Re: [Teem-users] Fwd: Ready to release Teem 1.10?

[James B. <jam...@gm...>]

I'm all for it.  I would advocate releasing, fix any minor issues for 1.10.1
that come up and release more often from now on out.

James

On Sun, Dec 7, 2008 at 9:36 PM, Gordon Kindlmann <gk...@bw...> wrote:

> Hello-
>
> Any major last-minute requests?  On Dec 10 I'd like to call the svn
> trunk "Teem 1.10".
>
> Gordon
>
> Begin forwarded message:
>
> > From: Gordon Kindlmann <gk...@bw...>
> > Date: November 22, 2008 11:07:20 PM EST
> > To: Teem Users <tee...@li...>
> > Subject: [Teem-users] Ready to release Teem 1.10?
> >
> > Hi-
> >
> > I'm nearly finished with the things that I'd like to get done before
> > releasing Teem 1.10, which I'd like to do before Dec 10.
> >
> > Below is the summary of 3 years worth of changes, culled from all the
> > messages to teem-commit.
> >
> > Are there are other significantly broken things that people want
> > fixing?
> >
> > Gordon
> >
> >
> > It has been about three years since the last release 1.9.  Since that
> > time, Gordon has been working on getting publications and a job (bye
> > Red Sox, hello White Sox), but Teem development has continued.  Here
> > is a summary of the changes that people might notice since Teem 1.9.
> > The major API changes are likely to affect Teem-using software, the
> > smaller API changes less so.  Only the most important API additions
> > are listed.
> >
> > It is unlikely that there are functionality changes that are not
> > accompanied by an API change.  So teem-using code should break first
> > because of failures to link, not because of subtler behavioral chages.
> > Best of luck, and remember to email teem-users:
> >
> > http://lists.sourceforge.net/lists/listinfo/teem-users
> >
> > in case of problems or questions.
> >
> > ====================================================================
> > Over-all Changes ===================================================
> > ====================================================================
> >
> > Thanks to the efforts of James Bigler and Andy Cedilnik, The CMake
> > build system for Teem is mature, and should most certainly be used
> > instead of the old GNUMakefiles.
> >
> > In particular, CMake now builds for Teem a single "mega" library that
> > puts all the sub-libraries (air, biff, hest, etc) into a single place.
> > There is currently no single "mega" *header* file.
> >
> > Thanks to Steve Pieper, there's a new demo of how CMake projects can
> > use Teem in teem/UseTeemCMakeDemo
> >
> > Also thanks to Steve Pieper, Teem can now link with VTK's name-mangled
> > versions of the PNG and zlib libraries, via the TEEM_VTK_* options in
> > CMakeLists.txt
> >
> > Teem's CMake now generally refers to Teem as "Teem" instead of "TEEM".
> > This may break existing things that used CMake to build and use Teem.
> >
> > Teem now optionally uses the "levmar" library from
> > http://www.ics.forth.gr/~lourakis/levmar/<http://www.ics.forth.gr/%7Elourakis/levmar/>
> > as a new "external" for non-linear least-squares fitting.
> >
> > Anticipating the eventual removal of the GNUMakefile-based system for
> > building Teem, all the architecture-specific directories (darwin.32,
> > irix6.64, linux.32, linux.ia64, cygwin, darwin.64, irix6.n32,
> > linux.amd64, solaris) have beem moved from the top-level teem
> > directory into a new teem/arch subdirectory.  Perhaps confusingly,
> > this includes the win32 directory, even though that was (directly)
> > handled by GNUMake.
> >
> > ====================================================================
> > Major API Change ==================================================-
> > ====================================================================
> >
> > gage ---------
> >
> > gage_t is gone.  Use "double" instead.
> >
> > GAGE_ITEM_PREREQ_NUM changed from 5 to 6, then to 8, and also
> > renamed to GAGE_ITEM_PREREQ_MAXNUM
> >
> > If a volume doesn't identify itself as cell- or node-centered, gage
> > now assumes cell-centered (in Teem 1.9 gaged assumed node-centered).
