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IMOD - Boulder Laboratory for 3-D Electron Microscopy of Cells
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See the file BUILDING for building instructions. The setup program makes configuration files based on machine-specific details in the "machines" directory. Upon unpacking the source, you will find the following directories: autodoc Autodoc files for programs using PIP package for input clip Source for Command Line Image Processing com Command files, mostly used by copytomocoms for tomography ctfplotter Source for ctfplotter program dist Files for installation and distribution Etomo eTomo package tree Etomo/doc Program documentation files Etomo/scripts Has an eTomo testing script Etomo/src Top of source tree Etomo/src/etomo All java source is under here .../comscript Command script classes .../logic .../process Process-running classes .../storage File-related classes .../type Classes to handle specific data items .../ui/swing Dialog classes .../uitest Classes for the UI testing .../util Utility functions Etomo/src/images Has icons flib Fortran program source tree flib/beadtrack Source for bead tracker program flib/blend Source for montage blending program and montage reducer flib/distort Source for distortion-finding program flib/graphics Source for several programs using line graphics flib/image Source for many programs that do not use models or graphics flib/man Master directory for man pages of Fortran programs flib/model Source for many programs that use IMOD models flib/ndasda Source for nda, sda, and mtk spatial analysis programs flib/subrs Top of source tree for Fortran libraries .../blas Source for blas routines needed by lapack .../compat Source for compatibility routines where needed .../dtrigs Source for cosd, sind, etc. functions for Linux (libdtrigs) .../graphics Source for graphics subroutines (libdnmncar) .../hvem Source for miscellaneous subroutines developed here .../ifftsub Source for FFT subroutines (libifft - no longer used) .../imsubs Source for basic image I/O routines (libim) .../imsubs2 Source for other image manipulation routines (libim) .../lapack Source for subset of lapack needed by ctfplotter .../linetrack Source for line tracker subroutines .../model Source for model-related subroutines (libwmod) .../piecesubs Source for routines that work with piece coordinates (libhvem) .../randm Source for Linux replacement for RAN function (librandm) .../smallmodel Derived source for library that has a small model (libsmlmod) .../statsubs Source for statistical subroutines .../xfsubs Source for routines that work with transformations flib/tilt Source for back-projection program flib/tilt/fbplib Source for library of routines for fast back-projection flib/tiltalign Source for tilt alignmnet program html All html documents and files that they link to html/3dmodHelp Help files for 3dmod html/3dmodimages Images for introduction to 3dmod html/ctfHelp Help files for ctfplotter html/etomoImages Images for etomo tutorial html/joinImages Images for join tutorial html/libdoc Framework files for library documentation html/midasHelp Help files for midas 3dmod Source for 3dmod program imodutil Source for utility programs for working with IMOD models include Include files for IMOD programs libcfft Source for C version of FFT library libcfshr Source for library of utilities shared with Fortran libdiaqt Source for Qt dialog and utility library libiimod Source for IMOD image library libimod Source for IMOD model library libmesh Source for meshing library libwarp Source for warping library, includes natural neighbor interpolation and Delaunay triangulation code machines Machine-specific files included by setup script manpages Master source for man pages of C programs, in nroff format midas Source for midas program mrc Source for various programs manipulating MRC image files plugs Source tree for imod plugins plugs/analysistools Source for Andrew Noske's analysis tools plugin plugs/beadfix Source for old version of bead fixer plugin used to test build plugs/beadhelper Source for Noske's bead helper plugin plugs/drawingtools Source for Noske's drawing tools plugin plugs/interpolator Source for Noske's interpolator plugin plugs/namewizard Source for Noske's namewizard plugin plugs/noskecommon Source for common files for Noske's plugins plugs/stereology Source for Noske's stereology plugin processchunks Source for processchunks program pysrc Python scripts qtassist Source for imodqtassist program raptor Source for RAPTOR scripts Shell scripts sendevent Source for imodsendevent program sourcedoc Source for sourcedoc program (Qt-based) sysdep System dependent files needed for builds sysdep/mac Files for OS X build - not currently needed sysdep/win Files for Windows build - Tiff-related files and manifests After doing a "make" and default "make install", you will have: buildlib Newly built but uninstalled libraries, needed to make programs man Top directory for man pages (contains a cat1 and cat5) html/man Html versions of man pages html/libhelp Processed library documentation files html/plughelp Copies of plugin help files, needed for inclusion in IMOD.qch bin Installation directory for executable programs and scripts lib Installation directory for libraries (old 32-bit on SGI) lib/imodplug Installation directory for imod plugins pylib Installation directory for Python modules Other files in top directory: BUILDING Details for building IMOD on all platforms History Has the complete history of changes installqtlib Does post-install copying of libraries and startup files Makefile Master Makefile for build packMacApps For a Mac install, puts Qt programs into .app directories setup Starting script for configuring for build setup2 Real configure script; setup runs dos2unix on it in Cygwin vcimod.dsw Workspace for midas, 3dmod, imodsendevent in Visual C++
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