debian/0000755000000000000000000000000012232020121007147 5ustar debian/Doxyfile0000644000000000000000000002640012203642665010704 0ustar # Doxyfile 1.7.1 #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- DOXYFILE_ENCODING = UTF-8 PROJECT_NAME = Teem PROJECT_NUMBER = "1.11.0" OUTPUT_DIRECTORY = doc CREATE_SUBDIRS = NO OUTPUT_LANGUAGE = English BRIEF_MEMBER_DESC = YES REPEAT_BRIEF = YES ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ is \ provides \ specifies \ contains \ represents \ a \ an \ the ALWAYS_DETAILED_SEC = NO INLINE_INHERITED_MEMB = NO FULL_PATH_NAMES = YES STRIP_FROM_PATH = STRIP_FROM_INC_PATH = SHORT_NAMES = NO JAVADOC_AUTOBRIEF = NO QT_AUTOBRIEF = NO MULTILINE_CPP_IS_BRIEF = NO INHERIT_DOCS = YES SEPARATE_MEMBER_PAGES = NO TAB_SIZE = 8 ALIASES = OPTIMIZE_OUTPUT_FOR_C = YES OPTIMIZE_OUTPUT_JAVA = NO OPTIMIZE_FOR_FORTRAN = NO OPTIMIZE_OUTPUT_VHDL = NO EXTENSION_MAPPING = BUILTIN_STL_SUPPORT = NO CPP_CLI_SUPPORT = NO SIP_SUPPORT = NO IDL_PROPERTY_SUPPORT = YES DISTRIBUTE_GROUP_DOC = NO SUBGROUPING = YES TYPEDEF_HIDES_STRUCT = NO SYMBOL_CACHE_SIZE = 0 #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- EXTRACT_ALL = YES EXTRACT_PRIVATE = YES EXTRACT_STATIC = YES EXTRACT_LOCAL_CLASSES = YES EXTRACT_LOCAL_METHODS = NO EXTRACT_ANON_NSPACES = NO HIDE_UNDOC_MEMBERS = NO HIDE_UNDOC_CLASSES = NO HIDE_FRIEND_COMPOUNDS = NO HIDE_IN_BODY_DOCS = NO INTERNAL_DOCS = NO CASE_SENSE_NAMES = YES HIDE_SCOPE_NAMES = NO SHOW_INCLUDE_FILES = YES FORCE_LOCAL_INCLUDES = NO INLINE_INFO = YES SORT_MEMBER_DOCS = YES SORT_BRIEF_DOCS = NO SORT_MEMBERS_CTORS_1ST = NO SORT_GROUP_NAMES = NO SORT_BY_SCOPE_NAME = NO GENERATE_TODOLIST = YES GENERATE_TESTLIST = YES GENERATE_BUGLIST = YES GENERATE_DEPRECATEDLIST= YES ENABLED_SECTIONS = MAX_INITIALIZER_LINES = 30 SHOW_USED_FILES = YES SHOW_DIRECTORIES = NO SHOW_FILES = YES SHOW_NAMESPACES = YES FILE_VERSION_FILTER = LAYOUT_FILE = #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- QUIET = NO WARNINGS = YES WARN_IF_UNDOCUMENTED = YES WARN_IF_DOC_ERROR = YES WARN_NO_PARAMDOC = NO WARN_FORMAT = "$file:$line: $text" WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- INPUT = src INPUT_ENCODING = UTF-8 FILE_PATTERNS = *.c \ *.cc \ *.cxx \ *.cpp \ *.c++ \ *.d \ *.java \ *.ii \ *.ixx \ *.ipp \ *.i++ \ *.inl \ *.h \ *.hh \ *.hxx \ *.hpp \ *.h++ \ *.idl \ *.odl \ *.cs \ *.php \ *.php3 \ *.inc \ *.m \ *.mm \ *.dox \ *.py \ *.f90 \ *.f \ *.vhd \ *.vhdl \ *.C \ *.CC \ *.C++ \ *.II \ *.I++ \ *.H \ *.HH \ *.H++ \ *.CS \ *.PHP \ *.PHP3 \ *.M \ *.MM \ *.PY \ *.F90 \ *.F \ *.VHD \ *.VHDL RECURSIVE = YES EXCLUDE = EXCLUDE_SYMLINKS = NO EXCLUDE_PATTERNS = EXCLUDE_SYMBOLS = EXAMPLE_PATH = EXAMPLE_PATTERNS = * EXAMPLE_RECURSIVE = NO IMAGE_PATH = INPUT_FILTER = FILTER_PATTERNS = FILTER_SOURCE_FILES = NO #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- SOURCE_BROWSER = NO INLINE_SOURCES = NO STRIP_CODE_COMMENTS = YES REFERENCED_BY_RELATION = NO REFERENCES_RELATION = NO REFERENCES_LINK_SOURCE = YES USE_HTAGS = NO VERBATIM_HEADERS = NO #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- ALPHABETICAL_INDEX = NO COLS_IN_ALPHA_INDEX = 5 IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- GENERATE_HTML = YES HTML_OUTPUT = html HTML_FILE_EXTENSION = .html HTML_HEADER = HTML_FOOTER = HTML_STYLESHEET = HTML_COLORSTYLE_HUE = 220 HTML_COLORSTYLE_SAT = 100 HTML_COLORSTYLE_GAMMA = 80 HTML_TIMESTAMP = YES HTML_ALIGN_MEMBERS = YES HTML_DYNAMIC_SECTIONS = NO GENERATE_DOCSET = NO DOCSET_FEEDNAME = "Doxygen generated docs" DOCSET_BUNDLE_ID = org.doxygen.Project DOCSET_PUBLISHER_ID = org.doxygen.Publisher DOCSET_PUBLISHER_NAME = Publisher GENERATE_HTMLHELP = NO CHM_FILE = HHC_LOCATION = GENERATE_CHI = NO CHM_INDEX_ENCODING = BINARY_TOC = NO TOC_EXPAND = NO GENERATE_QHP = NO QCH_FILE = QHP_NAMESPACE = org.doxygen.Project QHP_VIRTUAL_FOLDER = doc QHP_CUST_FILTER_NAME = QHP_CUST_FILTER_ATTRS = QHP_SECT_FILTER_ATTRS = QHG_LOCATION = GENERATE_ECLIPSEHELP = NO ECLIPSE_DOC_ID = org.doxygen.Project DISABLE_INDEX = NO ENUM_VALUES_PER_LINE = 4 GENERATE_TREEVIEW = ALL USE_INLINE_TREES = NO TREEVIEW_WIDTH = 250 EXT_LINKS_IN_WINDOW = NO FORMULA_FONTSIZE = 10 FORMULA_TRANSPARENT = YES SEARCHENGINE = NO SERVER_BASED_SEARCH = NO #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- GENERATE_LATEX = NO LATEX_OUTPUT = latex LATEX_CMD_NAME = latex MAKEINDEX_CMD_NAME = makeindex COMPACT_LATEX = NO PAPER_TYPE = a4wide EXTRA_PACKAGES = LATEX_HEADER = PDF_HYPERLINKS = YES USE_PDFLATEX = YES LATEX_BATCHMODE = NO LATEX_HIDE_INDICES = NO LATEX_SOURCE_CODE = NO #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- GENERATE_RTF = NO RTF_OUTPUT = rtf COMPACT_RTF = NO RTF_HYPERLINKS = NO RTF_STYLESHEET_FILE = RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- GENERATE_MAN = NO MAN_OUTPUT = man MAN_EXTENSION = .3 MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- GENERATE_XML = NO XML_OUTPUT = xml XML_SCHEMA = XML_DTD = XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- GENERATE_PERLMOD = NO PERLMOD_LATEX = NO PERLMOD_PRETTY = YES PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- ENABLE_PREPROCESSING = YES MACRO_EXPANSION = NO EXPAND_ONLY_PREDEF = NO SEARCH_INCLUDES = YES INCLUDE_PATH = INCLUDE_FILE_PATTERNS = PREDEFINED = EXPAND_AS_DEFINED = SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- TAGFILES = GENERATE_TAGFILE = ALLEXTERNALS = NO EXTERNAL_GROUPS = YES PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- CLASS_DIAGRAMS = NO MSCGEN_PATH = HIDE_UNDOC_RELATIONS = YES HAVE_DOT = YES DOT_NUM_THREADS = 0 DOT_FONTNAME = FreeSans DOT_FONTSIZE = 10 DOT_FONTPATH = CLASS_GRAPH = YES COLLABORATION_GRAPH = YES GROUP_GRAPHS = YES UML_LOOK = NO TEMPLATE_RELATIONS = NO INCLUDE_GRAPH = YES INCLUDED_BY_GRAPH = YES CALL_GRAPH = NO CALLER_GRAPH = NO GRAPHICAL_HIERARCHY = YES DIRECTORY_GRAPH = YES DOT_IMAGE_FORMAT = png DOT_PATH = DOTFILE_DIRS = DOT_GRAPH_MAX_NODES = 50 MAX_DOT_GRAPH_DEPTH = 1000 DOT_TRANSPARENT = YES DOT_MULTI_TARGETS = NO GENERATE_LEGEND = YES DOT_CLEANUP = YES debian/copyright0000644000000000000000000002531612203642665011136 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Debianized-By: Dominique Belhachemi Debianized-Date: Fri, 21 Mar 2008 09:41:47 +0000 Original-Source: http://teem.sourceforge.net/ Files: * Copyright: Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah License: Simple Library Usage License ---------------------------------------------------------------------- Simple Library Usage License Version 1, Nov 6 2005 . Copyright (c) 2005 Gordon Kindlmann . Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. . SIMPLE LIBRARY USAGE LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION . This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License (LGPL) as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU Lesser General Public License can be found in `/usr/share/common-licenses/LGPL'. . . . EXCEPTION NOTICE . 1. As a special exception, the copyright holders of this library give permission for additional uses of the text contained in this release of the library as licensed under the Simple Library Usage License, applying either version 1 of the License, or (at your option) any later version of the License as published by the copyright holders of version 1 of the License document. . 2. The exception is that you may combine or link a "work that uses the Library" (as defined by the LGPL) with the Library to produce a work containing portions of the Library in binary form, and distribute that work under terms of your choice, provided that: . a) You give prominent notice with each copy of the work that the Library is used in it. . b) If the work during execution displays copyright notices, you must include the copyright notice for the Library among them. . 3. If you copy code from files distributed under the terms of the GNU General Public License or the GNU Lesser General Public License into a copy of this library, as this license permits, the exception does not apply to the code that you add in this way. To avoid misleading anyone as to the status of such modified files, you must delete this exception notice from such code and/or adjust the licensing conditions notice accordingly. . 