> >
> > GAGE_KERNEL_NUM #define gone, now GAGE_KERNEL_MAX+1 plays its role
> >
> > rename GAGE_PERVOLUME_NUM --> GAGE_PERVOLUME_MAXNUM
> > rename GAGE_ITEM_PREREQ_NUM --> GAGE_ITEM_PREREQ_MAXNUM
> > rename GAGE_KERNEL_NUM --> GAGE_KERNEL_MAX
> > rename GAGE_CTX_FLAG_NUM --> GAGE_CTX_FLAG_MAX
> > rename GAGE_PVL_FLAG_NUM --> GAGE_PVL_FLAG_MAX
> >
> > The GAGE_PERVOLUME_MAXNUM (called GAGE_PERVOLUME_NUM in Teem-1.9)
> > #define
> > compile-time limit on the number of pervolumes in a context is
> > gone. The pvl[] array (and ctx->pvlNum) is now dynamically managed
> > with an airArray (ctx->pvlArr). As a result, the stackFslw[] array is
> > now also allocated dynamically (whenever the stack is attached)
> >
> > FIXED long-standing bug (how long I don't know) in how the derivatives
> > were normalized in volumes with only per-axis spacing (that is,
> > lacking full orientation info)- some users have noticed this change
> >
> > added matrices ItoWSubInvTransp and ItoWSubInv to gageShape, to handle
> > more general transforms from index to world space (now gage correctly
> > handles shear from gantry tilt, for example).  Thus, REMOVED fwScale[]
> > from gageShape, because its role has been taken over by
> > ItoWSubInvTransp and ItoWSubInv.
> >
> > gageScl3PFilter2, gageScl3PFilter4, and gageScl3PFilterN now take a
> > gageShape* as a mandatory first argument, because this stores the
> > ItoWSubInvTransp and ItoWSubInv matrices used to transform gradients
> > and hessians from index space to world space.  Note that this also
> > shifts the responsibility for this transform from something that is
> > strictly internal to gage, to something that is not strictly internal:
> > each gageKind is now responsible for doing this transform as part of
> > its filter() callback. In practice, there is no real change, because
> > all existing kinds ended calling the same gageScl3PFilter2,
> > gageScl3PFilter4, and gageScl3PFilterN functions, since they all
> > operate per-component.
> >
> > ten -----------
> >
> > renamed enum value tenEstimateMethod* -> tenEstimate1Method*
> >
> > tenFiberTypeEvec1 now refers to the medium eigenvector NOT the
> > principal one (that's tenFiberTypeEvec0)
> >
> > tenInvariantGradients_d() gone, replaced by more specific
> > tenInvariantGradientsK_d() and tenInvariantGradientsR_d()
> >
> > The tenAnisoCalc_f function has been removed. It was one of the
> > earliest
> > and stupidest functions in the ten library, it was incapable of high
> > accuracy
> > for mode-related invariants, and it has been superceded by other
> > functions.
> >
> > Specifically, use tenAnisoEval_f() or tenAnisoEval_d() to go from pre-
> > computed
> > eigenvalues to a particular anisotropy value, or use tenAnisoTen_f
> > () or
> > tenAnisoTen_d() to go from the full tensor value to an anisotropy
> > value.
> > Some functions (like tenAniso_Cl1 and related) make more sense
> > computed from
> > the individual eigenvalues, but others (like tenAniso_FA) can be
> > quickly
> > computed directly from the tensor value, no eigensolution required.
> >
> > The tenAniso_* enum and tenAniso airEnum are alive and well, and are
> > used
> > with the tenAniso{Eval,Ten}_{f,d} to identify which anisotropy to
> > compute.
> >
> > ====================================================================
> > Minor API change, no one probably notices ==========================
> > ====================================================================
> >
> > air ---------
> > airRandMTStateGlobal is no longer allocated at compile time. Now it is
> > both allocated and initialized as needed at run time. This will create
> > a memory-in-use-at-exit situation in valgrind.
> >
> > renames
> > airBesselI0Scaled --> airBesselI0ExpScaled
> > airBesselI1Scaled --> airBesselI1ExpScaled
> > airBesselInScaled --> airBesselInExpScaled
> >
> > nrrd ------
> > removed nrrdSpaceGet() (or its public declaration)- Teem's structs
> > are open for reading.
> >
> > changed nrrdResample_t from float to double; whatever is released
> > should use higher precision by default; other people can make it lower
> > precision for their own builds if they want.
