mops
Mops allow users to perform morphological operations and restrict rendering to specific regions in the data.
Mop specifies the morphological operations to be performed on the empty space skipping volume. This volume is used as a mask. The rendering is limited to within the non-zero regions of this mask. This buffer is generated by applying contributing transfer functions to drag volume. Voxels that contribute to the final image are set to 255. In the final rendering, values from mask buffer are multiplied with the opacities. 0 is completely transparent i.e. will not contribute to final image.
In the final rendering, values in channel 0 from mask buffer are multiplied with the opacities. 0 is completely transparent - will not contribute to final image. For non-zero values (tags) in channel 2, appropriate tag color and opacity (change tag color/opacity via Preferences widget) is mixed to generate the final color and opacity.
The mask buffer is saved in keyframes, when there is a mop operation performed on the mask buffer, so they can be animated. The mask buffer resides on GPU and needs to be downloaded onto CPU side. GPU-CPU transfer are very slow, therefore saving and restoring keyframes will be slower for large datasets, whenever mop is employed. When there is no mop involved the mask buffer is not saved, which is the default case. User also has option of not interpolating the mask buffer - use None option for interpolate Mop. This option is available when spacebar is pressed for selected keyframe. Mask buffers can also be copied from one keyframe to another.
All morphological commands start with mop and are entered via the command dialog.
Morphologcal operations can be performed in stages. For example to remove top skin one can follow the following protocol
- shrinkwrap mop shrinkwrap 10 based on size of the hole you would like to plug.
- invert mop invert invert current mask
- thicken mop thicken 4 thicken current mask - this will catch 4 voxel deep top layer
- invert mop invert this will expose interior by removing top layer - that thicken 4 voxel layer.
Another way could be
- shrinkwrap mop shrinkwrap 10
- cityblock cityblock 4 distance transform will be evaluated only 4 voxels deep
- saturate 0 mop sat0 5 voxel masks below 5 are set to 0 - this will remove 4 voxel deep top layer.
Users can also specify transfer function set to use while creating the mask buffer.
Various options that are supported are listed below.
* [average](#average) * [blend](#blend) * [carve](#carve) * [carverad](#carverad) * [chessboard](#chessboard) * [cityblock](#cityblock) * [close](#close) * [copy](#copy) * [copyfromsaved](#copyfromsaved) * [copytosaved](#copytosaved) * [dilateedge](#dilateedge) * [dilate](#dilate) * [edge](#edge) * [erode](#erode) * [fusepatch](#fusepatch) * [hatch](#hatch) * [histogram](#histogram) * [invert](#invert) * [itk](#itk) * [localmax](#localmax) * [localthickness](#localthickness) * [masktf](#masktf) * [max](#max) * [maxvalue](#maxvalue) * [min](#min) * [nop](#nop) * [open](#open) * [paint](#paint) * [rdilate](#rdilate) * [removepatch](#removepatch) * [sat0](#sat0) * [sat1](#sat1) * [save](#save) * [setvalue](#setvalue) * [shrink](#shrink) * [shrinkwrap](#shrinkwrap) * [smoothchannel](#smoothchannel) * [swap](#swap) * [tag](#tag) * [thicken](#thicken) * [update](#update) * [xor](#xor)### average average (chan1) (chan2) (dst)
dst = (chan1 + chan2)/2
### blend blend (off)
Switch on/off blend mode.
When blend mode is switched on, the paint tags that users have painted on the data are used as reference to the transfer functions for blending. Appropriate transfer functions will be blended in place of tag colors - tag value refers to the transfer function set. If the tag value is greater than the total number of transfer function sets, then set 0 is chosen.
When multiple volumes are loaded, appropriate transfer functions from different sets are applied to the volumes with the tag value refering volume 0 transfer functions. In the case of multiple volumes, user need to take care of choosing appropriate tag values for painting, so that there is no overlap between transfer function sets.
### carve carve (off)
Switch on/off carve mode.
Using carve users can modify values in channel 1. Only the mask values in a sperical region around mouse cursor and those that have non-zero channel 1 are affected. Channel 1 values are normally set for non-zero opacity voxels when mask texture gets updated with transfer function change.
When in carve mode, users can remove spherical portions of the data by using shift+left mouse drag. Normally shift+left mouse click add a point - this normal function is disabled when carving is switched on. Only mask values that have non-zero channel 1 are carved.
Shift+right (or Ctrl+left) mouse drag will restore mask buffer values in the spherical region defined by carve radius. Only mask values that have non-zero channel 1 are restored.
Shift+middle (or Alt+left) mouse drag will set mask buffer values in the spherical region defined by carve radius to 255.
