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From: Chourasia, A. <am...@sd...> - 2013-10-03 15:51:51
|
Hi Gordon, A fresh checkout from new repo address worked https://svn.code.sf.net/p/teem/code/teem/trunk While I was updating my earlier checkout version with older address, some stuff may not be updating, hence the issue. None the less thanks for helping out. Cheers -A On Oct 3, 2013, at 2:26 AM, Gordon L. Kindlmann wrote: > Hi Amit, > > You've run into the problem that sourceforge continues to serve some version, an old and un-update-able version, from https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem > but you really should only be using, as SF said, > https://svn.code.sf.net/p/teem/code/teem/trunk > > Try checking that code out and building it. With that, when I do your command, I get: > > min: 0 > max: 4.0885190722395799e-11 > > Or with this: > unu make -h -t double -s 393 892 23 -i dump.bin \ > | unu axmerge -a 0 1 \ > | unu project -a 0 -m sum \ > | unu save -f text > > 6.1351656e-08 > > Let me know if you get something different. > > Gordon > > On Oct 2, 2013, at 4:07 PM, Chourasia, Amit wrote: > >> David: Nice, that works. >> >> Gordon: unu minmax is not reporting correct result for a binary data with doubles >> Here is an example >> >> unu make -h -t double -s 393 892 23 -i dump.bin \ >> | unu minmax - >> min: 0 >> max: 0.000000 >> >> Whereas the correct result should be >>> Min = 0 >>> Max = 4.08852e-11 >> >> >> The data dump.bin is available here >> http://users.sdsc.edu/~amit/forums/dump.bin >> >> Could this be a bug or my teem compilation is borked (In cmake configuration I see that its linking to 64 bit libraries.) >> >> -A >> >> >> >> >> >> On Oct 2, 2013, at 1:45 PM, David Weinstein wrote: >> >>> Hi Amit, >>> >>> Another solution, which will work with older version of Teems, is to insert a last stub axis before projecting: >>> >>> unu make -t float -s 1000000 -i vol.bin \ >>> | unu axinsert -a 1 \ >>> | unu project -a 0 -m sum \ >>> | unu save -f text >>> >>> Cheers, >>> Dave >>> >>> >>> On Oct 2, 2013, at 10:56 AM, "Chourasia, Amit" <am...@sd...> wrote: >>> >>>> Gordon, >>>> >>>> I checked out revision 6124, via >>>> %svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem >>>> >>>> I still get the error with unu project that it cannot sum 1-D array >>>> % unu make -t float -s 1000000 -i vol.bin \ >>>> | unu project -a 0 -m sum -i - >>>> (_nrrdFormatNRRD_read: reading raw data ... done) >>>> unu project: error projecting nrrd: >>>> [nrrd] nrrdProject: sorry, currently need at least 2-D array to project >>>> >>>> Could you tell me which version has this capability and how to fetch it? >>>> >>>> House keeping note: I get the following warning with SVN perhaps make this change on the webpage >>>> svn: Repository moved permanently to 'https://svn.code.sf.net/p/teem/code/teem/trunk'; please relocate >>>> >>>> I have the following work around, but a full unu solution like you mentioned will be perfect >>>> unu make -t float -s 10000 100 -i vol.bin \ >>>> | unu project -a 0 -m sum -i - \ >>>> | unu save -f text \ >>>> | paste -sd + - \ >>>> | bc >>>> >>>> BTW, thanks for reminding the -h option, one less pipe can save a lot of time for large data. >>>> >>>> Cheers >>>> --Amit >>>> >>>> >>>> >>>> On Oct 2, 2013, at 10:19 AM, Gordon L. Kindlmann wrote: >>>> >>>>> Hi Amit, >>>>> >>>>> As of some recent revision on the SVN trunk, you can unu project 1D arrays, and get out a singleton 1-element 1-D array. >>>>> >>>>> Also, you can use unu axmerge to lose the raster structure, so for your data, you could: >>>>> >>>>> unu make -h -t float -s 64 64 64 -i blob \ >>>>> | unu axmerge -a 0 1 \ >>>>> | unu project -a 0 -m sum \ >>>>> | unu save -f text >>>>> >>>>> Note the -h on "unu make"; it delays the actual read of blob and saves you one piping of data. Probably a minor difference but might help with larger data. >>>>> >>>>> But if all you care about is the sum, and you're creating the nrrd as needed (with unu make), you could also just: >>>>> >>>>> unu make -h -t float -s 262144 -i blob | unu project -a 0 -m sum | unu save -f text >>>>> >>>>> I'm using "unu save -f text" here as a way of getting out a textual representation, but that's only a 32-bit float in ASCII; you could also save it (the 1-element 1-D array) to a .nrrd file to record the value exactly. Or you could pipe to "unu minmax" which does an exact ASCII representation of a 64-bit double (via printf with %.17g). >>>>> >>>>> Gordon >>>>> >>>>> On Oct 1, 2013, at 2:25 PM, Chourasia, Amit wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> Is there a way to find the sum of all values in a volume? >>>>>> I thought this method may be there in unu 1op, but its not. >>>>>> >>>>>> Say I have a binary floating point 3D scalar data as "blob" . >>>>>> I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. >>>>>> >>>>>> unu make -t float -s 64 64 64 -i blob | \ >>>>>> unu project -a 0 -m sum -i - | \ >>>>>> unu project -a 0 -m sum -i - >>>>>> ??? >>>>>> >>>>>> I would appreciate any pointers. >>>>>> >>>>>> Thanks >>>>>> -Amit >>>>>> >>>>>> PS: I am writing a very short documentation for quickly inspecting binary data using teem. >>>>>> ------------------------------------------------------------------------------ >>>>>> October Webinars: Code for Performance >>>>>> Free Intel webinars can help you accelerate application performance. >>>>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >>>>>> the latest Intel processors and coprocessors. See abstracts and register > >>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >>>>>> _______________________________________________ >>>>>> teem-users mailing list >>>>>> tee...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/teem-users >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> October Webinars: Code for Performance >>>> Free Intel webinars can help you accelerate application performance. >>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >>>> the latest Intel processors and coprocessors. See abstracts and register > >>>> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >>>> _______________________________________________ >>>> teem-users mailing list >>>> tee...@li... >>>> https://lists.sourceforge.net/lists/listinfo/teem-users >>> >> >> >> ------------------------------------------------------------------------------ >> October Webinars: Code for Performance >> Free Intel webinars can help you accelerate application performance. >> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >> the latest Intel processors and coprocessors. See abstracts and register > >> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >> _______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users > |
From: Gordon L. K. <gl...@uc...> - 2013-10-03 07:26:18
|
Hi Amit, You've run into the problem that sourceforge continues to serve some version, an old and un-update-able version, from https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem but you really should only be using, as SF said, https://svn.code.sf.net/p/teem/code/teem/trunk Try checking that code out and building it. With that, when I do your command, I get: min: 0 max: 4.0885190722395799e-11 Or with this: unu make -h -t double -s 393 892 23 -i dump.bin \ | unu axmerge -a 0 1 \ | unu project -a 0 -m sum \ | unu save -f text 6.1351656e-08 Let me know if you get something different. Gordon On Oct 2, 2013, at 4:07 PM, Chourasia, Amit wrote: > David: Nice, that works. > > Gordon: unu minmax is not reporting correct result for a binary data with doubles > Here is an example > > unu make -h -t double -s 393 892 23 -i dump.bin \ > | unu minmax - > min: 0 > max: 0.000000 > > Whereas the correct result should be >> Min = 0 >> Max = 4.08852e-11 > > > The data dump.bin is available here > http://users.sdsc.edu/~amit/forums/dump.bin > > Could this be a bug or my teem compilation is borked (In cmake configuration I see that its linking to 64 bit libraries.) > > -A > > > > > > On Oct 2, 2013, at 1:45 PM, David Weinstein wrote: > >> Hi Amit, >> >> Another solution, which will work with older version of Teems, is to insert a last stub axis before projecting: >> >> unu make -t float -s 1000000 -i vol.bin \ >> | unu axinsert -a 1 \ >> | unu project -a 0 -m sum \ >> | unu save -f text >> >> Cheers, >> Dave >> >> >> On Oct 2, 2013, at 10:56 AM, "Chourasia, Amit" <am...@sd...