Removing ImageMath dependency #53

stnava · 2015-06-09T15:47:45Z

ANTsR will be "broken" for a while ... Being tired of this ongoing issue, I did the aggressive thing and removed imageMath and src/ImageMath.cpp and also updated the antstag s.t. ImageMath is not compiled in core. here are the current issues:

* checking R code for possible problems ... NOTE
aslCensoring : aslOutlierRejection: no visible global function
  definition for ‘imageMath’
basicInPaint: no visible global function definition for ‘imageMath’
compcor: no visible global function definition for ‘imageMath’
getCentroids: no visible global function definition for ‘imageMath’
getTemplateCoordinates: no visible global function definition for
  ‘imageMath’
projectImageAlongAxis: no visible global function definition for
  ‘imageMath’
sliceTimingCorrection: no visible global function definition for
  ‘imageMath’
* checking Rd files ... OK

relating to:

ANTsR/R/aslCensoring.R:    imageMath(4, diffs, "TimeSeriesSimpleSubtraction", asl)
ANTsR/R/basicInPaint.R:  imageMath(img@dimension, temp, "MD", temp, 1)
ANTsR/R/basicInPaint.R:  # imageMath(img@dimension,paintMaskUse,'GD',paintMask,1)
ANTsR/R/basicInPaint.R:  imageMath(inpainted@dimension, inpainted, "FastMarchingExtension", speedimage,
ANTsR/R/compcor.R:    imageMath(4, myoutfn, "CompCorrAuto", fmri, mask, ncompcor)
ANTsR/R/getCentroids.R:  imageMath(imagedim, pointfile, "LabelStats", img, img, clustparam)
ANTsR/R/getTemplateCoordinates.R:  imageMath(milab@dimension, pointfile, "LabelStats",
ANTsR/R/pairwiseImageDistanceMatrix.R:        # broken !!  metric <- capture.output(imageMath(dim, 'j', metrictype, i1,
ANTsR/R/projectImageAlongAxis.R:  imageMath(imageND@dimension, downimg, "Project", imageND, axis, projtype)
ANTsR/R/sliceTimingCorrection.R:    imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
ANTsR/R/sliceTimingCorrection.R:    imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
ANTsR/R/sliceTimingCorrection.R:    imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime)

here is a commit that deals with some of these:

3713fd8

however it would be good to get the rest as well ...

@jeffduda a few pieces of functionality in iMath

Project operator from ImageMath
FastMarchingExtension

@bkandel add x, y, z, t to labelStats ... the output is always 4D centroids ... e.g. in 2D it will contain x_i, y_i, 0, 0 ( or maybe NA, NA ) ....

the other issues should be self explanatory.

The text was updated successfully, but these errors were encountered:

bkandel · 2015-06-09T15:59:42Z

sounds good. i already fixed the aslCensoring dependency, just waiting on
test suite to run before committing.

for the labelStats xyz coords, should i just use the raw output from
labelgeometryimagefilter, or is there some other space that the coordinates
should be drawn from?

2015-06-09 11:47 GMT-04:00 stnava notifications@github.com:

@jeffduda https://github.com/jeffduda @bkandel
https://github.com/bkandel

ANTsR will be "broken" for a while ... Being tired of this ongoing issue,
I did the aggressive thing and removed imageMath and src/ImageMath.cpp and
also updated the antstag s.t. ImageMath is not compiled in core. here are
the current issues:

checking R code for possible problems ... NOTE
aslCensoring : aslOutlierRejection: no visible global function
definition for ‘imageMath’
basicInPaint: no visible global function definition for ‘imageMath’
compcor: no visible global function definition for ‘imageMath’
getCentroids: no visible global function definition for ‘imageMath’
getTemplateCoordinates: no visible global function definition for
‘imageMath’
projectImageAlongAxis: no visible global function definition for
‘imageMath’
sliceTimingCorrection: no visible global function definition for
‘imageMath’

checking Rd files ... OK

relating to:

ANTsR/R/aslCensoring.R: imageMath(4, diffs, "TimeSeriesSimpleSubtraction", asl)
ANTsR/R/basicInPaint.R: imageMath(img@dimension, temp, "MD", temp, 1)
ANTsR/R/basicInPaint.R: # imageMath(img@dimension,paintMaskUse,'GD',paintMask,1)
ANTsR/R/basicInPaint.R: imageMath(inpainted@dimension, inpainted, "FastMarchingExtension", speedimage,
ANTsR/R/compcor.R: imageMath(4, myoutfn, "CompCorrAuto", fmri, mask, ncompcor)
ANTsR/R/getCentroids.R: imageMath(imagedim, pointfile, "LabelStats", img, img, clustparam)
ANTsR/R/getTemplateCoordinates.R: imageMath(milab@dimension, pointfile, "LabelStats",
ANTsR/R/pairwiseImageDistanceMatrix.R: # broken !! metric <- capture.output(imageMath(dim, 'j', metrictype, i1,
ANTsR/R/projectImageAlongAxis.R: imageMath(imageND@dimension, downimg, "Project", imageND, axis, projtype)
ANTsR/R/sliceTimingCorrection.R: imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
ANTsR/R/sliceTimingCorrection.R: imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
ANTsR/R/sliceTimingCorrection.R: imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime)

here is a commit that deals with some of these:

3713fd8
3713fd8

however it would be good to get the rest as well ...