Users can also employ paths and points for carving operations. Path can also be used to patchup big holes. Points can be used to fillup large empty spaces before shrinkwrap operations.
### carverad carverad (radius) (decay)
Specify carve radius and decay parameters. Carving allows users to remove spherical portions of the data by setting mask buffer values to 0 in that region. Carve radius defines the sphere of influence. The decay parameter specifies the smoothing near the edges - mask buffer values are set to 0 near the central region and are smoothstepped to original values near edge. Decay value 0 implies sharp boundary.
Users can also change carve radius and decay using up/down and left/right arrows respectively.
For example :
mop carverad 20 5 : influence sphere of radius 20, with 0 values within sphere of radius 15 and gradually climbing to original values near the edge.
### chessboard chessboard (sz)
Chessboard distance transform. The values start with 0 on the surface of the object and increasing inside the object. Default value for sz is 100.
### cityblock cityblock (sz)
Cityblock distance transform. The values start with 0 on the surface of the object and increasing inside the object. Default value for sz is 100.
### close close (sz) (chan)
Morphological closing of channel chan - dilate followed by erode dictated by size parameter. Default value for sz is 1 and chan is 0.
### copy copy (src) (dst)
Copy mask buffer channel src to mask buffer channel dst. src and dst can be either 0,1,2.
### copyfromsaved copyfromsaved (src) (dst)
Copy savedbuffer channel src to mask buffer channel dst. If specified, src and dst can be either 0,1,2. If not specified, all channels from savedbuffer are copied to mask buffer.
### copytosaved copytosaved (src) (dst)
Copy mask buffer channel src to savedbuffer channel dst. If specified, src and dst can be either 0,1,2. If not specified, all channels from mask buffer are copied to savedbuffer.
### dilateedge diateedge (val1) (val2)
Very similar to erode - values near the edge are set to zero based on current mask values at those positions. User needs to provide two parameters to this operation which will specify range of values that can be eroded. If only one value is provided then the range of values is taken as [1, val].
For example :
mop dilateedge 100 : erode edge where values are between 1 and 100
mop dilateedge 230 253 : erode edge where values are between 230 and 253
### dilate dilate (sz) (chan)
Dilate mask buffer channel chan by sz. Default is dilate by 1 for chan 0.
### edge edge (val) (thickness)
Set edges of mask buffer to val. Parameter thickness controls how thick edge would be. By default val is 0 and thickness is 1.
For example :
mop edge 0 2 : set 2-voxel thick edge to 0
### erode erode (sz) (chan)
Erode mask buffer channel chan by sz. Default value for sz is 1 and chan is 0.
### fusepatch fusepatch
Merge patches that were added using paths with the rest of the mask. Patches are usually added to help contain the interior region during shrinkwrap process.
### hatch hatch (box | grid) (xn) (xd) (yn) (yd) (zn) (zd)
This action etched a box or grid hatching pattern on channel 0 based on "box" or "grid" option and integer values xn,xd,yn,yd,zn,zd.
Pseudo code to set channel value to 0 is as follows :
zeroit = true;
if (xn > 0 and xd > 0) zeroit .and. (xcoord%xn < xd);
if (yn > 0 and yd > 0) zeroit .and. (ycoord%yn < yd);
if (zn > 0 and zd > 0) zeroit .and. (zcoord%zn < zd);
if (box selected and zeroit is true) then set value to 0;
if (grid selected and zeroit is false) then set value to 0;
### histogram histogram (chan)
Calculate frequency histogram for channel chan. Default value for chan is 2.
### invert invert
Inverts the mask buffer : 255-current mask value.
### itk itk
Apply ITK (Insight Tool Kit) filters. Several filter are implemented. Channel 1 (which usually stores opacity information) is passed on to the filter. The results are passed back in channel 2. The filter is performed over the opacity information - users can tweek data in channel 1 (for e.g. carving) to achieve the required result.
### localmax localmax
Find locally maximum values.
### localthickness localthickness (sz)
Finds local thickness - channel 0 mask buffer values are used to calculate the local thickness and these values are stored in channel 2 of the mask buffer. Default value for sz is 100.
### masktf masktf (tf)
Specify which transfer function set to use for generating the mask buffer. If the tf parameter is -1, then contributing transfer functions from all the sets are considered for generating the empty space skipping mask buffer. -1 is default value, if no value is specified.
For example :
mop masktf -1 - use transfer function from all the sets.
mop masktf 1 - use transfer funtions from set 1 only.