> wrote: >> >>> Gordon, >>> >>> I checked out revision 6124, via >>> %svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem >>> >>> I still get the error with unu project that it cannot sum 1-D array >>> % unu make -t float -s 1000000 -i vol.bin \ >>> | unu project -a 0 -m sum -i - >>> (_nrrdFormatNRRD_read: reading raw data ... done) >>> unu project: error projecting nrrd: >>> [nrrd] nrrdProject: sorry, currently need at least 2-D array to project >>> >>> Could you tell me which version has this capability and how to fetch it? >>> >>> House keeping note: I get the following warning with SVN perhaps make this change on the webpage >>> svn: Repository moved permanently to 'https://svn.code.sf.net/p/teem/code/teem/trunk'; please relocate >>> >>> I have the following work around, but a full unu solution like you mentioned will be perfect >>> unu make -t float -s 10000 100 -i vol.bin \ >>> | unu project -a 0 -m sum -i - \ >>> | unu save -f text \ >>> | paste -sd + - \ >>> | bc >>> >>> BTW, thanks for reminding the -h option, one less pipe can save a lot of time for large data. >>> >>> Cheers >>> --Amit >>> >>> >>> >>> On Oct 2, 2013, at 10:19 AM, Gordon L. Kindlmann wrote: >>> >>>> Hi Amit, >>>> >>>> As of some recent revision on the SVN trunk, you can unu project 1D arrays, and get out a singleton 1-element 1-D array. >>>> >>>> Also, you can use unu axmerge to lose the raster structure, so for your data, you could: >>>> >>>> unu make -h -t float -s 64 64 64 -i blob \ >>>> | unu axmerge -a 0 1 \ >>>> | unu project -a 0 -m sum \ >>>> | unu save -f text >>>> >>>> Note the -h on "unu make"; it delays the actual read of blob and saves you one piping of data. Probably a minor difference but might help with larger data. >>>> >>>> But if all you care about is the sum, and you're creating the nrrd as needed (with unu make), you could also just: >>>> >>>> unu make -h -t float -s 262144 -i blob | unu project -a 0 -m sum | unu save -f text >>>> >>>> I'm using "unu save -f text" here as a way of getting out a textual representation, but that's only a 32-bit float in ASCII; you could also save it (the 1-element 1-D array) to a .nrrd file to record the value exactly. Or you could pipe to "unu minmax" which does an exact ASCII representation of a 64-bit double (via printf with %.17g). >>>> >>>> Gordon >>>> >>>> On Oct 1, 2013, at 2:25 PM, Chourasia, Amit wrote: >>>> >>>>> Hi, >>>>> >>>>> Is there a way to find the sum of all values in a volume? >>>>> I thought this method may be there in unu 1op, but its not. >>>>> >>>>> Say I have a binary floating point 3D scalar data as "blob" . >>>>> I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. >>>>> >>>>> unu make -t float -s 64 64 64 -i blob | \ >>>>> unu project -a 0 -m sum -i - | \ >>>>> unu project -a 0 -m sum -i - >>>>> ??? >>>>> >>>>> I would appreciate any pointers. >>>>> >>>>> Thanks >>>>> -Amit >>>>> >>>>> PS: I am writing a very short documentation for quickly inspecting binary data using teem. >>>>> ------------------------------------------------------------------------------ >>>>> October Webinars: Code for Performance >>>>> Free Intel webinars can help you accelerate application performance. >>>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >>>>> the latest Intel processors and coprocessors. See abstracts and register > >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >>>>> _______________________________________________ >>>>> teem-users mailing list >>>>> tee...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/teem-users >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> October Webinars: Code for Performance >>> Free Intel webinars can help you accelerate application performance. >>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >>> the latest Intel processors and coprocessors. See abstracts and register > >>> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> teem-users mailing list >>> tee...@li... >>> https://lists.sourceforge.net/lists/listinfo/teem-users >> > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk > _______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Chourasia, A. <am...@sd...> - 2013-10-02 21:07:43
|
David: Nice, that works. Gordon: unu minmax is not reporting correct result for a binary data with doubles Here is an example unu make -h -t double -s 393 892 23 -i dump.bin \ | unu minmax - min: 0 max: 0.000000 Whereas the correct result should be > Min = 0 > Max = 4.08852e-11 The data dump.bin is available here http://users.sdsc.edu/~amit/forums/dump.bin Could this be a bug or my teem compilation is borked (In cmake configuration I see that its linking to 64 bit libraries.) -A On Oct 2, 2013, at 1:45 PM, David Weinstein wrote: > Hi Amit, > > Another solution, which will work with older version of Teems, is to insert a last stub axis before projecting: > > unu make -t float -s 1000000 -i vol.bin \ > | unu axinsert -a 1 \ > | unu project -a 0 -m sum \ > | unu save -f text > > Cheers, > Dave > > > On Oct 2, 2013, at 10:56 AM, "Chourasia, Amit" <am...@sd...> wrote: > >> Gordon, >> >> I checked out revision 6124, via >> %svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem >> >> I still get the error with unu project that it cannot sum 1-D array >> % unu make -t float -s 1000000 -i vol.bin \ >> | unu project -a 0 -m sum -i - >> (_nrrdFormatNRRD_read: reading raw data ... done) >> unu project: error projecting nrrd: >> [nrrd] nrrdProject: sorry, currently need at least 2-D array to project >> >> Could you tell me which version has this capability and how to fetch it? >> >> House keeping note: I get the following warning with SVN perhaps make this change on the webpage >> svn: Repository moved permanently to 'https://svn.code.sf.net/p/teem/code/teem/trunk'; please relocate >> >> I have the following work around, but a full unu solution like you mentioned will be perfect >> unu make -t float -s 10000 100 -i vol.bin \ >> | unu project -a 0 -m sum -i - \ >> | unu save -f text \ >> | paste -sd + - \ >> | bc >> >> BTW, thanks for reminding the -h option, one less pipe can save a lot of time for large data. >> >> Cheers >> --Amit >> >> >> >> On Oct 2, 2013, at 10:19 AM, Gordon L. Kindlmann wrote: >> >>> Hi Amit, >>> >>> As of some recent revision on the SVN trunk, you can unu project 1D arrays, and get out a singleton 1-element 1-D array. >>> >>> Also, you can use unu axmerge to lose the raster structure, so for your data, you could: >>> >>> unu make -h -t float -s 64 64 64 -i blob \ >>> | unu axmerge -a 0 1 \ >>> | unu project -a 0 -m sum \ >>> | unu save -f text >>> >>> Note the -h on "unu make"; it delays the actual read of blob and saves you one piping of data. Probably a minor difference but might help with larger data. >>> >>> But if all you care about is the sum, and you're creating the nrrd as needed (with unu make), you could also just: >>> >>> unu make -h -t float -s 262144 -i blob | unu project -a 0 -m sum | unu save -f text >>> >>> I'm using "unu save -f text" here as a way of getting out a textual representation, but that's only a 32-bit float in ASCII; you could also save it (the 1-element 1-D array) to a .nrrd file to record the value exactly. Or you could pipe to "unu minmax" which does an exact ASCII representation of a 64-bit double (via printf with %.17g). >>> >>> Gordon >>> >>> On Oct 1, 2013, at 2:25 PM, Chourasia, Amit wrote: >>> >>>> Hi, >>>> >>>> Is there a way to find the sum of all values in a volume? >>>> I thought this method may be there in unu 1op, but its not. >>>> >>>> Say I have a binary floating point 3D scalar data as "blob" . >>>> I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. >>>> >>>> unu make -t float -s 64 64 64 -i blob | \ >>>> unu project -a 0 -m sum -i - | \ >>>> unu project -a 0 -m sum -i - >>>> ??? >>>> >>>> I would appreciate any pointers. >>>> >>>> Thanks >>>> -Amit >>>> >>>> PS: I am writing a very short documentation for quickly inspecting binary data using teem. >>>> ------------------------------------------------------------------------------ >>>> October Webinars: Code for Performance >>>> Free Intel webinars can help you accelerate application performance. >>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >>>> the latest Intel processors and coprocessors. See abstracts and register > >>>> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >>>> _______________________________________________ >>>> teem-users mailing list >>>> tee...@li... >>>> https://lists.sourceforge.net/lists/listinfo/teem-users >>> >> >> >> ------------------------------------------------------------------------------ >> October Webinars: Code for Performance >> Free Intel webinars can help you accelerate application performance. >> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >> the latest Intel processors and coprocessors. See abstracts and register > >> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >> _______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users > |
From: David W. <dm...@sc...> - 2013-10-02 19:45:20
|
Hi Amit, Another solution, which will work with older version of Teems, is to insert a last stub axis before projecting: unu make -t float -s 1000000 -i vol.bin \ | unu axinsert -a 1 \ | unu project -a 0 -m sum \ | unu save -f text Cheers, Dave On Oct 2, 2013, at 10:56 AM, "Chourasia, Amit" <am...@sd...> wrote: > Gordon, > > I checked out revision 6124, via > %svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem > > I still get the error with unu project that it cannot sum 1-D array > % unu make -t float -s 1000000 -i vol.bin \ > | unu project -a 0 -m sum -i - > (_nrrdFormatNRRD_read: reading raw data ... done) > unu project: error projecting nrrd: > [nrrd] nrrdProject: sorry, currently need at least 2-D array to project > > Could you tell me which version has this capability and how to fetch it? > > House keeping note: I get the following warning with SVN perhaps make this change on the webpage > svn: Repository moved permanently to 'https://svn.code.sf.net/p/teem/code/teem/trunk'; please relocate > > I have the following work around, but a full unu solution like you mentioned will be perfect > unu make -t float -s 10000 100 -i vol.bin \ > | unu project -a 0 -m sum -i - \ > | unu save -f text \ > | paste -sd + - \ > | bc > > BTW, thanks for reminding the -h option, one less pipe can save a lot of time for large data. > > Cheers > --Amit > > > > On Oct 2, 2013, at 10:19 AM, Gordon L. Kindlmann wrote: > >> Hi Amit, >> >> As of some recent revision on the SVN trunk, you can unu project 1D arrays, and get out a singleton 1-element 1-D array. >> >> Also, you can use unu axmerge to lose the raster structure, so for your data, you could: >> >> unu make -h -t float -s 64 64 64 -i blob \ >> | unu axmerge -a 0 1 \ >> | unu project -a 0 -m sum \ >> | unu save -f text >> >> Note the -h on "unu make"; it delays the actual read of blob and saves you one piping of data. Probably a minor difference