Fie:
Fabrication d’imagerie extraordinaireFie:
Fabrication d’imagerie extraordinaireTable of contents
Fie is a programme for various image-editing and related tasks. Its main purpose these days is for 3-D segmentation.
The drawing operations in Fie can be used to trace structure outlines in stacks of images. The outlines are maintained in text files suitable for subsequent surface triangulation using Tr3, for either visualization (VRML) or finite-element simulation.
The use of open contours (in addition to the usual closed contours) facilitates the controlled handling of complex structures with shared surfaces. An important feature is that one can specify that a line should start and/or finish at the start or finish of some other line. This provides a mechanism for specifying and ensuring topological continuity and integrity. This continuity is specified for a particular line within groups of slices, and is displayed graphically, so the user can visually verify connections. Since the connectivity often changes from slice to slice, a mechanism is provided to specify Joins across such divisions, and Caps can be defined to close the beginnings and ends of 3-D surfaces.
The alignment operations in Fie can be used to align histological serial sections for subsequent segmentation and 3-D reconstruction.
The .tr3 file produced by Fie contains
specifications for visualization and mechanical properties together with the
basic geometry, so complete models can be generated in one
operation.
Two different colours (an editing
colour and a separate rendering colour)
and a transparency can be specified for each line.
Nodal boundary conditions (whether free or
clamped) and applied pressure can be specified. Material properties for the 3-D
surfaces can be specified for each line by reference to a list of
material types, and specification of thickness.
A syntax is available for specifying the triangulation of subsets of a whole model, and for specifying different mesh resolutions for different parts of a model or for different versions of a model. Algorithms have been developed for resolving start-at/finish-at dependencies and detecting circular indeterminacy, and for detecting and removing duplicate nodes (essential to ensuring mechanical continuity for simulations).
Triangulated models are generated in both VRML format (for interactive visualization) and SAP format (for finite-element simulation). The VRML models include dynamic labels with two levels of granularity, one well suited for debugging and the other for teaching purposes.
Additional features include:
Fie is implemented in Fortran. It was originally developed under VMS and later under Unix for Alpha. It is currently being developed under Debian GNU/Linux for x86 and x86_64, and (alas) under Microsoft Windows; the binaries are available for downloading below. It can be used for any purpose as long as I am informed of its use. So far there is no documentation beyond what you're looking at.
Fie has been evolving gradually since 1989, and I have added various features as I needed them for various projects. (The ‘F’ originally stood for Fancy or Fortran or Funnell, depending on the phase of the moon and other factors; these days maybe it would stand for Funky. The ‘IE’ stood for Image Editor. These days we don't use Fie much for image editing, but more for creating 3-D models, so I came up with Fabrication d'imagerie extraordinaire as a new excuse for the name Fie.)
Section 2 explains how to install the software. Section 3 gives some general information about the graphical user interface, file saving and automatic backups. Section 4 then presents the functions of every menu and submenu. Section 5 describes the detailed format of the .tr3 file produced by Fie; although much of the file is created and modified by Fie, there are some sections which still need to be created and edited directly by the user.
Section 6 presents an example to illustrate the use of Fie. Section 7 presents a history of changes to Fie.
[New] When new information is added to this documentation, it is flagged as [New]. You can find new items by using the Find feature of your Web browser to look for ‘[New]’. If you hover over the [New] indicator with the mouse, your Web browser will display the date when the item was added or modified.
Either download the Fie executable for 32-bit Windows (about 1.5 Mbytes) or (if your computer is part of the McGill BME network) create a shortcut to the executable on probeShare. Follow the general instructions for installation of Dip software.
If you are using a copy of Fie installed on your local hard disk,
then you must also provide the Glib library and two
associated libraries. Download the following DLL files into the same
directory that fie.exe is in:
Fie has been used with MS Windows 95, 98, NT, 2000, XP and Vista.
If your computer is part of the McGill BME network, create a
symbolic link (ln -s) to the executable on
probeShare. Otherwise download the Fie executable from here and do
chmod u+x fie to make it executable.
Follow the general instructions for installation of Dip software.
Fie has a menu-based graphical user interface. The interface is identical under different operating systems. As shown at right, the interface consists of
Repaint button in the lower left corner which can
be used to repaint the screen if it becomes corrupted for some
reason (this should not happen)
Repaint button
where queries and messages are displayed
See the Dip documentation for a general discussion of how to use the menus. Note that every menu button has a shortcut key, indicated by underlining in the button label.
In some cases when a menu is displayed in Fie, you can either
click on one of the menu items or click in one of the image windows.
For example, when selecting a line for some purpose, you can either click
on the appropriate button in the menu or click near the line within
either the main image window or the overview window.
When Fie saves a file, if a file already exists with the same name
then the old file is renamed by adding a version number. The version
number is of the form #n# and is appended to the
file name. For example, if three versions of the file
test.tr3 exist, called test.tr3#1#,
test.tr3#2# and test.tr3, when a new version
is saved it will be called test.tr3 and the previous
version will be renamed to test.tr3#3#. If you ever need
to recover an older version, just use your operating system to delete
the later version (or rename it to something else if you're not sure)
and then rename the version you want by removing the version number.
As you are doing operations (or
operations)
Fie will automatically back up the
.tr3 file from time to time. The backup is done to a file called
fie_tr3.tmp in your HOME directory. If something goes wrong
during a session (e.g., Fie crashes or your computer crashes), or
you accidentally quit without saving your latest changes,
you can recover the contents of the
last automatic backup:
fie_tr3.tmp from
your HOME directory to the directory where your .tr3 file normally
resides.
fie_tr3.tmp to have the name of your normal .tr3 file.
The frequency with which automatic backups are done can be controlled by the item in the settings menu (which is available from within several menus). Specify how many interactive operations you want to have happen between backups.
| File |
| Set |
| Focus |
| Filter |
| Paint |
| Draw |
| Stats |
| Tailor |
| Combine |
| Surface |
| Quit |
| ? |
The following summarizes the functionality of Fie, organised according to the items on the top-level menu (shown at right).
includes file opening, saving, etc.
includes a number of settings. Other than font size, the important ones for most current uses are included at various places under .
allows the specification of focus regions for operations like filtering and statistics. includes various image-processing operations.
provides a number of image filters.
provides some simple pixel-painting operations.
provides a sophisticated set of drawing and segmentation operations.
provides various kinds of statistics for pixels and clusters of pixels.
provides a number of image operations like resizing, reshaping, distortion removal and alignment.
produces a combination image by combining selected images from a stack of images, using either average or maximum pixel values.
generates a 3-D surface from a stack of images using a user-specified threshold and a marching-tetrahedra algorithm. The surface is output as a VRML file.
just quits, after checking for any unsaved modifications, and with saving of session settings.
Note that all of the
contour-tracing things are located under
, and the alignment tools for stacks of
histological images are under .
| Open |
| New |
| Import |
| Save |
Fie can read in several different types of files, as described in
the following subsections. When Open is selected from the
File menu, Fie will display a list of recently opened
files (if any). If the desired file appears on that list, select it.
If not (or if no such list is available) click on
or use the + shortcut key.
Fie will then display a list of the
subdirectories and files within some starting directory. (The
particular starting directory used may depend on which files have been
opened recently, on whether the HOME environment variable
is defined, and on the phase of the moon.)
Browse to find the file to
be opened and click on it.
Currently (for historical reasons) Fie handles JPEG images
differently from the way it handles other types of images. JPEG images
can be handled only by opening a .tr3 file which includes
a list of a set of JPEG images. For other types of images, open the
image file itself; Fie will then automatically open the corresponding
.tr3 file if it finds one with the same name as the image
file.
For new datasets that we create ourselves, the format of choice is JPEG. It provides greater image compression and more flexibility.
.jpg)Fie can read both grey-scale and colour JPEG images. A 3-D stack consists of a set of image files, one image for each slice.
The images in a stack must all have the same numbers of rows and columns of pixels.
The usual practice is to have all of the image files
in a subdirectory of the directory where the .tr3
file is. The name of that subdirectory, and the names of the
image files, are specified in the SLICES
section of the .tr3 file.
.tif)Fie can read several types of TIFF-encoded images: 8-bit grey-level or paletted, and 24-bit RGB, either uncompressed or with run-length-encoding compression.
A 3-D stack of TIFF-encoded images must be stored in a single multi-image TIFF file. The images must all have the same numbers of rows and columns of pixels, and must all be of the same type.
If the file name.tif is opened, then Fie
will look for a file name.tr3 in the same
directory, and open it if found.
.raw)Fie can read images, or stacks of images, stored as raw byte streams.
If the file name.raw is opened, then Fie
will look for a file name.fie in the same
directory. This is an auxiliary plain-text file which provides
the image size and other characteristics.
