Added parse_3dinfo

core/util/parse_3dinfo.py

@@ -0,0 +1,105 @@
+#!/usr/bin/env python
+
+"""
+If given 1 input argument (FILEN), lists all the sub-BRIKs in that file.
+
+If given 2 input arguments (FILEN, SUBBRIKNAME), returns the zero-indexed
+BRIK number for that sub-brik.
+
+e.g.
+
+  > greg% python /path/to/parse_3dinfo.py my_bucket+orig
+  Full_Fstat
+  cat2_conv_c1#0_Coef
+  cat2_conv_c1#0_Tstat
+  ...
+  statmap_3dDeconvolve_GLT_Fstat
+  
+  OR
+  
+  > greg% python /path/to/parse_3dinfo.py my_bucket+orig 'cat2_conv_c1#0_Coef'
+  1
+  
+  > greg% python /path/to/parse_3dinfo.py my_bucket+orig 'nonexistent_brik'
+  [no output]
+  
+It runs a simple regular expression to extract the brik numbers and
+names from 3dinfo, e.g.:
+
+  -- At sub-brick #11 'statmap_3dDeconvolve_GLT_Fstat' datum type is short: ...
+ 
+  -> 11, 'statmap_3dDeconvolve_GLT_Fstat'
+
+N.B. I'm assuming that your sub-brik names consist only of
+non-whitespace characters, e.g. they don't have spaces or tabs. I'm
+not sure if AFNI even allows whitespace in sub-brik names - but you'll
+have to tweak the main re.search() regular expression if you need to
+find them.
+"""
+
+import os, sys, re, tempfile, pdb
+
+
+############################################################
+def create_name2num(filen):
+    """
+    Creates a dictionary of sub-brik names -> nums (zero-indexed) by
+    calling 3dinfo on the BRIK in FILEN, and parsing its output.
+    """
+
+    # create a temporary file into which we can write the output from
+    # 3DINFO. this is easier than being clever about piping the system process
+    tfile = tempfile.NamedTemporaryFile('w')    
+    # we want to write both STDOUT and STDERR from 3dinfo so that when
+    # we're done, all we print to STDOUT is the number of the SUBBRIKNAME,
+    # hence the weird >& redirect. see
+    # http://tomecat.com/jeffy/tttt/cshredir.html
+    cmd = '3dinfo -verb %s >& %s' % (filen,tfile.name)
+    os.system(cmd)
+    txt = open(tfile.name,'r').read()
+    lines = txt.split('\n')
+    tfile.close()
+    # TFILE gets automatically deleted by close() in python 2.6+, but
+    # let's be sure
+    if os.path.exists(tfile.name): delete(tfile.name)
+
+    name2num = {}
+    for line in lines:
+        matches = re.search("At sub-brick #(\d+) '(\S*)' datum", line)
+        if matches:
+            num, name = matches.groups()
+            num = int(num)
+            # sanity-check that we haven't already found a sub-brik like
+            # this before
+            assert not name2num.has_key(name)
+            assert not num in name2num.values()
+            name2num[name] = num
+
+    return name2num
+
+
+############################################################
+if __name__=="__main__":
+
+    args = sys.argv[1:]
+    if len(args)==0 or len(args)>2:
+        print 'USAGE:\n%s\n' % (__doc__.strip())
+        sys.exit(0)    
+    filen = args[0]
+    if len(args)==2: subbrikname = args[1]
+    else: subbrikname = None
+
+    name2num = create_name2num(filen)
+
+    if subbrikname:
+        # print the NUM for the subbrik we're interested in, if we found
+        # it
+        if name2num.has_key(subbrikname):
+            print name2num[subbrikname]
+    else:
+        # no subbrik specified, so just print them all (sorted by NUM)
+        nums_names = name2num.items()
+        nums_names.sort(key=lambda x : x[1])
+        for nn in nums_names: print '%s' % nn[0]
+
+