but might help with larger data. >> >> But if all you care about is the sum, and you're creating the nrrd as needed (with unu make), you could also just: >> >> unu make -h -t float -s 262144 -i blob | unu project -a 0 -m sum | unu save -f text >> >> I'm using "unu save -f text" here as a way of getting out a textual representation, but that's only a 32-bit float in ASCII; you could also save it (the 1-element 1-D array) to a .nrrd file to record the value exactly. Or you could pipe to "unu minmax" which does an exact ASCII representation of a 64-bit double (via printf with %.17g). >> >> Gordon >> >> On Oct 1, 2013, at 2:25 PM, Chourasia, Amit wrote: >> >>> Hi, >>> >>> Is there a way to find the sum of all values in a volume? >>> I thought this method may be there in unu 1op, but its not. >>> >>> Say I have a binary floating point 3D scalar data as "blob" . >>> I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. >>> >>> unu make -t float -s 64 64 64 -i blob | \ >>> unu project -a 0 -m sum -i - | \ >>> unu project -a 0 -m sum -i - >>> ??? >>> >>> I would appreciate any pointers. >>> >>> Thanks >>> -Amit >>> >>> PS: I am writing a very short documentation for quickly inspecting binary data using teem. >>> ------------------------------------------------------------------------------ >>> October Webinars: Code for Performance >>> Free Intel webinars can help you accelerate application performance. >>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >>> the latest Intel processors and coprocessors. See abstracts and register > >>> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> teem-users mailing list >>> tee...@li... >>> https://lists.sourceforge.net/lists/listinfo/teem-users >> > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk > _______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Chourasia, A. <am...@sd...> - 2013-10-02 16:57:32
|
Gordon, I checked out revision 6124, via %svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem I still get the error with unu project that it cannot sum 1-D array % unu make -t float -s 1000000 -i vol.bin \ | unu project -a 0 -m sum -i - (_nrrdFormatNRRD_read: reading raw data ... done) unu project: error projecting nrrd: [nrrd] nrrdProject: sorry, currently need at least 2-D array to project Could you tell me which version has this capability and how to fetch it? House keeping note: I get the following warning with SVN perhaps make this change on the webpage svn: Repository moved permanently to 'https://svn.code.sf.net/p/teem/code/teem/trunk'; please relocate I have the following work around, but a full unu solution like you mentioned will be perfect unu make -t float -s 10000 100 -i vol.bin \ | unu project -a 0 -m sum -i - \ | unu save -f text \ | paste -sd + - \ | bc BTW, thanks for reminding the -h option, one less pipe can save a lot of time for large data. Cheers --Amit On Oct 2, 2013, at 10:19 AM, Gordon L. Kindlmann wrote: > Hi Amit, > > As of some recent revision on the SVN trunk, you can unu project 1D arrays, and get out a singleton 1-element 1-D array. > > Also, you can use unu axmerge to lose the raster structure, so for your data, you could: > > unu make -h -t float -s 64 64 64 -i blob \ > | unu axmerge -a 0 1 \ > | unu project -a 0 -m sum \ > | unu save -f text > > Note the -h on "unu make"; it delays the actual read of blob and saves you one piping of data. Probably a minor difference but might help with larger data. > > But if all you care about is the sum, and you're creating the nrrd as needed (with unu make), you could also just: > > unu make -h -t float -s 262144 -i blob | unu project -a 0 -m sum | unu save -f text > > I'm using "unu save -f text" here as a way of getting out a textual representation, but that's only a 32-bit float in ASCII; you could also save it (the 1-element 1-D array) to a .nrrd file to record the value exactly. Or you could pipe to "unu minmax" which does an exact ASCII representation of a 64-bit double (via printf with %.17g). > > Gordon > > On Oct 1, 2013, at 2:25 PM, Chourasia, Amit wrote: > >> Hi, >> >> Is there a way to find the sum of all values in a volume? >> I thought this method may be there in unu 1op, but its not. >> >> Say I have a binary floating point 3D scalar data as "blob" . >> I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. >> >> unu make -t float -s 64 64 64 -i blob | \ >> unu project -a 0 -m sum -i - | \ >> unu project -a 0 -m sum -i - >> ??? >> >> I would appreciate any pointers. >> >> Thanks >> -Amit >> >> PS: I am writing a very short documentation for quickly inspecting binary data using teem. >> ------------------------------------------------------------------------------ >> October Webinars: Code for Performance >> Free Intel webinars can help you accelerate application performance. >> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from >> the latest Intel processors and coprocessors. See abstracts and register > >> http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk >> _______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users > |
From: Gordon L. K. <gl...@uc...> - 2013-10-02 15:40:40
|
Hi Amit, As of some recent revision on the SVN trunk, you can unu project 1D arrays, and get out a singleton 1-element 1-D array. Also, you can use unu axmerge to lose the raster structure, so for your data, you could: unu make -h -t float -s 64 64 64 -i blob \ | unu axmerge -a 0 1 \ | unu project -a 0 -m sum \ | unu save -f text Note the -h on "unu make"; it delays the actual read of blob and saves you one piping of data. Probably a minor difference but might help with larger data. But if all you care about is the sum, and you're creating the nrrd as needed (with unu make), you could also just: unu make -h -t float -s 262144 -i blob | unu project -a 0 -m sum | unu save -f text I'm using "unu save -f text" here as a way of getting out a textual representation, but that's only a 32-bit float in ASCII; you could also save it (the 1-element 1-D array) to a .nrrd file to record the value exactly. Or you could pipe to "unu minmax" which does an exact ASCII representation of a 64-bit double (via printf with %.17g). Gordon On Oct 1, 2013, at 2:25 PM, Chourasia, Amit wrote: > Hi, > > Is there a way to find the sum of all values in a volume? > I thought this method may be there in unu 1op, but its not. > > Say I have a binary floating point 3D scalar data as "blob" . > I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. > > unu make -t float -s 64 64 64 -i blob | \ > unu project -a 0 -m sum -i - | \ > unu project -a 0 -m sum -i - > ??? > > I would appreciate any pointers. > > Thanks > -Amit > > PS: I am writing a very short documentation for quickly inspecting binary data using teem. > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk > _______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Chourasia, A. <am...@sd...> - 2013-10-01 20:00:55
|
Hi, Is there a way to find the sum of all values in a volume? I thought this method may be there in unu 1op, but its not. Say I have a binary floating point 3D scalar data as "blob" . I could use project and sum along axes to get a 1d data, but is there a way to sum 1D data using teem. unu make -t float -s 64 64 64 -i blob | \ unu project -a 0 -m sum -i - | \ unu project -a 0 -m sum -i - ??? I would appreciate any pointers. Thanks -Amit PS: I am writing a very short documentation for quickly inspecting binary data using teem. |
From: Murat M. <ma...@uw...> - 2013-09-11 19:28:22
|
Just create a detach nrrd header (.nhdr) to describe your volume. http://teem.sourceforge.net/nrrd/format.html -----Original Message----- From: Alessandro Candini [mailto:ca...@me...] Sent: Friday, February 01, 2013 6:15 AM To: tee...@li... Subject: [Teem-users] Create a nrrd file from png images Hi everyone. I have a set of png images wich defines a parallelepiped in the space: 720 png for X axis, 361 for y axis and 240 for Z axis. I would like to convert them in a nrrd file, to obtain something like this: http://lessons.goxtk.com/11/ If is that possible using the teem-unu tool, can you give me some indications on how to get it? Thanks in advance, Alessandro ---------------------------------------------------------------------------- -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan _______________________________________________ teem-users mailing list tee...@li... https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Taylor Braun-J. <ta...@br...> - 2013-08-25 14:36:22
|
I'm looking at the process for registering the NRRD media type with IANA[1]. The hope is that the registered type would eventually propagate to web browsers and /etc/mime.types so that downloads are handled better by default. To get in the "Standards Tree" (rather than the Vendor or Personal trees) it looks like an IETF specification would need to be approved. Has any one considered writing an RFC for the NRRD format? Does it even make sense? There is always the "Vendor" tree as an option (so the MIME type would be image/vnd.nrrd) that doesn't require any sort of standardization. I could do this, but it probably makes sense for the "owner" of the format to do these applications. Thanks, Taylor [1] http://www.iana.org/cgi-bin/mediatypes.pl |
From: Martin M. <Mar...@ut...> - 2013-07-30 00:21:24
|
