[ViewVC] Annotation of: OpenMD/trunk/src/applications/utilities/md2md

#!@PYTHON_EXECUTABLE@
"""MetaData file remapper

Takes a MetaData file and maps all StuntDoubles back to the periodic box.
Will optionally replicate the system in the three box directions, or 
translate every object in the box and before writing out a new MetaData file.

Usage: md2md

Options:
  -h,  --help             show this help
  -m,  --meta-data=...    use specified meta-data (.md, .eor) file
  -o,  --output-file=...  use specified output file
  -x,  --repeatX=...      make the system repeat in the x direction
  -y,  --repeatY=...      make the system repeat in the y direction
  -z,  --repeatZ=...      make the system repeat in the z direction
  -t,  --translateX=...   translate all x coordinates by some amount 
  -u,  --translateY=...   translate all y coordinates by some amount
  -v,  --translateZ=...   translate all z coordinates by some amount

Example:
  md2md -m lipidSystem.md -o bigLipidSystem.md -x 2 -y 2 -z 1 -v 35.0

"""

__author__ = "Dan Gezelter (gezelter@nd.edu)"
__version__ = "$Revision$"
__date__ = "$Date$"
__copyright__ = "Copyright (c) 2009 by the University of Notre Dame"
__license__ = "OpenMD"

import sys
import getopt
import string
import math
import random
from sets import *

metaData = []
frameData = []
indices = []
pvqj = []
p = []
v = []
q = []
j = []
Hmat = []
BoxInv = []

def usage():
    print __doc__

def readFile(mdFileName):
    mdFile = open(mdFileName, 'r')        
    # Find OpenMD version info first
    line = mdFile.readline()
    while 1:
        if '<OOPSE version=' in line or '<OpenMD version=' in line:
            OpenMDversion = line
            break
        line = mdFile.readline()
        
        # Rewind file and find start of MetaData block
        
    mdFile.seek(0)
    line = mdFile.readline()
    print "reading MetaData"
    while 1:
        if '<MetaData>' in line:
            while 2:
                metaData.append(line)
                line = mdFile.readline()
                if '</MetaData>' in line:
                    metaData.append(line)
                    break
            break
        line = mdFile.readline()

    mdFile.seek(0)
    print "reading Snapshot"
    line = mdFile.readline()
    while 1:
        if '<Snapshot>' in line:
            line = mdFile.readline()
            while 1:
                print "reading FrameData"
                if '<FrameData>' in line:
                    while 2:
                        frameData.append(line)
                        if 'Hmat:' in line:
                            L = line.split()
                            Hxx = float(L[2].strip(','))
                            Hxy = float(L[3].strip(','))
                            Hxz = float(L[4].strip(','))
                            Hyx = float(L[7].strip(','))
                            Hyy = float(L[8].strip(','))
                            Hyz = float(L[9].strip(','))
                            Hzx = float(L[12].strip(','))
                            Hzy = float(L[13].strip(','))
                            Hzz = float(L[14].strip(','))
                            Hmat.append([Hxx, Hxy, Hxz])
                            Hmat.append([Hyx, Hyy, Hyz])
                            Hmat.append([Hzx, Hzy, Hzz])
                            BoxInv.append(1.0/Hxx)
                            BoxInv.append(1.0/Hyy)
                            BoxInv.append(1.0/Hzz)
                        line = mdFile.readline()
                        if '</FrameData>' in line:
                            frameData.append(line)
                            break
                    break