It contains lines with the following syntax:
NPIXH nh
| nh = no. pixels horizontally |
NPIXV nv
| nv = no. pixels vertically |
NSLICE ns
| ns = no. slices in image stack |
NBITS nb [nbu [{
| nb = no. bits/pixel = 8 or 16. If nb=16, then nbu = no. bits actually
used/pixel = 8 or 16; and byte order is specified as either SWAP or NOSWAP.
Default no. bits/pixel = 8. If no. bits/pixel = 16, default no. bits
used/pixel = 16 and default byte order = NOSWAP.
|
TYPE t
| t = image type: GREY or RGB.
Default = grey.
|
Any line which starts with a semicolon is interpreted as a comment.
Example. A stack of 8-bit grey images might have this
.fie file:
;15516.fie
|
NPIXH 228
|
NPIXV 186
|
NSLICE 168
|
NBITS 8
|
TYPE GREY
|
If no .fie file is found, Fie will query the user
for the image characteristics.
Fie
will also look for a file name.tr3 in the same
directory, and open it if found.
.den)These are grey-level files as used in
VolPack.
The .den file format includes a header which specifies, among
other things, the numbers of rows, columns and slices.
If the file name.den is opened, then Fie
will look for a file name.tr3 in the same
directory, and open it if found.
| Image |
| Tr3 file |
Fie can generate test images or new .tr3 files.
Fie can generate test images and image stacks with user-specified size and various contents:
Fie can generate a new .tr3 file corresponding to
an existing set of .jpg files. It will first ask
to confirm that you have such a set of files. If you answer
, it will ask you to select the
first file in the set, and then to select the last file in the
set. All the files must be in the same directory.
Fie assumes that the filenames of every file in the set
consist of the same text followed by a sequence number (with leading zeros if
required), e.g., cat01.jpg, cat02.jpg,
… cat20.jpg. It asks what increment to
use for the sequence numbers; the default is 1, but you could
specify, e.g., 2 if you only wanted to use every second image,
or if you only had cat02.jpg, cat04.jpg, etc.
Fie will then ask for the file path and name to use for the new
.tr3 file. It will offer a default path and name based on
the path and names of the image files.
Fie will then ask for the z coördinate to use for the first slice, and for the z spacing between slices. It will then ask for the x-y pixel size, which should be measured in the same units as the z coördinates. If you don't know the actual dimensions at this point, you can just accept the defaults and then adjust things later.
Finally, Fie will ask for your initials and a line of comment, and
create the new .tr3 file. The file can now be opened
using .
| SurfDriver v. 2 (.txt) |
| SurfDriver v. 4 (.txt) |
| MRP |
Fie can import contours traced by SurfDriver. The contours
must first have been Exported from SurfDriver to .txt files,
and the corresponding set of .bmp files used by SurfDriver must
have been combined into an image stack
(TIFF, raw or .den).
To import the contours, first use to open the image stack. Then do . You will then be asked for
0 13502 27000 [landmarks] [nodes] 2.0781 2.3786 1.9818 2.0789 2.3786 1.9924 2.0753 2.3647 1. … 2.4724 2.9489 2.3444 2.468 2.9474 2.3474 2.4756 2.9458 2.3422 [surface] 1 2 3 1 3 4 5 6 7 5 7 8 … |
Fie can import .mrp files. This is a rather primitive
surface-definition file format; an extract from an example file is shown
on the right.
Fie assumes that an image-stack file is available;
the stack should be opened before doing the import.
Landmarks are ignored. It is assumed that nodes come before triangles.
Fie can save data in various formats:
See the descriptions above in the
Open section for more details
about some of the file formats.
When using Fie to do image segmentation, the only file that needs
to be saved is the .tr3 file. The images themselves are
not modified.
Saving a stack of images is a convenient way of converting the images to a different format, e.g., converting a TIFF or raw image stack to a set of JPEG images. When a stack of images is saved, they will not include any changes made to them within Fie.
| Grey |
| False colour |
| 3-3-2 |
| 5-6-5 |
| RGB-CMY |
| B & w |
| TIFF |
Choose from several palette options. For 3-D segmentation, the Grey palette is the usual choice.
For grey-scale images, the palette controls how the grey levels are displayed, possibly with colour. Normally one would choose either a grey-level palette (possibly specifying a gamma and thresholds) or a false-colour palette.
For full-colour (3 bytes/pixel, RGB) images, the grey-level mapping defined by the palette is applied to any pixel which is a shade of grey, i.e., for which the red, green and blue values are the same.
For paletted images (1 byte/pixel colour) the selected palette controls
the mapping from the single-byte pixel value to colour.
Currently this applies only to TIFF images which are paletted;
such an image will set up its palette when it is read in.
| Black | ||||||
| White | ||||||
| Gamma | ||||||
| Blue | ||||||
| Yellow | ||||||
| Quit | ||||||
| [< | << | <( | ? | )> | >> | >] |
The grey-level palette controls the mapping of 8-bit pixel values
to displayed grey levels or colours.
A submenu and thumbwheel are provided for adjusting the black level,
white level, gamma, low (blue) threshold and high (yellow) threshold.
The default palette just maps
pixel values of 0-255 linearly to the same range of greys.
allows adjustment of the pixel value below which all values are displayed as completely black. By default the black level is 0.
allows adjustment of the pixel value above
which all values are displayed as completely white. By default the
white level is 255 (i.e., the maximum pixel value).
| 
|
| γ=0.5 | γ=1.5 |
and
correspond to two thresholds.
Pixels are set to shades of
blue if their values are less than the
first threshold, and to shades of yellow if their
grey-level values are greater than the second threshold.
Such thresholds can be used to assist segmentation.
The sample image shown here has the thresholds set to
differentiate among bone, soft tissue and no tissue.
As here, the distinction will generally be only approximate
and in itself cannot provide accurate segmentation.
False-colour palette ranging from black
through blue, green and yellow to white.
This palette provides
monotonically increasing brightness. It can be used
to enhance visual contrast and to make images prettier.
RGB encoded with 3, 3 and 2 bits, respectively
RGB encoded with ranges of 0 to 5, 6 and 5,
respectively
Palette starting with black and white; then
saturated red,
green, blue, cyan, magenta and yellow; then six
unsaturated colours having combinations of
0, 0.5 and 1 for r, g and b; then two greys;
then 30 shades each for grey, red, green, blue,
cyan, magenta, yellow and orange
Black and white
Uses palette embedded in TIFF image (if any).
Pen size and shape for painting. Partially broken and not used much these days.
Font size (an integer) used in the interface.
| [< | << | <( | ? | )> | >> | >] |
Normally adjusted using the New image function within .
Same as Zoom.
Specify whether certain operations are to be applied to all of the image, to the visible part of the image, or to specified foci.
Set size of main image window (currently broken)
Sets or unsets watch mode for watching the progress of certain operations.
Allows user to specify the name of a command file for executing scripts (currently broken)
Specify various regions of ‘focus’, which can be used to restrict the part(s) of the image involved in other operations
Apply various filtering operations
Paint things into the image, actually changing the pixels. this is here for historical reasons, and for playing with algorithms, and isn't really very useful at the moment.
| ! Zoom |
| @ Pan |
| # New image |
| $ Settings |
| ~ Show lines = Yes |
| " Copy lines |
| : Paste lines |
| Edit attributes |
| Edit joins |
| Edit caps |
| Add line |
| Edit lines |
| Delete lines |
| Locate line |
| Transform Z's |
| Mark voxels |
Draw things ‘over’ the image, not actually changing the pixel values in the underlying image. In addition to the windows described above, two additional windows appear. They are used for displaying side views of either the stack of images or (as shown on the right) the lines used to segment the images.
In Draw mode a scale bar
is displayed in the main image window. The units used for this scale
bar are specified in the XY_CALC command.
The image on the left shows how lines are displayed when not being edited.
Their colours, the line thickness and the symbol sizes can all be
controlled by the user. The first point of a line is indicated by
a triangle pointing to the right
and the last point of a line is indicated by a
triangle pointing to the left
. First and last points
of lines which start at or
finish at the ends
of other lines are displayed as right-pointing
and left-pointing
3-pointed stars
(like dehydrated triangles).
Other points are shown
as squares. Connections due to
start-at/finish-at commands are shown
as thinner lines.
The image on the right shows how lines are displayed when being edited. All lines in the current slice are green, except for the currently active segment which is red. Lines in the previous slice are shown as thin blue lines; those in the next slice are shown as thin magenta lines. The user can control whether all lines in the previous and following slices are shown, or just the currently active line, or none at all.