Hi Dr. Kindlmann, Thank you for this detailed reply. No I wasn't expecting it to be a GUI app. I am the software designer here at a small geophysics company, so software library and command line is fine. If I find it looks useful for either job (time series graph, or magnetic field maps) I can code around it to do what I want and present what I want. I guess my comment on the starting web page (http://teem.sourceforge.net/) would be that it took too many clicks to find any tangible examples or demos (like http://teem.sourceforge.net/nrrd/demo.html), and (as I see now) they were only under the specific library links (nrrd, gage, mite, ten as linked from that start page), so I initially glossed over the demo-y links because I figured I didn't want to drill down that specifically to individual libraries right away. I have now read through a lot of the demo pages and the paper on curvature based transfer functions so it makes a lot more sense. My scenario is airborne geophysical surveys (magnetic and radiometric). We're flying sensors around on helicopters in a grid pattern over regions on the order of tens of kilometers, with line spacings usually 50 to 200 m. So although the scale is vastly different from medical, the tasks seem somewhat similar. Also this is not a 3d grid of data points like an MRI, only 2d. There is also the issue of the idealized flight path (perfectly straight at constant altitude) which we intend to send our sensors through, versus the actual flight lines affected by the vagaries of topography, wind, weather, pilot skill, etc. So we have many filters and corrections from many sources and methods, which it strikes me must be similar to tasks done in medical imaging. Thanks again for your time in replying, and for providing this impressive looking tool. Martin Muc On 26/07/13 05:22 PM, Gordon L. Kindlmann wrote: > Hello Martin, > > Thanks for the query and the opportunity to describe Teem. > > One of the first things to know about Teem is that it is a collection of libraries, and a few command-line tools, but there is no GUI, or anything with a network connection. Nor is there much stuff that is specific to any one field of study, with the notable exception of the diffusion-weighted MRI stuff in the "ten", and "elf" libraries. So without doing any research, my guess about the answer to "is Teem used for geophysics" is "probably not, but you could try coding something up :) ". > > Teem is probably more low-level that you think - being a set of libraries, it is used by people who write applications that link against libraries, not by people looking for applications. You can write applications that are useful for various domains, and draw on functions in Teem, but there's nothing "out of the box" that suits your stated needs (web-accessible graphing of time-series data and mapping magnetic fields). > > This may be an unsatisfying answer, and it doesn't answer the "what is it good for" question. I would say that in Teem, just to highlight a few of the libraries: "nrrd" is good for raster data manipulation (see the unu commands), "gage" is good for creating the abstraction of continuous fields from raster data via convolution, "ten" is good for doing things with tensor fields (see the tend commands), and "pull" is good for particle-based feature extraction in continuous fields. Except for possibly "ten", none of these are very application specific, because they weren't coded or designed for specific applications. They are just libraries. > > The mailing list traffic is low because most people who pick up Teem figure out how to use it by experimentation or looking at the source code. Also, Teem has a relatively small user community (compared to things like VTK or ITK). But don't mistake this for being moribund: > > https://www.ohloh.net/p/Teem > > this documents some general properties of the project. It says there haven't been recent commits because Sourceforge recently switched to new SVN servers. Prompted by your email, I just updated the ohloh page to include the new SVN server. > > The last release was in December: > > http://sourceforge.net/projects/teem/files/teem/1.11.0/ > > and that page lists what is new relative to the previous release. A patch release is coming out next month. > > Answering "how many people use Teem" is tricky. Anyone can get the source and use it without telling us, so there's no central accounting of number of users. > > Good luck, > Gordon > > > On Jul 25, 2013, at 4:36 PM, mar...@ut... wrote: > >> Hey list, >> >> I've stumbled on teem because of a coincidence in your file format >> name, nrrd, matching a search for "rrd". I was actually looking for >> Debian packages similar to rrdtool (round robin database - for storing >> and graphing time-series data). >> >> Actually I have two tasks, web-accessible graphing of time-series data >> that is more frequent than 1 Hz (which is a limitation of rrdtool), >> and mapping magnetic fields (or, technically, magnetic intensity). >> And reading about teem has gotten me intrigued about teem's potential >> suitability for both of these tasks. >> >> I've clicked around and read on teem.sourceforge.net. Clicked on >> "air"... fairly terse... okay it's got some macros. I clicked on >> "ell"... okay it's for linear algebra... fairly terse. I've clicked a >> smattering of teem-users@ mailing list threads in the archive, >> randomly from 2004, 2008, 2012, mostly discussing compile problems, >> bug fixes, etc... Screen shots on >> http://sourceforge.net/projects/teem/ are text output of processing >> steps. >> >> So, aside from "Teem is a coordinated group of libraries for >> representing, processing, and visualizing scientific raster data", >> what _IS_ teem? What is it being used for? Aside from mentioning >> "Healthcare Industry" in the intended audience, and a few of the >> thumbnail images (not the Mr. T one) for the different libraries being >> slightly suggestive of medical X-rays or MRIs, I can't tell what teem >> really does or is good at, It is all so general (as science and math >> of course are), I can't tell what teem _is_ or what it _does_. >> >> Okay, never mind. I've just found >> http://teem.sourceforge.net/nrrd/demo.html I will read some of these >> examples and I guess if it looks promising, will download and try teem >> with some of these tutorials. >> >> Also, is anyone using teem for geophysics? Broadly, parts of our >> geophysics output (mapping) _are_ "scientific raster data", so I >> suppose I can answer my own question that teem should be useful. But >> I don't see any mention in the mailing list archive (assuming the >> search is working). >> >> Also also, mailing list traffic seems low for 2012 and especially >> 2013. Is the project falling out of use, or just stable and good at >> what it does with no new features lately? >> >> Cheers. >> >> Martin Muc >> >> >> >> P.S. are you aware there is another unrelated project called teem? >> (googled "teem usage examples" in trying to answer my own question) >> and found http://lis2.epfl.ch/resources/download/doc1.0/teem/index.html >> >> >> ------------------------------------------------------------------------------ >> See everything from the browser to the database with AppDynamics >> Get end-to-end visibility with application monitoring from AppDynamics >> Isolate bottlenecks and diagnose root cause in seconds. >> Start your free trial of AppDynamics Pro today! >> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk >> _______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users >> |
From: Gordon L. K. <gl...@uc...> - 2013-07-26 21:22:12
|
Hello Martin, Thanks for the query and the opportunity to describe Teem. One of the first things to know about Teem is that it is a collection of libraries, and a few command-line tools, but there is no GUI, or anything with a network connection. Nor is there much stuff that is specific to any one field of study, with the notable exception of the diffusion-weighted MRI stuff in the "ten", and "elf" libraries. So without doing any research, my guess about the answer to "is Teem used for geophysics" is "probably not, but you could try coding something up :) ". Teem is probably more low-level that you think - being a set of libraries, it is used by people who write applications that link against libraries, not by people looking for applications. You can write applications that are useful for various domains, and draw on functions in Teem, but there's nothing "out of the box" that suits your stated needs (web-accessible graphing of time-series data and mapping magnetic fields). This may be an unsatisfying answer, and it doesn't answer the "what is it good for" question. I would say that in Teem, just to highlight a few of the libraries: "nrrd" is good for raster data manipulation (see the unu commands), "gage" is good for creating the abstraction of continuous fields from raster data via convolution, "ten" is good for doing things with tensor fields (see the tend commands), and "pull" is good for particle-based feature extraction in continuous fields. Except for possibly "ten", none of these are very application specific, because they weren't coded or designed for specific applications. They are just libraries. The mailing list traffic is low because most people who pick up Teem figure out how to use it by experimentation or looking at the source code. Also, Teem has a relatively small user community (compared to things like VTK or ITK). But don't mistake this for being moribund: https://www.ohloh.net/p/Teem this documents some general properties of the project. It says there haven't been recent commits because Sourceforge recently switched to new SVN servers. Prompted by your email, I just updated the ohloh page to include the new SVN server. The last release was in December: http://sourceforge.net/projects/teem/files/teem/1.11.0/ and that page lists what is new relative to the previous release. A patch release is coming out next month. Answering "how many people use Teem" is tricky. Anyone can get the source and use it without telling us, so there's no central accounting of number of users. Good luck, Gordon On Jul 25, 2013, at 4:36 PM, mar...