            line = mdFile.readline()
            while 1:
                if '<StuntDoubles>' in line:
                    line = mdFile.readline()
                    while 2:
                        L = line.split()
                        myIndex = int(L[0])
                        indices.append(myIndex)
                        pvqj.append(L[1])
                        i = 2
                        if 'p' in L[1]:                              
                            x = float(L[i])
                            y = float(L[i+1])
                            z = float(L[i+2])                            
                            p.append([x, y, z])
                            i = i+3
                        else:
                            p.append([0.0, 0.0, 0.0])
                        if 'v' in L[1]:                              
                            vx = float(L[i])                                
                            vy = float(L[i+1])
                            vz = float(L[i+2])
                            v.append([vx, vy, vz])
                            i = i+3
                        else:
                            v.append([0.0, 0.0, 0.0])
                        if 'q' in L[1]:
                            qw = float(L[i])
                            qx = float(L[i+1])
                            qy = float(L[i+2])
                            qz = float(L[i+3])
                            q.append([qw, qx, qy, qz])
                            i = i+4
                        else:
                            q.append([0.0, 0.0, 0.0, 0.0])
                        if 'j' in L[1]:
                            jx = float(L[i])
                            jy = float(L[i+1])
                            jz = float(L[i+2])
                            j.append([jx, jy, jz])
                            i = i+3
                        else:
                            j.append([0.0, 0.0, 0.0])
                                               
                        line = mdFile.readline()
                        if '</StuntDoubles>' in line:
                            break
                    break
        line = mdFile.readline()
        if not line: break
    
    mdFile.close()

def writeFile(outputFileName,repeatX,repeatY,repeatZ):
    outputFile = open(outputFileName, 'w')

    outputFile.write("<OpenMD version=1>\n");

    print "writing MetaData"
    for metaline in metaData:
        if 'nMol' in metaline:
            metasplit = metaline.split()
            nMol = float(metasplit[2].strip(';'))
            newNmol = nMol * repeatX * repeatY * repeatZ
            outputFile.write('  nMol = %10d;\n' % (newNmol))
        else:
            outputFile.write(metaline)

    print "writing Snapshot"
    outputFile.write("  <Snapshot>\n")

    print "writing FrameData"
    for frameline in frameData:
        if 'Hmat:' in frameline:
            myH = []
            myH.append([repeatX * Hmat[0][0], repeatX * Hmat[0][1], repeatX * Hmat[0][2]])
            myH.append([repeatY * Hmat[1][0], repeatY * Hmat[1][1], repeatY * Hmat[1][2]])
            myH.append([repeatZ * Hmat[2][0], repeatZ * Hmat[2][1], repeatZ * Hmat[2][2]])
            outputFile.write("        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (myH[0][0], myH[0][1], myH[0][2], myH[1][0], myH[1][1], myH[1][2], myH[2][0], myH[2][1], myH[2][2]))
        else:
            outputFile.write(frameline)

    print "writing StuntDoubles"
    outputFile.write("    <StuntDoubles>\n")

    print repeatX, repeatY, repeatZ

    deco = [ (index, i) for i, index in enumerate(indices) ]
    deco.sort()
    whichSD = 0
    for ii in range(repeatX):
        for jj in range(repeatY):
            for kk in range(repeatZ):
                for index in range(len(deco)):
                    (index,i) = deco[index]
                    print i
                    myP = [] 
                    myP.append(p[i][0] + ii*Hmat[0][0] + jj*Hmat[1][0] + kk*Hmat[2][0])
                    myP.append(p[i][1] + ii*Hmat[0][1] + jj*Hmat[1][1] + kk*Hmat[2][1])
                    myP.append(p[i][2] + ii*Hmat[0][2] + jj*Hmat[1][2] + kk*Hmat[2][2])
    
                    if (pvqj[i] == 'p'):
                        outputFile.write("%10d %7s %18.10g %18.10g %18.10g\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2]))

                    elif (pvqj[i] == 'pv'):
                        outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2]))
                    elif (pvqj[i] == 'pq'):
                        outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], q[i][0], q[i][1], q[i][2], q[i][3]))
                    elif (pvqj[i] == 'pvqj'):
                        outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2], q[i][0], q[i][1], q[i][2], q[i][3], j[i][0], j[i][1], j[i][2]))
                    whichSD = whichSD + 1

    outputFile.write("    </StuntDoubles>\n")
    outputFile.write("  </Snapshot>\n")
    outputFile.write("</OpenMD>\n")
    outputFile.close()

def roundMe(x):
    if (x >= 0.0):
        return math.floor(x + 0.5)
    else:
        return math.ceil(x - 0.5)

def wrapVector(myVect):
    scaled = [0.0, 0.0, 0.0]
    for i in range(3):
        scaled[i] = myVect[i] * BoxInv[i]
        scaled[i] = scaled[i] - roundMe(scaled[i])
        myVect[i] = scaled[i] * Hmat[i][i]
    return myVect