The rest of this section describes the various items in the Draw menu.
| In |
| Out |
| Specify |
| ▶ |
| ! Zoom |
Zoom in or out by factors of two, or specify an integer zoom factor. Zoom factors ≥ 1 correspond to magnifications. Negative zoom factors ≤ −1 correspond to reductions; e.g., −2 corresponds to a magnification of ½.
As seen in the examples above, when zoomed in, the original pixels are shown enlarged (rather than smoothly interpolated) so one doesn't lose sight of the resolution limitations of the data.
| @ Pan |
If the image is larger than the displayed area, shift the display window by clicking in either the overview window or the main image window, at the point that you'd like to have centred in the display window.
One can also recentre the displayed area by right-clicking in the overview window when the main menu is active, but not when the menu is active.
A 7-button navigation menu pops up, allowing selection of a new image from the stack of images.
| [< | << | <( | ? | )> | >> | >] |
| ▶ |
| # New image |
| Sideview: lines or Images |
| Sideview: which lines |
| Sideview: nodes on/off |
| Next/previous slices: which lines |
| Next/previous slices: line Colours |
| Marked-voxel colours |
| Marked voxels on/off |
| Pen size = size |
| Symbol size = size |
| Visibility of lines |
| No. slices for big step = n_slices |
| Grey-level mapping |
| RGB channel display |
| Image-window limits |
| Autobackup frequency = n_ops |
Set various parameters. Many of the parameters are optionally stored in a session-settings files when the user exits from the programme. The file is used to restore the settings when the programme is run again.
| [< | << | <( | ? | )> | >> | >] |
| Red | ||
| Green | ||
| Blue | ||
| 1 red minus green | ||
| 2 green minus blue | ||
| 3 blue minus red | ||
| *All | ~Inv | |
| ~ Show lines = Yes |
This button can be used to quickly toggle on or off the display of lines in the main image window.
Copy lines to an internal clipboard
Paste lines from internal clipboard
| Edit line attributes |
| Edit slice attributes |
Use this function to edit the attributes of either lines or slices.
| 1 line |
| Multiple lines |
You can choose to edit the attributes of either a single line or multiple lines.
| * Copy attributes from another line |
| Name = line_name |
| Description = descriptive_text |
| Open/Closed = open_or_closed |
| Interpolation = straight_or_bezier |
| Colour = colour1;colour2 |
| Transparency = 0_to_1 |
| Start-at = independent_or_dependent |
| Finish-at = independent_or_dependent |
| X-Y mesh resolution = nel_per_diam |
| Z mesh resolution = n_slices |
| Material type = material_type |
| Boundary conditions = bc_code |
| Pressure = value |
| Thickness = value |
| /OK |
If you choose to edit the attributes for a single line, a menu will appear which permits selection of one line. After you select the line, a menu will appear in which each button displays the current value of an attribute. Click on the appropriate button to change an attribute. Clicking on will allow you to select some other line from which all attributes (except the name) will be copied to the line whose attributes are being edited. For some attributes (e.g., Open/Closed, Interpolation, Boundary conditions), a menu will appear for selecting the new attribute value. For most other attributes a simple text prompt will appear asking for the new value.
If you choose to edit the attributes for multiple lines, a menu will appear which permits selection of the lines to be affected. After you select some lines, a menu will appear for editing only those attributes which can sensibly be applied to multiple lines. The attribute values will be preset to those for the first of the selected lines. The only attributes whose values will be transferred to the multiple lines are those whose menu buttons you use (whether or not you actually change their values).
For the Colour attribute, a colour-selection tool will appear.
Find and click on the desired editing colour (the colour used within
Fie), then click outside the tool to make the selection. The
colour-selection tool will then appear again, this time for selecting
the rendering colour (the colour used for the 3-D models produced by
Tr3).
| A −big |
| B < |
| C <= |
| D 5. |
| E Finish of |
| F wallextfr_001 |
| G Up |
| H Down |
| I Delete |
| J Quit |
For the start-at and finish-at attributes, each of the two menu
buttons displays the word Dependent if there are any such
conditions, and how many there are; or the word
Independent if there are none. Clicking on the button
causes a menu to be presented which displays the current start-at
or finish-at specifications, and a
button which can be used to create a new start-at or finish-at
specification with default settings. Clicking on the button for an
existing specification causes a menu to appear which displays
the current settings. For example, the menu shown on the right
corresponds to a connection to the finish-of
the line wallextfr_001. The first four buttons
indicate that the specification should be applied to the
range –∞ < z ≤ 5.
Clicking on button or
permits specification of a new z value. Clicking on button
or toggles
between < and ≤. Clicking on button
offers a choice of ,
or .
The and buttons
move the current start-at or finish-at specification up or down in the
original list; the specifications
should be arranged in order of increasing z.
The button causes the current specification
to be deleted.
Choose whether to edit the attributes for one slice at a time, or for a range of slices: the current slice and all preceding ones, the current slice and all following ones, or all slices. If one slice at a time, the usual slice-choosing tool appears - use the tool to position yourself to the desired slice and then click outside the tool to make the selection. You will then be prompted for new attribute values for the slice: z value, slice name, rotation, and x and y offsets. The slice-choosing tool then appears again; either select a new slice, or select the same slice to quit.
If editing attributes for a range of slices, the values requested are a z scale factor and a z shift.
The editing of Joins is not yet documented.
The editing of Caps is not yet documented.
| ! Zoom |
| @ Pan |
| # New image |
| Flood |
| Autotrace |
| Delete last pt |
| Trim tail |
| Cut |
| Median filter |
| Smooth |
| Resample |
| Quit |
Add a new line to this image. You can either use an existing line definition or add a new one; you can then use the following functions to specify the new line:
| Lower threshold | ||||||
| Upper threshold | ||||||
| New seed | ||||||
| Quit | ||||||
| [< | << | <( | ? | )> | >> | >] |
![[grey scale]](fie_draw_greyscale.png)
| ||||||
For lines which are small and/or difficult, the line is best specified manually point by point.
For long stretches of clear boundaries, the autotrace function works well. It continues until it runs into the edge of the visible image, or until it runs into itself, or until it has generated too many points. Usually it will go too far, and it may also run off course. In either case the trim function can be used to cut off the unwanted part, and then the line tracing can be continued.
For closed regions with clear boundaries, the flood function works well.
The manual and automatic tracing methods can be mixed in any order, although the flood method is normally used by itself, and will overwrite any previous tracing.
The median-filter and smooth operations are particularly useful after the flood and autotrace functions, which tend to produce jagged curves and many more points that are required. The snake method of fitting ( ▶ ▶ ) may also be useful after tracing here.
The 2×/5×/10× resample function may be useful to add smoothly interpolated points after a few points have been specified manually.
Edit the existing lines in this image. Left-clicking within the image selects the closest point to be the active point. Right-clicking within the image repositions the currently active point.
B in slices 10 to 15
should be considered to be a continuation of
line A that already appears in slices 5 to 9:
go to slice 10,
do ,
select line B, and then
select line A and specify
A
that appears in slices 5 to 15
needs to be treated differently in slices 10 to 15
than in slices 5 to 9: go to slice 10,
do ,
select line A,
then select
to create line B, and specify
| Manual adjustment |
| Force weighting: ext,int = 0.6, 0.5 |
| Pressure (e.g. 0.03) = 0. |
| Gradient/GVF = Gradient |
| Vertex spacing = 5. |
| Downsampling ratio = 1 |
| Blurring (e.g. 1.) = 0. |
| Blue/Yellow thresholds = 19,inactive |
| Threshold strength (0.-1.) = 0.5 |
| Image displayed = Original |
| Damping = 1. |
| Time step = 0.5 |
| Open/Closed = Open |
| No. iterations = 100 |
| Slither ahead |
| Undo & slither again |
| Restore original line |
| Quit |
| ! Zoom (don't use) |
| @ Pan (don't use) |
| Next point |
| Previous point |
| Delete point |
| Insert point |
| Append point |
| Trim all following points |
| Cut some following points |
| Quit |
Delete some or all of the lines in some or all slices.
Determine which slices a particular line occurs in. If a line never appears and is never referenced, it can be marked for deletion.
Some functions repeated from
Apply scale factor and offset
An image stack is resliced perpendicular to the original plane of section, and x-z and z-y views are displayed. The side views are slices through a user-specified point. The user can select that point by right-clicking in any of the three image windows, or by using the menu.
Voxels can be ‘marked’, in which case they will be displayed in a distinctive colour. Once you exit from the Reslice mode the marked voxels can continue to be displayed in the main image window. One use for this is to help with the segmentation of structures which are difficult to visualise in the x-y images. Another use of this feature is to mark particular voxels for display as blocks in the VRML models produced by Tr3.
The remainder of this section explains the use of the menu.