4. If you write modifications of your own for this library, it is your choice whether to permit this exception to apply to your modifications. If you do not wish that, you must delete the exception notice from such code and/or adjust the licensing conditions notice accordingly. ---------------------------------------------------------------------- Files: UseTeemCMakeDemo/sanity.c Copyright: Copyright (C) 2008 Gordon Kindlmann License: WTFPL Version 2, December 2004 DO WHAT THE FUCK YOU WANT TO PUBLIC LICENSE Version 2, December 2004 . Copyright (C) 2004 Sam Hocevar 14 rue de Plaisance, 75014 Paris, France Everyone is permitted to copy and distribute verbatim or modified copies of this license document, and changing it is allowed as long as the name is changed. . DO WHAT THE FUCK YOU WANT TO PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION . 0. You just DO WHAT THE FUCK YOU WANT TO. ----------------------------------------------------------- Files: src/nrrd/gzio.c Copyright: Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah Copyright (C) 1995-2002 Jean-loup Gailly and Mark Adler License: This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License (LGPL) as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. The terms of redistributing and/or modifying this software also include exceptions to the LGPL that facilitate static linking. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA --- This file is a modified version of the 'gzio.c' and 'zutil.h' source files from the zlib 1.1.4 distribution. . zlib.h -- interface of the 'zlib' general purpose compression library version 1.1.4, March 11th, 2002 . Copyright (C) 1995-2002 Jean-loup Gailly and Mark Adler . This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. . Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu . The data format used by the zlib library is described by RFCs (Request for Comments) 1950 to 1952 in the files ftp://ds.internic.net/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format). ---------------------------------- Files: src/air/randMT.c Copyright: Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura, Copyright (C) 2000 - 2003, Richard J. Wagner License: This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License (LGPL) as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. The terms of redistributing and/or modifying this software also include exceptions to the LGPL that facilitate static linking. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA --- This file is a modified version of the MersenneTwister.h source file written by Richard J. Wagner. The original copyright notice follows. . Mersenne Twister random number generator -- a C++ class MTRand Based on code by Makoto Matsumoto, Takuji Nishimura, and Shawn Cokus Richard J. Wagner v1.0 15 May 2003 rjwagner@writeme.com . The Mersenne Twister is an algorithm for generating random numbers. It was designed with consideration of the flaws in various other generators. The period, 2^19937-1, and the order of equidistribution, 623 dimensions, are far greater. The generator is also fast; it avoids multiplication and division, and it benefits from caches and pipelines. For more information see the inventors' web page at http://www.math.keio.ac.jp/~matumoto/emt.html . Reference M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator", ACM Transactions on Modeling and Computer Simulation, Vol. 8, No. 1, January 1998, pp 3-30. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. . The original code included the following notice: . When you use this, send an email to: matumoto@math.keio.ac.jp with an appropriate reference to your work. . It would be nice to CC: rjwagner@writeme.com and Cokus@math.washington.edu when you write. ---------------------------------- Files: debian/* Copyright: Copyright 2008, Dominique Belhachemi License: GPL-2+ The Debian packaging is licensed under the GPL, see `/usr/share/common-licenses/GPL' debian/teem-doc.doc-base0000644000000000000000000000231112203642665012265 0ustar Document: teem-doc Title: TEEM class documentation Author: Various Abstract: Teem - Tools to process and visualize scientific data and images Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are: . * Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information. * Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.) * Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure * Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods. Section: Programming Format: HTML Index: /usr/share/doc/teem-doc/html/index.html Files: /usr/share/doc/teem-doc/html/*.html debian/source/0000755000000000000000000000000012203642666010475 5ustar debian/source/format0000644000000000000000000000001412203642665011702 0ustar 3.0 (quilt) debian/man/0000755000000000000000000000000012203642666007750 5ustar debian/man/teem-vprobe.10000644000000000000000000000606012203642665012260 0ustar .TH "teem-vprobe" "1" "December 10, 2008" "1.10.0" "User Commands" .SH "NAME" teem\-vprobe \- Shows off the functionality of the gage library. .SH "SYNOPSIS" .B teem\-vprobe \fI\-i \-k \fR[\fI\-v \fR] \fI\-q \fR[\fI\-s ] [\-k00 ] [\-k11 ] [\-k22 ] [\-seed ] \e [\-ssn ] [\-ssr ] [\-sss ] [\-ssw ] [\-kssblur ] [\-kss ] [\-ssrn ] [\-ssu] [\-rn] \e [\-gmc ] [\-t ] [\-o ] .IP \fB\-i\fR = input volume .IP \fB\-k\fR = "kind" of volume ("scalar", "vector", "tensor", or .IP "dwi") .HP \fB\-v\fR = verbosity level (int); default: "1" .IP \fB\-q\fR = the quantity (scalar, vector, or matrix) to learn by .IP probing (string) .TP \fB\-s\fR = scaling factor for resampling on each axis (>1.0 : supersampling) (3 doubles); default: "1.0 1.0 1.0" .HP \fB\-k00\fR = kernel for gageKernel00; default: "tent" .HP \fB\-k11\fR = kernel for gageKernel11; default: "cubicd:1,0" .HP \fB\-k22\fR = kernel for gageKernel22; default: "cubicdd:1,0" .IP \fB\-seed\fR = RNG seed; mostly for debugging (unsigned int); .IP default: "42" .IP \fB\-ssn\fR = how many scale\-space samples to evaluate, or, 0 to .IP turn\-off all scale\-space behavior (unsigned int); default: "0" .TP \fB\-ssr\fR = range of scales in scale\-space (2 doubles); default: "nan nan" .PP \fB\-sss\fR = give a non\-empty path string (like "./") to save out .IP the pre\-blurred volumes computed for the stack (string); default: "" .TP \fB\-ssw\fR = "world"\-space position (true sigma) at which to sample in scale\-space (double); default: "0" .TP \fB\-kssblur\fR = blurring kernel, to sample scale space; default: "dgauss:1,5" .TP \fB\-kss\fR = kernel for reconstructing from scale space samples; default: "tent" .TP \fB\-ssrn\fR = enable derivative normalization based on scale space (int); default: "0" .IP \fB\-ssu\fR = do uniform samples along sigma, and not (by default) .IP samples according to the logarithm of diffusion time .IP \fB\-rn\fR = renormalize kernel weights at each new sample .IP location. "Accurate" kernels don't need this; doing it always makes things go slower .TP \fB\-gmc\fR = For curvature\-based queries, use zero when gradient magnitude is below this (double); default: "0.0" .IP \fB\-t\fR = type of output volume (type); default: "float" \fB\-o\fR = output volume (string); default: "\-" .SH "SEE ALSO" The full documentation for .B teem\-vprobe is maintained as a Texinfo manual. If the .B info and .B teem\-vprobe programs are properly installed at your site, the command .IP .B info teem\-vprobe .PP should give you access to the complete manual. debian/man/teem-tend.10000644000000000000000000000332612203642665011717 0ustar .TH "teem-tend" "1" "December 10, 2008" "1.10.0" "User Commands" .SH "NAME" teem\-tend \- Diffusion Image Processing and Analysis .SH "DESCRIPTION" .IP "tend" is a command\-line interface to much of the functionality in "ten", .IP a C library for diffusion image processing. Ten is one library in the "Teem" collection of libraries. More information about Teem is at . .IP Users are strongly encouraged to join the teem\-users mailing list: .IP . This is the primary forum for feedback, questions, and feature requests. .IP Like "unu", another Teem command\-line binary, it is often useful to chain .IP together invocations of tend with pipes, as in the following, which estimates tensors from DWIs, takes a slice of the tensor volume, computes the standard RGB colormap of the principal eigenvector, and then quantizes it to an 8\-bit PNG: .IP tend estim \fB\-i\fR dwi.nhdr \fB\-B\fR kvp \fB\-knownB0\fR true \e .IP | tend slice \fB\-a\fR 2 \fB\-p\fR 30 \e | tend evecrgb \fB\-c\fR 0 \fB\-a\fR cl2 \fB\-gam\fR 1.2 \e | unu quantize \fB\-b\fR 8 \fB\-min\fR 0 \fB\-max\fR 1 \fB\-o\fR z30\-rgb.png .IP If tend repeatedly proves itself useful for your research, an .IP acknowledgment to that effect in your publication would be greatly appreciated, such as (for LaTeX): "Dataset processing performed with the {\ett tend} tool part of the {\ett Teem} toolkit available at {\ett $<$http://teem.sf.net$>$}" .SH "SEE ALSO" The full documentation for .B Teem is maintained as a Texinfo manual. If the .B info and .B teem\-tend programs are properly installed at your site, the command .IP .B info teem\-tend .PP should give you access to the complete manual. debian/man/teem-ilk.10000644000000000000000000000604112203642665011541 0ustar .TH TEEM "1" "April 2012" "Teem version 1.11.0" "User Commands" .SH NAME teem\-ilk \- (I)mage (L)inear Trans(X\-\->K)forms. .SH SYNOPSIS .B teem-ilk [\fI@file \fR...] [\fI-i \fR] [\fI-0 \fR] \fI\\fR .SH DESCRIPTION /usr/bin/teem\-ilk: (I)mage (L)inear Trans(X\-\->K)forms. Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling. .HP \fB\-t\fR [\-k ] [\-min ] [\-max ] \e .IP [\-b ] [\-bg ] [\-s ] [\-a ] \e [\-o ] .IP @file ... = response file(s) containing command\-line arguments .HP \fB\-i\fR = input image; default: "\-" .TP \fB\-0\fR = where to location (0,0) prior to applying transforms. o "u:," locate origin in a unit box [0,1]x[0,1] which covers the original image o "p:," locate origin at a particular pixel location, in the index space of the image default: "p:0,0" .TP \fB\-t\fR = transform(s) to apply to image. Transforms are applied in the order in which they appear. o "identity": no geometric transform, just resampling o "translate:x,y": shift image by vector (x,y), as measured in pixels o "rotate:ang": rotate CCW by ang degrees o "scale:xs,ys": scale by xs in X, and ys in Y o "shear:fix,amnt": shear by amnt, keeping fixed the pixels along a direction degrees from the X axis o "flip:ang": flip along axis an angle degrees from the X axis o "a,b,tx,c,d,ty": specify the transform explicitly in row\-major order (opposite of PostScript) (1 or more 2D transforms) .HP \fB\-k\fR = reconstruction kernel; default: "cubic:0,0.5" .TP \fB\-min\fR = lower bounding corner of output image. Default (by not using this option) is the lower corner of input image. (2 doubles) .TP \fB\-max\fR = upper bounding corner of output image. Default (by not using this option) is the upper corner of input image. (2 doubles) .TP \fB\-b\fR = what to do when sampling outside original image. o "bleed": copy values at image border outward o "wrap": do wrap\-around on image locations o "pad": use a given background value (via "\-bg") default: "bleed" .PP \fB\-bg\fR = background color to use with boundary behavior "pad". .IP Defaults to all zeroes. (1 or more floats) .TP \fB\-s\fR = For each axis, information about how many samples in output: o "x": number of output samples is some scaling of the number input of samples; multiplied by o "": specify exact number of samples (2 sampling specifications) default: "x1 x1" .TP \fB\-a\fR = number of averages (if there there is only one rotation) (unsigned int); default: "0" .HP \fB\-o\fR = file to write output nrrd to (string); default: "\-" .SH "SEE ALSO" The full documentation for .B Teem is maintained as a Texinfo manual. If the .B info and .B Teem programs are properly installed at your site, the command .IP .B info Teem .PP should give you access to the complete manual. debian/man/teem-nrrdSanity.10000644000000000000000000000163712203642665013125 0ustar .TH "teem-nrrdSanity" "1" "December 10, 2008" "1.10.0" "User Commands" .SH "NAME" teem\-nrrdSanity \- Nearly Raw Raster Data Sanity Check .SH "DESCRIPTION" .IP Usage: teem\-nrrdSanity .IP nrrdSanity calls the nrrdSanity() check to verify the correctness of all .IP the information (set at compile\-time) about the architecture, such as endianness, 32/64\-bit, and the size of various types, as well as running sanity checks on the global default (nrrdDefault*) and state (nrrdState*) variables. .IP As a convenience, nrrdSanity also list the availability of the different .IP formats and data encodings (for Nrrd files) supported by this build. .SH "SEE ALSO" The full documentation for .B teem\-nrrdSanity is maintained as a Texinfo manual. If the .B info and .B teem\-nrrdSanity programs are properly installed at your site, the command .IP .B info teem\-nrrdSanity .PP should give you access to the complete manual. debian/man/teem-puller.10000644000000000000000000002257212203642665012274 0ustar .TH TEEM "1" "April 2012" "Teem version 1.11.0" "User Commands" .SH NAME /usr/bin/teem\-puller \- Command\-line interface to the "pull" library. .SH SYNOPSIS .B teem-puller [\fI@file \fR...] [\fI-int \fR] [\fI-enr \fR] \fI\\fR .SH DESCRIPTION /usr/bin/teem\-puller: Command\-line interface to the "pull" library. Published research using this tool or the "pull" library should cite the paper: .IP Gordon L. Kindlmann, Ra{\e'u}l San Jos{\e'e} Est{\e'e}par, Stephen M. Smith, Carl\-Fredrik Westin. Sampling and Visualizing Creases with Scale\-Space Particles. IEEE Trans. on Visualization and Computer Graphics, 15(6):1415\-1424 (2009). .IP [\-ens ] [\-enw ] [\-efs ] [\-nave ] [\-cbst ] \e [\-noadd] [\-usa ] [\-pcet ] [\-nobin] [\-lti ] \e [\-por ] [\-npcwza ] [\-ubfgl ] [\-ratb ] \e [\-svec ] [\-gssr ] [\-v ] \fB\-vol\fR \e \fB\-info\fR [\-k00 ] [\-k11 ] [\-k22 ] \e [\-sscp ] [\-kssb ] [\-kssr ] [\-nss <# scl smpls>] \e [\-np <# points>] [\-halton] [\-ppv <# pnts/vox>] [\-ppvzr ] \e [\-jit ] [\-pi ] [\-step ] [\-csm ] [\-snap <# \e iters>] [\-maxi <# iters>] [\-stim <# iters>] [\-maxci <# iters>] \e [\-irad ] [\-srad ] [\-bws ] [\-alpha ] \e [\-beta ] [\-gamma ] [\-theta ] [\-wall ] [\-eip ] \e [\-ess ] [\-oss ] [\-edmin ] [\-edpcmin ] \e [\-fnnm ] [\-pcp ] [\-iad <# iters>] [\-icb <# iters>] \e [\-ac3c ] [\-sit ] [\-rng ] [\-pbm ] [\-eiphl ] \e [\-nt <# threads>] [\-nprob ] [\-pprob ] [\-addlog ] \e [\-o ] [\-eob ] .IP @file ... = response file(s) containing command\-line arguments .IP \fB\-int\fR = inter\-particle energy type (interaction type); .IP default: "justr" .IP \fB\-enr\fR = inter\-particle energy, radial component (energy .IP specification); default: "cotan" .IP \fB\-ens\fR = inter\-particle energy, scale component (energy .IP specification); default: "zero" .IP \fB\-enw\fR = windowing to create locality with additive .IP scale\-space interaction ("\-int add") (energy specification); default: "butter:16,0.8" .IP \fB\-efs\fR = whether or not strength contributes to .IP particle\-image energy (bool); default: "false" .IP \fB\-nave\fR = whether or not to nix points at edge of volume, .IP where gage had to invent values for kernel support (bool); default: "false" .IP \fB\-cbst\fR = during initialization, try constraint satisfaction .IP before testing seedThresh (bool); default: "false" .IP \fB\-noadd\fR = turn off adding during population control .IP \fB\-usa\fR = allow volumes to have different shapes (false is .IP safe as different volume sizes are often accidental) (bool); default: "false" .IP \fB\-pcet\fR = use neighbor\-counting "enough" heuristic to bail out .IP of pop cntl (bool); default: "true" .IP \fB\-nobin\fR = turn off spatial binning (which prevents .IP multi\-threading from being useful), for debugging or speed\-up measurement .IP \fB\-lti\fR = impose liveThresh on initialization (bool); .IP default: "true" .IP \fB\-por\fR = permute points during rebinning (bool); .IP default: "true" .HP \fB\-npcwza\fR = no pop cntl with zero alpha (bool); default: "false" .HP \fB\-ubfgl\fR = use beta for gamma learning (bool); default: "false" .IP \fB\-ratb\fR = be choosy when adding points to bins to avoid .IP overlap (bool); default: "true" .IP \fB\-svec\fR = if non\-zero (length), vector to use for displaying .IP scale in 3\-space (3 doubles); default: "0 0 0" .IP \fB\-gssr\fR = if non\-zero (length), scaling of scale to .IP cylindrical tensors (double); default: "0.0" .HP \fB\-v\fR = verbosity level (int); default: "1" .TP \fB\-vol\fR = input volumes, in format :: (1 or more meetPullVols) .PP \fB\-info\fR = info definitions, in format .IP [\-c]::[::] (1 or more meetPullInfos) .TP \fB\-k00\fR = kernel for gageKernel00 (kernel specification); default: "cubic:1,0" .TP \fB\-k11\fR = kernel for gageKernel11 (kernel specification); default: "cubicd:1,0" .TP \fB\-k22\fR = kernel for gageKernel22 (kernel specification); default: "cubicdd:1,0" .IP \fB\-sscp\fR = path (without trailing /) for where to read/write .IP pre\-blurred volumes for scale\-space (string); default: "./" .TP \fB\-kssb\fR = blurring kernel, to sample scale space (kernel specification); default: "ds:1,5" .TP \fB\-kssr\fR = kernel for reconstructing from scale space samples (kernel specification); default: "hermite" .TP \fB\-nss\fR <# scl smpls> = if using "\-ppv", number of samples along scale axis for each spatial position (unsigned int); default: "1" .TP \fB\-np\fR <# points> = number of points to start in system (unsigned int); default: "1000" .IP \fB\-halton\fR = use Halton sequence initialization instead of .IP uniform random .TP \fB\-ppv\fR <# pnts/vox> = number of points per voxel to start in simulation (need to have a seed thresh vol, overrides "\-np") (unsigned int); default: "0" .TP \fB\-ppvzr\fR = range of Z slices (1st num < 2nd num) to do ppv in, or, "1 0" for whole volume (2 unsigned ints); default: "1 0" .TP \fB\-jit\fR = amount of jittering to do with ppv (double); default: "0" .IP \fB\-pi\fR = 4\-by\-N array of positions to start at (overrides .IP "\-np") (nrrd); default: "" .IP \fB\-step\fR = initial step size for gradient descent (double); .IP default: "1" .IP \fB\-csm\fR = convergence criterion for constraint satisfaction .IP (double); default: "0.0001" .TP \fB\-snap\fR <# iters> = if non\-zero, # iters between saved snapshots (unsigned int); default: "0" .TP \fB\-maxi\fR <# iters> = if non\-zero, max # iterations to run whole system (unsigned int); default: "0" .TP \fB\-stim\fR <# iters> = if non\-zero, max # iterations to allow a particle to be stuck before nixing (unsigned int); default: "5" .TP \fB\-maxci\fR <# iters> = if non\-zero, max # iterations for contraint enforcement (unsigned int); default: "15" .TP \fB\-irad\fR = particle radius in spatial domain (double); default: "1" .TP \fB\-srad\fR = particle radius in scale domain (double); default: "1" .TP \fB\-bws\fR = spatial bin width as multiple of spatial radius (double); default: "1.001" .TP \fB\-alpha\fR = blend between particle\-image (alpha=0) and inter\-particle (alpha=1) energies (double); default: "0.5" .IP \fB\-beta\fR = when using Phi2 energy, blend between pure space .IP repulsion (beta=0) and scale attraction (beta=1) (double); default: "1.0" .TP \fB\-gamma\fR = scaling factor on energy from strength (double); default: "1.0" .TP \fB\-theta\fR = slope of increasing livethresh wrt scale (double); default: "0.0" .IP \fB\-wall\fR = spring constant on walls (double); default: "0.0" .IP \fB\-eip\fR = amount by which its okay for *per\-particle* energy .IP to increase during gradient descent process (double); default: "0.0" .IP \fB\-ess\fR = when energy goes up instead of down, scale step size .IP by this (double); default: "0.5" .IP \fB\-oss\fR = opportunistic scaling (hopefully up, >1) of step .IP size on every iteration (double); default: "1.0" .TP \fB\-edmin\fR = convergence threshold: stop when fractional improvement (decrease) in energy dips below this (double); default: "0.0001" .TP \fB\-edpcmin\fR = population control is triggered when energy improvement goes below this threshold (double); default: "0.01" .IP \fB\-fnnm\fR = don't nix if this fraction (or more) of neighbors .IP have been nixed (double); default: "0.25" .TP \fB\-pcp\fR = # iters to wait between attempts at population control (unsigned int); default: "20" .TP \fB\-iad\fR <# iters> = # iters to run descent on tentative new points during PC (unsigned int); default: "10" .TP \fB\-icb\fR <# iters> = periodicity of calling rendering callback (unsigned int); default: "1" .IP \fB\-ac3c\fR = allow codimensions 3 constraints (bool); .IP default: "false" .IP \fB\-sit\fR = scale is tau (bool); default: "false" .IP \fB\-rng\fR = base seed value for RNGs (unsigned int); .IP default: "42" .IP \fB\-pbm\fR = progress bin mod (unsigned int); default: "50" .IP \fB\-eiphl\fR = half\-life of energyIncreasePermute ("\-eip") .IP (unsigned int); default: "0" .TP \fB\-nt\fR <# threads> = number of threads hoover should use (int); default: "1" .TP \fB\-nprob\fR = do full neighbor discovery with this probability (double); default: "1.0" .TP \fB\-pprob\fR = probe local image values with this probability (double); default: "1.0" .TP \fB\-addlog\fR = name of file in which to log all particle additions (string); default: "" .IP \fB\-o\fR = output volume (string); default: "\-" .IP \fB\-eob\fR = save extra info (besides position), and use this .IP string as the base of the filenames. Not using this means the extra info is not saved. (string); default: "" .SH "SEE ALSO" The full documentation for .B Teem is maintained as a Texinfo manual. If the .B info and .B Teem programs are properly installed at your site, the command .IP .B info Teem .PP should give you access to the complete manual. debian/man/teem-unu.10000644000000000000000000000537112203642665011576 0ustar .TH "teem-unu" "1" "December 10, 2008" "1.10.0" "User Commands" .SH "NAME" teem\-unu \- Utah Nrrd Utilities command\-line interface .SH "DESCRIPTION" .HP "teem\-unu" is a command\-line interface to much of the functionality in "nrrd", .IP a C library for raster data processing. Nrrd is one library in the "Teem" collection of libraries. More information about Teem is at . .IP Users are strongly encouraged to join the teem\-users mailing list: .IP . This is the primary forum for feedback, questions, and feature requests. .IP The utility of unu is mainly as a pre\-processing tool for getting data .IP into a type, encoding, format, or dimensions best suited for some visualization or rendering task. Also, slices and projections are effective ways to visually inspect the contents of a dataset. Especially useful commands include make, resample, crop, slice, project, histo, dhisto, quantize, and save. Full documentation for each command is shown by typing the command alone, e.g., "unu make". Unu can process CT and MRI volume datasets, grayscale and color images, time\-varying volumes of vector fields (5\-D arrays), and more. Currently supported formats are plain text files (2\-D float arrays), NRRD, VTK structured points, and PNG and PNM images. "unu make \fB\-bs\fR \fB\-1\fR" can read from DICOM files. "unu save" can generate EPS files. Supported encodings are raw, ascii, hex, gzip, and bzip2. .IP Much of the functionality of unu derives from chaining multiple .IP invocations together with pipes ("|"), minimizing the need to save out intermediate files. For example, if "data.raw.gz" is a gzip'ed 256 x 256 x 80 volume of raw floats written from a PC, then the following will save to "zsum.png" a histogram equalized summation projection along the slowest axis: .IP unu make \fB\-i\fR data.raw.gz \fB\-t\fR float \fB\-s\fR 256 256 80 \fB\-e\fR gzip \fB\-en\fR little \e .IP | unu project \fB\-a\fR 2 \fB\-m\fR sum \e | unu heq \fB\-b\fR 2000 \fB\-s\fR 1 \e | unu quantize \fB\-b\fR 8 \fB\-o\fR zsum.png .IP If unu or nrrd repeatedly proves itself useful for your research, an .IP acknowledgment to that effect in your publication would be greatly appreciated, such as (for LaTeX): "Dataset processing performed with the {\ett unu} tool (or the {\ett nrrd} library), part of the {\ett Teem} toolkit available at {\ett $<$http://teem.sf.net$>$}" .IP Formats available: nrrd pnm png vtk text eps Nrrd data encodings available: raw ascii hex gz bz2 .SH "SEE ALSO" The full documentation for .B teem\-unu is maintained as a Texinfo manual. If the .B info and .B teem\-unu programs are properly installed at your site, the command .IP .B info teem\-unu .PP should give you access to the complete manual. debian/man/teem-gprobe.10000644000000000000000000001037512203642665012245 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH TEEM "1" "May 2011" "Teem version 1.11.0 (late 2009 or early 2010)" "User Commands" .SH NAME Teem\-gprobe \- Shows off the functionality of the gage library .SH SYNOPSIS .B teem-gprobe \fI\-i \-k \fR[\fI\-v \fR] \fI\-q \\fR .SH DESCRIPTION \&./teem\-gprobe: Shows off the functionality of the gage library. Uses gageProbe() to query various kinds of volumes to learn various measured or derived quantities. .IP [\-gmc ] [\-ofs] [\-seed ] [\-k00 ] [\-k11 ] \e [\-k22 ] [\-rn] [\-ssn ] [\-ssr ] \e [\-kssb ] [\-kssr ] [\-ssu] [\-sso] [\-ssnd] [\-ssf ] [\-s ] [\-ssp ] [\-pg ] \e [\-pi ] [\-pp ] [\-eps ] [\-psi

