MantisBT - Bender
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IDProjectCategoryView StatusDate SubmittedLast Update
0013882BenderWorkflowpublic2013-01-25 19:202013-03-04 15:36
ReporterJulien Finet 
Assigned Tojohan andruejol 
PrioritynormalSeverityfeatureReproducibilityN/A
StatusclosedResolutionfixed 
PlatformOSOS Version
Product Version0.1 
Target Version1.0Fixed in Version1.0 
Summary0013882: Add workflow module
DescriptionThere must be a workflow module to guide the user step by step in the repositioning of its labelmap.
It notably should take care of the pre-processing.
Steps To Reproduce
Additional Information
TagsNo tags attached.
Relationships
parent of 0013890closed Julien Finet Integrate Slicer changes into Workflow modules 
parent of 0013891resolved johan andruejol Apply PoseBody anytime the armature is changed 
parent of 0013971closed johan andruejol Advanced workflow tweaks 
Attached Files
Issue History
Date ModifiedUsernameFieldChange
2013-01-25 19:20Julien FinetNew Issue
2013-01-25 19:20Julien FinetStatusnew => assigned
2013-01-25 19:20Julien FinetAssigned To => Julien Finet
2013-02-04 09:45Julien FinetRelationship addedparent of 0013890
2013-02-04 16:04Julien FinetRelationship addedparent of 0013891
2013-02-12 15:54Julien FinetNote Added: 0032251
2013-02-12 15:54Julien FinetAssigned ToJulien Finet => johan andruejol
2013-02-13 10:21johan andruejolNote Added: 0032256
2013-02-22 17:57Julien FinetNote Added: 0032363
2013-02-22 17:58Julien FinetNote Edited: 0032363bug_revision_view_page.php?bugnote_id=32363#r1046
2013-02-22 18:13Julien FinetNote Edited: 0032363bug_revision_view_page.php?bugnote_id=32363#r1047
2013-02-24 18:11Julien FinetNote Edited: 0032363bug_revision_view_page.php?bugnote_id=32363#r1048
2013-02-24 19:42Julien FinetNote Edited: 0032363bug_revision_view_page.php?bugnote_id=32363#r1049
2013-02-25 10:22Julien FinetNote Edited: 0032363bug_revision_view_page.php?bugnote_id=32363#r1050
2013-02-26 17:02johan andruejolNote Added: 0032388
2013-02-26 17:02johan andruejolStatusassigned => resolved
2013-02-26 17:02johan andruejolResolutionopen => fixed
2013-02-26 18:42Julien FinetNote Added: 0032390
2013-02-26 18:42Julien FinetStatusresolved => assigned
2013-03-03 22:22Julien FinetProduct Version => 0.1
2013-03-03 22:22Julien FinetTarget Version => 1.0
2013-03-03 22:35Julien FinetRelationship addedparent of 0013971
2013-03-03 22:36Julien FinetNote Deleted: 0032390
2013-03-03 22:36Julien FinetNote Added: 0032431
2013-03-03 22:36Julien FinetStatusassigned => resolved
2013-03-03 22:36Julien FinetFixed in Version => 1.0
2013-03-04 15:36Julien FinetStatusresolved => closed

Notes
(0032251)
Julien Finet   
2013-02-12 15:54   
a) Armatures page:
  * Change the layout to 3D view before going to Armature module
  * Set the purple (Right, Left, Anterior, Posterior, Inforior, Superior) box around the bones model (-> same as the "center" button in the 3D view toolbar.
  * Advanced feature
  ** (TBD) Create automatically an armature node
  ** (TBD) the created armature node could have a node initialized as the root node (coccyx)
(0032256)
johan andruejol   
2013-02-13 10:21   
There are two branches (merge into the main branch workflow):

http://public.kitware.com/gitweb?p=Bender/Bender.git;a=commit;h=7b6a577ff5d8b5f08b7fd4c3c556d723f7bf43e7 [^]

http://public.kitware.com/gitweb?p=Bender/Bender.git;a=commit;h=0e25af8f681e414d0b8a130136d8182ae062a8b0 [^]