@jeffduda https://github.com/jeffduda a few pieces of functionality in
iMath

Project operator from ImageMath

FastMarchingExtension

@bkandel https://github.com/bkandel add x, y, z, t to labelStats ...
the output is always 4D centroids ... e.g. in 2D it will contain x_i, y_i,
0, 0 ( or maybe NA, NA ) ....

the other issues should be self explanatory.

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#53.

stnava · 2015-06-09T16:44:09Z

i forgot about labelGeometryMeasures, in part because it was broken. so i will fix the calls to labelStats by using this instead. so never mind about labelStats ....

stnava · 2015-06-09T17:01:22Z

done.

stnava · 2015-06-09T17:43:01Z

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R:    imageMath(4, diffs, "TimeSeriesSimpleSubtraction", asl)
R/sliceTimingCorrection.R:    imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R:    imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R:    imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime)

jeffduda · 2015-06-09T18:46:16Z

We should probably just get rid of sliceTimingCorrection.R for now. It
makes a number of assumption which aren't true for data that is currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs, "TimeSeriesSimpleSubtraction", asl)
R/sliceTimingCorrection.R: imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected, "SliceTimingCorrection", fmri, sliceTime)

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stnava · 2015-06-09T19:10:38Z

i am ok with that and will implement now.

any thoughts on the other 2: (1) projection (2) fast marching extension ?

brian

On Tue, Jun 9, 2015 at 2:46 PM, Jeffrey Duda notifications@github.com
wrote:

We should probably just get rid of sliceTimingCorrection.R for now. It
makes a number of assumption which aren't true for data that is currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs, "TimeSeriesSimpleSubtraction", asl)
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime)

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jeffduda · 2015-06-09T19:13:20Z

I can work on those today.

On Tue, Jun 9, 2015 at 3:10 PM stnava notifications@github.com wrote:

i am ok with that and will implement now.

any thoughts on the other 2: (1) projection (2) fast marching extension ?

brian

On Tue, Jun 9, 2015 at 2:46 PM, Jeffrey Duda notifications@github.com
wrote:

We should probably just get rid of sliceTimingCorrection.R for now. It
makes a number of assumption which aren't true for data that is currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs, "TimeSeriesSimpleSubtraction",
asl)
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime)

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jeffduda · 2015-06-09T21:15:48Z

rather than make "project" part of iMath, i wrote apply.antsImage. This has
the advantage of being much more R-like and allowing an arbitrary function
to be used for the projection. It's just a wrapper for apply that handles
the header info.

On Tue, Jun 9, 2015 at 3:13 PM Jeffrey Duda jeff.duda@gmail.com wrote:

I can work on those today.

On Tue, Jun 9, 2015 at 3:10 PM stnava notifications@github.com wrote:

i am ok with that and will implement now.

any thoughts on the other 2: (1) projection (2) fast marching extension ?

brian

On Tue, Jun 9, 2015 at 2:46 PM, Jeffrey Duda notifications@github.com
wrote:

We should probably just get rid of sliceTimingCorrection.R for now. It
makes a number of assumption which aren't true for data that is
currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs, "TimeSeriesSimpleSubtraction",
asl)
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime)

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#53 (comment).

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#53 (comment).

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stnava · 2015-06-09T21:19:03Z

that makes sense, of course. probably very useful if we can figure out
what to do with it.

one issue is how to take care of the header info - guess you can wrap that
into apply.

brian

On Tue, Jun 9, 2015 at 5:15 PM, Jeffrey Duda notifications@github.com
wrote:

rather than make "project" part of iMath, i wrote apply.antsImage. This has
the advantage of being much more R-like and allowing an arbitrary function
to be used for the projection. It's just a wrapper for apply that handles
the header info.

On Tue, Jun 9, 2015 at 3:13 PM Jeffrey Duda jeff.duda@gmail.com wrote:

I can work on those today.

On Tue, Jun 9, 2015 at 3:10 PM stnava notifications@github.com wrote:

i am ok with that and will implement now.

any thoughts on the other 2: (1) projection (2) fast marching extension
?

brian

On Tue, Jun 9, 2015 at 2:46 PM, Jeffrey Duda notifications@github.com
wrote:

We should probably just get rid of sliceTimingCorrection.R for now. It
makes a number of assumption which aren't true for data that is
currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com
wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs, "TimeSeriesSimpleSubtraction",
asl)
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime)

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#53 (comment).

