Add CLI for transforming files (and minor nsd_mapdata.py tweak)

nsdcode/nsd_mapdata.py

@@ -29,6 +29,7 @@ def fit(self,
             outputfile=None,
             outputclass=None,
             fsdir=None,
+            transformfile=None,
             ):
         """nsa_mapdata is used to map functional data between coordinate systems
 
@@ -211,6 +212,8 @@ def fit(self,
             res = None
 
         # load transform
+        if transformfile is not None:
+            tfile=transformfile
         a1_data = load_transform(casenum, tfile)
 
         # load sourcedata

nsdcode/nsdmapcli.py

@@ -0,0 +1,55 @@
+import os
+import sys
+import argparse
+import textwrap
+from nsdcode.nsd_mapdata import NSDmapdata
+from nsdcode.nsd_datalocation import nsd_datalocation
+
+def argument_parse():
+    parser=argparse.ArgumentParser(description='Transform NSD data from the command line',
+        epilog=textwrap.dedent('''\
+        --sourcespace and --targetspace options include: 
+            anat0pt5, anat0pt8, anat1pt0, func1pt0, func1pt8, MNI,
+            [lh,rh].white, [lh,rh].pial, [lh,rh].layerB1, [lh,rh].layerB2, [lh,rh].layerB3, fsaverage'''))
+
+    parser.add_argument('--sourcespace',action='store',dest='sourcespace',help="One of the volume/surface space options below",required=True)
+    parser.add_argument('--targetspace',action='store',dest='targetspace',help="One of the volume/surface space options below",required=True)
+    parser.add_argument('--inputfile',action='store',dest='inputfile',help="Input file in <sourcespace>",required=True)
+    parser.add_argument('--outputfile',action='store',dest='outputfile',help="Output file in <targetspace>",required=True)
+    parser.add_argument('--nsdlocation',action='store',dest='basedir',default=None,help='Directory containing ppdata/, etc')
+    parser.add_argument('--subjix',action='store',dest='subjix',type=int,help="NSD subject index 1-8")
+    parser.add_argument('--interptype',action='store',dest='interptype',default='cubic',
+        choices=['nearest','linear','cubic','wta','surfacewta'],
+        help="default: 'cubic'. See nsd_mapdata.py for wta details")
+    parser.add_argument('--badval',action='store',dest='badval',default=None)
+    parser.add_argument('--outputclass',action='store',dest='outputclass',default=None)
+    parser.add_argument('--fsdir',action='store',dest='fsdir',default=None)
+    parser.add_argument('--transformfile',action='store',dest='transformfile',default=None,
+        help="Manually-specified transformation file (ignores --nsdlocation and --subjix)")
+
+    return parser.parse_args()
+
+def main():
+    args=argument_parse()
+    #if transform file was provided, we can ignore the basedir and subjix and just set defaults
+    if args.transformfile is not None:
+        if args.basedir is None:
+            args.basedir=nsd_datalocation(".")
+        if args.subjix is None:
+            args.subjix=1
+    NSD=NSDmapdata(args.basedir)
+    NSD.fit(subjix=args.subjix,
+            sourcespace=args.sourcespace,
+            targetspace=args.targetspace,
+            sourcedata=args.inputfile,
+            interptype=args.interptype,
+            badval=args.badval,
+            outputfile=args.outputfile,
+            outputclass=args.outputclass,
+            fsdir=args.fsdir,
+            transformfile=args.transformfile,
+            )
+
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -25,7 +25,12 @@ def local_version(version):
 opts = dict(
     use_scm_version={"root": ".", "relative_to": __file__,
                      "write_to": op.join("nsdcode", "version.py"),
-                     "local_scheme": local_version}
+                     "local_scheme": local_version},
+    entry_points={
+            'console_scripts': [
+                'nsdmapdata = nsdcode.nsdmapcli:main',
+            ],
+        },
             )