From 2e4d0f536519737070851718f80c5dfbf409aa63 Mon Sep 17 00:00:00 2001 From: nebula Date: Sun, 12 Feb 2017 20:08:41 +0900 Subject: [PATCH] update readme --- README.md | 18 ++++++++++-------- registration/BahRegistration.py | 1 + registration/ParaRegistration.py | 4 ++-- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index c17f0aa..f2e937e 100644 --- a/README.md +++ b/README.md @@ -12,16 +12,18 @@ Developed by Brain Atlas Hackathon Registration Team (https://www.neuroinf.jp/ba ## Files and Directories - Parallel registration **input** files and dirs - - ImageRegistration9: program from ITK - - filelist_all.txt: write down all TIF file name of *in situ* hybridization images - - work3: Monochromed (and resized) TIF files of *in situ* hybridization images - - SB_bin: resliced standard brain files (from Waxholm Space) + - `ImageRegistration9`: registration program from ITK + - `filelist.txt`: write down all TIF file name of *in situ* hybridization images + - `work3`: Monochromed (and resized) TIF files of *in situ* hybridization images + - `SB_bin`: resliced standard brain files (from Waxholm Space) - Parallel registration **output** files and dirs - - work4: results of registration for all standard brain slices - - log4: registration log - - metric: metric value for each slice - - metric_fig: graph of metric value + - `work4`: results of registration for all standard brain slices + - `log4`: registration log + - `metric`: metric value for each slice + - `metric_fig`: graph of metric value + + ## usage diff --git a/registration/BahRegistration.py b/registration/BahRegistration.py index 1abbf10..ad07d81 100644 --- a/registration/BahRegistration.py +++ b/registration/BahRegistration.py @@ -36,6 +36,7 @@ def __init__(self, homedir=None, reg_program=None): sys.exit('Error : %s not found.' % self.registration_in) # output dirs + # TODO: this mkdir methods is not good for parallelization if not os.path.exists(self.registration_out): os.mkdir(self.registration_out) if not os.path.exists(self.registration_log): diff --git a/registration/ParaRegistration.py b/registration/ParaRegistration.py index 0db8163..69d002f 100644 --- a/registration/ParaRegistration.py +++ b/registration/ParaRegistration.py @@ -41,7 +41,7 @@ def wrap_registration(filename): reg = BahRegistration.BahRegistration(homedir='/data/registration/Processed20170212') # metric = reg.single_registration(filename) - metric = reg.single_registration(filename, sb_reslice_end=129) + metric = reg.single_registration(filename, sb_reslice_start=80, sb_reslice_end=129) reg.draw_metric_graph() return metric @@ -54,7 +54,7 @@ def read_filelist(filelistname): filelist = [str.rstrip() for str in filelist] return filelist - filelistname = os.path.join('/', 'data', 'registration', 'Processed20170212', 'filelist.txt') + filelistname = '/data/registration/Processed20170212/filelist.txt' filelist = read_filelist(filelistname) pec = ParaExec()