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#53 (comment).

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stnava · 2015-06-09T21:29:14Z

looks like FastMarchingExtension may be the only thing left ... that may
also be better off in a separate location than iMath ...

brian

On Tue, Jun 9, 2015 at 5:18 PM, brian avants stnava@gmail.com wrote:

that makes sense, of course. probably very useful if we can figure out
what to do with it.

one issue is how to take care of the header info - guess you can wrap that
into apply.

brian

On Tue, Jun 9, 2015 at 5:15 PM, Jeffrey Duda notifications@github.com
wrote:

rather than make "project" part of iMath, i wrote apply.antsImage. This
has
the advantage of being much more R-like and allowing an arbitrary function
to be used for the projection. It's just a wrapper for apply that handles
the header info.

On Tue, Jun 9, 2015 at 3:13 PM Jeffrey Duda jeff.duda@gmail.com wrote:

I can work on those today.

On Tue, Jun 9, 2015 at 3:10 PM stnava notifications@github.com wrote:

i am ok with that and will implement now.

any thoughts on the other 2: (1) projection (2) fast marching
extension ?

brian

On Tue, Jun 9, 2015 at 2:46 PM, Jeffrey Duda <notifications@github.com

wrote:

We should probably just get rid of sliceTimingCorrection.R for now.
It
makes a number of assumption which aren't true for data that is
currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com
wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs,
"TimeSeriesSimpleSubtraction",
asl)
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime)

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<#53 (comment)
.

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#53 (comment).

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jeffduda · 2015-06-09T21:36:18Z

Was thinking the same. Will make it, it's own .cpp

On Tue, Jun 9, 2015 at 5:29 PM stnava notifications@github.com wrote:

looks like FastMarchingExtension may be the only thing left ... that may
also be better off in a separate location than iMath ...

brian

On Tue, Jun 9, 2015 at 5:18 PM, brian avants stnava@gmail.com wrote:

that makes sense, of course. probably very useful if we can figure out
what to do with it.

one issue is how to take care of the header info - guess you can wrap
that
into apply.

brian

On Tue, Jun 9, 2015 at 5:15 PM, Jeffrey Duda notifications@github.com
wrote:

rather than make "project" part of iMath, i wrote apply.antsImage. This
has
the advantage of being much more R-like and allowing an arbitrary
function
to be used for the projection. It's just a wrapper for apply that
handles
the header info.

On Tue, Jun 9, 2015 at 3:13 PM Jeffrey Duda jeff.duda@gmail.com
wrote:

I can work on those today.

On Tue, Jun 9, 2015 at 3:10 PM stnava notifications@github.com
wrote:

i am ok with that and will implement now.

any thoughts on the other 2: (1) projection (2) fast marching
extension ?

brian

On Tue, Jun 9, 2015 at 2:46 PM, Jeffrey Duda <
notifications@github.com

wrote:

We should probably just get rid of sliceTimingCorrection.R for now.
It
makes a number of assumption which aren't true for data that is
currently
being collected.

On Tue, Jun 9, 2015 at 1:43 PM stnava notifications@github.com
wrote:

Remaining issues

MacBook-Pro:ANTsR stnava$ grep imageMath R/*
R/aslCensoring.R: imageMath(4, diffs,
"TimeSeriesSimpleSubtraction",
asl)
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime, interpolation,
R/sliceTimingCorrection.R: imageMath(4, corrected,
"SliceTimingCorrection", fmri, sliceTime)

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#53 (comment)
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stnava · 2015-06-10T14:04:36Z

added some documentation to FastMarchingExtension and updated basicInPaint ...

not sure the documentation has the right usage of the mask ... you might want clean that up / make sure it works with an example .... if you get a chance to do so, let me know.

jeffduda · 2015-06-10T19:40:20Z

Looks like apply isn't a generic so we can't make it work like we do with
plot, but as it is, apply.antsImage should handle all the header info and
work the same as a call to apply with an array

On Wed, Jun 10, 2015 at 10:04 AM stnava notifications@github.com wrote:

added some documentation to FastMarchingExtension and updated basicInPaint
...

not sure the documentation has the right usage of the mask ... you might
want clean that up / make sure it works with an example .... if you get a
chance to do so, let me know.

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stnava · 2015-06-10T21:48:12Z

this is pretty close to done ... will close the issue once we get both codeship and travis passing ...

stnava · 2015-06-11T15:28:30Z

fixed an example bug. this appears to be ready to close now.

stnava closed this as completed Jun 11, 2015

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Removing ImageMath dependency #53

Removing ImageMath dependency #53

stnava commented Jun 9, 2015

bkandel commented Jun 9, 2015

Project operator from ImageMath

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stnava commented Jun 11, 2015

Removing ImageMath dependency #53

Removing ImageMath dependency #53

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stnava commented Jun 9, 2015

bkandel commented Jun 9, 2015

Project operator from ImageMath

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