@ut... wrote: > Hey list, > > I've stumbled on teem because of a coincidence in your file format > name, nrrd, matching a search for "rrd". I was actually looking for > Debian packages similar to rrdtool (round robin database - for storing > and graphing time-series data). > > Actually I have two tasks, web-accessible graphing of time-series data > that is more frequent than 1 Hz (which is a limitation of rrdtool), > and mapping magnetic fields (or, technically, magnetic intensity). > And reading about teem has gotten me intrigued about teem's potential > suitability for both of these tasks. > > I've clicked around and read on teem.sourceforge.net. Clicked on > "air"... fairly terse... okay it's got some macros. I clicked on > "ell"... okay it's for linear algebra... fairly terse. I've clicked a > smattering of teem-users@ mailing list threads in the archive, > randomly from 2004, 2008, 2012, mostly discussing compile problems, > bug fixes, etc... Screen shots on > http://sourceforge.net/projects/teem/ are text output of processing > steps. > > So, aside from "Teem is a coordinated group of libraries for > representing, processing, and visualizing scientific raster data", > what _IS_ teem? What is it being used for? Aside from mentioning > "Healthcare Industry" in the intended audience, and a few of the > thumbnail images (not the Mr. T one) for the different libraries being > slightly suggestive of medical X-rays or MRIs, I can't tell what teem > really does or is good at, It is all so general (as science and math > of course are), I can't tell what teem _is_ or what it _does_. > > Okay, never mind. I've just found > http://teem.sourceforge.net/nrrd/demo.html I will read some of these > examples and I guess if it looks promising, will download and try teem > with some of these tutorials. > > Also, is anyone using teem for geophysics? Broadly, parts of our > geophysics output (mapping) _are_ "scientific raster data", so I > suppose I can answer my own question that teem should be useful. But > I don't see any mention in the mailing list archive (assuming the > search is working). > > Also also, mailing list traffic seems low for 2012 and especially > 2013. Is the project falling out of use, or just stable and good at > what it does with no new features lately? > > Cheers. > > Martin Muc > > > > P.S. are you aware there is another unrelated project called teem? > (googled "teem usage examples" in trying to answer my own question) > and found http://lis2.epfl.ch/resources/download/doc1.0/teem/index.html > > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users > |
From: <mar...@ut...> - 2013-07-25 21:36:30
|
Hey list, I've stumbled on teem because of a coincidence in your file format name, nrrd, matching a search for "rrd". I was actually looking for Debian packages similar to rrdtool (round robin database - for storing and graphing time-series data). Actually I have two tasks, web-accessible graphing of time-series data that is more frequent than 1 Hz (which is a limitation of rrdtool), and mapping magnetic fields (or, technically, magnetic intensity). And reading about teem has gotten me intrigued about teem's potential suitability for both of these tasks. I've clicked around and read on teem.sourceforge.net. Clicked on "air"... fairly terse... okay it's got some macros. I clicked on "ell"... okay it's for linear algebra... fairly terse. I've clicked a smattering of teem-users@ mailing list threads in the archive, randomly from 2004, 2008, 2012, mostly discussing compile problems, bug fixes, etc... Screen shots on http://sourceforge.net/projects/teem/ are text output of processing steps. So, aside from "Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data", what _IS_ teem? What is it being used for? Aside from mentioning "Healthcare Industry" in the intended audience, and a few of the thumbnail images (not the Mr. T one) for the different libraries being slightly suggestive of medical X-rays or MRIs, I can't tell what teem really does or is good at, It is all so general (as science and math of course are), I can't tell what teem _is_ or what it _does_. Okay, never mind. I've just found http://teem.sourceforge.net/nrrd/demo.html I will read some of these examples and I guess if it looks promising, will download and try teem with some of these tutorials. Also, is anyone using teem for geophysics? Broadly, parts of our geophysics output (mapping) _are_ "scientific raster data", so I suppose I can answer my own question that teem should be useful. But I don't see any mention in the mailing list archive (assuming the search is working). Also also, mailing list traffic seems low for 2012 and especially 2013. Is the project falling out of use, or just stable and good at what it does with no new features lately? Cheers. Martin Muc P.S. are you aware there is another unrelated project called teem? (googled "teem usage examples" in trying to answer my own question) and found http://lis2.epfl.ch/resources/download/doc1.0/teem/index.html |
From: Gordon L. K. <gl...@uc...> - 2013-07-24 21:34:26
|
Thanks for the further ideas. "mutate" is a great verb! For the time being I want to go with nrrdCastClampRound(), which is bulky, but its completely honest, and specific. Its also forward-compatible with renaming nrrdConvert --> nrrdCast and nrrdClampConvert --> nrrdCastClamp. The Teem naming convention is to put commonalities at the beginning of the name, instead of the end, with a hopeful eye towards IDEs with tab completion. nrrdClampConvert is in violation of this convention. The flexibility of nrrdCastClampRound() is different than the non-flexibility of nrrdClampConvert(), but that's a small wart. I think "Generic" could imply something more than the very limited functionality that nrrdCastClampRound() offers, and "mutate" is even more open-ended in its meaning. Longer term, there ought to be some more flexible way of creating efficient combinations of these kinds of low-level functions. Chains of "unu 1op" commands (or corresponding sequences of nrrdArithUnaryOp calls) can replicate the functionality of nrrdCastClampRound(), but will be slower because that would mean three sweeps through array memory instead of one. This is a special case of the general problem of compiling unu commands to efficient C code, which I've given some thought to. The first pass of "unu compile" will likely amount to a sequential calls to the unrrdu_CMDMain function calls that underly "unu CMD" (thereby avoid all disk IO, though as some of you know, that's all buffered in disk caches anyway, so it might not represent much of a performance win). Gordon On Jul 24, 2013, at 1:19 PM, Sam Quinan wrote: > Interjecting a little late here, but the digest just showed up in my email. > Another option might be nrrdMutate(), linking to the idea of 'mutation' as triggering changes at various gradations of discernibility through a wide variety of processes > > - Sam > On Wednesday, July 24, 2013 at 11:55 AM, tee...@li... wrote: > >> Send teem-users mailing list submissions to >> tee...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/teem-users >> or, via email, send a message with subject or body 'help' to >> tee...@li... >> >> You can reach the person managing the list at >> tee...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of teem-users digest..." >> >> >> Today's Topics: >> >> 1. suggestions for nrrd function name? (Gordon L. Kindlmann) >> 2. Re: suggestions for nrrd function name? (Xavier Tricoche) >> 3. Re: Bug in Teem (Gordon L. Kindlmann) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 21 Jul 2013 02:33:32 -0500 >> From: "Gordon L. Kindlmann" <gl...@uc...> >> Subject: [Teem-users] suggestions for nrrd function name? >> To: "tee...@li... Users" >> <tee...@li...> >> Message-ID: <D43...@uc...> >> Content-Type: text/plain; charset=us-ascii >> >> Hello, >> >> There is currently a function nrrdConvert() which is basically just a per-value cast of the values from one type to another type. This is the basis of "unu convert". >> >> Recognizing the need to sometimes avoid value wrap-around in integer types, there is also nrrdClampConvert(), which clamps values to the representable range of the output type prior to casting. This is accessed via "unu convert -clamp". >> >> However, sometimes you want to convert an array to an integer type via rounding, rather than plain casting. And at that point you could very well want a function that converts from one type to another, with the ability to turn on rounding and/or clamping, or neither. >> >> I'd want to call that function nrrdConvert(), and rename the old nrrdConvert() to nrrdCast(). But that be a needless loss of backwards compatibility. >> >> Strictly following Teem conventions, this function could be called something like nrrdMaybeRoundMaybeClampConvert, which is obviously silly, so the question is: what should this function be called? >> >> thanks, >> Gordon >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 21 Jul 2013 10:02:08 -0400 >> From: Xavier Tricoche <tri...@sc...> >> Subject: Re: [Teem-users] suggestions for nrrd function name? >> To: "Gordon L. Kindlmann" <gl...@uc...> >> Cc: "tee...@li... Users" >> <tee...@li...> >> Message-ID: <3F4...@sc...> >> Content-Type: text/plain; charset=us-ascii >> >> What about nrrdGenericConvert()? >> >> Xavier >> >> On Jul 21, 2013, at 3:33 AM, "Gordon L. Kindlmann" <gl...@uc...