Gregory Jefferis jefferis
jefferis
/ gjdevtools.R
Created
November 20, 2013 22:48
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| #' Release an R package to our local repository on ourserver | |
| #' | |
| #' from where it can then be installed (without this package) by | |
| #' install.packages(pkg,repos='http://ourserver.com/R',type='source') | |
| #' | |
| #' Modified from release function in devtools. | |
| #' @param pkg package description see \link[devtools]{release} | |
| #' @param check if TRUE, run checking, otherwise omit it. This is useful if | |
| #' you've just checked your package and you're ready to release it. | |
| #' @param user defaults to myuser |
jefferis
/ decomposecomposebug.sh
Created
November 25, 2013 00:59
Test possible round trip bug in CMTK Compose/Decompose methods exposed by dof2mat/mat2dof
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| #!/usr/bin/env bash | |
| # The idea of this script is to do a round trip test on a CMTK affine | |
| # registration using the dof2mat/mat2dof tools | |
| mkdir -p testinit.list | |
| cat <<EOF > testinit.list/registration | |
| ! TYPEDSTREAM 1.1 | |
| registration { |
jefferis
/ cmtk_bspline_example.sh
Last active
January 2, 2016 03:49
Trying to use CMTK fit_spline_xform to fit the inverse of an existing transform
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| #!/bin/bash | |
| # Setup | |
| mkdir images | |
| mkdir refbrain | |
| curl -o images/A.nrrd http://flybrain.mrc-lmb.cam.ac.uk/cmtk/A.nrrd | |
| curl -o refbrain/B.nrrd http://flybrain.mrc-lmb.cam.ac.uk/cmtk/B.nrrd | |
| AREG="B_A_9dof.list" | |
| REG="B_A_warp.list" |
jefferis
/ reformatted.JFRC2_brightest_slices.txt
Created
March 7, 2014 13:16
Marta and I wrote something to calculate the brightest slice for each stack in the flycircuit set in response to Douglas' suggestion. Spreadsheet and summary histogram attached.
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| ff brightest | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000001_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 156 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000002_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 58 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000003_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 23 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000004_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 93 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000005_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 51 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000006_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 63 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000007_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 52 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000007_seg002_03_warp_m0g80c8e1e-1x26r4.nrrd 48 | |
| reformatted.JFRC2/JFRC2_FCWB_5HT1bMARCM-F000008_seg001_03_warp_m0g80c8e1e-1x26r4.nrrd 45 |
jefferis
/ fc_good_images.txt
Last active
August 29, 2015 13:57
Preprocessed and registered images based on raw data from http://flycircuit.tw (16229 images. ids can be translated using R code/data at https://github.com/jefferis/flycircuit
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| FruMARCM-M002262_seg001 | |
| FruMARCM-M002262_seg002 | |
| FruMARCM-M002278_seg001 | |
| FruMARCM-M002287_seg001 | |
| FruMARCM-M002507_seg001 | |
| FruMARCM-M002522_seg001 | |
| FruMARCM-M002578_seg001 | |
| FruMARCM-M002578_seg002 | |
| FruMARCM-M002579_seg001 | |
| FruMARCM-M002579_seg002 |
jefferis
/ gist:a7a9de4d058866368940
Created
July 16, 2014 16:43
Sample winbuilder output for 05349fd57c
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| R Under development (unstable) (2014-07-14 r66149) -- "Unsuffered Consequences" | |
| Copyright (C) 2014 The R Foundation for Statistical Computing | |
| Platform: i386-w64-mingw32/i386 (32-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| R is a collaborative project with many contributors. |
jefferis
/ install_all_nat.R
Last active
December 4, 2015 21:27
Install all neuroanatomy toolbox (nat) R packages
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| devtools::install_github("jefferis/nat") | |
| # dependencies = TRUE should install the suggested package git2r as well | |
| devtools::install_github("jefferislab/nat.templatebrains", dependencies=TRUE) | |
| devtools::install_github(paste0("jefferislab/", c("nat.nblast", "nat.flybrains"))) | |
| # download our standard set of registrations | |
| nat.flybrains::download_jefferislab_registrations() | |
| devtools::install_github("jefferis/flycircuit") | |
| devtools::install_github("jefferis/vfbr") |
jefferis
/ Install_all_rappdirs.R
Created
September 3, 2014 14:37
install nat code using rappdirs to locate downloaded data
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| devtools::install_github("jefferis/nat") | |
| devtools::install_github(c("nat.nblast","nat.templatebrains","nat.flybrains"), username="jefferislab") | |
| devtools::install_github("rappdirs") | |
| devtools::install_github("jefferis/flycircuit", ref="feature/rappdirs") |
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| #!/bin/sh | |
| # | |
| # An example hook script to prepare a packed repository for use over | |
| # dumb transports. | |
| # | |
| # To enable this hook, rename this file to "post-update". | |
| # Jekyll update code | |
| # always runs in .git dir |
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| # straight from: | |
| # https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/rgl/R/obj.R?revision=1197&root=rgl | |
| # see: | |
| # https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/rgl/DESCRIPTION?revision=1234&root=rgl | |
| # for authorship/license information | |
| readOBJ <- function(con, ...) { | |
| lines <- readLines(con) | |
| instrs <- sub(" .*", "", lines) | |
| vertices <- read.table(textConnection(lines[instrs == "v"]), | |
| col.names = c("instr", "x", "y", "z"), |
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