> >
> > changed NrrdIoState->byteSkip from int to long int, in keeping with
> > type of offset argument to fseek
> >
> > changed _nrrdContainsPercentDAndMore(const char *str) to the slightly
> > more general purpose: _nrrdContainsPercentThisAndMore(const char *str,
> > char this) The only reason this was a public function was so that
> > unrrdu/dice could use it, but unrrdu/dice should be changed to use the
> > new nrrdSaveMulti anyway.
> >
> > As part of cleaning up kernels, some single-letter kernel
> > identifications were removed from _nrrdKernelStrToKern(), because they
> > were too clever, and too apt to be confused:
> >
> > - if (!strcmp("z", str)) return nrrdKernelZero;
> > - if (!strcmp("b", str)) return nrrdKernelBox;
> > - if (!strcmp("t", str)) return nrrdKernelTent;
> > - if (!strcmp("c", str)) return nrrdKernelBCCubic;
> > - if (!strcmp("cd", str)) return nrrdKernelBCCubicD;
> > - if (!strcmp("cdd", str)) return nrrdKernelBCCubicDD;
> > - if (!strcmp("q", str)) return nrrdKernelAQuartic;
> > - if (!strcmp("qd", str)) return nrrdKernelAQuarticD;
> > - if (!strcmp("qdd", str)) return nrrdKernelAQuarticDD;
> > - if (!strcmp("g", str)) return nrrdKernelGaussian;
> >
> > unrrdu / unu -------
> >
> > nrrdStateKeyValuePairsPropagate is now set to AIR_TRUE if user hasn't
> > already tried to set it via environment variable
> > NRRD_STATE_KEYVALUEPAIRS_PROPAGATE
> >
> > gage --------
> >
> > GAGE_QUERY_BYTES_NUM changed from 8 to 16, then to 24
> >
> > Some variables in the gageContext that were "int" have now been
> > changed to "unsigned int"; should have been done a lot time ago.
> > * gageContext->fd
> > * gagePoint->xi, yi, zi
> >
> > removed gageShapeUnitWtoI() and gageShapeUnitItoW() (the latter is
> > still used internally as _gageShapeUnitItoW) because they were never
> > outside of gage
> >
> > tweaked the logic of how continuous index-space space positions are
> > mapped to discrete index space and offsets (in _gageLocationSet),
> > and added test/indx function for debugging it.
> >
> > nixed the _gageStandardPadder() and _gageStandardNixer() functions
> > that have long since been made obsolete (ever since gage stopped doing
> > its own padding prior to probing)
> >
> > limn ---------
> > limnPolyData completely reorganized to have multiple per-attribute
> > arrays, but hopefully no one is using this as yet.
> >
> > limn now depends on gage.  In previous Teem versions, this was because
> > of how the feaure extraction needed gage, but now it is simply because
> > there is some plan of having more gage-specific per-vertex attribute
> > information stored in the limnPolyData
> >
> > renames:
> > limnObjectOFFRead -> limnObjectReadOFF
> > limnObjectOFFWrite -> limnObjectWriteOFF
> > limnPolyDataIVWrite -> limnPolyDataWriteIV
> > limnPolyDataLMPDRead -> limnPolyDataReadLMPD
> > limnPolyDataLMPDWrite -> limnPolyDataWriteLMPD
> > limnPolyDataVTKWrite -> limnPolyDataWriteVTK
> > limnPolyDataOFFRead -> limnPolyDataReadOFF
> >
> > ten ---------
> >
> > tenGradientParm no longer has "srand" flag, and now has an explicit
> > "seed" value, to allow reproducible results. "tend grads" has
> > different
> > command-line options accordingly
> >
> > tenAnisoPlot(Nrrd *nout, int aniso, unsigned int res,
> > int hflip, int whole, int nanout) now has the "hflip" horizontal
> > flip flag.
> >
> > Removed the tenAniso_Cz anisotropy measure. It was never used in Teem,
> > its not used in the literature, and its odd because its unbounded.
> >
> > renames:
> > tenEvqOne --> tenEvqSingle
> > tenMakeOne_f --> tenMakeSingle_f
> > tenMakeOne_d --> tenMakeSingle_d
> > tenSimulateOne_f --> tenSimulateSingle_f
> > various tenPath... -> tenInterp...