> wrote: >> >>> Hello, >>> >>> There is currently a function nrrdConvert() which is basically just a per-value cast of the values from one type to another type. This is the basis of "unu convert". >>> >>> Recognizing the need to sometimes avoid value wrap-around in integer types, there is also nrrdClampConvert(), which clamps values to the representable range of the output type prior to casting. This is accessed via "unu convert -clamp". >>> >>> However, sometimes you want to convert an array to an integer type via rounding, rather than plain casting. And at that point you could very well want a function that converts from one type to another, with the ability to turn on rounding and/or clamping, or neither. >>> >>> I'd want to call that function nrrdConvert(), and rename the old nrrdConvert() to nrrdCast(). But that be a needless loss of backwards compatibility. >>> >>> Strictly following Teem conventions, this function could be called something like nrrdMaybeRoundMaybeClampConvert, which is obviously silly, so the question is: what should this function be called? >>> >>> thanks, >>> Gordon >>> >>> >>> ------------------------------------------------------------------------------ >>> See everything from the browser to the database with AppDynamics >>> Get end-to-end visibility with application monitoring from AppDynamics >>> Isolate bottlenecks and diagnose root cause in seconds. >>> Start your free trial of AppDynamics Pro today! >>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> teem-users mailing list >>> tee...@li... >>> https://lists.sourceforge.net/lists/listinfo/teem-users >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 24 Jul 2013 12:54:55 -0500 >> From: "Gordon L. Kindlmann" <gl...@uc...> >> Subject: Re: [Teem-users] Bug in Teem >> To: Michael G?tz <m....@dk...> >> Cc: "tee...@li... Users" >> <tee...@li...> >> Message-ID: <71E...@uc...> >> Content-Type: text/plain; charset="windows-1252" >> >> >> The bug has been fixed in Teem, and Teem's distribution of NrrdIO, and now also in ITK's NrrdIO: >> >> http://review.source.kitware.com/#/c/12072/ >> >> Thanks again, >> Gordon >> >> On Jul 6, 2013, at 4:44 PM, Gordon L. Kindlmann wrote: >> >>> >>> On Jul 5, 2013, at 1:57 PM, Gordon L. Kindlmann wrote: >>> >>>> Hello, >>>> >>>> I'm planning on a June 1 patch release of Teem 1.11.1 ... >>> >>> By which I meant an August 1 release (thanks Xavier). >>> >>> Do let me know if you find any other bugs! >>> >>> Thanks, >>> Gordon >>> >>>> , and before then I will go through the process of making sure ITK's NrrdIO has the same bug fix. >>>> >>>> Thanks, >>>> Gordon >>>> >>>> On Jul 5, 2013, at 5:23 AM, G?tz, Michael wrote: >>>> >>>>> Hello Gordon, >>>>> this bug was discovered using MITK, which in returns uses ITK for nrrd-support >>>>> Regards >>>>> Michael >>>>> Von: Gordon L. Kindlmann [mailto:gl...@uc...] >>>>> Gesendet: Freitag, 5. Juli 2013 12:12 >>>>> An: G?tz, Michael >>>>> Cc: tee...@li... >>>>> Betreff: Re: [Teem-users] Bug in Teem >>>>> Hello, >>>>> Thank you very much for the bug report and the very specific information on fixing it. >>>>> I've just committed a fix to the svn trunk. >>>>> May I ask - was this bug discovered through ITK's NrrdIO, or something separate? >>>>> Gordon >>>>> On Jul 3, 2013, at 9:45 AM, G?tz, Michael wrote: >>>>> >>>>> >>>>> Hi list, >>>>> i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) >>>>> If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the ?remove-nonprintable?-part again and again. -> Endless loop. >>>>> The problem can be solved by checking for \0 in the loop: >>>>> for (i=0; i<len && s[i] != \0; i++) { >>>>> if (isspace(AIR_CAST(int, s[i]))) { >>>>> s[i] = ' '; >>>>> continue; >>>>> } >>>>> if (!isprint(AIR_CAST(int, s[i]))) { >>>>> for (j=i; j<len; j++) { >>>>> /* this will copy the '\0' at the end */ >>>>> s[j] = s[j+1]; >>>>> } >>>>> i--; >>>>> continue; >>>>> } >>>>> } >>>>> Best Regards >>>>> Michael Goetz >>>>> -------------- >>>>> M.Sc. Michael G?tz >>>>> Computational Disease Analysis Group >>>>> Div. Medical and Biological Informatics (E130) >>>>> German Cancer Research Center (DKFZ) >>>>> Im Neuenheimer Feld 280 >>>>> 69120 Heidelberg, Germany >>>>> Email: m....@dk... >>>>> Phone: (+49) 6221/42-3559 >>>>> Fax: (+49) 6221/42-2345 >>>>> http://www.dkfz.de/de/mbi/people/Michael_Goetz.html >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> See everything from the browser to the database with AppDynamics >> Get end-to-end visibility with application monitoring from AppDynamics >> Isolate bottlenecks and diagnose root cause in seconds. >> Start your free trial of AppDynamics Pro today! >> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk >> >> ------------------------------ >> >> _______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users >> >> >> End of teem-users Digest, Vol 65, Issue 5 >> ***************************************** > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Sam Q. <sam...@gm...> - 2013-07-24 18:19:21
|
Interjecting a little late here, but the digest just showed up in my email. Another option might be nrrdMutate(), linking to the idea of 'mutation' as triggering changes at various gradations of discernibility through a wide variety of processes - Sam On Wednesday, July 24, 2013 at 11:55 AM, tee...@li... wrote: > Send teem-users mailing list submissions to > tee...@li... (mailto:tee...@li...) > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/teem-users > or, via email, send a message with subject or body 'help' to > tee...@li... (mailto:tee...@li...) > > You can reach the person managing the list at > tee...@li... (mailto:tee...@li...) > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of teem-users digest..." > > > Today's Topics: > > 1. suggestions for nrrd function name? (Gordon L. Kindlmann) > 2. Re: suggestions for nrrd function name? (Xavier Tricoche) > 3. Re: Bug in Teem (Gordon L. Kindlmann) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Jul 2013 02:33:32 -0500 > From: "Gordon L. Kindlmann" <gl...@uc... (mailto:gl...@uc...)> > Subject: [Teem-users] suggestions for nrrd function name? > To: "tee...@li... (mailto:tee...@li...) Users" > <tee...@li... (mailto:tee...@li...)> > Message-ID: <D43...@uc... (mailto:D43...@uc...)> > Content-Type: text/plain; charset=us-ascii > > Hello, > > There is currently a function nrrdConvert() which is basically just a per-value cast of the values from one type to another type. This is the basis of "unu convert". > > Recognizing the need to sometimes avoid value wrap-around in integer types, there is also nrrdClampConvert(), which clamps values to the representable range of the output type prior to casting. This is accessed via "unu convert -clamp". > > However, sometimes you want to convert an array to an integer type via rounding, rather than plain casting. And at that point you could very well want a function that converts from one type to another, with the ability to turn on rounding and/or clamping, or neither. > > I'd want to call that function nrrdConvert(), and rename the old nrrdConvert() to nrrdCast(). But that be a needless loss of backwards compatibility. > > Strictly following Teem conventions, this function could be called something like nrrdMaybeRoundMaybeClampConvert, which is obviously silly, so the question is: what should this function be called? > > thanks, > Gordon > > > > > ------------------------------ > > Message: 2 > Date: Sun, 21 Jul 2013 10:02:08 -0400 > From: Xavier Tricoche <tri...@sc... (mailto:tri...@sc...)> > Subject: Re: [Teem-users] suggestions for nrrd function name? > To: "Gordon L. Kindlmann" <gl...@uc... (mailto:gl...@uc...)> > Cc: "tee...@li... (mailto:tee...@li...) Users" > <tee...@li... (mailto:tee...@li...)> > Message-ID: <3F4...@sc... (mailto:3F4...@sc...)> > Content-Type: text/plain; charset=us-ascii > > What about nrrdGenericConvert()? > > Xavier > > On Jul 21, 2013, at 3:33 AM, "Gordon L. Kindlmann" <gl...@uc... (mailto:gl...@uc...)> wrote: > > > Hello, > > > > There is currently a function nrrdConvert() which is basically just a per-value cast of the values from one type to another type. This is the basis of "unu convert". > > > > Recognizing the need to sometimes avoid value wrap-around in integer types, there is also nrrdClampConvert(), which clamps values to the representable range of the output type prior to casting. This is accessed via "unu convert -clamp". > > > > However, sometimes you want to convert an array to an integer type via rounding, rather than plain casting. And at that point you could very well want a function that converts from one type to another, with the ability to turn on rounding and/or clamping, or neither. > > > > I'd want to call that function nrrdConvert(), and rename the old nrrdConvert() to nrrdCast(). But that be a needless loss of backwards compatibility. > > > > Strictly following Teem conventions, this function could be called something like nrrdMaybeRoundMaybeClampConvert, which is obviously silly, so the question is: what should this function be called? > > > > thanks, > > Gordon > > > > > > ------------------------------------------------------------------------------ > > See everything from the browser to the database with AppDynamics > > Get end-to-end visibility with application monitoring from AppDynamics > > Isolate bottlenecks and diagnose root cause in seconds. > > Start your free trial of AppDynamics Pro today! > > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > > _______________________________________________ > > teem-users mailing list > > tee...@li... (mailto:tee...@li...) > > https://lists.sourceforge.net/lists/listinfo/teem-users > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 24 Jul 2013 12:54:55 -0500 > From: "Gordon L. Kindlmann" <gl...