Calculate density histograms
-
align the slices in a stack
by applying rotations
and translations. The main alignment display shows either
the current
image in shades of green overlaid on the previous image in
shades of red, or the contours in the current and previous
slices. Auxiliary windows display the contours in the previous,
current and next slice, and side views of the contours. The
current slice can be aligned manually or by using
an algorithm based on selected traced contours.
The model definitions created by Fie are stored in plain-text files with the
filename extension .tr3. These files are used by the Tr3
programme to create VRML and finite-element models.
A .tr3 file may contain the following sections:
| Section | END?*
| Notes |
|---|---|---|
| Comments | No | Any line starting with a semicolon is interpreted as a comment. Only the comments at the beginning of the file, before the first non-comment line, are preserved when Fie (or Tr3) saves a new version of the file. Whenever Fie (or Tr3) saves a revised version of the file, the user is asked for initials and a comment, which are added (with the current date) to the end of the initial comments. |
LINES
| Yes | See Lines |
SCALE
| No | See Scaling |
XY_CALC
| No | See Scaling |
Z_CALC
| No | See Scaling |
SLICES
| Yes | See Slices |
JOINS
| Yes | See Joins |
CAPS
| Yes | See Caps |
SUBSETS
| Yes | See Subsets |
VOLUMES
| Yes | See Volumes |
MATERIALS
| Yes | See Material properties |
SPRINGS
| Yes | See Springs |
CONC_LOADS
| Yes | See Concentrated loads |
LABELS
| Yes | See Labels |
VIEWPOINTS
| Yes | See Viewpoints |
DATA
| Yes | The actual x and y coördinates of lines are stored in this section. |
COSTS
| Yes | Used by Tr3 to record cost functions chosen by user for triangulation. Normally not directly modified by the user. |
GLOBAL_RANGES
| Obsolete | |
MERGES
| Obsolete |
*Whether section must be terminated by END record.
In the syntax specifications here, square brackets
([ ]) denote optional
elements and { | } denotes alternative values.
Roman (upright) characters denote actual strings to be used, while
italic (slanted) characters denote values to be chosen by the user.
Within the LINES section of a .tr3 file,
the syntax for a line definition is:
name: [qualifiers] descriptive_text
|
The possible qualifiers are:
-openclosed
| { OPEN | CLOSED }
|
-on
|
|
-off
|
|
-reverse
|
|
-do_slices
| { ALL | FIRST | LAST }
|
-colour
| ecolour[;rcolour]
|
-transparency
| transp |
-boundary_condition
| {F |
C[{S|F|B}[{F|L|B}]]}
|
-pressure
| press |
-material
| itype |
-thickness
| thick |
-mtt
| itype thick [deprecated] |
-m
| itype thick [deprecated] |
-xyresolution
| ires_xy |
-zresolution
| ires_z |
-resolution
| ires_xy ires_z [deprecated] |
-linetype
| { STRAIGHT |
BEZIER |
ELLIPTICAL }
|
-start
| [([[=]zmin][,
[=]zmax])]
{START|FINISH|NEAREST}
line_name
|
-finish
| [([[=]zmin][,
[=]zmax])]
{START|FINISH|NEAREST}
line_name
|
-url
| URL |
The attributes are discussed in more detail below. All qualifier
names may be abbreviated to any unambiguous degree. In fact, they can
all be abbreviated to a single character except
-openclosed, -on and -off,
which require at least two characters.
Open or Closed. (There
used to also be values of Filled,
Head, Tail and Both
but they are no longer used.)
-on is not required in line definitions
because it is implied;
it will be overridden if -off is present.
In subset records -on is not implied,
so it must be given explicitly if that is the intent.
If for some reason both -on and -off
are present in the same line definition or subset record,
whichever comes last will take effect.
If no -start is specified then the starting point
of the line is independent of any other line.
If line A starts at, say, the start of line B, but line B
itself starts at the finish of line C, then line A will not
start at the start of line C but rather at the first
‘real’ point of line B. It is recommended that
lines be specified to start at a start or finish
which doesn't itself depend on some other line.
-start specification applies to all slices in which
the line appears. Optionally, a range of z values
can be included in a -start specification, and there
can be multiple -start specifications for a line.
A z range is specified by a zmin
and a zmax. If zmin
is not specified, it is taken to be equal to the
zmax of the previous -start
of the line, or to –∞
for the first -start.
If zmax is not specified, it is taken to be
equal to +∞. If zmin is preceded by
= then the -start applies for
zmin ≤ z; otherwise
it applies for
zmin < z.
Similarly, if zmax is preceded by
= then the -start applies for
z ≤ zmax; otherwise
it applies for
z < zmin.
If there are multiple -start specifications for
a line, then their z ranges should not overlap and
they should be arranged in order of increasing z.
do_slices by default has the value
ALL, which means that the line will be eligible
for triangulation in all slices in which it appears (subject
to the effects of the z resolution ires_z). If
do_slices has the value FIRST or
LAST then
only the first (or last) occurrence of the line (subject to the effects
of ires_z) will be included in the triangulation process.
This means that no triangles will be generated for the line itself,
but that it will be available for use in joins and caps.
diprgb.txt file.
F | Free at all nodes |
C | Clamped at all nodes |
CS | Clamped at start node |
CSF | Clamped at start node and along all of first slice |
CSL | Clamped at start node and along all of last slice |
CSB | Clamped at start node and along all of first and last slices |
CF | Clamped at finish node |
CFF | Clamped at finish node and along all of first slice |
CFL | Clamped at finish node and along all of last slice |
CFB | Clamped at finish node and along all of first and last slices |
CB | Clamped at both ends |
CBF | Clamped at both ends and along all of first slice |
CBL | Clamped at both ends and along all of last slice |
CBB | Clamped at both ends and along all of first and last slices |
MATERIALS
section of the file
incus1: -op CL -c yellow;bone -r 100 1 -m 1 .04 ;Incus top
|
incus1 demonstrates a closed line which will be shown as
yellow in Fie and rendered as bone coloured in the 3-D models; which
is to be triangulated using every slice at 100 elements/diameter; and
which consists of material type 1 with a thickness of 0.04.
tm_inf: -op OP -c green;white -t .5 -r 50 2 -m 4 .001 -s f annlig -f s manub ;TM
|
tm_inf demonstrates an open line which will be shown
as green in Fie, but in the VRML model as translucent white with a
transparency of 0.5; it is to be triangulated using only every second
slice at 50 elements/diameter; it consists of material type 4 with
a thickness of 0.001; and it starts at the finish of line annlig
and finishes at the start of line manub.
The first line of the SLICES section may be of the form
IMAGE_PATH path
|
path can be used to specify where to find the image files if they are not in the same directory as the .tr3 file. It will be prefixed to the image names before the path of the .tr3 file is prefixed, so it will specify a path relative to the path of the .tr3 file. (Neither the image-path name nor the path of the .tr3 file will be used if the image name itself contains a path specification.) The image-path name should not include leading or trailing path delimiters; it will be system independent if it does not include any path delimiters, i.e., it specifies only a single directory name. This path is used only when there is a separate image file for each slice. The usual method is to put all of the image files into a subdirectory of the directory where the .tr3 file is, and then give the subdirectory name as the path.
The rest of the SLICES section consists of records of the form
i, name, [z, [rotate, offsetx, offsety]]
|
There should be one record for each image (slice). i is the slice sequence number. name is a descriptive name for the slice (or an actual file name when the slices are stored as separate files). z is the z coördinate for the slice. rotate, offsetx and offsety optionally specify the offset and orientation required to align the image with the rest of the stack (usually for histological images).
As a structure subdivides from slice to slice, or becomes connected to other structures, multiple line names must be used for the same structure. The Join mechanism is provided to specify how triangulation should be done across such changes of line name. The syntax for Joins allows concatenation of multiple lines; forward or backward traversal of lines; and incorporation of only the first or last point of a line. The syntax permits transitions between Closed and Open lines. Joins can either inherit properties from the lines which constitute them, or take on new properties.
Within the JOINS section of a .tr3 file,
the syntax for a Join definition is:
name: [qualifiers]
[-]i1[{>|<}] [-]i2[{>|<}] … to
[-]j1[{>|<}] [-]j2[{>|<}] …
[;description]
|
i1, i2, etc., are the names of the lines to be concatenated in order to form multiline 1. j1, j2, etc., are the names of the lines to be concatenated in order to form multiline 2. A surface is triangulated between multiline 1 and multiline 2.
A minus sign (-) before a
line name means that that line is to be traversed backwards when being
concatenated to its multiline.
The symbol > after a
line name means that only the first node of that line is used.
The symbol < after a
line name means that only the last node of that line is used.
The following attributes (qualifiers) can be defined for Joins. Their meanings are the same as for line attributes.
