Merge branch 'release-0.1.8'

Makefile.am

@@ -1,5 +1,9 @@
 ACLOCAL_AMFLAGS = -I m4
 
+# we are not conforming to gnu standards:
+# we have README.md instead of README
+AUTOMAKE_OPTIONS = foreign
+
 SUBDIRS = src perl data
 
 m4_files = m4/mni_REQUIRE_LIB.m4 m4/mni_REQUIRE_MNILIBS.m4	 \

NEWS

@@ -1,3 +1,7 @@
+New in Version 0.1.8
+====================
+* clobber option in pmincaverage is activated
+
 New in Version 0.1.7
 ====================
 * added vtk_meshconvert.py a program that can be used to convert between BIC obj, stl and vtk meshes

README.md

@@ -24,14 +24,20 @@ git submodule update --init --recursive
 
 To build and install the perl and src code:
 ------------------------------------------
+<pre><code>
 ./autogen.sh
 ./configure
 make
 make install
+</pre></code>
+
 
 To build and install the python scripts:
 ---------------------------------------
+<pre><code>
 python setup.py install
+</pre></code>
+
 
 Installation Notes:
 -------------------

python/pmincaverage

@@ -2,8 +2,9 @@
 
 from pyminc.volumes.factory import *
 from numpy import *
-#from scipy.stats import *
-from optparse import OptionParser
+from argparse import ArgumentParser
+import os.path
+import sys
 import multiprocessing as mp
 
 def getslice(volhandle, slice, q,nslices):
@@ -31,31 +32,34 @@ def getfile(q, filename):
 
 if __name__ == "__main__":
 
-    usage = "Usage text"
-    description = "Description text"
-
-    parser = OptionParser(usage=usage, description=description)
-    parser.add_option("--clobber", dest="clobber",
-                      help="clobber output file",
-                      type="string")
-
-    (options, args) = parser.parse_args()
-
-    if len(args) < 4:
+    parser = ArgumentParser()
+    g = parser.add_mutually_exclusive_group()
+    g.add_argument("--clobber", dest="clobber",
+                        action="store_true",
+                        help="clobber output file")
+    g.add_argument("--noclobber", dest="clobber",
+                        action="store_false",
+                        help="don't clobber output file (default)")
+    g.set_defaults(clobber=False)
+    parser.add_argument("infile", nargs="+", type=str, help="files to average")
+    parser.add_argument("outfile", type=str, help="name of file to output")
+
+    args = parser.parse_args()
+
+    infiles     = args.infile
+    nfiles      = len(infiles)
+    outfilename = args.outfile
+
+    if len(infiles) < 2:
         parser.error("Incorrect number of arguments")
 
-    outfilename = args[-1]
-    # clobber check should go here
+    if not(args.clobber) and os.path.exists(outfilename):
+        sys.exit("Output file already exists; use --clobber to overwrite.")
 
-    volhandles = []
-
     # open all the file handles
-    nfiles = len(args)-1
-    for i in range( nfiles ):
-        print("VOLHANDLES: %d" % i)
-        volhandles.append(volumeFromFile(args[i], dtype='double'))
+    volhandles = [volumeFromFile(f, dtype='double') for f in infiles]
 
-    outfile = volumeLikeFile(args[0], outfilename, volumeType='short')
+    outfile = volumeLikeFile(infiles[0], outfilename, volumeType='short')
 
     # create the slice array
     nslices = 10
@@ -122,5 +126,3 @@ if __name__ == "__main__":
     outfile.writeFile()
     outfile.closeVolume()
 
-
-

setup.py

@@ -13,7 +13,7 @@
     m.Extension.__dict__ = m._Extension.__dict__
 
 setup(name="python-stuffs",
-      version='0.1.7',
+      version='0.1.8',
       scripts=["python/TFCE",
                "python/smooth_vector",
                "python/measure_xcorr",