] [\-t ] \e [\-o ] .IP \fB\-i\fR = input volume .IP \fB\-k\fR = "kind" of volume ("scalar", "vector", "tensor", .IP or "dwi") .IP \fB\-v\fR = verbosity level (int); default: "1" .IP \fB\-q\fR = the quantity (scalar, vector, or matrix) to learn .IP by probing (string) .TP \fB\-gmc\fR = For curvature\-based queries, use zero when gradient magnitude is below this (double); default: "0.0" .IP \fB\-ofs\fR = If only per\-axis spacing is available, use that .IP to contrive full orientation info .IP \fB\-seed\fR = RNG seed; mostly for debugging (unsigned int); .IP default: "42" .IP \fB\-k00\fR = kernel for gageKernel00; default: "tent" \fB\-k11\fR = kernel for gageKernel11; default: "cubicd:1,0" \fB\-k22\fR = kernel for gageKernel22; default: "cubicdd:1,0" .IP \fB\-rn\fR = renormalize kernel weights at each new sample .IP location. "Accurate" kernels don't need this; doing it always makes things go slower .IP \fB\-ssn\fR = how many scale\-space samples to evaluate, or, 0 .IP to turn\-off all scale\-space behavior (unsigned int); default: "0" .TP \fB\-ssr\fR = range of scales in scale\-space (2 doubles); default: "nan nan" .IP \fB\-kssb\fR = blurring kernel, to sample scale space; .IP default: "dgauss:1,5" .IP \fB\-kssr\fR = kernel for reconstructing from scale space .IP samples; default: "hermite" .IP \fB\-ssu\fR = do uniform samples along sigma, and not (by .IP default) samples according to the effective diffusion scale .IP \fB\-sso\fR = if not using "\-ssu", use pre\-computed optimal .IP sigmas when possible .IP \fB\-ssnd\fR = normalize derivatives by scale .PP \fB\-ssf\fR = printf\-style format (including a "%u") for the .IP filenames from which to read pre\-blurred volumes computed for the stack, if they exist and match the stack parameters, and where to save them if they had to be re\-computed. Leave this as empty string to disable this. (string); default: "" .TP \fB\-s\fR = scaling factor for resampling on each axis (>1.0 : supersampling); use "\-ssp" (and "\-psi")to specify scale position of sampling (3 doubles); default: "1 1 1" .IP \fB\-ssp\fR = when using scale\-space, scale\-position at which .IP to probe (double); default: "0" .IP \fB\-pg\fR = overrides "\-s": 2\-D nrrd which specifies origin .IP and direction vectors for sampling grid; default: "" .IP \fB\-pi\fR = overrides "\-pv": probes at this list of 3\-vec or .IP 4\-vec positions; default: "" .IP \fB\-pp\fR = overrides "\-pi": only sample at this specified .IP point (3..4 doubles); default: "nan nan nan" .IP \fB\-eps\fR = if non\-zero, and if query is a scalar, and if .IP using "pp" to query at a single point, then do epsilon offset probes to calculate discrete differences, to find the numerical gradient and hessian (for debugging) (double); default: "0" .IP \fB\-psi\fR

= whether the probe location specification (by any .IP of the four previous flags) are in index space (bool); default: "true" .IP \fB\-t\fR = type of output volume (type); default: "float" \fB\-o\fR = output volume (string); default: "\-" .SH "SEE ALSO" The full documentation for .B Teem is maintained as a Texinfo manual. If the .B info and .B Teem programs are properly installed at your site, the command .IP .B info Teem .PP should give you access to the complete manual. debian/man/teem-overrgb.10000644000000000000000000000361612203642665012435 0ustar .TH TEEM "1" "December 10, 2008" "1.10.0" "User Commands" .SH NAME teem\-overrgb \- Composites an RGBA nrrd over a background color. .SH SYNOPSIS .B teem-overrgb \fI-i \fR[\fI-c \fR] [\fI-cfp \fR] \fI\\fR .SH DESCRIPTION \&./teem\-overrgb: Composites an RGBA nrrd over a background color (or image), after doing gamma correction, then quantizes to an 8\-bit image. Actually, the input nrrd can have more than 4 values per pixel, but only the first four are used. If the RGBA nrrd is floating point, the values are taken at face value; if it is fixed point, the values interpreted as having been quantized (so that 8\-bit RGBA images will act as you expect). When compositing with a background image, the given background image does not have to be the same size as the input image; it will be resampled (with linear interpolation) to fit. .IP [\-g ] [\-b ] [\-bi ] \fB\-o\fR .HP \fB\-i\fR = input nrrd to composite (nrrd) .TP \fB\-c\fR = contrast to apply to RGB values, before gamma. "0.0" means no change, "1.0" means thresholding, "\-1.0" means a complete washout. (double); default: "0.0" .PP \fB\-cfp\fR = component level that doesn't change with contrast .IP (double); default: "0.5" .TP \fB\-g\fR = gamma to apply to image data, after contrast (double); default: "1.0" .TP \fB\-b\fR = background color to composite against; white is 1 1 1, not 255 255 255. (3 doubles); default: "0 0 0" .TP \fB\-bi\fR = 8\-bit RGB background image to composite against (nrrd); default: "" .HP \fB\-o\fR = file to write output PPM image to (string) .SH "SEE ALSO" The full documentation for .B teem-overrgb is maintained as a Texinfo manual. If the .B info and .B teem-overrgb programs are properly installed at your site, the command .IP .B info teem-overrgb .PP should give you access to the complete manual. debian/man/teem.10000644000000000000000000001417012203642665010766 0ustar .TH "teem" "1" "April 2008" "" "" .SH "NAME" teem \- simple command\-line tools which provide fast and easy access to the functionality in the various libraries .SH "DESCRIPTION" \fBteem\-affine\fR: This uses air's AIR_AFFINE macro to print out the value which stands in the same relationship with the interval [, ] as has with the interval [minIn, maxOut]. \fBteem\-deconv\fR: Does deconvolution. \fBteem\-airSanity\fR: \fBteem\-cubic\fR: \fBteem\-emap\fR: Creates environment maps based on limn's "checker" normal quantization methods. By taking into account camera parameters, this allows for both lights in both world and view space. Solely out of laziness, the nrrd format is used for specifying the lights, but not to worry: you can use a simple un\-adorned text file, defining one light per line, with 7 values per light: 0/1 (world/view space), R G B color, and X Y Z position. \fBteem\-gkms\fR: Semi\-Automatic Generation of Transfer Functions \fBteem\-idx2pos\fR: Converts from floating\-point "index" to floating\-point "position", given the centering of the data (cell vs. node), the range of positions, and the number of intervals into which position has been quantized. \fBteem\-ilk\fR: (I)mage (L)inear Trans(X\-\->K)forms. Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling. \fBteem\-miter\fR: A simple but effective little volume renderer. \fBteem\-mrender\fR: A demonstration of hoover, gage, and nrrd measures. Uses hoover to cast rays through a volume (scalar, vector, or tensor), gage to measure one of various quantities along the rays, and a specified nrrd measure to reduce all the values along a ray down to one scalar, which is saved in the output (double) image. \fBteem\-ninspect\fR: Quick way of seeing what's inside a 3D volume. A color image of three axis\-aligned projections is composed of histogram\-equalized and quantized images of the summation (red), variance (green), and maximum (blue) intensity projections. If volume is orientation in RAS space, then a standard orientation is used for projections and projections are upsampled (with box kernel) to have isotropic pixels. \fBteem\-ninspect\fR: Quick way of seeing what's inside a 3D volume. A color image of three axis\-aligned projections is composed of histogram\-equalized and quantized images of the summation (red), variance (green), and maximum (blue) intensity projections. If volume is orientation in RAS space, then a standard orientation is used for projections and projections are upsampled (with box kernel) to have isotropic pixels. \fBteem\-nrrdSanity\fR: \fBteem\-overrgb\fR: Composites an RGBA nrrd over a background color (or image), after doing gamma correction, then quantizes to an 8\-bit image. Actually, the input nrrd can have more than 4 values per pixel, but only the first four are used. If the RGBA nrrd is floating point, the values are taken at face value; if it is fixed point, the values interpreted as having been quantized (so that 8\-bit RGBA images will act as you expect). When compositing with a background image, the given background image does not have to be the same size as the input image; it will be resampled (with linear interpolation) to fit. \fBteem\-pos2idx\fR: Converts