Example. If you had a structure defined by
two open lines, bone_ant_50 and bone_post_50,
from slices 50 to 79, and then at slice 80 they combined into a
single closed line,
bone_80, you could define the join
between them as
bone_50: bone_ant_50 bone_post_50 to bone_80 ;Bone
|
If you wanted to specify a distinctive colour for the triangles corresponding to the join, you could use, for example,
bone_50: -c red bone_ant_50 bone_post_50 to bone_80 ;Bone
|
Within the CAPS section of a .tr3 file,
the syntax for a Cap definition is:
name: {HEAD|TAIL} [qualifiers]
[-]i1[{>|<}] [-]i2[{>|<}] …
[;description]
|
HEAD means that the cap is to created at the first slice
for which all of the component lines are present.
TAIL means that the cap is to created at the last slice
for which all of the component lines are present.
i1, i2, etc., are the names of the lines to be concatenated in order to form the cap. A flat surface is triangulated within the resulting multiline.
A minus sign (-) before a
line name means that that line is to be traversed backwards when being
concatenated to the multiline.
The symbol > after a
line name means that only the first node of that line is used.
The symbol < after a
line name means that only the last node of that line is used.
The following attributes (qualifiers) can be defined for Caps. Their meanings are the same as for line attributes.
F or C)
Example. If you had a structure defined by
two open lines, bone_ant_50 and bone_post_50,
from slices 50 to 79, you could a define a cap at slice 50 as
bone: HEAD bone_ant_50 bone_post_50 ;Bone
|
bone: TAIL bone_ant_50 bone_post_50 ;Bone
|
The syntax for the VOLUMES section of a .tr3 file
is the following:
| ||||||||||||||||||||||||||||||||||||||
i1, i2, etc., are the names of the lines to be concatenated in order to form a closed multiline. These closed multilines should be specified in the order in which they are encountered in processing from the first slice to the last.
The syntax for specifying a multiline is the same as for Joins and Caps.
A minus sign (-) before a
line name means that that line is to be traversed backwards when being
concatenated to the multiline.
The symbol > after a
line name means that only the first node of that line is used;
the symbol < after a
line name means that only the last node of that line is used.
The purpose of this section is to produce surface
model definitions suitable for use by volume-mesh generators.
This section has essentially been superseded by the use of the
Volume qualifier for subsets.
The syntax of the SUBSETS section of a .tr3 file
is the following:
| ||||||||||||||||||||||||||||||||||||||
The optional VOLUME qualifier is intended to result in the
output of the model in file formats for use by volume-mesh
generators.
(Currently no such formats are output because a separate application,
sap2gmsh, is used to convert .sap files
to Gmsh format.)
This qualifier
should be used only for a subset which defines a single, simple closed
surface.
The optional MIRROR qualifier causes the model to
be flipped to become a mirror image: the z coördinates
are all multiplied by –1 and the node numbering is reversed in each
triangle.
The syntax for each subset record is one of the following:
linename: [qualifiers]
descriptive_text
|
(cap) capname: [qualifiers]
descriptive_text
|
(join) joinname: [qualifiers]
descriptive_text
|
(vol) volname: { -on | -off }
|
(clip) { xmin val | xmax val |
xrange val1 val2 |
ymin val | ymax val |
yrange val1 val2 |
zmin val | zmax val |
zrange val1 val2 }
|
(rot) θx θy
θz
|
(tran) tx ty tz
|
@[-]subsetname
|
SUBSETS
| ||
SUBSET Bone
| ||
*: -off
| ||
bone*: -on -c red
| ||
(join) bone1: -off
| ||
(join) bone2: -on
| ||
End of subset
| ||
End of subsets
| ||
Each line, cap and join name field can contain any number
of (*) or ? wildcard characters. The
* matches any number of characters, including zero
characters, and the ? matches exactly one character.
For example, inc?_*med_* would match
incA_antmed_050,
incB_postmed_100, etc.
Any of the line, cap and join attributes which are specified here will over-ride those specified in the original line, cap and join definitions.
The (vol) lines are used to turn specified volumes on
or off.
The (clip) line is used to exclude ranges
of x and y, or slices
based on their z values, from the 3-D model. For example,
(clip) zmin 5. would cause all slices with z
less than 5. to be dropped;
(clip) zmax 10. would cause all slices with z
greater than 10. to be dropped; and
(clip) zrange 5. 10. would result in keeping
only slices with 5. ≤ z ≤ 10.
The (rot) and (tran) lines are used to
apply specified rotations and translations to the overall model.
The @ line is used to include another subset
within this subset. Subsets can be nested to any depth; that is,
the included subset can itself include other subsets.
The optional - (minus sign) can
be used to reverse the numbering of all of the triangles in the
included subset.
The usual practice is to begin each subset definition with
*: -off (i.e., turn off all lines) and then turn on
the desired lines, turn caps and joins on or off as required,
etc. When some other subset is included using an @ line,
the *: -off line of the included subset is ignored
(to avoid turning off the lines that have already been turned on in
the subset requesting the inclusion).
As an example, the SUBSET definition shown at the right would suppress all
lines and then reactivate (and turn red) all those whose names start
with ‘bone’. It would also turn off Join bone1
and replace it with join bone2 (which presumably would
initially have been defined with -off.
Within the MATERIALS section of a .tr3 file,
the syntax for a record is:
nmat ym pr den
descriptive_text
|
nmat is a sequence number for the material type, normally starting at 1 and incremented for each material type. ym is the Young's modulus, pr is Poisson's ratio, and den is the mass density of the material. The value of Young's modulus may be expressed with a metric suffix, e.g., 2G or 2.G for 2 GPa, or 1.5M for 1.5 MPa.
Everything after the density value is taken as descriptive text.
If no material properties are defined, then no .sap finite-element model will be generated by Tr3.
Within the SPRINGS section of a .tr3 file,
the syntax for a record is:
{D|R} stiffness [-]line0(n0)
[-]line1(n1) …
[[-]line4(n4)]
|
If the first item in the spring definition is D
then the spring is a translational one (e.g., N/m);
if it's an R then the spring is a
rotational one (e.g., N/rad).
stiffness is the actual stiffness
of the spring.
The spring will be attached to the model at the first node of line line0 in slice n0, or at its last node if the line name is preceded by a minus sign.
The direction of the spring is determined by the position(s) of from 1 to
4 other nodes, each of which is specified using the same syntax as node 0.
The following table describes how the direction of the spring is determined.
The notation Vmn indicates a vector from node m to
node n.
| No. other nodes | Direction of spring |
|---|---|
| 1 | parallel to V01 |
| 2 | parallel to V12 |
| 3 | perpendicular to the plane formed by V12 and V13 |
| 4 | perpendicular to the plane formed by V12 and V34 |
Note that the length of the spring is immaterial.
Within the CONC_LOADS section of a .tr3 file,
the syntax for a record is:
{F|M} load [-]line0(n0)
[-]line1(n1) …
[[-]line4(n4)]
|
If the first item in the concentrated-load definition is F
then the load is a force (e.g., N);
if it's an M then the load is a
moment (torque, e.g., N m).
load is the actual value
of the load.
The load will be applied to the model at the first node of line line0 in slice n0, or at its last node if the line name is preceded by a minus sign.
The direction of the load is determined in the same way as for springs.
Within the LABELS section of a .tr3 file,
the syntax for a record is:
label_text [-size size] [-colour colour]
[-family family]
[-]line0(n0)
[[-]line1(n1)]
|
label_text is the text that will be displayed as the
label. If the text contains any space characters, it should be enclosed
in double quotation marks, e.g., "Label 1".
size is the font size used for the label, measured in the same units as the model. If unspecified, the default value is 1.
colour is the colour used for the text of the label, specified by name. If unspecified, the default value depends on the browser. The colour names available are the same as those offered by menu as line, join and cap colours.
family specifies the font family to be used
for the label. It can specify the name of any font on the user's
computer, but the only values guaranteed to work are the generic
values SERIF, SANS
and TYPEWRITER.
If unspecified, the default value is SERIF.
The label will be attached to the model at the first node of line line0 in slice n0, or at its last node if the line name is preceded by a minus sign.
Within the VIEWPOINTS section of a .tr3 file,
the syntax for a record is one of the following:
name XYZ rotx roty rotz
description
|
name AA posx posy posz
axisx axisy axisz angle
description
|
(reldist) relative_distance
|
The xyz option defines a viewpoint corresponding to what
one sees in Fad after the specified x, y and
z rotations (in that order). In other words, one can use
the rotation angles displayed in Fad in order to re-create a
view from the same direction.
