update readme

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
 

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):

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()