Elliptical Fourier Analysis - OrigOutline Worksheet & Importing Data


Worksheet Structure
Outline Data Limitations
Importing Outline Data

Worksheet Structure

Data associated with each valve outline are stored in two adjacent columns, such as, A & B, C & D, ..., which are alternately shaded and unshaded in pairs (see Figure below). Outline data for any new valve are imported into the first pair of empty columns moving to the right across the worksheet.

Rows 1-5 of the OrigOutline worksheet contain basic information about the valve and its outline; rows 6-9 are reserved for the coordinates of the Orientation Landmarks.

Row\Col
LEFT (e.g., A)
RIGHT (e.g., B)
1
 sample name or number valve ID number assigned by CDiatomEFA program
2
 image path & directory [tpsDIG2 only] valve ID number [assigned only in tpsDIG2]
3
 taxon name  
4
 image file name scaling factor [tpsDIG2 only]
5
 digitization mode. number of coordinates ]
6
 Orientation Landmark 1
(x-coordinate)

Orientation Landmark 1
(y-coordinate)
7
 Orientation Landmark 2
(x-coordinate)		 Orientation Landmark 2
(y-coordinate)
8
 Orientation Landmark 3
(x-coordinate)		 Orientation Landmark 3
(y-coordinate)
9
 Orientation Landmark 4
(x-coordinate)		 Orientation Landmark 4
(y-coordinate)
10
This grayed row serves as a header for the beginning of outline coordinates in row 11 and holds only "x" and "y" labels for the coordinates in their respective columns.
11-
Outline coordinates begin in row 11, the x-coordinate in the left column, the y-coordinate in the right column, and proceed down the worksheet. Rows 11-7511 in all columns on the worksheet are reserved for outline coordinates.
 

None of the above descriptors is necessary to run the program as long as there are coordinate data in rows 11 on down; however, the user will be find it difficult to interpret the results without at least some of them. Minimally, valve (specimen) ID numbers will be assigned by the CartesianDiatom-EFA program (cells B1, D1, F1, ...).

In the absence of an entry for a scaling factor (row 4), the program will default to using the value "1".

Scaling factor: All imported values are mulitplied by this factor; a value of 1 leaves all numbers unchanged; this is the default value. Landmark and outline coordinates are exported from tpsDIG2 in pixel units; the scaling factor is used to convert pixels to micrometers (or whatever units in which you are working), where, micrometers = scaling factor * pixels. The scaling factor is based on the calibration made at the beginning of the image analysis session in tpsDIG2. So, x, y coordinates will normally have the units of micrometers when they are entered in the Excel cells. For ImageJ the units in which the specimens were digitized (pixels, micrometers, etc.) will be the units in which they will be entered on the Excel worksheets.

Orientation Landmarks (OL) 1 and 2 are user-chosen coordinates defining a line, commonly the apical axis, used to normalize differences in rotation among outlines. All outlines are initially rotated to bring this "orientation line" to a slope of zero and to coincide with the x-axis. In the absence of these Orientation Landmarks outline orientation is normalized based on the slope of the first principal axis of all the coordinates in the original outline. Valve length is calculated as the distance between Orientation Landmarks 1 and 2, if they are present. Orientation Landmark 3 is used to rotate the specimen around the apical axis formed by Landmarks 1 and 2, such that in the final orientation it is "above" the axis, i.e., OL 3 has a positive y-coordinate. Orientation Landmark 4 permits the user to define the center of the specimen. The point chosen as the center of the specimen will be that point on the apical-axis defined by the perpendicular projection of OL 4 onto the axis; OL 4 may thus be used to define the location of a transapical axis.


The Digitization Mode classifies the outline as to the image digitizing program and the tools within the program used to generate the outline coordinates:

  ijC Crosshair Tool in ImageJ
  ijW WandAuto Tool in ImageJ
  tpsL Landmark Tool in tpsDIG2
  tpsC Curves Tool in tpsDIG2
  tpsO Outline Tool in tpsDIG2


 




Outline Data Limitations

The OrigOutline worksheet holds up to 128 contiguous sets of outline data (= 256 columns with 2 columns per valve data set); this program was written before Excel 2007 was released, which accomodates many more columns.

There must be a set of outline data in columns A & B or the program will abort in attempting to execute the EFA. In batch mode the program will process all outlines (pairs of columns) until it reaches the first blank column (searching to the right on the worksheet from column A), and then it stops. When the worksheet is full, copy the data to a new worksheet named anything except "OrigOutline". Confirm that the data were copied successfully, and then clear the data from the "OrigOutline" worksheet, that is, clear the contents of the worksheet cells; if you by mistake also clear the formatting, then click on the Reformat button on the Import Outlines form. The program will only read data for EFA from the OrigOutline worksheet. So you are limited to processing 128 valves (specimens) at a time.

The number of x,y coordinates read in each column is limited to 7500.
The program stops reading coordinates when the first blank row below row 10 is encountered.
Therefore, all rows of x, y coordinates of an outline must also be contiguous

Importing Outline Data

In the Data Source Frame on the Import Outlines Form select one of the 3 option buttons or enter the data manually onto the worksheet:

tpsDIG2 & ImageJ
Custom
Manual

tpsdDI2 & ImageJ

Outline data are imported from an appropriately formatted *.tps or *.txt file containing one or many specimens.

(1) From the CDiatom Menu, select Outlines | Import
(2) On the Import Outlines Form in the

(i) Data Source Frame: select either tpsDIG2 or ImageJ as is appropriate to the structure of your data file.
For ImageJ-derived files only, select the tool used to digitize the outline: Crosshair (=Point) Tool or WandAutoMeasure Tool. The tool used in tpsDIG2 can be determined from the *.tps data file.

If the 4 Orientation Landmarks have been included in the data file, then the Orientation Landmarks box should be checked. This is the default option. Uncheck it if the 4 landmarks are absent.

The require formats of the imported files are explained in Generating Outlines & Data Files in the program documentation.
(ii) Sample: This sample code/name will be used for all imported valves.
(iii) Taxon: This name will be used for all outlines imported in a batch.
(iv) User ID: The users's name or initials.
(3) Click on Get Data button to import the outline data. The user will be asked to select the data file to be imported.
(4) Data can be edited after they are imported using conventional Excel tools.
Delete Seletion button: Valves (specimens) can be deleted from the OrigOutlines worksheet by selecting their columns and then clicking this button on the form. Such action results in not only deletion of the data selected, but a shift in the remaining data to close the gap on the worksheet and a re-numbering of the valve's ID assigned by the program.
Reformat button: If you clear columns using Excel tools, clear only their contents. If you mistakenly clear the formatting (font style, font size, row and column shadings, ....), clicking this button will re-establish it.











 

 

 

 

 

 

 

Custom

This option requires a customized procedure to import the data from files with a specific format. Customized procedures can be supplied by CartesianDiatom at diatom.org; we do so on limited basis. If they are relatively simple, the addition is free; if not, there is a charge. Use of the customized procedure requires entry of a three-letter code in the textbox adjacent to the option; these codes are supplied with the procedures we provide.

If an unrecognized code is entered, the Import Outlines procedure aborts.


Manual

Outline data can be entered directly into Excel cells by typing, using cut/paste tools or any combination of them, as long as they conform to the worksheet cell assignments and constraints described in Outline Worksheet Structure and Outline Data Limitations. If there are no Orientation Landmark coordinates, simply leave those cells blank.



Updated 6 July 2009 RKE