If one is starting from an orientation in
Thrup’ny, one can use
to display the rotation angles, apply them in the order z,
y and x in Fad using the interactive rotation
tool, and then use the angles displayed
by Fad.
The aa option defines a viewpoint using the same method
used by VRML itself. The required parameters can be determined by
requesting Tr3 to include code in the VRML file which causes the
current position
(posx posy posz) and
orientation
(axisx axisy axisz angle)
of the viewpoint to be continuously
displayed.
Whether or not any viewpoints are defined in the .tr3 file, six standard viewpoints are generated, in both directions along each of the x, y and z axes.
A (reldist) line defines the relative distance from the
centre of the model to any xyz-type viewpoint and
to the six standard viewpoints along the axes. The actual distance
is the relative distance multiplied by an estimate of the size of the model.
The default value for the relative distance is 2.
Fie needs to handle two different ways of thinking about x, y and z coördinates. On the one hand, line nodes need to be positioned with respect to pixel positions (columns and rows) within images and with respect to slice numbers within a stack of images. On the other hand, the x, y and z coördinates of the final model normally need to be expressed in real-world coördinates, e.g., millimetres.
There are two ways to manage Fie's scaling between the real-world x and y coördinates of a model and the row and column pixel positions:
XY_CALC parameters (below)
to map the real-world coördinates
to pixel positions when displaying lines within images; or
SCALE parameters (below)
to convert to real-world coördinates when creating the
final triangulated models.
There is also a set of Z_CALC
parameters (below)
which is concerned with mapping between z
coördinates and slice numbers.
XY_CALC
|
ux and uy are scaling parameters (in units/pixel). ox and oy are offsets (in pixels). These parameters are used by Fie to transform real-world x and y coördinates in the .tr3 file to match the images. The z coördinates of the slices are assumed to be given using the same real-world coördinates.
The directive XY_CALC is on one line and the parameter values
are on the next line.
By default, ux and uy are 1., and ox and oy are 0., implying that the x and y coördinates in the .tr3 file, and presumably also the z coördinates, are measured in pixels. If the z coördinates were measured in, say, mm, then ux and uy would normally specify the pixel size in mm.
If uy is not specified, it is assumed to be the same as ux, i.e., the x and y units are assumed to be the same.
The -u parameter is an optional name for the units, e.g.,
-u m for metres, or -u um for micrometres.
Example. If you had images with a pixel size of 0.5 mm, then you might use the following:
XY_CALC
|
SCALE
|
These scaling parameters are not actually used within Fie. Tr3 uses them to scale the x, y and z coördinates that it reads from the .tr3 file.
Normally only sx needs to be specified, and sy and sz will be taken to be the same as sx. By default, sx = 1.
The directive SCALE is on one line and the parameter values
are on the next line.
One use for these parameters is to produce real-world coördinates in the VRML and SAP files produced by Tr3 when the coördinates in the .tr3 file are expressed in pixels.
Example. If you had images with a pixel size of 0.5 mm, then you might use the following:
SCALE
|
The SCALE parameters could also be used to convert from
one set of units to another, say from mm in
the .tr3 file to m in the VRML and SAP files.
Z_CALC
|
z1 is the z coördinate for the first image of a stack of images, measured in the same units as used for x and y. dz indicates the nominal spacing between slices.
The directive Z_CALC is on one line and the parameter values
are on the next line.
Note that these parameters are just used to guess an appropriate z coördinate for a slice which has not yet had a z coördinate assigned, and to assign slice numbers to contours read from an old .tr3 file which does not contain explicit slice-number/z-coördinate information.
The main image shows part of slice 127 from a magnetic-resonance microscopy dataset for a cat middle ear. The data are courtesy of Drs. M.M. and O.W. Henson (UNC) and the CIVM (Duke University). The image shown is a small part of the original image. Click on the image for a larger version.
Below the main image window are x-z and z-y views showing a selected subset of the lines that have been created by the user. The lines shown in the side views correspond to parts of the eardrum, malleus, tensor tympani muscle and stapes.
Each line in the image is represented by a set of vertices. The first vertex of a line is represented by a rightward-pointing triangle; the last vertex is represented by a leftward-pointing triangle; and the others are represented by squares. The straight-line segments between the vertices of a line are relatively thick. When a line is specified as starting at, or finishing at, some other line, then that connection is drawn as a thin straight-line segment.
In the centre of the image are seen a part of the malleus bone (yellow) and
the tensor tympani muscle (red) attached to it. Notice that the shared surface
between the two is represented as a separate line. These lines could be
defined as shown in the following table: mallmuscinf
and mallmuscsup represent the inferior (lower) and superior
(upper) lines defining the part of the malleus to which the muscle is
attached, and ttymp represents the tensor tympani muscle.
The lines mallmuscsup and ttymp are both
defined as starting at the finish of mallmuscinf and
finishing at the start of mallmuscinf. Note that the bone
has a material type of 1 while the muscle has a material type of 2.
mallmuscinf: -op OP -c yellow;bone -xyr 100 -mat 1 Malleus
|
mallmuscsup: -op OP -c yellow;bone -xyr 100 -mat 1 -s f mallmuscinf -f s mallmuscinf Malleus
|
ttymp: -op OP -c red;muscle -xyr 100 -mat 2 -s f mallmuscinf -f s mallmuscinf Tensor tympani
|
This section is the beginning of a collection of mini-tutorials on specific tasks. Links are given to the Menus documentation for details on the various menu items used.
For now, at least, this section focusses on working with stacks of images like X-ray CT scans, MR scans, serial-section histology or optical-sectioning microscopy.
Enter or Return key.
Unfortunately, copying and pasting of text is not possible
within Fie, and the only editing available while typing such
text is the use of the delete-left (or Backspace) key.
| ! Zoom |
| @ Pan |
| # New image |
| $ Settings |
Quit
or Cancel button, clicking outside the menu
will have the same effect.
This section assumes that you already have a .tr3 file
and the corresponding stack of images. Look at the following two sections if
that's not the case.
If your images are in either JPEG or PNG format, you need to tell Fie to
open the .tr3 file. If the images are in the form of
a TIFF or raw stack, you need to tell Fie to open the stack file.
Start by clicking on and then . The first time you work with a dataset in Fie, you need to browse to find it. Click on the menu button. The first button in the next menu will be and will display what Fie considers to be the current directory. You can navigate from there by using the button or by clicking on one of the buttons indicating a subdirectory. (Each button in a file-selection menu contains, after its shortcut key, either for directory or for file.) Use the buttons at the bottom of the menu to scroll up and down as required.
If you want to go directly to some other directory (or don't recognize what
directory you're in) click on the
button. You will then be asked to type in the name of a directory, e.g.,
/home or C:\users. You can then start browsing
from there.
Once you're looking at the right directory, click on the button corresponding
to the desired .tr3, .tif or .raw file.
Next time you run Fie, the most recently opened file will be at the top of a list of all of your previously opened files, so you don't need to browse for it again.
Mañana.
Mañana.
Once you have opened a .tr3 file
for the first time, you will see some or all of the first
image in the stack.
To look at the other images, click on
in the main Fie menu and then
.
Use the 7-button navigation menu to move back and forth in the
stack. Next time you use Fie to look at this dataset, it will start at
the image that you were looking at last.
The first time you look at a dataset, the images will be displayed at 100% scaling. If the images are very large, you may see only part of the image; you can zoom out to see more of the images. If the images are quite small, they may take up only a small area of the screen; you can zoom in to make them bigger or to focus on a small area. To zoom in or out, use the button. If you are viewing less than the whole image, the Overview window will show you which part you are viewing.
If you are looking at only part of an image (because you have zoomed in) you can choose which part to look at by using the button.
If you have not already done so, click on
in the main Fie menu, then click on
.
If lines already exist in this .tr3 file, a list of
them will appear as a menu, with
at the top of the list. If no lines exist yet, only the
button will appear. Click on it and then on
.
When the menu for specifying line attributes appears, click on . A prompt will appear near the bottom of the window, asking for the name of the new line to be added. Type in a name. You can set other attributes either now or later. Click on to continue. There are three different methods available for adding the points that define a line: manual, autotrace and flood. The manual method is the most straightforward but also the most tedious. The autotrace and flood methods can greatly speed things up – when they're successful. They work best for structures with good contrast.
To add points to a new line manually, simply left-click in the image window. The prompt near the bottom of the screen will show the number of the point to be added next. At any time the last point in the line can be deleted using the button.
The function will attempt to trace a boundary automatically. It will use the last point so far as its starting point; if no points have been added yet it will ask for a starting point. It will ask you to point to a point that lies in the direction in which it should go. It will then attempt to trace a boundary that has properties similar to the boundary defined by the two points that it has been given to start with. It will continue tracing until it hits the edge of the visible image or until it runs into itself. Often it will trace successfully for a while and then go off course. In that case the function can be used to delete all of the points following a point that you specify. You can then add some points manually and perhaps try autotracing again.