def dot(L1, L2):
    myDot = 0.0
    for i in range(len(L1)):
        myDot = myDot + L1[i]*L2[i]
    return myDot

def normalize(L1):
    L2 = []
    myLength = math.sqrt(dot(L1, L1))
    for i in range(len(L1)):
        L2.append(L1[i] / myLength)
    return L2

def cross(L1, L2):
    # don't call this with anything other than length 3 lists please
    # or you'll be sorry
    L3 = [0.0, 0.0, 0.0]
    L3[0] = L1[1]*L2[2] - L1[2]*L2[1] 
    L3[1] = L1[2]*L2[0] - L1[0]*L2[2]
    L3[2] = L1[0]*L2[1] - L1[1]*L2[0]
    return L3

def mapToBox(translateX, translateY, translateZ):
    print "translating by %f\t%f\t%f" % (translateX, translateY, translateZ)
    for i in range(len(indices)):
        dpos = []
        dpos.append(p[i][0] + translateX)
        dpos.append(p[i][1] + translateY)
        dpos.append(p[i][2] + translateZ)
        p[i] = wrapVector(dpos)

def main(argv):
    repeatX = 1
    repeatY = 1
    repeatZ = 1
    translateX = 0.0
    translateY = 0.0
    translateZ = 0.0
    _haveMDFileName = 0
    _haveOutputFileName = 0
    try:                                
        opts, args = getopt.getopt(argv, "hm:o:x:y:z:t:u:v:", ["help", "meta-data=", "output-file=", "repeatX=", "repeatY=", "repeatZ=","translateX=","translateY=","translateZ="]) 
    except getopt.GetoptError:           
        usage()                          
        sys.exit(2)                     
    for opt, arg in opts:                
        if opt in ("-h", "--help"):      
            usage()                     
            sys.exit()                  
        elif opt in ("-m", "--meta-data"): 
            mdFileName = arg
            _haveMDFileName = 1
        elif opt in ("-o", "--output-file"): 
            outputFileName = arg
            _haveOutputFileName = 1
        elif opt in ("-x", "--repeatX"):
            repeatX = int(arg)
        elif opt in ("-y", "--repeatY"): 
            repeatY = int(arg)
        elif opt in ("-z", "--repeatZ"): 
            repeatZ = int(arg)
        elif opt in ("-t", "--translateX"):
            translateX = float(arg)
        elif opt in ("-u", "--translateY"): 
            translateY = float(arg)
        elif opt in ("-v", "--translateZ"): 
            translateZ = float(arg)
    if (_haveMDFileName != 1):
        usage() 
        print "No meta-data file was specified"
        sys.exit()
    if (_haveOutputFileName != 1):
        usage()
        print "No output file was specified"
        sys.exit()

    readFile(mdFileName)
    mapToBox(translateX, translateY, translateZ)    
    writeFile(outputFileName, repeatX, repeatY, repeatZ)