### max max (ch1) (ch2)
Take maximum of current mask buffer channel ch1 and saved buffer channel ch2 - behaves as union of current buffer and saved buffer. If specified, ch1 and ch2 can be either 0,1,2. If not specified, all channels are considered.
### maxvalue maxvalue
Displays maximum buffer value for each channel.
### min min (ch1) (ch2)
Take minimum of current mask buffer channel ch1 and saved buffer channel ch2 - behaves as intersection of current buffer and saved buffer. If specified, ch1 and ch2 can be either 0,1,2. If not specified, all channels are considered.
### nop nop
Dilate mask buffer by 1. This is the default option.
### open open (sz) (chan)
Morphological opening of channel chan - erode followed by dilate dictated by size parameter. Default value for sz is 1 and chan is 0.
### paint paint (off)
Switch on/off paint mode. When in paint mode, users can paint tags on the data. Tags are shown as colours mixed on top of the transfer function. Tag colours are mixed based on opacity parameter of the colour, which can be set individually for each tag color. The tag colours are set via Preferences - Tag Colour menu.
### rdilate rdilate (val) (sz)
Restricted dilate - dilate mask buffer by sz only for voxels with value val. Default values for sz and val are 1 and 255 resp.
### removepatch removepatch
Remove the patches that were added using paths. Patches are usually added to help contain the interior region during shrinkwrap process.
### sat0 sat0 (val) (chan)
Mask value of channel chan less than val will be set to 0. Some mask value will be greater than 0 but less than 255 for cityblock, thicken or shrinkwrap operations. Default value for val is 255 and chan is 0
### sat1 sat1 (val) (chan)
Mask value of channel chan greater than val will be set to 255. Some mask value will be greater than 0 but less than 255 for cityblock, thicken or shrinkwrap operations. Default value for val is 0 and chan is also 0.
### save save
Save mask buffer to raw file or image. The data will be save as 1-byte per voxel. The mask value will range from 0 to 255.
### setvalue setvalue (val) (minval) (maxval) (chan)
If channel chan maskbuffer value lies between minval and maxval, then set it to val. Default value for chan is 0.
This option can be used to create a shell - for example :
apply distance transform : mop cityblock 20
set voxels away from surface to 0 : mop setvalue 0 5 255 - all 5 and above voxel deep are set to 0
set non-zero voxels to 1 : mop sat1 0 - (or : mop setvalue 255 0 255)
### shrink shrink (sz) (chan)
Erode channel 0 by sz based on values in channel chan. Erosion operation is only applied at voxels where value of chan is zero. Default value for sz is 10 and chan is 1.
This operation is useful for eroding filled cavities on the exterior of the structure by shrinkwrap operation.
### shrinkwrap shrinkwrap (sz)
Very similar to close, except erosion starts from the edge of the subvolume box. Default value for sz is 50.
This operation applies following protocol :
thicken current buffer by sz
set 1-voxel thin edges of the bounding box to 0
thicken 0 valued edge by sz
### smoothchannel smoothchannel (chan)
Apply 3x3x3 averaging for mask buffer values in channel chan. Only non-zero values are considered for smoothing.
### swap swap (ch1) (ch2)
Swap mask buffer channel ch1 and savedbuffer channel ch2.
### tag tag (val)
Set tag value for painting. Value must be between 0 and 255.
### thicken thicken (sz
Very similar to dilate - except mask buffer values decrease as one goes into empty region away from original surface like distance transform. Default value for sz is 1.
### update update (off)
Switch on/off updating of mask buffer. By default the mask buffer will be updated every time a transfer function is changed. Users can switch off these updates and freeze the mask buffer by specifying "off" or "no" for the parameter. If no parameter is specified the updates will be swithed on. The mask buffer will always be updated whenever any morphological operaion (listed below) are performed.
For example :
mop update off - to turn of updates to mask buffer.
mop update - to turn on updates for every transfer function change.
Even when updates to the buffer via transfer function changes are switched off, all morphological operations do update the current buffer. This enables user to perform multiple operations one after another.
### xor xor (ch1) (ch2)
XOR mask buffer channel ch1 with savedbuffer channel ch2. Result is stored in channel ch1 of mask buffer. If specified, ch1 and ch2 can be either 0,1,2. If not specified, all channels from mask buffer are xored with savedbuffer.
File Formats
. .pvl.nc file format
Panels
. Keyframe Editor
Main Window Dialog
Main Window Keyboard and Mouse bindings
Mops - morphological/mask operations
Clip Planes
Clip Planes - Property Dialog
Clip Planes - Commands
Clip Planes - Keyboard and Mouse bindings
Paths
Paths - Property Dialog
Paths - Keyboard and Mouse bindings