> >
> > push -------
> > The whole library is still under major revision, may get nixed
> > entirely if "pull" does everythings its supposed to
> >
> > ====================================================================
> > Major API New ======================================================
> > ====================================================================
> >
> > nrrd -------
> > negative byteskip now compatible with gzip encoding. Functionality
> > contributed by Katharina Quintus
> >
> > nrrdDistanceL2() and nrrdDistanceL2Signed() are fast separable
> > Euclidean distance transforms, based on code by Pedro Felzenszwalb,
> > accessible in "unu dist"
> >
> > added nrrdKernelDiscreteGaussian, which implements the discrete
> > Gaussian described by Lindeberg.  Thanks to Raul San Jose.
> >
> > added nrrdKernelSpecSprint(), which is like the opposite of
> > nrrdKernelSpecParse(): it prints the kernel specification to a
> > string. New code added to test/tkernel.c to demo this (as well as
> > adding airMop use).  To make the sprinted result parse'able, it was
> > discovered that sometimes the kernel's self-identification wasn't
> > actually recognized as identifying that kernel by
> > nrrdKernelParse(). This has been fixed
> >
> > gage -------
> >
> > added the ability to probe in "stacks"- where a single volume is
> > replaced by an array of volumes, with some kind of kernel-based
> > interpolation between volumes.  This could be used for generic 4-D
> > volumes, but more importantly it allows probing in scale-space.
> > Implementing this functionality was made possibly only because gage
> > has always allowed multiple per-volumes to be probed simultaneously
> > in a single context.  This needs to be documented elsewhere in detail,
> > but briefly:
> > gageStackBlur() pre-computes the stack with different blurring levels,
> > gageStackPerVolumeNew() allocates the per-volume array
> > gageStackPerVolumeAttach() attaches the per-volume array
> > gageStackProbe() does the probing at given 4-D position
> > gageStackProbeSpace() does 4-D probing, with extra tricks
> >
> > Internal change that shouldn't be much of an API change if at all: the
> > value of the first, unknown, item (e.g. gageSclUnknown) changes from
> > -1 to 0, and gageKinds have a new dynamicAlloc member to indicate if
> > the kind is dynamically allocated. The semantics of other gageKind
> > members has been clarified relative to this, and the initialization of
> > the item tables (e.g. _gageSclTable in teem/src/gage/scl.c) is simpler
> > now that the pre-requisite lists don't have to be filled out with -1s
> > (because C guarantees that uninitialized struct members will be
> > zero). If gage users assumed that the unknown item had value -1 (and
> > in fact, vprobe and pprobe stupidly did make this assumption), then
> > your code has to change.
> >
> > The reason that gageSclUnknown used to be -1 was that in the earliest
> > days of gage (when its brains were actually part of the bane library),
> > queries were represented by bitflags stored in int or a long long int,
> > and I didn't want to waste a bit (the first one) on representing an
> > item value that would never be used.
> >
> > limn ----------
> >
> > limnPolyDataSave() does auto-magic format detection based on filename
> > suffix.
> >
> > ten --------
> >
> > tenDwiGageKind is the first dynamic gageKind, meaning that information
> > is actually allocated in the gageKind, rather than being completely
> > set at compile time (as is gageKindScl, gageKindScl, and tenGage).
> > This is because the number of DWIs is set at run-time.  You currently
> > create a tenDwiGageKind with tenDwiGageKindNew() and kill it with
> > tenDwiGageKindNix().  You set all the stuff that needs to be set at
> > run-time with tenDwiGageKindSet(), but the API of this function is
> > pretty much guaranteed to change in future releases.  tenDwiGageKind
> > also represents the first use of gageKind->data and
> > gagePerVolume->data, which were added to gage long ago, but never
> > exploited until now.
> >
> > added tenFiberSingle, a new struct (based on a class previously in
> > Deft) for handling all information about a single tractography result
> > (following a single direction from a single seedpoint). Also added
> > functions for this: tenFiberSingleInit(), tenFiberSingleDone(),
> > tenFiberSingleNew(), tenFiberSingleNix(), and most importantly,
> > tenFiberSingleTrace(), which actually does tractography.
> >
> > added tenFiberMulti, a new struct for containing an array of
> > tenFiberSingles (basically an airArray), which is the output of
> > tenFiberMultiTrace().  The main purpose of this function is to break
> > the existing one-to-one correspondance between seed points and fibers,
> > which happens with multi-fiber tractography.