if __name__ == "__main__":
    if len(sys.argv) == 1:
        usage()
        sys.exit()
    main(sys.argv[1:])
Revision:	2043
Committed:	Fri Nov 14 19:04:27 2014 UTC (10 years, 8 months ago) by gezelter
File size:	11981 byte(s)
Log Message:	Another md2md fix
#	User	Rev	Content
1	gezelter	1782	#!@PYTHON_EXECUTABLE@
2	gezelter	1227	"""MetaData file remapper
3
4			Takes a MetaData file and maps all StuntDoubles back to the periodic box.
5	gezelter	1383	Will optionally replicate the system in the three box directions, or
6			translate every object in the box and before writing out a new MetaData file.
7	gezelter	1227
8			Usage: md2md
9
10			Options:
11	gezelter	1383	-h, --help show this help
12			-m, --meta-data=... use specified meta-data (.md, .eor) file
13			-o, --output-file=... use specified output file
14			-x, --repeatX=... make the system repeat in the x direction
15			-y, --repeatY=... make the system repeat in the y direction
16			-z, --repeatZ=... make the system repeat in the z direction
17			-t, --translateX=... translate all x coordinates by some amount
18			-u, --translateY=... translate all y coordinates by some amount
19			-v, --translateZ=... translate all z coordinates by some amount
20	gezelter	1227
21			Example:
22	gezelter	1383	md2md -m lipidSystem.md -o bigLipidSystem.md -x 2 -y 2 -z 1 -v 35.0
23	gezelter	1227
24			"""
25
26			__author__ = "Dan Gezelter (gezelter@nd.edu)"
27	gezelter	1442	__version__ = "$Revision$"
28			__date__ = "$Date$"
29	gezelter	1383	__copyright__ = "Copyright (c) 2009 by the University of Notre Dame"
30	gezelter	1390	__license__ = "OpenMD"
31	gezelter	1227
32			import sys
33			import getopt
34			import string
35			import math
36			import random
37			from sets import *
38
39			metaData = []
40			frameData = []
41			indices = []
42			pvqj = []
43			p = []
44			v = []
45			q = []
46			j = []
47			Hmat = []
48			BoxInv = []
49
50			def usage():
51			print __doc__
52
53			def readFile(mdFileName):
54			mdFile = open(mdFileName, 'r')
55	gezelter	1390	# Find OpenMD version info first
56	gezelter	1227	line = mdFile.readline()
57			while 1:
58	gezelter	1390	if '<OOPSE version=' in line or '<OpenMD version=' in line:
59			OpenMDversion = line
60	gezelter	1227	break
61			line = mdFile.readline()
62
63			# Rewind file and find start of MetaData block
64
65			mdFile.seek(0)
66			line = mdFile.readline()
67			print "reading MetaData"
68			while 1:
69			if '<MetaData>' in line:
70			while 2:
71			metaData.append(line)
72			line = mdFile.readline()
73			if '</MetaData>' in line:
74			metaData.append(line)
75			break
76			break
77			line = mdFile.readline()
78
79			mdFile.seek(0)
80			print "reading Snapshot"
81			line = mdFile.readline()
82			while 1:
83			if '<Snapshot>' in line:
84			line = mdFile.readline()
85			while 1:
86			print "reading FrameData"
87			if '<FrameData>' in line:
88			while 2:
89			frameData.append(line)
90			if 'Hmat:' in line:
91			L = line.split()
92			Hxx = float(L[2].strip(','))
93			Hxy = float(L[3].strip(','))
94			Hxz = float(L[4].strip(','))
95			Hyx = float(L[7].strip(','))
96			Hyy = float(L[8].strip(','))
97			Hyz = float(L[9].strip(','))
98			Hzx = float(L[12].strip(','))
99			Hzy = float(L[13].strip(','))
100			Hzz = float(L[14].strip(','))
101			Hmat.append([Hxx, Hxy, Hxz])
102			Hmat.append([Hyx, Hyy, Hyz])
103			Hmat.append([Hzx, Hzy, Hzz])
104			BoxInv.append(1.0/Hxx)
105			BoxInv.append(1.0/Hyy)
106			BoxInv.append(1.0/Hzz)
107			line = mdFile.readline()
108			if '</FrameData>' in line:
109			frameData.append(line)
110			break
111			break
112
