R/W model

R/W model

AppMgr

AppMgr

open Dialog

open Dialog

Dialog Box

Dialog Box

Panel?

Panel?

Validation

Script

Program

Const

Initializer

Updater

load

save

load

save

get

set

get

set


eraser

ccderaser

x

x

x

x

x

x

x

x

x

x

x


xcorr

tiltxcorr

x

x

x

x

x

x

x

x

x

x

x


prenewst

xftoxt














newst













track

beadtrack

x

x

x

x

x

x

x

x

x

x

x


align

tiltalign

x

x

x










newst

newst














mrctaper













findsec

findsection













sample

newst













tilt

tilt













tomopitch

tomopitch

















Standard input parameter => attribute mapping

Beadtrack

Number

Description

Attribute name

Attribute type

1

Image file name

inputFile

String

2

Piece list file name if the file is montaged (or if it is digitizedout of order), otherwise enter a blank line

pieceListFile

String

3

Name of model file with starting bead coordinates

seedModelFile

String

4

Name of output model file

outputModelFile

String

5

List of views to skip over. Model objects will pass through these views; points will need to be added by hand afterwards. Ranges may be entered, e.g. 1,4-6. Views are numbered from 1.

viewSkipList

String

6

Angle of rotation of the tilt axis in the images; specifically, the angle from the vertical to the tilt axis (counterclockwise positive).

imageRotation

double

7

Number of sets of views to treat separately from the main set of views when automapping the tilt angle and magnification variables. Enter 0 if all views can be treated together when automapping. These sets would typically be lists of views that were reshot.

nAdditionalViewSets#

int

8

IF a number other than 0 was entered, next enter one line for each separate set, giving a list of the views included in that set. Ranges are allowed here.

additionalViewGroups

String[]

9

-1 to enter individual tilt angle for each view, 1 to specify a starting and increment tilt, or 0 to read tilt angles from a file

tiltAngleSpec

TiltAngleSpec

10

IF you entered 1, next enter the starting and incremental tilt angles. IF you entered -1, enter the tilt angle of each view. IF you entered 0, enter name of file with tilt angles#

tiltAngleSpec

TiltAngleSpec

11

The default number of views to group together in solving for tilt angles, and the number of ranges of views that should have some grouping other than the default. If a negative number of views is entered, then reshoot sets will NOT be segregated from the rest of the views in this default mapping.

tiltAngleGroupParams

FortranInputString

12

IF you entered a non-zero number of ranges to be treated separately, then for each such range, enter the starting and ending view number and the number of views that should be grouped in that range. If a negative number of views is entered, then reshoot sets will NOT be segregated from the rest of the views in this range

tiltAngleGroups

String[]

13

The default number of views to group together in solving for magnifications, and the number of ranges of views to group in some other way.

magnificationGroupParams

FortranInputString

14

If you enter a non-zero number of ranges, then for each one, enter starting and emding view numbers and group size. Note that extensive grouping of tilt angle and magnification variables is desirable, but the grouping should be adjusted if there are known places where magnification or the deviation from the ideal tilt angle changes abruptly.

magnificationGroups

String[]

15

Minimum number of views with bead positions available before trying to do a tilt alignment. To skip the tilt alignment computations, set this to a number higher than the number of views.

nMinViews

int

16

Radius for centroid calculation, and 0 if beads are darker or 1 if they are lighter than background. The radius need not be a whole number; e.g., 4.5 is acceptable.

fiducialParams

FortranInputString

17

1 to fill in gaps in the seed model, or 0 not to fill in gaps

fillGaps

boolean

18

Maximum size of gap to create in the model. If a bead cannot be tracked through some views, the tracking may be resumed as long as the gap thus created is no larger than this amount.

maxGap

int

19

Minimum range of tilt angles for which data must be available before trying to find the angle of the tilt axis, and minimum range of angles required before trying to solve for tilt angles. Suggestedvalues are 10 and 20.

tiltAngleMinRange

FortranInputString

20

X and Y dimensions of the box used to search for a bead (32,32 suggested)

searchBoxPixels

FortranInputString

21

Maximum number of views over which to average a bead (4 suggested) A running average is kept of the appearance of the bead over the most recent views examined; this parameter specifies the maximum number of views averaged.

maxBeadsAvg

int

22

Number of positions to use for extrapolating the bead position to the next view, and minimum required to do extrapolation rather than simply taking the mean of positions on the last few views. Suggested values 7 and 5.

fiducialExtrapolationParams

FortranInputString

23

Fraction of mean bead integral, and number of standard deviations below mean, to use as the criterion for when to attempt a rescue based on bead density.

rescueAttemptParams

FortranInputString

24

Distance in pixels away from expected position at which to attempt a rescue based on excessive distance

minRangeRescuePixels

int

25

Factors by which to adjust (relax) the density criterion when trying to rescue. Enter one factor for density rescue and one for distance rescue. A value of 1 does not relax the criterion.

rescueRelaxationParams

FortranInputString

26

Criterion distance for deletion of a point after tilt alignment. Points with residuals greater than this amount will be deleted on the first pass, and a rescue search performed on the second pass.

residualLimit

double

27

Factor by which to relax the density criterion on the second pass, and maximum distance to search from the expected position on this pass.

secondPassParams

FortranInputString

28

Maximum and minimum number of changes in mean residual to use in finding the mean and SD of changes in the mean residual for a bead as more points have been added. Suggested values 9 and 5.

meanResidChange

FortranInputString

29

Minimum change in residual, and criterion number of SD's from the mean residual change, to require for deletion of apoint on pass 1 or 2.

deletionParams

FortranInputString





tiltalign