Advanced features mentioned above not covered yet.
(0032363)
Julien Finet   
2013-02-22 17:57   
(edited on: 2013-02-25 10:22)
0: Workflow generalities
 * a) Use (create) progress bar pushbutton for all the "Apply" buttons running CLIs
 * b) or reuse the CLI progress bar of all the CLI modules (above the Previous/Next buttons
 * c) Bender Workflow should be the first module of the module list, and should be the first module to show up
 * d) "Advanced workflow" checkbox should be to the left of the text (or reduce the space between the text and the checkbox)
 * e) Add tooltip for each button
 * f) Move "Volume Render" section in 2:B) into general section
 * g) When "Go To Module" is clicked, the CLI node should be updated

1: Adjust labelmap
 * a) Set automatically layout to 2x2
A) Labelmap
 * a) Add GenericColors entry as it is the default color node when loading a volume as labelmap
 * b) Automatically select the current color node at startup
B) Merge labels
 * a) Merge bones into "Bone.cancellous" instead of "Bone.MARROW"

2: Extract bones and skin
A) Bone model maker
 * a) Reset camera after bone is generated
 * b) Automatically create a model hierarchy if needed
 * c) After "Generate bone model" is executed, why "Model Hierarchy" is created? (After "Generate skin model" too).
 * d) Rename "Skeleton" into "Bones", for consistency
 * e) Add "Go to Models" pushbutton

3: Create rest armature
 * a) Add a "Load Armature" button (for now loads a mrml scene).
 * b) Add a "Save Armature" button (for now manually create a MRML scene with the armature and bones into it)
 * c) Add "Toggle Skin Visibility" pushbutton

4: Skinning
 * a) Remove annoying top level tooltip
 * b) Merge 4: with 3: ?
A) Segment bones
 * a) Output should be renamed into "Output body partition"
 * b) Armature should be selected by default
 * c) "Go To Armature Bones Module" goes to "Armature Weight" instead of "Armature Bones"
B) Armature Weights
 * a) Rename "Body partition" into "Input body partition"
 * b) "Go to Armature Weights" module should be advanced
 * c) parameters in "Bender Workflow" are different from the ones in Armature Weights module.
 * d) in "Armature Weights" module, "Controls" parameters should not be "advanced"->collapsed
 * e) Armature should be selected by default

5: Pose armature
A) Armatures
 * a) select "Pose" mode from Armature module when "5: Pose armature" page is current
B) Evaluate Weight
 * a) "B) Evaluate Weight" should be before "A) Armatures"
 * b) Automatically choose the Skin model
C) Pose Body
 * a) Rename into "C) Pose Surface"
 * b) Automatically choose the Skin model as input
 * c) Automatically choose an output other than input, but with a "-posed" suffix
 
6: Pose labelmap
A) Resample labelmap in pose
 * a) Armature should be selected by default
 * b) Should have a Weight directory input in advanced workflow mode
 * c) Integrate PoseLabelmap module
(0032388)
johan andruejol   
2013-02-26 17:02   
Julien's Work: 0) to 3)

http://public.kitware.com/gitweb?p=Bender/Bender.git;a=commit;h=60e2d8c14aa27982ee9b2dbc7a8beee2b77e442a [^]

4): http://public.kitware.com/gitweb?p=Bender/Bender.git;a=commit;h=bfdb43e0cbf8a84d0ba1f7b761399e332b712b49 [^]

5):http://public.kitware.com/gitweb?p=Bender/Bender.git;a=commit;h=7cb12bc22319ac3ff2f5191154bee85199fd0ba8 [^]

6): Merged heat diffusion and http://public.kitware.com/gitweb?p=Bender/Bender.git;a=commit;h=a66595e4178995baa3ff8e3e20256ac705e1a016 [^]
(0032431)
Julien Finet   
2013-03-03 22:36   
Remaining issues are tracked in 0013971