113			line = mdFile.readline()
114			while 1:
115			if '<StuntDoubles>' in line:
116			line = mdFile.readline()
117			while 2:
118			L = line.split()
119			myIndex = int(L[0])
120			indices.append(myIndex)
121			pvqj.append(L[1])
122	gezelter	2043	i = 2
123	gezelter	2041	if 'p' in L[1]:
124	gezelter	2043	x = float(L[i])
125			y = float(L[i+1])
126			z = float(L[i+2])
127	gezelter	2041	p.append([x, y, z])
128	gezelter	2043	i = i+3
129	gezelter	2041	else:
130			p.append([0.0, 0.0, 0.0])
131			if 'v' in L[1]:
132	gezelter	2043	vx = float(L[i])
133			vy = float(L[i+1])
134			vz = float(L[i+2])
135	gezelter	2041	v.append([vx, vy, vz])
136	gezelter	2043	i = i+3
137	gezelter	2041	else:
138			v.append([0.0, 0.0, 0.0])
139			if 'q' in L[1]:
140	gezelter	2043	qw = float(L[i])
141			qx = float(L[i+1])
142			qy = float(L[i+2])
143			qz = float(L[i+3])
144	gezelter	1227	q.append([qw, qx, qy, qz])
145	gezelter	2043	i = i+4
146	gezelter	2041	else:
147			q.append([0.0, 0.0, 0.0, 0.0])
148			if 'j' in L[1]:
149	gezelter	2043	jx = float(L[i])
150			jy = float(L[i+1])
151			jz = float(L[i+2])
152	gezelter	1227	j.append([jx, jy, jz])
153	gezelter	2043	i = i+3
154	gezelter	1227	else:
155			j.append([0.0, 0.0, 0.0])
156
157			line = mdFile.readline()
158			if '</StuntDoubles>' in line:
159			break
160			break
161			line = mdFile.readline()
162			if not line: break
163
164			mdFile.close()
165
166	gezelter	1383	def writeFile(outputFileName,repeatX,repeatY,repeatZ):
167	gezelter	1227	outputFile = open(outputFileName, 'w')
168
169	gezelter	1390	outputFile.write("<OpenMD version=1>\n");
170	gezelter	1227
171			print "writing MetaData"
172			for metaline in metaData:
173			if 'nMol' in metaline:
174			metasplit = metaline.split()
175			nMol = float(metasplit[2].strip(';'))
176			newNmol = nMol * repeatX * repeatY * repeatZ
177			outputFile.write(' nMol = %10d;\n' % (newNmol))
178			else:
179			outputFile.write(metaline)
180
181			print "writing Snapshot"
182			outputFile.write(" <Snapshot>\n")
183
184			print "writing FrameData"
185			for frameline in frameData:
186			if 'Hmat:' in frameline:
187			myH = []
188			myH.append([repeatX * Hmat[0][0], repeatX * Hmat[0][1], repeatX * Hmat[0][2]])
189			myH.append([repeatY * Hmat[1][0], repeatY * Hmat[1][1], repeatY * Hmat[1][2]])
190			myH.append([repeatZ * Hmat[2][0], repeatZ * Hmat[2][1], repeatZ * Hmat[2][2]])
191			outputFile.write(" Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (myH[0][0], myH[0][1], myH[0][2], myH[1][0], myH[1][1], myH[1][2], myH[2][0], myH[2][1], myH[2][2]))
192			else:
193			outputFile.write(frameline)
194
195			print "writing StuntDoubles"
196			outputFile.write(" <StuntDoubles>\n")
197
198	xsun	1243	print repeatX, repeatY, repeatZ
199
200	gezelter	1383	deco = [ (index, i) for i, index in enumerate(indices) ]
201			deco.sort()
202			whichSD = 0
203	gezelter	1390	for ii in range(repeatX):
204			for jj in range(repeatY):
205			for kk in range(repeatZ):
206			for index in range(len(deco)):
207			(index,i) = deco[index]
208			print i
209	gezelter	1383	myP = []
210			myP.append(p[i][0] + iiHmat[0][0] + jjHmat[1][0] + kk*Hmat[2][0])
211			myP.append(p[i][1] + iiHmat[0][1] + jjHmat[1][1] + kk*Hmat[2][1])
212			myP.append(p[i][2] + iiHmat[0][2] + jjHmat[1][2] + kk*Hmat[2][2])
213	gezelter	2041
214			if (pvqj[i] == 'p'):
215			outputFile.write("%10d %7s %18.10g %18.10g %18.10g\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2]))
216
217			elif (pvqj[i] == 'pv'):
218			outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2]))
219			elif (pvqj[i] == 'pq'):