The function traces a line around a closed region based on a range of pixel intensities. This method cannot be combined with the manual and autotrace methods. When you invoke the flood method, you are asked to specify a ‘seed rectangle’ by pointing to two diagonally opposite corners. The pixels within that rectangle will be used to determine the range of desired intensities, and a line will be traced around the corresponding region. A menu is then presented which permits adjustment of the thresholds in case the line isn't quite right (or is terribly wrong). Click on when the line is satisfactory (or as satisfactory as it's going to get). If the line is mostly acceptable but part is not, function can be used to remove that part by pointing to each end of it.
The Autotrace and Flood methods often produce excessive numbers of points and very jagged lines. The and functions can be used to clean things up somewhat. The more powerful Snake function can also be used for this.
When using the Manual method, it is sometimes useful to manually specify only a small number of points and then use the or function to interpolate additional points.
When a line has been satisfactorily traced in one image, it is often useful to immediately use the button to advance to another image, rather than doing . This way a line can be added to multiple slices without having to specify the line name each time. The flood method works particularly effectively this way because it automatically attempts to use the same location and intensity range for the next slice.
Once a line has been added, it can be manually edited by clicking on .
Note that the Undo facility is extremely primitive. It can only be used
to undo the positioning of a single point, and only if undone immediately.
The best protection against errors is to save frequently. Every time
you save a .tr3 file, Fie creates a backup version with
a version number, so you can retrieve older versions. Fie also
automatically creates a temporary backup file periodically, which
may be useful for getting yourself out of trouble if you haven't saved
recently.
If an existing line needs to be split into two lines, first position yourself at the first slice (or only slice) in which you want to do the splitting. Also zoom and pan so that you'll be able to see the place where the split is to be made. Then use . You will then specify which line is to be split.
You will next specify which lines will correspond to parts 1 and 2 after the split. Often you will select for one or both lines. In that case you will be presented with the menu for editing line attributes. Change the line name and then click on . Notes:
You will next specify which slice or slices you want to do the splitting in, by selecting a choice from a menu.
| Prev |
| Next |
| Point -> part 1 |
| Point -> part 2 |
| Point delete |
| Cancel |
The actual splitting is done with a menu which allows you to select the node where the split will be performed and then to associate that node with one (or neither) of the two resulting line parts. Select the node by using the and buttons or by left-clicking on the node in the main image window, then press , or .
If you have chosen to do the split in more than one slice, you will immediately be moved to another slice, ready to select the node and do the split. This continues until the requested slices have been processed. If at a certain slice you can no longer see the place where the split is to be made, press , do the required pan, and then restart the split operation. You'll find that the appropriate line-selection buttons have already been pressed.
A similar operation is also available.
This corresponds to snipping out part of a line to form a second line.
There is also a operation
for combining two lines together.
After lines have been split or snipped, it will probably be necessary to
specify appropriate
start at or finish at
attributes.
An existing line can also be refined using the semi-automatic line-fitting functions. The snake method is especially useful. There are several ways of taking advantage of it:
Invoke the snake method by doing then then . Choose the line to be fitted from the menu that appears. A menu then appears that offers a number of settings that can be adjusted. See the detailed documentation for how to use the various adjustments.
The actual fitting is done by using the the button. If the results of that slithering are bad, use either or to back up and try again.
If the snake algorithm is having trouble getting part of the line to fit the desired boundary, then can be used to help it along. The functions are similar to those for manually editing lines.
Once you are satisfied with the fit, or have given up, click on . In the menu that then appears, you can choose to keep the results of the fitting and go directly to another slice. This allows efficient fitting of the same line in a number of slices after having added it using, say, the flood method. If the line that you were fitting does not already appear in the new slice, the line will be pasted into the new slice, ready for fitting. This allows efficient addition of a line to a number of slices without having to do an explicit for each slice. Whether it's better to do a series of floods followed by a series of snakes, or just do a series of snakes, depends on the nature of the data and on personal preference.
When fitting an open (as opposed to closed) line in a sequence of images, it is often useful to do a manual adjustment of the first and last points before slithering in each new image. When you click on the first point in the line will be the active point. You can reposition it by right-clicking, then use to move to the last point in the line and reposition it. Then click on and try slithering.
History of changes, in chronological order, starting in 2003 Jun.
Minor bug fixes and menu changes are not all included. Some changes listed here actually reflect changes in the Dip library.
Fixed so multiple saves per session won't lose comments; truncate long comments if necessary to make space for initials and date. Fixed so autosaves don't add comments.
Implemented function for concatenating lines.
Revised surface-smoothing function, to hopefully give better results when multiple Bézier segments are used; the number of Bézier segments must now be a power of 2.
Implemented -on/off qualifiers for Joins. This means that joins, as well as caps and lines, can be initialized On then turned Off in subsets, and vice versa.
When lines are reversed, start-at and finish-at connections are adjusted accordingly. Multiple lines can be reversed at the same time.
The shortcut keys for Black and Blue are now different in the colour-selection menu. (This is actually a change in the Dip library.)
Enforce restriction that line names may contain only letters, digits and '_'.
Implemented specification of Volumes.
Implemented checking of date & time of .tr3 file when first change is made and before saving.
Increased maximum number of Joins.
Increased maximum number of lines from 500 to 1000.
In snake fitting, implemented option of carrying newly modifed contour to next slice and applying snake again; added option of using GVF for snake; changed line colouring.
Added Copy & Paste to Edit-lines menu.
Implemented median filter in Filter.
Removed an obscure Dip feature which permitted menu-button selection by typing " or ' followed by button text. Now " can be used as a shortcut key in menus.
Allow customisation of colours to be used for contours in previous and next slices.
In snake fitting, added manual-adjustment facility for snake; allow fitted contour to be carried to previous slice as well as to next contour, and also backward or forward several slices; implemented adjustable downsampling (to get reasonable speed and attraction to boundaries over large areas); fixed normalisation in GVF, so it works better now, and fixed memory leak.
In line splitting, removed special treatment for closed lines because it was confusing, user now must set starting point appropriately before splitting a closed line; added to menus that it's deprecated to assign point to both parts.
Display Bézier lines properly in overview and sideview windows.
Use of a different shade of green for inactive lines when editing.
Implemented interpretation of Shift-click as selecting or unselecting a range of buttons, in all multiple-selection menus.
Save low (blue) and high (yellow) thresholds in session settings. Added advice to use -1 if no threshold is wanted.
Revised shortcut keys in Preferences menu.
Comments from the .tr3 file are now stored in memory rather than in a temporary file (avoiding conflicts between, e.g., Fie and Tr3 running at the same time). The user's initials are now requested only the first time changes are saved, and are then re-used for subsequent saves during that session.
Pressure (-p) is now recorded using metric prefixes,
e.g., 3.m instead of 0.3E-2. Changed internal logic so negative
and zero pressures can be specified. (The value of -666. is now
used to mean undefined, and therefore will not be preserved when
a new .tr3 file is written.)
Allow longer file names in certain places.
In the Reslice function for viewing sideview images:
Added saving of session setting for whether lines or images are displayed in sideviews.
No longer clear the text-terminal screen when starting up.
Named colour definitions are now created internally, rather than all being taken from a diprgb.txt file. (That file is no longer required, but it can still be used for overriding or supplementing the internal definitions.) The colours are now displayed in a somewhat different (hopefully better) order than before.
Implemented proper clipping of polygons in Dip library; this mainly affects Fad but may also affect symbol display in Fie.
Implemented mirror attribute for subsets.
Implemented separate -material and -thickness
line attributes; the attribute abbreviations -m and
-t are recognised as, and converted to, -mtt
(both material type and thickness) and -tr (transparency).
Implemented separate -xyresolution and -zresolution.
Old -resolution (both xy and z) is still recognised.
Changed contour_names and slice_descriptors
to lines and slices, but still recognise old
forms.
Made indenting more consistent in .tr3 files as saved by Fie & Tr3.
The -op (open/closed) and -c (colour) are
no longer written to .tr3 file if they have the default values,
viz., open and 1;white. The -op filled
attribute is changed to -op closed.
Implemented viewpoints, for generating extra viewpoints
in the VRML file.
Revised handling of Dip initialisation errors. Kill Fie if there are too many invalid mouse clicks or keyboard presses at the main menu, to avoid a possible infinite loop when Dip has not been properly initialised.
Added -url line attribute, which can be used to specify
a URL which the browser will display if the user clicks on a structure.
In Tr3: ask about Separate vs. Combined before starting triangulation; added option of adding code to VRML file to continuously display the position and orientation of the viewpoint, to facilitate defining viewpoints in the .tr3 file.