> >
> > added tenFiberMultiPolyData(), which converts an airArray of
> > tenFiberSingle's into limnPolyData. Like the tenFiberSingle, this is
> > another example of code moving from Deft into Teem.
> >
> > "tend fiber" has been enhanced to make more of this functionality
> > available, so it is finally able to do multiple tracts from a
> > given list of seedpoints, instead of being merely a one-track-pony.
> >
> > There are many, many more tenGage items now, including some from
> > Thomas Schultz, see teem/src/ten/ten.h for the full details.  The
> > proliferation of these has actually led to some changes in gage's
> > compile-time limits, and in the future we may have to move to a more
> > modular system where items are added dynamically at run-time.  How to
> > do this without breaking the existing API will be tricky.
> >
> > seek --------
> > New library for doing things like isosurfacing and ridge surface
> > extraction.  API will be in flux for some time.
> >
> > pull --------
> > New library for particle systems. API will be in flux.
> >
> > ====================================================================
> > Minor API New, not such a big deal =================================
> > ====================================================================
> >
> > air ---------
> > addded airRandMTSanity() to check return of airUIrandMT_r against
> > sequence of known values
> >
> > airInsane_AIR_NAN_f, and airInsane_AIR_NAN_d represent new ways that
> > airSanity() can fail
> >
> > airMode3_d() returns the "mode" of three values- really the skewness
> > scaled to fit in [-1,1]
> >
> > airEqvAdd() and airEqvSettle() might be useful for managing
> > information
> > about equivalence classes
> >
> > airIntPow(v,p) == pow(v,p), but optimized for integral p
> >
> > airEnumLast() returns the last (valid) value in an airEnum
> >
> > airFastExp(), a fast but crude (and buggy?) approximation to exp()
> >
> > nrrd --------
> >
> > added nrrdUnaryOpIf and "unu 1op if"
> >
> > nrrdFormatEPS (an output-only format) now understands 4-channel
> > images as CMYK, exploiting the same implicit semantics as the
> > PostScript colorimage operator, it turns out.
> >
> > nrrdClampConvert() is like nrrdConvert() (which is essentially per-
> > value
> > casting), but now values are clamped so that they don't wrap-around
> > due to casting.  "unu convert -clamp" calls this.
> >
> > Fixed memory leak in nrrdProject(): scan-line buffer wasn't being
> > freed (reported by Jorik Blaas)
> >
> > added nrrdKernelC4Hexic, nrrdKernelC4HexicD, nrrdKernelC4HexicDD- the
> > unique 6-sample support C4 3rd-order accurate 6th-order polynomial
> >
> > added nrrdSaveMulti(), which is like nrrdSave(), but saves
> > an array of Nrrds to some set of files, based on a sprintf-style
> > formatted string.  Eventually "unu dice" will use this.
> >
> > added nrrdBinaryOpNormalRandScaleAdd, for adding scaled gaussian noise
> > to given data.  Accessible with "unu 2op nrand"
> >
> > gage --------
> >
> > gageDeconvolve is a super-dumb way to deconvolve a given volume
> > (of any gageKind) with a given kernel.  Can be used to pre-sharpen
> > an image so that convolution with, e.g., cubic:1,0 is interpolating.
> >
> > "vprobe" program now has TEEM_VPROBE_HACK_ZI environmental variable
> > hack which allows probing to only be done on a single Z slice
> >
> > added gageScl3PFilter_t typedef, which simplifies the declaration of
> > gageScl3PFilter2 and gageScl3PFilter4 and: added gageScl3PFilter6,
> > gageScl3PFilter8, which were easy to implement now that the body of
> > these functions is in the new file scl3pfilterbody.c, which is
> > included as if its a macro (bad hack!)