220			outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], q[i][0], q[i][1], q[i][2], q[i][3]))
221	gezelter	1383	elif (pvqj[i] == 'pvqj'):
222			outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2], q[i][0], q[i][1], q[i][2], q[i][3], j[i][0], j[i][1], j[i][2]))
223			whichSD = whichSD + 1
224	gezelter	1227
225			outputFile.write(" </StuntDoubles>\n")
226			outputFile.write(" </Snapshot>\n")
227	gezelter	1390	outputFile.write("</OpenMD>\n")
228	gezelter	1227	outputFile.close()
229
230			def roundMe(x):
231			if (x >= 0.0):
232			return math.floor(x + 0.5)
233			else:
234			return math.ceil(x - 0.5)
235
236			def wrapVector(myVect):
237			scaled = [0.0, 0.0, 0.0]
238			for i in range(3):
239			scaled[i] = myVect[i] * BoxInv[i]
240			scaled[i] = scaled[i] - roundMe(scaled[i])
241			myVect[i] = scaled[i] * Hmat[i][i]
242			return myVect
243
244			def dot(L1, L2):
245			myDot = 0.0
246			for i in range(len(L1)):
247			myDot = myDot + L1[i]*L2[i]
248			return myDot
249
250			def normalize(L1):
251			L2 = []
252			myLength = math.sqrt(dot(L1, L1))
253			for i in range(len(L1)):
254			L2.append(L1[i] / myLength)
255			return L2
256
257			def cross(L1, L2):
258			# don't call this with anything other than length 3 lists please
259			# or you'll be sorry
260			L3 = [0.0, 0.0, 0.0]
261			L3[0] = L1[1]L2[2] - L1[2]L2[1]
262			L3[1] = L1[2]L2[0] - L1[0]L2[2]
263			L3[2] = L1[0]L2[1] - L1[1]L2[0]
264			return L3
265
266	gezelter	1383	def mapToBox(translateX, translateY, translateZ):
267			print "translating by %f\t%f\t%f" % (translateX, translateY, translateZ)
268	gezelter	1227	for i in range(len(indices)):
269	gezelter	1383	dpos = []
270			dpos.append(p[i][0] + translateX)
271			dpos.append(p[i][1] + translateY)
272			dpos.append(p[i][2] + translateZ)
273	gezelter	1227	p[i] = wrapVector(dpos)
274
275			def main(argv):
276	gezelter	1383	repeatX = 1
277			repeatY = 1
278			repeatZ = 1
279			translateX = 0.0
280			translateY = 0.0
281			translateZ = 0.0
282			_haveMDFileName = 0
283			_haveOutputFileName = 0
284	gezelter	1227	try:
285	gezelter	1383	opts, args = getopt.getopt(argv, "hm:o:x:y:z:t:u:v:", ["help", "meta-data=", "output-file=", "repeatX=", "repeatY=", "repeatZ=","translateX=","translateY=","translateZ="])
286	gezelter	1227	except getopt.GetoptError:
287			usage()
288			sys.exit(2)
289			for opt, arg in opts:
290			if opt in ("-h", "--help"):
291			usage()
292			sys.exit()
293			elif opt in ("-m", "--meta-data"):
294			mdFileName = arg
295			_haveMDFileName = 1
296			elif opt in ("-o", "--output-file"):
297			outputFileName = arg
298			_haveOutputFileName = 1
299	xsun	1243	elif opt in ("-x", "--repeatX"):
300	gezelter	1227	repeatX = int(arg)
301			elif opt in ("-y", "--repeatY"):
302			repeatY = int(arg)
303			elif opt in ("-z", "--repeatZ"):
304			repeatZ = int(arg)
305	gezelter	1383	elif opt in ("-t", "--translateX"):
306			translateX = float(arg)
307			elif opt in ("-u", "--translateY"):
308			translateY = float(arg)
309			elif opt in ("-v", "--translateZ"):
310			translateZ = float(arg)
311	gezelter	1227	if (_haveMDFileName != 1):
312			usage()
313			print "No meta-data file was specified"
314			sys.exit()
315			if (_haveOutputFileName != 1):
316			usage()
317			print "No output file was specified"
318			sys.exit()
319	chuckv	1293
320	gezelter	1227	readFile(mdFileName)
321	gezelter	1383	mapToBox(translateX, translateY, translateZ)
322			writeFile(outputFileName, repeatX, repeatY, repeatZ)
323	gezelter	1227
324			if __name__ == "__main__":
325			if len(sys.argv) == 1:
326			usage()
327			sys.exit()
328			main(sys.argv[1:])