@uc... (mailto:gl...@uc...)> > Subject: Re: [Teem-users] Bug in Teem > To: Michael G?tz <m....@dk... (mailto:m....@dk...)> > Cc: "tee...@li... (mailto:tee...@li...) Users" > <tee...@li... (mailto:tee...@li...)> > Message-ID: <71E...@uc... (mailto:71E...@uc...)> > Content-Type: text/plain; charset="windows-1252" > > > The bug has been fixed in Teem, and Teem's distribution of NrrdIO, and now also in ITK's NrrdIO: > > http://review.source.kitware.com/#/c/12072/ > > Thanks again, > Gordon > > On Jul 6, 2013, at 4:44 PM, Gordon L. Kindlmann wrote: > > > > > On Jul 5, 2013, at 1:57 PM, Gordon L. Kindlmann wrote: > > > > > Hello, > > > > > > I'm planning on a June 1 patch release of Teem 1.11.1 ... > > > > By which I meant an August 1 release (thanks Xavier). > > > > Do let me know if you find any other bugs! > > > > Thanks, > > Gordon > > > > > , and before then I will go through the process of making sure ITK's NrrdIO has the same bug fix. > > > > > > Thanks, > > > Gordon > > > > > > On Jul 5, 2013, at 5:23 AM, G?tz, Michael wrote: > > > > > > > Hello Gordon, > > > > > > > > this bug was discovered using MITK, which in returns uses ITK for nrrd-support > > > > > > > > Regards > > > > Michael > > > > > > > > Von: Gordon L. Kindlmann [mailto:gl...@uc...] > > > > Gesendet: Freitag, 5. Juli 2013 12:12 > > > > An: G?tz, Michael > > > > Cc: tee...@li... (mailto:tee...@li...) > > > > Betreff: Re: [Teem-users] Bug in Teem > > > > > > > > Hello, > > > > > > > > Thank you very much for the bug report and the very specific information on fixing it. > > > > > > > > I've just committed a fix to the svn trunk. > > > > > > > > May I ask - was this bug discovered through ITK's NrrdIO, or something separate? > > > > > > > > Gordon > > > > > > > > > > > > On Jul 3, 2013, at 9:45 AM, G?tz, Michael wrote: > > > > > > > > > > > > Hi list, > > > > > > > > i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) > > > > > > > > If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the ?remove-nonprintable?-part again and again. -> Endless loop. > > > > > > > > The problem can be solved by checking for \0 in the loop: > > > > for (i=0; i<len && s[i] != \0; i++) { > > > > if (isspace(AIR_CAST(int, s[i]))) { > > > > s[i] = ' '; > > > > continue; > > > > } > > > > if (!isprint(AIR_CAST(int, s[i]))) { > > > > for (j=i; j<len; j++) { > > > > /* this will copy the '\0' at the end */ > > > > s[j] = s[j+1]; > > > > } > > > > i--; > > > > continue; > > > > } > > > > } > > > > > > > > Best Regards > > > > Michael Goetz > > > > > > > > > > > > -------------- > > > > M.Sc. Michael G?tz > > > > Computational Disease Analysis Group > > > > Div. Medical and Biological Informatics (E130) > > > > German Cancer Research Center (DKFZ) > > > > Im Neuenheimer Feld 280 > > > > 69120 Heidelberg, Germany > > > > > > > > Email: m....@dk... (mailto:m....@dk...) > > > > Phone: (+49) 6221/42-3559 > > > > Fax: (+49) 6221/42-2345 > > > > http://www.dkfz.de/de/mbi/people/Michael_Goetz.html > > > > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > > ------------------------------ > > _______________________________________________ > teem-users mailing list > tee...@li... (mailto:tee...@li...) > https://lists.sourceforge.net/lists/listinfo/teem-users > > > End of teem-users Digest, Vol 65, Issue 5 > ***************************************** > > |
From: Gordon L. K. <gl...@uc...> - 2013-07-24 17:55:06
|
The bug has been fixed in Teem, and Teem's distribution of NrrdIO, and now also in ITK's NrrdIO: http://review.source.kitware.com/#/c/12072/ Thanks again, Gordon On Jul 6, 2013, at 4:44 PM, Gordon L. Kindlmann wrote: > > On Jul 5, 2013, at 1:57 PM, Gordon L. Kindlmann wrote: > >> Hello, >> >> I'm planning on a June 1 patch release of Teem 1.11.1 ... > > By which I meant an August 1 release (thanks Xavier). > > Do let me know if you find any other bugs! > > Thanks, > Gordon > >> , and before then I will go through the process of making sure ITK's NrrdIO has the same bug fix. >> >> Thanks, >> Gordon >> >> On Jul 5, 2013, at 5:23 AM, Götz, Michael wrote: >> >>> Hello Gordon, >>> >>> this bug was discovered using MITK, which in returns uses ITK for nrrd-support >>> >>> Regards >>> Michael >>> >>> Von: Gordon L. Kindlmann [mailto:gl...@uc...] >>> Gesendet: Freitag, 5. Juli 2013 12:12 >>> An: Götz, Michael >>> Cc: tee...@li... >>> Betreff: Re: [Teem-users] Bug in Teem >>> >>> Hello, >>> >>> Thank you very much for the bug report and the very specific information on fixing it. >>> >>> I've just committed a fix to the svn trunk. >>> >>> May I ask - was this bug discovered through ITK's NrrdIO, or something separate? >>> >>> Gordon >>> >>> >>> On Jul 3, 2013, at 9:45 AM, Götz, Michael wrote: >>> >>> >>> Hi list, >>> >>> i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) >>> >>> If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the “remove-nonprintable”-part again and again. -> Endless loop. >>> >>> The problem can be solved by checking for \0 in the loop: >>> for (i=0; i<len && s[i] != \0; i++) { >>> if (isspace(AIR_CAST(int, s[i]))) { >>> s[i] = ' '; >>> continue; >>> } >>> if (!isprint(AIR_CAST(int, s[i]))) { >>> for (j=i; j<len; j++) { >>> /* this will copy the '\0' at the end */ >>> s[j] = s[j+1]; >>> } >>> i--; >>> continue; >>> } >>> } >>> >>> Best Regards >>> Michael Goetz >>> >>> >>> -------------- >>> M.Sc. Michael Götz >>> Computational Disease Analysis Group >>> Div. Medical and Biological Informatics (E130) >>> German Cancer Research Center (DKFZ) >>> Im Neuenheimer Feld 280 >>> 69120 Heidelberg, Germany >>> >>> Email: m....@dk... >>> Phone: (+49) 6221/42-3559 >>> Fax: (+49) 6221/42-2345 >>> http://www.dkfz.de/de/mbi/people/Michael_Goetz.html >>> >>> |
From: Xavier T. <tri...@sc...> - 2013-07-21 14:18:04
|
What about nrrdGenericConvert()? Xavier On Jul 21, 2013, at 3:33 AM, "Gordon L. Kindlmann" <gl...@uc...> wrote: > Hello, > > There is currently a function nrrdConvert() which is basically just a per-value cast of the values from one type to another type. This is the basis of "unu convert". > > Recognizing the need to sometimes avoid value wrap-around in integer types, there is also nrrdClampConvert(), which clamps values to the representable range of the output type prior to casting. This is accessed via "unu convert -clamp". > > However, sometimes you want to convert an array to an integer type via rounding, rather than plain casting. And at that point you could very well want a function that converts from one type to another, with the ability to turn on rounding and/or clamping, or neither. > > I'd want to call that function nrrdConvert(), and rename the old nrrdConvert() to nrrdCast(). But that be a needless loss of backwards compatibility. > > Strictly following Teem conventions, this function could be called something like nrrdMaybeRoundMaybeClampConvert, which is obviously silly, so the question is: what should this function be called? > > thanks, > Gordon > > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Gordon L. K. <gl...@uc...> - 2013-07-21 07:33:40
|
Hello, There is currently a function nrrdConvert() which is basically just a per-value cast of the values from one type to another type. This is the basis of "unu convert". Recognizing the need to sometimes avoid value wrap-around in integer types, there is also nrrdClampConvert(), which clamps values to the representable range of the output type prior to casting. This is accessed via "unu convert -clamp". However, sometimes you want to convert an array to an integer type via rounding, rather than plain casting. And at that point you could very well want a function that converts from one type to another, with the ability to turn on rounding and/or clamping, or neither. I'd want to call that function nrrdConvert(), and rename the old nrrdConvert() to nrrdCast(). But that be a needless loss of backwards compatibility. Strictly following Teem conventions, this function could be called something like nrrdMaybeRoundMaybeClampConvert, which is obviously silly, so the question is: what should this function be called? thanks, Gordon |
From: Gordon L. K. <gl...@uc...> - 2013-07-06 21:44:51
|
On Jul 5, 2013, at 1:57 PM, Gordon L. Kindlmann wrote: > Hello, > > I'm planning on a June 1 patch release of Teem 1.11.1 ... By which I meant an August 1 release (thanks Xavier). Do let me know if you find any other bugs! Thanks, Gordon > , and before then I will go through the process of making sure ITK's NrrdIO has the same bug fix. > > Thanks, > Gordon > > On Jul 5, 2013, at 5:23 AM, Götz, Michael wrote: > >> Hello Gordon, >> >> this bug was discovered using MITK, which in returns uses ITK for nrrd-support >> >> Regards >> Michael >> >> Von: Gordon L. Kindlmann [mailto:gl...@uc...] >> Gesendet: Freitag, 5. Juli 2013 12:12 >> An: Götz, Michael >> Cc: tee...@li... >> Betreff: Re: [Teem-users] Bug in Teem >> >> Hello, >> >> Thank you very much for the bug report and the very specific information on fixing it. >> >> I've just committed a fix to the svn trunk. >> >> May I ask - was this bug discovered through ITK's NrrdIO, or something separate? >> >> Gordon >> >> >> On Jul 3, 2013, at 9:45 AM, Götz, Michael wrote: >> >> >> Hi list, >> >> i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) >> >> If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the “remove-nonprintable”-part again and again. -> Endless loop. >> >> The problem can be solved by checking for \0 in the loop: >> for (i=0; i<len && s[i] != \0; i++) { >> if (isspace(AIR_CAST(int, s[i]))) { >> s[i] = ' '; >> continue; >> } >> if (!isprint(AIR_CAST(int, s[i]))) { >> for (j=i; j<len; j++) { >> /* this will copy the '\0' at the end */ >> s[j] = s[j+1]; >> } >> i--; >> continue; >> } >> } >> >> Best Regards >> Michael Goetz >> >> >> -------------- >> M.Sc. Michael Götz >> Computational Disease Analysis Group >> Div. Medical and Biological Informatics (E130) >> German Cancer Research Center (DKFZ) >> Im Neuenheimer Feld 280 >> 69120 Heidelberg, Germany >> >> Email: m....@dk... >> Phone: (+49) 6221/42-3559 >> Fax: (+49) 6221/42-2345 >> http://www.dkfz.de/de/mbi/people/Michael_Goetz.html >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev_______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users > |
