select more than two bins with the field “Number of bins”.

2

MESH OPERATIONS – PHASIC

INTERPRETATION

Phasic interpretation allows a manual creation of an indicator image by

mouse clicking on screen. 1

By clicking the “Interpret” button on the new frame you’ll get a smaller one (which can be maximized)

where you click the vertices of the shape you want to make. To close a shape just click the first vertices (it will

appear as a red dot instead of white). You can do more than one shape on the same phase (selected in the “Phasic interpretation” frame). To finish mouse click interpretation just press the “X” . When you finish

interpretation of all your phases just press the “Mark as object” button. Notice the preview panel will always show the interpretation of all phases with different

colors.

2

Example of phasic interpretation. 3

MESH OPERATIONS – POINT

SCENARIOS

Create point scenario is an algorithm to generate point data from a mesh. 1

Pressing the “Pick markers” button a new window will appear where you press in the locations you intend to have a point in a new point set. The selected locations will appear as red dots. Once the locations are selected just click the “X” to close the pick screen and then press

the “Mark as object” to put the object in the object manager.

2

POINT OPERATIONS – POINT

SCENARIOS

Now we have a point set in the object manager. Again right mouse click over it to get the point context

menu. The first option is “Use to create point scenario”.

1

This procedure is used when you want to add new points to an existing point set. I functions pretty much the same way as the one shown on the previous slide with the exception that it shows the older markers (as

big red dots instead of small) in the picking screen.

2

POINT OPERATIONS – GENERATE

WEB

A web is a new kind of object (used to create blocks). This procedure is

used to create a web from the point markers.

1

From this frame the for the blocks is created. If you chose as “Web style” constant than the point markers won’t be

used. But both VSQ (void quadtree selection) use the markers as can be shown on this preview. Notice the

smaller blocks are closer to the markers.

2

We’ll talk more about

webs in a moment.

POINT OPERATIONS –

INTERPOLATE FOR ERROR

Block error can be mapped, for example by using the distance to the markers. That is why this procedure is

used.

1

Using distance to poit set a map was created where the greatest value (error, for instance) is farther from the

points. 2

WEB OPERATIONS – CREATE BLOCK

SET

In this software version it’s a lonely position to the web options. From a

web you can create blocks. 1

Remember that

this is a web.

Here we can see the preview of a created block set (notice that only centroid are shown over a block map). Since we have blocks and point-set from the same study we can now do simulation which is a point operation.

2

BLOCK OPERATIONS – ERASE BLOCKS

Sometimes we have block set but its too dense or we just want to create high uncertainty areas. The solution is to erase some of the blocks from

the block set.

1

Erase works pretty much like phasic interpretation when you do shapes. But now every block whose centroid is

inside a shape is eliminated. 2

BLOCK OPERATIONS – ERROR

MAPPING

Finally error mapping lets you add some error to your blocks by using a

mesh to locate the error to the centroids.

1

This is an update to the object and not a new object. The block set will simply have error. Any mesh will do (it

doesn’t need to be a mesh from error interpolation) since you chose the minimum and maximum error and the map variable is linearly transformed into error and

retrieved to the blocks.

2

POINT OPERATIONS - SIMULATION

Since now we have both point and block data the simulations procedure

is possible. 1

Most parameters are pretty common to any sequential simulation procedure. For now you must give the

number of points/nodes and blocks to search for each to be simulated node, number of simulations and output directory (only the most likely image will be

automatically imported to the software).

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This block characterization

was the main objective for the

development of this software.

IMPORTANT INFORMATION

Some procedures where never included in the software although that was the

intention (the development phase was getting to long). This is the case for both

the mesh and point variogram. The buttons exist but they were never

implemented.

Also some other things were pointed out by the alpha users such as:

1) Visualizing blocks from its centroids is not easy.

2) “Use all VSQ” method not using all blocks available.

3) In the error mapping frame the first image is not being updated when the

object is changed.

4) While exporting some headers may not be correct.

NOTICE that this documentation was written in the 10th of September, 2013. It is

unlikely that this developer will add new functionalities to the software unless its

utterly necessary for the research project for which it was built to. The software is,

therefore, considered adequate to its purpose and its continuous development

halted.