from floating\-point "position" to floating\-point "index", given the centering of the data (cell vs. node), the range of positions, and the number of intervals into which position has been quantized. \fBteem\-pprobe\fR: Uses gageProbe() to query scalar or vector volumes at a single probe location. \fBteem\-qbert\fR: Generates volume datasets friendly to hardware\-based volume renderers. The main value of this is a means of combining the functions of resampling a dataset to a particular size, measuring first (and optionally second) derivatives, and doing some semi\-intelligent quantization of the derivative values down to 8\-bits (if quantization is desired). The various up and down sampling, as well as the the VGH measurements, can be done with various nrrd kernels. Also, histogram\-equalized VG and VH scatterplots can be generated at a specified resolution. \fBteem\-talkweb\fR: Generates HTML pages from slide images and text. This program takes multiple inputs: a template for the table of contents that will become "index.html" ("\-i"), a template for the pages generated for each slide e.g. "slide000.html" ("\-t"), and a script text file that contains all the information that will go into the slide pages. The format of this file is: \- Separator line indicating slide transitions, e.g. "\-\-\-\-\-\-\-\-\-\-\-\-\-" \- Title of first slide (one line) \- Filename for image to put on first slide (one line) \- Body of HTML text to put with the slide image (multiple lines) \- Separator followed by information for the second slide, and so forth. Textual subtitutions are performed in the template files, according to the replacement tags ("\-r", see below). Within the slide pages, navigation arrows are based on remaining command\-line options. \fBteem\-tend\fR: Diffusion Tensor Processing and Analysis \fBteem\-undos\fR undos: Converts from DOS text files to normal (converting LF\-CR pairs to just CR), or, with the "\-r" option, convert back to DOS, for whatever sick and twisted reason you'd have to do that. Can also handle legacy MAC text files (only LF). Unlike the simple sed or perl scripts for this purpose, this program is careful to be idempotent. Also, this makes an effort to not meddle with binary files (on which this may be mistakenly invoked). A message is printed to stderr for all the files actually modified. \fBteem\-ungantry\fR: Gantry tilt be gone! This program is actually of limited utility: it can only change the tilt by shearing with the X and Z axis fixed, by some angle "around" the X axis, assuming that (X,Y,Z) is a right\-handed frame. \fBteem\-unu\fR: Utah Nrrd Utilities command\-line interface \fBteem\-vprobe\fR: Shows off the functionality of the gage library. Uses gageProbe() to query various kinds of volumes to learn various measured or derived quantities. Can set environment variable TEEM_VPROBE_HACK_ZI to limit probing to a single z slice. .SH "SEE ALSO" slicer(1) debian/man/teem-miter.10000644000000000000000000001176712203642665012115 0ustar .TH "teem-miter" "1" "December 10, 2008" "1.10.0" "User Commands" .SH "NAME" teem\-miter \- A simple but effective little volume renderer .SH "SYNOPSIS" .B teem\-miter [\fI@file \fR...] [\fI\-i \fR] [\fI\-vi \fR] [\fI\-ti \fR] \fI\\fR .HP \fB\-txf\fR \fB\-fr\fR [\-at ] [\-up ] [\-rh] [\-or] \e .HP \fB\-dn\fR \fB\-di\fR \fB\-df\fR [\-ar] [\-ur ] [\-vr ] [\-fv ] [\-offfr] [\-ffr ] \e [\-turn ] [\-am ] [\-ld ] [\-is ] \e [\-iss ] [\-ads ] [\-sp ] [\-k00 ] \e [\-k11 ] [\-k22 ] [\-ss ] [\-ns ] [\-side ] [\-rn] [\-gmc ] [\-step ] \e [\-ref ] [\-vp ] [\-n1 ] [\-nt <# threads>] \e \fB\-o\fR .IP @file ... = response file(s) containing command\-line arguments \fB\-i\fR = input scalar volume to render (nrrd); default: "" .HP \fB\-vi\fR = input vector volume to render (nrrd); default: "" .HP \fB\-ti\fR = input tensor volume to render (nrrd); default: "" .HP \fB\-txf\fR = one or more transfer functions (1 or more nrrds) .HP \fB\-fr\fR = camera eye point (3 doubles) .HP \fB\-at\fR = camera look\-at point (3 doubles); default: "0 0 0" .HP \fB\-up\fR = camera pseudo\-up vector (3 doubles); default: "0 0 1" .IP \fB\-rh\fR = use a right\-handed UVN frame (V points down) \fB\-or\fR = orthogonal (not perspective) projection .HP \fB\-dn\fR = distance to near clipping plane (double) .HP \fB\-di\fR = distance to image plane (double) .HP \fB\-df\fR = distance to far clipping plane (double) .IP \fB\-ar\fR = near, image, and far plane distances are relative to the .IP *at* point, instead of the eye point .HP \fB\-ur\fR = range in U direction of image plane (2 doubles) .HP \fB\-vr\fR = range in V direction of image plane (2 doubles) .PP \fB\-fv\fR = angle (in degrees) vertically subtended by view window .IP (double); default: "20" .IP \fB\-offfr\fR = the given eye point ("\-fr") is to be interpreted as an .IP offset from the at point. .TP \fB\-ffr\fR = eye point to use for view\-dependent transfer functions. By default (not using this option), the point used is the normally specified camera eye point. (3 doubles) .TP \fB\-turn\fR = angle (degrees) by which to rotate the from point around true up, for making stereo pairs. Positive means move towards positive U (the right) (double); default: "0.0" .HP \fB\-am\fR = ambient light color (3 floats); default: "1 1 1" .TP \fB\-ld\fR = view space light position (extended to infinity) (3 floats); default: "0 0 \fB\-1\fR" .HP \fB\-is\fR = image dimensions (2 ints); default: "256 256" .TP \fB\-iss\fR = scaling of image size (from "is") (float); default: "1.0" .HP \fB\-ads\fR = phong components (3 floats); default: "0.1 0.6 0.3" .HP \fB\-sp\fR = phong specular power (double); default: "30" .TP \fB\-k00\fR = value reconstruction kernel (kernel specification); default: "tent" .TP \fB\-k11\fR = first derivative kernel (kernel specification); default: "cubicd:1,0" .TP \fB\-k22\fR = second derivative kernel (kernel specification); default: "cubicdd:1,0" .TP \fB\-ss\fR = how to do shading (string); default: "phong:gage(scalar:n)" .TP \fB\-ns\fR = "normal" to use for those miteVal's that need one (string); default: "" .SS "\-side = how to interpret gradients as normals:" .IP o "1": normal points to lower values (higher == more "inside") o "0": "two\-sided": dot\-products are abs()'d o "\-1": normal points to higher values (lower == more "inside") (int) default: "1" .IP \fB\-rn\fR = renormalize kernel weights at each new sample location. .IP "Accurate" kernels don't need this; doing it always makes things go slower .TP \fB\-gmc\fR = For curvature\-based transfer functions, set curvature to zero when gradient magnitude is below this (double); default: "0.0" .TP \fB\-step\fR = step size along ray in world space (double); default: "0.01" .TP \fB\-ref\fR = "reference" step size (world space) for doing opacity correction in compositing (double); default: "0.01" .PP \fB\-vp\fR = pixel for which to turn on verbose messages (2 ints); .IP default: "\-1 \fB\-1\fR" .TP \fB\-n1\fR = opacity close enough to 1.0 to terminate ray (double); default: "0.99" .HP \fB\-nt\fR <# threads> = number of threads hoover should use (int); default: "1" .HP \fB\-o\fR = file to write output nrrd to (string) .SH "SEE ALSO" The full documentation for .B teem\-miter is maintained as a Texinfo manual. If the .B info and .B teem\-miter programs are properly installed at your site, the command .IP .B info teem\-miter .PP should give you access to the complete manual. debian/man/teem-mrender.10000644000000000000000000001113712203642665012420 0ustar .TH "teem\-mrender" "1" "December 10, 2008" "1.10.0" "User Commands" .SH "NAME" teem\-mrender \- A demonstration of hoover, gage, and nrrd measures. .SH "SYNOPSIS" .B teem\-mrender [\fI@file \fR...] \fI\-i \-k \-fr \fR[\fI\-at ] [\-up ] [\-rh] [\-or] \fB\-dn\fR \fB\-di\fR \fB\-df\fR [\-ar] \e [\-ur ] [\-vr ] [\-fv ] [\-offfr] \e [\-turn ] [\-is ] [\-k00 ] [\-k11 ] \e [\-k22 ] [\-rn] \fB\-q\fR \fB\-m\fR [\-gmc ] \e [\-fn ] [\-step ] [\-nt <# threads>] [\-vp ] \e [\-o ] .IP @file ... = response file(s) containing command\-line arguments .IP \fB\-i\fR = input nrrd to render (nrrd) .TP \fB\-k\fR = "kind" of volume ("scalar", "vector", or "tensor") (kind) .HP \fB\-fr\fR = camera eye point (3 doubles) .HP \fB\-at\fR = camera look\-at point (3 doubles); default: "0 0 0" .HP \fB\-up\fR = camera pseudo\-up vector (3 doubles); default: "0 0 1" .IP \fB\-rh\fR = use a right\-handed