From: Gordon L. K. <gl...@uc...> - 2013-07-05 18:57:54
|
Hello, I'm planning on a June 1 patch release of Teem 1.11.1, and before then I will go through the process of making sure ITK's NrrdIO has the same bug fix. Thanks, Gordon On Jul 5, 2013, at 5:23 AM, Götz, Michael wrote: > Hello Gordon, > > this bug was discovered using MITK, which in returns uses ITK for nrrd-support > > Regards > Michael > > Von: Gordon L. Kindlmann [mailto:gl...@uc...] > Gesendet: Freitag, 5. Juli 2013 12:12 > An: Götz, Michael > Cc: tee...@li... > Betreff: Re: [Teem-users] Bug in Teem > > Hello, > > Thank you very much for the bug report and the very specific information on fixing it. > > I've just committed a fix to the svn trunk. > > May I ask - was this bug discovered through ITK's NrrdIO, or something separate? > > Gordon > > > On Jul 3, 2013, at 9:45 AM, Götz, Michael wrote: > > > Hi list, > > i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) > > If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the “remove-nonprintable”-part again and again. -> Endless loop. > > The problem can be solved by checking for \0 in the loop: > for (i=0; i<len && s[i] != \0; i++) { > if (isspace(AIR_CAST(int, s[i]))) { > s[i] = ' '; > continue; > } > if (!isprint(AIR_CAST(int, s[i]))) { > for (j=i; j<len; j++) { > /* this will copy the '\0' at the end */ > s[j] = s[j+1]; > } > i--; > continue; > } > } > > Best Regards > Michael Goetz > > > -------------- > M.Sc. Michael Götz > Computational Disease Analysis Group > Div. Medical and Biological Informatics (E130) > German Cancer Research Center (DKFZ) > Im Neuenheimer Feld 280 > 69120 Heidelberg, Germany > > Email: m....@dk... > Phone: (+49) 6221/42-3559 > Fax: (+49) 6221/42-2345 > http://www.dkfz.de/de/mbi/people/Michael_Goetz.html > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev_______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Gordon L. K. <gl...@uc...> - 2013-07-05 10:43:19
|
Hello, Thank you very much for the bug report and the very specific information on fixing it. I've just committed a fix to the svn trunk. May I ask - was this bug discovered through ITK's NrrdIO, or something separate? Gordon On Jul 3, 2013, at 9:45 AM, Götz, Michael wrote: > Hi list, > > i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) > > If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the “remove-nonprintable”-part again and again. -> Endless loop. > > The problem can be solved by checking for \0 in the loop: > for (i=0; i<len && s[i] != \0; i++) { > if (isspace(AIR_CAST(int, s[i]))) { > s[i] = ' '; > continue; > } > if (!isprint(AIR_CAST(int, s[i]))) { > for (j=i; j<len; j++) { > /* this will copy the '\0' at the end */ > s[j] = s[j+1]; > } > i--; > continue; > } > } > > Best Regards > Michael Goetz > > > -------------- > M.Sc. Michael Götz > Computational Disease Analysis Group > Div. Medical and Biological Informatics (E130) > German Cancer Research Center (DKFZ) > Im Neuenheimer Feld 280 > 69120 Heidelberg, Germany > > Email: m....@dk... > Phone: (+49) 6221/42-3559 > Fax: (+49) 6221/42-2345 > http://www.dkfz.de/de/mbi/people/Michael_Goetz.html > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev_______________________________________________ > teem-users mailing list > tee...@li... > https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Götz, M. <m....@dk...> - 2013-07-05 10:24:10
|
Hello Gordon, this bug was discovered using MITK, which in returns uses ITK for nrrd-support Regards Michael Von: Gordon L. Kindlmann [mailto:gl...@uc...] Gesendet: Freitag, 5. Juli 2013 12:12 An: Götz, Michael Cc: tee...@li... Betreff: Re: [Teem-users] Bug in Teem Hello, Thank you very much for the bug report and the very specific information on fixing it. I've just committed a fix to the svn trunk. May I ask - was this bug discovered through ITK's NrrdIO, or something separate? Gordon On Jul 3, 2013, at 9:45 AM, Götz, Michael wrote: Hi list, i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the "remove-nonprintable"-part again and again. -> Endless loop. The problem can be solved by checking for \0 in the loop: for (i=0; i<len && s[i] != \0; i++) { if (isspace(AIR_CAST(int, s[i]))) { s[i] = ' '; continue; } if (!isprint(AIR_CAST(int, s[i]))) { for (j=i; j<len; j++) { /* this will copy the '\0' at the end */ s[j] = s[j+1]; } i--; continue; } } Best Regards Michael Goetz -------------- M.Sc. Michael Götz Computational Disease Analysis Group Div. Medical and Biological Informatics (E130) German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg, Germany Email: m....@dk...<mailto:m....@dk...> Phone: (+49) 6221/42-3559 Fax: (+49) 6221/42-2345 http://www.dkfz.de/de/mbi/people/Michael_Goetz.html ------------------------------------------------------------------------------ This SF.net<http://SF.net/> email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev_______________________________________________ teem-users mailing list tee...@li...<mailto:tee...@li...> https://lists.sourceforge.net/lists/listinfo/teem-users |
From: Götz, M. <m....@dk...> - 2013-07-03 14:45:54
|
Hi list, i found a bug in the NrrdIO-library. It is in the file NrrdIO/string.c in the function airOneLinify() (be more specific in line 274-278) If a non-printable character is in the given string, every element it is replaced by copying the following elements back by one and reading the given position again. The problem is, that \0 will also be copied and therefore s[len-1] will be \0. Since \0 is non-printable the algorithm will continue to repeat the "remove-nonprintable"-part again and again. -> Endless loop. The problem can be solved by checking for \0 in the loop: for (i=0; i<len && s[i] != \0; i++) { if (isspace(AIR_CAST(int, s[i]))) { s[i] = ' '; continue; } if (!isprint(AIR_CAST(int, s[i]))) { for (j=i; j<len; j++) { /* this will copy the '\0' at the end */ s[j] = s[j+1]; } i--; continue; } } Best Regards Michael Goetz -------------- M.Sc. Michael Götz Computational Disease Analysis Group Div. Medical and Biological Informatics (E130) German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg, Germany Email: m....@dk... Phone: (+49) 6221/42-3559 Fax: (+49) 6221/42-2345 http://www.dkfz.de/de/mbi/people/Michael_Goetz.html |
From: Chourasia, A. <am...@sd...> - 2013-07-02 23:02:11
|
This may be of interest to some folks on this mail list. FYI - The annual IEEE Scientific Visualization Contest is happening now! This year's contest covers gene expression in the developing mouse brain, courtesy of the Allen Institute for Brain Science. The data set tracks the level of gene expression for ~2000 genes in a 3D mouse brain from embryonic stages through adulthood. These expression levels are recorded within annotated 3D anatomical regions that change size and shape (and even divide) during development. The goals for contest participants is to help identify spatial and temporal gene expression patterns in this complex data set. Have a look at the contest website for more details: http://sciviscontest.ieeevis.org/2013/ Submissions are due at the end of July, 2013. We look forward to your submissions! Cheers - IEEE SciVis Contest 2013 Team |
From: J C. P. <jpo...@ri...> - 2013-03-27 19:15:31
|
Hi all, I have a question about the preservation of key/value pairs. Operations that have one input nrrd preserve k/v pairs but operations that take more than one (eg unu join) seem to strip all k/v pairs even if the pair is in all input files. Is there something I'm missing thats "stronger" than the environment variable NRRD_STATE_KEYVALUEPAIRS_PROPAGATE that can force the preservation of k/v pairs? Thanks, Collin The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. |
From: Dr G. J. <jef...@mr...> - 2013-03-13 15:17:19
|
Great! I hadn't seen the exists operator. Thanks a lot to both, Greg. On 13 Mar 2013, at 12:19, Gordon L. Kindlmann wrote: > Or this, which is a few characters shorter: > > unu 2op exists input.nrrd NaN -o output.nrrd > > a demo (commands at % prompt): > > % echo 1 2 +inf 3 4 -inf 5 6 nan | unu save -f text > 1 2 inf 3 4 -inf 5 6 nan > > % echo 1 2 +inf 3 4 -inf 5 6 nan | unu 2op exists - nan | unu save -f > text > 1 2 nan 3 4 nan 5 6 nan > > Gordon > > On Mar 13, 2013, at 4:51 AM, Thomas Schultz wrote: > >> Hi, >> >> On Tue, 2013-03-12 at 23:39 +0000, Dr Gregory Jefferis wrote: >> >>> I have some float nrrds with positive and negative infinity at some >>> voxels. I would like to convert any infinite values to NaNs. Could >>> anyone suggest a simple approach with unu? Many thanks, >> >> This converts all non-existent values to NaN: >> >> unu 3op exists input.nrrd input.nrrd NaN -o output.nrrd >> >> Hope this helps >> Thomas >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> _______________________________________________ >> teem-users mailing list >> tee...@li... >> https://lists.sourceforge.net/lists/listinfo/teem-users >> -- PLEASE NOTE CHANGE OF CONTACT DETAILS FROM MON 4TH MARCH: Gregory Jefferis, PhD Tel: 01223 267048 Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://flybrain.stanford.edu |