> >
> > added gageErr airEnum, and now gage's ctx->errNum takes values from
> > the gageErr* enum
> >
> > ell --------
> >
> > added ell_3v_angle_f() and ell_3v_angle_d() for properly measuring
> > angle between two unit vectors
> >
> > more stupid macros
> > ELL_3V_SCALE_ADD2_TT, ELL_3V_SCALE_ADD3_TT, ELL_3M_SCALE_INCR
> > ELL_3M_SCALE_ADD3, ELL_3MV_SCALE_OUTER_INCR, ELL_2V_COPY, ELL_4V_INCR,
> > ELL_3M_LERP, ELL_3MV_CONTR
> >
> > added ell_6m_mul_d, and ell_6ms_eigensolve_d for doing Jacobi-based
> > eigensolves of symmetric 6-by-6 matrices
> >
> > limn --------
> >
> > limnPolyDataVertexWindingFix() might work to fix vertex winding
> > problems
> >
> > limnPolyDataVertexNormals() might compute per-vertex normals
> >
> > limnPolyDataCCFind() might find connected components in polydata
> >
> > limnPolyDataWriteIV() can kind of save polydata to Inventor files
> >
> > limnPolyDataLMPDRead() and limnPolyDataLMPDWrite() read and write a
> > stupid new "LMPD" polydata format, which will probably change a lot,
> > but I needed a way of saving limnPolyData that took a long time to
> > compute
> >
> > limnPolyDataVTKWrite() is mostly a VTK writer for limnPolyData
> >
> > limnPolyDataOFFRead() is mostly a OFF reader of limnPolyData
> >
> > limnPolyDataClip(), limnPolyDataVertexWindingSplit() do what the names
> > suggest, but badly
> >
> > limnPolyDataSpiralTubeWrap() is new Teem home for the clever single
> > tri-strip tube wrapping that used to be in Deft.
> >
> > ten ---------
> >
> > "tend grads" is now based on a much faster gradient descent algorithm
> >
> > added teem/src/ten/test/tensorDotDat, which is designed to generate
> > the information that can replace GE's broken tensor.dat DWI gradient
> > list file
> >
> > tenEstimateContext functionality can now handle skipping some of the
> > data
> >
> > various strings associated with key/value pairs in DWMRI headers
> > TEN_EXPORT const char *tenDWMRIModalityKey;
> > TEN_EXPORT const char *tenDWMRIModalityVal;
> > TEN_EXPORT const char *tenDWMRIBValueKey;
> > TEN_EXPORT const char *tenDWMRIGradKeyFmt;
> > TEN_EXPORT const char *tenDWMRIBmatKeyFmt;
> > TEN_EXPORT const char *tenDWMRINexKeyFmt;
> >
> > tenFiber: added tenFiberStopRadius termination criterion based on
> > radius of curvature of fiber tracks, and tenFiberStopStub to represent
> > the fact that although the seedpoint was okay, neither direction of
> > the fiber went far enough to matter.
> >
> > Added midpoint integration (AKA 2nd order Runge-Kutta)
> > tenFiberIntgMidpoint, and an airEnum for tenFiberIntg
> >
> > "tend satin" teem/src/ten/tendSatin.c now uses full orientation,
> > instead of just axis-aligned spacing
> >
> > tenExp() and tenLog() take exp() and log() of tensors
> >
> > added enum values tenEstimate2Method*
> >
> > more macros:
> > TEN_T_SUB, TEN_T_AFFINE, TEN_T_ADD, TEN_T_LERP, and TEN_T_INCR
> >
> > Added the _tenAnisoTen_f[] and _tenAnisoTen_d[] arrays of functions,
> > and the associated tenAnisoTen_f() and tenAnisoTen_d() function
> > wrappers,
> > to complement tenAnisoEval_{f,d}(): these provide a way of
> > evaluating a
> > given anisotropy measure given the tensor, whereas tenAnisoEval_
> > {f,d}()
> > provide a way of evaluating a given aniosotropy given the soted
> > eigenvalues.
> >
> > added tenPath* functions and enums, including geodesic-loxodrome
> > functionality.  All still very much under construction...
> >
> > tenFiberContextDwiNew() returns a fiber context wrapped around a DWI
> > volume, instead of a tensor volume, for some new functionality of
> > deterministic tractography on DWIs instead of single tensors.
> >
> > added tenTripleConvert_d() and tenTripleConvert_f() for converting
> > between the various triples of scalars that come up in DTI
> > (J, R, and K invariants, eigenvalues)
> >
> > tenDoubleContract_d() for double contraction of a fourth-order
> > tensor with two 2nd-order tensors
> >
> > added tenFiberStopAnisoSet(), tenFiberStopDoubleSet(),
> > tenFiberStopUIntSet() so that stop criteria can be set without using
> > var-args
> >
> >
> > ----------------------------------------------------------------------
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