UVN frame (V points down) \fB\-or\fR = orthogonal (not perspective) projection .HP \fB\-dn\fR = distance to near clipping plane (double) .HP \fB\-di\fR = distance to image plane (double) .HP \fB\-df\fR = distance to far clipping plane (double) .IP \fB\-ar\fR = near, image, and far plane distances are relative to the .IP *at* point, instead of the eye point .TP \fB\-ur\fR = range in U direction of image plane (2 doubles); default: "nan nan" .TP \fB\-vr\fR = range in V direction of image plane (2 doubles); default: "nan nan" .PP \fB\-fv\fR = angle (in degrees) vertically subtended by view window .IP (double); default: "20" .IP \fB\-offfr\fR = the given eye point ("\-fr") is to be interpreted as an .IP offset from the at point. .TP \fB\-turn\fR = angle (degrees) by which to rotate the from point around true up, for making stereo pairs. Positive means move towards positive U (the right) (double); default: "0.0" .HP \fB\-is\fR = image dimensions (2 ints); default: "256 256" .TP \fB\-k00\fR = value reconstruction kernel (kernel specification); default: "tent" .TP \fB\-k11\fR = first derivative kernel (kernel specification); default: "cubicd:1,0" .TP \fB\-k22\fR = second derivative kernel (kernel specification); default: "cubicdd:1,0" .IP \fB\-rn\fR = renormalize kernel weights at each new sample location. .IP "Accurate" kernels don't need this; doing it always makes things go slower .TP \fB\-q\fR = the quantity (scalar, vector, or matrix) to learn by probing (string) .TP \fB\-m\fR = how to collapse list of ray samples into one scalar. Possibilities include: o "min", "max", "mean", "median", "mode", "variance", "skew" (self\-explanatory) o "intc", "slope", "error": intercept, slope, and error from line fitting o "sd": standard deviation o "product", "sum": product or sum of all values o "L1", "L2", "Linf": different norms o "histo\-min", "histo\-max", "histo\-mean", "histo\-median", "histo\-mode", "histo\-product", "histo\-l2", "histo\-sum", "histo\-variance", "histo\-sd": same measures, but for situations where we're given not the original values, but a histogram of them. (measure) .TP \fB\-gmc\fR = For curvature\-related queries, set answer to zero when gradient magnitude is below this (double); default: "0.0" .TP \fB\-fn\fR = When histo\-based measures generate NaN answers, the value that should be substituted for NaN. (double); default: "nan" .TP \fB\-step\fR = step size along ray in world space (double); default: "0.01" .HP \fB\-nt\fR <# threads> = number of threads hoover should use (int); default: "1" .TP \fB\-vp\fR = pixel coordinates for which to turn on all verbose debugging messages, or "\-1 \fB\-1\fR" to disable this. (2 ints); default: "\-1 \fB\-1\fR" .TP \fB\-o\fR = file to write output nrrd to. Defaults to stdout ("\-"). (string); default: "\-" .SH "DESCRIPTION" Uses hoover to cast rays through a volume (scalar, vector, or tensor), gage to measure one of various quantities along the rays, and a specified nrrd measure to reduce all the values along a ray down to one scalar, which is saved in the output (double) image. .SH "SEE ALSO" The full documentation for .B teem\-mrender is maintained as a Texinfo manual. If the .B info and .B teem\-mrender programs are properly installed at your site, the command .IP .B info teem\-mrender .PP should give you access to the complete manual. debian/changelog0000644000000000000000000000544112232020121011025 0ustar teem (1.11.0~svn6057-1ubuntu1) trusty; urgency=low * Merge from Debian unstable. Remaining changes: - Fix FTBFS on ppc, arm64, and s390 with -ffp-contract=off - Fix testsuite failure on any-i386 with -ffloat-store -- Adam Conrad Wed, 23 Oct 2013 13:00:43 -0600 teem (1.11.0~svn6057-1) unstable; urgency=low * new upstream snapshot * updated repository location in debian/get-orig-source -- Dominique Belhachemi Fri, 16 Aug 2013 17:12:11 -0400 teem (1.11.0~svn5906-1ubuntu1) raring; urgency=low * Fix FTBFS on powerpc and s390 with -ffp-contract=off * Fix testsuite failure on any-i386 with -ffloat-store -- Adam Conrad Sun, 21 Apr 2013 08:36:10 -0600 teem (1.11.0~svn5906-1) unstable; urgency=low * new upstream snapshot -- Dominique Belhachemi Wed, 09 Jan 2013 07:28:21 -0500 teem (1.11.0~svn5226-1) unstable; urgency=low * new upstream snapshot * upload to unstable * removed DM upload rights * removed teem-doc package and dependencies -- Dominique Belhachemi Fri, 06 Apr 2012 21:46:12 -0400 teem (1.11.0~svn5112-1) experimental; urgency=low * new upstream snapshot * updating mail address * bump standards version -- Dominique Belhachemi Tue, 20 Sep 2011 21:46:17 -0400 teem (1.11.0~svn5079-1) experimental; urgency=low * new upstream snapshot -- Dominique Belhachemi Tue, 30 Aug 2011 23:33:19 -0400 teem (1.11.0~svn5054-1) experimental; urgency=low * new upstream snapshot * debian/control: Bump compat level, fix Vcs-Browser field -- Dominique Belhachemi Wed, 10 Aug 2011 17:26:47 -0400 teem (1.11.0~svn4425-2) experimental; urgency=low * move documentation build process to different target -- Dominique Belhachemi Sun, 08 May 2011 00:18:53 -0400 teem (1.11.0~svn4425-1) experimental; urgency=low * New upstream snapshot * Switch to dpkg-source 3.0 (quilt) format * Remove static libraries * Added debug package * Removed DM-Upload-Allowed: yes * Bump Standards-Version: 3.9.1 * Changed package name libteem1-dev -> libteem-dev * Bump ABI version, libteem1 -> libteem2 -- Dominique Belhachemi Sun, 06 Mar 2011 17:21:11 -0500 teem (1.10.0.dfsg1-2) unstable; urgency=low [ Mathieu Malaterre ] * Add DEB_BUILD_OPTIONS options [ Dominique Belhachemi ] * added README.source * patch added to fix a bug that caused segfaults * debian/control: changed package description -- Dominique Belhachemi Thu, 18 Dec 2008 15:49:57 -0500 teem (1.10.0-1) unstable; urgency=low * Initial release (Closes: #473044) -- Dominique Belhachemi Tue, 16 Dec 2008 14:11:30 -0500 debian/compat0000644000000000000000000000000212203642665010372 0ustar 8 debian/rules0000755000000000000000000000324112232016323010240 0ustar #!/usr/bin/make -f # Set this value to 0/1 to turn off/on verbose mode. export DH_VERBOSE=0 include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/cmake.mk include /usr/share/cdbs/1/rules/patchsys-quilt.mk ABI_VERSION := 2 DEB_DH_STRIP_ARGS := --dbg-package=libteem${ABI_VERSION}-dbg DEB_BUILD_PARALLEL := true ifneq (,$(filter $(DEB_HOST_ARCH_CPU), i386)) CFLAGS += -ffloat-store endif ifneq (,$(filter $(DEB_HOST_ARCH_CPU), arm64 powerpc ppc64 ppc64el s390 s390x)) CFLAGS += -ffp-contract=off endif DEB_CMAKE_EXTRA_FLAGS = \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo \ -DCMAKE_VERBOSE_MAKEFILE=$(DH_VERBOSE) \ -DCMAKE_SKIP_RPATH:BOOL=ON \ -DBUILD_EXPERIMENTAL_APPS:BOOL=OFF \ -DBUILD_EXPERIMENTAL_LIBS:BOOL=OFF \ -DBUILD_TESTING:BOOL=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR:BOOL=ON \ -DBUILD_SHARED_LIBS:BOOL=ON \ build/libteem${ABI_VERSION}:: cd $(DEB_BUILDDIR) && LD_LIBRARY_PATH=`pwd`/bin:$$LD_LIBRARY_PATH ctest -VV -D ExperimentalTest install/libteem${ABI_VERSION}:: dh_install -plibteem${ABI_VERSION} debian/tmp/usr/lib/Teem-1.11.0/*so.* usr/lib install/libteem-dev:: dh_install -plibteem-dev debian/tmp/usr/lib/Teem-1.11.0/*.so usr/lib dh_install -plibteem-dev debian/tmp/usr/lib/Teem-1.11.0/*.cmake usr/lib/Teem-1.11.0 dh_install -plibteem-dev debian/tmp/usr/include/teem/* usr/include/teem install/teem-apps:: dh_install -pteem-apps debian/tmp/usr/bin/* usr/bin get-orig-source: /bin/sh $(CURDIR)/debian/get-orig-source debian/get-orig-source0000644000000000000000000000212412203642665012131 0ustar #!/bin/sh set -ex PACKAGE=teem VERSION=${VERSION:-$2} TARFILE=${TARFILE:-$3} if [ -z ${VERSION}]; then VERSION=`dpkg-parsechangelog | sed -n -e 's/^Version: \(.*\)-[^-]*$/\1/p'` fi REVISION=`echo $VERSION | sed -e 's/^.