Extended features for marking voxels.
Further extended features for marking voxels. Added reading and saving of marked voxels in .tr3 file.
Implemented Labels.
Implemented display of scale bar.
Implemented unit-name specification in XY_CALC.
Added 'saving' to progress message when saving resliced files.
Fix to cursor handling.
In _read_tr3_fie, don't try to get file date/time if no file
For Volumes, added use of * to specify that multiline is Open.
Added Reverse flag for lines, caps & joins.
Added side-view display of selected line even if not in list of lines to display
Added Do_slices attribute (= all, first or last).
Implemented Volume qualifier for subsets.
Cosmetic change in user query for new .tr3 file.
For snake, added 'keep & go to specified slice'.
In _reslice, do z-y reslicing in a separate loop, in an attempt to speed things up
Made top-level directives case-insensitive in .tr3 file.
Allow editing of slice attributes for a range of slices at one time.
Fixed handling of file names when reslicing images.
Use TEMP environment variable for log file if
HOME not found.
Minor changes in saving of resliced image stacks.
Added explicit error message for excessively long subset name.
Revised reslicing to use multiple passes, to speed things up by using memory better.
Minor fixes in error checking.
Implemented saving and re-use of resliced .jpg files. If images are in TIFF or .raw stack, always save resliced stacks, don't bother to ask.
For reslicing, calculate block sizes for multiple passes based on image size and use of 200 MB of memory.
Fixes and refinements in session save and restore; image and palette initialisation; import.
Fixed logic for retrieving previous reslicing for .jpg images.
Implemented display of sideview images when resliced images are in JPEG images rather than stacks
Fix to drawing of scale bar.
Implemented consistent & graceful handling of Nxy too big
Added 'No lines available' message when trying to ask user which line(s) to use.
Added checks to make sure start-at and finish-at names for a line are not the same as the name of the line.
Use of thumbwheel for adjusting grey palette; removed query re using rarely used densities for r,g,b,c,m,y; don't ask about converting pixels to grey if it's already a grey-scale image.
When reslicing, base amount of memory used on amount of physical memory available, rather than always using 200 MB
For snake, added option of deleting line; in manual mode, added Trim function.
Fix to z scaling.
For side views, fixed handling of .jpg images, revised menu text and one shortcut key.
Keep history of .jpg files that have been opened (when creating new .tr3 files) separate from history of datasets opened by Fie.
For reslicing, fixed specification of amount of memory used, and reverted to using a single pass for TIFF and .raw datasets.
For splitting lines, removed option of assigning split point to both parts (had side effect of making accidentally hidden Cancel button appear; reworded '-> neither part' to 'delete'.
For snake, divide internal weight by vertex spacing to prevent stiffening for vertex spacing > 1.
For image side views, added option of not showing marked voxels (because it slows things down); count voxel marking and unmarking as modifications (for purpose of auto backup).
In line side views, if line is being displayed only because it's currently active, display it as light grey.
Use of grey palette for rgb images when pixels are grey.
Added snake threshold-strength feature.
Added adjustment of blue/yellow thresholds from within Snake, and adjustment of all grey-palette settings from within Preferences (rather than just Gamma).
When reading .tr3 file, fixed handling of slice spacing < 0 when trying to match z; output extra info to log file in case of error matching z.
Changed order in menu for setting palette, putting Grey and False Colour first.
Added font size to session settings that are saved and restored.
Fixed logic for initialising palette superbutton; fixes problem when font size is changed.
Added saving of images in JPEG format.
Added flood filling. Fixed bug in smoothing and resampling.
Added display of name of .tr3 file at top, along with image name.
Fixed scaling bugs in line smoothing and resampling.
Use of deferred mode rather than immediate mode when choosing colours; a couple of other minor colour-related changes.
Changed initial value of Err_smooth(2) from 0.5 to 0.25.
Fix to output of statistics.
When editing line attributes, added check for name already used.
No longer accept Filled as a line type.
For line colours within Fie, allow same colours as for rendering in VRML.
For colours of caps and joins, allow conversion of old-style colour codes to colour names.
Enhanced scale bar.
Don't allow ‘\’ character in descriptive text.
Added ability to specify zmin and/or zmax for subsets.
Reworded msg if image not open when importing SurfDriver .txt file(s); check for Nmodifications_tr3 > 0 rather than Nlindes or Nxy > 0; added setting of slice z's, offsets, rotations and name lengths.
Started implementing import of .mrp files.
Minor code improvements for reading files.
Fixes related to scale bar, and to drawing if pen size ≤ 0.
Continued implementing import of .mrp files. Minor improvements to logic in import.
Minor code improvements for reading files.
Increased maximum number of joins.
Added error checking when parsing file names.
Added control over display of red, green and blue channels. Enabled their recognition by snake algorithm, and use better conversion from colour to grey scale for passing image to snake algorithm.
Added setting of colours and transparency for marked voxels, and added auto-set function for marking voxels.
Increased maximum number of subset records.
Some improved error messages when reading files.
Additional checking of colour names when reading files.
Fixed saving of colour raw images.
Added information to saved/restored session settings.
Modified session save/restore so each dataset has saved settings. Don't call session_restore at beginning; always save session settings when quitting.
When reading a file, check if a modified file is already open; if a file is already open, save session settings before opening another file. Additional call to restore session.
Internal change to passing of parent ID's to subroutines.
Improved initialisation.
Internal improvements to menu handling.
Check for Islice ≤ 0 before trying to read image
In all menus where it appeared, replaced Preferences
by Settings (in consistent position and with consistent
shortcut key $); changed shortcut key for Reslice
from 's' to 'R' (which used to be for Preferences)
Improved user interface for side-view images; implemented option of auto setting in all slices at once
Added control over visibility of lines.
Improved session saving and restoration.
Improved re-initialisation of menus (especially for font-size changes).
Increased maximum number of marked voxels.
When saving files, use ; rather than : for marked-voxel colour.
Fixes to handling of colours, gammas, etc.
Implemented option of doing statistics for all slices; added display of number ≥ threshold; added drawing of line at threshold; ask for bin size before threshold, changed default bin size from 4 to 1; after last focus, loop to ask for different threshold; added calculation of total densities <, = and > threshold; rearranged display of numbers.
Added display of difference pseudo-channels R-G, G-B and B-R.
Fixed logic for handling cancellation when editing start-at and finish-at.
For side-view images, added Zoom, Pan and Settings to menu; implemented filling; fixed some logic problems.
For snake algorithm, implemented option of displaying either original image or prepared image; improved interface.
Some improved error messages when reading files.
Improvement to checking of colour names.
Additional error checking when saving files.
Fixes and added checks for statistics.
Improved handling of too-long or empty material-type descriptors.
Bug fix: in _redisp, added missing Ierrsw=0 at beginning
Started implementing display of join specifications.
Improved handling of default and unspecified attributes.
In main menu, use of " and : rather than C and P as shortcut keys for Copy and Paste (as in edit-line menu).
Implementing Set command for directly setting node coördinates from keyboard; added coördinates to information displayed for a node.
Added ability to display lines in 'next' or 'previous' slices either in one slice or all slices.
Started implemented new-style start-at and finish-at.
When reversing a line, no longer reverse its start-at and finish-at specifications, because the line may not be being reversed in all slices.
Disabled 'C' short-cut key for palette to avoid conflicts. For creating new .tr3 file, fixed problem when only 1 image, then extended to permit re-use of 1 image for multiple slices.
Finished implementing new-style start-at and finish-at, which allow multiple specifications per line, with specified z ranges. Implemented editing of start-at and finish-at specifications.
Further work on displaying join specifications.
Implemented ability to click in image windows to select a line or lines, supplementing use of menus.
When saving session, output window limits before zoom and pan so pan setting will be better preserved across sessions
When editing line attributes, redisplay lines after each interaction. Implemented editing of attributes for multiple lines.
Fix to avoid saving of corrupted session settings if error occurs reading file.
Fixed error handling start-at and finish-at specifications which affected only i386 Linux version.
...
Fixed handling of the reversals caused by using
- when invoking a subset with @.
The implementation of the -on, -off and
-reverse attribute specifiers has changed. The main goal
was that -on should no longer be implied in every
subset record. Thus, an explicit -on is now required
in subset records if that is the
intent. The advantage is that a subset record can now be used to modify
attributes of a set of lines without unintentionally turning back on
lines that have been turned off. -on is still implied
in the actual line definitions.
The implementation of wildcards in subset-record interpretation has changed. The wildcards '*' (standing for zero or more characters) and '?' (standing for a single character) can now be anywhere in the line specifier. Previously only '*' was recognized and it had to be at the end of the line specifier.
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