*svn//g'` #REVISION=10509 FOLDER=${PACKAGE}-${VERSION} if [ -z ${TARFILE}]; then TARFILE=${PACKAGE}_${VERSION}.orig.tar.gz fi svn export --quiet --revision ${REVISION} http://svn.code.sf.net/p/teem/code/teem/trunk ${FOLDER} #svn export --quiet --revision ${REVISION} https://teem.svn.sourceforge.net/svnroot/teem/teem/branches/Teem-1.11 ${FOLDER} #find teem/ -depth -type d -name ".svn" | xargs rm -rf #find teem/ -depth -name "GNUmakefile" | xargs rm -rf rm -rf ${FOLDER}/arch/ rm -rf ${FOLDER}/src/make/ GZIP=-9 tar czf ${TARFILE} ${FOLDER} rm -rf ${FOLDER} exit VERSIONDFSG=1.11.0.dfsg1 wget http://downloads.sourceforge.net/teem/teem-$VERSION-src.tar.gz tar xvzf teem-$VERSION-src.tar.gz rm teem-$VERSION-src.tar.gz mv teem-$VERSION-src teem-$VERSIONDFSG rm -rf teem-$VERSIONDFSG/arch GZIP=-9 tar cvzf teem_$VERSIONDFSG.orig.tar.gz teem-$VERSIONDFSG rm -rf teem-$VERSIONDFSG debian/Notes0000644000000000000000000000055012203642665010207 0ustar help2man ./teem-miter -oteem-miter.1 help2man ./teem-mrender -oteem-mrender.1 help2man ./teem-nrrdSanity -oteem-nrrdSanity.1 help2man ./teem-overrgb -oteem-overrgb.1 help2man ./teem-tend -oteem-tend.1 help2man ./teem-unu -oteem-unu.1 help2man ./teem-vprobe -oteem-vprobe.1 help2man ./teem-gprobe -oteem-gprobe.1 debian/control0000644000000000000000000001304612203642665010603 0ustar Source: teem Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Science Team Uploaders: Dominique Belhachemi Build-Depends: debhelper (>= 8), cmake, zlib1g-dev, libpng-dev, libbz2-dev, cdbs, quilt Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-science/packages/teem/trunk/ Vcs-Svn: svn://svn.debian.org/svn/debian-science/packages/teem/trunk/ Section: libs Homepage: http://teem.sourceforge.net/ Package: libteem-dev Section: libdevel Provides: libteem1-dev Replaces: libteem1-dev Conflicts: libteem1-dev Architecture: any Depends: libteem2 (= ${binary:Version}), ${misc:Depends} Description: Tools to process and visualize scientific data and images - development Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are: . * Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information. * Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.) * Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure * Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods. . This package provides the Teem header files required to compile C++ programs that use Teem to do 3D visualisation. Package: teem-apps Section: libdevel Architecture: any Depends: libteem2 (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} Description: Tools to process and visualize scientific data and images - command line tools Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are: . * Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information. * Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.) * Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure * Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods. . This package contains some simple command-line tools which provide fast and easy access to the functionality in the various libraries. Package: libteem2 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Tools to process and visualize scientific data and images - runtime Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are: . * Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information. * Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.) * Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure * Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods. . This package provides the runtime files required to run programs that use Teem to do 3D visualisation. Package: libteem2-dbg Architecture: any Section: debug Priority: extra Depends: libteem2 (= ${binary:Version}), ${misc:Depends} Description: debugging symbols for libteem2 Teem is a coordinated group of libraries for representing, processing, and visualizing scientific raster data. Teem includes command-line tools that permit the library functions to be quickly applied to files and streams, without having to write any code. The most important and useful libraries in Teem are: . * Nrrd (and the unu command-line tool on top of it) supports a range of operations for transforming N-dimensional raster data (resample, crop, slice, project, histogram, etc.), as well as the NRRD file format for storing arrays and their meta-information. * Gage: fast convolution-based measurements at arbitrary point locations in volume datasets (scalar, vector, tensor, etc.) * Mite: a multi-threaded ray-casting volume render with transfer functions based on any quantity Gage can measure * Ten: for estimating, processing, and visualizing diffusion tensor fields, including fiber tractography methods. . This package contains the debugging symbols for libteem2. debian/watch0000644000000000000000000000012612203642665010224 0ustar version=3 opts="dversionmangle=s/\.dfsg1//" http://sf.net/teem/teem-(.*)-src\.tar\.gz debian/teem-apps.manpages0000644000000000000000000000041112203642665012600 0ustar debian/man/teem.1 debian/man/teem-gprobe.1 debian/man/teem-ilk.1 debian/man/teem-miter.1 debian/man/teem-mrender.1 debian/man/teem-nrrdSanity.1 debian/man/teem-overrgb.1 debian/man/teem-puller.1 debian/man/teem-tend.1 debian/man/teem-unu.1 debian/man/teem-vprobe.1 debian/docs0000644000000000000000000000001312203642665010041 0ustar README.txt debian/patches/0000755000000000000000000000000012203642666010624 5ustar debian/patches/10_all_changes.diff0000644000000000000000000000666012203642665014225 0ustar Index: teem-1.11.0~svn5906/CMakeLists.txt =================================================================== --- teem-1.11.0~svn5906.orig/CMakeLists.txt 2013-01-09 12:24:33.075791490 -0500 +++ teem-1.11.0~svn5906/CMakeLists.txt 2013-01-09 12:24:33.000000000 -0500 @@ -376,7 +376,7 @@ BUILD_WITH_INSTALL_RPATH OFF INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/lib - SOVERSION 1 + SOVERSION 2 VERSION ${Teem_VERSION_STRING} ) Index: teem-1.11.0~svn5906/src/bin/CMakeLists.txt =================================================================== --- teem-1.11.0~svn5906.orig/src/bin/CMakeLists.txt 2013-01-09 12:24:33.043790944 -0500 +++ teem-1.11.0~svn5906/src/bin/CMakeLists.txt 2013-01-09 12:24:33.000000000 -0500 @@ -33,36 +33,36 @@ MACRO(CREATE_EXEC name sources) ENDMACRO(CREATE_EXEC) # These binaries should not be depending on BUILD_EXPERIMENTAL_LIBS -CREATE_EXEC(nrrdSanity nrrdSanity.c) -CREATE_EXEC(overrgb overrgb.c) -CREATE_EXEC(ilk ilk.c) -CREATE_EXEC(mrender mrender.c) -CREATE_EXEC(miter miter.c) -CREATE_EXEC(vprobe vprobe.c) -CREATE_EXEC(gprobe gprobe.c) -CREATE_EXEC(unu unu.c) -CREATE_EXEC(puller puller.c) -CREATE_EXEC(tend tend.c) +CREATE_EXEC(teem-nrrdSanity nrrdSanity.c) +CREATE_EXEC(teem-overrgb overrgb.c) +CREATE_EXEC(teem-ilk ilk.c) +CREATE_EXEC(teem-mrender mrender.c) +CREATE_EXEC(teem-miter miter.c) +CREATE_EXEC(teem-vprobe vprobe.c) +CREATE_EXEC(teem-gprobe gprobe.c) +CREATE_EXEC(teem-unu unu.c) +CREATE_EXEC(teem-puller puller.c) +CREATE_EXEC(teem-tend tend.c) # NOTE: The BUILD_EXPERIMENTAL_LIBS-dependent inclusion of binaries has to be # done with knowledge of how BUILD_EXPERIMENTAL_LIBS behaves in the top-level # CMakeLists.txt file IF(BUILD_EXPERIMENTAL_APPS) - CREATE_EXEC(airSanity airSanity.c) - CREATE_EXEC(cubic cubic.c) - CREATE_EXEC(qbert qbert.c) - CREATE_EXEC(emap emap.c) - CREATE_EXEC(talkweb talkweb.c) - CREATE_EXEC(pprobe pprobe.c) - CREATE_EXEC(ninspect ninspect.c) - CREATE_EXEC(ungantry ungantry.c) - CREATE_EXEC(deconv deconv.c) + CREATE_EXEC(teem-airSanity airSanity.c) + CREATE_EXEC(teem-cubic cubic.c) + CREATE_EXEC(teem-qbert qbert.c) + CREATE_EXEC(teem-emap emap.c) + CREATE_EXEC(teem-talkweb talkweb.c) + CREATE_EXEC(teem-pprobe pprobe.c) + CREATE_EXEC(teem-ninspect ninspect.c) + CREATE_EXEC(teem-ungantry ungantry.c) + CREATE_EXEC(teem-deconv deconv.c) IF(BUILD_EXPERIMENTAL_LIBS) - CREATE_EXEC(gkms gkms.c) - CREATE_EXEC(spots spots.c) + CREATE_EXEC(teem-gkms gkms.c) + CREATE_EXEC(teem-spots spots.c) ENDIF(BUILD_EXPERIMENTAL_LIBS) ENDIF(BUILD_EXPERIMENTAL_APPS) #IF(BUILD_TESTING) -# ADD_TEST(nrrd.Sanity ${EXECUTABLE_OUTPUT_PATH}/nrrdSanity) +# ADD_TEST(nrrd.Sanity ${EXECUTABLE_OUTPUT_PATH}/teem-nrrdSanity) #ENDIF(BUILD_TESTING) Index: teem-1.11.0~svn5906/Testing/CMakeLists.txt =================================================================== --- teem-1.11.0~svn5906.orig/Testing/CMakeLists.txt 2013-01-09 12:24:33.063791286 -0500 +++ teem-1.11.0~svn5906/Testing/CMakeLists.txt 2013-01-09 12:24:33.000000000 -0500 @@ -47,7 +47,7 @@ # This just runs nrrdSanity as test called "nrrd.Sanity" # We don't do the same for airSanity because that's an # "experimental app" . . . -ADD_TEST(nrrd.Sanity ${EXECUTABLE_OUTPUT_PATH}/nrrdSanity) +ADD_TEST(nrrd.Sanity ${EXECUTABLE_OUTPUT_PATH}/teem-nrrdSanity) # Hope to eventually have tests in all directories; until then # many of these are commented out. (TEEM_LIB_LIST) debian/patches/series0000644000000000000000000000002412203642665012034 0ustar 10_all_changes.diff